 
REBASE version 901                                              procitea.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
 
@D	Aagaard, C.//Awayez, M.J.//Garrett, R.A. 	Profile of the DNA recognition site of the archaeal homing endonuclease I-DmoI.	Nucleic Acids Res.	1997	25		1523-1530			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. 		
@D	Aagaard, C.//Dalgaard, J.Z.//Garrett, R.A. 	Intercellular mobility and homing of an archaeal rDNA intron confers a selective advantage over intron- cells of Sulfolobus acidocaldarius.	Proc. Natl. Acad. Sci. U. S. A.	1995	92		12285-12289			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. 		
@D	Aalbaek, B.//Jensen, L.K.//Jensen, H.E.//Olsen, J.E.//Christensen, H. 	Whole-Genome Sequence of Staphylococcus aureus S54F9 Isolated from a Chronic Disseminated Porcine Lung Abscess and Used in Human Infection Models.	Genome Announcements	2015	3		e01207-15			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. 		
@D	Aapola, U.//Kawasaki, K.//Scott, H.S.//Ollila, J.//Vihinen, M.//Heino, M.//Shintani, A.//Kawasaki, K.//Minoshima, S.//Krohn, K.//Antonarakis, S.E.//Shimizu, N.//Kudoh, J.//Peterson, P. 	Isolation and initial characterization of a novel zinc finger gene, DNMT3L, on 21q22.3, related to the cytosine-5-methyltransferase 3 gene family.	Genomics	2000	65		293-298			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. 		
@D	Aapola, U.//Liiv, I.//Peterson, P. 	Imprinting regulator DNMT3L is a transcriptional repressor associated with histone deacetylase activity.	Nucleic Acids Res.	2002	30		3602-3608			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. 		
@D	Aapola, U.//Lyle, R.//Krohn, K.//Antonarakis, S.E.//Peterson, P. 	Isolation and initial characterization of the mouse Dnmt3L gene.	Cytogenet. Cell Genet.	2001	92		122-126			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. 		
@D	Aapola, U.//Maenpaa, K.//Kaipia, A.//Peterson, P. 	Epigenetic modifications affect the Dnmt3L expression.	Biochem. J.	2004	380		705-713			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. 		
@D	Aarab, S.//Arakrak, A.//Ollero, F.J.//Megias, M.//Gomes, D.F.//Ribeiro, R.A.//Hungria, M. 	Draft Genome Sequence of Pseudomonas fluorescens Strain ET76, Isolated from Rice  Rhizosphere in Northwestern Morocco.	Genome Announcements	2016	4		e00356-16			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. 		
@D	Abadjieva, A.//Patel, J.//Webb, M.//Zinkevich, V.//Firman, K. 	A deletion mutant of the type IC restriction endonuclease EcoR124I expressing a novel DNA specificity.	Nucleic Acids Res.	1993	21		4435-4443			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. 		
@A	Abadjieva, A.//Patel, J.//Zinkevich, V.//Weiserova, M.//Firman, K. 		The domain structure of the DNA specificity subunit of type I restriction endonucleases.  II.  Mutations affecting subunit assembly.			Balla, E.//Berencsi, G.//Szentirmai, A. 		DNA Transfer and Gene Expression in Microorganisms				Andover	Intercept	1993		0		189-196									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. 		
@D	Abadjieva, A.//Scarlett, G.//Janscak, P.//Dutta, C.F.//Firman, K. 	Characterization of an EcoR1241 restriction-modification enzyme produced from a deleted form of the DNA-binding subunit, which results in a novel DNA specificity.	Folia Microbiol. (Praha)	2003	48		319-328			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. 		
@D	Abadjieva, A.//Webb, M.//Patel, J.//Zinkevich, V.//Firman, K. 	Deletions within the DNA recognition subunit of M.EcoR124I that identify a region involved in protein-protein interactions between HsdS and HsdM.	J. Mol. Biol.	1994	241		35-43			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. 		
@D	Abaev, I.//Skryabin, Y.//Kislichkina, A.//Bogun, A.//Korobova, O.//Dyatlov, I. 	Draft Genome Sequences of Eight Staphylococcus aureus Strains Isolated during Foodborne Outbreaks.	Genome Announcements	2018	6		e01557-17			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. 		
@D	Abaev, I.//Skryabin, Y.//Kislichkina, A.//Bogun, A.//Korobova, O.//Mayskaya, N.//Shemyakin, I.//Dyatlov, I. 	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.	Genome Announcements	2016	4		e00064-16			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. 		
@D	Abbasalizadeh, S.//Salehi, J.G.//Motamedi, J.M.//Azarbaijani, R.//Parsa, Y.L.//Ahmad, R.M.//Mardi, M.//Salekdeh, G.H. 	Draft Genome Sequence of Ureibacillus thermosphaericus Strain Thermo-BF, Isolated from Ramsar Hot Springs in Iran.	J. Bacteriol.	2012	194		4431			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. 		
@D	Abbasifar, R.//Kropinski, A.M.//Sabour, P.M.//Ackermann, H.W.//Lingohr, E.J.//Griffiths, M.W. 	Complete Genome Sequence of Cronobacter sakazakii Bacteriophage vB_CsaM_GAP161.	J. Virol.	2012	86		13806-13807			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. 		
@D	Abdallah, A.M.//Rashid, M.//Adroub, S.A.//Arnoux, M.//Ali, S.//van Soolingen, D.//Bitter, W.//Pain, A. 	Complete Genome Sequence of Mycobacterium phlei Type Strain RIVM601174.	J. Bacteriol.	2012	194		3284-3285			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. 		
@D	Abdallah, A.M.//Rashid, M.//Adroub, S.A.//Elabdalaoui, H.//Ali, S.//van Soolingen, D.//Bitter, W.//Pain, A. 	Complete Genome Sequence of Mycobacterium xenopi Type Strain RIVM700367.	J. Bacteriol.	2012	194		3282-3283			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. 		
@D	Abdel-Haleem, A.M.//Rchiad, Z.//Khan, B.K.//Abdallah, A.M.//Naeem, R.//Nikhat, S.S.//Solovyev, V.//Ahmed, A.//Pain, A. 	Genome Sequence of a Multidrug-Resistant Strain of Stenotrophomonas maltophilia with Carbapenem Resistance, Isolated from King Abdullah Medical City, Makkah, Saudi Arabia.	Genome Announcements	2015	3		e01166-15			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. 		
@D	Abdelbary, M.M.H.//Prod'hom, G.//Greub, G.//Senn, L.//Blanc, D.S. 	Draft Genome Sequences of Two Carbapenemase-Producing Acinetobacter baumannii Clinical Strains Isolated from Albanian and Togolese Patients.	Genome Announcements	2017	5		e00115-17			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. 		
@D	Abdelhamed, H.//Ozdemir, O.//Tekedar, H.C.//Arick, M.A.I.I.//Hsu, C.Y.//Karsi, A.//Lawrence, M.L. 	Complete Genome Sequence of Multidrug-Resistant Plesiomonas shigelloides Strain MS-17-188.	Genome Announcements	2018	6		e00387-18			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. 		
@D	Abdelhamed, H.//Tekedar, H.C.//Ozdemir, O.//Hsu, C.Y.//Arick, M.A.I.I.//Karsi, A.//Lawrence, M.L. 	Complete Genome Sequence of Multidrug-Resistant Edwardsiella ictaluri Strain MS-17-156.	Genome Announcements	2018	6		e00477-18			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. 		
@D	Abdul-Majid, S.//Graw, M.F.//Nguyen, H.//Hay, A.G. 	Draft Whole-Genome Sequence of Urease-Producing Sporosarcina koreensis.	Genome Announcements	2016	4		e00096-16			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. 		
@D	Abdul-Momin, M.H.F.//Liakopoulos, A.//Wareham, D.W. 	Draft Genome Sequence of a Multidrug-Resistant Sequence Type 231 Outbreak-Associated Clone of Klebsiella pneumoniae, KP41-2015, Producing OXA-232 Carbapenemase.	Genome Announcements	2017	5		e00604-17			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. 		
@D	Abdurashitov, M.A.//Belichenko, O.A.//Lebedeva, N.A.//Degtyarev, S.K. 	PsiI, a novel restriction endonuclease recognizing the DNA sequence 5'-TTA^TAA-3'.	Biokhimiia	1999	64		574-576			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. 		
@D	Abdurashitov, M.A.//Belichenko, O.A.//Shevchenko, A.V.//Dedkov, V.S.//Degtyarev, S.K. 	BstAPI, an ApaBI isoschizomer, cleaves DNA at 5'-GCANNNN/NTGC-3'.	Nucleic Acids Res.	1997	25		2301-2302			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. 		
@D	Abdurashitov, M.A.//Belichenko, O.A.//Shevchenko, A.V.//Degtyarev, S.K. 	N.BstSE - site-specific nuclease from Bacillus stearothermophilus SE-589 - restriction endonuclease production.	Mol. Biol. (Mosk)	1996	30		1261-1267			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. 		
@D	Abdurashitov, M.A.//Belichenko, O.A.//Shevchenko, A.V.//Degtyarev, S.K. 	SimI, a new restriction endonuclease that recognizes non-palindromic sequence 5'-GGGTC-3'(-3/0).	Nucleic Acids Res.	1995	23		2571-2572			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'. 		
@D	Abdurashitov, M.A.//Kileva, E.V.//Myakisheva, T.V.//Dedkov, V.S.//Shevchenko, A.V.//Degtyarev, S.K. 	AccBSI: A new restriction endonuclease from Acinetobacter calcoaceticus BS.	Prikl. Biokhim. Mikrobiol.	1997	33		556-558			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. 		
@D	Abdurashitov, M.A.//Kileva, E.V.//Shinkarenko, N.M.//Shevchenko, A.V.//Dedkov, V.S.//Degtyarev, S.K. 	BstF5I, an unusual isoschizomer of FokI.	Gene	1996	172		49-51			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. 		
@D	Abdurashitov, M.A.//Netesova, N.A.//Golikova, L.N.//Gutorov, V.V.//Belavin, P.A.//Degtyarev, S.K. 	The second methyltransferase of the BstF5I restriction-modification system is homologous to the C-terminal domains of FokI and StsI methylases.	Mol. Biol. (Mosk)	2000	34		87-94			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. 		
@D	Abdurashitov, M.A.//Okhapkina, S.S.//Netesova, N.A.//Golikova, L.N.//Gonchar, D.A.//Degtyarev, S.K. 	The unique FauI restriction-modification system: Cloning and protein sequence comparisons.	Mol. Biol. (Mosk)	2003	37		619-624			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. 		
@D	Abdurashitov, M.A.//Tomilov, V.N.//Chernukhin, V.A.//Gonchar, D.A.//Degtyarev, S.K. 	Comparative analysis of human chromosomal DNA digestion with restriction endonucleases in vitro and in silico.	Medical Genetics	2007	6		29-36			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. 		
@D	Abeijon, M.M.C.//Saavedra, L.//Gauffin, C.M.P.//Hebert, E.M.//Medina, R.B. 	Draft Genome Sequence of the Feruloyl Esterase-Producing Strain Lactobacillus fermentum CRL1446, a Probiotic for Malnutrition.	Genome Announcements	2018	6		e00225-18			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. 		
@D	Abendroth, C.//Hahnke, S.//Codoner, F.M.//Klocke, M.//Luschnig, O.//Porcar, M. 	Complete Genome Sequence of a New Firmicutes Species Isolated from Anaerobic Biomass Hydrolysis.	Genome Announcements	2017	5		e00686-17			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. 		
@D	Abicht, H.K.//Mancini, S.//Karnachuk, O.V.//Solioz, M. 	Genome Sequence of Desulfosporosinus sp. OT, an Acidophilic Sulfate-Reducing Bacterium from Copper Mining Waste in Norilsk, Northern  Siberia.	J. Bacteriol.	2011	193		6104-6105			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. 		
@D	Abin, C.A.//Hollibaugh, J.T. 	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.	Genome Announcements	2016	4		e01246-16			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. 		
@D	Abin, C.A.//Hollibaugh, J.T. 	Draft Genome Sequence of the Type Strain Desulfuribacillus alkaliarsenatis AHT28, an Obligately Anaerobic, Sulfidogenic Bacterium Isolated from Russian Soda Lake  Sediments.	Genome Announcements	2016	4		e01244-16			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. 		
@D	Abo-Aba, S.E.//Sabir, J.S.//Baeshen, M.N.//Sabir, M.J.//Mutwakil, M.H.//Baeshen, N.A.//D'Amore, R.//Hall, N. 	Draft Genome Sequence of Bacillus Species from the Rhizosphere of the Desert Plant Rhazya stricta.	Genome Announcements	2015	3		e00957-15			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. 		
@D	Abolnik, C.//Beylefeld, A. 	Complete Genome Sequence of Mycoplasma gallinaceum.	Genome Announcements	2015	3		e00712-15			Mycoplasma gallinaceum strain B2096 8B was isolated from domestic chickens in South Africa. The 845,307-bp full genome was sequenced, assembled, and annotated. 		
@D	Aboubaker, O.D.//Phelippeau, M.//Musso, D.//Robert, C.//Michelle, C.//Croce, O.//Drancourt, M. 	Draft Genome Sequence of Mycobacterium tuberculosis Strain MT43, a Representative of the Manu2 Genotype.	Genome Announcements	2015	3		e00579-15			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. 		
@D	Aboubaker, O.D.//Phelippeau, M.//Musso, D.//Robert, C.//Michelle, C.//Croce, O.//Drancourt, M. 	Draft Genome Sequence of Mycobacterium tuberculosis Strain MT11, Which Represents a New Lineage.	Genome Announcements	2015	3		e00573-15			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. 		
@D	Abouelkhair, M.A.//Riley, M.C.//Bemis, D.A.//Kania, S.A. 	Complete Genome Sequence of Staphylococcus pseudintermedius Type Strain LMG 22219.	Genome Announcements	2017	5		e01651-16			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. 		
@D	Abouelkhair, M.A.//Thompson, R.//Riley, M.C.//Bemis, D.A.//Kania, S.A. 	Complete Genome Sequences of Three Staphylococcus pseudintermedius Strains Isolated from Botswana.	Genome Announcements	2018	6		e01599-17			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. 		
@D	Abraham, S.//O'Dea, M.//Trott, D.J.//Abraham, R.J.//Hughes, D.//Pang, S.//McKew, G.//Cheong, E.Y.//Merlino, J.//Saputra, S.//Malik, R.//Gottlieb, T. 	Isolation and plasmid characterization of carbapenemase (IMP-4) producing Salmonella enterica Typhimurium from cats.	Sci. Rep.	2016	6		35527			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. 		
@D	Abraham, W.P.//Thomas, S. 	Draft Genome Sequence of Pseudomonas psychrophila MTCC 12324, Isolated from the Arctic at 79 degrees N.	Genome Announcements	2015	3		e00578-15			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. 		
@D	Abrahante, J.E.//Hunter, S.S.//Maheswaran, S.K.//Hauglund, M.J.//Tatum, F.M.//Briggs, R.E. 	Draft Genome Sequence of Pasteurella multocida Isolate P1062, Isolated from Bovine Respiratory Disease.	Genome Announcements	2015	3		e01254-15			Here, we report the draft genome of Pasteurella multocida isolate P1062 recovered from pneumonic bovine lung in the United States in 1959. 		
@D	Abrahante, J.E.//Johnson, T.J.//Hunter, S.S.//Maheswaran, S.K.//Hauglund, M.J.//Bayles, D.O.//Tatum, F.M.//Briggs, R.E. 	Draft Genome Sequences of Two Virulent Serotypes of Avian Pasteurella multocida.	Genome Announcements	2013	1		e00058-12			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. 		
@D	Abrahante, J.E.//Veeregowda, B.M.//Hogtapur, S.S.//Briggs, R.E.//Maheswaran, S.K.//Sreevatsan, S. 	Draft Genome Sequences of Two Pasteurella multocida Strains Isolated from Buffaloes in India with Hemorrhagic Septicemia Disease.	Genome Announcements	2014	2		e00798-14			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. 		
@D	Abrams, A.J.//Trees, D.L.//Nicholas, R.A. 	Complete Genome Sequences of Three Neisseria gonorrhoeae Laboratory Reference Strains, Determined Using PacBio Single-Molecule Real-Time Technology.	Genome Announcements	2015	3		e01052-15			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. 		
@D	Abriouel, H.//Benomar, N.//Perez, P.R.//Canamero, M.M.//Galvez, A. 	Annotated genome sequence of Lactobacillus pentosus MP-10, which has probiotic potential, from naturally fermented Alorena green table olives.	J. Bacteriol.	2011	193		4559-4560			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. 		
@D	Abriouel, H.//Perez, M.B.//Casado, M.M.C.//Lavilla, L.L.//Hidalgo, P.M.//Caballero, G.N.//Franz, C.M.//Galvez, A.//Benomar, N. 	Complete Genome Sequence of a Potential Probiotic, Lactobacillus pentosus MP-10,  Isolated from Fermented Alorena Table Olives.	Genome Announcements	2016	4		e00854-16			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. 		
@D	Abrol, S.//Chaudhary, V.K. 	Excess PCR primers inhibit DNA cleavage by some restriction endonucleases.	Biotechniques	1993	15		630-632			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. 		
@D	Abrosimova, L.//Monakhova, M.//Schierling, B.//Volkov, E.//Romanova, E.//Wende, W.//Pingoud, A.//Kubareva, E.//Oretskaya, T. 	Light dependent activity of restriction endonucleases.	FEBS J.	2013	280		597			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). 		
@D	Abrosimova, L.A.//Monakhova, M.V.//Migur, A.Y.//Wolfgang, W.//Pingoud, A.//Kubareva, E.A.//Oretskaya, T.S. 	Thermo-switchable Activity of the Restriction Endonuclease SsoII Achieved by Site-Directed Enzyme Modification.	Life	2013	65		1012-1016			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. 		
@D	Abt, B. et al. 	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.	Standards in Genomic Sciences	2012	6		194-209			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. 		
@D	Abt, B. et al. 	Complete genome sequence of Cellulomonas flavigena type strain (134).	Standards in Genomic Sciences	2010	3		15-25			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. 		
@D	Abt, B. et al. 	Complete genome sequence of Leadbetterella byssophila type strain (4M15).	Standards in Genomic Sciences	2011	4		2-12			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. 		
@D	Abt, B. et al. 	Complete genome sequence of Cellulophaga algicola type strain (IC166).	Standards in Genomic Sciences	2011	4		72-80			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. 		
@D	Abt, B. et al. 	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.	Standards in Genomic Sciences	2013	8		88-105			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. 		
@D	Abu, C.M.//Wailan, A.M.//Sidjabat, H.E.//Zhang, L.//Marsh, N.//Rickard, C.M.//Davies, M.R.//McMillan, D.J. 	Draft Genome Sequence of Roseomonas mucosa Strain AU37, Isolated from a Peripheral Intravenous Catheter.	Genome Announcements	2017	5		e00128-17			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. 		
@D	AbuLaban, N.//Tan, B.//Dao, A.//Foght, J. 	Draft Genome Sequence of Uncultivated Toluene-Degrading Desulfobulbaceae Bacterium Tol-SR, Obtained by Stable Isotope Probing Using [13C6]Toluene.	Genome Announcements	2015	3		e01423-14			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. 		
@D	AbuLaban, N.//Tan, B.//Dao, A.//Foght, J. 	Draft Genome Sequence of Uncultivated Desulfosporosinus sp. Strain Tol-M, Obtained by Stable Isotope Probing Using [13C6]Toluene.	Genome Announcements	2015	3		e01422-14			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. 		
@D	Abulencia, C.B.//Wyborski, D.L.//Garcia, J.A.//Podar, M.//Chen, W.//Chang, S.H.//Chang, H.W.//Watson, D.//Brodie, E.L.//Hazen, T.C.//Keller, M. 	Environmental whole-genome amplification to access microbial populations in contaminated sediments.	Appl. Environ. Microbiol.	2006	72		3291-3301			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. 		
@D	Accetto, T.//Peterka, M.//Avgustin, G. 	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.	FEMS Microbiol. Lett.	2005	247		177-183			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. 		
@D	Acedo, J.Z.//Ibarra, R.C.//Miyata, S.T.//Blaine, A.H.//McMullen, L.M.//Vederas, J.C.//van Belkum, M.J. 	Draft Genome Sequence of Enterococcus canintestini 49, a Potential Probiotic That Produces Multiple Bacteriocins.	Genome Announcements	2017	5		e01131-17			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. 		
@D	Acharya, A.S.//Roy, K.B. 	An alternative approach for screening active Bam HI variants: Overexpression in T-7 RNA polymerase based system.	Indian J. Biochem. Biophys.	2001	38		303-308			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. 		
@D	Acharya, A.S.//Roy, K.B. 	Reduced activity of BamHI variants C54I, C64W, and C54D/C64R is consistent with the substrate-assisted catalysis model.	Biochem. Biophys. Res. Commun.	2001	287		153-159			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. 		
@D	Acuna-Amador, L.//Primot, A.//Cadieu, E.//Roulet, A.//Barloy-Hubler, F. 	Genomic repeats, misassembly and reannotation: a case study with long-read resequencing of Porphyromonas gingivalis reference strains.	BMC Genomics	2018	19		54			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. 		
@D	Adaikpoh, B.I.//Dowd, S.E.//Stevens, D.C. 	Draft Genome Sequence of Archangium sp. Strain Cb G35.	Genome Announcements	2017	5		e01678-16			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. 		
@D	Adam, E.//Muller, H.//Erlacher, A.//Berg, G. 	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.	Standards in Genomic Sciences	2016	11		61			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. 		
@D	Adam, Z.//Chen, Q.//Xu, R.//Diange, A.E.//Bromfield, E.S.//Tambong, J.T. 	Draft Genome Sequence of Pseudomonas simiae Strain 2-36, an In Vitro Antagonist of Rhizoctonia solani and Gaeumannomyces graminis.	Genome Announcements	2015	3		e01534-14			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. 		
@D	Adam, Z.//Tambong, J.T.//Chen, Q.//Lewis, C.T.//Levesque, C.A.//Xu, R. 	Draft Genome Sequence of Pseudomonas sp. Strain 2-92, a Biological Control Strain Isolated from a Field Plot Under Long-Term Mineral Fertilization.	Genome Announcements	2014	2		e01121-13			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. 		
@D	Adam, Z.//Tambong, J.T.//Lewis, C.T.//Levesque, C.A.//Chen, W.//Bromfield, E.S.//Khan, I.U.//Xu, R. 	Draft Genome Sequence of Pantoea ananatis Strain LMG 2665T, a Bacterial Pathogen  of Pineapple Fruitlets.	Genome Announcements	2014	2		e00489-14			We report the draft genome sequence of Pantoea ananatis LMG 2665(T), the bacterial causal agent of pineapple fruitlet rot. 		
@D	Adam, Z.//Whiteduck-Leveillee, K.//Cloutier, M.//Chen, W.//Lewis, C.T.//Levesque, C.A.//Topp, E.//Lapen, D.R.//Tambong, J.T.//Talbot, G.//Khan, I.U. 	Draft Genome Sequence of Arcobacter cibarius Strain LMG21996T, Isolated from Broiler Carcasses.	Genome Announcements	2014	2		e00034-14					
@D	Adam, Z.//Whiteduck-Leveillee, K.//Cloutier, M.//Chen, W.//Lewis, C.T.//Levesque, C.A.//Topp, E.//Lapen, D.R.//Tambong, J.T.//Talbot, G.//Khan, I.U. 	Draft genome sequences of two arcobacter strains isolated from human feces.	Genome Announcements	2014	2		e00113-14			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. 		
@D	Adam, Z.//Whiteduck-Leveillee, K.//Cloutier, M.//Tambong, J.T.//Chen, W.//Lewis, C.T.//Levesque, C.A.//Topp, E.//Lapen, D.R.//Talbot, G.//Khan, I.U. 	Draft genome sequences of three arcobacter strains of pig and dairy cattle manure origin.	Genome Announcements	2014	2		e00377-14			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. 		
@D	Adamczyk-Poplawska, M.//Kondrzycka, A.//Urbanek, K.//Piekarowicz, A. 	Tetra-amino-acid tandem repeats are involved in HsdS complementation in type IC restriction-modification systems.	Microbiology	2003	149		3311-3319			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. 		
@D	Adamczyk-Poplawska, M.//Lower, M.//Piekarowicz, A. 	Characterization of the NgoAXP: phase-variable type III restriction-modification system in Neisseria gonorrhoeae.	FEMS Microbiol. Lett.	2009	300		25-35			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. 		
@D	Adamczyk-Poplawska, M.//Lower, M.//Piekarowicz, A. 	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.	J. Bacteriol.	2011	193		6750-6759			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. 		
@D	Adams, G.M. 	Preventing autorestriction: A functional analysis of the pvuIIM and pvuIIW gene products.	Diss. Abstr.	1996	57		108			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. 		
@D	Adams, G.M.//Blumenthal, R.M. 	The PvuII DNA (cytosine-N4)-methyltransferase comprises two trypsin-defined domains, each of which binds a molecule of S-adenosyl-L-methionine.	Biochemistry	1997	36		8284-8292			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. 		
@D	Adams, G.M.//Blumenthal, R.M. 	Gene pvuIIW: a possible modulator of PvuII endonuclease subunit association.	Gene	1995	157		193-199			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. 		
@D	Adams, G.M.//Blumenthal, R.M. 	What is the significance of the internal duplication in the PvuII DNA methyltransferase?	FASEB J.	1995	9		A1399			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. 		
@D	Adams, K.L.//Clements, M.J.//Vaughn, J.C. 	The Peperomia mitochondrial coxI group I intron: Timing of horizontal transfer and subsequent evolution of the intron.	J. Mol. Evol.	1998	46		689-696			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. 		
@D	Adams, M.D. et al. 	The genome sequence of Drosophila melanogaster.	Science	2000	287		2185-2195			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. 		
@D	Adams, M.D.//Chan, E.R.//Molyneaux, N.D.//Bonomo, R.A. 	Genomewide analysis of divergence of antibiotic resistance determinants in closely related isolates of Acinetobacter baumannii.	Antimicrob. Agents Chemother.	2010	54		3569-3577			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. 		
@D	Adams, M.D.//Goglin, K.//Molyneaux, N.//Hujer, K.M.//Lavender, H.//Jamison, J.J.//MacDonald, I.J.//Martin, K.M.//Russo, T.//Campagnari, A.A.//Hujer, A.M.//Bonomo, R.A.//Gill, S.R. 	Comparative genome sequence analysis of multidrug-resistant Acinetobacter baumannii.	J. Bacteriol.	2008	190		8053-8064			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. 		
@D	Adams, R.L.P. 	Eukaryotic DNA methyltransferases - structure and function.	Bioessays	1995	17		139-145			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. 		
@A	Adams, R.L.P.//Pradhan, S.//Johnson, C.A.//Lindsay, H.//Shek, E.W.L.//Jenkins, G.I.//Urwin, N.A.R. 		Plant methyltransferases and their targets in the plant genome.			Russo, V.E.A.//Martienssen, R.A.//Riggs, A.D. 		Epigenetic Mechanisms of Gene Regulation				Cold Spring Harbor	Cold Spring Harbor Laboratory Press	1996		0		95-108									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. 		
@D	Adegboye, M.F.//Lobb, B.//Babalola, O.O.//Doxey, A.C.//Ma, K. 	Draft Genome Sequences of Two Novel Cellulolytic Streptomyces Strains Isolated from South African Rhizosphere Soil.	Genome Announcements	2018	6		e00632-18			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. 		
@D	Adelskov, J.//Patel, B.K. 	Draft Genome Sequence of Bacillus subtilis Strain D7XPN1, Isolated from Commercial Bioreactor-Degrading Food Waste.	Genome Announcements	2014	2		e00989-14			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. 		
@D	Adelskov, J.//Patel, B.K. 	Draft Genome Sequence of Paenibacillus Strain P1XP2, a Polysaccharide-Degrading,  Thermophilic, Facultative Anaerobic Bacterium Isolated from a Commercial  Bioreactor Degrading Food Waste.	Genome Announcements	2015	3		e01484-14			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. 		
@D	Adelskov, J.//Patel, B.K. 	Draft Genome Sequence of Cellulosilyticum sp. I15G10I2, a Novel Bacterium Isolated from a Coal Seam Gas Water Treatment Pond.	Genome Announcements	2017	5		e01616-16			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. 		
@D	Adelskov, J.//Patel, B.K.C. 	Draft Genome Sequence of the 1,2-Dichloroethane-Utilizing Micrococcus sp. Strain  NDB3Y10, Isolated from an Australian Bore Well Producing Coal Seam Gas.	Genome Announcements	2017	5		e00255-17			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. 		
@D	Adelskov, J.//Patel, B.K.C. 	Draft Genome Sequence of Microbacterium sp. TNHR37B Isolated from a Heated Aquifer Bore Well of the Great Artesian Basin, Australia.	Genome Announcements	2017	5		e00251-17			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. 		
@D	Adeniji, J.A.//Faleye, T.O.C.//Adewumi, O.M.//Olayinka, O.A.//Donbraye, E.//Oluremi, B.//George, U.E.//Arowolo, O.A.//Omoruyi, E.C.//Ifeorah, M.I.//Akande, A. 	Draft Genome Sequence of Mycoplasma arginini Strain NGR_2017.	Genome Announcements	2018	6		e00577-18			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. 		
@D	Adessi, A.//Spini, G.//Presta, L.//Mengoni, A.//Viti, C.//Giovannetti, L.//Fani, R.//De Philippis, R. 	Draft genome sequence and overview of the purple non sulfur bacterium Rhodopseudomonas palustris 42OL.	Standards in Genomic Sciences	2016	11		24			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. 		
@D	Adimpong, D.B.//Sorensen, K.I.//Nielsen, D.S.//Thorsen, L.//Rasmussen, T.B.//Derkx, P.M.//Jespersen, L. 	Draft Whole-Genome Sequence of Bacillus sonorensis Strain L12, a Source of Nonribosomal Lipopeptides.	Genome Announcements	2013	1		e0009713			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. 		
@D	Adlakha, N.//Ritturaj, K.H.//Rajagopal, R.//Yazdani, S.S. 	Draft Genome Sequence of the Paenibacillus sp. Strain ICGEB2008 (MTCC 5639) Isolated from the Gut of Helicoverpa armigera.	Genome Announcements	2013	1		e00026-12			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. 		
@D	Adler, S.P.//Nathans, D. 	Studies of SV40 DNA: V. Conversion of circular to linear SV40 DNA by restriction endonuclease from Escherichia coli B.	Biochim. Biophys. Acta	1973	299		177-188			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. 		
@D	Adnani, N.//Braun, D.R.//McDonald, B.R.//Chevrette, M.G.//Currie, C.R.//Bugni, T.S. 	Draft Genome Sequence of Micromonospora sp. Strain WMMB235, a Marine Ascidian-Associated Bacterium.	Genome Announcements	2017	5		e01369-16			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. 		
@D	Adnani, N.//Braun, D.R.//McDonald, B.R.//Chevrette, M.G.//Currie, C.R.//Bugni, T.S. 	Complete Genome Sequence of Rhodococcus sp. Strain WMMA185, a Marine Sponge-Associated Bacterium.	Genome Announcements	2016	4		e01406-16			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. 		
@D	Adriaenssens, E.M.//Guerrero, L.D.//Makhalanyane, T.P.//Aislabie, J.M.//Cowan, D.A. 	Draft Genome Sequence of the Aromatic Hydrocarbon-Degrading Bacterium Sphingobium sp. Strain Ant17, Isolated from Antarctic Soil.	Genome Announcements	2014	2		e00212-14			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. 		
@D	Advani, S.//Mishra, P.//Dubey, S.//Thakur, S. 	Categoric prediction of metal ion mechanisms in the active sites of 17 select type II restriction endonucleases.	Biochem. Biophys. Res. Commun.	2010	402		177-179			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. 		
@D	Advani, S.//Roy, K.B. 	Properties and secondary structure analysis of BanI endonuclease: identification of putative active site.	Biochem. Biophys. Res. Commun.	2000	279		11-16			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. 		
@D	Advani, S.//Roy, K.B. 	BanI restriction endonuclease binds in the major groove of DNA: An inhibition kinetic study using substrates with mismatch basepairs.	Biochem. Biophys. Res. Commun.	2000	269		35-40			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. 		
@D	Aeling, K.A.//Steffen, N.R.//Johnson, M.//Hatfield, G.W.//Lathrop, R.H.//Senear, D.F. 	DNA deformation energy as an indirect recognition mechanism in protein-DNA interactions.	IEEE/ACM Trans. Comput. Biol. Bioinform.	2007	4		117-125			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. 		
@D	Aertsen, A.//Mebrhatu, M.T.//Michiels, C.W. 	Activation of the Salmonella Typhimurium Mrr protein.	Biochem. Biophys. Res. Commun.	2008	367		435-439			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. 		
@D	Aertsen, A.//Michiels, C.W. 	Mrr instigates the SOS response after high pressure stress in Escherichia coli.	Mol. Microbiol.	2005	58		1381-1391			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. 		
@D	Afouda, P.//Dubourg, G.//Labas, N.//Raoult, D.//Fournier, P.E. 	Draft Genome Sequence of Agrococcusbaldri Strain Marseille-P2731.	Genome Announcements	2017	5		e00015-17			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. 		
@D	Agarkova, I.V.//Dunigan, D.D.//Van Etten, J.L. 	Virion-associated restriction endonucleases of Chloroviruses.	J. Virol.	2006	80		8114-8123			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. 		
@D	Agarwal, B.//Agarwala, N.//Saikia, S.//Sarkar, S.//Ahmed, G. 	Draft Genome Sequence of a Polymyxin B-Resistant Sequence Type 195 Clinical Isolate of Acinetobacter baumannii from India.	Genome Announcements	2018	6		e00031-18			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. 		
@D	Agarwal, L.//Purohit, H.J. 	Genome Sequence of Rhizobium lupini HPC(L) Isolated from Saline Desert Soil, Kutch (Gujarat).	Genome Announcements	2013	1		e00071-12			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. 		
@D	Agarwal, P.K.//Bhattacharya, S.K. 	Construction of a multi RE module: Exploitation of mechanochemistry of restriction endonucleases.	Biotechnol. Bioeng.	1999	65		233-239			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. 		
@D	Aggarwal, A.K. 	Crystallization of DNA binding proteins with oligodeoxynucleotides.	Methods	1990	1		83-90			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. 		
@D	Aggarwal, A.K. 	Structure and function of restriction endonucleases.	Curr. Opin. Struct. Biol.	1995	5		11-19			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. 		
@D	Aggarwal, A.K.//Wah, D.A. 	Novel site-specific DNA endonucleases.	Curr. Opin. Struct. Biol.	1998	8		19-25			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. 		
@D	Aggarwal, R.K.//Dawar, C.//Das, S.//Sharma, S. 	Draft Genome Sequences of Two Drug-Resistant Isolates of Pseudomonas aeruginosa Obtained from Keratitis Patients in India.	Genome Announcements	2015	3		e01404-14			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. 		
@D	Aggarwal, R.K.//Dawar, C.//Phanindranath, R.//Mutnuri, L.//Dayal, A.M. 	Draft Genome Sequence of a Versatile Hydrocarbon-Degrading Bacterium, Rhodococcus pyridinivorans Strain KG-16, Collected from Oil Fields in India.	Genome Announcements	2016	4		e01704-15			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. 		
@D	Aghnatios, R.//Cayrou, C.//Garibal, M.//Robert, C.//Azza, S.//Raoult, D.//Drancourt, M. 	Draft genome of Gemmata massiliana sp. nov, a water-borne Planctomycetes species  exhibiting two variants.	Standards in Genomic Sciences	2015	10		120			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. 		
@D	Agren, J.//Finn, M.//Bengtsson, B.//Segerman, B. 	Microevolution during an Anthrax Outbreak Leading to Clonal Heterogeneity and Penicillin Resistance.	PLoS ONE	2014	9		E89112			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. 		
@D	Agron, P.G.//Sobecky, P.//Andersen, G.L. 	Establishment of uncharacterized plasmids in Escherichia coli by in vitro transposition.	FEMS Microbiol. Lett.	2002	217		249-254			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. 		
@D	Aguado-Urda, M.//Lopez-Campos, G.H.//Blanco, M.M.//Fernandez-Garayzabal, J.F.//Cutuli, M.T.//Aspiroz, C.//Lopez-Alonso, V.//Gibello, A. 	Genome sequence of Lactococcus garvieae 21881, isolated in a case of human septicemia.	J. Bacteriol.	2011	193		4033-4034			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. 		
@D	Aguado-Urda, M.//Lopez-Campos, G.H.//Gibello, A.//Cutuli, M.T.//Lopez-Alonso, V.//Fernandez-Garayzabal, J.F.//Blanco, M.M. 	Genome Sequence of Lactococcus garvieae 8831, Isolated from Rainbow Trout Lactococcosis Outbreaks in Spain.	J. Bacteriol.	2011	193		4263-4264			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%. 		
@D	Aguilar-Bultet, L.//Calderon-Copete, S.P.//Frey, J.//Falquet, L. 	Draft Genome Sequence of the Virulent Avibacterium paragallinarum Serotype A Strain JF4211 and Identification of Two Toxins.	Genome Announcements	2013	1		e00592-13			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. 		
@D	Aguirre-Arteta, A.M.//Grunewald, I.//Cardoso, M.C.//Leonhardt, H. 	Expression of an alternative Dnmt1 isoform during muscle differentiation.	Cell Growth Differ.	2000	11		551-559			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. 		
@D	Ahad, R.//Zhou, T.//Lepp, D.//Pauls, K.P. 	Draft Genome Sequence of Citrobacter freundii Strain A47, Resistant to the Mycotoxin Deoxynivalenol.	Genome Announcements	2017	5		e00019-17			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). 		
@D	Aherfi, S.//Pagnier, I.//Fournous, G.//Raoult, D.//La Scola, B.//Colson, P. 	Complete genome sequence of Cannes 8 virus, a new member of the proposed family 'Marseilleviridae'.	Virus Genes	2013	47		550-555			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." 		
@D	Ahir, V.B.//Roy, A.//Jhala, M.K.//Bhanderi, B.B.//Mathakiya, R.A.//Bhatt, V.D.//Padiya, K.B.//Jakhesara, S.J.//Koringa, P.G.//Joshi, C.G. 	Genome Sequence of Pasteurella multocida subsp. gallicida Anand1_poultry.	J. Bacteriol.	2011	193		5604			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. 		
@D	Ahlert, D.//Stegemann, S.//Kahlau, S.//Ruf, S.//Bock, R. 	Insensitivity of chloroplast gene expression to DNA methylation.	Mol. Genet. Genomics	2009	282		17-24			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. 		
@D	Ahlgren, N.A.//Chen, Y.//Needham, D.M.//Parada, A.E.//Sachdeva, R.//Trinh, V.//Chen, T.//Fuhrman, J.A. 	Genome and epigenome of a novel marine Thaumarchaeota strain suggest viral infection, phosphorothioation DNA modification and multiple restriction systems.	Environ. Microbiol.	2017	19		2434-2452			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. 		
@D	Ahmad, F.//Huang, X.//Lan, H.X.//Huma, T.//Bao, Y.M.//Huang, J.//Zhang, H.S. 	Comprehensive gene expression analysis of the DNA (cytosine-5) methyltransferase family in rice (Oryza sativa L.).	Gen. Mol. Res.	2014	13		5159-5172			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. 		
@D	Ahmad, I.//Krishnamurthy, V.//Rao, D.N. 	DNA recognition by the EcoP15I and EcoPI modification methyltransferases.	Gene	1995	157		143-147			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. 		
@D	Ahmad, I.//Kulkarni, M.//Gopinath, A.//Saikrishnan, K. 	Single-site DNA cleavage by Type III restriction endonuclease requires a site-bound enzyme and a trans-acting enzyme that are ATPase-activated.	Nucleic Acids Res.	2018	46		6229-6237			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. 		
@D	Ahmad, I.//Rao, D.N. 	Photolabeling of the EcoP15 DNA methyltransferase with S-adenosyl-L-methionine.	Gene	1994	142		67-71			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. 		
@D	Ahmad, I.//Rao, D.N. 	Chemistry and biology of DNA methyltransferases.	Crit. Rev. Biochem. Mol. Biol.	1996	31		361-380			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. 		
@D	Ahmad, I.//Rao, D.N. 	Interaction of EcoP15I DNA methyltransferase with oligonucleotides containing the asymmetric sequence 5'-CAGCAG-3'.	J. Mol. Biol.	1994	242		378-388			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. 		
@D	Ahmad, I.//Rao, D.N. 	Functional analysis of conserved motifs in EcoP15I DNA methyltransferase.	J. Mol. Biol.	1996	259		229-240			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. 		
@D	Ahmad, N.//Hii, S.Y.//Hashim, R.//Issa, R. 	Draft Genome Sequence of Salmonellaenterica Serovar Typhi IMR_TP298/15, a Strain  with Intermediate Susceptibility to Ciprofloxacin, Isolated from a Typhoid  Outbreak.	Genome Announcements	2017	5		e01740-16			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. 		
@D	Ahmad, N.//Hii, S.Y.//Mohd, K.M.K.//Abd, W.M.A.//Hashim, R.//Tang, S.N.//Liow, Y.L.//Hamzah, H.//Dahalan, N.A.//Seradja, V. 	First Draft Genome Sequences of Malaysian Clinical Isolates of Corynebacterium diphtheriae.	Genome Announcements	2017	5		e01670-16			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. 		
@D	Ahmed, A.//Earl, J.//Retchless, A.//Hillier, S.L.//Rabe, L.K.//Cherpes, T.L.//Powell, E.//Janto, B.//Eutsey, R.//Hiller, N.L.//Boissy, R.//Dahlgren, M.E.//Hall, B.G.//Costerton, J.W.//Post, J.C.//Hu, F.Z.//Ehrlich, G.D. 	Comparative Genomic Analyses of 17 Clinical Isolates of Gardnerella vaginalis Provide Evidence of Multiple Genetically Isolated Clades Consistent with  Subspeciation into Genovars.	J. Bacteriol.	2012	194		3922-3937			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. 		
@D	Ahmed, I.//Oshima, K.//Suda, W.//Kitamura, K.//Iida, T.//Ohmori, Y.//Fujiwara, T.//Hattori, M.//Ohkuma, M. 	Draft Genome Sequence of the Boron-Tolerant and Moderately Halotolerant Bacterium Gracilibacillus boraciitolerans JCM 21714T.	Genome Announcements	2014	2		e00097-14			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. 		
@D	Ahmed, I.H.//Manning, G.//Wassenaar, T.M.//Cawthraw, S.//Newell, D.G. 	Identification of genetic differences between two Campylobacter jejuni strains with different colonization potentials.	Microbiology	2002	148		1203-1212			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. 		
@D	Ahmed, N.//Saini, V.//Raghuvanshi, S.//Khurana, J.P.//Tyagi, A.K.//Tyagi, A.K.//Hasnain, S.E. 	Molecular analysis of a leprosy immunotherapeutic bacillus provides insights into Mycobacterium evolution.	PLoS ONE	2007	2		E968			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. 		
@D	Ahmed, S.A. et al. 	Genomic comparison of Escherichia coli O104:H4 isolates from 2009 and 2011 reveals plasmid, and prophage heterogeneity, including shiga toxin encoding phage  stx2.	PLoS ONE	2012	7		e48228			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. 		
@D	Ahn, Y.S.//Piamsomboon, P.//Tang, K.F.J.//Han, J.E.//Kim, J.H. 	Complete Genome Sequence of Acute Hepatopancreatic Necrosis Disease-Causing Vibrio campbellii LA16-V1, Isolated from Penaeus vannamei Cultured in a Latin  American Country.	Genome Announcements	2017	5		e01011-17			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. 		
@D	Ahrenfeldt, J.//Skaarup, C.//Hasman, H.//Pedersen, A.G.//Aarestrup, F.M.//Lund, O. 	Bacterial whole genome-based phylogeny: construction of a new benchmarking dataset and assessment of some existing methods.	BMC Genomics	2017	18		19			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 . 		
@D	Ahuja, Y.R. 	Bacterial infection restriction endonucleases, genetic damage and cancer.	Biol. Zentralbl.	1991	110		179-187			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. 		
@D	Ahuja, Y.R.//Obe, G. 	Are rogue cells an indicator of cancer risk due to the action of bacterial restriction endonucleases?	Mutat. Res.	1994	310		103-112			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. 		
@D	Ai, C.//McCarthy, S.//Schackwitz, W.//Martin, J.//Lipzen, A.//Blum, P. 	Complete Genome Sequences of Evolved Arsenate-Resistant Metallosphaera sedula Strains.	Genome Announcements	2015	3		e01142-15			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. 		
@D	Ai, H.//Zhang, J.//Yang, M.//Yu, P.//Li, S.//Zhu, M.//Dong, H.//Wang, S.//Wang, J. 	Draft Genome Sequence of an Anaerobic, Thermophilic Bacterium, Thermoanaerobacterium aotearoense SCUT27, Isolated from a Hot Spring in China.	Genome Announcements	2014	2		e00041-14			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. 		
@D	Ai, L.//Chen, C.//Zhou, F.//Wang, L.//Zhang, H.//Chen, W.//Guo, B. 	Complete genome sequence of probiotic Lactobacillus casei BD-II.	J. Bacteriol.	2011	193		3160-3161			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. 		
@D	Aiba, Y.//Sumaoka, J.//Komiyama, M. 	Artificial DNA cutters for DNA manipulation and genome engineering.	Chem. Soc. Rev.	2011	40		5657-5668			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. 		
@D	Aigle, A.//Michotey, V.//Bonin, P. 	Draft-genome sequence of Shewanella algae strain C6G3.	Standards in Genomic Sciences	2015	10		43			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. 		
@D	Aikawa, C.//Furukawa, N.//Watanabe, T.//Minegishi, K.//Furukawa, A.//Eishi, Y.//Oshima, K.//Kurokawa, K.//Hattori, M.//Nakano, K.//Maruyama, F.//Nakagawa, I.//Ooshima, T. 	Complete Genome Sequence of the Serotype k Streptococcus mutans Strain LJ23.	J. Bacteriol.	2012	194		2754-2755			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. 		
@D	Aiken, C.//Gumport, R.I. 	Restriction endonuclease RsrI from Rhodobacter sphaeroides, an isoschizomer of EcoRI:  purification and properties.	Nucleic Acids Res.	1988	16		7901-7916			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. 		
@D	Aiken, C.//Gumport, R.I. 	Interaction of RsrI endonuclease, an isoschizomer of EcoRI, with oligodeoxyribonucleotides containing base analogues.	J. Cell Biochem. Suppl.	1989	13D		79			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. 		
@D	Aiken, C.//Milarski-Brown, K.//Gumport, R.I. 	RsrI and EcoRI are two different restriction endonucleases that recognize the same DNA sequence.	Fed. Proc.	1986	45		1914			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. 		
@D	Aiken, C.R. 	Sequence-specific recognition of DNA by RsrI endonuclease of Rhodobacter sphaeroides, an isoschizomer of EcoRI.	Diss. Abstr.	1991	52		1399			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. 		
@D	Aiken, C.R.//Fisher, E.W.//Gumport, R.I. 	The specific binding, bending, and unwinding of DNA by RsrI endonuclease, an isoschizomer of EcoRI endonuclease.	J. Biol. Chem.	1991	266		19063-19069			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. 		
@D	Aiken, C.R.//Gumport, R.I. 	Base analogs in study of restriction enzyme-DNA interactions.	Methods Enzymol.	1991	208		433-457			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. 		
@D	Aiken, C.R.//McLaughlin, L.W.//Gumport, R.I. 	The highly homologous isoschizomers RsrI endonuclease and EcoRI endonuclease do not recognize their target sequence identically.	J. Biol. Chem.	1991	266		19070-19078			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. 		
@D	Ailloud, F.//Lowe, T.M.//Robene, I.//Cruveiller, S.//Allen, C.//Prior, P. 	In planta comparative transcriptomics of host-adapted strains of Ralstonia solanacearum.	PeerJ	2016	4		e1549			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. 		
@D	Ainala, S.K.//Ashok, S.//Ko, Y.//Park, S. 	Glycerol assimilation and production of 1,3-propanediol by Citrobacter amalonaticus Y19.	Appl. Microbiol. Biotechnol.	2013	97		5001-5011			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. 		
@D	Ainala, S.K.//Somasundar, A.//Park, S. 	Complete Genome Sequence of Pseudomonas denitrificans ATCC 13867.	Genome Announcements	2013	1		e00257-13			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. 		
@D	Ainsworth, S.//Mahony, J.//van Sinderen, D. 	The Plasmid Complement of Lactococcus lactis UC509.9 Encodes Multiple Bacteriophage Resistance Systems.	Appl. Environ. Microbiol.	2014	80		4341-4349			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. 		
@D	Ainsworth, S.//Zomer, A.//de Jager, V.//Bottacini, F.//van Hijum, S.A.//Mahony, J.//van Sinderen, D. 	Complete Genome of Lactococcus lactis subsp. cremoris UC509.9, Host for a Model Lactococcal P335 Bacteriophage.	Genome Announcements	2013	1		e00119-12			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. 		
@D	Aizawa, Y.//Xiang, Q.//Pyle, A.M. 	Kinetic dissection of the multistep process in L1.ltrB intron mobility.	Nucleic Acids Res. Suppl.	2001	1		249-250			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. 		
@D	Aizenberg-Gershtein, Y.//Izhaki, I.//Lapidus, A.//Copeland, A.//Reddy, T.//Huntemann, M.//Pillay, M.//Markowitz, V.//Goker, M.//Woyke, T.//Klenk, H.P.//Kyrpides, N.C.//Halpern, M. 	High quality permanent draft genome sequence of Phaseolibacter flectens ATCC 12775(T), a plant pathogen of French bean pods.	Standards in Genomic Sciences	2016	11		4			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. 		
@D	Ajdic, D.//McShan, W.M.//McLaughlin, R.E.//Savic, G.//Chang, J.//Carson, M.B.//Primeaux, C.//Tian, R.//Kenton, S.//Jia, H.//Lin, S.//Qian, Y.//Li, S.//Zhu, H.//Najar, F.//Lai, H.//White, J.//Roe, B.A.//Jerretti, J.J. 	Genome sequence of Streptococcus mutans UA159, a cariogenic dental pathogen.	Proc. Natl. Acad. Sci. U. S. A.	2002	99		14434-14439			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. 		
@D	Akamatsu, M.A.//Nishiyama, M.Y. Jr.//Morone, M.//Oliveira, U.C.//Bezerra, M.F.//Sakauchi, M.A.//Raw, I.//Junqueira-de-Azevedo, I.L.//Kitajima, J.P.//Carvalho, E.//Ho, P.L. 	Whole-Genome Sequence of a Bordetella pertussis Brazilian Vaccine Strain.	Genome Announcements	2015	3		e01570-14			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). 		
@D	Akasaka, T.//Matsuura, K.//Emi, N.//Kobayashi, K. 	Conjugation of plasmid DNAs with lactose via diazocoupling enhances resistance to restriction enzymes and acquires binding affinity to galactose-specific lectin.	Biochem. Biophys. Res. Commun.	1999	260		323-328			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. 		
@D	Akatov, A.K.//Zueva, V.S.//Dmitrenko, O.A. 	A new approach to establishing the set of phages for typing methicillin-resistant Staphylococcus aureus.	J. Chemother.	1991	3		275-278			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. 		
@D	Akbar, S.//Dowd, S.E.//Stevens, D.C. 	Draft Genome Sequence of Cystobacter ferrugineus Strain Cbfe23.	Genome Announcements	2017	5		e01601-16			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. 		
@D	Akbar, S.//Rout, S.P.//Humphreys, P.N. 	Draft Genome Sequence of the Biofilm-Forming Stenotrophomonas maltophilia Strain  53.	Genome Announcements	2015	3		e00312-15			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. 		
@D	Akbar, S.//Rout, S.P.//Humphreys, P.N. 	Draft Genome Sequences of Pseudomonas aeruginosa Strain PS3 and Citrobacter freundii Strain SA79 Obtained from a Wound Dressing-Associated Biofilm.	Genome Announcements	2015	3		e00561-15			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. 		
@D	Akcelik, M. 	The conjugal plasmid pLL10236 encodes lactose fermentation ability, restriction/modification activity, bacteriocin production and immunity in Lactococcus lactis subsp. Lactis LL102.	Food Microbiol.	1999	16		487-494			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. 		
@D	Akcelik, M.//Sanlibaba, P.//Tukel, C. 	Phage resistance in Lactococcus lactis subsp lactis strains isolated from traditional fermented milk products in Turkey.	Int. J. Food Sci. Technol.	2000	35		473-481			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. 		
@D	Akhtar, M.//Perehinec, T.M.//Nazli, A.//Hill, P.J.//Rees, C.E.D. 	Partial DNA methylation in Listeria monocytogenes creates variable populations of cells with altered virulence.	Abstr. Gen. Meet. Am. Soc. Microbiol.	2001	101		411			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. 		
@D	Akita, H.//Kimura, Z.//Yusoff, M.Z.//Nakashima, N.//Hoshino, T. 	Draft Genome Sequence of Burkholderia sp. Strain CCA53, Isolated from Leaf Soil.	Genome Announcements	2016	4		e00630-16			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. 		
@D	Akita, H.//Kimura, Z.I.//Hoshino, T. 	Draft Genome Sequence of Pseudomonas sp. Strain CCA1, Isolated from Leaf Soil.	Genome Announcements	2016	4		e01371-16			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%. 		
@D	Akita, H.//Kimura, Z.I.//Matsushika, A. 	Complete Genome Sequence of Ureibacillus thermosphaericus A1, a Thermophilic Bacillus Isolated from Compost.	Genome Announcements	2017	5		e00910-17			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. 		
@D	Akiyama, T.//Ishige, T.//Kanesaki, Y.//Ito, S.//Oinuma, K.//Takaya, N.//Sasaki, Y.//Yajima, S. 	Draft Genome Sequence of Microbacterium sp. Strain HM58-2, Which Hydrolyzes Acylhydrazides.	Genome Announcements	2016	4		e00554-16			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. 		
@D	Aklujkar, M.//Young, N.D.//Holmes, D.//Chavan, M.//Risso, C.//Kiss, H.E.//Han, C.S.//Land, M.L.//Lovley, D.R. 	The genome of Geobacter bemidjiensis, exemplar for the subsurface clade of Geobacter species that predominate in Fe(III)-reducing subsurface environments.	BMC Genomics	2010	11		490			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. 		
@D	Akman, L.//Rio, R.V.M.//Beard, C.B.//Aksoy, S. 	Genome size determination and coding capacity of Sodalis glossinidius, an enteric symbiont of Tsetse flies, as revealed by hybridization to Escherichia coli gene arrays.	J. Bacteriol.	2001	183		4517-4525			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. 		
@D	Akman, L.//Yamashita, A.//Watanabe, H.//Oshima, K.//Shiba, T.//Hattori, M.//Aksoy, S. 	Genome sequence of the endocellular obligate symbiont of tsetse flies, Wigglesworthia glossinidia.	Nat. Genet.	2002	32		402-407			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. 		
@D	Akopyants, N.S.//Clifton, S.W.//Kersulyte, D.//Crabtree, J.E.//Youree, B.E.//Reece, C.A.//Bukanov, N.O.//Drazek, E.S.//Roe, B.A.//Berg, D.E. 	Analyses of the cag pathogenicity island of Helicobacter pylori.	Mol. Microbiol.	1998	28		37-53			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. 		
@D	Akopyants, N.S.//Fradkov, A.//Diatchenko, L.//Hill, J.E.//Siebert, P.D.//Lukyanov, S.A.//Sverdlov, E.D.//Berg, D.E. 	PCR-based subtractive hybridization and differences in gene content among strains of Helicobacter pylori.	Proc. Natl. Acad. Sci. U. S. A.	1998	95		13108-13113			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. 		
@D	Akter, A. et al. 	Extremely low genomic diversity of Rickettsia japonica distributed in Japan.	Genome Biol. Evol.	2017	9		124-133			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. 		
@D	Akulenko, N.V.//Ivashina, T.V.//Shaloiko, L.A.//Shlyapnikov, M.G.//Ksenzenko, V.N. 	New site-specific endonucleases F-TflI, F-TflII, and F-TflIV encoded by bacteriophage T5.	Mol. Biol. (Mosk)	2004	38		530-537			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. 		
@D	Akulinin, G.E.//Getko, G.A.//Repin, V.E.//Degtyarev, S.K. 	New restriction endonuclease from the soil strain Bacillus megaterium 12.	Izv. Sib. Otd. Akad. Nauk SSSR	1988	14		105-108			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. 		
@D	Akuzawa, S.//Nagaoka, J.//Kanekatsu, M.//Kanesaki, Y.//Suzuki, T. 	Draft Genome Sequence of Oceanobacillus picturae Heshi-B3, Isolated from Fermented Rice Bran in a Traditional Japanese Seafood Dish.	Genome Announcements	2016	4		e01621-15			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. 		
@D	Akuzawa, S.//Nagaoka, J.//Kanekatsu, M.//Kubota, E.//Ohtake, R.//Suzuki, T.//Kanesaki, Y. 	Draft Genome Sequence of Paenibacillus amylolyticus Heshi-A3, Isolated from Fermented Rice Bran in a Japanese Fermented Seafood Dish.	Genome Announcements	2016	4		e00218-16			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. 		
@D	Al-Awadhi, S.//Welch, S.G.//Smith, K.E.//Williams, R.A.D. 	BstB7SI (R/CCGGY), a thermostable isoschizomer of Cfr10I, from a strain of Bacillus stearothermophilus isolated from oil-contaminated soil in Kuwait.	FEMS Microbiol. Lett.	1998	160		205-208			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. 		
@D	Al-Rashdi, A.S.A.//Jadhav, B.L.//Deshpande, T.//Deshpande, U. 	Whole-Genome Sequencing and Annotation of a Clinical Isolate of Mycobacterium tuberculosis from Mumbai, India.	Genome Announcements	2014	2		e00154-14			We report here the annotated genome sequence of a clinical isolate of Mycobacterium tuberculosis from Mumbai, India. 		
@D	Al-Saari, N.//Meirelles, P.M.//Mino, S.//Suda, W.//Oshima, K.//Hattori, M.//Ohkuma, M.//Thompson, F.L.//Gomez-Gil, B.//Sawabe, T.//Sawabe, T. 	Draft Genome Sequences of Two Vibrionaceae Species, Vibrio ponticus C121 and Photobacterium aphoticum C119, Isolated as Coral Reef Microbiota.	Genome Announcements	2014	2		e01095-14			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. 		
@D	Al-Sayegh, A.//Al-Wahaibi, Y.//Joshi, S.//Al-Bahry, S.//Elshafie, A.//Al-Bemani, A. 	Draft Genome Sequence of Bacillus subtilis AS2, a Heavy Crude Oil-Degrading and Biosurfactant-Producing Bacterium Isolated from a Soil Sample.	Genome Announcements	2017	5		e00969-17			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. 		
@D	Alam, M.//Roy, C.//Pyne, P.//Agarwal, A.//George, A.//Ghosh, W. 	Whole-Genome Shotgun Sequence of the Sulfur-Oxidizing Chemoautotroph Pseudaminobacter salicylatoxidans KCT001.	J. Bacteriol.	2012	194		4743-4744			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. 		
@D	Alam, N.//Sittman, D.B. 	Characterization of the cytotoxic effect of a chimeric restriction enzyme, H1 degrees-FokI.	Gene Ther. Mol. Biol.	2006	10A		147-159			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. 		
@D	Alatossava, T.//Klaenhammer, T.R. 	Molecular characterization of three small isometric-headed bacteriophages which vary in their sensitivity to the lactococcal phage resistance plasmid pTR2030.	Appl. Environ. Microbiol.	1991	57		1346-1353			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. 		
@D	Alawi, M.//Shapiro, N.//Woyke, T.//Horn, F.//Bakermans, C.//Wagner, D. 	Genome Sequence of Methanosarcina soligelidi SMA-21, Isolated from Siberian Permafrost-Affected Soil.	Genome Announcements	2015	3		e00270-15			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. 		
@D	Alba, J.//Marcaida, M.J.//Prieto, J.//Montoya, G.//Molina, R.//D'Abramo, M. 	Structure and dynamics of mesophilic variants from the homing endonuclease I-DmoI.	J. Comput. Aided Mol. Des.	2017	31		1063-1072			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. 		
@D	Albalat, R. 	Evolution of DNA-methylation machinery: DNA methyltransferases and methyl-DNA binding proteins in the amphioxus Branchiostoma floridae.	Dev. Genes Evol.	2008	218		691-701			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. 		
@D	Albarracin, O.A.G.//Tobares, R.A.//Ducasse, D.A.//Smania, A.M. 	Draft Genome Sequence of Bacillus subtilis ALBA01, a Strain with Antagonistic Activity against the Soilborne Fungal Pathogen of Onion Setophoma terrestris.	Genome Announcements	2016	4		e00455-16			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. 		
@D	Albersmeier, A.//Bomholt, C.//Glaub, A.//Ruckert, C.//Soriano, F.//Fernandez-Natal, I.//Tauch, A. 	Draft Genome Sequence of the Multidrug-Resistant Clinical Isolate Dermabacter hominis 1368.	Genome Announcements	2014	2		e00728-14			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. 		
@D	Albert, K.//Sela, D.A. 	Draft Genome Sequence of Bifidobacterium longum UMA026, Isolated from Holstein Dairy Cow Feces.	Genome Announcements	2018	6		e00559-18			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%. 		
@D	Albert, K.//Sela, D.A. 	Draft Genome Sequences of Alloscardovia macacae UMA81211 and UMA81212, Isolated from the Feces of a Rhesus Macaque (Macaca mulatta).	Genome Announcements	2017	5		e00581-17			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%. 		
@D	Albert, P.//Varga, B.//Zsibrita, N.//Kiss, A. 	Circularly permuted variants of two CG-specific prokaryotic DNA methyltransferases.	PLoS ONE	2018	13		e0197232			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. 		
@D	Albertsen, H.M.//Le Paslier, D.//Abderrahim, H.//Dausset, J.//Cann, H.//Cohen, D. 	Improved control of partial DNA restriction enzyme digest in agarose using limiting concentrations of Mg++.	Nucleic Acids Res.	1989	17		808			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. 		
@D	Albertsen, M.//Hugenholtz, P.//Skarshewski, A.//Nielsen, K.L.//Tyson, G.W.//Nielsen, P.H. 	Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes.	Nat. Biotechnol.	2013	31		533-538			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. 		
@D	Albu, R.F.//Jurkowski, T.P.//Jeltsch, A. 	The Caulobacter crescentus DNA-(adenine-N6)-methyltransferase CcrM methylates DNA in a distributive manner.	Nucleic Acids Res.	2012	40		1708-1716					
@D	Albu, R.F.//Zacharias, M.//Jurkowski, T.P.//Jeltsch, A. 	DNA Interaction of the CcrM DNA Methyltransferase: A Mutational and Modeling Study.	Chembiochem	2012	13		1304-1311			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. 		
@D	Albuquerque, G.M.R.//Souza, E.B.//Silva, A.M.F.//Lopes, C.A.//Boiteux, L.S.//Fonseca, M.E.N. 	Genome Sequence of Ralstonia pseudosolanacearum Strains with Compatible and Incompatible Interactions with the Major Tomato Resistance Source Hawaii 7996.	Genome Announcements	2017	5		e00982-17			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. 		
@D	Alcaraz, L.D. et al. 	The genome of Bacillus coahuilensis reveals adaptations essential for survival in the relic of an ancient marine environment.	Proc. Natl. Acad. Sci. U. S. A.	2008	105		5803-5808			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. 		
@D	Alcaraz, L.D.//Moreno-Hagelsieb, G.//Eguiarte, L.E.//Souza, V.//Herrera-Estrella, L.//Olmedo-Alvarez, G. 	Understanding the evolutionary relationships and major traits of Bacillus through comparative genomics.	BMC Genomics	2010	11		332			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. 		
@D	Alegado, R.A.//Ferriera, S.//Nusbaum, C.//Young, S.K.//Zeng, Q.//Imamovic, A.//Fairclough, S.R.//King, N. 	Complete Genome Sequence of Algoriphagus sp. PR1, Bacterial Prey of a Colony-Forming Choanoflagellate.	J. Bacteriol.	2011	193		1485-1486			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. 		
@D	Alegre, M.T.//Rodriguez, M.C.//Mesas, J.M. 	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.	Plasmid	2009	61		130-134			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. 		
@D	Alejo-Viderique, A.//Contreras-Castro, L.//Felix-Gastelum, R.//Maldonado, L.A.//Quintana, E.T. 	Draft Genome Sequence of a Streptomycete Isolated from Potato Common Scab Lesions in the State of Sinaloa, Mexico.	Microbiol. Resour. Announc.	2018	7		e00827-18			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. 		
@D	Aleksandrzak-Piekarczyk, T.//Koryszewska-Baginska, A.//Bardowski, J. 	Genome Sequence of the Probiotic Strain Lactobacillus rhamnosus (Formerly Lactobacillus casei) LOCK900.	Genome Announcements	2013	1		e00640-13			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. 		
@D	Alencar, V.C.//Barbosa, D.//Santos, D.S.//Oliveira, A.C.//de Oliveira, R.C.//Nunes, L.R. 	Genomic Sequencing of Two Coffee-Infecting Strains of Xylella fastidiosa Isolated from Brazil.	Genome Announcements	2014	2		e01190-13			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). 		
@D	Alenezi, F.N.//Weitz, H.J.//Belbahri, L.//Ben Rebah, H.//Luptakova, L.//Jaspars, M.//Woodward, S. 	Draft Genome Sequence of Aneurinibacillus migulanus Strain Nagano.	Genome Announcements	2015	3		e00232-15			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. 		
@D	Alenezi, F.N.//Weitz, H.J.//Belbahri, L.//Nidhal, J.//Luptakova, L.//Jaspars, M.//Woodward, S. 	Draft Genome Sequence of Aneurinibacillus migulanus NCTC 7096.	Genome Announcements	2015	3		e00234-15			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. 		
@D	Aleshkin, G.I.//Skavronskaya, A.G. 	R.M.EcoRI coding plasmids derived from recombinant R factor.	Genetika	1978	14		1466-1469			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. 		
@D	Aleshkin, G.I.//Strikhanov, S.N.//Skavronskaya, A.G. 	Plasmid recombination stimulated by restriction endonuclease EcoRI in vivo: formation of recombinant plasmids in recA+-cells of E. coli.	Mol. Gen. Mikrobiol. Virusol.	1985	4		15-21			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. 		
@D	Aleti, G.//Antonielli, L.//Corretto, E.//Nikolic, B.//Sessitsch, A.//Brader, G. 	The Draft Genome Sequence of Paenibacillus polymyxa Strain CCI-25 Encompasses High Potential for Secondary Metabolite Production.	Genome Announcements	2016	4		e00366-16			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. 		
@D	Alexander, K.A.//Larsen, M.H.//Robbe-Austerman, S.//Stuber, T.P.//Camp, P.M. 	Draft Genome Sequence of the Mycobacterium tuberculosis Complex Pathogen M. mungi, Identified in a Banded Mongoose (Mungos mungo) in Northern Botswana.	Genome Announcements	2016	4		e00471-16			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. 		
@D	Alexander, S.//Fazal, M.A.//Burnett, E.//Deheer-Graham, A.//Oliver, K.//Holroyd, N.//Parkhill, J.//Russell, J.E. 	Complete Genome Sequence of Neisseria weaveri Strain NCTC13585.	Genome Announcements	2016	4		e00815-16			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. 		
@D	Alexander, S.//Fazal, M.A.//Burnett, E.//Deheer-Graham, A.//Oliver, K.//Holroyd, N.//Parkhill, J.//Russell, J.E. 	Complete Genome Sequence of Plesiomonas shigelloides Type Strain NCTC10360.	Genome Announcements	2016	4		e01031-16			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. 		
@D	Alexandraki, V.//Kazou, M.//Blom, J.//Pot, B.//Tsakalidou, E.//Papadimitriou, K. 	The complete genome sequence of the yogurt isolate Streptococcus thermophilus ACA-DC 2.	Standards in Genomic Sciences	2017	12		18			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. 		
@D	Alexandraki, V.//Kazou, M.//Pot, B.//Tsakalidou, E.//Papadimitriou, K. 	Complete Genome Sequence of the Yogurt Isolate Lactobacillus delbrueckii subsp. bulgaricus ACA-DC 87.	Genome Announcements	2017	5		e00868-17			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. 		
@D	Alexandrino, P.M.//Mendonca, T.T.//Guaman, B.L.P.//Cherix, J.//Lozano-Sakalauskas, G.C.//Fujita, A.//Ramos, F.E.//Long, P.//Padilla, G.//Taciro, M.K.//Gomez, J.G.//Silva, L.F. 	Draft Genome Sequence of the Polyhydroxyalkanoate-Producing Bacterium Burkholderia sacchari LMG 19450 Isolated from Brazilian Sugarcane Plantation  Soil.	Genome Announcements	2015	3		e00313-15			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%. 		
@D	Alexeyev, M.F.//Gunkovskaya, N.V.//Romanovskaya, V.A.//Malashenko, Y.R. 	Methylococcus whittenburyi - producer of MwhI, new isoschizomer of HpaI.	Mikrobiol. Zh.	1992	54		70-73			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. 		
@D	Alexiev, A.//Coil, D.A.//Badger, J.H.//Enticknap, J.//Ward, N.//Robb, F.T.//Eisen, J.A. 	Complete Genome Sequence of Coprothermobacter proteolyticus DSM 5265.	Genome Announcements	2014	2		e00470-14			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. 		
@D	Alexiev, A.//Coil, D.A.//Jospin, G.//Eisen, J.A.//Adams, J.Y. 	Draft Genome Sequence of Klebsiella pneumoniae UCD-JA29 Isolated from a Patient with Sepsis.	Genome Announcements	2016	4		e00234-16			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. 		
@D	Alexiev, A.//Krusor, M.L.//Jospin, G.//Lang, J.M.//Eisen, J.A.//Coil, D.A. 	Draft Genome Sequence of Cobetia sp. UCD-24C, Isolated from Roots and Leaves of the Seagrass Zostera marina.	Genome Announcements	2016	4		e00116-16			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. 		
@D	Alexiev, A.//Krusor, M.L.//Jospin, G.//Lang, J.M.//Eisen, J.A.//Coil, D.A. 	Draft Genome Sequences of Two Pseudoalteromonas Strains Isolated from Roots and Leaf Blades of the Seagrass Zostera marina.	Genome Announcements	2016	4		e00010-16			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. 		
@D	Alfan-Guzman, R.//Ertan, H.//Manefield, M.//Lee, M. 	Genome Sequence of Dehalobacter sp. Strain TeCB1, Able To Respire Chlorinated Benzenes.	Genome Announcements	2017	5		e01681-16			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. 		
@D	Algire, M.A.//Montague, M.G.//Vashee, S.//Lartigue, C.//Merryman, C. 	A type III restriction-modification system in Mycoplasma mycoides subsp. capri.	Open Biology	2012	2		120115			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. 		
@D	Algowaihi, R.//Ashgar, S.//Sirag, B.//Shalam, S.//Nassir, A.//Ahmed, A. 	Draft Genome Sequence of a Multidrug-Resistant Klebsiella pneumoniae Strain Isolated from King Abdullah Medical City, Makkah, Saudi Arabia.	Genome Announcements	2016	4		e00375-16			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. 		
@D	Ali, F.//Hu, H.//Xu, P.//Tang, H. 	Complete Genome Sequence of Pseudomonas aeruginosa FA-HZ1, an Efficient Dibenzofuran-Degrading Bacterium.	Genome Announcements	2017	5		e01634-16			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. 		
@D	Ali, M.//Haroon, M.F.//Narita, Y.//Zhang, L.//Rangel, S.D.//Okabe, S.//Saikaly, P.E. 	Draft Genome Sequence of the Anaerobic Ammonium-Oxidizing Bacterium 'Candidatus Brocadia sp. 40'.	Genome Announcements	2016	4		e01377-16			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. 		
@D	Ali, S.A.//Kumar, S.//Mohanty, A.K.//Behare, P. 	Draft Genome Sequence of Lactobacillus fermentum NCDC 400, Isolated from a Traditional Indian Dairy Product.	Genome Announcements	2018	6		e01492-17			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. 		
@D	Alic, S.//Naglic, T.//Llop, P.//Toplak, N.//Koren, S.//Ravnikar, M.//Dreo, T. 	Draft Genome Sequences of Dickeya sp. Isolates B16 (NIB Z 2098) and S1 (NIB Z 2099) Causing Soft Rot of Phalaenopsis Orchids.	Genome Announcements	2015	3		e00973-15			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. 		
@D	Aliyu, H.//De Maayer, P.//Rees, J.//Tuffin, M.//Cowan, D.A. 	Draft Genome Sequence of the Antarctic Polyextremophile Nesterenkonia sp. Strain  AN1.	Genome Announcements	2014	2		e00197-14			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. 		
@D	Alkahem, A.T.H.//Rhoads, D.D.//Barabote, R.D. 	Draft Genome Sequence of Anoxybacillus sp. Strain UARK-01, a New Thermophilic Lignin-Utilizing Bacterium Isolated from Soil in Arkansas, USA.	Genome Announcements	2017	5		e00588-17			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. 		
@D	Alkhalili, R.N.//Hatti-Kaul, R.//Canback, B. 	Genome Sequence of Geobacillus sp. Strain ZGt-1, an Antibacterial Peptide-Producing Bacterium from Hot Springs in Jordan.	Genome Announcements	2015	3		e00799-15			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. 		
@D	Allam, M.//Joseph, L.//Ismail, F.//Said, H.//Ismail, N.A.//Ismail, A.//Mtshali, S.//Mnyameni, F.//Goussard, P.//Pekeur, J.C.//Lourens, A.//Omar, S.V. 	Whole-Genome Sequence of a Mycobacterium goodii Isolate from a Pediatric Patient  in South Africa.	Genome Announcements	2018	6		e01478-17			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. 		
@D	Allam, M.//Tau, N.//Smouse, S.L.//Mtshali, P.S.//Mnyameni, F.//Khumalo, Z.T.H.//Ismail, A.//Govender, N.//Thomas, J.//Smith, A.M. 	Whole-Genome Sequences of Listeria monocytogenes Sequence Type 6 Isolates Associated with a Large Foodborne Outbreak in South Africa, 2017 to 2018.	Genome Announcements	2018	6		e00538-18			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. 		
@D	Allan, B.W. 	The dynamic origin of sequence discrimination by the EcoRI DNA methyltransferase.	Diss. Abstr.	1999	59		3407B			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. 		
@D	Allan, B.W.//Beechem, J.M.//Lindstrom, W.M.//Reich, N.O. 	Direct real time observation of base flipping by the EcoRI DNA methyltransferase.	J. Biol. Chem.	1998	273		2368-2373			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. 		
@D	Allan, B.W.//Garcia, R.//Maegley, K.//Mort, J.//Wong, D.//Lindstrom, W.//Beechem, J.M.//Reich, N.O. 	DNA bending by EcoRI DNA methyltransferase accelerates base flipping but compromises specificity.	J. Biol. Chem.	1999	274		19269-19275			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. 		
@D	Allan, B.W.//Reich, N.O. 	Targeted base stacking disruption by the EcoRI DNA methyltransferase.	Biochemistry	1996	35		14757-14762			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. 		
@D	Allan, B.W.//Reich, N.O.//Beechem, J.M. 	Measurement of the absolute temporal coupling between DNA binding and base flipping.	Biochemistry	1999	38		5308-5314			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. 		
@D	Allan, B.W.//Reich, N.O.//Beechem, J.M. 	Simultaneous real-time measurement of binding base-flipping, and dissociation base unflipping in EcoRI DNA methyltransferase.	Biophys. J.	1998	74		A69			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. 		
@D	Allard, M.W.//Luo, Y.//Strain, E.//Li, C.//Keys, C.E.//Son, I.//Stones, R.//Musser, S.M.//Brown, E.W. 	High resolution clustering of Salmonella enterica serovar Montevideo strains using a next-generation sequencing approach.	BMC Genomics	2012	13		32			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. 		
@D	Allard, M.W.//Luo, Y.//Strain, E.//Pettengill, J.//Timme, R.//Wang, C.//Li, C.//Keys, C.E.//Zheng, J.//Stones, R.//Wilson, M.R.//Musser, S.M.//Brown, E.W. 	On the evolutionary history, population genetics and diversity among isolates of Salmonella Enteritidis PFGE pattern JEGX01.0004.	PLoS ONE	2013	8		E55254			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. 		
@D	Allard, M.W.//Muruvanda, T.//Strain, E.//Timme, R.//Luo, Y.//Wang, C.//Keys, C.E.//Payne, J.//Cooper, T.//Luong, K.//Song, Y.//Chin, C.S.//Korlach, J.//Roberts, R.J.//Evans, P.//Musser, S.M.//Brown, E.W. 	Fully Assembled Genome Sequence for Salmonella enterica subsp. enterica Serovar Javiana CFSAN001992.	Genome Announcements	2014	2		e00293-14			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." 		
@D	Allard, M.W.//Muruvanda, T.//Strain, E.//Timme, R.//Luo, Y.//Wang, C.//Keys, C.E.//Payne, J.//Cooper, T.//Luong, K.//Song, Y.//Chin, C.S.//Korlach, J.//Roberts, R.J.//Evans, P.//Musser, S.M.//Brown, E.W. 	Fully Assembled Genome Sequence for Salmonella enterica subsp. enterica Serovar Javiana CFSAN001992.	Genome Announcements	2013	1		e00081-13			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. 		
@D	Allen, E.E.//Tyson, G.W.//Whitaker, R.J.//Detter, J.C.//Richardson, P.M.//Banfield, J.F. 	Genome dynamics in a natural archaeal population.	Proc. Natl. Acad. Sci. U. S. A.	2007	104		1883-1888			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. 		
@D	Allen, M.J.//Tait, K.//Muhling, M.//Weynberg, K.//Bradley, C.//Trivedi, U.//Gharbi, K.//Nissimov, J.//Mavromatis, K.//Jensen, C.N.//Grogan, G.//Ali, S.T. 	Genome Sequence of Stenotrophomonas maltophilia PML168, Which Displays Baeyer-Villiger Monooxygenase Activity.	J. Bacteriol.	2012	194		4753-4754			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. 		
@D	Allen-Daniels, M.J.//Serrano, M.G.//Pflugner, L.P.//Fettweis, J.M.//Prestosa, M.A.//Koparde, V.N.//Brooks, J.P.//Strauss, J.F. III//Romero, R.//Chaiworapongsa, T.//Eschenbach, D.A.//Buck, G.A.//Jefferson, K.K. 	Identification of a gene in Mycoplasma hominis associated with preterm birth and microbial burden in intra-amniotic infection.	Am. J. Obstet. Gynecol.	2015	212		779.e1-779.e13			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. 		
@D	Allet, B. 	Fragments produced by cleavage of lambda deoxyribonucleic acid with the Hemophilus parainfluenzae restriction enzyme HpaII.	Biochemistry	1973	12		3972-3977			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. 		
@D	Allet, B.//Jeppesen, P.G.N.//Katagiri, K.J.//Delius, H. 	Mapping the DNA fragments produced by cleavage of lambda DNA with endonuclease RI.	Nature	1973	241		120-123			None 		
@D	Allet, B.//Rochaix, J.-D. 	Structure analysis at the ends of the intervening DNA sequences in the chloroplast 23S ribosomal genes of C. reinhardii.	Cell	1979	18		55-60			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. 		
@D	Allison, D.P.//Kerper, P.S.//Doktycz, M.J.//Spain, J.A.//Modrich, P.//Larimer, F.W.//Thundat, T. 	Direct atomic force microscope imaging of EcoRI endonuclease site specifically bound to plasmid DNA molecules.	Proc. Natl. Acad. Sci. U. S. A.	1996	93		8826-8829			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. 		
@D	Allison, G.E.//Angeles, D.//Tran-Dinh, N.//Verma, N.K. 	Complete genomic sequence of SfV, a serotype-converting temperate bacteriophage of Shigella flexneri.	J. Bacteriol.	2002	184		1974-1987			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. 		
@D	Allison, G.E.//Klaenhammer, T.R. 	Phage resistance mechanisms in lactic acid bacteria.	Int. Dairy Journal	1998	8		207-226			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. 		
@D	Allison, L.//Yee, C.N. 	Restriction site mapping is in separation theory.	Comput. Appl. Biosci.	1988	4		97-101			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. 		
@D	Allnutt, T.R.//Bradbury, M.I.//Fanning, S.//Chandry, P.S.//Fox, E.M. 	Draft Genome Sequences of 15 Isolates of Listeria monocytogenes Serotype 1/2a, Subgroup ST204.	Genome Announcements	2016	4		e00935-16			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. 		
@D	Allue-Guardia, A.//Echazarreta, M.//Koenig, S.S.K.//Klose, K.E.//Eppinger, M. 	Closed Genome Sequence of Vibrio cholerae O1 El Tor Inaba Strain A1552.	Genome Announcements	2018	6		e00098-18			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. 		
@D	Alm, E.//Advani, A.//Brave, A.//Wahab, T. 	Draft Genome Sequence of Strain R13-38 from a Francisella tularensis Outbreak in Sweden.	Genome Announcements	2015	3		e01517-14			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. 		
@D	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. 	Genomic-sequence comparison of two unrelated isolates of the human gastric pathogen Helicobacter pylori.	Nature	1999	397		176-180			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. 		
@D	Alm, R.A.//Trust, T.J. 	Analysis of the genetic diversity of Helicobacter pylori: the tale of two genomes.	J. Mol. Med.	1999	77		834-846			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. 		
@D	Almeida, E.L.//Margassery, L.M.//Kennedy, J.//Dobson, A.D.W. 	Draft Genome Sequence of the Antimycin-Producing Bacterium Streptomyces sp. Strain SM8, Isolated from the Marine Sponge Haliclona simulans.	Genome Announcements	2018	6		e01535-17			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. 		
@D	Almeida, E.L.//Margassery, L.M.//O'Leary, N.//Dobson, A.D.W. 	Draft Genome Sequence of Pseudomonas putida CA-3, a Bacterium Capable of Styrene  Degradation and Medium-Chain-Length Polyhydroxyalkanoate Synthesis.	Genome Announcements	2018	6		e01534-17			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. 		
@D	Almeida, F.//Medeiros, M.I.//Rodrigues, D.P.//Payne, J.//Timme, R.E.//Allard, M.W.//Falcao, J.P. 	Draft Genome Sequences of 40 Salmonella enterica Serovar Typhimurium Strains Isolated from Humans and Food in Brazil.	Genome Announcements	2016	4		e00892-16			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. 		
@D	Almeida, N.F.//Yan, S.//Lindeberg, M.//Studholme, D.J.//Schneider, D.J.//Condon, B.//Liu, H.//Viana, C.J.//Warren, A.//Evans, C.//Kemen, E.//Maclean, D.//Angot, A.//Martin, G.B.//Jones, J.D.//Collmer, A.//Setubal, J.C.//Vinatzer, B.A. 	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.	Mol. Plant Microbe Interact.	2009	22		52-62			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. 		
@D	Almeida, S. et al. 	The genome anatomy of Corynebacterium pseudotuberculosis VD57 a highly virulent strain causing Caseous lymphadenitis.	Standards in Genomic Sciences	2016	11		29			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. 		
@D	Almeida, S.//Loureiro, D.//Portela, R.W.//Mariano, D.C.//Sousa, T.J.//Pereira, F.L.//Dorella, F.A.//Carvalho, A.F.//Moura-Costa, L.F.//Leal, C.A.//Figueiredo, H.C.//Meyer, R.//Azevedo, V. 	Complete Genome Sequence of the Attenuated Corynebacterium pseudotuberculosis Strain T1.	Genome Announcements	2016	4		e00947-16			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. 		
@D	Almstrand, R.//Pinto, A.J.//Figueroa, L.A.//Sharp, J.O. 	Draft Genome Sequence of a Novel Desulfobacteraceae Member from a Sulfate-Reducing Bioreactor Metagenome.	Genome Announcements	2016	4		e01540-15			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. 		
@D	Alonso-Carmona, S.//Vera-Gargallo, B.//de la Haba, R.R.//Ventosa, A.//Sandoval-Trujillo, H.//Ramirez-Duran, N. 	Draft Genome Sequence of Saccharomonospora sp. Strain LRS4.154, a Moderately Halophilic Actinobacterium with the Biotechnologically Relevant Polyketide  Synthase and Nonribosomal Peptide Synthetase Systems.	Genome Announcements	2017	5		e00392-17			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. 		
@D	Alonso-Vega, P.//Normand, P.//Bacigalupe, R.//Pujic, P.//Lajus, A.//Vallenet, D.//Carro, L.//Coll, P.//Trujillo, M.E. 	Genome Sequence of Micromonospora lupini Lupac 08, Isolated from Root Nodules of  Lupinus angustifolius.	J. Bacteriol.	2012	194		4135			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. 		
@D	Alouane, T.//Uwingabiye, J.//Lemnouer, A.//Lahlou, L.//Laamarti, M.//Kartti, S.//Benhrif, O.//El Misbahi, H.//Frikh, M.//Benlahlou, Y.//Bssaibis, F.//El Abbassi, S.//Kabbage, S.//Maleb, A.//Elouennass, M.//Ibrahimi, A. 	First Whole-Genome Sequences of Two Multidrug-Resistant Acinetobacter baumannii Strains Isolated from a Moroccan Hospital Floor.	Genome Announcements	2017	5		e00298-17			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. 		
@D	Aloui, A.//Tagourti, J.//El May, A.//Petit, D.J.//Landoulsi, A. 	The effect of methylation on some biological parameters in Salmonella enterica serovar Typhimurium.	Pathol. Biol. (Paris)	2011	59		192-198			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. 		
@D	Aloyo, M.C.//Campbell, D.//Combates, N.J.//Gonzalez, J.//Kwok, Y.//Sheardy, R.D.//Winkle, S.A. 	Restriction enzymes have altered cleavage rates at sites near certain sequences.	Biophys. J.	1993	64		A280			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. 		
@D	Alpert, C.A.//Crutz-Le, C.A.M.//Malleret, C.//Zagorec, M. 	Characterization of a theta-type plasmid from Lactobacillus sakei: a potential basis for low-copy-number vectors in lactobacilli.	Appl. Environ. Microbiol.	2003	69		5574-5584			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. 		
@D	Alt, D.P.//Wilson-Welder, J.H.//Bayles, D.O.//Cameron, C.//Adler, B.//Bulach, D.M.//Seemann, T.//Lehane, M.J.//Haines, L.R.//Darby, A.C.//Hall, N.//Radford, A.D.//Zuerner, R.L. 	Complete Genome Sequence of Leptospira interrogans Serovar Bratislava, Strain PigK151.	Genome Announcements	2015	3		e00678-15			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). 		
@D	Altermann, E.//Russell, W.M.//Azcarate-Peril, M.A.//Barrangou, R.//Buck, B.L.//McAuliffe, O.//Souther, N.//Dobson, A.//Duong, T.//Callanan, M.//Lick, S.//Hamrick, A.//Cano, R.//Klaenhammer, T.R. 	Inaugural Article: From the Cover: Complete genome sequence of the probiotic lactic acid bacterium Lactobacillus acidophilus NCFM.	Proc. Natl. Acad. Sci. U. S. A.	2005	102		3906-3912			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. 		
@D	Althabegoiti, M.J.//Lozano, L.//Torres-Tejerizo, G.//Ormeno-Orrillo, E.//Rogel, M.A.//Gonzalez, V.//Martinez-Romero, E. 	Genome Sequence of Rhizobium grahamii CCGE502, a Broad-Host-Range Symbiont with Low Nodulation Competitiveness in Phaseolus vulgaris.	J. Bacteriol.	2012	194		6651-6652			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. 		
@D	Altin, G.//Nikerel, E.//Sahin, F. 	Draft Genome Sequence of Magnesium-Dissolving Lactococcus garvieae A1, Isolated from Soil.	Genome Announcements	2017	5		e00386-17			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. 		
@D	Altintas, M.M.//Ozer, N.//Ulgen, K.O. 	Purification of TaqI endonuclease from Thermus aquaticus.	J. Chromatogr. A	1998	828		373-381			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. 		
@D	Altintas, M.M.//Ulgen, K.O. 	Growth of Thermus aquaticus and its TaqI endonuclease production.	Acta Biotechnol.	1999	19		45-56			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. 		
@D	Altman, D.R. et al. 	Genome plasticity of agr-defective Staphylococcus aureus during clinical infection.	Infect. Immun.	2018	86		e00331-18			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. 		
@D	Altschmied, J.//Volff, J.//Winkler, C.//Gutbrod, H.//Korting, C.//Pagany, M.//Schartl, M. 	Primary structure and expression of the Xiphophorus DNA-(cytosine-5)-methyltransferase XDNMT-1.	Gene	2000	249		75-82			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. 		
@D	Alvarez, C.//Kukutla, P.//Jiang, J.//Yu, W.//Xu, J. 	Draft Genome Sequence of Pseudomonas sp. Strain Ag1, Isolated from the Midgut of  the Malaria Mosquito Anopheles gambiae.	J. Bacteriol.	2012	194		5449			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. 		
@D	Alvarez, M.A.//Chater, K.F.//Rosario, M.R. 	Complex transcription of an operon encoding the Sall restriction-modification system of Streptomyces albus G.	Mol. Microbiol.	1993	8		243-252			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. 		
@D	Alvarez, M.A.//Gomez, A.//Gomez, P.//Brooks, J.E.//Rodicio, M.R. 	Comparative analysis of expression of the SalI restriction-modification system in Escherichia coli and Streptomyces.	Mol. Gen. Genet.	1996	253		74-80			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. 		
@D	Alvarez, M.A.//Gomez, A.//Gomez, P.//Rodicio, M.R. 	Expression of the SalI restriction-modification system of Streptomyces albus G in Escherichia coli.	Gene	1995	157		231-232			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. 		
@D	Alvarez, N.//Haft, D.//Hurtado, U.A.//Robledo, J.//Rouzaud, F. 	Whole-Genome Sequence of a Beijing Extensively Drug-Resistant Mycobacterium tuberculosis Clinical Isolate from Buenaventura, Colombia.	Genome Announcements	2016	4		e01549-15			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. 		
@D	Alvarez, N.//Haft, D.//Hurtado, U.A.//Robledo, J.//Rouzaud, F. 	Whole-Genome Sequencing of a Haarlem Extensively Drug-Resistant Mycobacterium tuberculosis Clinical Isolate from Medellin, Colombia.	Genome Announcements	2016	4		e00566-16			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. 		
@D	Alvarez, N.//Haft, D.//Hurtado, U.A.//Robledo, J.//Rouzaud, F. 	Whole-Genome Sequencing of Two Latin American-Mediterranean Extensively Drug-Resistant Mycobacterium tuberculosis Clinical Isolates from Medellin,  Colombia.	Genome Announcements	2016	4		e00192-16			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. 		
@D	Alvarez-Fraga, L.//Lopez, M.//Merino, M.//Rumbo-Feal, S.//Tomas, M.//Bou, G.//Poza, M. 	Draft Genome Sequence of the Biofilm-Hyperproducing Acinetobacter baumannii Clinical Strain MAR002.	Genome Announcements	2015	3		e00824-15			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%. 		
@D	Alvarez-Ponce, D.//Weitzman, C.L.//Tillett, R.L.//Sandmeier, F.C.//Tracy, C.R. 	High quality draft genome sequences of Mycoplasma agassizii strains PS6(T) and 723 isolated from Gopherus tortoises with upper respiratory tract disease.	Standards in Genomic Sciences	2018	13		12			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. 		
@D	Alves, J.//Kohler, E.//Selent, U.//Thielking, V.//Wolfes, H.//Pingoud, A. 	The recognition of DNA by the EcoRV restriction endonuclease: Accuracy and cation dependence.	Biol. Chem. Hoppe Seyler	1991	372		627			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). 		
@D	Alves, J.//Pingoud, A.//Haupt, W.//Langowski, J.//Peters, F.//Maass, G.//Wolff, C. 	The influence of sequences adjacent to the recognition site on the cleavage of oligodeoxynucleotides by the EcoRI endonuclease.	Eur. J. Biochem.	1984	140		83-92			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. 		
@D	Alves, J.//Pingoud, A.//Langowski, J.//Urbanke, C.//Maass, G. 	Two identical subunits of the EcoRI restriction endonuclease co-operate in the binding and cleavage of the palindromic substrate.	Eur. J. Biochem.	1982	124		139-142			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. 		
@D	Alves, J.//Ruter, T.//Geiger, R.//Fliess, A.//Maass, G.//Pingoud, A. 	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.	Biochemistry	1989	28		2678-2684			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. 		
@D	Alves, J.//Selent, U.//Wolfes, H. 	Accuracy of the EcoRV restriction endonuclease: binding and cleavage studies with oligodeoxynucleotide substrates containing degenerate recognition sequences.	Biochemistry	1995	34		11191-11197			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. 		
@D	Alves, J.//Thielking, V.//Selent, U.//Kohler, E.//Wolfes, H.//Pingoud, A. 	The recognition of DNA by the EcoRV restriction endonuclease:  accuracy and cation dependence.	J. Biomol. Struct. Dyn.	1991	8		a007			None 		
@D	Alves, J.//Urbanke, C.//Fliess, A.//Maass, G.//Pingoud, A. 	Fluorescence stopped-flow kinetics of the cleavage of synthetic oligodeoxynucleotides by the EcoRI restriction endonuclease.	Biochemistry	1989	28		7879-7888			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. 		
@A	Alves, J.//Vennekohl, P. 		Protein engineering of restriction enzymes.			Pingoud, A. 		Nucleic Acids Mol. Biol.				Berlin Heidelberg	Springer-Verlag	2004		14		393-411									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. 		
@D	Alves, J.M.//Serrano, M.G.//Maia-da-Silva, F.//Voegtly, L.J.//Matveyev, A.V.//Teixeira, M.M.//Camargo, E.P.//Buck, G.A. 	Genome evolution and phylogenomic analysis of candidatus kinetoplastibacterium, the betaproteobacterial endosymbionts of strigomonas and angomonas.	Genome Biol. Evol.	2013	5		338-350			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. 		
@D	Alves, J.T.//Veras, A.A.//Cavalcante, A.L.//de Sa, P.H.//Dias, L.M.//Guimaraes, L.C.//Morais, E.//Silva, A.G.//Azevedo, V.//Ramos, R.T.//Silva, A.//Carneiro, A.R. 	Complete Genome Sequence of Corynebacterium pseudotuberculosis Strain PA01, Isolated from Sheep in Para, Brazil.	Genome Announcements	2016	4		e01664-15			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. 		
@D	Alzhanov, D.T.//Alzhanova, D.V.//Zheleznaya, L.A.//Matvienko, N.I. 	Thermophilic strain Bacillus species AA contains several site-specific endonucleases.	Biokhimiia	1998	63		636-645			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. 		
@D	Alzhanova, D.V.//Alzhanov, D.T.//Zheleznaya, L.A.//Matvienko, N.I. 	Isolation and characterization of site-specific endonuclease Bsp123I from thermophilic strain Bacillus species 123.	Biokhimiia	1998	63		207-211			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. 		
@D	Amachawadi, R.G.//Thomas, M.//Nagaraja, T.G.//Scaria, J. 	Genome Sequences of Salmonella enterica subsp. enterica Serovar Lubbock Strains Isolated from Liver Abscesses of Feedlot Cattle.	Genome Announcements	2016	4		e00319-16			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. 		
@D	Amadio, A.F.//Amigo, N.//Puebla, A.F.//Farber, M.D.//Cataldi, A.A. 	Draft Genome Sequences of Escherichia coli O157:H7 Strains Rafaela_II (Clade 8) and 7.1_Anguil (Clade 6) from Cattle in Argentina.	Genome Announcements	2015	3		e00617-15			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. 		
@D	Amadio, A.F.//Benintende, G.B.//Zandomeni, R.O. 	Complete sequence of three plasmids from Bacillus thuringiensis INTA-FR7-4 environmental isolate and comparison with related plasmids from the Bacillus cereus group.	Plasmid	2009	62		172-182			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. 		
@D	Amano, N.//Yamamuro, A.//Miyahara, M.//Kouzuma, A.//Abe, T.//Watanabe, K. 	Methylomusa anaerophila gen. nov., sp. nov., an anaerobic methanol-utilizing bacterium isolated from a microbial fuel cell.	Int. J. Syst. Evol. Microbiol.	2018	68		1118-1122			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)). 		
@D	Amaral, G.R.//Silva, B.S.//Santos, E.O.//Dias, G.M.//Lopes, R.M.//Edwards, R.A.//Thompson, C.C.//Thompson, F.L. 	Genome Sequence of the Bacterioplanktonic, Mixotrophic Vibrio campbellii Strain PEL22A, Isolated in the Abrolhos Bank.	J. Bacteriol.	2012	194		2759-2760			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. 		
@D	Amari, M.//Laguerre, S.//Vuillemin, M.//Robert, H.//Loux, V.//Klopp, C.//Morel, S.//Gabriel, B.//Remaud-Simeon, M.//Gabriel, V.//Moulis, C.//Fontagne-Faucher, C. 	Genome Sequence of Weissella confusa LBAE C39-2, Isolated from a Wheat Sourdough.	J. Bacteriol.	2012	194		1608-1609			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. 		
@D	Amaro, F.//Gilbert, J.A.//Owens, S.//Trimble, W.//Shuman, H.A. 	Whole-Genome Sequence of the Human Pathogen Legionella pneumophila Serogroup 12 Strain 570-CO-H.	J. Bacteriol.	2012	194		1613-1614			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. 		
@D	Ambalam, P.//Pithva, S.//Kothari, C.//Kothari, R.//Parmar, N.//Nathani, N.M.//Koringa, P.G.//Joshi, C.G.//Dave, J.M.//Vyas, B.R. 	Insight into the Draft Genome Sequence of Human Isolate Lactobacillus rhamnosus LR231, a Bacterium with Probiotic Potential.	Genome Announcements	2014	2		e00111-14			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. 		
@D	Ambrosini, A.//Sant'Anna, F.H.//de Souza, R.//Tadra-Sfeir, M.//Faoro, H.//Alvarenga, S.M.//Pedrosa, F.O.//Souza, E.M.//Passaglia, L.M. 	Genome Sequence of Bacillus mycoides B38V, a Growth-Promoting Bacterium of Sunflower.	Genome Announcements	2015	3		e00245-15			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. 		
@D	Amin, O.//Fardeau, M.L.//Valette, O.//Hirschler-Rea, A.//Barbe, V.//Medigue, C.//Vacherie, B.//Ollivier, B.//Bertin, P.N.//Dolla, A. 	Genome Sequence of the Sulfate-Reducing Bacterium Desulfotomaculum hydrothermale  Lam5(T).	Genome Announcements	2013	1		e00114-12			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. 		
@D	Amin, S.//Shah, B.//Jain, K.//Patel, A.//Patel, N.//Joshi, C.G.//Madamwar, D. 	Draft Genome Sequence of Achromobacter sp. Strain DMS1, Capable of Degrading Polyaromatic Hydrocarbons Isolated from the Industrially Perturbed Environment of Amlakhadi Canal, India.	Genome Announcements	2015	3		e01264-15			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. 		
@D	Amitsur, M.//Benjamin, S.//Rosner, R.//Chapman-Shimshoni, D.//Meidler, R.//Blanga, S.//Kaufmann, G. 	Bacteriophage T4-encoded Stp can be replaced as activator of anticodon nuclease by a normal host cell metabolite.	Mol. Microbiol.	2003	50		129-143			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. 		
@D	Amitsur, M.//Morad, I.//Chapman-Shimshoni, D.//Kaufmann, G. 	HSD restriction-modification proteins partake in latent anticodon nuclease.	EMBO J.	1992	11		3129-3134			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. 		
@D	Amran, F.//Mohd, K.M.K.//Mohamad, S.//Mat, R.A.//Ahmad, N.//Goris, M.G.//Muhammad, A.H.//Noor, H.N.A. 	Draft Genome Sequence of Leptospira interrogans Serovar Bataviae Strain LepIMR 22 Isolated from a Rodent in Johor, Malaysia.	Genome Announcements	2016	4		e00956-16			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. 		
@D	An, L.//Li, Y.//Chen, Z.//Chang, D.//Zhang, X.//Guo, Y.//Wang, J.//Li, T.//Dai, W.//Liu, C. 	Genome Sequence of Enterococcus faecium Strain LCT-EF297, Which Has Specific Biochemical Features.	Genome Announcements	2014	2		e00102-14			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. 		
@D	An, R.//Lin, P.//Bougouffa, S.//Essack, M.//Boxrud, D.//Bajic, V.B.//Vidovic, S. 	Draft Genome Sequences of Four Salmonella enterica subsp. enterica Serovar Enteritidis Strains Implicated in Infections of Avian and Human Hosts.	Genome Announcements	2018	6		e01550-17			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. 		
@D	An, T.T.//Picardal, F.W. 	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.	Genome Announcements	2015	3		e00970-15			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. 		
@D	Anand, S.//Sangwan, N.//Lata, P.//Kaur, J.//Dua, A.//Singh, A.K.//Verma, M.//Kaur, J.//Khurana, J.P.//Khurana, P.//Mathur, S.//Lal, R. 	Genome Sequence of Sphingobium indicum B90A, a Hexachlorocyclohexane-Degrading Bacterium.	J. Bacteriol.	2012	194		4471-4472			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. 		
@D	Ancora, M.//Marcacci, M.//Orsini, M.//Zilli, K.//Di Giannatale, E.//Garofolo, G.//Camma, C. 	Complete Genome Sequence of a Brucella ceti ST26 Strain Isolated from a Striped Dolphin (Stenella coeruleoalba) on the Coast of Italy.	Genome Announcements	2014	2		e00068-14			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. 		
@D	Anda, M.//Ohtsubo, Y.//Okubo, T.//Sugawara, M.//Nagata, Y.//Tsuda, M.//Minamisawa, K.//Mitsui, H. 	Bacterial clade with the ribosomal RNA operon on a small plasmid rather than the chromosome.	Proc. Natl. Acad. Sci. U. S. A.	2015	112		14343-14347			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. 		
@D	Andersen, M.T.//Liefting, L.W.//Havukkala, I.//Beever, R.E. 	Comparison of the complete genome sequence of two closely related isolates of 'Candidatus Phytoplasma australiense' reveals genome plasticity.	BMC Genomics	2013	14		529			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. 		
@D	Andersen, P.S.//Stegger, M.//Aziz, M.//Contente-Cuomo, T.//Gibbons, H.S.//Keim, P.//Sokurenko, E.V.//Johnson, J.R.//Price, L.B. 	Complete Genome Sequence of the Epidemic and Highly Virulent CTX-M-15-Producing H30-Rx Subclone of Escherichia coli ST131.	Genome Announcements	2013	1		e00988-13			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. 		
@D	Anderson, B.//McDonald, G. 	Construction of DNA libraries of A-T rich organisms using EcoRI star activity.	Anal. Biochem.	1993	211		325-327			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. 		
@D	Anderson, E.S.//Felix, A. 	Variation in Vi-Phage II of Salmonella typhi.	Nature	1952	170		492-494			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. 		
@D	Anderson, E.S.//Threlfall, E.J.//Carr, J.M.//Savoy, L.G. 	Bacteriophage restriction in Salmonella typhimurium by R factors and transfer factors.	J. Hyg. (Lond)	1973	71		619			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. 		
@D	Anderson, I. et al. 	Genome sequence of Frateuria aurantia type strain (Kondo 67(T)), a xanthomonade isolated from Lilium auratium Lindl.	Standards in Genomic Sciences	2013	9		83-92			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. 		
@D	Anderson, I. et al. 	Complete genome sequence of Methanothermus fervidus type strain (V24S).	Standards in Genomic Sciences	2010	3		315-324			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. 		
@D	Anderson, I. et al. 	Complete genome sequence of Staphylothermus hellenicus P8.	Standards in Genomic Sciences	2011	5		12-20			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. 		
@D	Anderson, I. et al. 	Complete genome sequence of Ferroglobus placidus AEDII12DO.	Standards in Genomic Sciences	2011	5		50-60			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. 		
@D	Anderson, I. et al. 	Complete genome sequence of Halorhabdus utahensis type strain (AX-2).	Standards in Genomic Sciences	2009	1		218-225			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. 		
@D	Anderson, I. et al. 	Genome sequence of the flexirubin-pigmented soil bacterium Niabella soli type strain (JS13-8(T)).	Standards in Genomic Sciences	2012	7		210-220			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. 		
@D	Anderson, I. et al. 	Complete genome sequence of the moderately thermophilic mineral-sulfide-oxidizing firmicute Sulfobacillus acidophilus type strain (NAL(T)).	Standards in Genomic Sciences	2012	6		1-13			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. 		
@D	Anderson, I. et al. 	Genome sequence of the homoacetogenic bacterium Holophaga foetida type strain (TMBS4(T)).	Standards in Genomic Sciences	2012	6		174-184			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. 		
@D	Anderson, I. et al. 	Complete genome sequence of the thermophilic sulfate-reducing ocean bacterium Thermodesulfatator indicus type strain (CIR29812(T)).	Standards in Genomic Sciences	2012	6		155-164			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. 		
@D	Anderson, I. et al. 	Complete genome sequence of Halopiger xanaduensis type strain (SH-6T).	Standards in Genomic Sciences	2012	6		31-42			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. 		
@D	Anderson, I. et al. 	Complete genome sequence of Nitratifractor salsuginis type strain (E9I37-1).	Standards in Genomic Sciences	2011	4		322-330			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. 		
@D	Anderson, I. et al. 	Complete genome sequence of the hyperthermophilic chemolithoautotroph Pyrolobus fumarii type strain (1A).	Standards in Genomic Sciences	2011	4		381-392			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. 		
@D	Anderson, I.J. et al. 	Complete genome sequence of Methanoculleus marisnigri Romesser et al. 1981 type strain JR1.	Standards in Genomic Sciences	2009	1		189-196			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. 		
@D	Anderson, I.J. et al. 	The complete genome sequence of Staphylothermus marinus reveals differences in sulfur metabolism among heterotrophic Crenarchaeota.	BMC Genomics	2009	10		145			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. 		
@D	Anderson, I.J. et al. 	Complete genome sequence of the Antarctic Halorubrum lacusprofundi type strain ACAM 34.	Standards in Genomic Sciences	2016	11		70			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. 		
@D	Anderson, I.J.//Sieprawska-Lupa, M.//Goltsman, E.//Lapidus, A.//Copeland, A.//Glavina Del Rio, T.//Tice, H.//Dalin, E.//Barry, K.//Pitluck, S.//Hauser, L.//Land, M.//Lucas, S.//Richardson, P.//Whitman, W.B.//Kyrpides, N.C. 	Complete genome sequence of Methanocorpusculum labreanum type strain Z.	Standards in Genomic Sciences	2009	1		197-203			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. 		
@D	Anderson, I.J.//Sun, H.//Lapidus, A.//Copeland, A.//Glavina Del Rio, T.//Tice, H.//Dalin, E.//Lucas, S.//Barry, K.//Land, M.//Richardson, P.//Huber, H.//Kyrpides, N.C. 	Complete genome sequence of Staphylothermus marinus Stetter and Fiala 1986 type strain F1.	Standards in Genomic Sciences	2009	1		183-188			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. 		
@D	Anderson, J.E. 	Restriction endonucleases and modification methylases.	Curr. Opin. Struct. Biol.	1993	3		24-30			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. 		
@D	Anderson, M.T.//Mitchell, L.A.//Zhao, L.//Mobley, H.L. 	Citrobacter freundii fitness during bloodstream infection.	Sci. Rep.	2018	8		11792			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. 		
@D	Anderson, M.T.//Mitchell, L.A.//Zhao, L.//Mobley, H.L.T. 	Capsule Production and Glucose Metabolism Dictate Fitness during Serratia marcescens Bacteremia.	MBio	2017	8		e00740-17			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. 		
@D	Andersson, S.G.E.//Zomorodipour, A.//Andersson, J.O.//Sicheritz-Ponten, T.//Alsmark, U.C.M.//Podowski, R.M.//Naslund, A.K.//Eriksson, A.-S.//Winkler, H.H.//Kurland, C.G. 	The genome sequence of Rickettsia prowazekii and the origin of mitochondria.	Nature	1998	396		133-140			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. 		
@D	Ando, T. 	Novel DNA enzymes:  specificity and application.	Reports Inst. Phys. Chem. Res.	1985	61		239-255			None 		
@D	Ando, T.//Aras, R.//Kusugami, K.//Peek, R.M.//Blaser, M.J.//Wassenaar, T.M. 	Presence of hrgA and hrgB (iceA2) differentially associated with Helicobacter pylori virulence.	Gastroenterology	2003	124		A272-A273			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. 		
@D	Ando, T.//Aras, R.A.//Kusugami, K.//Blaser, M.J.//Wassenaar, T.M. 	Evolutionary history of hrgA, which replaces the restriction gene hpyIIIR in the hpyIII locus of Helicobacter pylori.	J. Bacteriol.	2003	185		295-301			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. 		
@A	Ando, T.//Hayase, E.//Ikawa, S.//Shibata, T. 		Site-specific restriction endodeoxyribonucleases in Bacilli.			Schlessinger, D. 		Microbiology-1982				Washington	American Society for Microbiology	1982		0		66-70									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. 		
@D	Ando, T.//Ishiguro, K.//Watanabe, O.//Miyake, N.//Kato, T.//Hibi, S.//Mimura, S.//Nakamura, M.//Miyahara, R.//Ohmiya, N.//Niwa, Y.//Goto, H. 	Restriction-modification systems may be associated with Helicobacter pylori virulence.	J. Gastroenterol. Hepatol.	2010	25		S95-S98			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. 		
@D	Ando, T.//Peek, R.M. Jr.//Kusugami, K.//Van Doorn, L.-J.//Wassenaar, T.//Kim, S.-K.//Blaser, M.J. 	H. pylori strains with the novel gene MboX are correlated with gastric cancer in Asian patients.	Gastroenterology	2001	120		A652			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. 		
@D	Ando, T.//Shibata, T. 	Host-controlled modification and restriction and the relating enzymes in Bacillus subtilis and other Bacillus strains.	Tanpakushitsu Kakusan Koso	1977	22		1012-1019					
@D	Ando, T.//Shibata, T.//Kazami, J. 	Restriction endonucleases.	Tanpakushitsu Kakusan Koso	1985	30		1429-1444			Review - in Japanese 		
@D	Ando, T.//Wassenaar, T.M.//Peek, R.M. Jr.//Aras, R.A.//Tschumi, A.I.//van Doorn, L.-Jan.//Kusugami, K.//Blaser, M.J. 	A Helicobacter pylori restriction endonuclease-replacing gene, hrgA, is associated with gastric cancer in Asian strains.	Cancer Res.	2002	62		2385-2389			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. 		
@D	Ando, T.//Wassenaar, T.M.//Peek, R.M.//Aras, R.A.//Kusugami, K.//van Doom, L.//Blaser, M.J. 	hypX shares a genomic locus with the restriction endonuclease gene hpyIIIR in Helicobacter pylori.	Int. J. Med. Microbiol.	2001	291S		28			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. 		
@D	Ando, T.//Xu, Q.//Torres, M.//Kusugami, K.//Israel, D.A.//Blaser, M.J. 	Restriction-modification system differences in Helicobacter pylori are a barrier to interstrain plasmid transfer.	Mol. Microbiol.	2000	37		1052-1065			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. 		
@D	Andreeva, I.S.//Afinogenova, G.N.//Lebedev, I.R.//Nadolinnaya, I.G.//Pustoshilova, N.M. 	Kpn378I - a type II restriction endonuclease from Klebsiella pneumoniae.	Mol. Gen. Mikrobiol. Virusol.	1991	2		31-32			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. 		
@D	Andreeva, I.S.//Afinogenova, G.N.//Lebedev, L.R.//Pustoshilova, N.M.//Gordienko, N.Y.//Maistrenko, G.G. 	Site specific restriction endonuclease Rme21I from Rhizobium meliloti.	Mol. Gen. Mikrobiol. Virusol.	1991	0		30-31			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. 		
@D	Andreevskaya, M.//Hultman, J.//Johansson, P.//Laine, P.//Paulin, L.//Auvinen, P.//Bjorkroth, J. 	Complete genome sequence of Leuconostoc gelidum subsp. gasicomitatum KG16-1, isolated from vacuum-packaged vegetable sausages.	Standards in Genomic Sciences	2016	11		40			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. 		
@D	Andres, S.//Skoglund, A.//Nilsson, C.//Krabbe, M.//Bjorkholm, B.//Engstrand, L. 	Type I Restriction-Modification Loci Reveal High Allelic Diversity in Clinical Helicobacter pylori Isolates.	Helicobacter	2010	15		114-125			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. 		
@D	Andres-Barrao, C.//Falquet, L.//Calderon-Copete, S.P.//Descombes, P.//Ortega, P.R.//Barja, F. 	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).	J. Bacteriol.	2011	193		2670-2671			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. 		
@D	Andrews, K.T.//Patel, B.K.C.//Clarke, F.M. 	FgoI, a type II restriction endonuclease from the thermoanaerobe Fervidobacterium gondwanense AB39T.	Anaerobe	1998	4		227-232			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. 		
@D	Andriashvili, I.A.//Kvachadze, L.I.//Vashakidze, R.P.//Adamiya, R.S.//Chanishvili, T.G. 	Molecular mechanism of the protection of phage DNA from restriction endonuclease of Staphylococcus aureus cells.	Mol. Gen. Mikrobiol. Virusol.	1986	0		43-45			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. 		
@D	Andrievskaia, O.//Duceppe, M.O.//Lloyd, D. 	Genome Sequences of Five Mycobacterium bovis Strains Isolated from Farmed Animals and Wildlife in Canada.	Genome Announcements	2018	6		e00258-18			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. 		
@D	Andryuschenko, S.V.//Zdvizhkova, I.A.//Perunova, N.B.//Bukharin, O.V. 	Draft Genome Sequence of Klebsiella pneumoniae Strain ICIS-278_PBV, Isolated from the Feces of a Healthy 59-Year-Old Man from Orenburg, Russia.	Genome Announcements	2018	6		e00576-18			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. 		
@D	Ang, M.Y.//Dymock, D.//Tan, J.L.//Thong, M.H.//Tan, Q.K.//Wong, G.J.//Paterson, I.C.//Choo, S.W. 	Genome Sequence of Parvimonas micra Strain A293, Isolated from an Abdominal Abscess from a Patient in the United Kingdom.	Genome Announcements	2013	1		e01025-13			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. 		
@D	Ang, M.Y.//Dymock, D.//Tan, J.L.//Thong, M.H.//Tan, Q.K.//Wong, G.J.//Paterson, I.C.//Choo, S.W. 	Genome Sequence of Fusobacterium nucleatum Strain W1481, a Possible New Subspecies Isolated from a Periodontal Pocket.	Genome Announcements	2014	2		e00009-14			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. 		
@D	Angelakis, E.//Bibi, F.//Ramasamy, D.//Azhar, E.I.//Jiman-Fatani, A.A.//Aboushoushah, S.M.//Lagier, J.C.//Robert, C.//Caputo, A.//Yasir, M.//Fournier, P.E.//Raoult, D. 	Non-contiguous finished genome sequence and description of Clostridium saudii sp. nov.	Standards in Genomic Sciences	2014	9		8			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. 		
@D	Angelov, A.//Liebl, S.//Ballschmiter, M.//Bomeke, M.//Lehmann, R.//Liesegang, H.//Daniel, R.//Liebl, W. 	Genome Sequence of the Polysaccharide-Degrading, Thermophilic Anaerobe Spirochaeta thermophila DSM 6192.	J. Bacteriol.	2010	192		6492-6493			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. 		
@D	Angelov, A.//Voss, J.//Liebl, W. 	Characterization of Plasmid pPO1 from the Hyperacidophile Picrophilus oshimae.	Archaea	2011	0		723604			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. 		
@D	Anglana, M.//Bacchetti, S. 	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.	Nucleic Acids Res.	1999	27		4276-4281			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. 		
@D	Aniello, F.//Locascio, A.//Fucci, L.//Geraci, G.//Branno, M. 	Isolation of cDNA clones encoding DNA methyltransferase of sea urchin P. lividus: expression during embryonic development.	Gene	1996	178		57-61			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. 		
@D	Aniello, F.//Villano, G.//Corrado, M.//Locascio, A.//Russo, M.T.//D'Aniello, S.D.//Francone, M.//Fucci, L.//Branno, M. 	Structural organization of the sea urchin DNA (cytosine-5)-methyltransferase gene and characterization of five alternative spliced transcripts.	Gene	2003	302		1-9			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. 		
@D	Anjum, A.//Brathwaite, K.J.//Aidley, J.//Connerton, P.L.//Cummings, N.J.//Parkhill, J.//Connerton, I.//Bayliss, C.D. 	Phase variation of a Type IIG restriction-modification enzyme alters site-specific methylation patterns and gene expression in Campylobacter jejuni  strain NCTC11168.	Nucleic Acids Res.	2016	44		4581-4594			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. 		
@D	Ankrah, N.Y.//Lane, T.//Budinoff, C.R.//Hadden, M.K.//Buchan, A. 	Draft Genome Sequence of Sulfitobacter sp. CB2047, a Member of the Roseobacter Clade of Marine Bacteria, Isolated from an Emiliania huxleyi Bloom.	Genome Announcements	2014	2		e01125-14			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. 		
@D	Ankri, S.//Reyes, O.//Leblon, G. 	Improved electro-transformation of highly DNA-restrictive corynebacteria with DNA extracted from starved Escherichia coli.	FEMS Microbiol. Lett.	1996	140		247-251			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. 		
@D	Annapurna, K.//Govindasamy, V.//Sharma, M.//Rajrana, Y.//Swarnalakshmi, K.//Paul, S.//Ghosh, A.//Chikara, S.K. 	Draft Genome Sequence of Pseudomonas stutzeri Strain KMS 55, an Endophytic Diazotroph Isolated from Rice Roots.	Genome Announcements	2017	5		e00972-17			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. 		
@D	Anselmo, A.//Buttinelli, G.//Ciammaruconi, A.//Midulla, F.//Nicolai, A.//Fortunato, A.//Palozzi, A.//Fillo, S.//Lista, F.//Stefanelli, P. 	Draft Genome Sequence of a Bordetella pertussis Strain with the Virulence-Associated Allelic Variant ptxP3, Isolated in Italy.	Genome Announcements	2015	3		e00944-15			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. 		
@D	Anselmo, A.//Ciammaruconi, A.//Carannante, A.//Neri, A.//Fazio, C.//Fortunato, A.//Palozzi, A.M.//Vacca, P.//Fillo, S.//Lista, F.//Stefanelli, P. 	Draft Genome Sequence of Neisseria gonorrhoeae Sequence Type 1407, a Multidrug-Resistant Clinical Isolate.	Genome Announcements	2015	3		e00903-15			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. 		
@D	Anton, B.P. 	Phylogenomic analysis of Escherichia coli methyltransferases and characterization of a novel subfamily of enzymes performing methyl transfer.	Ph.D. Thesis, Boston University	2011			1-271			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. 		
@D	Anton, B.P.//Fomenkov, A.//Raleigh, E.A.//Berkmen, M. 	Complete Genome Sequence of the Engineered Escherichia coli SHuffle Strains and Their Wild-Type Parents.	Genome Announcements	2016	4		e00230-16			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. 		
@D	Anton, B.P.//Harhay, G.P.//Smith, T.P.//Blom, J.//Roberts, R.J. 	Comparative Methylome Analysis of the Occasional Ruminant Respiratory Pathogen Bibersteinia trehalosi.	PLoS ONE	2016	11		e0161499			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. 		
@D	Anton, B.P.//Heiter, D.F.//Benner, J.S.//Hess, E.J.//Greenough, L.//Moran, L.S.//Slatko, B.E.//Brooks, J.E. 	Cloning and characterization of the BglII restriction-modification system reveals a possible evolutionary footprint.	Gene	1997	187		19-27			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. 		
@D	Anton, B.P.//Mongodin, E.F.//Agrawal, S.//Fomenkov, A.//Byrd, D.R.//Roberts, R.J.//Raleigh, E.A. 	Complete Genome Sequence of ER2796, a DNA Methyltransferase-Deficient Strain of Escherichia coli K-12.	PLoS ONE	2015	10		E0127446			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. 		
@D	Anton, B.P.//Raleigh, E.A. 	Complete Genome Sequence of NEB 5-alpha, a Derivative of Escherichia coli K-12 DH5alpha.	Genome Announcements	2016	4		e01245-16			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. 		
@D	Anton, B.P.//Raleigh, E.A. 	Transposon-mediated linker insertion scanning mutagenesis of the Escherichia coli McrA endonuclease.	J. Bacteriol.	2004	186		5699-5707			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. 		
@D	Antonenko, V.//Pawlow, V.//Heesemann, J.//Rakin, A. 	Characterization of a novel unique restriction-modification system from Yersinia enterocolitica O:8 1B.	FEMS Microbiol. Lett.	2003	219		249-252			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. 		
@D	Antonopoulos, D.A.//Nelson, K.E.//Morrison, M.//White, B.A. 	Strain-specific genomic regions of Ruminococcus flavefaciens FD-1 as revealed by combinatorial random-phase genome sequencing and suppressive subtractive hybridization.	Environ. Microbiol.	2004	6		335-346			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. 		
@D	Antoshkina, N.V.//Vorob'eva, L.I.//Bur'ianov, Ia.I. 	[Methylcobalamin-dependent enzymatic methylation of DNA in a cell-free extract of Propionibacterium shermanii].	Mikrobiologiia	1981	50		631-635			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. 		
@D	Antoshkina, N.V.//Vorob'eva, L.I.//Iordan, E.P. 	[Participation of methylcobalamin in the methylation of Propionibacterium shermanii DNA].	Mikrobiologiia	1979	48		217-221			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. 		
@D	Antunes, A.//Alam, I.//Bajic, V.B.//Stingl, U. 	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.	J. Bacteriol.	2011	193		4555-4556			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. 		
@D	Antunes, A.//Alam, I.//Bajic, V.B.//Stingl, U. 	Genome sequence of Halorhabdus tiamatea, the first archaeon isolated from a deep-sea anoxic brine lake.	J. Bacteriol.	2011	193		4553-4554			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. 		
@D	Antunes, A.//Alam, I.//El Dorry, H.//Siam, R.//Robertson, A.//Bajic, V.B.//Stingl, U. 	Genome sequence of Haloplasma contractile, an unusual contractile bacterium from a deep-sea anoxic brine lake.	J. Bacteriol.	2011	193		4551-4552			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. 		
@D	Antwerpen, M.//Elschner, M.//Gaede, W.//Schliephake, A.//Grass, G.//Tomaso, H. 	Genome Sequence of Bacillus anthracis Strain Stendal, Isolated from an Anthrax Outbreak in Cattle in Germany.	Genome Announcements	2016	4		e00219-16			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. 		
@D	Antwerpen, M.//Georgi, E.//Zimmermann, P.//Hoermansdorfer, S.//Meyer, H.//Grass, G. 	Draft Genome Sequence of Strain BF-4, a Lysinibacillus-Like Bacillus Isolated during an Anthrax Outbreak in Bavaria.	Genome Announcements	2014	2		e00918-14			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. 		
@D	Antwerpen, M.//Proenca, D.N.//Ruckert, C.//Licht, K.//Kalinowski, J.//Hanczaruk, M.//Tiemann, C.//Grass, G. 	Draft Genome Sequence of Bacillus anthracis BF-1, Isolated from Bavarian Cattle.	J. Bacteriol.	2012	194		6360-6361			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. 		
@D	Antwerpen, M.//Wolfel, R.//Grass, G. 	Genome Sequence of Historical Bacillus anthracis Strain Tyrol 4675 Isolated from  a Bovine Anthrax Case in Austria.	Genome Announcements	2017	5		e00002-17			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. 		
@D	Antwerpen, M.H.//Schacht, E.//Kaysser, P.//Splettstoesser, W.D. 	Complete Genome Sequence of a Francisella tularensis subsp. holarctica Strain from Germany Causing Lethal Infection in Common Marmosets.	Genome Announcements	2013	1		e00135-12			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. 		
@D	Anvar, S.Y.//Frank, J.//Pol, A.//Schmitz, A.//Kraaijeveld, K.//den Dunnen, J.T.//Op den Camp, H.J. 	The genomic landscape of the verrucomicrobial methanotroph Methylacidiphilum fumariolicum SolV.	BMC Genomics	2014	15		914			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. 		
@D	Aoki, A.//Suetake, I.//Miyagawa, J.//Fujio, T.//Chijiwa, T.//Sasaki, H.//Tajima, S. 	Enzymatic properties of de novo-type mouse DNA (cytosine-5) methyltransferases.	Nucleic Acids Res.	2001	29		3506-3512			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. 		
@D	Aoki, K.//Harada, S.//Yahara, K.//Ishii, Y.//Motooka, D.//Nakamura, S.//Akeda, Y.//Iida, T.//Tomono, K.//Iwata, S.//Moriya, K.//Tateda, K. 	Molecular Characterization of IMP-1-Producing Enterobacter cloacae Complex Isolates in Tokyo.	Antimicrob. Agents Chemother.	2018	62		e02091-17			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. 		
@D	Aoki, T.//Teru, Y.//Morimoto, N.//Kono, T.//Sakai, M.//Takano, T.//Hawke, J.P.//Fukuda, Y.//Takeyama, H.//Hikima, J.I. 	Complete Genome Sequence of Photobacterium damselae subsp. piscicida Strain OT-51443 Isolated from Yellowtail (Seriola quinqueradiata) in Japan.	Genome Announcements	2017	5		e00404-17			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. 		
@D	Aoyagi, T.//Koike, H.//Morita, T.//Sato, Y.//Habe, H.//Hori, T. 	Draft Genome Sequence of Geobacter pelophilus Strain Dfr2, a Ferric Iron-Reducing Bacterium.	Genome Announcements	2017	5		e00537-17			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. 		
@D	Aparicio, J.F.//Barbes, C.//Hardisson, C.//Sanchez, J. 	Sensitivity to phages of Streptomyces coelicolor strains harbouring type II restriction endonucleases.	Microbiol. Sem.	1990	6		71-75			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. 		
@D	Arabyan, N.//Huang, B.C.//Weimer, B.C. 	Amylases and Their Importance during Glycan Degradation: Genome Sequence Release  of Salmonella Amylase Knockout Strains.	Genome Announcements	2017	5		e00355-17			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. 		
@D	Arabyan, N.//Huang, B.C.//Weimer, B.C. 	Draft Genome Sequences of Salmonella Lysozyme Gene Knockout Mutants.	Genome Announcements	2017	5		e00519-17			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. 		
@D	Arabyan, N.//Huang, B.C.//Weimer, B.C. 	Draft Genome Sequences of Salmonella enterica Serovar Typhimurium LT2 with Deleted Chitinases That Are Emerging Virulence Factors.	Genome Announcements	2017	5		e00659-17			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. 		
@D	Arabyan, N.//Weis, A.M.//Huang, B.C.//Weimer, B.C. 	Implication of Sialidases in Salmonella Infection: Genome Release of Sialidase Knockout Strains from Salmonella enterica Serovar Typhimurium LT2.	Genome Announcements	2017	5		e00341-17			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. 		
@D	Arahal, D.R.//Pujalte, M.J.//Rodrigo-Torres, L. 	Draft genomic sequence of Nereida ignava CECT 5292(T), a marine bacterium of the  family Rhodobacteraceae.	Standards in Genomic Sciences	2016	11		21			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. 		
@D	Arahal, D.R.//Rodrigo-Torres, L.//Lucena, T.//Pujalte, M.J. 	Draft Genome Sequences of Vibrio renopiscarius Strains CECT 8603T and CECT 8604,  Two Marine Gammaproteobacteria Isolated from Cultured Gilthead Sea Bream (Sparus   aurata).	Genome Announcements	2015	3		e00099-15			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. 		
@D	Arahal, D.R.//Shao, Z.//Lai, Q.//Pujalte, M.J. 	Draft Genome Sequence of Actibacterium mucosum KCTC 23349, a Marine Alphaproteobacterium with Complex Ionic Requirements Isolated from Mediterranean   Seawater at Malvarrosa Beach, Valencia, Spain.	Genome Announcements	2014	2		e00486-14			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%. 		
@D	Arai, H.//Kanbe, H.//Ishii, M.//Igarashi, Y. 	Complete genome sequence of the thermophilic, obligately chemolithoautotrophic hydrogen-oxidizing bacterium Hydrogenobacter  thermophilus TK-6.	J. Bacteriol.	2010	192		2651-2652			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. 		
@D	Arai, H.//Shomura, Y.//Higuchi, Y.//Ishii, M. 	Complete Genome Sequence of a Moderately Thermophilic Facultative Chemolithoautotrophic Hydrogen-Oxidizing Bacterium, Hydrogenophilus  thermoluteolus TH-1.	Microbiol. Resour. Announc.	2018	7		e00857-18			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. 		
@D	Arai, T.//Aoki, T. 	New R plasmid-mediated restriction-modification system of deoxyribonucleic acid conferred by group E R plasmids.	J. Bacteriol.	1977	130		529-531			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. 		
@D	Aranda, J.//Roca, M.//Lopez-Canut, V.//Tunon, I. 	Theoretical Study of the Catalytic Mechanism of DNA-(N4-Cytosine)-Methyltransferase from the Bacterium Proteus vulgaris.	J. Phys. Chem. B	2010	114		8467-8473			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. 		
@D	Aranda, J.//Roca, M.//Tunon, I. 	Substrate promiscuity in DNA methyltransferase M.PvuII. A mechanistic insight.	Org. Biomol. Chem.	2012	10		5395-5400			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. 		
@D	Aranda, J.//Zinovjev, K.//Roca, M.//Tunon, I. 	Dynamics and Reactivity in Thermus aquaticus N6-Adenine Methyltransferase.	J. Am. Chem. Soc.	2014	136		16227-16239			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. 		
@D	Aranda, J.//Zinovjev, K.//Swiderek, K.//Roca, M.//Tunon, I. 	Molecular dynamics and QM/MM free energy profiles of cytosine C5-methyltransferase M.Hhai.	FEBS J.	2013	280		105			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. 		
@D	Aras, R.A. 	Helicobacter pylori regulates hpyII restriction-modification function using gene deletion and horizontal reacquisition.	Int. J. Med. Microbiol.	2001	291S		95			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. 		
@D	Aras, R.A.//Blaser, M.J. 	Conservation of a type IIs restriction-modification system in Helicobacter pylori with homology to the MboII R-M system in Moraxella bovis.	Abstr. Gen. Meet. Am. Soc. Microbiol.	2000	100		290-291			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. 		
@D	Aras, R.A.//Small, A.J.//Ando, T.//Blaser, M.J. 	Horizontal transfer of the Helicobacter pylori restriction-modification system, HpyII, by a conjugation-like mechanism.	Abstr. Gen. Meet. Am. Soc. Microbiol.	2002	102		165-166			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. 		
@D	Aras, R.A.//Small, A.J.//Ando, T.//Blaser, M.J. 	Helicobacter pylori interstrain restriction-modification diversity prevents genome subversion by chromosomal DNA from competing strains.	Nucleic Acids Res.	2002	30		5391-5397			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. 		
@D	Aras, R.A.//Takata, T.//Ando, T.//van der Ende, A.//Blaser, M.J. 	Regulation of the HpyII restriction-modification system of Helicobacter pylori by gene deletion and horizontal reconstitution.	Mol. Microbiol.	2001	42		369-382			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. 		
@D	Aras, R.A.//Takata, T.//van der Ende, A.//Blaser, M.J. 	Helicobacter pylori variants from a single host that differ in the presence of the hpyII restriction-modification system.	Abstr. Gen. Meet. Am. Soc. Microbiol.	2001	101		296			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. 		
@D	Araujo, C.L.//Dias, L.M.//Veras, A.A.//Alves, J.T.//Cavalcante, A.L.//Dowson, C.G.//Azevedo, V.//Ramos, R.T.//Silva, A.//Carneiro, A.R. 	Whole-Genome Sequence of Corynebacterium pseudotuberculosis 262 Biovar equi Isolated from Cow Milk.	Genome Announcements	2016	4		e00176-16			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. 		
@D	Araujo, F.A.//Marques, J.M.//de Moura, V.A.//Schneider, M.P.//Andrade, S.S.//Lima, A.C.//Guimaraes, L.C.//Folador, A.R.//Silva, A.//Ramos, R.T. 	Draft Genome Sequence of Corynebacterium pseudotuberculosis Strain PA07 Biovar ovis, Isolated from a Sheep Udder in Amazonia.	Genome Announcements	2017	5		e00040-17			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. 		
@D	Araujo, F.D.//Croteau, S.//Slack, A.D.//Milutinovic, S.//Bigey, P.//Price, G.B.//Zannis-Hajopoulos, M.//Szyf, M. 	The dnmt1 target recognition domain resides in the n terminus.	J. Biol. Chem.	2001	276		6930-6936			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. 		
@D	Araujo, F.D.//Knox, J.D.//Ramchandrani, S.//Pelletier, R.//Bigey, P.//Price, G.//Szyf, M.//Zannis-Hadjopoulos, M. 	Identification of initiation sites for DNA replication in the human dnmt1 (DNA-methyltransferase) locus.	J. Biol. Chem.	1999	274		9335-9341			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. 		
@D	Aravind, L.//Makarova, K.S.//Koonin, E.V. 	Holliday junction resolvases and related nucleases: identification of new families, phyletic distribution and evolutionary trajectories.	Nucleic Acids Res.	2000	28		3417-3432			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. 		
@D	Arber, W. 	On the generation of genetic diversity in microorganisms.	Proc. Indian Natn. Sci. Acad.	1994	B60		357-364			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. 		
@D	Arber, W. 	DNA Modification and Restriction.	Prog. Nucleic Acid Res. Mol. Biol.	1974	14		1-37			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. 		
@D	Arber, W. 	Host-controlled modification of bacteriophage.	Annu. Rev. Microbiol.	1965	19		365-378			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. 		
@D	Arber, W. 	Strain-specific restriction and modification of DNA.	Bull. Schweiz. Akad. Med. Wiss.	1970	25		99-100			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]. 		
@D	Arber, W. 	Host-controlled modification of DNA.	Naturwissenschaften	1969	56		155-160			None 		
@D	Arber, W. 	Promotion and limitation of genetic exchange.	Science	1979	205		361-365			None 		
@D	Arber, W. 	Specificites biologiques de l'acide desoxyribonucleique.	Pathol. Microbiol. (Basel)	1962	25		668-681			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. 		
@D	Arber, W. 	Host specificity of DNA produced by Escherichia coli V. The role of Methionine in the Production of Host Specificity.	J. Mol. Biol.	1965	11		247-256			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. 		
@D	Arber, W. 	Host-controlled restriction and modification of bacteriophage.	Symp. Soc. Gen. Microbiol.	1968	18		295-314			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. 		
@D	Arber, W. 	Host specificity of DNA produced by Escherichia coli.   9. Host-controlled modification of bacteriophage fd.	J. Mol. Biol.	1966	20		483-496			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. 		
@D	Arber, W. 	Host specificity of DNA produced by Escherichia coli.  III.  Effects on transduction mediated by lambda dg.	Virology	1964	23		173-182			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. 		
@D	Arber, W. 	What is the function of DNA restriction enzymes?	Trends Biochem. Sci.	1977	2		N176-N178			None 		
@D	Arber, W. 	Origin and properties of type A host specificity in Escherichia coli.	Pathol. Microbiol. (Basel)	1969	34		147					
@D	Arber, W. 	Roots, strategies and prospects of functional genomics - functional genomics, human genome, bioinformatic software and polymerase chain  reaction; a review.	Curr. Sci.	2002	83		826-828			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) 		
@D	Arber, W. 	Genetically encoded generators of genetic variants.	J. Proteomics	2009	72		836-837			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. 		
@D	Arber, W. 	Elements in microbial evolution.	J. Mol. Evol.	1991	33		4-12			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. 		
@D	Arber, W. 	Genetic variation: molecular mechanisms and impact on microbial evolution.	FEMS Microbiol. Rev.	2000	24		1-7			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. 		
@A	Arber, W. 		Genetic Variation and Molecular Evolution.			Meyers, R.A. 		Encyclopedia of Molecular Cell Biology and Molecular Medicine.					Wiley-VCH Verlag	2004		5		331-352									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. 		
@A	Arber, W. 		Host-controlled variation.			Hershey, A.D. 		Bacteriophage Lambda				Cold Spring Harbor, New York	Cold Spring Harbor Laboratory Press	1971		0		83-96									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. 		
@A	Arber, W. 		Restriction Enzymes: From Their Discovery to Their Applications.			Piguet, P.//Poindron, P. 		Biovalley Monographs				Basel, Switzerland	Karger, Postfach, CH-4009	2012		3		33-38									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. 		
@D	Arber, W.//Dussoix, D. 	Host Specificity of DNA Producted by Escherichia Coli:  I. Host controlled modification of bacteriophage lambda.	J. Mol. Biol.	1962	5		18-36			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. 		
@D	Arber, W.//Hattman, S.//Dussoix, D. 	On the host-controlled modification of bacteriophage lambda.	Virology	1963	21		30-35			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. 		
@D	Arber, W.//Kuhnlein, U. 	Mutational loss of B-specific restriction of the bacteriophage fd.	Pathol. Microbiol. (Basel)	1967	30		946-952			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. 		
@D	Arber, W.//Kuhnlein, U. 	Repair and modification of genetic material:  DNA modification and restriction.	Int. Congr. Biochem.	1970	8		180			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. 		
@D	Arber, W.//Linn, S. 	DNA modification and restriction.	Annu. Rev. Biochem.	1969	38		467-500			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. 		
@D	Arber, W.//Morse, M.L. 	Host specificity of DNA produced by Escherichia coli.  VI.  Effects on bacterial conjugation.	Genetics	1965	51		137-148			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). 		
@D	Arber, W.//Rifat, A.//Wauters-Willems, D.//Kuhnlein, U. 	Host specificity of DNA produced by Escherichia coli.	Mol. Gen. Genet.	1972	115		195-207			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. 		
@D	Arber, W.//Smith, J.D. 	Kinetics of reproduction of nucleic acids and their role in biosynthesis of proteins.	Int. Congr. Microbiol.	1966	5		5			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. 		
@D	Arber, W.//Wauters-Willems, D. 	Host specificity of DNA produced by Escherichia coli. XII.  The two restriction and modification systems of strain 15T-.	Mol. Gen. Genet.	1970	108		203-217			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. 		
@A	Arber, W.//Yuan, R.//Bickle, T.A. 		Strain-specific modification and restriction of DNA in bacteria.			Antoni, F.//Farago, A. 		Post Synthetic Modification of Macromolecules.  Symposium at 9th FEBS Meeting, Budapest. 1974				New York	Elsevier	1975		34		3-22									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). 		
@D	Arbulu, S.//Frantzen, C.//Lohans, C.T.//Cintas, L.M.//Herranz, C.//Holo, H.//Diep, D.B.//Vederas, J.C.//Hernandez, P.E. 	Draft Genome Sequence of the Bacteriocin-Producing Strain Enterococcus faecium M3K31, Isolated from Griffon Vultures (Gyps fulvus subsp. fulvus).	Genome Announcements	2016	4		e00055-16			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. 		
@D	Arbulu, S.//Jimenez, J.J.//Borrero, J.//Sanchez, J.//Frantzen, C.//Herranz, C.//Nes, I.F.//Cintas, L.M.//Diep, D.B.//Hernandez, P.E. 	Draft Genome Sequence of the Bacteriocinogenic Strain Enterococcus faecalis DBH18, Isolated from Mallard Ducks (Anas platyrhynchos).	Genome Announcements	2016	4		e00663-16			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. 		
@D	Archer, C.T.//Kim, J.F.//Jeong, H.//Park, J.H.//Vickers, C.E.//Lee, S.Y.//Nielsen, L.K. 	The genome sequence of E. coli W (ATCC 9637): comparative genome analysis and an improved genome-scale reconstruction of E. coli.	BMC Genomics	2011	12		9			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. 		
@D	Arden, S.B.//Barksdale, L. 	Restriction and modification and the phage typing of true Corynebacteria.	Abstr. Gen. Meet. Am. Soc. Microbiol.	1971	71		181			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. 		
@D	Ardley, J.//Tian, R.//Howieson, J.//Yates, R.//Brau, L.//Han, J.//Lobos, E.//Huntemann, M.//Chen, A.//Mavromatis, K.//Markowitz, V.//Ivanova, N.//Pati, A.//Goodwin, L.//Woyke, T.//Kyrpides, N.//Reeve, W. 	Genome sequence of the dark pink pigmented Listia bainesii microsymbiont Methylobacterium sp. WSM2598.	Standards in Genomic Sciences	2014	9		5			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. 		
@D	Ardley, J.//Tian, R.//O'Hara, G.//Seshadri, R.//Reddy, T.B.//Pati, A.//Woyke, T.//Markowitz, V.//Ivanova, N.//Kyrpides, N.//Howieson, J.//Reeve, W. 	High-quality permanent draft genome sequence of Ensifer medicae strain WSM244, a  microsymbiont isolated from Medicago polymorpha growing in alkaline soil.	Standards in Genomic Sciences	2015	10		126			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. 		
@D	Areechon, N.//Kannika, K.//Hirono, I.//Kondo, H.//Unajak, S. 	Draft Genome Sequences of Streptococcus agalactiae Serotype Ia and III Isolates from Tilapia Farms in Thailand.	Genome Announcements	2016	4		e00122-16			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. 		
@D	Arena, F.//Henrici, De.A.L.//Pieralli, F.//Di Pilato, V.//Giani, T.//Torricelli, F.//D'Andrea, M.M.//Rossolini, G.M. 	Draft Genome Sequence of the First Hypermucoviscous Klebsiella quasipneumoniae subsp. quasipneumoniae Isolate from a Bloodstream Infection.	Genome Announcements	2015	3		e00952-15			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. 		
@D	Arens, J.C.//Haltli, B.//Kerr, R.G. 	Draft Genome Sequence of Kitasatospora griseola Strain MF730-N6, a Bafilomycin, Terpentecin, and Satosporin Producer.	Genome Announcements	2015	3		e00208-15			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. 		
@D	Argast, G.M.//Stephens, K.M.//Emond, M.J.//Monnat, R.J. Jr. 	I-PpoI and I-CreI homing site sequence degeneracy determined by random mutagenesis and sequential in vitro enrichment.	J. Mol. Biol.	1998	280		345-353			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. 		
@D	Argemi, X.//Martin, V.//Loux, V.//Dahyot, S.//Lebeurre, J.//Guffroy, A.//Martin, M.//Velay, A.//Keller, D.//Riegel, P.//Hansmann, Y.//Paul, N.//Prevost, G. 	Whole genome sequencing of 7 strains of Staphylococcus lugdunensis allows identification of mobile genetic elements.	Genome Biol. Evol.	2017	9		0			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. 		
@D	Argos, P. 	Evidence for a repeating domain in type I restriction enzymes.	EMBO J.	1985	4		1351-1355			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. 		
@D	Arimondo, P.B. 	IDENTIFICATION AND DESIGN OF NEW C5-DNA METHYLTRANSFERASE INHIBITORS AND THEIR BIOLOGICAL ACTIVITY.	Anticancer Res.	2014	34		5813-5814			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. 		
@D	Arivett, B.A.//Fiester, S.E.//Ream, D.C.//Centron, D.//Ramirez, M.S.//Tolmasky, M.E.//Actis, L.A. 	Draft Genome of the Multidrug-Resistant Acinetobacter baumannii Strain A155 Clinical Isolate.	Genome Announcements	2015	3		e00212-15			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. 		
@D	Arivett, B.A.//Ream, D.C.//Fiester, S.E.//Kidane, D.//Actis, L.A. 	Draft Genome Sequences of Pseudomonas aeruginosa Isolates from Wounded Military Personnel.	Genome Announcements	2016	4		e00829-16			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. 		
@D	Arivett, B.A.//Ream, D.C.//Fiester, S.E.//Kidane, D.//Actis, L.A. 	Draft Genome Sequences of Escherichia coli Isolates from Wounded Military Personnel.	Genome Announcements	2016	4		e00828-16			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. 		
@D	Arivett, B.A.//Ream, D.C.//Fiester, S.E.//Kidane, D.//Actis, L.A. 	Draft Genome Sequences of Acinetobacter baumannii Isolates from Wounded Military  Personnel.	Genome Announcements	2016	4		e00773-16			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. 		
@D	Arivett, B.A.//Ream, D.C.//Fiester, S.E.//Mende, K.//Murray, C.K.//Thompson, M.G.//Kanduru, S.//Summers, A.M.//Roth, A.L.//Zurawski, D.V.//Actis, L.A. 	Draft Genome Sequences of Klebsiella pneumoniae Clinical Type Strain ATCC 13883 and Three Multidrug-Resistant Clinical Isolates.	Genome Announcements	2015	3		e01385-14			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. 		
@D	Armalyte, E.//Bujnicki, J.M.//Giedriene, J.//Gasiunas, G.//Kosinski, J.//Lubys, A. 	Mva1269I: A monomeric type IIS restriction endonuclease from micrococcus varians with two EcoRI- and FokI-like catalytic domains.	J. Biol. Chem.	2005	280		41584-41594			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. 		
@D	Armbrust, E.V. et al. 	The genome of the diatom Thalassiosira pseudonana: ecology, evolution, and metabolism.	Science	2004	306		79-86			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. 		
@D	Armbruster, C.E.//Smith, S.N.//Johnson, A.O.//DeOrnellas, V.//Eaton, K.A.//Yep, A.//Mody, L.//Wu, W.//Mobley, H.L. 	The Pathogenic Potential of Proteus mirabilis is Enhanced by Other Uropathogens During Polymicrobial Urinary Tract Infection.	Infect. Immun.	2017	85		e00808-16			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. 		
@D	Armitano, R.I.//Zerbetto, De.P.G.//Matteo, M.J.//Revale, S.//Romero, S.//Traglia, G.M.//Catalano, M. 	Draft Genome Sequences of Helicobacter pylori Strains HPARG63 and HPARG8G, Cultured from Patients with Chronic Gastritis and Gastric Ulcer Disease.	Genome Announcements	2013	1		e00700-13			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. 		
@D	Armstrong, K.//Bauer, W.R. 	Preferential site-dependent cleavage by restriction endonuclease PstI.	Nucleic Acids Res.	1982	10		993-1007			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. 		
@D	Armstrong, K.A.//Bauer, W.R. 	Site-dependent cleavage of pBR322 DNA by restriction endonuclease HinfI.	Nucleic Acids Res.	1983	11		4109-4126			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. 		
@D	Arnold, H.P.//Ziese, U.//Zillig, W. 	SNDV, a novel virus of the extremely thermophilic and acidophilic archaeon Sulfolobus.	Virology	2000	272		409-416			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. 		
@D	Arnold, J.W.//Monteagudo-Mera, A.//Altermann, E.//Cadenas, M.B.//Thompson, A.L.//Azcarate-Peril, M.A. 	Genome Sequences of Potential Probiotic Lactobacillus rhamnosus Isolates from Human Infants.	Genome Announcements	2017	5		e00107-17			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. 		
@D	Arnold, M.//Wibberg, D.//Blom, J.//Schatschneider, S.//Winkler, A.//Kutter, Y.//Ruckert, C.//Albersmeier, A.//Albaum, S.//Goesmann, A.//Zange, S.//Heesemann, J.//Puhler, A.//Hogardt, M.//Vorholter, F.J. 	Draft Genome Sequence of Pseudomonas aeruginosa Strain WS136, a Highly Cytotoxic  ExoS-Positive Wound Isolate Recovered from Pyoderma Gangrenosum.	Genome Announcements	2015	3		e00680-15			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. 		
@D	Arnould, S.//Chames, P.//Perez, C.//Lacroix, E.//Duclert, A.//Epinat, J.C.//Stricher, F.//Petit, A.S.//Patin, A.//Guillier, S.//Rolland, S.//Prieto, J.//Blanco, F.J.//Bravo, J.//Montoya, G.//Serrano, L.//Duchateau, P.//Paques, F. 	Engineering of large numbers of highly specific homing endonucleases that induce recombination on novel DNA targets.	J. Mol. Biol.	2005	355		443-458			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. 		
@D	Arnould, S.//Delenda, C.//Grizot, S.//Desseaux, C.//Paques, F.//Silva, G.H.//Smith, J. 	The I-CreI meganuclease and its engineered derivatives: applications from cell modification to gene therapy.	Protein Eng. Des. Sel.	2011	24		27-31			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. 		
@D	Arnould, S.//Perez, C.//Cabaniols, J.-P.//Smith, J.//Gouble, A.//Grizot, S.//Epinat, J.-C.//Duclert, A.//Duchateau, P.//Paques, F. 	Engineered I-Crel derivatives cleaving sequences from the human XPC gene can induce highly efficient gene correction in mammalian cells.	J. Mol. Biol.	2007	371		49-65			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. 		
@D	Arraj, J.A.//Marinus, M.G. 	Phenotypic reversal in dam mutants of Escherichia coli K-12 by a recombinant plasmid containing the dam+ gene.	J. Bacteriol.	1983	153		562-565			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. 		
@D	Arraj, J.A.//Wu, T.-H.//Marinus, M.G. 	Expression of a DNA methylation (dam) gene in Escherichia coli K-12.	Curr. Microbiol.	1990	20		133-136			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. 		
@D	Arrand, J.R.//Myers, P.A.//Roberts, R.J. 	A new restriction endonuclease from Streptomyces albus G.	J. Mol. Biol.	1978	118		127-135			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. 		
@D	Arsene-Ploetze, F. et al. 	Structure, function, and evolution of the Thiomonas spp. genome.	PLoS Genet.	2010	6		e1000859			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. 		
@D	Artyukhin, A.B.//Woo, Y.H. 	DNA extraction method with improved efficiency and specificity using DNA methyltransferase and 'click' chemistry.	Anal. Biochem.	2012	425		169-174			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. 		
@D	Arushothy, R.//Ahmad, N.//Amran, F.//Hashim, R.//Samsuddin, N.//Che, A.C.R. 	Draft Genome Sequence of a Highly Resistant Streptococcus pneumoniae Serotype 15A Strain Isolated from Blood.	Genome Announcements	2018	6		e00167-18			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). 		
@D	Arutyunyan, E.E.//Gonchar, N.A.//Gruber, I.M.//Nikolskaya, N.I. 	Purification and characterization of DNA methyltransferase Sau6782 of Staphylococcus aureus.	Mol. Gen. Mikrobiol. Virusol.	1992	11-1		26-29					
@D	Arutyunyan, E.E.//Gonchar, N.A.//Levchenko, I.Y.//Gruber, I.M.//Nikolskaya, I.I. 	Isoelectrofocusing of methylation and restriction enzymes of Staphylococcus aureus 6782.	Biokhimiia	1991	56		281-288			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. 		
@D	Arutyunyan, E.E.//Gruber, I.M.//Polyachenko, V.M.//Kvachadze, L.J.//Andriashvili, I.A.//Chanishvili, T.G.//Nikolskaya, I.I. 	Restricting Endonuclease SAU 6782.	Vopr. Med. Khim.	1985	31		127-132			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. 		
@D	Arutyunyan, E.E.//Gruber, I.M.//Polyachenko, V.M.//Nikolskaya, I.I.//Debov, S.S. 	Isolation of methylases from Sau 6782 strain.	Vopr. Med. Khim.	1990	36		75-79			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. 		
@D	Arwert, F.//Rutberg, L. 	Restriction and modification in Bacillus subtilis.  Induction of a modifying activity in Bacillus subtilis 168.	Mol. Gen. Genet.	1974	133		175-177			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. 		
@D	Arya, G.//Petronella, N.//Crosthwait, J.//Carrillo, C.D.//Shwed, P.S. 	Draft Genome Sequence of Bacillus megaterium Type Strain ATCC 14581.	Genome Announcements	2014	2		e01124-14			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. 		
@D	Aryantini, N.P.//Prajapati, J.B.//Urashima, T.//Fukuda, K. 	Complete Genome Sequence of Lactobacillus fermentum MTCC 25067 (Formerly TDS030603), a Viscous Exopolysaccharide-Producing Strain Isolated from Indian  Fermented Milk.	Genome Announcements	2017	5		e00091-17			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. 		
@D	Asahina, A.Y.//Hadfield, M.G. 	Complete Genome Sequence of Cellulophaga lytica HI1 Using PacBio Single-Molecule  Real-Time Sequencing.	Genome Announcements	2014	2		e01148-14			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. 		
@D	Asahina, A.Y.//Hadfield, M.G. 	Draft Genome Sequence of Pseudoalteromonas luteoviolacea HI1, Determined Using Roche 454 and PacBio Single-Molecule Real-Time Hybrid Sequencing.	Genome Announcements	2015	3		e01590-14			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. 		
@D	Asahina, Y.//Shiroma, A.//Nakano, K.//Tamotsu, H.//Ashimine, N.//Shinzato, M.//Minami, M.//Shimoji, M.//Nakanishi, T.//Ohki, S.//Teruya, K.//Satou, K.//Kobayashi, M.//Hagi, T.//Moriya, N.//Suzuki, C.//Tajima, A.//Nomura, M.//Hirano, T. 	Complete Genome Sequence of Lactobacillus paracasei EG9, a Strain Accelerating Free Amino Acid Production during Cheese Ripening.	Genome Announcements	2018	6		e00627-18			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. 		
@D	Asai, A.//Hirai, H.//Bodell, W.J.//Hoshino, T. 	Restriction endonuclease recognition and Southern hybridization of bromodeoxyuridine-substituted genomic DNA.	Cell Prolif.	1993	26		271-280			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. 		
@D	Asakura, H.//Ikeda, T.//Yamamoto, S.//Kabeya, H.//Sugiyama, H.//Takai, S. 	Draft Genome Sequence of Five Shiga Toxin-Producing Escherichia coli Strains Isolated from Wild Deer in Japan.	Genome Announcements	2017	5		e01455-16			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. 		
@D	Asakura, H.//Takahashi, N.//Yamamoto, S.//Maruyama, H. 	Draft Genome Sequence of Campylobacter jejuni CAM970 and C. coli CAM962, Associated with a Large Outbreak of Foodborne Illness in Fukuoka, Japan, in 2016.	Genome Announcements	2017	5		e00508-17			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. 		
@D	Asakura, H.//Yamamoto, S.//Momose, Y.//Kato, H.//Iwaki, M.//Shibayama, K. 	Genome Sequence of Clostridium botulinum Strain Adk2012 Associated with a Foodborne Botulinum Case in Tottori, Japan, in 2012.	Genome Announcements	2017	5		e00872-17			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. 		
@D	Asakura, Y.//Kobayashi, I. 	From damaged genome to cell surface: transcriptome changes during bacterial cell death triggered by loss of a restriction-modification gene  complex.	Nucleic Acids Res.	2009	37		3021-3031			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. 		
@D	Asakura, Y.//Kojima, H.//Kobayashi, I. 	Evolutionary genome engineering using a restriction-modification system.	Nucleic Acids Res.	2011	39		9034-9046			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. 		
@D	Asamizu, E.//Sato, S.//Kaneko, T.//Nakamura, Y.//Kotani, H.//Miyajima, N.//Tabata, S. 	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.	DNA Res.	1998	5		379-391			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/. 		
@D	Aserse, A.A.//Woyke, T.//Kyrpides, N.C.//Whitman, W.B.//Lindstrom, K. 	Draft genome sequences of Bradyrhizobium shewense sp. nov. ERR11(T) and Bradyrhizobium yuanmingense CCBAU 10071(T).	Standards in Genomic Sciences	2017	12		74			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. 		
@D	Aserse, A.A.//Woyke, T.//Kyrpides, N.C.//Whitman, W.B.//Lindstrom, K. 	Draft genome sequence of type strain HBR26T and description of Rhizobium aethiopicum sp. nov.	Standards in Genomic Sciences	2017	12		14			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. 		
@D	Ashapkin, V.V.//Kutueva, L.I.//Vanyushin, B.F. 	Is the cytosine DNA methyltransferase gene MET1 regulated by DNA methylation in Arabidopsis thaliana plants?	Genetika	2011	47		279-288			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. 		
@D	Ashapkin, V.V.//Kutueva, L.I.//Vanyushin, B.F. 	The gene for domains rearranged methyltransferase (DRM2) in Arabidopsis thaliana plants is methylated at both cytosine and adenine residues.	FEBS Lett.	2002	532		367-372			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. 		
@D	Ashraf, M.//Altschuler, M.//Galasinski, S.//Griffiths, T.D. 	Alteration of gene expression by restriction enzymes electroporated into plant cells.	Mutat. Res.	1993	302		75-82			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. 		
@D	Ashworth, J.//Havranek, J.J.//Duarte, C.M.//Sussman, D.//Monnat, R.J.//Stoddard, B.L.//Baker, D. 	Computational redesign of endonuclease DNA binding and cleavage specificity.	Nature	2006	441		656-659			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. 		
@D	Ashworth, J.//Taylor, G.K.//Havranek, J.J.//Quadri, S.A.//Stoddard, B.L.//Baker, D. 	Computational reprogramming of homing endonuclease specificity at multiple adjacent base pairs.	Nucleic Acids Res.	2010	38		5601-5608			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. 		
@D	Asim, M.//Chikara, S.K.//Ghosh, A.//Vudathala, S.//Romero-Gallo, J.//Krishna, U.S.//Wilson, K.T.//Israel, D.A.//Peek, R.M. Jr.//Chaturvedi, R. 	Draft Genome Sequence of Gerbil-Adapted Carcinogenic Helicobacter pylori Strain 7.13.	Genome Announcements	2015	3		e00641-15			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. 		
@D	Aslam, F.//Yasmin, A.//Thomas, T. 	Genome Sequence of Klebsiella quasipneumoniae subsp. similipneumoniae MB373, an Effective Bioremediator.	Genome Announcements	2016	4		e01068-16			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. 		
@D	Asmar, S.//Phelippeau, M.//Robert, C.//Croce, O.//Drancourt, M. 	Draft Genome Sequence of Mycobacterium bohemicum Strain DSM 44277T.	Genome Announcements	2015	3		e00878-15			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. 		
@D	Asmar, S.//Rascovan, N.//Robert, C.//Drancourt, M. 	Draft Genome Sequence of Mycobacterium peregrinum Strain CSUR P2098.	Genome Announcements	2015	3		e01274-15			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. 		
@D	Asmar, S.//Rascovan, N.//Robert, C.//Drancourt, M. 	Draft Genome Sequence of Mycobacterium acapulcensis Strain CSURP1424.	Genome Announcements	2016	4		e00836-16			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. 		
@D	Asmar, S.//Rascovan, N.//Robert, C.//Drancourt, M. 	Draft Genome Sequence of Mycobacterium mucogenicum Strain CSUR P2099.	Genome Announcements	2015	3		e01369-15			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. 		
@D	Asmar, S.//Robert, C.//Croce, O.//Caputo, A.//Drancourt, M. 	Draft Genome Sequence of Mycobacterium neworleansense Strain ATCC 49404T.	Genome Announcements	2015	3		e01314-15			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. 		
@D	Assis-das-Gracas, D.//Thiago-Juca-Ramos, R.//Vieira-Araujo, A.C.//Zahlouth, R.//Ribeiro-Carneiro, A.//Souza-Lopes, T.//Azevedo-Barauna, R.//Azevedo, V.//Cruz-Schneider, M.P.//Pellizari, V.H.//Silva, A. 	Complete Genome of a Methanosarcina mazei Strain Isolated from Sediment Samples from an Amazonian Flooded Area.	Genome Announcements	2013	1		e00271-13			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. 		
@D	Astolfi, M.C.T.//Carvalho, E.B.S.//de Barros, A.M.//Pinto, M.V.//de Lacerda, L.B.//Nogueira, V.B.//Lopes, E.F.//Astolfi-Filho, S. 	Draft Genome Sequence of the Novel Enterobacter cloacae Strain amazonensis, a Highly Heavy Metal-Resistant Bacterium from a Contaminated Stream in Amazonas,  Brazil.	Genome Announcements	2018	6		e00450-18			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. 		
@D	Aswani, V.//Mau, B.//Shukla, S.K. 	Complete Genome Sequence of Staphylococcus aureus MCRF184, a Necrotizing Fasciitis-Causing Methicillin-Sensitive Sequence Type 45 Staphylococcus Strain.	Genome Announcements	2016	4		e00374-16			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. 		
@D	Atack, J.M.//Srikhanta, Y.N.//Fox, K.L.//Jurcisek, J.A.//Brockman, K.L.//Clark, T.A.//Boitano, M.//Power, P.M.//Jen, F.E.//McEwan, A.G.//Grimmond, S.M.//Smith, A.L.//Barenkamp, S.J.//Korlach, J.//Bakaletz, L.O.//Jennings, M.P. 	A biphasic epigenetic switch controls immunoevasion, virulence and niche adaptation in non-typeable Haemophilus influenzae.	Nat. Commun.	2015	6		7828			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. 		
@D	Atack, J.M.//Tan, A.//Bakaletz, L.O.//Jennings, M.P.//Seib, K.L. 	Phasevarions of Bacterial Pathogens: Methylomics Sheds New Light on Old Enemies.	Trends Microbiol.	2018	26		715-726			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. 		
@D	Atack, J.M.//Weinert, L.A.//Tucker, A.W.//Husna, A.U.//Wileman, T.M.//Hadjirin, N.F.//Hoa, N.T.//Parkhill, J.//Maskell, D.J.//Blackall, P.J.//Jennings, M.P. 	Streptococcus suis contains multiple phase-variable methyltransferases that show  a discrete lineage distribution.	Nucleic Acids Res.	2018	46		11466-11476			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. 		
@D	Atack, J.M.//Yang, Y.//Seib, K.L.//Zhou, Y.//Jennings, M.P. 	A survey of Type III restriction-modification systems reveals numerous, novel epigenetic regulators controlling phase-variable regulons; phasevarions.	Nucleic Acids Res.	2018	46		3532-3542			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. 		
@D	Atanasiu, C.//Byron, O.//McMiken, H.//Sturrock, S.S.//Dryden, D.T.F. 	Characterisation of the structure of ocr, the gene 0.3 protein of bacteriophage T7.	Nucleic Acids Res.	2001	29		3059-3068			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. 		
@D	Atanasiu, C.//Su, T.-J.//Sturrock, S.S.//Dryden, D.T.F. 	Interaction of the ocr gene 0.3 protein of bacteriophage T7 with EcoKI restriction/modification enzyme.	Nucleic Acids Res.	2002	30		3936-3944			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. 		
@D	Athanasiadis, A.//Gregoriu, M.//Thanos, D.//Kokkinidis, M.//Papamatheakis, J. 	Complete nucleotide sequence of the PvuII restriction enzyme gene from Proteus vulgaris.	Nucleic Acids Res.	1990	18		6434			None 		
@D	Athanasiadis, A.//Kokkinidis, M. 	Purification, crystallization and preliminary X-ray diffraction studies of the PvuII endonuclease.	J. Mol. Biol.	1991	222		451-453			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. 		
@D	Athanasiadis, A.//Papanikolau, Y.//Rina, M.//Papadovasilaki, M.//Dauter, Z.//Petratos, K.//Bouriotis, V.//Kokkindis, M. 	Purification, crystallization and preliminary x-ray analysis of the M.BseCI DNA methyltransferase from Bacillus stearothermophilus.	Acta Crystallogr. D Biol. Crystallogr.	1997	53		477-479			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. 		
@D	Athanasiadis, A.//Vlassi, M.//Kotsifaki, D.//Tucker, P.A.//Wilson, K.S.//Kokkinidis, M. 	Crystal structure of PvuII endonuclease reveals extensive structural homologies to EcoRV.	Nat. Struct. Biol.	1994	1		469-475			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. 		
@D	Atkins, L.M.//Holder, M.E.//Ajami, N.J.//Metcalf, G.A.//Weissenberger, G.M.//Wang, M.//Vee, V.//Han, Y.//Muzny, D.M.//Gibbs, R.A.//Petrosino, J.F. 	High-Quality Draft Genome Sequence of Francisella tularensis subsp. holarctica Strain OR96-0246.	Genome Announcements	2015	3		e00898-15			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. 		
@D	Attar, N. 	SMRT-seq reveals an epigenetic switch.	Nat. Rev. Microbiol.	2016	14		546			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. 		
@D	Attie, O.//Jayaprakash, A.//Shah, H.//Paulsen, I.T.//Morino, M.//Takahashi, Y.//Narumi, I.//Sachidanandam, R.//Satoh, K.//Ito, M.//Krulwich, T.A. 	Draft Genome Sequence of Bacillus alcalophilus AV1934, a Classic Alkaliphile Isolated from Human Feces in 1934.	Genome Announcements	2014	2		e01175-14			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. 		
@D	Attwood, G.T.//Kelly, W.J.//Altermann, E.H.//Leahy, S.C. 	Analysis of the Methanobrevibacter ruminantium draft genome: understanding methanogen biology to inhibit their action in the rumen.	Aust. J. Exp. Agr.	2008	48		83-88			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. 		
@D	Atyame, C.M.//Delsuc, F.//Pasteur, N.//Weill, M.//Duron, O. 	Diversification of Wolbachia endosymbiont in the Culex pipiens mosquito.	Mol. Biol. Evol.	2011	28		2761-2772			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. 		
@D	Atyame, C.M.//Duron, O.//Tortosa, P.//Pasteur, N.//Fort, P.//Weill, M. 	Multiple Wolbachia determinants control the evolution of cytoplasmic incompatibilities in Culex pipiens mosquito populations.	Mol. Ecol.	2011	20		286-298			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. 		
@D	Auad, L.//Peril, M.A.A.//de Ruiz Holgado, A.A.P.//Raya, R.R. 	Evidence of a restriction/modification system in Lactobacillus delbrueckii subsp. lactis CNRZ 326.	Curr. Microbiol.	1998	36		271-273			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. 		
@D	Aubert, E.//Spurgeon, S.//Ray, W.//Davies, J. 	Purification and characterization of an isoschizomer of SphI from Bacillus circulans.	Nucleic Acids Res.	1990	18		6152			None 		
@D	Aubin, G.G.//Kambarev, S.//Bemer, P.//Lawson, P.A.//Corvec, S. 	Draft Genome Sequence of Highly Rifampin-Resistant Propionibacterium namnetense NTS 31307302T Isolated from a Patient with a Bone Infection.	Genome Announcements	2016	4		e00819-16			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. 		
@D	Aubin, G.G.//Kambarev, S.//Guillouzouic, A.//Khammari, A.//Dreno, B.//Corvec, S. 	Draft Genome Sequence of an Erythromycin-Resistant Propionibacterium acnes Isolate Recovered from Folliculitis of the Scalp.	Genome Announcements	2017	5		e01490-16			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). 		
@D	Aubin, G.G.//Kambarev, S.//Guillouzouic, A.//Lepelletier, D.//Bemer, P.//Corvec, S. 	Draft Genome Sequences of Four Propionibacterium acnes Strains Isolated from Implant-Related Infections.	Genome Announcements	2016	4		e01395-16			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). 		
@D	Aubol, B.E.//Reich, N.O. 	Murine DNA cytosine C5-methyltransferase: in vitro studies of de novo methylation spreading.	Biochem. Biophys. Res. Commun.	2003	310		209-214			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. 		
@D	Aubol, B.E.//Reich, N.O. 	Exploring the N-terminal function of murine methyltransferase.	ACS Abstracts	1999	217		453			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. 		
@D	Auchtung, T.A.//Holder, M.E.//Gesell, J.R.//Ajami, N.J.//Duarte, R.T.//Itoh, K.//Caspi, R.R.//Petrosino, J.F.//Horai, R.//Zarate-Blades, C.R. 	Complete Genome Sequence of Turicibacter sp. Strain H121, Isolated from the Feces of a Contaminated Germ-Free Mouse.	Genome Announcements	2016	4		e00114-16			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. 		
@D	Audic, S.//Lescot, M.//Claverie, J.M.//Cloeckaert, A.//Zygmunt, M.S. 	The genome sequence of Brucella pinnipedialis B2/94 sheds light on the evolutionary history of the genus Brucella.	BMC Evol. Biol.	2011	11		200			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. 		
@D	Audic, S.//Lescot, M.//Claverie, J.M.//Scholz, H.C. 	Brucella microti: the genome sequence of an emerging pathogen.	BMC Genomics	2009	10		352			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. 		
@D	Audisio, M.C.//Albarracin, L.//Torres, M.J.//Saavedra, L.//Hebert, E.M.//Villena, J. 	Draft Genome Sequences of Lactobacillus salivarius A3iob and Lactobacillus johnsonii CRL1647, Novel Potential Probiotic Strains for Honeybees (Apis  mellifera L.).	Microbiol. Resour. Announc.	2018	7		e00975-18			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. 		
@D	Auer, B.//Schweiger, M. 	Evidence that Escherichia coli virus T1 induces a DNA methyltransferase.	J. Virol.	1984	49		588-590			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. 		
@D	Auffret, P.//Segura, A.//Bertin, Y.//Klopp, C.//Bouchez, O.//Kerouredan, M.//Bibbal, D.//Brugere, H.//Forano, E. 	Draft Genome Sequence of Enterohemorrhagic Escherichia coli O157:H7 Strain MC2 Isolated from Cattle in France.	Genome Announcements	2017	5		e01097-17			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). 		
@D	Augelletti, F.//Tremblay, J.//Agathos, S.N.//Stenuit, B. 	Draft Whole-Genome Sequence of the Fluorene-Degrading Sphingobium sp. Strain LB126, Isolated from Polycyclic Aromatic Hydrocarbon-Contaminated Soil.	Genome Announcements	2018	6		e00249-18			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. 		
@D	Auger, S.//Galleron, N.//Segurens, B.//Dossat, C.//Bolotin, A.//Wincker, P.//Sorokin, A. 	Complete Genome Sequence of the Highly Hemolytic Strain Bacillus cereus F837/76.	J. Bacteriol.	2012	194		1630			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. 		
@D	Augustyniak, D.//Seredynski, R.//McClean, S.//Roszkowiak, J.//Roszniowski, B.//Smith, D.L.//Drulis-Kawa, Z.//Mackiewicz, P. 	Virulence factors of Moraxella catarrhalis outer membrane vesicles are major targets for cross-reactive antibodies and have adapted during evolution.	Sci. Rep.	2018	8		4955			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. 		
@D	Aung, H.L.//Tun, T.//Permina, E.//Nyunt, W.W.//Aung, S.T.//Thinn, K.K.//Crump, J.A.//Cook, G.M. 	Draft Genome Sequences of Two Drug-Resistant Mycobacterium tuberculosis Isolates  from Myanmar.	Genome Announcements	2016	4		e00850-16			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. 		
@D	Aurass, P.//Karste, S.//Trost, E.//Glaeser, S.P.//Kampfer, P.//Flieger, A. 	Genome Sequence of Paracoccus contaminans LMG 29738T, Isolated from a Water Microcosm.	Genome Announcements	2017	5		e00487-17			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. 		
@D	Avalos, M.//Boetzer, M.//Pirovano, W.//Arenas, N.E.//Douthwaite, S.//van Wezel, G.P. 	Complete Genome Sequence of Escherichia coli AS19, an Antibiotic-Sensitive Variant of E. coli Strain B REL606.	Genome Announcements	2018	6		e00385-18			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(). 		
@D	Avasthi, T.S.//Devi, S.H.//Taylor, T.D.//Kumar, N.//Baddam, R.//Kondo, S.//Suzuki, Y.//Lamouliatte, H.//Megraud, F.//Ahmed, N. 	Genomes of the two chronological isolates (Helicobacter pylori 2017 and 2018) of the West African Helicobacter pylori strain 908, obtained from a  single patient.	J. Bacteriol.	2011	193		3385-3386			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. 		
@D	Avasthi, T.S.//Kumar, N.//Baddam, R.//Hussain, A.//Nandanwar, N.//Jadhav, S.//Ahmed, N. 	Genome of Multidrug-Resistant Uropathogenic Escherichia coli Strain NA114 from India.	J. Bacteriol.	2011	193		4272-4273			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. 		
@D	Avci, B.//Hahnke, R.L.//Chafee, M.//Fischer, T.//Gruber-Vodicka, H.//Tegetmeyer, H.E.//Harder, J.//Fuchs, B.M.//Amann, R.I.//Teeling, H. 	Genomic and physiological analyses of 'Reinekea forsetii' reveal a versatile opportunistic lifestyle during spring algae blooms.	Environ. Microbiol.	2017	19		1209-1221			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. 		
@D	Avendano-Herrera, R.//Poblete-Morales, M. 	Genome Sequence of Streptococcus phocae subsp. phocae Strain ATCC 51973T Isolated from a Harbor Seal (Phoca vitulina).	Genome Announcements	2015	3		e01307-15			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. 		
@D	Avendano-Herrera, R.//Suarez, R.//Lazo, E.//Bravo, D.//Llegues, K.O.//Romalde, J.L.//Godoy, M.G. 	Genome Sequence of Streptococcus phocae subsp. salmonis Strain C-4T, Isolated from Atlantic Salmon (Salmo salar).	Genome Announcements	2014	2		e01269-14			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. 		
@D	Aw, Y.K.//Ong, K.S.//Yule, C.M.//Gan, H.M.//Lee, S.M. 	Draft Genome Sequence of Paenibacillus sp. Strain MSt1 with Broad Antimicrobial Activity, Isolated from Malaysian Tropical Peat Swamp Soil.	Genome Announcements	2014	2		e01024-14			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. 		
@D	Axelsson, L.//Rud, I.//Naterstad, K.//Blom, H.//Renckens, B.//Boekhorst, J.//Kleerebezem, M.//van Hijum, S.//Siezen, R.J. 	Genome Sequence of the Naturally Plasmid-Free Lactobacillus plantarum Strain NC8  (CCUG 61730).	J. Bacteriol.	2012	194		2391-2392			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. 		
@D	Axenov-Gribanov, D.V.//Tokovenko, B.T.//Rebets, Y.V.//Voytsekhovskaya, I.V.//Shatilina, Z.M.//Protasov, E.S.//Luzhetskyy, A.N.//Timofeyev, M.A. 	Draft Genome Sequence of Streptomyces sp. Strain IB2014011-1, Isolated from Trichoptera sp. Larvae of Lake Baikal.	Genome Announcements	2017	5		e00062-17			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. 		
@D	Aya-Castaneda, M.R.//Sarnacki, S.H.//Noto-Llana, M.//Lopez-Guerra, A.G.//Giacomodonato, M.N.//Cerquetti, M.C. 	Dam methylation is required for efficient biofilm production in Salmonella enterica serovar Enteritidis.	Int. J. Food Microbiol.	2015	193		15-22			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. 		
@D	Ayala, D.I.//Cook, P.W.//Campos, D.L.//Brashears, M.M.//den Bakker, H.//Nightingale, K.K. 	Draft Genome Sequence of Lactobacillus salivarius L28 Isolated from Ground Beef.	Genome Announcements	2017	5		e00955-17			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. 		
@D	Ayala, D.I.//Cook, P.W.//Campos, D.L.//Franco, J.G.//Brashears, M.M.//den Bakker, H.//Nightingale, K.K. 	Draft Genome Sequence of Enterococcus faecium Strain J19, Isolated from Cabbage.	Genome Announcements	2018	6		e00213-18			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. 		
@D	Ayala, M.//Segovia, C.//Rojas, R.//Miranda, C.//Santander, J. 	Draft Genome Sequence of Epilithonimonas sp. FP211-J200, Isolated from an Outbreak Episode on a Rainbow Trout (Oncorhynchus mykiss) Farm.	Genome Announcements	2017	5		e00819-17			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. 		
@D	Ayalew, S.//Confer, A.W.//Hansen, R.D.//Couger, M.B. 	Genome Sequence of Mannheimia haemolytica Serotype 1 Strain 16041065 BH.	Genome Announcements	2017	5		e01721-16			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. 		
@D	Ayalew, S.//Confer, A.W.//Hansen, R.D.//Couger, M.B. 	Genome Sequence of a Spontaneous Nonhemolytic Mutant of Mannheimia haemolytica 16041065 GH.	Genome Announcements	2017	5		e01720-16			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. 		
@D	Ayano, H.//Kuroda, M.//Soda, S.//Ike, M. 	Draft Genome Sequence of Pseudomonas aeruginosa Strain RB, a Bacterium Capable of Synthesizing Cadmium Selenide Nanoparticles.	Genome Announcements	2014	2		e00368-14			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. 		
@D	Ayarza, J.M.//Figuerola, E.L.//Erijman, L. 	Draft Genome Sequences of Type Strain Sediminibacterium salmoneum NJ-44 and Sediminibacterium sp. Strain C3, a Novel Strain Isolated from Activated Sludge.	Genome Announcements	2014	2		e01073-13			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. 		
@D	Aylward, F.O. et al. 	Complete Genome of Serratia sp. Strain FGI 94, a Strain Associated with Leaf-Cutter Ant Fungus Gardens.	Genome Announcements	2013	1		e0023912			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. 		
@D	Aylward, F.O. et al. 	Complete Genome of Enterobacteriaceae Bacterium Strain FGI 57, a Strain Associated with Leaf-Cutter Ant Fungus Gardens.	Genome Announcements	2013	1		e00238-12			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. 		
@D	Azarinskas, A.//Maneliene, Z.//Jakubauskas, A. 	Hin4II, a new prototype restriction endonuclease from Haemophilus influenzae RFL4: Discovery, cloning and expression in Escherichia coli.	J. Biotechnol.	2006	123		288-296			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. 		
@D	Azarov, D.//Goncharov, A.//Karaseva, A.//Brodina, T.//Lebedeva, E.//Taranenko, I.//Feting, A.//Bakaev, M.//Brusina, E.//Zueva, L. 	Draft Genome Sequence of a Multidrug-Resistant Nosocomial Serratia marcescens Strain That Persisted in a Hospital in Kemerovo, Russian Federation.	Genome Announcements	2017	5		e01764-16			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. 		
@D	Azcarate-Peril, M.A.//Altermann, E.//Goh, Y.J.//Tallon, R.//Sanozky-Dawes, R.B.//Pfeiler, E.A.//O'Flaherty, S.//Buck, B.L.//Dobson, A.//Duong, T.//Miller, M.J.//Barrangou, R.//Klaenhammer, T.R. 	Analysis of the genome sequence of Lactobacillus gasseri ATCC 33323 reveals the molecular basis of an autochthonous intestinal organism.	Appl. Environ. Microbiol.	2008	74		4610-4625			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. 		
@D	Azeddoug, H.//Hubert, J.//Reysset, G. 	Characterization of a methyl-specific restriction system in Clostridium acetobutylicum strain N1-4081.	FEMS Microbiol. Lett.	1989	65		323-326			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. 		
@A	Azeddoug, H.//Hubert, J.//Reysset, G. 		Restriction endonuclease in Clostridium acetobutylicum strain NI-4081.			Borriello, S.P. 		Clinical and Molecular Aspects of Anaerobes				Petersfield	Wrightson Biomedical Publishing Ltd.	1990		0		249-250									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. 		
@D	Azeddoug, H.//Reysset, G. 	Recognition sequence of a new methyl-specific restriction system from Clostridium acetobutylicum strain ABKn8.	FEMS Microbiol. Lett.	1991	78		153-156			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. 		
@D	Azeddoug, H.//Reysset, G.//Sebald, M. 	Characterization of restriction endonuclease BfrBI from Bacteroides fragilis strains BE3 and AIP 10006.	FEMS Microbiol. Lett.	1992	95		133-136			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. 		
@D	Azevedo, A.C.//Bento, C.B.//Ruiz, J.C.//Queiroz, M.V.//Mantovani, H.C. 	Draft Genome Sequence of Streptococcus equinus (Streptococcus bovis) HC5, a Lantibiotic Producer from the Bovine Rumen.	Genome Announcements	2015	3		e00085-15			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. 		
@D	Azevedo-Antunes, C.//Richardson, E.J.//Quick, J.//Fuentes-Utrilla, P.//Isom, G.L.//Goodall, E.C.//Moller, J.//Hoskisson, P.A.//Mattos-Guaraldi, A.L.//Cunningham, A.F.//Loman, N.J.//Sangal, V.//Burkovski, A.//Henderson, I.R. 	Complete Closed Genome Sequence of Nontoxigenic Invasive Corynebacterium diphtheriae bv. mitis Strain ISS 3319.	Genome Announcements	2018	6		e01566-17			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. 		
@D	Aziz, S.//Mast, Y.//Wohlleben, W.//Gross, H. 	Draft Genome Sequence of the Pristinamycin-Producing Strain Streptomyces sp. SW4, Isolated from Soil in Nusa Kambangan, Indonesia.	Microbiol. Resour. Announc.	2018	7		e00912-18			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. 		
@D	Azizbekyan, R.R.//Rebentish, B.A.//Netyksa, E.M. 	Bacillus thuringiensis restrictase sensitive to dam-methylation.	Biotekhnologiya	1988	4		197-198			A new restriction enzyme from Bacillus thuringiensis is described. It is an isoschizomer of ClaI and is sensitive to dam methylation. 		
@D	Azizbekyan, R.R.//Rebentish, B.A.//Netyksa, E.M.//Bychkova, M.A.//Bolotin, A.P. 	Site-specific restriction endonuclease from Bacillus thuringiensis var. Kumantoenis.	Mol. Gen. Mikrobiol. Virusol.	1992	1-2		13-15			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. 		
@D	Azizbekyan, R.R.//Rebentish, B.A.//Stepanova, T.V.//Netyksa, E.M.//Bychkova, M.A. 	Site specific restriction endonuclease from a Bacillus thuringiensis strain.	Dokl. Akad. Nauk.	1984	274		742-744			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. 		
@D	Azorin, F.//Hahn, R.//Rich, A. 	Restriction endonucleases can be used to study B-Z junctions in supercoiled DNA.	Proc. Natl. Acad. Sci. U. S. A.	1984	81		5714-5718			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. 		
@D	Azuma, Y.//Hosoyama, A.//Matsutani, M.//Furuya, N.//Horikawa, H.//Harada, T.//Hirakawa, H.//Kuhara, S.//Matsushita, K.//Fujita, N.//Shirai, M. 	Whole-genome analyses reveal genetic instability of Acetobacter pasteurianus.	Nucleic Acids Res.	2009	37		5768-5783			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. 		
@D	Azwani, F.//Suzuki, K.//Honjyo, M.//Tashiro, Y.//Futamata, H. 	Draft Genome Sequence of Comamonas testosteroni R2, Consisting of Aromatic Compound Degradation Genes for Phenol Hydroxylase.	Genome Announcements	2017	5		e00875-17			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. 		
@D	Baar, C.//Eppinger, M.//Raddatz, G.//Simon, J.//Lanz, C.//Klimmek, O.//Nandakumar, R.//Gross, R.//Rosinus, A.//Keller, H.//Jagtap, P.//Linke, B.//Meyer, F.//Lederer, H.//Schuster, S.C. 	Complete genome sequence and analysis of Wolinella succinogenes.	Proc. Natl. Acad. Sci. U. S. A.	2003	100		11690-11695			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. 		
@D	Baaziz, H.//Lemaire, O.N.//Jourlin-Castelli, C.//Iobbi-Nivol, C.//Mejean, V.//Alatou, R.//Fons, M. 	Draft Genome Sequence of Shewanella algidipiscicola H1, a Highly Chromate-Resistant Strain Isolated from Mediterranean Marine Sediments.	Microbiol. Resour. Announc.	2018	7		e00905-18			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. 		
@D	Baba, T.//Bae, T.//Schneewind, O.//Takeuchi, F.//Hiramatsu, K. 	Genome sequence of Staphylococcus aureus strain Newman and comparative analysis of staphylococcal genomes: polymorphism and evolution of two major pathogenicity    islands.	J. Bacteriol.	2008	190		300-310			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. 		
@D	Baba, T.//Kuwahara-Arai, K.//Uchiyama, I.//Takeuchi, F.//Ito, T.//Hiramatsu, K. 	Complete genome sequence of Macrococcus caseolyticus strain JSCS5402, reflecting the ancestral genome of the human-pathogenic staphylococci.	J. Bacteriol.	2009	191		1180-1190			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. 		
@D	Baba, T.//Takeuchi, F.//Kuroda, M.//Yuzawa, H.//Aoki, K.//Oguchi, A.//Nagai, Y.//Iwama, N.//Asano, K.//Naimi, T.//Kuroda, H.//Cui, L.//Yamamoto, K.//Hiramatsu, K. 	Genome and virulence determinants of high virulence community-acquired MRSA.	Lancet	2002	359		1819-1827			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. 		
@D	Babbar, A.//Nitsche-Schmitz, D.P.//Pieper, D.H.//Barrantes, I. 	Draft Genome Sequence of Streptococcus dysgalactiae subsp. equisimilis Strain C161L1 Isolated in Vellore, India.	Genome Announcements	2017	5		e00336-17			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. 		
@D	Babcock, M.J.//Schottel, J.L. 	SsbI, an isoschizomer of HindIII isolated from Streptomyces scabies.	Nucleic Acids Res.	1991	19		3457			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. 		
@D	Babic, A.C.//Little, E.J.//Manohar, V.M.//Bitinaite, J.//Horton, N.C. 	DNA Distortion and Specificity in a Sequence-Specific Endonuclease.	J. Mol. Biol.	2008	383		186-204			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. 		
@D	Babinger, P.//Volkl, R.//Cakstina, I.//Maftei, A.//Schmitt, R. 	Maintenance DNA methyltransferase (Met1) and silencing of CpG-methylated foreign DNA in Volvox carteri.	Plant Mol. Biol.	2007	63		325-336			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. 		
@D	Babkina, O.V.//Chutko, C.A.//Shashkov, A.A.//Dzhidzhoev, M.S.//Eritja, R.//Gromova, E.S. 	Iodouracil-mediated photocrosslinking of DNA to EcoRII restriction endonuclease in catalytic conditions.	Photochem. Photobiolog.	2002	1		636-640			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. 		
@D	Babkina, O.V.//Evstafieva, A.G.//Chichkova, N.V.//Vartapetian, A.B.//Muller, S.//Baskunov, V.B.//Petrauskene, O.V.//Kochetkov, S.N.//Gromova, E.S. 	Recombinant components of the EcoRII restriction-modification system: Restriction endonuclease can interact with DNA-RNA duplexes.	Mol. Biol. (Mosk)	2000	34		1065-1073			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. 		
@D	Babkina, O.V.//Petrauskene, O.V.//Gromova, E.S. 	Restriction endonuclease EcoRII hydrolyzes one of the two DNA restriction sites forming the catalytic complex.	Mol. Biol. (Mosk)	1998	32		793-796			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. 		
@D	Baby, V.//Matteau, D.//Knight, T.F.//Rodrigue, S. 	Complete Genome Sequence of the Mesoplasma florum W37 Strain.	Genome Announcements	2013	1		e00879-13			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. 		
@D	Bachi, B.//Reiser, J.//Pirrotta, V. 	Methylation and cleavage sequences of the EcoP1 restriction-modification enzyme.	J. Mol. Biol.	1979	128		143-163			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. 		
@D	Bachman, K.E.//Rountree, M.R.//Baylin, S.B. 	Dnmt3a and Dnmt3b are transcriptional repressors that exhibit unique localization properties to heterochromatin.	J. Biol. Chem.	2001	276		32282-32287			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. 		
@D	Backman, K. 	A cautionary note on the use of certain restriction endonucleases with methylated substrates.	Gene	1980	11		169-171			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. 		
@D	Backus, L.//Wels, M.//Boekhorst, J.//Dijkstra, A.R.//Beerthuyzen, M.//Kelly, W.J.//Siezen, R.J.//van Hijum, S.A.//Bachmann, H. 	Draft Genome Sequences of 24 Lactococcus lactis Strains.	Genome Announcements	2017	5		e01737-16			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. 		
@D	Bacolla, A.//Pradhan, S.//Larson, J.E.//Roberts, R.J.//Wells, R.D. 	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.	J. Biol. Chem.	2001	276		18605-18613			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. 		
@D	Bacolla, A.//Pradhan, S.//Roberts, R.J.//Wells, R.D. 	Recombinant human DNA (cytosine-5) methyltransferase. II. Steady-state kinetics reveal allosteric activation by methylated DNA.	J. Biol. Chem.	1999	274		33011-33019			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. 		
@D	Badalamenti, J.P.//Bond, D.R. 	Complete Genome of Geobacter pickeringii G13T, a Metal-Reducing Isolate from Sedimentary Kaolin Deposits.	Genome Announcements	2015	3		e00038-15			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. 		
@D	Badalamenti, J.P.//Erickson, J.D.//Salomon, C.E. 	Complete Genome Sequence of Streptomyces albus SM254, a Potent Antagonist of Bat  White-Nose Syndrome Pathogen Pseudogymnoascus destructans.	Genome Announcements	2016	4		e00290-16			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). 		
@D	Badalamenti, J.P.//Hunter, R.C. 	Complete Genome Sequence of Achromobacter xylosoxidans MN001, a Cystic Fibrosis Airway Isolate.	Genome Announcements	2015	3		e00947-15			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. 		
@D	Badalamenti, J.P.//Krajmalnik-Brown, R.//Torres, C.I.//Bond, D.R. 	Genomes of Geoalkalibacter ferrihydriticus Z-0531T and Geoalkalibacter subterraneus Red1T, Two Haloalkaliphilic Metal-Reducing Deltaproteobacteria.	Genome Announcements	2015	3		e00039-15			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. 		
@D	Baddam, R.//Kumar, N.//Thong, K.L.//Ngoi, S.T.//Teh, C.S.//Yap, K.P.//Chai, L.C.//Avasthi, T.S.//Ahmed, N. 	Genetic Fine Structure of a Salmonella enterica Serovar Typhi Strain Associated with the 2005 Outbreak of Typhoid Fever in Kelantan, Malaysia.	J. Bacteriol.	2012	194		3565-3566			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. 		
@D	Baddam, R.//Thong, K.L.//Avasthi, T.S.//Shaik, S.//Yap, K.P.//Teh, C.S.//Chai, L.C.//Kumar, N.//Ahmed, N. 	Whole-Genome Sequences and Comparative Genomics of Salmonella enterica Serovar Typhi Isolates from Patients with Fatal and Nonfatal Typhoid Fever in Papua New  Guinea.	J. Bacteriol.	2012	194		5122-5123			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. 		
@D	Badger, J.H. et al. 	Comparative genomic evidence for a close relationship between the dimorphic prosthecate bacteria Hyphomonas neptunium and Caulobacter  crescentus.	J. Bacteriol.	2006	188		6841-6850			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. 		
@D	Badhai, J.//Narayan, K.D.//Whitman, W.B.//Das, S.K. 	Draft Genome Sequence of Gulbenkiania indica Strain HT27T (DSM 17901T) Isolated from a Sulfur Spring in India.	Genome Announcements	2016	4		e00830-16			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. 		
@D	Badhai, J.//Whitman, W.B.//Das, S.K. 	Draft Genome Sequence of Chelatococcus sambhunathii Strain HT4T (DSM 18167T) Isolated from a Hot Spring in India.	Genome Announcements	2016	4		e00825-16			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. 		
@D	Badhai, J.//Whitman, W.B.//Das, S.K. 	Draft Genome Sequence of Rhizobiumpusense Strain NRCPB10T (LMG 25623T) Isolated from Rhizosphere Soil of Chickpeas (Cicer arietinum L.) Grown in India.	Genome Announcements	2017	5		e00282-17			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. 		
@D	Badie, G. 	Role of DNA adenine methylase in regulation of bacterial gene expression, virulence, and the elicitation of immune responses.	Ph.D. Thesis, Univ. of California, Santa Barbara	2005			1-149			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. 		
@D	Badie, G.//Heithoff, D.M.//Mahan, M.J. 	LcrV synthesis is altered by DNA adenine methylase overproduction in Yersinia pseudotuberculosis and is required to confer immunity in  vaccinated hosts.	Infect. Immun.	2004	72		6707-6710			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. 		
@D	Badie, G.//Heithoff, D.M.//Sinsheimer, R.L.//Mahan, M.J. 	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.	J. Bacteriol.	2007	189		1556-1564			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. 		
@D	Badran, S.//Morales, N.//Schick, P.//Jacoby, B.//Villella, W.//Lorenz, T. 	Complete Genome Sequence of the Bacillus pumilus Phage Leo2.	Genome Announcements	2018	6		e00066-18			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. 		
@D	Badrun, R.//Abu, B.N.//Laboh, R.//Redzuan, R.//Bala, J.I. 	Draft Genome Sequence of Blood Disease Bacterium A2 HR-MARDI, a Pathogen Causing  Banana Bacterial Wilt.	Genome Announcements	2017	5		e00408-17			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. 		
@D	Bae, H.//Kim, K.P.//Lee, J.I.//Song, J.G.//Kil, E.J.//Kim, J.S.//Kwon, S.T. 	Characterization of DNA polymerase from the hyperthermophilic archaeon Thermococcus marinus and its application to PCR.	Extremophiles	2009	13		657-667			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). 		
@D	Bae, H.//Kim, K.P.//Song, J.M.//Kim, J.H.//Yang, J.S.//Kwon, S.T. 	Characterization of intein homing endonuclease encoded in the DNA polymerase gene of Thermococcus marinus.	FEMS Microbiol. Lett.	2009	297		180-188			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. 		
@D	Bae, M.//Par, J.-O.//Hwang, H.-Y.//Yim, J. 	Purification and characterization of a restriction endonuclease from Streptomyces exfoliatus.	Korean J. Microbiol.	1993	31		544-549			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. 		
@D	Bae, M.//Song, E.-S. 	Purification of restriction endonuclease, SdiI, from Steptomyces diastatochromogenes.	Korean J. Microbiol.	1994	32		297-300			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. 		
@D	Bae, M.//Song, E.-S.//Hwang, H.-Y.//Yim, J. 	Characterization of the restriction endonuclease, SdiI, from Streptomyces diastatochromogenes.	Korean J. Microbiol.	1994	32		301-305			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'. 		
@D	Bae, M.//Suh, W.-N.//Park, J.-O.//Kim, H.T.//Lee, K.-J. 	Numerical identification of Streptomyces sp. 58 producing restriction endonuclease SexIII, a novel isoschizomer of SacII.	Korean J. Microbiol.	1993	31		465-470			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. 		
@D	Bae, M.//Suh, W.-N.//Song, E.-S.//Lee, K.-J. 	Numerical identification of a Streptomyces strain producing restriction endonuclease SdiI.	Korean J. Appl. Microbiol. Biotechnol.	1994	22		126-133			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. 		
@D	Bae, M.//Yun, M.-S.//Kim, H.-T.//Lee, K.-J. 	Numerical identification of a Streptomyces strain producing a thermotolerable restriction endonuclease SviI.	Korean J. Appl. Microbiol. Biotechnol.	1993	21		299-305			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. 		
@D	Baek, K.//Chung, E.J.//Choi, G.G.//Nam, Y.H.//Choi, A. 	Draft Genome Sequence of Deinococcus koreensis SJW1-2(T), a Gamma Radiation-Resistant Bacterium Isolated from River Water.	Microbiol. Resour. Announc.	2018	7		e00894-18			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. 		
@D	Bag, S.//Ghosh, T.S.//Das, B. 	Draft Genome Sequence of Prevotella copri Isolated from the Gut of a Healthy Indian Adult.	Genome Announcements	2017	5		e00834-17			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. 		
@D	Bag, S.//Ghosh, T.S.//Das, B. 	Whole-Genome Sequence of Bifidobacterium longum Strain Indica, Isolated from the  Gut of a Healthy Indian Adult.	Genome Announcements	2017	5		e01017-17			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. 		
@D	Bag, S.//Ghosh, T.S.//Das, B. 	Whole-Genome Sequence of a Megasphaera elsdenii Strain Isolated from the Gut of a Healthy Indian Adult Subject.	Genome Announcements	2017	5		e01033-17			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. 		
@D	Bag, S.//Ghosh, T.S.//Das, B. 	Complete Genome Sequence of Faecalibacterium prausnitzii Isolated from the Gut of a Healthy Indian Adult.	Genome Announcements	2017	5		e01286-17			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. 		
@D	Bag, S.//Ghosh, T.S.//Das, B. 	Complete Genome Sequence of Collinsella aerofaciens Isolated from the Gut of a Healthy Indian Subject.	Genome Announcements	2017	5		e01361-17			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. 		
@D	Bahari, Z.M.//Ibrahim, Z.//Jaafar, J.//Shahir, S. 	Draft Genome Sequence of Arsenic-Resistant Microbacterium sp. Strain SZ1 Isolated from Arsenic-Bearing Gold Ores.	Genome Announcements	2017	5		e01183-17			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. 		
@D	Bahr, M. 	Biophysical characterization and biochemical direction of methyltransferase-DNA-interactions.	Ph.D. Thesis, Germany	2009			1-192					
@D	Bahrami, T.//Zarvandi, S.//De Mot, R.//Gross, H.//Changi-Ashtiani, M.//Shahani, T.//Rokni-Zadeh, H. 	Draft Genome Sequence of Pseudomonas gingeri Strain LMG 5327, the Causative Agent of Ginger Blotch in Agaricus bisporus.	Genome Announcements	2018	6		e00196-18			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. 		
@D	Bai, J.//He, Z. 	Mammalian DNA methylase.	Shengli Kexue Jinzhan	1997	28		67-69					
@D	Bai, Y.//Muller, D.B.//Srinivas, G.//Garrido-Oter, R.//Potthoff, E.//Rott, M.//Dombrowski, N.//Munch, P.C.//Spaepen, S.//Remus-Emsermann, M.//Huttel, B.//McHardy, A.C.//Vorholt, J.A.//Schulze-Lefert, P. 	Functional overlap of the Arabidopsis leaf and root microbiota.	Nature	2015	528		364-369			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. 		
@D	Baik, S.C.//Lee, W.K.//Song, J.Y.//Choi, Y.J.//Rye, B.D.//Choi, S.H.//Cho, M.J.//Rhee, K.H. 	Purification and characterization of type II restriction endonuclease (HpyI) of Helicobacter pylori.	Abstr. Gen. Meet. Am. Soc. Microbiol.	1998	0		120			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. 		
@D	Bailey, A.C.//Kellom, M.//Poret-Peterson, A.T.//Noonan, K.//Hartnett, H.E.//Raymond, J. 	Draft Genome Sequence of Massilia sp. Strain BSC265, Isolated from Biological Soil Crust of Moab, Utah.	Genome Announcements	2014	2		e01199-14			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. 		
@D	Bailey, A.C.//Kellom, M.//Poret-Peterson, A.T.//Noonan, K.//Hartnett, H.E.//Raymond, J. 	Draft Genome Sequence of Bacillus sp. Strain BSC154, Isolated from Biological Soil Crust of Moab, Utah.	Genome Announcements	2014	2		e01198-14			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. 		
@D	Bailey, A.C.//Kellom, M.//Poret-Peterson, A.T.//Noonan, K.//Hartnett, H.E.//Raymond, J. 	Draft Genome Sequence of Microvirga sp. Strain BSC39, Isolated from Biological Soil Crust of Moab, Utah.	Genome Announcements	2014	2		e01197-14			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. 		
@D	Bailey, C.R.//Winstanley, D.J. 	Inhibition of restriction in Streptomyces clavuligerus by heat treatment.	J. Gen. Microbiol.	1986	132		2945-2947			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. 		
@D	Bailey, T.W.//do Nascimento, N.C.//Bhunia, A.K. 	Genome Sequence of Listeria monocytogenes Strain F4244, a 4b Serotype.	Genome Announcements	2017	5		e01324-17			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. 		
@D	Bair, C.L.//Black, L.W. 	A Type IV Modification Dependent Restriction Nuclease that Targets Glucosylated Hydroxymethyl Cytosine Modified DNAs.	J. Mol. Biol.	2007	366		768-778			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. 		
@D	Bair, C.L.//Black, L.W. 	Setting the phage for evolution: The mechanism of host exclusion of bacteriophage T4 IPI.	Abstr. Gen. Meet. Am. Soc. Microbiol.	2004	104		392			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. 		
@D	Bair, C.L.//Rifat, D.//Black, L.W. 	Exclusion of Glucosyl-Hydroxymethylcytosine DNA Containing Bacteriophages Is Overcome by the Injected Protein Inhibitor IPI*.	J. Mol. Biol.	2007	366		779-789			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. 		
@D	Bajpai, A.//Shende, K.K.//Meena, N.//Suravajhala, P.//Medicherla, K.M.//Johri, B.N. 	Draft Genome Sequence of the Plant Growth-Promoting Rhizobacterium Pseudomonas protegens Strain BNJ-SS-45, Isolated from Rhizosphere Soil of Wheat (Triticum  aestivum).	Microbiol. Resour. Announc.	2018	7		e00926-18			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. 		
@D	Bakenhus, I.//Voget, S.//Poehlein, A.//Brinkhoff, T.//Daniel, R.//Simon, M. 	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.	Standards in Genomic Sciences	2018	13		7			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. 		
@D	Baker, B.J.//Comolli, L.R.//Dick, G.J.//Hauser, L.J.//Hyatt, D.//Dill, B.D.//Land, M.L.//Verberkmoes, N.C.//Hettich, R.L.//Banfield, J.F. 	Enigmatic, ultrasmall, uncultivated Archaea.	Proc. Natl. Acad. Sci. U. S. A.	2010	107		8806-8811			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. 		
@D	Baker, D. 	Proteins by design.	The Scientist	2006	20		26-32			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. 		
@D	Baker, D.J.//Hardy, T.A.//Smith, S.S. 	The influence of the dT.dG mispair on the activity of the human DNA (cytosine-5) methyltransferase.	Biochem. Biophys. Res. Commun.	1987	146		596-602			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. 		
@D	Baker, D.J.//Kan, J.L.C.//Smith, S.S. 	Recognition of structural perturbations in DNA by human DNA(cytosine-5)methyltransferase.	Gene	1988	74		207-210			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). 		
@D	Baker, D.J.//Laayoun, A.//Smith, S.S. 	Transition state analogs as affinity labels for human DNA methyltransferases.	Biochem. Biophys. Res. Commun.	1993	196		864-871			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. 		
@D	Baker, K.S.//Parkhill, J.//Thomson, N.R. 	Draft Genome Sequence of 24570, the Type Strain of Shigella flexneri.	Genome Announcements	2015	3		e00393-15			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. 		
@D	Bakh, N.L.//Semina, I.E. 	Obtaining the preparations of immobilized restrictases SalI and PvuII.	Zh. Mikrobiol. Epidemiol. Immunobiol.	1985	2		32-34			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. 		
@D	Bakh, N.L.//Tsvetkova, N.V.//Semina, I.E.//Tarasov, A.P.//Mileikovskaya, M.M.//Gruber, I.M.//Polyachenko, V.M.//Romanenko, E.E. 	Isolation and Purification of Restriction Endonuclease PmiI from Pseudomonas Mirabilis 1667.	Antibiot. Med. Biotekhnol.	1985	30		342-344			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. 		
@D	Bakhrat, A.//Baranes, K.//Krichevsky, O.//Rom, I.//Schlenstedt, G.//Pietrokovski, S.//Raveh, D. 	Nuclear import of Ho endonuclease utilizes two nuclear localization signals and four importins of the ribosomal import system.	J. Biol. Chem.	2006	281		12218-12226			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. 		
@D	Bakhrat, A.//Jurica, M.S.//Stoddard, B.L.//Raveh, D. 	Homology modeling and mutational analysis of Ho endonuclease of yeast.	Genetics	2004	166		721-728			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. 		
@D	Baksi, K.//Rogerson, D.L.//Rushizky, G.W. 	Rapid, single-step purification of restriction endonucleases on Cibacron blue F3GA-agarose.	Biochemistry	1978	17		4136-4139			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. 		
@D	Baksi, K.//Rushizky, G.W. 	Rapid purification of restriction endonucleases on Cibacron Blue F3GA.	Fed. Proc.	1978	37		1414			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. 		
@D	Baksi, K.//Rushizky, G.W. 	Purification of the restriction endonuclease PalI.	Anal. Biochem.	1979	99		207-212			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. 		
@D	Bakthavatchalam, Y.D.//Veeraraghavan, B.//Peter, J.V.//Rajinikanth, J.//Inbanathan, F.Y.//Devanga, R.N.K.//Rajamani, S.S.K. 	Novel Observations in 11 Heteroresistant Vancomycin-Intermediate Methicillin-Resistant Staphylococcus aureus Strains from South India.	Genome Announcements	2016	4		e01425-16			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. 		
@D	Bala, M.//Kumar, S.//Raghava, G.P.//Mayilraj, S. 	Draft Genome Sequence of Rhodococcus ruber Strain BKS 20-38.	Genome Announcements	2013	1		e0013913			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. 		
@D	Bala, M.//Kumar, S.//Raghava, G.P.//Mayilraj, S. 	Draft Genome Sequence of Rhodococcus qingshengii Strain BKS 20-40.	Genome Announcements	2013	1		e0012813			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. 		
@D	Balabanov, V.P.//Kotova, V.Y.//Kholodii, G.Y.//Mindlin, S.Z.//Zavilgelsky, G.B. 	A novel gene, ardD, determines antirestriction activity of the non-conjugative transposon Tn5053 and is located antisense within the tniA gene.	FEMS Microbiol. Lett.	2012	337		55-60			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. 		
@D	Balabanov, V.P.//Pustovoit, K.S.//Zavilgelsky, G.B. 	Comparative analysis of antirestriction activity of the ArdA and ArdB proteins encoded by genes of the R64 transmissible plasmid (IncI1).	Mol. Biol. (Mosk)	2012	46		269-275			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. 		
@D	Balachandran, M.//Riley, M.C.//Bemis, D.A.//Kania, S.A. 	Complete Genome Sequence of Staphylococcus aureus Strain Wood 46.	Genome Announcements	2017	5		e00087-17			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. 		
@D	Balado, M.//Lemos, M.L.//Osorio, C.R. 	Integrating conjugative elements of the SXT/R391 family from fish-isolated Vibrios encode restriction-modification systems that confer resistance to bacteriophages.	FEMS Microbiol. Ecol.	2013	83		457-467			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. 		
@D	Balaji, V.//Rajenderan, S.//Anandan, S.//Biswas, I. 	Genome Sequences of Two Multidrug-Resistant Acinetobacter baumannii Clinical Strains Isolated from Southern India.	Genome Announcements	2015	3		e01010-15			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. 		
@D	Balakhonov, S.V.//Mironova, L.V.//Basov, E.A.//Gladkikh, A.S.//Afanasev, M.V.//Ganin, V.S.//Urbanovich, L.Y.//Sidorova, E.A. 	Whole-Genome Sequencing of a Vibrio cholerae El Tor Strain Isolated in the Imported Cholera Focus in Siberia.	Genome Announcements	2015	3		e01550-14			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. 		
@D	Balakrishna, P.A.//Jaya, K.A.//Thulasi, K.//Reghunathan, D.//Prasannakumar, M.//Kumarapillai, H. 	Draft Genome Sequence of Bacillus aryabhattai Strain PHB10, a Poly(3-Hydroxybutyrate)-Accumulating Bacterium Isolated from Domestic Sewerage.	Genome Announcements	2017	5		e01072-17			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. 		
@D	Balcarova, A.//Mrazek, J.//Kleinwachter, W.//Brabec, V. 	Cleavage by restriction enzymes of DNA modified with the antitumour drug cis-diamminedichloroplatinum (II).	Gen. Physiol. Biophys.	1992	11		579-588			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. 		
@D	Baldauf, F.//Kiss, A. 	Expression of cloned gene for methyltransferase from Bacillus subtilis bacteriophage SPbetaB.	Mol. Gen. Mikrobiol. Virusol.	1985	2		26-28			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. 		
@D	Baldwin, D.N.//Shepherd, B.//Kraemer, P.//Hall, M.K.//Sycuro, L.K.//Pinto-Santini, D.M.//Salama, N.R. 	Identification of Helicobacter pylori genes that contribute to stomach colonization.	Infect. Immun.	2007	75		1005-1016			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. 		
@A	Baldwin, G.S.//Gormley, N.A.//Halford, S.E. 		Manganese(II) as a probe for the mechanism and specificity of restriction endonucleases.			Sigel, A. & Sigel//H. 		Metal Ions in Biological Systems, Vol. 37: Manganese and its role in Biological Processes.				New York	Marcel Dekker	2000		37		345-364									A review of the role of metal ions in DNA cleavage by restriction enzymes and the experimental possibilities offered by substituting manganese for magnesium. 		
@D	Baldwin, G.S.//Halford, S.E. 	Rapid reaction kinetics on the EcoRV restriction endonuclease.	Biochem. Soc. Trans.	1994	22		300S			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. 		
@D	Baldwin, G.S.//Kelly, S.M.//Price, N.C.//Wilson, G.W.//Connolly, B.A.//Artymiuk, P.J.//Hornby, D.P. 	Ligand-induced conformational states of the cytosine-specific DNA methyltransferase M.HgaI-2.	J. Mol. Biol.	1994	235		545-553			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. 		
@D	Baldwin, G.S.//Sessions, R.B.//Erskine, S.G.//Halford, S.E. 	DNA cleavage by the EcoRV restriction endonuclease: Roles in divalent metal ions in specificity and catalysis.	J. Mol. Biol.	1999	288		87-103			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. 		
@D	Baldwin, G.S.//Vipond, I.B.//Halford, S.E. 	Rapid reaction analysis of the catalytic cycle of the EcoRV restriction endonuclease.	Biochemistry	1995	34		705-714			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. 		
@D	Bale, A.//d'Alarcao, M.//Marinus, M.G. 	Characterization of DNA adenine methylation mutants of Escherichia coli K12.	Mutat. Res.	1979	59		157-165			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. 		
@D	Balendiran, K.//Bonventre, J.//Knott, R.//Jack, W.//Benner, J.//Schildkraut, I.//Anderson, J.E. 	Expression, purification, and crystallization of restriction endonuclease PvuII with DNA containing its recognition site.	Proteins	1994	19		77-79			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. 		
@D	Balganesh, T.S.//Reiners, L.//Lauster, R.//Noyer-Weidner, M.//Wilke, K.//Trautner, T.A. 	Construction and use of chimeric SPR/Phi3T DNA methyltransferases in the definition of sequence recognizing enzyme regions.	EMBO J.	1987	6		3543-3549			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. 		
@D	Baliga, N.S.//Bonneau, R.//Facciotti, M.T.//Pan, M.//Glusman, G.//Deutsch, E.W.//Shannon, P.//Chiu, Y.//Weng, R.S.//Gan, R.R.//Hung, P.//Date, S.V.//Marcotte, E.//Hood, L.//Ng, W.V. 	Genome sequence of Haloarcula marismortui: A halophilic archaeon from the Dead Sea.	Genome Res.	2004	14		2221-2234			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. 		
@D	Ball, C.A.//Osuna, R.//Ferguson, K.C.//Johnson, R.C. 	Dramatic changes in Fis levels upon nutrient upshift in Escherichia coli.	J. Bacteriol.	1992	174		8043-8056			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. 		
@D	Ball, N.//Streeter, S.D.//Kneale, G.G.//McGeehan, J.E. 	Structure of the restriction-modification controller protein C.Esp1396I.	Acta Crystallogr. D Biol. Crystallogr.	2009	65		900-905			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. 		
@D	Ball, N.J.//McGeehan, J.E.//Streeter, S.D.//Thresh, S.J.//Kneale, G.G. 	The structural basis of differential DNA sequence recognition by restriction-modification controller proteins.	Nucleic Acids Res.	2012	40		10532-10542			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. 		
@D	Balmain, A. 	Exploring the bowels of DNA methylation.	Curr. Biol.	1995	5		1013-1016			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. 		
@D	Baltrus, D.A.//Amieva, M.R.//Covacci, A.//Lowe, T.M.//Merrell, D.S.//Ottemann, K.M.//Stein, M.//Salama, N.R.//Guillemin, K. 	The complete genome sequence of Helicobacter pylori strain G27.	J. Bacteriol.	2009	191		447-448			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. 		
@D	Baltrus, D.A.//Nishimura, M.T.//Romanchuk, A.//Chang, J.H.//Mukhtar, M.S.//Cherkis, K.//Roach, J.//Grant, S.R.//Jones, C.D.//Dangl, J.L. 	Dynamic evolution of pathogenicity revealed by sequencing and comparative genomics of 19 Pseudomonas syringae isolates.	PLoS Pathog.	2011	7		e1002132			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. 		
@D	Baltrus, D.A.//Yourstone, S.//Lind, A.//Guilbaud, C.//Sands, D.C.//Jones, C.D.//Morris, C.E.//Dangl, J.L. 	Draft Genome Sequences of a Phylogenetically Diverse Suite of Pseudomonas syringae Strains from Multiple Source Populations.	Genome Announcements	2014	2		e01195-13			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. 		
@A	Baltz, R.H.//McHenney, M.A. 		Transduction of plasmid DNA in Streptomyces spp.			Hershberger, C.L.//Queener, S.W.//Megeman, G. 		Genetics and Molecular Biology of Industrial Microorganisms				Washington, DC	American Society for Microbiology	1989		0		163-167									None 		
@D	Ban, C.//Yang, W. 	Structural basis for MutH activation in E. coli mismatch repair and relationship of MutH to restriction endonucleases.	EMBO J.	1998	17		1526-1534			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. 		
@D	Ban, E.//Yoshida, Y.//Wakushima, M.//Wajima, T.//Hamabata, T.//Ichikawa, N.//Abe, H.//Horiguchi, Y.//Hara-Kudo, Y.//Kage-Nakadai, E.//Yamamoto, T.//Wada, T.//Nishikawa, Y. 	Characterization of unstable pEntYN10 from enterotoxigenic Escherichia coli (ETEC) O169:H41.	Virulence	2015	6		735-744			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. 		
@D	Banas, J.A.//Biswas, S.//Zhu, M. 	Effects of DNA Methylation on Expression of Virulence Genes in Streptococcus mutans.	Appl. Environ. Microbiol.	2011	77		7236-7242			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. 		
@D	Banas, J.A.//Ferretti, J.J.//Progulske-Fox, A. 	Identification and sequence analysis of a methylase gene in Porphyromonas gingivalis.	Nucleic Acids Res.	1991	19		4189-4192			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'. 		
@D	Banas, J.A.//Ferretti, J.J.//Progulske-Fox, A. 	Identification of a methylase gene in Porphyromonas gingivalis.	Abstr. Gen. Meet. Am. Soc. Microbiol.	1991	91		174			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'. 		
@D	Banavali, N.K.//MacKerell, A.D. Jr. 	Free energy and structural pathways of base flipping in a DNA GCGC containing sequence.	J. Mol. Biol.	2002	319		141-160			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. 		
@D	Bancroft, I.//Smith, R.J. 	An analysis of restriction endonuclease sites in cyanophages infecting the heterocystous cyanobacteria Anabaena and Nostoc.	J. Gen. Virol.	1988	69		739-743			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. 		
@D	Bandaru, B. 	Study of cytosine to thymine mutations at the sites of dcm and M.HpaII methyltransferases.	Diss. Abstr.	1996	57		2535B-2536B			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. 		
@D	Bandaru, B.//Gopal, J.//Bhagwat, A.S. 	Overproduction of DNA cytosine methyltransferases causes methylation and C-T mutations at non-canonical sites.	J. Biol. Chem.	1996	271		7851-7859			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. 		
@D	Bandaru, B.//Wyszynski, M.//Bhagwat, A.S. 	HpaII methyltransferase is mutagenic in Escherichia coli.	J. Bacteriol.	1995	177		2950-2952			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. 		
@D	Bandyopadhyay, P.K.//Studier, F.W.//Hamilton, D.L.//Yuan, R. 	Inhibition of the type I restriction-modification enzymes EcoB and EcoK by the gene 0.3 protein of bacteriophage T7.	J. Mol. Biol.	1985	182		567-578			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. 		
@D	Bandyopadhyay, R.//Das, J. 	The DNA adenine methyltransferase-encoding gene (dam) of Vibrio cholerae.	Gene	1994	140		67-71			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%. 		
@D	Bandyopadhyay, R.//Sengupta, A.//Das, J. 	A mutation in the dam gene of Vibrio cholerae: 2-aminopurine sensitivity with intact GATC methylase activity.	Biochem. Biophys. Res. Commun.	1989	165		561-567			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. 		
@D	Bandyopadhyay, S.//Whitman, W.B.//Das, S.K. 	Draft Genome Sequence of Pannonibacter indicus Strain HT23T (DSM 23407T), a Highly Arsenate-Tolerant Bacterium Isolated from a Hot Spring in India.	Genome Announcements	2017	5		e00283-17			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. 		
@D	Banerjee, A.//Halder, U.//Chaudhry, V.//Varshney, R.K.//Mantri, S.//Bandopadhyay, R. 	Draft Genome Sequence of the Nonpathogenic, Thermotolerant, and Exopolysaccharide-Producing Bacillus anthracis Strain PFAB2 from Panifala Hot Water Spring in West Bengal, India.	Genome Announcements	2016	4		e01346-16			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. 		
@D	Banerjee, A.//Rao, D.N. 	Functional analysis of an acid adaptive DNA adenine methyltransferase from Helicobacter pylori 26695.	PLoS ONE	2011	6		e16810			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. 		
@D	Banerjee, S.//Chowdhury, R. 	An orphan DNA (cytosine-5-)-methyltransferase in Vibrio cholerae.	Microbiology	2006	152		1055-1062			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. 		
@D	Banerjee, S.//Fisher, O.//Lohia, A.//Ankri, S. 	Entamoeba histolytica DNA methyltransferase (Ehmeth) is a nuclear matrix protein that binds EhMRS2, a DNA that includes a scaffold/matrix  attachment region (S/MAR).	Mol. Biochem. Parasitol.	2005	139		91-97			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. 		
@D	Banerjee, S.//Petronella, N.//Chew, L.C.//Farber, J. 	Draft Genome Sequences of Four Vibrio parahaemolyticus Isolates from Clinical Cases in Canada.	Genome Announcements	2015	3		e01482-14			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. 		
@D	Banfalvi, G.//Sarkar, N. 	Effect of mercury substitution of DNA on its susceptibility to cleavage by restriction endonucleases.	DNA Cell Biol.	1995	14		445-450			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. 		
@D	Banfield, J.F.//Anantharaman, K.//Williams, K.H.//Thomas, B.C. 	Complete 4.55-Megabase-Pair Genome of 'Candidatus Fluviicola riflensis,' Curated  from Short-Read Metagenomic Sequences.	Genome Announcements	2017	5		e01299-17			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. 		
@D	Bang, M.S.//Jeong, H.W.//Lee, Y.J.//Lee, S.J.//Lee, S.C.//Shin, J.I.//Oh, C.H. 	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.	Genome Announcements	2018	6		e00525-18			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. 		
@D	Bang, M.S.//Jeong, H.W.//Lee, Y.J.//Oh, H.Y.//Lee, S.J.//Shim, M.S.//Shin, J.I.//Oh, C.H. 	Draft Genome Sequences of Bacillus subtilis Strain DKU_NT_01 Isolated from Traditional Korean Food Containing Soybean (Chung-gook-jang).	Genome Announcements	2017	5		e00769-17			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). 		
@D	Bangera, S.R.//Umakanth, S.//Mukhopadhyay, A.K.//Leekitcharoenphon, P.//Chowdhury, G.//Hendriksen, R.S.//Ballal, M. 	Draft Genome Sequence of Salmonella enterica subsp. enterica Serotype Typhimurium Sequence Type 313, Isolated from India.	Microbiol. Resour. Announc.	2018	7		e00990-18			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. 		
@D	Banks, D.J.//Porcella, S.F.//Barbian, K.D.//Beres, S.B.//Philips, L.E.//Voyich, J.M.//DeLeo, F.R.//Martin, J.M.//Somerville, G.A.//Musser, J.M. 	Progress toward Characterization of the Group A Streptococcus Metagenome: Complete Genome Sequence of a Macrolide-Resistant Serotype M6 Strain.	J. Infect. Dis.	2004	190		727-738			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. 		
@D	Banks, D.J.//Porcella, S.F.//Barbian, K.D.//Martin, J.M.//Musser, J.M. 	Structure and distribution of an unusual chimeric genetic element encoding macrolide resistance in phylogenetically diverse clones of group A Streptococcus.	J. Infect. Dis.	2003	188		1899-1909			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. 		
@D	Bannam, T.L.//Teng, W.L.//Bulach, D.//Lyras, D.//Rood, J.I. 	Functional Identification of Conjugation and Replication Regions of the Tetracycline Resistance Plasmid pCW3 from Clostridium perfringens.	J. Bacteriol.	2006	188		4942-4951			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. 		
@D	Bannam, T.L.//Yan, X.X.//Harrison, P.F.//Seemann, T.//Keyburn, A.L.//Stubenrauch, C.//Weeramantri, L.H.//Cheung, J.K.//McClane, B.A.//Boyce, J.D.//Moore, R.J.//Rood, J.I. 	Necrotic Enteritis-Derived Clostridium perfringens Strain with Three Closely Related Independently Conjugative Toxin and Antibiotic Resistance Plasmids.	MBio	2011	2		e00190-11			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. 		
@D	Bannantine, J.P.//Bayles, D.O.//Robbe-Austerman, S.//Burrell, A.M.//Stabel, J.R. 	Draft Genome Sequence of a Mycobacterium avium Complex Isolate from a Broadbill Bird.	Genome Announcements	2014	2		e01268-13			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. 		
@D	Bannantine, J.P.//Li, L.//Mwangi, M.//Cote, R.//Raygoza, G.J.A.//Kapur, V. 	Complete Genome Sequence of Mycobacterium avium subsp. paratuberculosis, Isolated from Human Breast Milk.	Genome Announcements	2014	2		e01252-13			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. 		
@D	Bannister, D. 	Analysis of an R+ strain carrying two fi- sex factors.	J. Gen. Microbiol.	1970	61		273-281			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. 		
@D	Bannister, D.//Glover, S.W. 	Restriction and modification of bacteriophages by R+ strains of Escherichia coli K12.	Biochem. Biophys. Res. Commun.	1968	30		735-738			None 		
@D	Bannister, D.//Glover, S.W. 	The isolation and properties of non-restricting mutants of two different host specificities associated with drug resistance factors.	J. Gen. Microbiol.	1970	61		63-71			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. 		
@D	Bao, G.//Wang, R.//Zhu, Y.//Dong, H.//Mao, S.//Zhang, Y.//Chen, Z.//Li, Y.//Ma, Y. 	Complete genome sequence of Clostridium acetobutylicum DSM 1731, a solvent-producing strain with multireplicon genome architecture.	J. Bacteriol.	2011	193		5007-5008			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. 		
@D	Bao, G.//Zhang, Y.//Du, C.//Chen, Z.//Li, Y.//Cao, Z.//Ma, Y. 	Genome Sequence of Klebsiella oxytoca M5al, a Promising Strain for Nitrogen Fixation and Chemical Production.	Genome Announcements	2013	1		e00074-12			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. 		
@D	Bao, H.X.//Tang, L.//Yu, L.//Wang, X.Y.//Li, Y.//Deng, X.//Li, Y.G.//Li, A.//Zhu, D.L.//Johnston, R.N.//Liu, G.R.//Feng, Y.//Liu, S.L. 	Differential efficiency in exogenous DNA acquisition among closely related Salmonella strains: implications in bacterial speciation.	BMC Microbiol.	2014	14		157			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. 		
@D	Bao, P.//Su, J.Q.//Hu, Z.Y.//Haggblom, M.M.//Zhu, Y.G. 	Genome sequence of the anaerobic bacterium Bacillus sp. strain ZYK, a selenite and nitrate reducer from paddy soil.	Standards in Genomic Sciences	2014	9		646-654			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. 		
@D	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. 	A complete sequence of the T. tengcongensis genome.	Genome Res.	2002	12		689-700			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. 		
@D	Bao, W.//Zhou, Y.//Jiang, J.//Xu, Z.//Hou, L.//Leung, F.C. 	Complete Genome Sequence of Raoultella ornithinolytica Strain S12, a Lignin-Degrading Bacterium Isolated from Forest Soil.	Genome Announcements	2015	3		e00104-15			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. 		
@D	Bao, Y.//Higgins, L.//Zhang, P.//Chan, S.H.//Laget, S.//Sweeney, S.//Lunnen, K.//Xu, S.Y. 	Expression and purification of BmrI restriction endonuclease and its N-terminal cleavage domain variants.	Protein Expr. Purif.	2008	58		42-52			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). 		
@D	Bao, Y.//Kwok, A.H.//He, L.//Jiang, J.//Huang, Z.//Leung, F.C.//Sheng, X. 	Complete Genome Sequence of Dyella jiangningensis Strain SBZ3-12, Isolated from the Surfaces of Weathered Rock.	Genome Announcements	2014	2		e00416-14			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. 		
@D	Bao, Y.//Liang, Z.//Booyjzsen, C.//Mayfield, J.A.//Li, Y.//Lee, S.W.//Ploplis, V.A.//Song, H.//Castellino, F.J. 	Unique Genomic Arrangements in an Invasive Serotype M23 strain of Streptococcus pyogenes Identify Genes that Induce Hypervirulence.	J. Bacteriol.	2014	196		4089-4102			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. 		
@D	Bao, Y.J.//Liang, Z.//Mayfield, J.A.//Donahue, D.L.//Carothers, K.E.//Lee, S.W.//Ploplis, V.A.//Castellino, F.J. 	Genomic Characterization of a Pattern D Streptococcus pyogenes emm53 Isolate Reveals a Genetic Rationale for Invasive Skin Tropicity.	J. Bacteriol.	2016	198		1712-1724			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. 		
@D	Bao, Z.//Shinoda, R.//Minamisawa, K. 	Draft Genome Sequence of Methylosinus sp. Strain 3S-1, an Isolate from Rice Root  in a Low-Nitrogen Paddy Field.	Genome Announcements	2016	4		e00932-16			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. 		
@D	Baptista, J.P.//Sanches, P.P.//Teixeira, G.M.//Morey, A.T.//Tavares, E.R.//Yamada-Ogatta, S.F.//da Rocha, S.P.D.//Hungria, M.//Ribeiro, R.A.//Balbi-Pena, M.I.//Chideroli, R.T.//Pereira, U.P.//de Oliveira, A.G. 	Complete Genome Sequence of Bacillus velezensis LABIM40, an Effective Antagonist  of Fungal Plant Pathogens.	Genome Announcements	2018	6		e00595-18			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. 		
@D	Barak-Gavish, N.//Frada, M.J.//Lee, P.A.//DiTullio, G.R.//Ku, C.//Malitsky, S.//Aharoni, A.//Green, S.J.//Kartvelishvily, E.//Sheyn, U.//Schatz, D.//Vardi, A. 	Bacterial virulence against an oceanic bloom-forming phytoplankter is mediated by algal DMSP.	Sci. Adv.	2018	4		eaau5716			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. 		
@D	Baranasic, D.//Gacesa, R.//Starcevic, A.//Zucko, J.//Blazic, M.//Horvat, M.//Gjuracic, K.//Fujs, S.//Hranueli, D.//Kosec, G.//Cullum, J.//Petkovic, H. 	Draft Genome Sequence of Streptomyces rapamycinicus Strain NRRL 5491, the Producer of the Immunosuppressant Rapamycin.	Genome Announcements	2013	1		e00581-13			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. 		
@D	Baranasic, D.//Zucko, J.//Nair, M.//Pain, A.//Long, P.F.//Hranueli, D.//Cullum, J.//Starcevic, A. 	Genome Sequences of the Oxytetracycline Production Strain Streptomyces rimosus R6-500 and Two Mutants with Chromosomal Rearrangements.	Genome Announcements	2014	2		e00517-14			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. 		
@D	Baranova, N.B.//Malygina, T.Y.//Medvedeva, E.S.//Boulygina, E.A.//Siniagina, M.N.//Dramchini, M.A.//Prottoy, R.A.//Mouzykantov, A.A.//Davydova, M.N.//Chernova, O.A.//Chernov, V.M. 	Genome Sequences of Acholeplasma laidlawii Strains with Increased Resistance to Tetracycline and Melittin.	Genome Announcements	2018	6		e01446-17			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. 		
@D	Barany, F. 	A genetic system for isolation and characterization of TaqI restriction endonuclease mutants.	Gene	1987	56		13-27			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. 		
@D	Barany, F. 	The TaqI star reaction:  strand preferences reveal hydrogen-bond donor and acceptor sites in canonical sequence recognition.	Gene	1988	65		149-165			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. 		
@D	Barany, F. 	Isolation and characterization of TaqI restriction endonuclease mutants.	J. Cell Biochem. Suppl.	1989	13A		82			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. 		
@D	Barany, F. 	How TaqI endonuclease recognizes its cognate sequence.	Gene	1988	74		63-65			Meeting Abstract 		
@D	Barany, F. 	Two codon insertion mutagenesis of the TaqI restriction endonuclease.	J. Cell Biochem. Suppl.	1987	11C		240			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. 		
@D	Barany, F. 	Overproduction, purification and crystallization of TaqI restriction endonuclease.	Gene	1988	65		167-177			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. 		
@D	Barany, F.//Danzitz, M.//Zebala, J.//Mayer, A. 	Cloning and sequencing of genes encoding the TthHB8I restriction and modification enzymes: comparison with the isoschizomeric TaqI enzymes.	Gene	1992	112		3-12			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. 		
@D	Barany, F.//Slatko, B.//Danzitz, M.//Cowburn, D.//Schildkraut, I.//Wilson, G.G. 	The corrected nucleotide sequences of the TaqI restriction and modification enzymes reveal a thirteen-codon overlap.	Gene	1992	112		91-95			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. 		
@D	Barany, F.//Zebala, J. 	Correlation between insertion mutant activities and amino acid sequence identities of the TaqI and TthHB8 restriction endonucleases.	Gene	1992	112		13-20			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. 		
@D	Baranyi, U.//Klein, R.//Lubitz, W.//Kruger, D.H.//Witte, A. 	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.	Mol. Microbiol.	2000	35		1168-1179			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. 		
@D	Baranzoni, G.M.//Fratamico, P.M.//Kim, G.H.//Reichenberger, E.R.//Funk, J.A.//Manning, S.D.//Bosilevac, J.M. 	Genome Sequences of 34 Shiga Toxin-Producing Escherichia coli Isolates from Swine and Other Sources.	Genome Announcements	2017	5		e01214-17			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. 		
@D	Baranzoni, G.M.//Fratamico, P.M.//Reichenberger, E.R.//Kim, G.H.//Breidt, F.//Kay, K.//Oh, D.H. 	Complete Genome Sequences of Escherichia coli O157:H7 Strains SRCC 1675 and 28RC, Which Vary in Acid Resistance.	Genome Announcements	2016	4		e00743-16			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. 		
@D	Barau, J.//Teissandier, A.//Zamudio, N.//Roy, S.//Nalesso, V.//Herault, Y.//Guillou, F.//Bourc'his, D. 	The DNA methyltransferase DNMT3C protects male germ cells from transposon activity.	Science	2016	354		909-912			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. 		
@D	Barauna, R.A.//Guimaraes, L.C.//Veras, A.A.//de Sa, P.H.//Gracas, D.A.//Pinheiro, K.C.//Silva, A.S.//Folador, E.L.//Benevides, L.J.//Viana, M.V.//Carneiro, A.R.//Schneider, M.P.//Spier, S.J.//Edman, J.M.//Ramos, R.T.//Azevedo, V.//Silva, A. 	Genome Sequence of Corynebacterium pseudotuberculosis MB20 bv. equi Isolated from a Pectoral Abscess of an Oldenburg Horse in California.	Genome Announcements	2014	2		e00977-14			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. 		
@D	Barauna, R.A.//Ramos, R.T.//Veras, A.A.//de Sa, P.H.//Guimaraes, L.C.//das Gracas, D.A.//Carneiro, A.R.//Edman, J.M.//Spier, S.J.//Azevedo, V.//Silva, A. 	Genomic analysis of four strains of Corynebacterium pseudotuberculosis bv. Equi isolated from horses showing distinct signs of infection.	Standards in Genomic Sciences	2017	12		16			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. 		
@D	Barauna, R.A.//Ramos, R.T.//Veras, A.A.//Pinheiro, K.C.//Benevides, L.J.//Viana, M.V.//Guimaraes, L.C.//Edman, J.M.//Spier, S.J.//Azevedo, V.//Silva, A. 	Assessing the Genotypic Differences between Strains of Corynebacterium pseudotuberculosis biovar equi through Comparative Genomics.	PLoS ONE	2017	12		E0170676			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. 		
@D	Barbato, M.//Mapelli, F.//Chouaia, B.//Crotti, E.//Daffonchio, D.//Borin, S. 	Draft Genome Sequence of the Hydrocarbon-Degrading Bacterium Alcanivorax dieselolei KS-293 Isolated from Surface Seawater in the Eastern Mediterranean  Sea.	Genome Announcements	2015	3		e01424-15			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. 		
@D	Barbau-Piednoir, E.//Bertrand, S.//Roosens, N.H.//De Keersmaecker, S.C. 	Genome Sequence of the Salmonella enterica subsp. enterica Serovar Namur Strain 05-2929, Lacking the Salmonella Atypical Fimbrial Operon.	Genome Announcements	2014	2		e00299-14			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. 		
@D	Barbau-Piednoir, E.//De Keersmaecker, S.C.//Wuyts, V.//Gau, C.//Pirovano, W.//Costessi, A.//Philipp, P.//Roosens, N.H. 	Genome Sequence of EU-Unauthorized Genetically Modified Bacillus subtilis Strain  2014-3557 Overproducing Riboflavin, Isolated from a Vitamin B2 80% Feed Additive.	Genome Announcements	2015	3		e00214-15			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. 		
@D	Barbe, V.//Bouzon, M.//Mangenot, S.//Badet, B.//Poulain, J.//Segurens, B.//Vallenet, D.//Marliere, P.//Weissenbach, J. 	Complete Genome Sequence of Streptomyces cattleya NRRL 8057, a Producer of Antibiotics and Fluorometabolites.	J. Bacteriol.	2011	193		5055-5056			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. 		
@D	Barbe, V.//Vallenet, D.//Fonknechten, N.//Kreimeyer, A.//Oztas, S.//Labarre, L.//Cruveiller, S.//Robert, C.//Duprat, S.//Wincker, P.//Ornston, L.N.//Weissenbach, J.//Marliere, P.//Cohen, G.N.//Medigue, C. 	Unique features revealed by the genome sequence of Acinetobacter sp. ADP1, a versatile and naturally transformation competent bacterium.	Nucleic Acids Res.	2004	32		5766-5779			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. 		
@D	Barber, R.D.//Zhang, L.//Harnack, M.//Olson, M.V.//Kaul, R.//Ingram-Smith, C.//Smith, K.S. 	Complete genome sequence of Methanosaeta concilii, a specialist in aceticlastic methanogenesis.	J. Bacteriol.	2011	193		3668-3669			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. 		
@D	Barbes, C.//Hardisson, C.//Novella, I.S.//Yebra, M.J.//Sanchez, J. 	DNA-methyltransferase activities in Streptomyces antibioticus.	FEMS Microbiol. Lett.	1988	55		59-64			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. 		
@D	Barbes, C.//Sanchez, J.//Yebra, M.J.//Robert-Gero, M.//Hardisson, C. 	Effects of sinefungin and S-adenosylhomocysteine on DNA and protein methyltransferases from Streptomyces and other bacteria.	FEMS Microbiol. Lett.	1990	69		239-244			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. 		
@D	Barbeyron, T.//Kean, K.//Forterre, P. 	DNA adenine methylation of GATC sequences appeared recently in the Escherichia coli lineage.	J. Bacteriol.	1984	160		586-590			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. 		
@D	Barbier, F.//Ruppe, E.//Hernandez, D.//Lebeaux, D.//Francois, P.//Felix, B.//Desprez, A.//Maiga, A.//Woerther, P.L.//Gaillard, K.//Jeanrot, C.//Wolff, M.//Schrenzel, J.//Andremont, A.//Ruimy, R. 	Methicillin-resistant coagulase-negative staphylococci in the community: high homology of SCCmec IVa between Staphylococcus epidermidis and major clones of methicillin-resistant Staphylococcus aureus.	J. Infect. Dis.	2010	202		270-281			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. 		
@D	Barbier, P.//Houel, A.//Loux, V.//Poulain, J.//Bernardet, J.F.//Touchon, M.//Duchaud, E. 	Complete Genome Sequence of Flavobacterium indicum GPSTA100-9T, Isolated from Warm Spring Water.	J. Bacteriol.	2012	194		3024-3025			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. 		
@D	Barbosa, B.G.//Fernandez-Garcia, L.//Gato, E.//Lopez, M.//Blasco, L.//Leao, R.S.//Albano, R.M.//Fernandez, B.//Cuenca, F.F.//Pascual, A.//Bou, G.//Marques, E.A.//Tomas, M. 	Genome Sequence of Airborne Acinetobacter sp. Strain 5-2Ac02 in the Hospital Environment, Close to the Species of Acinetobacter towneri.	Genome Announcements	2016	4		e01343-16			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. 		
@D	Barbosa, P.//Leao, C.//Usie, A.//Amaro, A.//Botelho, A.//Pinto, C.//Inacio, J.//Stevenson, K.//Ramos, A.M. 	Draft Genome Sequence of a Rare Pigmented Mycobacterium avium subsp. paratuberculosis Type C Strain.	Genome Announcements	2017	5		e01066-17			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. 		
@D	Barbour, A.G. 	Chromosome and Plasmids of the Tick-Borne Relapsing Fever Agent Borrelia hermsii.	Genome Announcements	2016	4		e00528-16			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. 		
@D	Barbour, A.G.//Campeau, M.S. 	Genome Sequence of Borrelia parkeri, an Agent of Enzootic Relapsing Fever in Western North America.	Genome Announcements	2014	2		e00018-14			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. 		
@A	Barcus, V.A.//Murray, N.E. 		Barriers to recombination: restriction.			Baumberg, S.//Young, J.P.W.//Saunders, S.R.//Wellington, E.M.H. 		Population Genetics of Bacteria				Cambridge	Cambridge University Press	1995		0		31-58									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. 		
@D	Barcus, V.A.//Titheradge, A.J.B.//Murray, N.E. 	The diversity of alleles at the hsd locus in natural populations of Escherichia coli.	Genetics	1995	140		1187-1197			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. 		
@D	Barke, J.//Seipke, R.F.//Gruschow, S.//Heavens, D.//Drou, N.//Bibb, M.J.//Goss, R.J.//Yu, D.W.//Hutchings, M.I. 	A mixed community of actinomycetes produce multiple antibiotics for the fungus farming ant Acromyrmex octospinosus.	BMC Biol.	2010	8		109			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. 		
@D	Barker, D.//Hoff, M.//Oliphant, A.//White, R. 	A second type II restriction endonuclease from Thermus aquaticus with an unusual sequence specificity.	Nucleic Acids Res.	1984	12		5567-5581			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'. 		
@D	Barker, E.N.//Helps, C.R.//Peters, I.R.//Darby, A.C.//Radford, A.D.//Tasker, S. 	Complete Genome Sequence of Mycoplasma haemofelis, a Hemotropic Mycoplasma.	J. Bacteriol.	2011	193		2060-2061			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. 		
@D	Barlow, D.P. 	Methylation and imprinting: from host defense to gene regulation?	Science	1993	260		309-310					
@D	Barlow, R.S.//Gobius, K.S. 	Diverse class 2 integrons in bacteria from beef cattle sources.	J. Antimicrob. Chemother.	2006	58		1133-1138			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. 		
@D	Barnaba, T.J.//Gangiredla, J.//Mammel, M.K.//Lacher, D.W.//Elkins, C.A.//Lampel, K.A.//Whitehouse, C.A.//Tartera, C. 	Draft Genome Sequences of Bifidobacterium Strains Isolated from Dietary Supplements and Cultured Food Products.	Genome Announcements	2018	6		e00610-18			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. 		
@D	Barnes, A.C.//Delamare-Deboutteville, J.//Gudkovs, N.//Brosnahan, C.//Morrison, R.//Carson, J. 	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.	Microbial Genomics	2016	2		E000095			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. 		
@D	Barnes, G.//Rine, J. 	Regulated expression of endonuclease EcoRI in Saccharomyces cerevisiae: Nuclear entry and biological consequences.	Proc. Natl. Acad. Sci. U. S. A.	1985	82		1354-1358			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. 		
@D	Barnes, H.E.//Liu, G.//Weston, C.Q.//King, P.//Pham, L.K.//Waltz, S.//Helzer, K.T.//Day, L.//Sphar, D.//Yamamoto, R.T.//Forsyth, R.A. 	Selective Microbial Genomic DNA Isolation Using Restriction Endonucleases.	PLoS ONE	2014	9		e109061			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. 		
@D	Barony, G.M.//Tavares, G.C.//Pereira, F.L.//Carvalho, A.F.//Dorella, F.A.//Leal, C.A.G.//Figueiredo, H.C.P. 	Large-scale genomic analyses reveal the population structure and evolutionary trends of Streptococcus agalactiae strains in Brazilian fish farms.	Sci. Rep.	2017	7		13538			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. 		
@D	Barra, R.//Chiong, M.//Gonzalez, E.//Vasquez, C. 	A DNA-modification methylase from Bacillus stearothermophilus V.	Biochem. J.	1988	255		699-703			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'. 		
@D	Barrado, L.//Viedma, E.//Vindel, A.//Otero, J.R.//Chaves, F. 	Draft Genome Sequence of Strain SA_ST125_MupR of Methicillin-Resistant Staphylococcus aureus ST125, a Major Clone in Spain.	Genome Announcements	2013	1		e00588-13			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. 		
@D	Barragan, V.//Sahl, J.W.//Wiggins, K.//Chiriboga, J.//Salinas, A.//Cantos, N.E.//Loor, M.N.//Intriago, B.I.//Morales, M.//Trueba, G.//Pearson, T. 	Draft Genome Sequence of the First Pathogenic Leptospira Isolates from Ecuador.	Genome Announcements	2016	4		e00271-16			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. 		
@D	Barrangou, R.//Briczinski, E.P.//Traeger, L.L.//Loquasto, J.R.//Richards, M.//Horvath, P.//Coute-Monvoisin, A.C.//Leyer, G.//Rendulic, S.//Steele, J.L.//Broadbent, J.R.//Oberg, T.//Dudley, E.G.//Schuster, S.//Romero, D.A.//Roberts, R.F. 	Comparison of the complete genome sequences of Bifidobacterium animalis subsp. lactis DSM 10140 and Bl-04.	J. Bacteriol.	2009	191		4144-4151			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. 		
@D	Barrangou, R.//van der Oost, J. 	Bacteriophage exclusion, a new defense system.	EMBO J.	2015	34		134-135			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 		
@D	Barras, F.//Marinus, M.G. 	The great GATC:  DNA methylation in E. coli.	Trends Genet.	1989	5		139-143			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. 		
@D	Barreau, G.//Tompkins, T.A.//de Carvalho, V.G. 	Draft Genome Sequence of Probiotic Strain Pediococcus acidilactici MA18/5M.	J. Bacteriol.	2012	194		901			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%. 		
@D	Barreiro, C. et al. 	Draft Genome of Streptomyces tsukubaensis NRRL 18488, the Producer of the Clinically Important Immunosuppressant Tacrolimus (FK506).	J. Bacteriol.	2012	194		3756-3757			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. 		
@D	Barrera, C.//Valot, B.//Rognon, B.//Zaugg, C.//Monod, M.//Millon, L. 	Draft Genome Sequence of the Principal Etiological Agent of Farmer's Lung Disease, Saccharopolyspora rectivirgula.	Genome Announcements	2014	2		e01340-14			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. 		
@D	Barrero, R.A.//Moolhuijzen, P.//Indjein, L.//Venus, B.//Keeble-Gagnere, G.//Power, J.//Bellgard, M.I.//Lew-Tabor, A.E. 	Draft Genome Sequences of Campylobacter fetus subsp. venerealis bv. venerealis Strain B6 and bv. intermedius Strain 642-21.	Genome Announcements	2014	2		e00943-14			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. 		
@D	Barreto-Hernandez, E.//Falquet, L.//Reguero, M.T.//Mantilla, J.R.//Valenzuela, E.M.//Gonzalez, E.//Cepeda, A.//Escalante, A. 	Draft Genome Sequences of Multidrug-Resistant Acinetobacter sp. Strains from Colombian Hospitals.	Genome Announcements	2013	1		e00868-13			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. 		
@D	Barretto, C.//Alvarez-Martin, P.//Foata, F.//Renault, P.//Berger, B. 	Genome Sequence of the Lantibiotic Bacteriocin Producer Streptococcus salivarius  Strain K12.	J. Bacteriol.	2012	194		5959-5960			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. 		
@D	Barretto, C.//Ngom-Bru, C.//Genevaz, A.//Fournier, C.//Moine, D.//Kassam, M.//Iltis, A.//Sagory-Zalkind, P.//Ciron, P.E.//Faucherand, G.//Descombes, P.//Duboux, S. 	Genome Sequence of Lactobacillus fermentum Strain NCC2970 (CNCM I-5068).	Genome Announcements	2016	4		e01254-16			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. 		
@D	Barshevsky, T.//Benner, J.S. 	Site-directed mutagenesis of the EcoRV methylase for the study of the functional role of the conserved sequences in N6-adenine methylases.	J. Cell Biochem. Suppl.	1989	13D		211			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. 		
@D	Barsomian, J.M.//Card, C.O.//Wilson, G.G. 	Cloning of the HhaI and HinPI restriction-modification systems.	Gene	1988	74		5-7			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. 		
@A	Bart, A. 		Genetic variation in Neisseria meningitidis.			 		Ph.D. Thesis, Univ. Amsterdam, Netherlands				Wageningen	Ponsen & Looijen, BV	1999				1-115									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". 		
@D	Bart, A.//Dankert, J.//van der Ende, A. 	Representational difference analysis of Neisseria meningitidis identifies sequences that are specific for the hyper-virulent lineage III clone.	FEMS Microbiol. Lett.	2000	188		111-114			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. 		
@D	Bart, A.//Dankert, J.//van der Ende, A. 	Operator sequences for the regulatory proteins of restriction modification systems.	Mol. Microbiol.	1999	31		1275-1281			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. 		
@D	Bart, A.//Pannekoek, Y.//Dankert, J.//van der Ende, A. 	NmeSI restriction-modification system identified by representational difference analysis of a hypervirulent Neisseria meningitidis strain.	Infect. Immun.	2001	69		1816-1820			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. 		
@D	Bart, A.//Pannekoek, Y.//Dankert, J.//van der Ende, A. 	The NmeSI restriction-modification system identified by representational difference analysis of a hypervirulent Neisseria  meningitidis strain.	Abstr. Gen. Meet. Am. Soc. Microbiol.	2001	101		303			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. 		
@D	Bart, A.//van Passel, M.W.//van Amsterdam, K.//van der Ende, A. 	Direct detection of methylation in genomic DNA.	Nucleic Acids Res.	2005	33		e124			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. 		
@D	Bart, M.J.//van der Heide, H.G.//Zeddeman, A.//Heuvelman, K.//van Gent, M.//Mooi, F.R. 	Complete Genome Sequences of 11 Bordetella pertussis Strains Representing the Pandemic ptxP3 Lineage.	Genome Announcements	2015	3		e01394-15			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. 		
@D	Bart, M.J.//van Gent, M.//van der Heide, H.G.//Boekhorst, J.//Hermans, P.//Parkhill, J.//Mooi, F.R. 	Comparative genomics of prevaccination and modern Bordetella pertussis strains.	BMC Genomics	2010	11		627			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. 		
@D	Bart, M.J.//Zeddeman, A.//van der Heide, H.G.//Heuvelman, K.//van Gent, M.//Mooi, F.R. 	Complete Genome Sequences of Bordetella pertussis Isolates B1917 and B1920, Representing Two Predominant Global Lineages.	Genome Announcements	2014	2		e01301-14			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. 		
@D	Bartee, L.//Bender, J. 	Two Arabidopsis methylation-deficiency mutations confer only partial effects on a methylated endogenous gene family.	Nucleic Acids Res.	2001	29		2127-2134			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. 		
@D	Bartee, L.//Malagnac, F.//Bender, J. 	Arabidopsis cmt3 chromomethylase mutations block non-CG methylation and silencing of an endogenous gene.	Genes Dev.	2001	15		1753-1758			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. 		
@D	Bartelme, R.P.//Barbier, P.//Lipscomb, R.S.//LaPatra, S.E.//Newton, R.J.//Evenhuis, J.P.//McBride, M.J. 	Draft Genome Sequence of the Fish Pathogen Flavobacterium columnare Strain MS-FC-4.	Genome Announcements	2018	6		e00429-18			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. 		
@D	Bartelme, R.P.//Newton, R.J.//Zhu, Y.//Li, N.//LaFrentz, B.R.//McBride, M.J. 	Complete Genome Sequence of the Fish Pathogen Flavobacterium columnare Strain C#2.	Genome Announcements	2016	4		e00624-16			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. 		
@D	Bartels, M.D.//Hansen, L.H.//Boye, K.//Sorensen, S.J.//Westh, H. 	An Unexpected Location of the Arginine Catabolic Mobile Element (ACME) in a USA300-Related MRSA StrainJ3 region.	PLoS ONE	2011	6		e16193			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. 		
@D	Bartoli, C.//Carrere, S.//Lamichhane, J.R.//Varvaro, L.//Morris, C.E. 	Whole-Genome Sequencing of 10 Pseudomonas syringae Strains Representing Different Host Range Spectra.	Genome Announcements	2015	3		e00379-15			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. 		
@D	Barton, J.K. 	Transition metal complexes in the design of synthetic restriction enzymes.	ACS Abstracts	1988	195		44			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. 		
@D	Barton, J.K.//Basile, L.A.//Paranawithana, S.R. 	The presence of zinc in the restriction enzyme EcoRI*.	J. Biol. Chem.	1982	257		7911-7914			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. 		
@D	Barton, J.K.//Paranawithana, S.R. 	Restriction endonuclease EcoRI alters the Enantiomeric Preference of Chiral Metallointercalators for DNA:  an illustration of a protein-induced DNA conformational change.	Biochemistry	1986	25		2205-2211			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. 		
@D	Baryshev, M.M.//Buryanov, Y.I.//Kosykh, V.G.//Bayev, A.A. 	Isolation, purification and some properties of restrictase and methylase BstNI from Bacillus stearothermophilus.	Biokhimiia	1989	54		1894-1903			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. 		
@D	Barzel, A.//Privman, E.//Peeri, M.//Naor, A.//Shachar, E.//Burstein, D.//Lazary, R.//Gophna, U.//Pupko, T.//Kupiec, M. 	Native homing endonucleases can target conserved genes in humans and in animal models.	Nucleic Acids Res.	2011	39		6646-6659			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. 		
@D	Barzilai, R. 	SV40 DNA:  Quantitative conversion of closed circular to open circular form by an ethidium bromide-restricted endonuclease.	J. Mol. Biol.	1973	74		739-742			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. 		
@D	Basavanna, U.//Gonzalez-Escalona, N.//Timme, R.//Datta, S.//Schoen, B.//Brown, E.W.//Zink, D.//Sharma, S.K. 	Draft Genome Sequence of a Clostridium botulinum Isolate from Water Used for Cooling at a Plant Producing Low-Acid Canned Foods.	Genome Announcements	2013	1		e00200-12			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. 		
@D	Basco, M.D.S.//Revollo, J.R.//McKinzie, P.B.//Agnihothram, S.//Kothari, A.//Saccente, M.//Hart, M.E. 	Draft Genome Sequences of Two Staphylococcus aureus Strains Isolated in Succession from a Case of Bacteremia.	Genome Announcements	2017	5		e00259-17			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. 		
@D	Bashir, A. et al. 	A hybrid approach for the automated finishing of bacterial genomes.	Nat. Biotechnol.	2012	30		701-707			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. 		
@D	Bashir, A.//Attie, O.//Sullivan, M.//Sebra, R.//Singh, K.V.//Altman, D.//Pak, T.//Dutta, J.//Chacko, K.//Webster, E.//Lewis, M.//Hamula, C.//Delli-Carpini, K.W.//Murray, B.E.//Kasarskis, A.//van Bakel, H.//Huprikar, S. 	Genomic confirmation of vancomycin-resistant Enterococcus transmission from deceased donor to liver transplant recipient.	PLoS ONE	2017	12		e0170449			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. 		
@D	Bashtrykov, P.//Jankevicius, G.//Jurkowska, R.Z.//Ragozin, S.//Jeltsch, A. 	The UHRF1 Protein Stimulates the Activity and Specificity of the Maintenance DNA Methyltransferase DNMT1 by an Allosteric Mechanism.	J. Biol. Chem.	2014	289		4106-4115			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. 		
@D	Bashtrykov, P.//Ragozin, S.//Jeltsch, A. 	Mechanistic details of the DNA recognition by the Dnmt1 DNA methyltransferase.	FEBS Lett.	2012	586		1821-1823			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. 		
@D	Baskunov, V.B.//Subach, F.V.//Kolbanovskiy, A.//Kolbanovskiy, M.//Eremin, S.A.//Johnson, F.//Bonala, R.//Geacintov, N.E.//Gromova, E.S. 	Effects of benzo[a]pyrene-deoxyguanosine lesions on DNA methylation catalyzed by EcoRII DNA methyltransferase and on DNA cleavage effected  by EcoRII restriction endonuclease.	Biochemistry	2005	44		1054-1066			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. 		
@D	Basnakyan, A.G.//Votrin, I.I. 	Restriction endonucleases as a possible factor in the evolution of DNA nucleotide composition.	Zh. Evol. Biokhim. Fiziol.	1983	19		20-24			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. 		
@D	Basra, P.//Koziol, A.//Wong, A.//Carrillo, C.D. 	Complete Genome Sequences of Citrobacter braakii Strains GTA-CB01 and GTA-CB04, Isolated from Ground Beef.	Genome Announcements	2015	3		e01307-14			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. 		
@D	Bassi, D.//Fontana, C.//Gazzola, S.//Pietta, E.//Puglisi, E.//Cappa, F.//Cocconcelli, P.S. 	Draft Genome Sequence of Clostridium tyrobutyricum Strain UC7086, Isolated from Grana Padano Cheese with Late-Blowing Defect.	Genome Announcements	2013	1		e00614-13			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. 		
@D	Bassil, N.M.//Lloyd, J.R. 	Draft Genome Sequences of Four Alkaliphilic Bacteria Belonging to the Anaerobacillus Genus.	Genome Announcements	2017	5		e01493-16			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. 		
@D	Bassing, C.H.//Kim, Y.-G.//Li, L.//Chandrasegaran, S. 	Overproduction, purification and characterization of M.HinfI methyltransferase and its deletion mutant.	Gene	1992	113		83-88			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. 		
@D	Bateman, A.C.//Perez-Osorio, A.C.//Li, Z.//Tran, M.//Greninger, A.L. 	Conservation and Recombination in the Genome Sequence of Haemophilus influenzae Type f WAPHL1.	Genome Announcements	2017	5		e00929-17			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. 		
@D	Bateman, M.D.//de Vries, S.P.W.//Gupta, S.//Guardabassi, L.//Cavaco, L.M.//Grant, A.J.//Holmes, M.A. 	Genome and Plasmid Sequences of Escherichia coli KV7, an Extended-Spectrum beta-Lactamase Isolate Derived from Feces of a Healthy Pig.	Genome Announcements	2017	5		e00595-17			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. 		
@D	Bates, P.J.//Hammond, G.B.//Xu, B.//Aponte, J.C.//Malik, M.T.//Martin, A.N.//Choi, E.W.//Thomas, S.D.//Casson, L.K.//Trent, J.O. 	Discovery of XB05, a potent antiproliferative agent and novel non-nucleoside inhibitor of DNA methyltransferase 1.	Proc. Amer. Assoc. Cancer Res.	2008	49		783			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. 		
@D	Bath, A.J.//Milsom, S.E.//Gormley, N.A.//Halford, S.E. 	Many type IIs restriction endonucleases interact with two recognition sites before cleaving DNA.	J. Biol. Chem.	2002	277		4024-4033			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. 		
@D	Batista, B.D.//Taniguti, L.M.//Almeida, J.R.//Azevedo, J.L.//Quecine, M.C. 	Draft Genome Sequence of Multitrait Plant Growth-Promoting Bacillus sp. Strain RZ2MS9.	Genome Announcements	2016	4		e01402-16			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. 		
@D	Batista, B.D.//Taniguti, L.M.//Monteiro-Vitorello, C.B.//Azevedo, J.L.//Quecine, M.C. 	Draft Genome Sequence of Burkholderia ambifaria RZ2MS16, a Plant Growth-Promoting Rhizobacterium Isolated from Guarana, a Tropical Plant.	Genome Announcements	2016	4		e00125-16			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. 		
@D	Batista, D.F.//Freitas, N.O.C.//Leite, L.R.//Varani, A.M.//Araujo, F.M.//Salim, A.//Almeida, A.M.//Ribeiro, S.A.//Oliveira, G.C.//Barrow, P.A.//Berchieri, J.A. 	Draft Genome Sequence of Salmonella enterica subsp. enterica Serovar Gallinarum Biovar Pullorum Strain FCAV198, a Brazilian Chicken Pathogen.	Genome Announcements	2014	2		e00028-14			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. 		
@D	Battisti, J.M.//Minnick, M.F. 	Development of a system for genetic manipulation of Bartonella bacilliformis.	Appl. Environ. Microbiol.	1999	65		3441-3448			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. 		
@D	Batzilla, J.//Hoper, D.//Antonenka, U.//Heesemann, J.//Rakin, A. 	Complete Genome Sequence of Yersinia enterocolitica subsp. palearctica Serogroup O:3.	J. Bacteriol.	2011	193		2067			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). 		
@D	Baubec, T.//Colombo, D.F.//Wirbelauer, C.//Schmidt, J.//Burger, L.//Krebs, A.R.//Akalin, A.//Schubeler, D. 	Genomic profiling of DNA methyltransferases reveals a role for DNMT3B in genic methylation.	Nature	2015	520		243-247			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. 		
@D	Baumgart, M. et al. 	Corynebacterium glutamicum chassis C1*: Building and testing a novel platform host for synthetic biology and industrial biotechnology.	ACS Synth. Biol.	2017	7		132-144			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. 		
@D	Baumgart, M.//Unthan, S.//Ruckert, C.//Sivalingam, J.//Grunberger, A.//Kalinowski, J.//Bott, M.//Noack, S.//Frunzke, J. 	Construction of a prophage-free variant of Corynebacterium glutamicum ATCC 13032 - a platform strain for basic research and industrial biotechnology.	Appl. Environ. Microbiol.	2013	79		6006-6015			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. 		
@D	Baumstark, B.R.//Roberts, R.J.//RajBhandary, U.L. 	Use of short synthetic DNA duplexes as substrates for the restriction endonucleases HpaII and MnoI.	J. Biol. Chem.	1979	254		8943-8950			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. 		
@D	Baxter, B.K.//Topal, M.D. 	Formation of a cleavasome: enhancer DNA-2 stabilizes an active conformation of NaeI dimer.	Biochemistry	1993	32		8291-8298			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. 		
@D	Baxter, S.//Lambert, A.R.//Kuhar, R.//Jarjour, J.//Kulshina, N.//Parmeggiani, F.//Danaher, P.//Gano, J.//Baker, D.//Stoddard, B.L.//Scharenberg, A.M. 	Engineering domain fusion chimeras from I-OnuI family LAGLIDADG homing endonucleases.	Nucleic Acids Res.	2012	40		7985-8000			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. 		
@D	Bayliss, C.D.//Bidmos, F.A.//Anjum, A.//Manchev, V.T.//Richards, R.L.//Grossier, J.P.//Wooldridge, K.G.//Ketley, J.M.//Barrow, P.A.//Jones, M.A.//Tretyakov, M.V. 	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.	Nucleic Acids Res.	2012	40		5876-5889			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. 		
@D	Bayliss, C.D.//Callaghan, M.J.//Moxon, E.R. 	High allelic diversity in the methyltransferase gene of a phase variable type III restriction-modification system has implications for the fitness  of Haemophilus influenzae.	Nucleic Acids Res.	2006	34		4046-4059			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. 		
@D	Bayona-Bafaluy, M.P.//Blits, B.//Battersby, B.J.//Shoubridge, E.A.//Moraes, C.T. 	Rapid directional shift of mitochondrial DNA heteroplasmy in animal tissues by a mitochondrially targeted restriction endonuclease.	Proc. Natl. Acad. Sci. U. S. A.	2005	102		14392-14397			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. 		
@D	Bayot-Custodio, A.N.//Alcantara, E.P.//Zulaybar, T.O. 	Draft Genome Sequence of Insecticidal Streptomyces sp. Strain PCS3-D2, Isolated from Mangrove Soil in Philippines.	Genome Announcements	2014	2		e00448-14			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. 		
@D	Beaber, J.W.//Hochhut, B.//Waldor, M.K. 	Genomic and Functional Analyses of SXT, an Integrating Antibiotic Resistance Gene Transfer Element Derived from Vibrio cholerae.	J. Bacteriol.	2002	184		4259-4269			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. 		
@D	Bean, D.C.//Wigmore, S.M.//Wareham, D.W. 	Draft Genome Sequence of a Canine Isolate of Methicillin-Resistant Staphylococcus haemolyticus.	Genome Announcements	2017	5		e00146-17			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. 		
@D	Bean, D.C.//Wigmore, S.M.//Wareham, D.W. 	Draft Genome Sequence of Staphylococcus cohnii subsp. urealyticus Isolated from a Healthy Dog.	Genome Announcements	2017	5		e01628-16			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. 		
@D	Beare, P.A.//Jeffrey, B.M.//Martens, C.A.//Heinzen, R.A. 	Draft Genome Sequences of Three Coxiella burnetii Strains Isolated from Q Fever Patients.	Genome Announcements	2017	5		e00986-17			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. 		
@D	Beare, P.A.//Jeffrey, B.M.//Martens, C.A.//Heinzen, R.A. 	Draft Genome Sequences of the Avirulent Coxiella burnetii Dugway 7D77-80 and Dugway 7E65-68 Strains Isolated from Rodents in Dugway, Utah.	Genome Announcements	2017	5		e00984-17			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. 		
@D	Beare, P.A.//Jeffrey, B.M.//Martens, C.A.//Pearson, T.//Heinzen, R.A. 	Draft Genome Sequences of Historical Strains of Coxiella burnetii Isolated from Cow's Milk and a Goat Placenta.	Genome Announcements	2017	5		e00985-17			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. 		
@D	Beary, T.P.//Braymer, H.D.//Achberger, E.C. 	Evidence of participation of McrBs in McrBC restriction in Escherichia coli K-12.	J. Bacteriol.	1997	179		7768-7775			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. 		
@D	Beary, T.P.//Ross, T.K.//Braymer, H.D.//Achberger, E.C. 	Characterization of genes involved in the McrB restriction system of Escherichia coli K12.	Abstr. Gen. Meet. Am. Soc. Microbiol.	1989	89		180			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. 		
@D	Beatson, S.A. et al. 	Molecular analysis of the asymptomatic bacteriuria Escherichia coli strain VR50 reveals adaptation to the urinary tract by gene acquisition.	Infect. Immun.	2015	83		1749-1764			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. 		
@D	Beatson, S.A.//Das-Gracas-de-Luna, M.//Bachmann, N.L.//Alikhanm, N.F.//Hanksm, K.R.//Sullivanm, M.J.//Weem, B.A.//Freitas-Almeida, A.C.//Dos Santos, P.A.//de Melo, J.T.//Squire, D.J.//Cunningham, A.F.//Fitzgerald, J.R.//Henderson, I.R. 	Genome sequence of the emerging pathogen Aeromonas caviae.	J. Bacteriol.	2010	193		1286-1287			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. 		
@D	Beattie, K.L.//Wakil, A.E.//Driggers, P.H. 	Action of restriction endonucleases on transforming DNA of Haemophilus influenzae.	J. Bacteriol.	1982	152		332-337			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. 		
@D	Beaty, J.S.//Mclean-Bowen, C.A.//Brown, L.R. 	BvuI: a site-specific endonuclease from Bacillus vulgatis.	Gene	1982	18		61-67			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. 		
@D	Beauchamp, J.M.//Leveque, R.M.//Dawid, S.//DiRita, V.J. 	Methylation-dependent DNA discrimination in natural transformation of Campylobacter jejuni.	Proc. Natl. Acad. Sci. U. S. A.	2017	114		E8053-E8061			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. 		
@D	Beaulaurier, J.//Zhang, X.S.//Zhu, S.//Sebra, R.//Rosenbluh, C.//Deikus, G.//Shen, N.//Munera, D.//Waldor, M.K.//Chess, A.//Blaser, M.J.//Schadt, E.E.//Fang, G. 	Single molecule-level detection and long read-based phasing of epigenetic variations in bacterial methylomes.	Nat. Commun.	2015	6		7438			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. 		
@D	Beaulaurier, J.//Zhu, S.//Deikus, G.//Mogno, I.//Zhang, X.S.//Davis-Richardson, A.//Canepa, R.//Triplett, E.W.//Faith, J.J.//Sebra, R.//Schadt, E.E.//Fang, G. 	Metagenomic binning and association of plasmids with bacterial host genomes using DNA methylation.	Nat. Biotechnol.	2017	36		61-69			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. 		
@D	Beaulieu, N.//Morin, S.//Chute, I.C.//Robert, M.-F.//Nguyen, H.//MacLeod, A.R. 	An essential role for DNA methyltransferase DNMT3B in cancer cell survival.	J. Biol. Chem.	2002	277		28176-28181			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. 		
@D	Beck, C.//Cranz, S.//Solmaz, M.//Roth, M.//Jeltsch, A. 	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.	Biochemistry	2001	40		10956-10965			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. 		
@D	Beck, C.//Jeltsch, A. 	Probing the DNA interface of the EcoRV DNA-(adenine-N6)-methyltransferase by site-directed mutagenesis, fluorescence spectroscopy, and UV cross-linking.	Biochemistry	2002	41		14103-14110			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. 		
@D	Beck, M.H.//Poehlein, A.//Bengelsdorf, F.R.//Schiel-Bengelsdorf, B.//Daniel, R.//Durre, P. 	Draft Genome Sequence of the Strict Anaerobe Clostridium homopropionicum LuHBu1 (DSM 5847).	Genome Announcements	2015	3		e01112-15			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. 		
@D	Beck, M.H.//Poehlein, A.//Bengelsdorf, F.R.//Schiel-Bengelsdorf, B.//Daniel, R.//Durre, P. 	Draft Genome Sequence of the Strict Anaerobe Clostridium neopropionicum X4 (DSM 3847T).	Genome Announcements	2016	4		e00209-16			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). 		
@D	Beck, R.//Burtscher, H. 	Introduction of arbitrary sequences into genes by use of class IIs restriction enzymes.	Nucleic Acids Res.	1994	22		886-887			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. 		
@D	Becker, L.//Bunk, B.//Eller, C.//Steglich, M.//Pfeifer, Y.//Werner, G.//Nubel, U. 	Complete Genome Sequence of a CTX-M-15-Producing Klebsiella pneumoniae Outbreak Strain from Multilocus Sequence Type 514.	Genome Announcements	2015	3		e00742-15			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). 		
@D	Becker, M.M.//Lesser, D.//Kurpiewski, M.//Baranger, A.//Jen-Jacobson, L. 	Ultraviolet footprinting accurately maps sequence-specific contacts and DNA kinking in the EcoRI endonuclease-DNA complex.	Proc. Natl. Acad. Sci. U. S. A.	1988	85		6247-6251			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. 		
@D	Bedford, D.J.//Laity, C.//Buttner, M.J. 	Two genes involved in the phase-variable phi C31 resistance mechanism of Streptomyces coelicolor A3(2).	J. Bacteriol.	1995	177		4681-4689			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. 		
@D	Beer, H.D.//Maschke, H.E.//Schugerl, K. 	Continuous production of restriction endonucleases: continuous two-stage cultivation with E. coli JM103; continuous cell disintegration and purification by affinity chromatography.	Appl. Microbiol. Biotechnol.	1992	38		220-225			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. 		
@D	Begley, T.J.//Cunningham, R.P. 	Methanobacterium thermoformicicum thymine DNA mismatch glycosylase: conversion of an N-glycosylase to an AP lyase.	Protein Eng.	1999	12		333-340			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. 		
@D	Begley, T.J.//Haas, B.J.//Morales, J.C.//Kool, E.T.//Cunningham, R.P. 	Kinetics and binding of the tymine-DNA mismatch glycosylase, Mig-Mth, with mismatch-containing DNA substrates.	DNA Repair	2003	2		107-120			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. 		
@D	Behar, A.//McCormick, L.J.//Perlman, S.J. 	Rickettsia felis infection in a common household insect pest, Liposcelis bostrychophila (Psocoptera: Liposcelidae).	Appl. Environ. Microbiol.	2010	76		2280-2285			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. 		
@D	Behera, B.K.//Das, P.//Maharana, J.//Paria, P.//Mandal, S.N.//Meena, D.K.//Sharma, A.P.//Jayarajan, R.//Dixit, V.//Verma, A.//Vellarikkal, S.K.//Scaria, V.//Sivasubbu, S.//Rao, A.R.//Mohapatra, T. 	Draft Genome Sequence of the Extremely Halophilic Bacterium Halomonas salina Strain CIFRI1, Isolated from the East Coast of India.	Genome Announcements	2015	3		e01321-14			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. 		
@D	Behr, J.//Geissler, A.J.//Schmid, J.//Zehe, A.//Vogel, R.F. 	The Identification of Novel Diagnostic Marker Genes for the Detection of Beer Spoiling Pediococcus damnosus Strains Using the BlAst Diagnostic Gene findEr.	PLoS ONE	2016	11		E0152747			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. 		
@D	Behrens, B.//Noyer-Weidner, M.//Pawlek, B.//Lauster, R.//Balganesh, T.S.//Trautner, T.A. 	Organization of multispecific DNA methyltransferases encoded by temperate Bacillus subtilis phages.	EMBO J.	1987	6		1137-1142			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. 		
@D	Behrens, B.//Pawlek, B.//Morelli, G.//Trautner, T.A. 	Restriction and modification in Bacillus subtilis:  construction of hybrid lambda and SPP1 phages containing a DNA methyltransferase gene from B. subtilis phage SPR.	Mol. Gen. Genet.	1983	189		10-16			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. 		
@D	Behrens, W.//Bonig, T.//Suerbaum, S.//Josenhans, C. 	Genome Sequence of Helicobacter pylori hpEurope Strain N6.	J. Bacteriol.	2012	194		3725-3726			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. 		
@D	Beja, O.//Aravind, L.//Koonin, E.V.//Suzuki, M.T.//Hadd, A.//Nguyen, L.P.//Jovanovich, S.B.//Gates, C.M.//Feldman, R.A.//Spudich, J.L.//Spudich, E.N.//DeLong, E.F. 	Bacterial rhodopsin: evidence for a new type of phototrophy in the sea.	Science	2000	289		1902-1906			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. 		
@D	Bekal, S.//Lin, A.//Vincent, A.//Berry, C.//Gilmour, M.//Fournier, E.//Cote, J.C.//Tremblay, C. 	Draft Genome Sequence of a Necrotoxigenic Escherichia coli Isolate.	Genome Announcements	2015	3		e01152-15			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. 		
@D	Beker, M.//Rose, S.//Lykkebo, C.A.//Douthwaite, S. 	Integrative and Conjugative Elements (ICEs) in Pasteurellaceae Species and Their  Detection by Multiplex PCR.	Front. Microbiol.	2018	9		1329			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. 		
@D	Bekker, O.B.//Klimina, K.M.//Vatlin, A.A.//Zakharevich, N.V.//Kasianov, A.S.//Danilenko, V.N. 	Draft Genome Sequence of Streptomyces fradiae ATCC 19609, a Strain Highly Sensitive to Antibiotics.	Genome Announcements	2014	2		e01247-14			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. 		
@D	Belavin, P.A.//Dedkov, V.S.//Degtyarev, S.K. 	A simple technique for detection of restriction endonucleases in bacterial colonies.	Prikl. Biokhim. Mikrobiol.	1988	24		121-124			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. 		
@D	Belavin, P.A.//Gorbunov, Y.A.//Malygin, E.G.//Rechkunova, N.I.//Degtyarev, S.K. 	Substrate specificity of DNA methylase from Flavobacterium okeanokoites.	Bioorg. Khim.	1989	15		417-418			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. 		
@D	Belbahri, L.//Alenezi, F.N.//Luptakova, L.//Rateb, M.E.//Woodward, S. 	Complete Genome Sequence of Aneurinibacillus migulanus E1, a Gramicidin S- and d-Phenylalanyl-l-Propyl Diketopiperazine-Deficient Mutant.	Genome Announcements	2015	3		e01441-15			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. 		
@D	Belcaid, M.//Kang, Y.//Tuanyok, A.//Hoang, T.T. 	Complete Genome Sequence of Burkholderia cepacia Strain LO6.	Genome Announcements	2015	3		e00587-15			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. 		
@D	Belduz, A.O.//Canakci, S.//Chan, K.G.//Kahar, U.M.//Chan, C.S.//Yaakop, A.S.//Goh, K.M. 	Genome sequence of Anoxybacillus ayderensis AB04(T) isolated from the Ayder hot spring in Turkey.	Standards in Genomic Sciences	2015	10		70			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. 		
@D	Beletskaya, I.V.//Zakharova, M.V.//Shlyapnikov, M.G.//Semenova, L.M.//Solonin, A.S. 	DNA methylation at the CfrBI site is involved in expression control in the CfrBI restriction-modification system.	Nucleic Acids Res.	2000	28		3817-3822			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. 		
@D	Beletskii, A.//Bhagwat, A.S. 	Transcription-induced mutations: increase in C to T mutations in the nontranscribed strand during transcription in Escherichia coli.	Proc. Natl. Acad. Sci. U. S. A.	1996	93		13919-13924			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. 		
@D	Belfort, M. 	Two for the price of one: a bifunctional intron-encoded DNA endonuclease-RNA maturase.	Genes Dev.	2003	17		2860-2863			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. 		
@A	Belfort, M. 		Back to Basics: Structure, function, evolution and application of homing endonucleases and inteins.			Belfort, M. 		Nucleic Acids Mol. Biol.				Berlin Heidelberg	Springer-Verlag	2005		16		1-10									"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. 		
@D	Belfort, M.//Bonocora, R.P. 	Homing Endonucleases: From Genetic Anomalies to Programmable Genomic Clippers.	Methods Mol. Biol.	2014	1123		1-26			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. 		
@D	Belfort, M.//Edgell, D.//Shub, D.//Van Roey, P.//Derbyshire, V. 	A multicomponent, multifunctional intron endonuclease, I-TevI.	J. Biomol. Struct. Dyn.	2003	20		834-835			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. 		
@D	Belfort, M.//Perlman, P.S. 	Mechanisms of intron mobility.	J. Biol. Chem.	1995	270		30237-30240			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. 		
@D	Belfort, M.//Reaban, M.E.//Coetzee, T.//Dalgaard, J.Z. 	Prokaryotic introns and inteins: a panoply of form and function.	J. Bacteriol.	1995	177		3897-3903			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. 		
@D	Belfort, M.//Roberts, R.J. 	Homing endonucleases: keeping the house in order.	Nucleic Acids Res.	1997	25		3379-3388			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. 		
@D	Belfort, M.//Van Roey, P.//Derbyshire, V. 	Modular assembly of a multi-functional homing endonuclease.	J. Biomol. Struct. Dyn.	2005	22		809			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. 		
@D	Belguesmia, Y.//Leclere, V.//Duban, M.//Auclair, E.//Drider, D. 	Draft Genome Sequence of Enterococcus faecalis DD14, a Bacteriocinogenic Lactic Acid Bacterium with Anti-Clostridium Activity.	Genome Announcements	2017	5		e00695-17			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. 		
@D	Belinsky, S.A.//Nikula, K.J.//Baylin, S.B.//Issa, J.-P. 	A microassay for measuring cytosine DNA methyltransferase activity during tumor progression.	Toxicol. Lett.	1995	82		335-340			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. 		
@D	Belinsky, S.A.//Nikula, K.J.//Baylin, S.B.//Issa, J.-P.J. 	Increased cytosine DNA-methyltransferase activity is target-cell-specific and an early event in lung cancer.	Proc. Natl. Acad. Sci. U. S. A.	1996	93		4045-4050			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. 		
@D	Belkebir, A.//Azeddoug, H. 	Purification and characterization of SepII a new restriction endonuclease from Staphylococcus epidermidis.	Microbiol. Res.	2012	167		90-94			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. 		
@D	Belkebir, A.//Azeddoug, H. 	Metal ion dependence of DNA cleavage by SepMI and EhoI restriction endonucleases.	Microbiol. Res.	2013	168		99-105			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. 		
@D	Belkhelfa, S.//Labadie, K.//Cruaud, C.//Aury, J.M.//Roche, D.//Bouzon, M.//Salanoubat, M.//Doring, V. 	Complete Genome Sequence of the Facultative Methylotroph Methylobacterium extorquens TK 0001 Isolated from Soil in Poland.	Genome Announcements	2018	6		e00018-18			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. 		
@D	Bell, D.C.//Cupples, C.G. 	Very-Short-Patch Repair in Escherichia coli Requires the dam Adenine Methylase.	J. Bacteriol.	2001	183		3631-3635			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. 		
@D	Bell, K.S. et al. 	Genome sequence of the enterobacterial phytopathogen Erwinia carotovora subsp. atroseptica and characterization of virulence factors.	Proc. Natl. Acad. Sci. U. S. A.	2004	101		11105-11110			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. 		
@D	Bell-Pedersen, D.//Quirk, S.//Clyman, J.//Belfort, M. 	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.	Nucleic Acids Res.	1990	18		3763-3770			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. 		
@D	Bell-Pedersen, D.//Quirk, S.M.//Aubrey, M.//Belfort, M. 	A site-secific endonuclease and co-conversion of flanking exons associated with the mobile td intron of phage T4.	Gene	1989	82		119-126			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. 		
@D	Bell-Pedersen, D.//Quirk, S.M.//Bryk, M.//Belfort, M. 	I-TevI, the endonuclease encoded by the mobile td intron, recognizes binding and cleavage domains on its DNA target.	Proc. Natl. Acad. Sci. U. S. A.	1991	88		7719-7723			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. 		
@D	Bellaiche, Y.//Mogila, V.//Perrimon, N. 	I-SceI endonuclease, a new tool for studying DNA double-strand break repair mechanisms in Drosophila.	Genetics	1999	152		1037-1044			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. 		
@D	Bellamy, S.R.//Kovacheva, Y.S.//Zulkipli, I.H.//Halford, S.E. 	Differences between Ca2+ and Mg2+ in DNA binding and release by the SfiI restriction endonuclease: implications for DNA looping.	Nucleic Acids Res.	2009	37		5443-5453			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+). 		
@D	Bellamy, S.R.//Milsom, S.E.//Kovacheva, Y.S.//Sessions, R.B.//Halford, S.E. 	A Switch in the Mechanism of Communication between the Two DNA-Binding Sites in the SfiI Restriction Endonuclease.	J. Mol. Biol.	2007	373		1169-1183			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. 		
@D	Bellamy, S.R.//Mina, P.//Retter, S.E.//Halford, S.E. 	Fidelity of DNA Sequence Recognition by the SfiI Restriction Endonuclease Is Determined by Communications between Its Two DNA-Binding Sites.	J. Mol. Biol.	2008	384		557-563			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. 		
@D	Bellamy, S.R.W.//Milsom, S.E.//Scott, D.J.//Daniels, L.E.//Wilson, G.G.//Halford, S.E. 	Cleavage of individual DNA strands by the different subunits of the heterodimeric restriction endonuclease BbvCI.	J. Mol. Biol.	2005	348		641-653			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. 		
@A	Belland, R.J.//Morrison, S.G.//Hogan, D. 		A phase-variable type III restriction-modification system in Neisseria gonorrhoeae.			Zollinger, W.D.//Frasch, C.E.//Deal, C.D. 		Abs. Tenth Int. Conf. Pathogenegic Neisseria				Baltimore, MD		1996		0		360-361									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). 		
@D	Bellemare, G.//Potvin, C. 	Classification of type-II restriction endonucleases and cloning of non-identical cohesive-end fragments without self-polymerization using nonpalindromic oligodeoxyribonucleotide adapters.	Gene	1991	101		67-74			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. 		
@D	Beller, H.R.//Chain, P.S.//Letain, T.E.//Chakicherla, A.//Larimer, F.W.//Richardson, P.M.//Coleman, M.A.//Wood, A.P.//Kelly, D.P. 	The genome sequence of the obligately chemolithoautotrophic, facultatively anaerobic bacterium Thiobacillus denitrificans.	J. Bacteriol.	2006	188		1473-1488			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. 		
@D	Bellgard, M.I.//Wanchanthuek, P.//La, T.//Ryan, K.//Moolhuijzen, P.//Albertyn, Z.//Shaban, B.//Motro, Y.//Dunn, D.S.//Schibeci, D.//Hunter, A.//Barrero, R.//Phillips, N.D.//Hampson, D.J. 	Genome sequence of the pathogenic intestinal spirochete brachyspira hyodysenteriae reveals adaptations to its lifestyle in the porcine large intestine.	PLoS ONE	2009	4		E4641			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. 		
@D	Bello-Akinosho, M.//Adeleke, R.//Swanevelder, D.//Thantsha, M. 	Draft Genome Sequence of Pseudomonas sp. Strain 10-1B, a Polycyclic Aromatic Hydrocarbon Degrader in Contaminated Soil.	Genome Announcements	2015	3		e00325-15			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. 		
@D	Bellon, B. 	Construction of restriction maps.	Comput. Appl. Biosci.	1988	4		111-116			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. 		
@D	Bellstein, F.//Dreiseikelmann, B. 	Temperate bacteriophage Phi O18P from an Aeromonas media isolate: Characterization and complete genome sequence.	Virology	2008	373		25-29			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. 		
@D	Belogurov, A.A.//Delver, E.P. 	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.	Nucleic Acids Res.	1995	23		785-787			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. 		
@D	Belogurov, A.A.//Delver, E.P.//Agafonova, O.V.//Belogurova, N.G.//Lee, L.Y.//Kado, C.I. 	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.	J. Mol. Biol.	2000	296		969-977			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. 		
@D	Belogurov, A.A.//Delver, E.P.//Rodzevich, O.V. 	Plasmid pKM101 encodes two nonhomologous antirestriction proteins (ArdA and ArdB) whose expression is controlled by homologous regulatory sequences.	J. Bacteriol.	1993	175		4843-4850			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. 		
@D	Belogurov, A.A.//Delver, E.P.//Rodzevich, O.V. 	IncN plasmid pKM101 and IncI1 Plasmid ColIb-P9 encode homologous antirestriction proteins in their leading regions.	J. Bacteriol.	1992	174		5079-5085			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. 		
@D	Belogurov, A.A.//Efimova, E.P.//Delver, E.P.//Zavilgelsky, G.B. 	Alleviation of type I restriction in Escherichia coli: Effect of 2-amino-purine and 5-bromouracil.	Mol. Gen. Mikrobiol. Virusol.	1987	12		34-40			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. 		
@D	Belogurov, A.A.//Efimova, E.P.//Delver, E.P.//Zavilgelsky, G.B. 	Alleviation of I type restriction in E. coli: Effect of a dam mutation.	Mol. Gen. Mikrobiol. Virusol.	1987	9		10-16			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. 		
@D	Belogurov, A.A.//Yussifov, T.N.//Kotova, V.U.//Zavilgelsky, G.B. 	The novel gene(s) ARD of plasmid pKM101: alleviation of EcoK restriction.	Mol. Gen. Genet.	1985	198		509-513			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. 		
@D	Belogurov, A.A.//Zavilgelskii, G.B. 	Effect of plasmid pKM101 on the K-specific restriction-modification of bacteriophage lambda DNA.	Dokl. Akad. Nauk.	1983	269		738-741					
@D	Belogurov, A.A.//Zavilgelsky, G.B. 	The repair of the interstrand cross links in DNA: Role of restriction system K.	Mol. Biol. (Mosk)	1979	13		160-168			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. 		
@D	Belova, T.S.//Surikov, N.N.//Prozorov, A.A. 	Transformation and transduction of Bacillus subtilis strains possessing the BsuR system of restriction-modification by nonmodified and modified plasmid pUB110 DNA.	Genetika	1981	17		794-800			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. 		
@D	Beltramo, C.//Oraby, M.//Bourel, G.//Garmyn, D.//Guzzo, J. 	A new vector, pGID052, for genetic transfer in Oenococcus oeni.	FEMS Microbiol. Lett.	2004	236		53-60			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. 		
@D	Ben Hania, W.//Fadhlaoui, K.//Brochier-Armanet, C.//Persillon, C.//Postec, A.//Hamdi, M.//Dolla, A.//Ollivier, B.//Fardeau, M.L.//Le Mer, J.//Erauso, G. 	Draft genome sequence of Mesotoga strain PhosAC3, a mesophilic member of the bacterial order Thermotogales, isolated from a digestor treating phosphogypsum in  Tunisia.	Standards in Genomic Sciences	2015	10		12			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. 		
@D	Ben Hania, W.//Joseph, M.//Schumann, P.//Bunk, B.//Fiebig, A.//Sproer, C.//Klenk, H.P.//Fardeau, M.L.//Spring, S. 	Complete genome sequence and description of Salinispira pacifica gen. nov., sp. nov., a novel spirochaete isolated form a hypersaline microbial mat.	Standards in Genomic Sciences	2015	10		7			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. 		
@D	Ben Zakour, N.L.//Bannoehr, J.//van den Broek, A.H.//Thoday, K.L.//Fitzgerald, J.R. 	Complete genome sequence of the canine pathogen Staphylococcus pseudintermedius.	J. Bacteriol.	2011	193		2363-2364			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. 		
@D	Ben-Hattar, J.//Jiricny, J. 	Effect of cytosine methylation on the cleavage of oligonucleotide duplexes with restriction endonucleases HpaII and MspI.	Nucleic Acids Res.	1988	16		4160			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. 		
@D	Benachour, A.//Frere, J.//Novel, G. 	pUCL287 plasmid from Tetragenococcus halophila (Pediococcus halophilus) ATCC 33315 represents a new theta-type replicon family of lactic acid bacteria.	FEMS Microbiol. Lett.	1995	128		167-175			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. 		
@D	Benahmed, F.H.//Gopinath, G.R.//Harbottle, H.//Cotta, M.A.//Luo, Y.//Henderson, C.//Teri, P.//Soppet, D.//Rasmussen, M.//Whitehead, T.R.//Davidson, M. 	Draft Genome Sequences of Streptococcus bovis Strains ATCC 33317 and JB1.	Genome Announcements	2014	2		e01012-14			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. 		
@D	Benahmed, F.H.//Gopinath, G.R.//Wang, H.//Jean-Gilles, B.J.//Grim, C.//Cheng, C.M.//McClelland, M.//Ayers, S.//Abbott, J.//Desai, P.//Frye, J.G.//Weinstock, G.//Hammack, T.S.//Hanes, D.E.//Rasmussen, M.A.//Davidson, M.K. 	Whole-Genome Sequencing of Salmonella enterica subsp. enterica Serovar Cubana Strains Isolated from Agricultural Sources.	Genome Announcements	2014	2		e01184-13			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. 		
@D	Benamar, S.//Cassir, N.//Caputo, A.//Cadoret, F.//La Scola, B. 	Complete Genome Sequence of Clostridium septicum Strain CSUR P1044, Isolated from the Human Gut Microbiota.	Genome Announcements	2016	4		e00922-16			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. 		
@D	Benamar, S.//Cassir, N.//La Scola, B. 	Genome Sequence of a Clostridium neonatale Strain Isolated in a Canadian Neonatal Intensive Care Unit.	Genome Announcements	2016	4		e01431-15			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. 		
@D	Benamar, S.//La Scola, B.//Croce, O. 	Genome Sequence of Afipia felis Strain 76713, Isolated in Hospital Water Using an Amoeba Co-Culture Procedure.	Genome Announcements	2014	2		e01367-14			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. 		
@D	Benbadis, L.//Faelen, M.//Slos, P.//Fazel, A.//Mercenier, A. 	Characterization and comparison of virulent bacteriophages of Streptococcus thermophilus isolated from yogurt.	Biochimie	1990	72		855-862			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. 		
@D	Benbadis, L.//Garel, J.R.//Hartley, D.L. 	Purification, properties, and sequence specificity of SslI, a new type II restriction endonuclease from Streptococcus salivarius subsp. thermophilus.	Appl. Environ. Microbiol.	1991	57		3677-3678			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. 		
@D	Bench, S.R.//Hanson, T.E.//Williamson, K.E.//Ghosh, D.//Radosovich, M.//Wang, K.//Wommack, K.E. 	Metagenomic characterization of Chesapeake Bay virioplankton.	Appl. Environ. Microbiol.	2007	73		7629-7641			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. 		
@D	Bendall, M.L.//Luong, K.//Wetmore, K.M.//Blow, M.//Korlach, J.//Deutschbauer, A.//Malmstrom, R.R. 	Exploring the roles of DNA methylation in the metal-reducing bacterium Shewanella oneidensis MR-1.	J. Bacteriol.	2013	195		4966-4974			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. 		
@D	Bender, J. 	A vicious cycle: RNA silencing and DNA methylation in plants.	Cell	2001	106		129-132			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. 		
@D	Bender, J.K.//Fiedler, S.//Klare, I.//Werner, G. 	Complete Genome Sequence of the Gut Commensal and Laboratory Strain Enterococcus faecium 64/3.	Genome Announcements	2015	3		e01275-15			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. 		
@D	Bendiks, Z.A.//Lang, J.M.//Darling, A.E.//Eisen, J.A.//Coil, D.A. 	Draft Genome Sequence of Microbacterium sp. Strain UCD-TDU (Phylum Actinobacteria).	Genome Announcements	2013	1		e0012013			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. 		
@D	Bendjama, E.//Loucif, L.//Diene, S.M.//Michelle, C.//Gacemi-Kirane, D.//Rolain, J.M. 	Non-contiguous finished genome sequence and description of Paucisalibacillus algeriensis sp. nov.	Standards in Genomic Sciences	2014	9		1352-1365			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. 		
@D	Bendjama, E.//Loucif, L.//Diene, S.M.//Michelle, C.//Gacemi-Kirane, D.//Rolain, J.M. 	Non-contiguous finished genome sequence and description of Bacillus massilioalgeriensis sp. nov.	Standards in Genomic Sciences	2014	9		1046-1061			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. 		
@D	Beneduzi, A.//Campos, S.//Ambrosini, A.//de Souza, R.//Granada, C.//Costa, P.//Arruda, L.//Moreira, F.//Vargas, L.K.//Weiss, V.//Tieppo, E.//Faoro, H.//de Souza, E.M.//Pedrosa, F.O.//Passaglia, L.M. 	Genome Sequence of the Diazotrophic Gram-Positive Rhizobacterium Paenibacillus riograndensis SBR5T.	J. Bacteriol.	2011	193		6391-6392			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. 		
@D	Benetti, R.//Gonzalo, S.//Jaco, I.//Munoz, P.//Gonzalez, S.//Schoeftner, S.//Murchison, E.//Andl, T.//Chen, T.//Klatt, P.//Li, E.//Serrano, M.//Millar, S.//Hannon, G.//Blasco, M.A. 	A mammalian microRNA cluster controls DNA methylation and telomere recombination via Rbl2-dependent regulation of DNA methyltransferases (vol 15, pg 268, 2008).	Nat. Struct. Mol. Biol.	2008	15		998			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. 		
@D	Benevides, L.J. et al. 	Genome Sequence of Corynebacterium ulcerans Strain FRC11.	Genome Announcements	2015	3		e00112-15			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. 		
@D	Bengelsdorf, F.R.//Poehlein, A.//Esser, C.//Schiel-Bengelsdorf, B.//Daniel, R.//Durre, P. 	Complete Genome Sequence of the Acetogenic Bacterium Moorella thermoacetica DSM 2955T.	Genome Announcements	2015	3		e01157-15			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). 		
@D	Bengelsdorf, F.R.//Poehlein, A.//Schiel-Bengelsdorf, B.//Daniel, R.//Durre, P. 	Genome Sequence of the Acetogenic Bacterium Butyribacterium methylotrophicum DSM  3468T.	Genome Announcements	2016	4		e01338-16			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. 		
@D	Bengelsdorf, F.R.//Poehlein, A.//Schiel-Bengelsdorf, B.//Daniel, R.//Durre, P. 	Genome Sequence of the Acetogenic Bacterium Oxobacter pfennigii DSM 3222T.	Genome Announcements	2015	3		e01408-15			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. 		
@A	Benight, A.S.//Gallo, F.J.//Paner, T.M.//Bishop, K.D.//Faldasz, B.D.//Lane, M.J. 		Sequence context and DNA reactivity: Application to sequence-specific cleavage of DNA.			Bush, C.A. 		Adv. Biophys. Chem.					JAI Press, Inc.	1995		5		1-55									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. 		
@D	Benkovic, S.J.//Baker, S.J.//Alley, M.R.K.//Woo, Y.H.//Zhang, Y.K.//Akama, T.//Mao, W.M.//Baboval, J.//Rajagopalan, P.T.R.//Wall, M.//Kahng, L.S.//Tavassoli, A.//Shapiro, L. 	Identification of borinic esters as inhibitors of bacterial cell growth and bacterial methyltransferases, CcrM and MenH.	J. Med. Chem.	2005	48		7468-7476			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. 		
@D	Bennett, G.M.//Abba, S.//Kube, M.//Marzachi, C. 	Complete Genome Sequences of the Obligate Symbionts 'Candidatus Sulcia muelleri'  and 'Ca. Nasuia deltocephalinicola' from the Pestiferous Leafhopper Macrosteles  quadripunctulatus (Hemiptera: Cicadellidae).	Genome Announcements	2016	4		e01604-15			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. 		
@D	Bennett, S.P. 	Restriction enzymes with asymmetrical recognition sites.	Diss. Abstr.	1988	49		722B			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. 		
@D	Bennett, S.P. 	Restriction enzymes with asymmetrical recognition sites.	Ph.D. Thesis, University of Bristol, UK	1987			1-196			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. 		
@D	Bennett, S.P.//Halford, S.E. 	Cytosine: cytosine formed in duplex DNA by the ligation of NciI- or CauII-cleaved DNA.	Biochem. Soc. Trans.	1986	14		259			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. 		
@D	Bennett, S.P.//Halford, S.E. 	Recognition of DNA by Type II restriction enzymes.	Curr. Top. Cell. Regul.	1989	30		57-104			A review 		
@A	Bennett, S.P.//Halford, S.E. 		Mechanism and specificity of two restriction enzymes, CauI and CauII, that recognize asymmetrical DNA sequences.			Guschlbauer, W.//Saenger, W. 		DNA-ligand interactions: from drugs to proteins.				New York	Plenum Press	1987				239-250									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. 		
@D	Bennke, C.M.//Kruger, K.//Kappelmann, L.//Huang, S.//Gobet, A.//Schuler, M.//Barbe, V.//Fuchs, B.M.//Michel, G.//Teeling, H.//Amann, R.I. 	Polysaccharide utilisation loci of Bacteroidetes from two contrasting open ocean sites in the North Atlantic.	Environ. Microbiol.	2016	18		4456-4470			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. 		
@D	Benomar, N.//Abriouel, H.//Lee, H.//Cho, G.S.//Huch, M.//Pulido, R.P.//Holzapfel, W.H.//Galvez, A.//Franz, C.M. 	Genome Sequence of Weissella thailandensis fsh4-2.	J. Bacteriol.	2011	193		5868			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. 		
@D	Bens, C.C.//Voss, A.//Klaassen, C.H. 	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.	J. Clin. Microbiol.	2006	44		1875-1876			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. 		
@D	Benson, M.A.//Ohneck, E.A.//Ryan, C.//Alonzo, F. III//Smith, H.//Narechania, A.//Kolokotronis, S.O.//Satola, S.W.//Uhlemann, A.C.//Sebra, R.//Deikus, G.//Shopsin, B.//Planet, P.J.//Torres, V.J. 	Evolution of hypervirulence by a MRSA clone through acquisition of a transposable element.	Mol. Microbiol.	2014	93		664-681			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. 		
@D	Bentley, S.D. et al. 	Complete genome sequence of the model actinomycete Streptomyces coelicolor A3(2).	Nature	2002	417		141-147			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. 		
@D	Bentley, S.D. et al. 	Sequencing and analysis of the genome of the Whipple's disease bacterium Tropheryma whipplei.	Lancet	2003	361		637-644			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. 		
@D	Bentzon-Tilia, M.//Riemann, L.//Gram, L. 	Draft Genome Sequence of Hoeflea sp. Strain BAL378, a Potential Producer of Bioactive Compounds.	Genome Announcements	2014	2		e01213-14			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. 		
@D	Benzinger, R. 	Restriction of infectious bacteriophage fd DNA's and an assay for in vitro host-controlled restriction and modification.	Proc. Natl. Acad. Sci. U. S. A.	1968	59		1294-1299			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. 		
@D	Bera, A.K.//Das, B.//Chattopadhyay, S.//Dasgupta, C. 	Refolding of denatured restriction endonucleases with ribosomal preparations from Methanosarcina barkeri.	Biochem. Mol. Biol. Int.	1994	32		315-323			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. 		
@D	Berben, T.//Sorokin, D.Y.//Ivanova, N.//Pati, A.//Kyrpides, N.//Goodwin, L.A.//Woyke, T.//Muyzer, G. 	Complete genome sequence of type strain ARh 1, an obligately chemolithoautotrophic haloalkaliphilic sulfur-oxidizing bacterium isolated from a  Kenyan soda lake.	Standards in Genomic Sciences	2015	10		105			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. 		
@D	Berben, T.//Sorokin, D.Y.//Ivanova, N.//Pati, A.//Kyrpides, N.//Goodwin, L.A.//Woyke, T.//Muyzer, G. 	Partial genome sequence of the haloalkaliphilic soda lake bacterium Thioalkalivibrio thiocyanoxidans ARh 2(T).	Standards in Genomic Sciences	2015	10		85			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. 		
@D	Berben, T.//Sorokin, D.Y.//Ivanova, N.//Pati, A.//Kyrpides, N.//Goodwin, L.A.//Woyke, T.//Muyzer, G. 	Partial genome sequence of Thioalkalivibrio thiocyanodenitrificans ARhD 1(T), a chemolithoautotrophic haloalkaliphilic sulfur-oxidizing bacterium capable of  complete denitrification.	Standards in Genomic Sciences	2015	10		84			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. 		
@D	Berdis, A.J.//Lee, I.//Coward, J.K.//Stephens, C.//Wright, R.//Shapiro, L.//Benkovic, S.J. 	A cell cycle-regulated adenine DNA methyltransferase from Caulobacter crescentus processively methylates GANTC sites on hemimethylated DNA.	Proc. Natl. Acad. Sci. U. S. A.	1998	95		2874-2879			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. 		
@D	Berendsen, E.M.//Wells-Bennik, M.H.//Krawczyk, A.O.//de Jong, A.//van Heel, A.//Eijlander, R.T.//Kuipers, O.P. 	Draft Genome Sequences of 10 Bacillus subtilis Strains That Form Spores with High or Low Heat Resistance.	Genome Announcements	2016	4		e00124-16			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. 		
@D	Berendsen, E.M.//Wells-Bennik, M.H.//Krawczyk, A.O.//de Jong, A.//van Heel, A.//Holsappel, S.//Eijlander, R.T.//Kuipers, O.P. 	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.	Genome Announcements	2016	4		e00105-16			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. 		
@D	Berenger, B.//Chen, J.//Bernier, A.M.//Bernard, K. 	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.	Genome Announcements	2016	4		e01442-16			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. 		
@D	Berent, L.M.//Messick, J.B. 	Physical Map and Genome Sequencing Survey of Mycoplasma haemofelis (Haemobartonella felis).	Infect. Immun.	2003	71		3657-3662			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. 		
@D	Beres, S.B.//Richter, E.W.//Nagiec, M.J.//Sumby, P.//Porcella, S.F.//DeLeo, F.R.//Musser, J.M. 	Molecular genetic anatomy of inter- and intraserotype variation in the human bacterial pathogen group A Streptococcus.	Proc. Natl. Acad. Sci. U. S. A.	2006	103		7059-7064			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. 		
@D	Beres, S.B.//Sesso, R.//Pinto, S.W.//Hoe, N.P.//Porcella, S.F.//Deleo, F.R.//Musser, J.M. 	Genome sequence of a Lancefield group C Streptococcus zooepidemicus strain causing epidemic nephritis: new information about an old disease.	PLoS ONE	2008	3		E3026			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. 		
@D	Beres, S.B.//Sylva, G.L.//Barbian, K.D.//Lei, B.//Hoff, J.S.//Mammarella, N.D.//Liu, M.-Y.//Smoot, J.C.//Porcella, S.F.//Parkins, L.D.//Campbell, D.S.//Smith, T.M.//McCormick, J.K.//Leung, D.Y.M.//Schlievert, P.M.//Musser, J.M. 	Genome sequence of a serotype M3 strain of group A Streptococcus: Phage-encoded toxins, the high-virulence phenotype, and clone emergence.	Proc. Natl. Acad. Sci. U. S. A.	2002	99		10078-10083			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. 		
@D	Berg, D.E.//Hoffman, P.S.//Appelmelk, B.J.//Kusters, J.G. 	The Helicobacter pylori genome sequence: genetic factors for long life in the gastric mucosa.	Trends Microbiol.	1997	5		468-474			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. 		
@D	Berg-Miller, M.E.//Antonopoulos, D.A.//Rincon, M.T.//Band, M.//Bari, A.//Akraiko, T.//Hernandez, A.//Thimmapuram, J.//Henrissat, B.//Coutinho, P.M.//Borovok, I.//Jindou, S.//Lamed, R.//Flint, H.J.//Bayer, E.A.//White, B.A. 	Diversity and strain specificity of plant cell wall degrading enzymes revealed by the draft genome of Ruminococcus flavefaciens FD-1.	PLoS ONE	2009	4		E6650			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. 		
@D	Berg-Miller, M.E.//Yeoman, C.J.//Chia, N.//Tringe, S.G.//Angly, F.E.//Edwards, R.A.//Flint, H.J.//Lamed, R.//Bayer, E.A.//White, B.A. 	Phage-bacteria relationships and CRISPR elements revealed by a metagenomic survey of the rumen microbiome.	Environ. Microbiol.	2012	14		207-227			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. 		
@D	Berge, T.//Ellis, D.J.//Dryden, D.T.F.//Edwardson, J.M.//Henderson, R.M. 	Translocation-independent dimerization of the EcoKI endonuclease visualized by atomic force microscopy.	Biophys. J.	2000	79		479-484			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. 		
@D	Bergemann, A.D.//Whitley, J.C.//Finch, L.R. 	Taxonomic significance of differences in DNA methylation within the Mycoplasma mycoides cluster' detected with restriction endonucleases MboI and DpnI.	Lett. Appl. Microbiol.	1990	11		48-51			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. 		
@D	Berger, S.//Alauzet, C.//Aissa, N.//Henard, S.//Rabaud, C.//Bonnet, R.//Lozniewski, A. 	Characterization of a new blaOXA-48-carrying Plasmid in Enterobacteriaceae.	Antimicrob. Agents Chemother.	2013	57		4064-4067			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. 		
@D	Berger, S.//Frank, J.//Dalcin, M.P.//Jetten, M.S.M.//Welte, C.U. 	High-Quality Draft Genome Sequence of 'Candidatus Methanoperedens sp.' Strain BLZ2, a Nitrate-Reducing Anaerobic Methane-Oxidizing Archaeon Enriched in an  Anoxic Bioreactor.	Genome Announcements	2017	5		e01159-17			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. 		
@D	Berger, S.L. 	Expanding the potential of restriction endonucleases: Use of hapaxoterministic enzymes.	Anal. Biochem.	1994	222		1-8			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. 		
@D	Berger, S.L. 	Gene modification with hapaxoterministic restriction enzymes.	Methods Mol. Biol.	2001	160		443-458			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. 		
@D	Bergerat, A.//Guschlbauer, W. 	The double role of methyl donor and allosteric effector of S-adenosyl-methionine for Dam methylase of E. coli.	Nucleic Acids Res.	1990	18		4369-4375			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. 		
@D	Bergerat, A.//Guschlbauer, W.//Fazakerley, G.V. 	Allosteric and catalytic binding of S-adenosylmethionine to Escherichia coli DNA adenine methyltransferase monitored by 3H NMR.	Proc. Natl. Acad. Sci. U. S. A.	1991	88		6394-6397			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. 		
@D	Bergerat, A.//Kriebardis, A.//Guschlbauer, W. 	Preferential site-specific hemimethylation of GATC sites in pBR322 DNA by dam methyltransferase from Escherichia coli.	J. Biol. Chem.	1989	264		4064-4070			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. 		
@D	Bergez, P.//Doignon, F.//Crouzet, M. 	The sequence of a 44,420 bp fragment located on the left arm of chromosome XIV from Saccharomyces cerevisiae.	Yeast	1995	11		967-974			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. 		
@D	Berglund, E.C.//Frank, A.C.//Calteau, A.//Vinnere, P.O.//Granberg, F.//Eriksson, A.S.//Naslund, K.//Holmberg, M.//Lindroos, H.//Andersson, S.G. 	Run-off Replication of Host-Adaptability Genes is Associated with Gene Transfer Agents in the Genome of Mouse-Infecting Bartonella grahamii.	PLoS Genet.	2009	5		e1000546			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. 		
@D	Bergman, Y.//Mostoslavsky, R. 	DNA demethylation: Turning genes on.	Biol. Chem.	1998	379		401-407			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. 		
@D	Bergottini, V.M.//Filippidou, S.//Junier, T.//Johnson, S.//Chain, P.S.//Otegui, M.B.//Zapata, P.D.//Junier, P. 	Genome Sequence of Kosakonia radicincitans Strain YD4, a Plant Growth-Promoting Rhizobacterium Isolated from Yerba Mate (Ilex paraguariensis St. Hill.).	Genome Announcements	2015	3		e00239-15			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. 		
@D	Bergsveinson, J.//Pittet, V.//Ewen, E.//Baecker, N.//Ziola, B. 	Genome Sequence of Rapid Beer-Spoiling Isolate Lactobacillus brevis BSO 464.	Genome Announcements	2015	3		e01411-15			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. 		
@D	Bergsveinson, J.//Thomson, E.//Jacoby, D.//Coady, Y.//Ziola, B. 	Genome Sequence of Megasphaera cerevisiae NSB1, a Bacterium Isolated from a Canning Line and Able To Grow in Beer with High Alcohol Content.	Genome Announcements	2017	5		e01686-16			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. 		
@D	Berkhout, B.//van Wamel, J. 	Accurate scanning of the BssHII endonuclease in search for its DNA cleavage site.	J. Biol. Chem.	1996	271		1837-1840			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. 		
@D	Berkner, K.L.//Folk, W.R. 	The effects of substituted pyrimidines in DNAs on cleavage by sequence-specific endonucleases.	J. Biol. Chem.	1979	254		2551-2560			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. 		
@D	Berkner, K.L.//Folk, W.R. 	Overmethylation of DNAs by the EcoRI methylase.	Nucleic Acids Res.	1978	5		435-450			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. 		
@D	Berkner, K.L.//Folk, W.R. 	EcoRI cleavage and methylation of DNAs containing modified pyrimidines in the recognition sequence.	J. Biol. Chem.	1977	252		3185-3193			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. 		
@D	Berkner, K.L.//Folk, W.R. 	Quantitation of the various termini generated by Type II restriction endonucleases using the polynucleotide kinase exchange reaction.	J. Biol. Chem.	1979	254		2561-2564			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. 		
@D	Berkner, K.L.//Folk, W.R. 	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.	Anal. Biochem.	1983	129		446-456			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. 		
@D	Berkyurek, A.C.//Suetake, I.//Arita, K.//Takeshita, K.//Nakagawa, A.//Shirakawa, M.//Tajima, S. 	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.	J. Biol. Chem.	2014	289		379-386			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. 		
@D	Berland, J.L.//de Carvalho, F.M.//de Almeida, L.G.//Bablishvili, N.//Gauthier, M.//Paranhos-Baccala, G.//de Vasconcelos, A.T. 	Draft Genome Sequence of Mycobacterium tuberculosis Clinical Strain G-12-005.	Genome Announcements	2014	2		e00385-14			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. 		
@D	Berlin, Y.A.//Butkus, V.V. 	Synthesis of oligodeoxynucleotides containing the sequence GGTACC and their interaction with KpnI restriction endonuclease.	Bioorg. Khim.	1981	7		1224-1232			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. 		
@D	Berna, L.//Iraola, G.//Greif, G.//Coitinho, C.//Rivas, C.M.//Naya, H.//Robello, C. 	Whole-Genome Sequencing of an Isoniazid-Resistant Clinical Isolate of Mycobacterium tuberculosis Strain MtURU-002 from Uruguay.	Genome Announcements	2014	2		e00655-14			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. 		
@D	Bernacchia, G.//Para, A.//Pedrali-Noy, G.//Cella, R. 	Isolation of a cDNA coding for DNA (cytosine-5)-methyltransferase (Accession No. AJ002140) from Lycopersicon esculentum.	Plant Physiol.	1998	116		446					
@D	Bernacchia, G.//Primo, A.//Giorgetti, L.//Pitto, L.//Cella, R. 	Carrot DNA-methyltransferase is encoded by two classes of genes with differing patterns of expression.	Plant J.	1998	13		317-329			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. 		
@D	Bernal, J.F.//Donado-Godoy, P.//Arevalo, A.//Duarte, C.//Realpe, M.E.//Diaz, P.L.//Gomez, Y.//Rodriguez, F.//Agarwala, R.//Landsman, D.//Marino-Ramirez, L. 	Whole-Genome Sequence of Multidrug-Resistant Campylobacter coli Strain COL B1-266, Isolated from the Colombian Poultry Chain.	Genome Announcements	2016	4		e00130-16			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. 		
@D	Bernal, J.F.//Donado-Godoy, P.//Valencia, M.F.//Leon, M.//Gomez, Y.//Rodriguez, F.//Agarwala, R.//Landsman, D.//Marino-Ramirez, L. 	Whole-Genome Sequences of Two Campylobacter coli Isolates from the Antimicrobial  Resistance Monitoring Program in Colombia.	Genome Announcements	2016	4		e00131-16			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. 		
@D	Bernal, W.M.//Raven, N.D.H.//Williams, R.A.D. 	Restriction endonuclease from Thermus ruber.	Proceedings 14th Int. Congress Microbiol.	1986	0		204			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. 		
@D	Bernal-Bayard, J.//Gomez-Valero, L.//Wessel, A.//Khanna, V.//Bouchier, C.//Ghigo, J.M. 	Short genome report of cellulose-producing commensal Escherichia coli 1094.	Standards in Genomic Sciences	2018	13		13			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. 		
@D	Bernan, V.//Sznyter, L.A.//Vaccaro, C.M.//Jager-Quinton, T.//Wilson, G.//Brooks, J.E. 	Cloning and characterization of the SphI restriction-modification system from S. phaeochromogenes.	Abstr. Gen. Meet. Am. Soc. Microbiol.	1989	89		206			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. 		
@D	Berndt, C.//Meier, P.//Wackernagel, W. 	DNA restriction is a barrier to natural transformation in Pseudomonas stutzeri JM300.	Microbiology	2003	149		895-901			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. 		
@D	Bernick, D.L.//Karplus, K.//Lui, L.M.//Coker, J.K.//Murphy, J.N.//Chan, P.P.//Cozen, A.E.//Lowe, T.M. 	Complete genome sequence of Pyrobaculum oguniense.	Standards in Genomic Sciences	2012	6		336-345			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. 		
@D	Bernier, A.M.//Bernard, K. 	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.	Genome Announcements	2016	4		e00989-16			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. 		
@D	Bernier, A.M.//Bernard, K. 	Draft Genome Sequence of Trueperella bernardiae LCDC 89-0504T, Isolated from a Human Blood Culture.	Genome Announcements	2016	4		e01634-15			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. 		
@D	Bernier, A.M.//Bernard, K. 	Draft Genome Sequence for the Type Strain of Corynebacterium afermentans LCDC 88-0199T, Isolated from a Human Blood Culture.	Genome Announcements	2016	4		e00661-16			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. 		
@D	Bernier, A.M.//Peters, G.A.//Bernard, K. 	Whole-Genome Sequences of Four Corynebacterium CDC Group F-1 Strains Isolated from Urine.	Genome Announcements	2017	5		e01537-16			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%. 		
@D	Bernstein, R.L.//Dharmgrongartama, B.//Srinivasan, P.R. 	Altered P2 bacteriophage restriction in E. coli B.	Fed. Proc.	1970	29		860			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. 		
@D	Bertalan, M. et al. 	Complete genome sequence of the sugarcane nitrogen-fixing endophyte Gluconacetobacter diazotrophicus Pal5.	BMC Genomics	2009	10		450			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. 		
@D	Bertani, G.//Bassi, D.//Gatti, M.//Cocconcelli, P.S.//Neviani, E. 	Draft Genome Sequence of Lactobacillus helveticus Strain Lh 12 Isolated from Natural Whey Starter.	Genome Announcements	2018	6		e00139-18			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. 		
@D	Bertani, G.//Weigle, J.J. 	Host controlled variation in bacterial viruses.	J. Bacteriol.	1953	65		113-121			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). 		
@D	Bertani, I.//Passos-da-Silva, D.//Abbruscato, P.//Piffanelli, P.//Venturi, V. 	Draft Genome Sequence of the Plant Pathogen Dickeya zeae DZ2Q, Isolated from Rice in Italy.	Genome Announcements	2013	1		e00905-13			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. 		
@D	Bertelli, C.//Collyn, F.//Croxatto, A.//Ruckert, C.//Polkinghorne, A.//Kebbi-Beghdadi, C.//Goesmann, A.//Vaughan, L.//Greub, G. 	The Waddlia Genome: A Window into Chlamydial Biology.	PLoS ONE	2010	5		e10890			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. 		
@D	Bertelli, C.//Goesmann, A.//Greub, G. 	Criblamydia sequanensis Harbors a Megaplasmid Encoding Arsenite Resistance.	Genome Announcements	2014	2		e00949-14			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. 		
@D	Bertinuson, A.//Illingworth, C.A.//Otto, C.J.//Hornemann, U. 	An apparently restriction deficient mutant of Streptomyces achromogenes var streptozoticus can be transformed by plasmid pIJ350.	Abstr. Gen. Meet. Am. Soc. Microbiol.	1984	84		H74			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. 		
@D	Bertolini, C.//van Aerle, R.//Lampis, S.//Moore, K.A.//Paszkiewicz, K.//Butler, C.S.//Vallini, G.//van der Giezen, M. 	Draft Genome Sequence of Stenotrophomonas maltophilia SeITE02, a Gammaproteobacterium Isolated from Selenite-Contaminated Mining Soil.	Genome Announcements	2014	2		e00331-14			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. 		
@D	Bertschinger, J.//Neri, D. 	Covalent DNA display as a novel tool for directed evolution of proteins in vitro.	Protein Eng. Des. Sel.	2004	17		699-707			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. 		
@D	Bertuzzi, A.S.//Guinane, C.M.//Crispie, F.//Kilcawley, K.N.//McSweeney, P.L.H.//Rea, M.C. 	Genome Sequence of Staphylococcus saprophyticus DPC5671, a Strain Isolated from Cheddar Cheese.	Genome Announcements	2017	5		e00193-17			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. 		
@D	Berube, P.M. et al. 	Single cell genomes of Prochlorococcus, Synechococcus, and sympatric microbes from diverse marine environments.	Sci. Data	2018	5		180154			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. 		
@D	Besaury, L.//Amato, P.//Sancelme, M.//Delort, A.M. 	Draft Genome Sequence of Pseudomonas syringae PDD-32b-74, a Model Strain for Ice-Nucleation Studies in the Atmosphere.	Genome Announcements	2017	5		e00742-17			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. 		
@D	Besaury, L.//Amato, P.//Wirgot, N.//Sancelme, M.//Delort, A.M. 	Draft Genome Sequence of Pseudomonas graminis PDD-13b-3, a Model Strain Isolated  from Cloud Water.	Genome Announcements	2017	5		e00464-17			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. 		
@D	Besnier, C.E.//Kong, H. 	Converting MlyI endonuclease into a nicking enzyme by changing its oligomerization state.	EMBO Rep.	2001	2		782-786			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. 		
@D	Bessen, D.E.//Kumar, N.//Hall, G.S.//Riley, D.R.//Luo, F.//Lizano, S.//Ford, C.N.//McShan, W.M.//Nguyen, S.V.//Dunning-Hotopp, J.C.//Tettelin, H. 	Whole Genome Association Study on Tissue Tropism Phenotypes in Group A Streptococcus.	J. Bacteriol.	2011	193		6651-6663			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. 		
@D	Bestor, T. 	Structure of mammalian DNA methyltransferase as deduced from the inferred amino acid sequence and direct studies of the protein.	Biochem. Soc. Trans.	1988	16		944-947			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. 		
@D	Bestor, T. 	Supercoiling-dependent sequence specificity of mammalian DNA mthyltransferase.	Nucleic Acids Res.	1987	15		3835-3843			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. 		
@D	Bestor, T.//Laudano, A.//Mattaliano, R.//Ingram, V. 	Cloning and sequencing of a cDNA encoding DNA methyltransferase of mouse cells.	J. Mol. Biol.	1988	203		971-983			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. 		
@D	Bestor, T.H. 	Activation of mammalian DNA methyltransferase by cleavage of a Zn binding regulatory domain.	EMBO J.	1992	11		2611-2617			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. 		
@D	Bestor, T.H. 	DNA methylation: evolution of a bacterial immune function into a regulator of gene expression and genome structure in higher eukaryotes.	Philos. Trans. R. Soc. Lond. B. Biol. Sci.	1990	326		179-187			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. 		
@D	Bestor, T.H. 	The DNA methyltransferases of mammals.	Hum. Mol. Genet.	2000	9		2395-2402			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. 		
@D	Bestor, T.H. 	Cloning of a mammalian DNA methyltransferase.	Gene	1988	74		9-12			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. 		
@D	Bestor, T.H. 	Methylation patterns in the vertebrate genome.	J. NIH Res.	1993	5		57-60			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. 		
@A	Bestor, T.H. 		DNA methyltransferases in mammalian development and genome defense.			Russo, V.E.A.//Martienssen, R.A.//Riggs, A.D. 		Epigenetic Mechanisms of Gene Regulation				Cold Spring Harbor	Cold Spring Harbor Laboratory Press	1996		0		61-76									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. 		
@D	Bestor, T.H.//Ingram, V.M. 	Two DNA methyltransferases from murine erythroleukemia cells: purification, sequence specificity, and mode of interaction with DNA.	Proc. Natl. Acad. Sci. U. S. A.	1983	80		5559-5563			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. 		
@D	Bestor, T.H.//Ingram, V.M. 	Growth-dependent expression of multiple species of DNA methyltransferase in murine erythroleukemia cells.	Proc. Natl. Acad. Sci. U. S. A.	1985	82		2674-2678			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. 		
@D	Bestor, T.H.//Verdine, G.L. 	DNA methyltransferases.	Curr. Opin. Cell Biol.	1994	6		380-389			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. 		
@D	Bethke, J.//Yanez, A.J.//Avendano-Herrera, R. 	Comparative Genomic Analysis of Two Chilean Renibacterium salmoninarum Isolates and the type strain ATCC 33209T.	Genome Biol. Evol.	2018	10		1816-1822			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. 		
@D	Betlach, M.//Hershfield, V.//Chow, L.//Brown, W.//Goodman, H.//Boyer, H.W. 	A restriction endonuclease analysis of the bacterial plasmid controlling the ecoRI restriction and modification of DNA.	Fed. Proc.	1976	35		2037-2043			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. 		
@D	Bettegowda, C.//Huang, X.//Lin, J.//Cheong, I.//Kohli, M.//Szabo, S.A.//Zhang, X.//Diaz, L.A. Jr.//Velculescu, V.E.//Parmigiani, G.//Kinzler, K.W.//Vogelstein, B.//Zhou, S. 	The genome and transcriptomes of the anti-tumor agent Clostridium novyi-NT.	Nat. Biotechnol.	2006	24		1573-1580			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. 		
@D	Bettina, A.M.//Doing, G.//O'Brien, K.//Perron, G.G.//Jude, B.A. 	Draft Genome Sequences of Phenotypically Distinct Janthinobacterium sp. Isolates  Cultured from the Hudson Valley Watershed.	Genome Announcements	2018	6		e01426-17			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. 		
@D	Betts, M.N.//Jospin, G.//Eisen, J.A.//Coil, D.A. 	Draft Genome Sequence of Planomicrobium glaciei UCD-HAM (Phylum Firmicutes).	Genome Announcements	2015	3		e01209-15			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%. 		
@D	Beuck, C.//Singh, I.//Bhattacharya, A.//Hecker, W.//Parmar, V.S.//Seitz, O.//Weinhold, E. 	Polycyclic Aromatic DNA-base surrogates: High-affinity binding to an adenine-specific base-flipping DNA methyltransferase.	Angew. Chem. Int. Ed. Engl.	2003	42		3958-3960			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. 		
@D	Beukers, A.G.//Zaheer, R.//Goji, N.//Cook, S.R.//Amoako, K.K.//Chaves, A.V.//Ward, M.P.//McAllister, T.A. 	Draft Genome Sequence of an Enterococcus thailandicus Strain Isolated from Bovine Feces.	Genome Announcements	2016	4		e00576-16			Here, we report the first draft genome sequence of Enterococcus thailandicus isolated from the feces of feedlot cattle in Southern Alberta. 		
@D	Beurmann, S.//Videau, P.//Ushijima, B.//Smith, A.M.//Aeby, G.S.//Callahan, S.M.//Belcaid, M. 	Complete Genome Sequence of Pseudoalteromonas sp. Strain OCN003, Isolated from Kane'ohe Bay, O'ahu, Hawaii.	Genome Announcements	2015	3		e01396-14			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. 		
@D	Beutin, L.//Hammerl, J.A.//Strauch, E.//Reetz, J.//Dieckmann, R.//Kelner-Burgos, Y.//Martin, A.//Miko, A.//Strockbine, N.A.//Lindstedt, B.A.//Horn, D.//Monse, H.//Huettel, B.//Muller, I.//Stuber, K.//Reinhardt, R. 	Spread of a Distinct Stx2-Encoding Phage Prototype among Escherichia coli O104:H4 Strains from Outbreaks in Germany, Norway, and Georgia.	J. Virol.	2012	86		10444-10455			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. 		
@D	Beutin, L.//Kruger, U.//Krause, G.//Miko, A.//Martin, A.//Strauch, E. 	Evaluation of major types of Shiga toxin 2E-producing Escherichia coli bacteria present in food, pigs, and the environment as potential pathogens for humans.	Appl. Environ. Microbiol.	2008	74		4806-4816			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. 		
@D	Bevan, M. et al. 	Analysis of 1.9 Mb of contiguous sequence from chromosome 4 of Arabidopsis thaliana.	Nature	1998	391		485-488			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. 		
@D	Bey, S.J.//Tsou, M.F.//Huang, C.H.//Yang, C.C.//Chen, C.W. 	The homologous terminal sequence of the Streptomyces lividans chromosome and SLP2 plasmid.	Microbiology	2000	146		911-922			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. 		
@D	Beye, M.//Bakour, S.//Labas, N.//Raoult, D.//Fournier, P.E. 	Draft Genome Sequence of Actinobaculum massiliense Strain FC3.	Genome Announcements	2016	4		e01537-15			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. 		
@D	Beye, M.//Bakour, S.//Traore, S.I.//Rathored, J.//Labas, N.//Raoult, D.//Fournier, P.E. 	Draft genome sequence of Fermentimonas caenicola strain SIT8, isolated from the human gut.	Standards in Genomic Sciences	2018	13		8			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. 		
@D	Beyersmann, P.G.//Chertkov, O.//Petersen, J.//Fiebig, A.//Chen, A.//Pati, A.//Ivanova, N.//Lapidus, A.//Goodwin, L.A.//Chain, P.//Detter, J.C.//Rohde, M.//Gronow, S.//Kyrpides, N.C.//Woyke, T.//Simon, M.//Goker, M.//Klenk, H.P.//Brinkhoff, T. 	Genome sequence of Phaeobacter caeruleus type strain (DSM 24564(T)), a surface-associated member of the marine Roseobacter clade.	Standards in Genomic Sciences	2013	8		403-419			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. 		
@D	Beylefeld, A.//Abolnik, C. 	Complete Genome Sequence of Mycoplasma pullorum Isolated from Domestic Chickens.	Genome Announcements	2017	5		e01647-16			The 1,007,172-bp complete genome of Mycoplasma pullorum strain B359_6, isolated from domestic chickens, has been sequenced, assembled, and annotated. 		
@D	Beylot, B.//Spassky, A. 	Chemical probing shows that the intron-encoded endonuclease I-SceI distorts DNA through binding in monomeric form to its homing site.	J. Biol. Chem.	2001	276		25243-25253			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. 		
@D	Bezuidt, O.K.//Gomri, M.A.//Pierneef, R.//Van Goethem, M.W.//Kharroub, K.//Cowan, D.A.//Makhalanyane, T.P. 	Draft genome sequence of Thermoactinomyces sp. strain AS95 isolated from a Sebkha in Thamelaht, Algeria.	Standards in Genomic Sciences	2016	11		68			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. 		
@D	Bezuidt, O.K.//Makhalanyane, T.P.//Gomri, M.A.//Kharroub, K.//Cowan, D.A. 	Draft Genome Sequence of Thermophilic Geobacillus sp. Strain Sah69, Isolated from Saharan Soil, Southeast Algeria.	Genome Announcements	2015	3		e01447-15			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. 		
@D	Bhagwat, A.S. 	Restriction enzymes: Properties and Use.	Methods Enzymol.	1992	216		199-224			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. 		
@D	Bhagwat, A.S.//Beletskii, A. 	Transcription is intrinsically mutagenic: Direct correlation between transcription and C to U or 5meC to T deaminations in the non-transcribed strand.	FASEB J.	1996	10		A962			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. 		
@D	Bhagwat, A.S.//Gabbara, S. 	The mechanism of activation of EcoRII endonuclease.	FASEB J.	1992	6		A281			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. 		
@D	Bhagwat, A.S.//Johnson, B.//Weule, K.//Roberts, R.J. 	Primary sequence of the EcoRII endonuclease and properties of its fusions with beta-galactosidase.	J. Biol. Chem.	1990	265		767-773			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. 		
@D	Bhagwat, A.S.//McClelland, M. 	DNA mismatch correction by very short patch repair may have altered the abundance of oligonucleotides in the E. coli genome.	Nucleic Acids Res.	1992	20		1663-1668			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. 		
@D	Bhagwat, A.S.//Person, S. 	Structure and properties of the region of homology between plasmids pMB1 and ColE1.	Mol. Gen. Genet.	1981	182		505-507			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. 		
@D	Bhagwat, A.S.//Roberts, R.J. 	Genetic analysis of the 5-azacytidine sensitivity of Escherichia coli K-12.	J. Bacteriol.	1987	169		1537-1546			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. 		
@D	Bhagwat, A.S.//Sohail, A.//Lieb, M. 	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.	J. Cell Biochem. Suppl.	1988	12A		282			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. 		
@A	Bhagwat, A.S.//Sohail, A.//Lieb, M. 		Methylation abilities of EcoRII and DCM methylases are not sufficient for their involvement in very short patch repair.			 		UCLA Symp. Mol. Cell. Biol.				New York	Alan R. Liss, Inc.	1988		83		173-178									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. 		
@D	Bhagwat, A.S.//Sohail, A.//Roberts, R.J. 	Cloning and characterization of the dcm locus of Escherichia coli K-12.	J. Bacteriol.	1986	166		751-755			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. 		
@D	Bhalla, A.//Kainth, A.S.//Sani, R.K. 	Draft Genome Sequence of Lignocellulose-Degrading Thermophilic Bacterium Geobacillus sp. Strain WSUCF1.	Genome Announcements	2013	1		e00595-13			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. 		
@D	Bhandare, S.G.//Warry, A.//Emes, R.D.//Hooton, S.P.T.//Barrow, P.A.//Atterbury, R.J. 	Complete Genome Sequences of Vibrio cholerae-Specific Bacteriophages 24 and X29.	Genome Announcements	2017	5		e01013-17			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. 		
@D	Bharadwaj, Sv.V.//Shrivastav, A.//Dubey, S.//Ghosh, T.//Paliwal, C.//Maurya, R.//Mishra, S. 	Draft Genome Sequence of Halomonas hydrothermalis MTCC 5445, Isolated from the West Coast of India.	Genome Announcements	2015	3		e01419-14			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. 		
@D	Bharat, A.//Martin, I.//Demczuk, W.//Allen, V.//Haldane, D.//Hoang, L.//Mulvey, M.R. 	Complete Genome Sequences of Neisseria gonorrhoeae with Coresistance to First-Line Antimicrobials.	Genome Announcements	2016	4		e00966-16			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. 		
@D	Bhat, A.//Tamuli, R.//Kasbekar, D.P. 	Genetic Transformation of Neurospora tetrasperma, Demonstration of Repeat-Induced Point Mutation (RIP) in Self-Crosses and a Screen for Recessive RIP-Defective Mutants.	Genetics	2004	167		1155-1164			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. 		
@D	Bhatia, U.//Robison, K.//Gilbert, W. 	Dealing with database explosion: A cautionary note.	Science	1997	276		1724-1725			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. 		
@D	Bhatnagar, S.//Badger, J.H.//Madupu, R.//Khouri, H.M.//O'Connor, E.M.//Robb, F.T.//Ward, N.L.//Eisen, J.A. 	Genome Sequence of a Sulfate-Reducing Thermophilic Bacterium, Thermodesulfobacterium commune DSM 2178T (Phylum Thermodesulfobacteria).	Genome Announcements	2015	3		e01490-14			Here, we present the complete genome sequence of Thermodesulfobacterium commune DSM 2178(T) of the phylum Thermodesulfobacteria. 		
@D	Bhatnagar, S.//Badger, J.H.//Madupu, R.//Khouri, H.M.//O'Connor, E.M.//Robb, F.T.//Ward, N.L.//Eisen, J.A. 	Genome Sequence of the Sulfate-Reducing Thermophilic Bacterium Thermodesulfovibrio yellowstonii Strain DSM 11347T (Phylum Nitrospirae).	Genome Announcements	2015	3		e01489-14			Here, we present the complete 2,003,803-bp genome of a sulfate-reducing thermophilic bacterium, Thermodesulfovibrio yellowstonii strain DSM 11347(T). 		
@D	Bhattacharjee, S.K.//Mahajan, S.K. 	The origin of adaptive mutations: Explaining the mutational spectra of Lac+ revertants of the Escherichia coli strain FC40.	Curr. Sci.	1998	74		583-590			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. 		
@D	Bhattacharya, P.//Barnebey, A.//Zemla, M.//Goodwin, L.//Auer, M.//Yannone, S.M. 	Complete genome sequence of the chromate-reducing bacterium Thermoanaerobacter thermohydrosulfuricus strain BSB-33.	Standards in Genomic Sciences	2015	10		74			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. 		
@D	Bhattacharya, S.//Dubey, A.K. 	Metabolic burden as reflected by maintenance coefficient of recombinant Escherichia coli overexpressing target gene.	Biotechnol. Lett.	1995	17		1155-1160			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. 		
@D	Bhattacharya, S.K.//Dubey, A.K. 	The N-terminus of m5C-DNA methyltransferase MspI is involved in its topoisomerase activity.	Eur. J. Biochem.	2002	269		2491-2497			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. 		
@D	Bhattacharya, S.K.//Dubey, A.K. 	Transient DNA binding by a proteolytic peptide from m5C-DNA methyltransferase MspI.	J. Biochem. Mol. Biol. Biophys.	2002	6		357-364			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. 		
@D	Bhattacharya, S.K.//Dubey, A.K. 	Effects of dissolved oxygen and oxygen mass transfer on overexpression of target gene in recombinant E. coli.	Enzyme Microb. Technol.	1997	20		355-360			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. 		
@D	Bhattacharya, S.K.//Dubey, A.K. 	High-level expression of a heterologous gene in Escherichia coli in response to carbon-nitrogen source and C/N ration in a batch bioreactor.	Biotechnol. Prog.	1997	13		151-155			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. 		
@D	Bhattacharya, S.K.//Dubey, A.K. 	Kinetic mechanism of cytosine DNA methyltransferase MspI.	J. Biol. Chem.	1999	274		14743-14749			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. 		
@D	Bhattacharya, S.K.//Dubey, A.K. 	Preparation and properties of restriction endonuclease SphI coupled to a nylon fabric filter.	Biotechnol. Appl. Biochem.	1994	20		141-146			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. 		
@D	Bhattacharya, S.K.//Dubey, A.K. 	Amino acid residues involved in catalysis and DNA binding by cytosine DNA methyltransferase MspI.	J. Biochem. Mol. Biol. Biophys.	2000	4		109-120			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. 		
@D	Bhattacharya, S.K.//Dubey, A.K. 	Expression parameters for target gene cloned in Escherichia coli in response to phosphate supply.	Biotechnol. Lett.	1996	18		1145-1148			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. 		
@D	Bhattacharya, S.K.//Ramchandani, S.//Cervoni, N.//Szyf, M. 	A mammalian protein with specific demethylase activity for mCpG DNA.	Nature	1999	397		579-583			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. 		
@D	Bhattacharyya, S.//Chandrababunaidu, M.M.//Sen, D.//Panda, A.//Ghorai, A.//Bhan, S.//Sanghi, N.//Tripathy, S. 	Draft Genome Sequence of Exopolysaccharide-Producing Cyanobacterium Aphanocapsa montana BDHKU 210001.	Genome Announcements	2015	3		e00057-15			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. 		
@D	Bhave, N.//Woodhead, J.L.//Malcolm, A.D.B. 	Cation-dependence of the restriction endodeoxyribonuclease EcoRI.	Biochem. Soc. Trans.	1980	8		634			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. 		
@D	Bheemanaik, S.//Bujnicki, J.M.//Nagaraja, V.//Rao, D.N. 	Functional analysis of amino acid residues at the dimerisation interface of Kpnl DNA methyltransferase.	Biol. Chem.	2006	387		515-523			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. 		
@D	Bheemanaik, S.//Chandrashekaran, S.//Nagaraja, V.//Rao, D.N. 	Kinetic and catalytic properties of dimeric KpnI DNA methyltransferase.	J. Biol. Chem.	2003	278		7863-7874			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. 		
@D	Bheemanaik, S.//Reddy, Y.V.R.//Rao, D.N. 	Structure, function and mechanism of exocyclic DNA methyltransferases.	Biochem. J.	2006	399		177-190			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. 		
@D	Bheemanaik, S.//Reddy, Y.V.R.//Rao, D.N. 	Structure, function and mechanism of exocyclic DNA methyltransferases (vol 399, pg 177, 2006).	Biochem. J.	2006	399		543			In Table 2, the Kd(DNA) values for the enzyme M.EcoRI were incorrect.  The correct table appears here. 		
@D	Bheemanaik, S.//Sistla, S.//Krishnamurthy, V.//Sampath, A.//Desirazu, N.R. 	Kinetics of methylation by EcoP1I DNA methyltransferase.	Enzyme Res.	2010	2010		302731			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. 		
@D	Bhotra, T.//Singh, D.V. 	Whole-Genome Sequence of Vibrio alginolyticus Isolated from the Mucus of the Coral Fungia danai in the Andaman Sea, India.	Genome Announcements	2016	4		e00339-16			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. 		
@D	Bhowmick, S.//Malar, M.//Das, A.//Kumar-Thakur, B.//Saha, P.//Das, S.//Rashmi, H.M.//Batish, V.K.//Grover, S.//Tripathy, S. 	Draft Genome Sequence of Lactobacillus casei Lbs2.	Genome Announcements	2014	2		e01326-14			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. 		
@D	Bhugra, B.//Voelker, L.L.//Zou, N.//Yu, H.//Dybvig, K. 	Mechanism of antigenic variation in Mycoplasma pulmonis: interwoven, site-specific DNA inversions.	Mol. Microbiol.	1995	18		703-714			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. 		
@D	Bian, F.//Qin, Q.L.//Xie, B.B.//Shu, Y.L.//Zhang, X.Y.//Yu, Y.//Chen, B.//Chen, X.L.//Zhou, B.C.//Zhang, Y.Z. 	Complete Genome Sequence of Seawater Bacterium Glaciecola nitratireducens FR1064T.	J. Bacteriol.	2011	193		7006-7007			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. 		
@D	Bian, F.//Xie, B.B.//Qin, Q.L.//Shu, Y.L.//Zhang, X.Y.//Yu, Y.//Chen, B.//Chen, X.L.//Zhou, B.C.//Zhang, Y.Z. 	Genome sequences of six pseudoalteromonas strains isolated from arctic sea ice.	J. Bacteriol.	2012	194		908-909			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. 		
@D	Bian, J.//Li, C. 	Disruption of a Type II Endonuclease (TDE0911) Enables Treponema denticola ATCC 35405 To Accept an Unmethylated Shuttle Vector.	Appl. Environ. Microbiol.	2011	77		4573-4578			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. 		
@D	Bianco, P.R.//Hurley, E.M. 	The type I restriction endonuclease EcoR124I, couples ATP hydrolysis to bidirectional DNA translocation.	J. Mol. Biol.	2005	352		837-859			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. 		
@D	Bianco, P.R.//Xu, C.//Chi, M. 	Type I restriction endonucleases are true catalytic enzymes.	Nucleic Acids Res.	2009	37		3377-3390			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. 		
@D	Bianconi, I.//D'Arcangelo, S.//Benedet, M.//Bailey, K.E.//Esposito, A.//Piffer, E.//Mariotto, A.//Baldo, E.//Dinnella, G.//Gualdi, P.//Schinella, M.//Donati, C.//Jousson, O. 	Draft Genome Sequences of 40 Pseudomonas aeruginosa Clinical Strains Isolated from the Sputum of a Single Cystic Fibrosis Patient Over an 8-Year Period.	Genome Announcements	2016	4		e01205-16			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. 		
@D	Bickle, T.//Arber, W. 	Host-controlled restriction and modification of filamentous I- and F-specific bacteriophages.	Virology	1969	39		605-607			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. 		
@D	Bickle, T.A. 	Restricting restriction.	Mol. Microbiol.	2004	51		3-5			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. 		
@D	Bickle, T.A. 	Adenosine triphosphate-requiring restriction enzymes.	Biochem. Soc. Trans.	1980	8		396-397			None 		
@D	Bickle, T.A. 	Phage introns on the hop: an alternative view.	Curr. Biol.	1992	2		150-151			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. 		
@A	Bickle, T.A. 		The ATP-dependent restriction enzymes.			Linn, S.M.//Lloyd, R.S.//Roberts, R.J. 		Nucleases				Cold Spring Harbor	Cold Spring Harbor Laboratory Press	1993		0		89-109									*
   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
 
 		
@A	Bickle, T.A. 		The ATP-dependent restriction endonucleases.			Linn, S.M.//Roberts, R.J. 		Nucleases				New York	Cold Spring Harbor Laboratory Press	1982		0		85-108									None 		
@A	Bickle, T.A. 		DNA restriction and modification systems.			Neidhardt, F.C. 		Escherichia coli and Salmonella typhimurium: Cellular and molecular biology.				Washington	Amer. Soc. Microbiology	1987		1		692-696									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. 		
@D	Bickle, T.A.//Brack, C.//Yuan, R. 	ATP-induced conformational changes in the restriction endonuclease from Escherichia coli K-12.	Proc. Natl. Acad. Sci. U. S. A.	1978	75		3099-3103			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. 		
@D	Bickle, T.A.//Ineichen, K. 	The DNA sequence recognised by BglI.	Gene	1980	9		205-212			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. 		
@D	Bickle, T.A.//Kruger, D.H. 	Biology of DNA Restriction.	Microbiol. Rev.	1993	57		434-450			*
 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
 
 		
@D	Bickle, T.A.//Pirrotta, V.//Imber, R. 	A simple, general procedure for purifying restriction endonucleases.	Nucleic Acids Res.	1977	4		2561-2572			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. 		
@D	Bickle, T.A.//Pirrotta, V.//Imber, R. 	Purification and properties of the BglI and II endonucleases.	Methods Enzymol.	1980	65		132-138			The presence of two distinct restriction endonucleases in Bacillus globigii, BglI and II, was first reported by Wilson and Young. 		
@D	Bickle, T.A.//Streiff, M. 	Methods for purification of restriction enzymes.	Nucleic Acid Biochem.	1983	B510		1-8			None 		
@D	Biddle, A.S. et al. 	The complete genome sequence of Clostridium indolis DSM 755(T.).	Standards in Genomic Sciences	2014	9		1089-1104			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. 		
@D	Bidle, K.D.//Lee, S.//Marchant, D.R.//Falkowski, P.G. 	Fossil genes and microbes in the oldest ice on earth.	Proc. Natl. Acad. Sci. U. S. A.	2007	104		13455-13460			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. 		
@D	Biedrzycka, I.//Sektas, M.//Kaczorowski, T. 	Characterization of pEC156, a ColE1-type plasmid from Escherichia coli E1585-68 that carries genes of the EcoVIII restriction-modification system.	Plasmid	2001	45		161			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. 		
@D	Bielas, J.H.//Loeb, L.A. 	Quantification of random genomic mutations.	Nat. Methods	2005	2		285-290			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. 		
@D	Bier, F.F.//Kleinjung, F.//Schmidt, P.M.//Scheller, F.W. 	Determination of the turnover number of the restriction endonuclease EcoRI using evanescent wave technology.	Anal. Bioanal. Chem.	2002	372		308-313			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. 		
@D	Bigey, P.//Knox, J.D.//Croteau, S.//Bhattacharya, S.K.//Theberge, J.//Szyf, M. 	Modified oligonucleotides as bona fide antagonists of proteins interacting with DNA.	J. Biol. Chem.	1999	274		4594-4606			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. 		
@D	Bigey, P.//Ramchandani, S.//Theberge, J.//Araujo, F.D.//Szyf, M. 	Transcriptional regulation of the human DNA methyltransferase (dnmt1) gene.	Gene	2000	242		407-418			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. 		
@D	Bigger, C.H.//Murray, K.//Murray, N.E. 	Recognition sequence of a restriction enzyme.	Nature New Biol.	1973	244		7-10			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. 		
@D	Bikandi, J.//San, M.R.//Rementeria, A.//Garaizar, J. 	In silico analysis of complete bacterial genomes: PCR, AFLP-PCR and endonuclease restriction.	Bioinformatics	2004	20		798-799			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 		
@D	Bilcock, D.T.//Daniels, L.E.//Bath, A.J.//Halford, S.E. 	Reactions of type II restriction endonucleases with 8-base pair recognition sites.	J. Biol. Chem.	1999	274		36379-36386			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. 		
@D	Bilcock, D.T.//Halford, S.E. 	DNA restriction dependent on two recognition sites: activities of the SfiI restriction-modification system in Escherichia coli.	Mol. Microbiol.	1999	31		1243-1254			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. 		
@D	Biller, S.J.//Coe, A.//Martin-Cuadrado, A.B.//Chisholm, S.W. 	Draft Genome Sequence of Alteromonas macleodii Strain MIT1002, Isolated from an Enrichment Culture of the Marine Cyanobacterium Prochlorococcus.	Genome Announcements	2015	3		e00967-15			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. 		
@D	Billings, A.F.//Fortney, J.L.//Hazen, T.C.//Simmons, B.//Davenport, K.W.//Goodwin, L.//Ivanova, N.//Kyrpides, N.C.//Mavromatis, K.//Woyke, T.//DeAngelis, K.M. 	Genome sequence and description of the anaerobic lignin-degrading bacterium sp. nov.	Standards in Genomic Sciences	2015	10		106			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. 		
@D	Billington, S.J.//Huggins, A.S.//Johanesen, P.A.//Crellin, P.K.//Cheung, J.K.//Katz, M.E.//Wright, C.L.//Haring, V.//Rood, J.I. 	Complete nucleotide sequence of the 27-kilobase virulence related locus (vrl) of Dichelobacter nodosus: evidence for extrachromosomal origin.	Infect. Immun.	1999	67		1277-1286			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. 		
@D	Billington, S.J.//Jost, B.H. 	Multiple genetic elements carry the tetracycline resistance gene, tet(W) in the animal pathogen, Arcanobacterium pyogenes.	Antimicrob. Agents Chemother.	2006	50		3580-3587			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. 		
@D	Bina, J.E.//Nano, F.//Hancock, R.E.W. 	Utilization of alkaline phosphatase fusions to identify secreted proteins, including potential efflux proteins and virulence factors from Helicobacter pylori.	FEMS Microbiol. Lett.	1997	148		63-68			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. 		
@D	Binetti, A.G.//Suarez, V.B.//Tailliez, P.//Reinheimer, J.A. 	Characterization of spontaneous phage-resistant variants of Streptococcus thermophilus by randomly amplified polymorphic DNA analysis and identification of phage-resistance mechanisms.	Int. Dairy Journal	2007	17		1115-1122			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. 		
@D	Bingham, A.H.A.//Atkinson, T. 	Restriction endonucleases and modification methylases in bacteria.	Biochem. Soc. Trans.	1978	6		315-324			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. 		
@D	Bingham, A.H.A.//Atkinson, T.//Sciaky, D.//Roberts, R.J. 	A specific endonuclease from Bacillus caldolyticus.	Nucleic Acids Res.	1978	5		3457-3467			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. 		
@D	Bingham, A.H.A.//Darbyshire, J. 	Isolation of two restriction endonucleases from Chloroflexus aurantiacus (CauI, CauII).	Gene	1982	18		87-91			The purification and characterization of two restriction endonucleases from the photosynthetic gliding bacterium Chloroflexus aurantiacus are described. 		
@D	Bingham, A.H.A.//Sharman, A.F.//Atkinson, T. 	The purification of restriction endonuclease EcoRI by precipitation involving polyethyleneimine.	FEBS Lett.	1977	76		250-256			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. 		
@D	Binh, T.T.//Suzuki, R.//Kwon, D.H.//Yamaoka, Y. 	Complete Genome Sequence of a Metronidazole-Resistant Helicobacter pylori Strain.	Genome Announcements	2015	3		e00051-15			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. 		
@D	Binh, T.T.//Suzuki, R.//Shiota, S.//Kwon, D.H.//Yamaoka, Y. 	Complete Genome Sequences of Helicobacter pylori Clarithromycin-Resistant Strains.	Genome Announcements	2013	1		e00912-13			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. 		
@D	Bini, E. et al. 	Complete genome sequence of Desulfurispirillum indicum stain S5.	Standards in Genomic Sciences	2011	5		371-378			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. 		
@D	Biniszkiewicz, D.//Cesnaviciene, E.//Shub, D.A. 	Self-splicing group I intron in cyanobacterial initiator methionine tRNA: evidence for lateral transfer of introns in bacteria.	EMBO J.	1994	13		4629-4635			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. 		
@D	Bioteau, A.//Huguet, K.//Burrus, V.//Banerjee, S. 	Genome Sequence of a Canadian Vibrio parahaemolyticus Isolate with Unique Mobilizing Capacity.	Genome Announcements	2018	6		e00520-18			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. 		
@D	Bircakova, M.//Truksa, M.//Scouten, W.H. 	Oriented immobilization of restriction endonuclease EcoRI.	J. Mol. Recognit.	1996	9		683-690			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. 		
@D	Bird, A. 	The essentials of DNA methylation.	Cell	1992	70		5-8			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. 		
@D	Bird, A. 	DNA methylation de novo.	Science	1999	286		2287-2288			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. 		
@D	Bird, A.//Taggart, M.//Frommer, M.//Miller, O.J.//Macleod, D. 	A fraction of the mouse genome that is derived from islands of nonmethylated, CpG-rich DNA.	Cell	1985	40		91-99			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. 		
@D	Bird, A.P. 	Gene number, noise reduction and biological complexity.	Trends Genet.	1995	11		94-100			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. 		
@D	Bird, A.P.//Taggart, M.H.//Smith, B.A. 	Methylated and unmethylated DNA compartments in the sea urchin genome.	Cell	1979	17		889-901			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. 		
@D	Bird, A.P.//Wolffe, A.P. 	Methylation-induced repression - belts, braces, and chromatin.	Cell	1999	99		451-454			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. 		
@D	Birdsell, D.N.//Antwerpen, M.//Keim, P.//Hanczaruk, M.//Foster, J.T.//Sahl, J.W.//Wagner, D.M.//Grass, G. 	Draft Genome Sequences of Two Bulgarian Bacillus anthracis Strains.	Genome Announcements	2013	1		e00152-13			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. 		
@D	Birkeland, N.K.//Schonheit, P.//Poghosyan, L.//Fiebig, A.//Klenk, H.P. 	Complete genome sequence analysis of Archaeoglobus fulgidus strain 7324 (DSM 8774), a hyperthermophilic archaeal sulfate reducer from a North Sea oil field.	Standards in Genomic Sciences	2017	12		79			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. 		
@D	Biro, J.C.//Biro, J.M. 	Frequent occurrence of recognition site-like sequences in the restriction endonucleases.	BMC Bioinformatics	2004	5		30			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. 		
@D	Bischofberger, N.//Ng, P.G.//Webb, T.R.//Matteucci, M.D. 	Cleavage of single stranded oligonucleotides by EcoRI restriction endonuclease.	Nucleic Acids Res.	1987	15		709-716			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. 		
@D	Bishnoi, U.//Polson, S.W.//Sherrier, D.J.//Bais, H.P. 	Draft Genome Sequence of a Natural Root Isolate, Bacillus subtilis UD1022, a Potential Plant Growth-Promoting Biocontrol Agent.	Genome Announcements	2015	3		e00696-15			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. 		
@D	Bishop, J.O. 	A DNA sequence cleaved by restriction endonuclease R.EcoRI in only one strand.	J. Mol. Biol.	1979	128		545-559			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. 		
@D	Bishop-Lilly, K.A.//Frey, K.G.//Daligault, H.E.//Davenport, K.W.//Bruce, D.C.//Chain, P.S.//Coyne, S.R.//Chertkov, O.//Freitas, T.//Jaissle, J.//Koroleva, G.I.//Ladner, J.T.//Minogue, T.D.//Palacios, G.F.//Redden, C.L.//Xu, Y.//Johnson, S.L. 	Complete Genome Sequence of Salmonella enterica subsp. enterica Serovar Enteritidis Strain SEJ.	Genome Announcements	2014	2		e01084-14			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. 		
@D	Bishop-Lilly, K.A.//Johnson, S.L.//Verratti, K.//Luu, T.//Khiani, A.//Awosika, J.//Mokashi, V.P.//Chain, P.S.//Sozhamannan, S. 	Genome sequencing of 15 clinical Vibrio isolates, including 13 non-o1/non-o139 serogroup strains.	Genome Announcements	2014	2		e00893-14			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. 		
@D	Bist, P.//Madhusoodanan, U.K.//Rao, D.N. 	A mutation in the Mod subunit of EcoP15I restriction enzyme converts the DNA methyltransferase to a site-specific endonuclease.	J. Biol. Chem.	2007	282		3520-3530			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. 		
@D	Bist, P.//Rao, D.N. 	Identification and mutational analysis of Mg2+ binding site in EcoP15I DNA methyltransferase: involvement in target base eversion.	J. Biol. Chem.	2003	278		41837-41848			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. 		
@D	Bist, P.//Sistla, S.//Krishnamurthy, V.//Acharya, A.//Chandrakala, B.//Rao, D.N. 	S-adenosyl-L-methionine is required for DNA cleavage by type III restriction enzymes.	J. Mol. Biol.	2001	310		93-109			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. 		
@D	Biswas, R.//Huntemann, M.//Clum, A.//Pillay, M.//Palaniappan, K.//Varghese, N.//Mikhailova, N.//Stamatis, D.//Reddy, T.B.K.//Daum, C.//Shapiro, N.//Ivanova, N.//Kyrpides, N.C.//Woyke, T.//Guss, A.M. 	Complete Genome Sequence of Thermoanaerobacterium sp. Strain RBIITD, a Butyrate-  and Butanol-Producing Thermophile.	Genome Announcements	2018	6		e01411-17			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. 		
@D	Biswas, R.K.//Kock, M.M.//Adelowotan, T.//Strasheim, W.//Mahomed, T.G.//Salawu, A.//Ehlers, M.M. 	Draft Genome Sequences of Five Clinical Methicillin-Resistant Staphylococcus aureus Isolates and a Methicillin-Resistant Staphylococcus epidermidis Isolate.	Genome Announcements	2015	3		e00836-15			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. 		
@D	Biswas, S.//Biswas, I. 	Complete Genome Sequence of Lactobacillus rhamnosus Strain LRB.	Genome Announcements	2016	4		e01208-16			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. 		
@D	Biswas, S.//Biswas, I. 	Complete Genome Sequence of Streptococcus mutans GS-5, a Serotype c Strain.	J. Bacteriol.	2012	194		4787-4788			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. 		
@D	Bitinaite, J.//Grigaite, R.//Maneliene, Z.//Butkus, V.//Janulaitis, A. 	Esp3I - a novel type IIs restriction endonuclease from Hafnia alvei that recognizes the sequence 5'-CGTCTC(N)1/5-3' .	Nucleic Acids Res.	1991	19		5076			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. 		
@D	Bitinaite, J.//Maneliene, Z.//Menkevicius, S.//Klimasauskas, S.//Butkus, V.//Janulaitis, A. 	Alw26I, Eco31I and Esp3I - type IIs methyltransferases modifying cytosine and adenine in complementary strands of the target DNA.	Nucleic Acids Res.	1992	20		4981-4985			*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.
 
 		
@D	Bitinaite, J.//Mitkaite, G.//Dauksaite, V.//Jakubauskas, A.//Timinskas, A.//Vaisvila, R.//Lubys, A.//Janulaitis, A. 	Evolutionary relationship of Alw261, Eco31I and Esp3I, restriction endonucleases that recognise overlapping sequences.	Mol. Genet. Genomics	2002	267		664-672			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. 		
@D	Bitinaite, J.//Schildkraut, I. 	Self-generated DNA termini relax the specificity of SgrAI restriction endonuclease.	Proc. Natl. Acad. Sci. U. S. A.	2002	99		1164-1169			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. 		
@D	Bitinaite, J.//Wah, D.A.//Aggarwal, A.K.//Schildkraut, I. 	FokI dimerization is required for DNA cleavage.	Proc. Natl. Acad. Sci. U. S. A.	1998	95		10570-10575			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. 		
@D	Bitinaite, J.B.//Klimasauskas, S.J.//Butkus, V.V.//Janulaitis, A. 	Characterization of restriction-modification enzymes Cfr13I from Citrobacter freundii RFL13.	FEBS Lett.	1985	182		509-513			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. 		
@D	Bittar, F.//Bibi, F.//Ramasamy, D.//Lagier, J.C.//Azhar, E.I.//Jiman-Fatani, A.A.//Al-Ghamdi, A.K.//Nguyen, T.T.//Yasir, M.//Fournier, P.E.//Raoult, D. 	Non contiguous-finished genome sequence and description of Bacillus jeddahensis sp. nov.	Standards in Genomic Sciences	2015	10		47			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). 		
@D	Bitzer, A.S.//Garbeva, P.//Silby, M.W. 	Draft Genome Sequence of Pedobacter sp. Strain V48, Isolated from a Coastal Sand  Dune in the Netherlands.	Genome Announcements	2014	2		e00094-14			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. 		
@D	Bjerga, G.E.//Hjerde, E.//De Santi, C.//Williamson, A.K.//Smalas, A.O.//Willassen, N.P.//Altermark, B. 	High quality draft genome sequence of Streptomyces sp. strain AW19M42 isolated from a sea squirt in Northern Norway.	Standards in Genomic Sciences	2014	9		676-686			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. 		
@D	Bjorkholm, B.M.//Guruge, J.L.//Oh, J.D.//Syder, A.J.//Salama, N.//Guillemin, K.//Falkow, S.//Nilsson, C.//Falk, P.G.//Engstrand, L.//Gordon, J.I. 	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.	J. Biol. Chem.	2002	277		34191-34197			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. 		
@D	Bjornsdottir-Butler, K.//Leon, M.S.//Benner, R.A. Jr. 	Draft Genome Sequences of Histamine-Producing Morganella psychrotolerans Strains.	Genome Announcements	2016	4		e01001-16			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. 		
@D	Bjornsdottir-Butler, K.//McCarthy, S.A.//Dunlap, P.V.//Timme, R.E.//Benner, R.A. Jr. 	Draft Genome Sequences of Histamine-Producing Photobacterium kishitanii and Photobacterium angustum, Isolated from Albacore (Thunnus alalunga) and Yellowfin   (Thunnus albacares) Tuna.	Genome Announcements	2015	3		e00400-15			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. 		
@D	Bjornsdottir-Butler, K.//Sanchez, L.M.//Dunlap, P.V.//Benner, R.A. Jr. 	Draft Genome Sequences of Histamine- and Non-Histamine-Producing Photobacterium Strains.	Genome Announcements	2016	4		e01008-16			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. 		
@D	Blakely, G.W.//Murray, N.E. 	Control of the endonuclease activity of type I restriction-modification systems is required to maintain chromosome integrity following  homologous recombination.	Mol. Microbiol.	2006	60		883-893			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. 		
@A	Blakesley, R.W. 		Restriction endonuclease:  cleavage, ligation, and sensitivity.			Chirikjian, J.G. 		Gene Amplif. Anal.					Elsevier North Holland	1987		5		51-102									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. 		
@A	Blakesley, R.W. 		Restriction endonuclease: specificities, diversities and computer analysis.			Chirikjian, J.G. 		Gene Amplif. Anal.					Elsevier North Holland	1981		1		1-43									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. 		
@D	Blakesley, R.W.//Dodgson, J.B.//Nes, I.F.//Wells, R.D. 	Duplex regions in "single-stranded" PhiX174 DNA are cleaved by a restriction endonuclease from Haemophilus aegyptius.	J. Biol. Chem.	1977	252		7300-7306			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. 		
@D	Blakesley, R.W.//Wells, R.D. 	Single-stranded DNA from PhiX174 and M13 is cleaved by certain restriction endonucleases.	Nature	1975	257		421-422			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. 		
@D	Blakeway, L.V.//Power, P.M.//Jen, F.E.//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.	FASEB J.	2014	28		5197-5207			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. 		
@D	Blanc, V.//Gil, P.//Bamas-Jacques, N.//Lorenzon, S.//Zagorec, M.//Schleuniger, J.//Bisch, D.//Blanche, F.//Debussche, L.//Crouzet, J.//Thibaut, D. 	Identification and analysis of genes from Streptomyces pristinaespiralis encoding enzymes involved in the biosynthesis of the 4-dimethylamino-L-phenylalanine precursor of pristinamycin I.	Mol. Microbiol.	1997	23		191-202			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. 		
@A	Blanck, A.//Gluck, B.//Wartbichler, R.//Bender, S.//Poll, M.//Brandl, A. 		Activity of restriction enzymes in a PCR mix.			 		Biochemica					Boehringer Mannheim GmbH	1995		2		14									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. 		
@D	Blanco-Massani, M.//Klumpp, J.//Widmer, M.//Lehmann, R.P.//Schuppler, M. 	Chromosomal Sil system contributes to silver resistance in E. coli ATCC 8739.	Biometals	2018	31		1101-1114			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. 		
@D	Blanga-Kanfi, S.//Amitsur, M.//Azem, A.//Kaufmann, G. 	PrrC-anticodon nuclease: functional organization of a prototypical bacterial restriction RNase.	Nucleic Acids Res.	2006	34		3209-3219			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. 		
@D	Blanks, R.//McLaughlin, L.W. 	An oligodeoxynucleotide affinity column for the isolation of sequence specific DNA binding proteins.	Nucleic Acids Res.	1988	16		10283-10299			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. 		
@D	Blasche, S.//Kim, Y.//Patil, K.R. 	Draft Genome Sequence of Corynebacterium kefirresidentii SB, Isolated from Kefir.	Genome Announcements	2017	5		e00877-17			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. 		
@D	Blaschitz, M.//Lepuschitz, S.//Wagner, L.//Allerberger, F.//Indra, A.//Ruppitsch, W.//Huhulescu, S. 	Draft Genome Sequence of a Vancomycin-Resistant and Vancomycin-Dependent Enterococcus faecium Isolate.	Genome Announcements	2016	4		e00059-16			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. 		
@D	Blaschke, U.//Skiebe, E.//Kaatz, M.//Higgins, P.G.//Pfeifer, Y.//Wilharm, G. 	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.	Genome Announcements	2018	6		e01405-17			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. 		
@D	Blaschke, U.//Wilharm, G. 	Complete Genome Sequence of Acinetobacter sp. Strain NCu2D-2 Isolated from a Mouse.	Genome Announcements	2017	5		e01415-16			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. 		
@D	Blasiak, J.//Kowalik, J. 	Interaction between organophosphorus compounds and DNA assayed by the restriction endonuclease EcoRI.	Acta Univ. Lodz. Folia Biochim. Biophys.	1998	13		61-67			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. 		
@D	Blattler, M.O.//Wenz, C.//Pingoud, A.//Benner, S.A. 	Distorting duplex DNA by dimethylenesulfone substitution: A new class of "transition state analog" inhibitors for restriction enzymes.	J. Am. Chem. Soc.	1998	120		2674-2675			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. 		
@D	Blattner, F.R.//Plunkett, G. III//Bloch, C.A.//Perna, N.T.//Burland, V.//Riley, M.//Collado-Vides, J.//Glasner, J.D.//Rode, C.K.//Mayhew, G.F.//Gregor, J.//Davis, N.W.//Kirkpatrick, H.A.//Goeden, M.A.//Rose, D.J.//Mau, B.//Shao, Y. 	The complete genome sequence of Escherichia coli K-12.	Science	1997	277		1453-1462			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. 		
@D	Bleckwedel, J.//Teran, L.C.//Bonacina, J.//Saavedra, L.//Mozzi, F.//Raya, R.R. 	Draft Genome Sequence of the Mannitol-Producing Strain Lactobacillus mucosae CRL573.	Genome Announcements	2014	2		e01292-14			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. 		
@D	Blom, J.//Rueckert, C.//Niu, B.//Wang, Q.//Borriss, R. 	The Complete Genome of Bacillus amyloliquefaciens subsp. plantarum CAU B946 Contains a Gene Cluster for Nonribosomal Synthesis of Iturin A.	J. Bacteriol.	2012	194		1845-1846			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. 		
@D	Bloodworth, R.A.//Selin, C.//Lopez, De.V.M.A.//Drevinek, P.//Galanternik, L.//Degrossi, J.//Cardona, S.T. 	Draft Genome Sequences of Burkholderia contaminans, a Burkholderia cepacia Complex Species That Is Increasingly Recovered from Cystic Fibrosis Patients.	Genome Announcements	2015	3		e00766-15			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. 		
@D	Blouin, Y.//Platonov, M.E.//Pourcel, C.//Evseeva, V.V.//Afanas'ev, M.V.//Balakhonov, S.V.//Anisimov, A.P.//Vergnaud, G. 	Draft Genome Sequences of Two Yersinia pseudotuberculosis ST43 (O:1b) Strains, B-7194 and B-7195.	Genome Announcements	2013	1		e00510-13			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. 		
@D	Blow, F.//Gioti, A.//Starns, D.//Ben-Yosef, M.//Pasternak, Z.//Jurkevitch, E.//Vontas, J.//Darby, A.C. 	Draft Genome Sequence of the Bactrocera oleae Symbiont 'Candidatus Erwinia dacicola'.	Genome Announcements	2016	4		e00896-16			'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. 		
@D	Blow, F.//Vontas, J.//Darby, A.C. 	Draft Genome Sequence of Stenotrophomonas maltophilia SBo1 Isolated from Bactrocera oleae.	Genome Announcements	2016	4		e00905-16			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. 		
@D	Blow, F.//Vontas, J.//Darby, A.C. 	Draft Genome Sequence of Chryseobacterium Strain CBo1 Isolated from Bactrocera oleae.	Genome Announcements	2017	5		e00177-17			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. 		
@D	Blow, M.J. et al. 	The Epigenomic Landscape of Prokaryotes.	PLoS Genet.	2016	12		e1005854			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. 		
@D	Blum, E.//Horst, G.//Kroger, M. 	PCR directed preparation and single step purification of highly active histidine-tagged restriction endonuclease HgiBI (GGWCC).	J. Biochem. Biophys. Methods	1994	29		113-121			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. 		
@D	Blum, E.//Horst, G.//Kroger, M. 	PCR-directed preparation and single-step purification of highly active histidine-tagged restriction endonuclease HgiBI (GGWCC).	Gene	1995	157		107-108			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. 		
@D	Blum, S.//Sela, N.//Heller, E.D.//Sela, S.//Leitner, G. 	Genome Analysis of Bovine-Mastitis-Associated Escherichia coli O32:H37 Strain P4.	J. Bacteriol.	2012	194		3732			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. 		
@D	Blumenthal, R.M. 	E. coli can restrict methylated DNA and may skew genomic libraries.	Trends Biotechnol.	1986	4		302-305			None 		
@D	Blumenthal, R.M. 	Cloning and restriction of methylated DNA in Escherichia coli.	BRL Focus	1989	11		41-46			A review of mcr systems. 		
@A	Blumenthal, R.M. 		The PvuII restriction-modification system:  cloning, characterization and use in revealing in E. coli barrier to certain methylases or methylated DNAs.			Chirikjian, J.G. 		Gene Amplif. Anal.					Elsevier North Holland	1987		5		227-245									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. 		
@D	Blumenthal, R.M.//Cheng, X. 	A Taq attack displaces bases.	Nat. Struct. Biol.	2001	8		101-103			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. 		
@D	Blumenthal, R.M.//Cotterman, M.M. 	Isolation of mutants in a DNA methyltransferase through mcr-B-mediated restriction.	Gene	1988	74		271-273			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. 		
@D	Blumenthal, R.M.//Gregory, S.A.//Cooperider, J.S. 	Cloning of a restriction-modification system from Proteus vulgaris and its use in analyzing a methylase-sensitive phenotype in Escherichia coli.	J. Bacteriol.	1985	164		501-509			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. 		
@D	Blumenthal, R.M.//Vijesurier, R.M.//Carlock, L.//Dunbar, J.C. 	C.PvuII, an unusual transcriptional activator conserved among restriction-modification systems.	Abstr. Gen. Meet. Am. Soc. Microbiol.	1999	99		354			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. 		
@D	Blumer-Schuette, S.E. et al. 	Complete Genome Sequences for the Anaerobic, Extremely Thermophilic Plant Biomass-Degrading Bacteria Caldicellulosiruptor hydrothermalis,  Caldicellulosiruptor kristjanssonii, Caldicellulosiruptor kronotskyensis,  Caldicellulosiruptor owensensis, and Cal.	J. Bacteriol.	2011	193		1483-1484			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. 		
@D	Bobst, A.M.//Pauly, G.T.//Keyes, R.S.//Bobst, E.V. 	Enzymatic sequence-specific spin labeling of a DNA fragment containing the recognition sequence of EcoRI endonuclease.	FEBS Lett.	1988	228		33-36			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. 		
@D	Boch, J.//Bonas, U. 	Xanthomonas AvrBs3 family-type III effectors: discovery and function.	Annu. Rev. Phytopathol.	2010	48		419-436			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. 		
@D	Bochow, S.//Elliman, J.//Owens, L. 	Bacteriophage adenine methyltransferase: a life cycle regulator? Modelled using Vibrio harveyi myovirus like.	J. Appl. Microbiol.	2012	113		1001-1013			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. 		
@D	Bochtler, M. 	Indirect DNA Sequence Readout by LAGLIDADG Homing Endonucleases.	Structure	2016	24		839-840			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. 		
@D	Bochtler, M.//Szczepanowski, R.H.//Tamulaitis, G.//Grazulis, S.//Czapinska, H.//Manakova, E.//Siksnys, V. 	Nucleotide flips determine the specificity of the Ecl18kI restriction endonuclease.	EMBO J.	2006	25		2219-2229			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. 		
@D	Bocklage, H.//Heeger, K.//Muller-Hill, B. 	Cloning and characterization of the MboII restriction-modification system.	Nucleic Acids Res.	1991	19		1007-1013			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. 		
@D	Bocsanczy, A.M.//Huguet-Tapia, J.C.//Norman, D.J. 	Whole-Genome Sequence of Ralstonia solanacearum P673, a Strain Capable of Infecting Tomato Plants at Low Temperatures.	Genome Announcements	2014	2		e00106-14			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. 		
@D	Bodaker, I.//Sharon, I.//Suzuki, M.T.//Feingersch, R.//Shmoish, M.//Andreishcheva, E.//Sogin, M.L.//Rosenberg, M.//Maguire, M.E.//Belkin, S.//Oren, A.//Beja, O. 	Comparative community genomics in the Dead Sea: an increasingly extreme environment.	ISME J.	2010	4		399-407			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. 		
@D	Boden, R. et al. 	Complete Genome Sequence of the Aerobic Marine Methanotroph Methylomonas methanica MC09.	J. Bacteriol.	2011	193		7001-7002			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. 		
@D	Boden, R.//Ferriera, S.//Johnson, J.//Kelly, D.P.//Murrell, J.C.//Schafer, H. 	Draft genome sequence of the chemolithoheterotrophic halophilic methylotroph Methylophaga thiooxydans DMS010.	J. Bacteriol.	2011	193		3154-3155			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. 		
@D	Boden, R.//Hutt, L.P.//Huntemann, M.//Clum, A.//Pillay, M.//Palaniappan, K.//Varghese, N.//Mikhailova, N.//Stamatis, D.//Reddy, T.//Ngan, C.Y.//Daum, C.//Shapiro, N.//Markowitz, V.//Ivanova, N.//Woyke, T.//Kyrpides, N. 	Permanent draft genome of Thermithiobaclillus tepidarius DSM 3134T, a moderately  thermophilic, obligately chemolithoautotrophic member of the Acidithiobacillia.	Standards in Genomic Sciences	2016	11		74			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. 		
@D	Bodi-Winn, C.//Dzink-Fox, J.//Feng, Y.//Shen, Z.//Bakthavatchalu, V.//Fox, J.G. 	Whole-Genome Sequences and Classification of Streptococcus agalactiae Strains Isolated from Laboratory-Reared Long-Evans Rats (Rattus norvegicus).	Genome Announcements	2017	5		e01435-16			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. 		
@D	Bodilis, J.//Youenou, B.//Briolay, J.//Brothier, E.//Favre-Bonte, S.//Nazaret, S. 	Draft Genome Sequences of Stenotrophomonas maltophilia Strains Sm32COP, Sm41DVV,  Sm46PAILV, SmF3, SmF22, SmSOFb1, and SmCVFa1, Isolated from Different Manures in   France.	Genome Announcements	2016	4		e00841-16			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. 		
@D	Bodnar, J.W.//Zempsky, W.//Warder, D.//Bergson, C.//Ward, D.C. 	Effect of nucleotide analogs on the cleavage of DNA by the restriction enzymes AluI, DdeI, HinfI, RsaI, and TaqI.	J. Biol. Chem.	1983	258		15206-15213			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. 		
@D	Bogdanova, E.//Djordjevic, M.//Papapanagiotou, I.//Heyduk, T.//Kneale, G.//Severinov, K. 	Transcription regulation of the type II restriction-modification system AhdI.	Nucleic Acids Res.	2008	36		1429-1442			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. 		
@D	Bogdanova, E.//Zakharova, M.//Streeter, S.//Taylor, J.//Heyduk, T.//Kneale, G.//Severinov, K. 	Transcription regulation of restriction-modification system Esp1396I.	Nucleic Acids Res.	2009	37		3354-3366			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. 		
@D	Bogdanove, A.J. et al. 	Two New Complete Genome Sequences Offer Insight into Host and Tissue Specificity of Plant Pathogenic Xanthomonas spp.	J. Bacteriol.	2011	193		5450-5464			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. 		
@D	Bogdanove, A.J.//Bohm, A.//Miller, J.C.//Morgan, R.D.//Stoddard, B.L. 	Engineering altered protein-DNA recognition specificity.	Nucleic Acids Res.	2018	46		4845-4871			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. 		
@D	Bogdarina, I.G.//Burianov, I.I.//Baev, A.A. 	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.	Dokl. Akad. Nauk.	1977	233		498-501					
@D	Bogdarina, I.G.//Buryanov, Y.I.//Bayev, A.A. 	Isolation and properties of DNA-cytosine-methyltransferase EcoRII and E. coli K12.	Biokhimiia	1979	44		440-452			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. 		
@D	Bogdarina, I.G.//Buryanov, Y.I.//Bayev, A.A. 	Isolation and properties of DNA-cytosine-methyl-transferase from Escherichia coli C.	Mol. Biol. (Mosk)	1979	13		281-291			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. 		
@D	Bogdarina, I.G.//Nadirova, I.M.//Buryanov, Y.I. 	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.	Mikrobiologiia	1986	55		699-700			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. 		
@D	Bogdarina, I.G.//Reuter, M.//Kruger, D.H.//Buryanov, Y.I.//Baev, A.A.A. 	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.	Dokl. Akad. Nauk.	1983	273		234-237			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. 		
@D	Bogdarina, I.G.//Vagabova, L.M.//Buryanov, Y.I. 	DNA-cytosine methylation in E. coli MRE 600 cells.	FEBS Lett.	1976	68		177-180			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. 		
@D	Bohle, H.//Henriquez, P.//Grothusen, H.//Navas, E.//Bustamante, F.//Bustos, P.//Mancilla, M. 	The Genome Sequence of an Oxytetracycline-Resistant Isolate of the Fish Pathogen  Piscirickettsia salmonis Harbors a Multidrug Resistance Plasmid.	Genome Announcements	2017	5		e01571-16			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. 		
@D	Bohle, H.//Henriquez, P.//Grothusen, H.//Navas, E.//Sandoval, A.//Bustamante, F.//Bustos, P.//Mancilla, M. 	Comparative Genome Analysis of Two Isolates of the Fish Pathogen Piscirickettsia  salmonis from Different Hosts Reveals Major Differences in Virulence-Associated  Secretion Systems.	Genome Announcements	2014	2		e01219-14			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. 		
@D	Bohm, M.E.//Huptas, C.//Krey, V.M.//Scherer, S. 	Draft Genome Sequence of Bacillus cytotoxicus CVUAS 2833, a Very Close Relative to Type Strain NVH 391-98 Isolated from a Different Location.	Genome Announcements	2015	3		e00901-15			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%). 		
@D	Boinett, C.J.//Harris, S.R.//Langridge, G.C.//Trainor, E.A.//Merkel, T.J.//Parkhill, J. 	Complete Genome Sequence of Bordetella pertussis D420.	Genome Announcements	2015	3		e00657-15			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. 		
@D	Bokor, A.A.//van Kan, J.A.//Poulter, R.T. 	Sexual mating of Botrytis cinerea illustrates PRP8 intein HEG activity.	Fungal. Genet. Biol.	2010	47		392-398			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. 		
@D	Boland, M.J. 	Identification and characterization of interactions between de novo DNA methyltransferase 3b and thymine-DNA glycosylase.	Ph.D. Thesis, University of Nebraska, USA	2007			1-141			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. 		
@D	Boland, M.J.//Christman, J.K. 	A novel interaction between thymine DNA-glycosylase and the de novo methyltransferase, Dnmt3b.	Proc. Amer. Assoc. Cancer Res.	2005	46		645			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. 		
@D	Boland, M.J.//Christman, J.K. 	Characterization of Dnmt3b:Thymine-DNA Glycosylase Interaction and Stimulation of Thymine Glycosylase-Mediated Repair by DNA  Methyltransferase(s) and RNA.	J. Mol. Biol.	2008	379		492-504			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. 		
@A	Boland, M.J.//Christman, J.K. 		Mammalian DNA methyltransferases Catalytic mechanism, structure, and functions.			Choi, S.W.//Friso, S. 		Nutrients and Epigenetics					CRC Press-Taylor and Francis Group	2009		0		37-65									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. 		
@D	Bolduc, J.M.//Spiegel, P.C.//Chatterjee, P.//Brady, K.L.//Downing, M.E.//Caprara, M.G.//Waring, R.B.//Stoddard, B.L. 	Structural and biochemical analyses of DNA and RNA binding by a bifunctional homing endonuclease and group I intron splicing factor.	Genes Dev.	2003	17		2875-2888			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. 		
@D	Bolhuis, H.H.//Palm, P.P.//Wende, A.A.//Falb, M.M.//Rampp, M.M.//Rodriguez-Valera, F.F.//Pfeiffer, F.F.//Oesterhelt, D.D. 	The genome of the square archaeon Haloquadratum walsbyi: life at the limits of water activity.	BMC Genomics	2006	7		169			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. 		
@D	Bolker, M.//Bohnert, H.U.//Braun, K.H.//Gorl, J.//Kahmann, R. 	Tagging pathogenicity genes in Ustilago maydis by restriction enzyme-mediated integration (REMI).	Mol. Gen. Genet.	1995	248		547-552			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. 		
@D	Bollmann, A. et al. 	Complete genome sequence of Nitrosomonas sp. Is79, an ammonia oxidizing bacterium adapted to low ammonium concentrations.	Standards in Genomic Sciences	2013	7		469-482			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. 		
@D	Bolot, S.//Cerutti, A.//Carrere, S.//Arlat, M.//Fischer-Le, S.M.//Portier, P.//Poussier, S.//Jacques, M.A.//Noel, L.D. 	Genome Sequences of the Race 1 and Race 4 Xanthomonas campestris pv. campestris Strains CFBP 1869 and CFBP 5817.	Genome Announcements	2015	3		e01023-15			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. 		
@D	Bolot, S.//Guy, E.//Carrere, S.//Barbe, V.//Arlat, M.//Noel, L.D. 	Genome Sequence of Xanthomonas campestris pv. campestris Strain Xca5.	Genome Announcements	2013	1		e00032-12			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. 		
@D	Bolot, S.//Munoz, B.A.//Cunnac, S.//Ortiz, E.//Szurek, B.//Noel, L.D.//Arlat, M.//Jacques, M.A.//Gagnevin, L.//Portier, P.//Fischer-Le, S.M.//Carrere, S.//Koebnik, R. 	Draft Genome Sequence of the Xanthomonas cassavae Type Strain CFBP 4642.	Genome Announcements	2013	1		e00679-13			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. 		
@D	Bolot, S.//Roux, B.//Carrere, S.//Jiang, B.L.//Tang, J.L.//Arlat, M.//Noel, L.D. 	Genome Sequences of Three Atypical Xanthomonas campestris pv. campestris Strains, CN14, CN15, and CN16.	Genome Announcements	2013	1		e00465-13			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. 		
@D	Bolotin, A.//de Wouters, T.//Schnupf, P.//Bouchier, C.//Loux, V.//Rhimi, M.//Jamet, A.//Dervyn, R.//Boudebbouze, S.//Blottiere, H.M.//Sorokin, A.//Snel, J.//Cerf-Bensussan, N.//Gaboriau-Routhiau, V.//van de Guchte, M.//Maguin, E. 	Genome Sequence of 'Candidatus Arthromitus' sp. Strain SFB-Mouse-NL, a Commensal  Bacterium with a Key Role in Postnatal Maturation of Gut Immune Functions.	Genome Announcements	2014	2		e00705-14			'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. 		
@D	Bolotin, A.//Quinquis, B.//Ehrlich, S.D.//Sorokin, A. 	Complete Genome Sequence of Lactococcus lactis subsp. cremoris A76.	J. Bacteriol.	2012	194		1241-1242			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. 		
@D	Bolotin, A.//Wincker, P.//Mauger, S.//Jaillon, O.//Malarme, K.//Weissenbach, J.//Ehrlich, S.D.//Sorokin, A. 	The complete genome sequence of the lactic acid bacterium Lactococcus lactis ssp. lactis IL1403.	Genome Res.	2001	11		731-753			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. 		
@D	Boltner, D.//MacMahon, C.//Pembroke, J.T.//Strike, P.//Osborn, A.M. 	R391: a Conjugative Integrating Mosaic Comprised of Phage, Plasmid, and Transposon Elements.	J. Bacteriol.	2002	184		5158-5169			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. 		
@D	Bolton, B.J.//Comer, M.//Kessler, C. 	Asp700I, a novel isoschizomer of XmnI from Achromobacter species 700 recognizing 5'-GAANN/NNTTC-3'.	Nucleic Acids Res.	1989	17		8879			None 		
@D	Bolton, B.J.//Holtke, H.-J.//Schmitz, G.G.//Jarsch, M.//Kessler, C. 	AspHI, a novel isoschizomer of HgiAI from Achromobacter species H recognizing 5'-GWGCW/C-3'.	Nucleic Acids Res.	1989	17		9500			None 		
@D	Bolton, B.J.//Kaluza, K.//Herz, M.J.//Berger, G.//Kessler, C.//Schmitz, G. 	Screening for novel type II restriction endonucleases.	Fresenius Z. Anal. Chem.	1988	330		376			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. 		
@D	Bolton, B.J.//Nesch, G.//Comer, M.J.//Wolf, W.//Kessler, C. 	Asp718 from a non-pathogenic species of the genus Achromobacter: a KpnI isoschizomer generating DNA-fragments with 5'-protruding ends.	FEBS Lett.	1985	182		130-134			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. 		
@D	Bolton, B.J.//Reischl, U.//Holtke, H.-J.//Schmitz, G.G.//Jarsch, M.//Kessler, C. 	EclXI, a novel isoschizomer of XmaIII from Enterobacter cloacae 590 recognizing 5'-C/GGCCG-3' .	Nucleic Acids Res.	1990	18		381			None 		
@D	Bolton, B.J.//Schmitz, G.G.//Jarsch, M.//Comer, M.J.//Kessler, C. 	Ksp632I: a novel class IIS restriction endonuclease from Kluyvera species 632 with the asymmetric hexanucleotide recognition sequence: 5'-CTCTTCN^-3' 3'-GAGAAGNNNN^-5' .	Gene	1988	66		31-43			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. 		
@D	Bolton, B.J.//Schmitz, G.G.//Jarsch, M.//Kessler, C. 	KspI, a novel isoschizomer of SacII from Kluyvera species recognizing 5'-CCGC/GG-3'.	Nucleic Acids Res.	1989	17		9476			None 		
@D	Bolton, B.J.//Schmitz, G.G.//Jarsch, M.//Kessler, C. 	AspI, a novel isoschizomer of Tht111l from Achromobacter species 699 recognizing 5'-GACN/NNGTC-3'.	Nucleic Acids Res.	1990	18		3422			None 		
@D	Bomar, L.//Stephens, W.Z.//Nelson, M.C.//Velle, K.//Guillemin, K.//Graf, J. 	Draft Genome Sequence of Aeromonas veronii Hm21, a Symbiotic Isolate from the Medicinal Leech Digestive Tract.	Genome Announcements	2013	1		e00800-13			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. 		
@D	Bomholt, C.//Glaub, A.//Gravermann, K.//Albersmeier, A.//Brinkrolf, K.//Ruckert, C.//Tauch, A. 	Whole-Genome Sequence of the Clinical Strain Corynebacterium argentoratense DSM 44202, Isolated from a Human Throat Specimen.	Genome Announcements	2013	1		e00793-13			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. 		
@D	Bonacina, J.//Saavedra, L.//Suarez, N.E.//Sesma, F. 	Draft Genome Sequence of the Nonstarter Bacteriocin-Producing Strain Enterococcus mundtii CRL35.	Genome Announcements	2014	2		e00444-14			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. 		
@D	Bonaldo, M.F.//Lennon, G.//Soares, M.B. 	Normalization and subtraction: two approaches to facilitate gene discovery.	Genome Res.	1996	6		791-806			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. 		
@D	Bonamy, C.//Guyonvarch, A.//Ryes, O.//David, F.//Leblon, G. 	Interspecies electro-transformation in Corynebacteria.	FEMS Microbiol. Lett.	1990	66		263-270			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. 		
@D	Bonfils, C.//Beaulieu, N.//Chan, E.//Cotton-Montpetit, J.//MacLeod, A.R. 	Characterization of the human DNA methyltransferase splice variant dnmt1b.	J. Biol. Chem.	2000	275		10754-10760			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. 		
@D	Bonitz, S.G.//Coruzzi, G.//Thalenfeld, B.E.//Tzagoloff, A. 	Assembly of the mitochondrial membrane system.	J. Biol. Chem.	1980	255		11927-11941			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. 		
@D	Bonnassie, S.//Burini, J.-F.//Oreglia, J.//Trautwetter, A.//Patte, J.-C.//Sicard, A.M. 	Transfer of plasmid DNA to Brevibacterium lactofermentum by electrotransformation.	J. Gen. Microbiol.	1990	136		2107-2112			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. 		
@D	Bonnassie, S.//Oreglia, J.//Trautwetter, A.//Sicard, A.M. 	Isolation and characterization of a restriction and modification deficient mutant of Brevibacterium lactofermentum.	FEMS Microbiol. Lett.	1990	72		143-146			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. 		
@D	Bonnet, I.//Biebricher, A.//Porte, P.L.//Loverdo, C.//Benichou, O.//Voituriez, R.//Escude, C.//Wende, W.//Pingoud, A.//Desbiolles, P. 	Sliding and jumping of single EcoRV restriction enzymes on non-cognate DNA.	Nucleic Acids Res.	2008	36		4118-4127			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. 		
@D	Bonnin, R.A.//Girlich, D.//Imanci, D.//Dortet, L.//Naas, T. 	Draft Genome Sequence of the Serratia rubidaea CIP 103234T Reference Strain, a Human-Opportunistic Pathogen.	Genome Announcements	2015	3		e01340-15			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. 		
@D	Bonnin, R.A.//Nordmann, P.//Carattoli, A.//Poirel, L. 	Comparative genomics of IncL/M-type plasmids; evolution by acquisition of resistance genes and insertion sequences.	Antimicrob. Agents Chemother.	2013	57		674-676			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).... 		
@D	Bonnin, R.A.//Poirel, L.//Carattoli, A.//Nordmann, P. 	Characterization of an IncFII Plasmid Encoding NDM-1 from Escherichia coli ST131.	PLoS ONE	2012	7		E34752			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. 		
@D	Bonnin, R.A.//Poirel, L.//Nordmann, P.//Eikmeyer, F.G.//Wibberg, D.//Puhler, A.//Schluter, A. 	Complete sequence of broad-host-range plasmid pNOR-2000 harbouring the metallo-beta-lactamase gene blaVIM-2 from Pseudomonas aeruginosa.	J. Antimicrob. Chemother.	2013	68		1060-1065			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). 		
@D	Bonnist, E.Y.M.//Liebert, K.//Dryden, D.T.F.//Jeltsch, A.//Jones, A.C. 	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.	Biophys. Chem.	2012	160		28-34			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. 		
@D	Bonocora, R.P.//Belfort, M. 	Mapping Homing Endonuclease Cleavage Sites Using In Vitro Generated Protein.	Methods Mol. Biol.	2014	1123		55-67			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. 		
@D	Bonocora, R.P.//Shub, D.A. 	A self-splicing group I intron in DNA polymerase genes of T7-like bacteriophages.	J. Bacteriol.	2004	186		8153-8155			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. 		
@D	Bonocora, R.P.//Shub, D.A. 	A likely pathway for formation of mobile group I introns.	Curr. Biol.	2009	19		223-228			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. 		
@D	Bonocora, R.P.//Shub, D.A. 	A novel group I intron-encoded endonuclease specific for the anticodon region of tRNA(fMet) genes.	Mol. Microbiol.	2001	39		1299-1306			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. 		
@D	Booker, A.E.//Johnston, M.D.//Daly, R.A.//Wrighton, K.C.//Wilkins, M.J. 	Draft Genome Sequences of Multiple Frackibacter Strains Isolated from Hydraulically Fractured Shale Environments.	Genome Announcements	2017	5		e00608-17			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. 		
@D	Boon, E.M.//Salas, J.E.//Barton, J.K. 	An electrical probe of protein-DNA interactions on DNA-modified surfaces.	Nat. Biotechnol.	2002	20		282-286			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. 		
@D	Boonma, P.//Spinler, J.K.//Qin, X.//Jittaprasatsin, C.//Muzny, D.M.//Doddapaneni, H.//Gibbs, R.//Petrosino, J.//Tumwasorn, S.//Versalovic, J. 	Draft genome sequences and description of Lactobacillus rhamnosus strains L31, L34, and L35.	Standards in Genomic Sciences	2014	9		744-754			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. 		
@D	Boonmak, C.//Takahasi, Y.//Morikawa, M. 	Draft Genome Sequence of Geobacillus thermoleovorans Strain B23.	Genome Announcements	2013	1		e00944-13			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. 		
@D	Borase, H.P.//Patil, C.D.//Salunkhe, R.B.//Suryawanshi, R.K.//Salunke, B.K.//Patil, S.V. 	Inhibition of restriction endonucleases by biofunctionalized silver nanoparticles: An in vitro study.	Mater. Lett.	2014	134		24-26			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. 		
@D	Borck, K.//Beggs, J.D.//Brammar, W.J.//Hopkins, A.S.//Murray, N.E. 	The construction in vitro of transducing derivatives of phage lambda.	Mol. Gen. Genet.	1976	146		199-207			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. 		
@D	Borek, E.//Srinivasan, P.R. 	The methylation of nucleic acids.	Annu. Rev. Biochem.	1966	35		275-298			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. 		
@D	Boreskov, Y.G.//Titeeva, G.R.//Berlin, Y.A. 	Synthetic oligodeoxynucleotides in studying MspI restriction endonuclease.	Bioorg. Khim.	1988	14		333-339			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. 		
@D	Borgaro, J.G.//Benner, N.//Zhu, Z.Y. 	Fidelity Index Determination of DNA Methyltransferases.	PLoS ONE	2013	8		e63866			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. 		
@D	Borgaro, J.G.//Zhu, Z. 	Characterization of the 5-hydroxymethylcytosine-specific DNA restriction endonucleases.	Nucleic Acids Res.	2013	41		4198-4206			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. 		
@D	Borges, K.M.//Wetterhahn, K.E. 	Chromium Bound to DNA alters cleavage by restriction endonucleases.	Chem. Res. Toxicol.	1991	4		638-641			None 		
@D	Bork, P.//Ouzounis, C.//Casari, G.//Schneider, R.//Sander, C.//Dolan, M.//Gilbert, W.//Gillevet, P.M. 	Exploring the Mycoplasma capricolum genome: a minimal cell reveals its physiology.	Mol. Microbiol.	1995	16		955-967			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. 		
@D	Borneman, A.R.//Bartowsky, E.J.//McCarthy, J.//Chambers, P.J. 	Genotypic diversity in Oenococcus oeni by high-density microarray comparative genome hybridization and whole genome sequencing.	Appl. Microbiol. Biotechnol.	2010	86		681-691			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. 		
@D	Boronin, A.M.//Kochetkov, V.V.//Kulakov, L.A.//Tusupbekova, G.A.//Alieva, R.M. 	PaeD253 restriction-modification system determined by pBS253 biodegradation plasmid of Pseudomonas aeruginosa.	Dokl. Akad. Nauk.	1989	304		1472-1474			None 		
@D	Borowczyk, E.//Mohan, K.N.//D'Aiuto, L.//Cirio, M.C.//Chaillet, J.R. 	Identification of a region of the DNMT1 methyltransferase that regulates the maintenance of genomic imprints.	Proc. Natl. Acad. Sci. U. S. A.	2009	106		20806-20811			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. 		
@D	Borowiak, M.//Fischer, J.//Baumann, B.//Hammerl, J.A.//Szabo, I.//Malorny, B. 	Complete Genome Sequence of a VIM-1-Producing Salmonella enterica subsp. enterica Serovar Infantis Isolate Derived from Minced Pork Meat.	Genome Announcements	2018	6		e00327-18			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. 		
@D	Borowiak, M.//Hammerl, J.A.//Fischer, J.//Szabo, I.//Malorny, B. 	Complete Genome Sequence of Salmonella enterica subsp. enterica Serovar Paratyphi B Sequence Type 28 Harboring mcr-1.	Genome Announcements	2017	5		e00991-17			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. 		
@D	Borowka, P.//Lach, J.//Bakula, Z.//van Ingen, J.//Safianowska, A.//Brzostek, A.//Dziadek, J.//Strapagiel, D.//Jagielski, T. 	Draft Genome Sequences of Mycobacterium kansasii Clinical Strains.	Genome Announcements	2017	5		e00406-17			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. 		
@D	Borrel, G.//Harris, H.M.//Parisot, N.//Gaci, N.//Tottey, W.//Mihajlovski, A.//Deane, J.//Gribaldo, S.//Bardot, O.//Peyretaillade, E.//Peyret, P.//O'Toole, P.W.//Brugere, J.F. 	Genome Sequence of 'Candidatus Methanomassiliicoccus intestinalis' Issoire-Mx1, a Third Thermoplasmatales-Related Methanogenic Archaeon from Human Feces.	Genome Announcements	2013	1		e00453-13			'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. 		
@D	Borrel, G.//Harris, H.M.//Tottey, W.//Mihajlovski, A.//Parisot, N.//Peyretaillade, E.//Peyret, P.//Gribaldo, S.//O'Toole, P.W.//Brugere, J.F. 	Genome Sequence of 'Candidatus Methanomethylophilus alvus' Mx1201, a Methanogenic Archaeon from the Human Gut Belonging to a Seventh Order of Methanogens.	J. Bacteriol.	2012	194		6944-6945			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. 		
@D	Borriss, M.//Lombardot, T.//Glockner, F.O.//Becher, D.//Albrecht, D.//Schweder, T. 	Genome and proteome characterization of the psychrophilic Flavobacterium bacteriophage 11b.	Extremophiles	2007	11		95-104			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. 		
@D	Borriss, R.//Chen, X.//Rueckert, C.//Blom, J.//Becker, A.//Baumgarth, B.//Fan, B.//Pukall, R.//Schumann, P.//Sproer, C.//Junge, H.//Vater, J.//Puhler, A.//Klenk, H.P. 	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.	Int. J. Syst. Evol. Microbiol.	2011	61		1786-1801			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. 		
@D	Borst, L.B.//Suyemoto, M.M.//Scholl, E.H.//Fuller, F.J.//Barnes, H.J. 	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.	PLoS ONE	2015	10		E0121294			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. 		
@D	Bose, S.//Mukherjee, T.//Sen, U.//Roy, C.//Rameez, M.J.//Ghosh, W.//Mukhopadhyay, S.K. 	Genome Sequence of the Multiple-Protease-Producing Strain Geobacillus thermoleovorans N7, a Thermophilic Bacterium Isolated from Paniphala Hot Spring,   West Bengal, India.	Genome Announcements	2016	4		e01202-16			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. 		
@D	Bosi, E.//Fondi, M.//Orlandini, V.//Perrin, E.//Maida, I.//de Pascale, D.//Tutino, M.L.//Parrilli, E.//Lo, G.A.//Filloux, A.//Fani, R. 	The pangenome of (Antarctic) Pseudoalteromonas bacteria: evolutionary and functional insights.	BMC Genomics	2017	18		93			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. 		
@D	Bosma, E.F.//Koehorst, J.J.//van Hijum, S.A.//Renckens, B.//Vriesendorp, B.//van de Weijer, A.H.//Schaap, P.J.//de Vos, W.M.//van der Oost, J.//van Kranenburg, R. 	Complete genome sequence of thermophilic Bacillus smithii type strain DSM 4216(T).	Standards in Genomic Sciences	2016	11		52			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. 		
@D	Bosse, J.T.//Chaudhuri, R.R.//Li, Y.//Leanse, L.G.//Fernandez, C.R.//Coupland, P.//Holden, M.T.//Bazzolli, D.M.//Maskell, D.J.//Tucker, A.W.//Wren, B.W.//Rycroft, A.N.//Langford, P.R. 	Complete Genome Sequence of MIDG2331, a Genetically Tractable Serovar 8 Clinical  Isolate of Actinobacillus pleuropneumoniae.	Genome Announcements	2016	4		e01667-15			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. 		
@D	Botelho, A.M.//Costa, M.O.//Beltrame, C.O.//Ferreira, F.A.//Cortes, M.F.//Bandeira, P.T.//Lima, N.C.//Souza, R.C.//Almeida, L.G.//Vasconcelos, A.T.//Nicolas, M.F.//Figueiredo, A.M. 	Complete genome sequence of an agr-dysfunctional variant of the ST239 lineage of  the methicillin-resistant Staphylococcus aureus strain GV69 from Brazil.	Standards in Genomic Sciences	2016	11		34			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. 		
@D	Bothma, L.//Gonzalez-Ibeas, D.//Mienie, C.//Bezuidenhout, C.C.//Adeleke, R. 	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.	Genome Announcements	2018	6		e00372-18			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. 		
@D	Bottacini, F.//Dal Bello, F.//Turroni, F.//Milani, C.//Duranti, S.//Foroni, E.//Viappiani, A.//Strati, F.//Mora, D.//van Sinderen, D.//Ventura, M. 	Complete Genome Sequence of Bifidobacterium animalis subsp. lactis BLC1.	J. Bacteriol.	2011	193		6387-6388			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. 		
@D	Bottacini, F.//Milani, C.//Turroni, F.//Sanchez, B.//Foroni, E.//Duranti, S.//Serafini, F.//Viappiani, A.//Strati, F.//Ferrarini, A.//Delledonne, M.//Henrissat, B.//Coutinho, P.//Fitzgerald, G.F.//Margolles, A.//van Sinderen, D.//Ventura, M. 	Bifidobacterium asteroides PRL2011 Genome Analysis Reveals Clues for Colonization of the Insect Gut.	PLoS ONE	2012	7		E44229			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. 		
@D	Bottacini, F.//Morrissey, R.//Roberts, R.J.//James, K.//van Breen, J.//Egan, M.//Lambert, J.//van Limpt, K.//Knol, J.//Motherway, M.O.//van Sinderen, D. 	Comparative genome and methylome analysis reveals restriction/modification system diversity in the gut commensal Bifidobacterium breve.	Nucleic Acids Res.	2018	46		1860-1877			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. 		
@D	Bottacini, F.//O'Connell-Motherway, M.//Casey, E.//McDonnell, B.//Mahony, J.//Ventura, M.//van Sinderen, D. 	Discovery of a conjugative megaplasmid in Bifidobacterium breve.	Appl. Environ. Microbiol.	2014	81		166-176			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. 		
@D	Bottacini, F.//O'Connell-Motherway, M.//Kuczynski, J.//O'Connell, K.J.//Serafini, F.//Duranti, S.//Milani, C.//Turroni, F.//Lugli, G.A.//Zomer, A.//Zhurina, D.//Riedel, C.//Ventura, M.//van Sinderen, D. 	Comparative genomics of the Bifidobacterium breve taxon.	BMC Genomics	2014	15		170			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. 		
@D	Bottagisio, M.//Soggiu, A.//Lovati, A.B.//Toscano, M.//Piras, C.//Romano, C.L.//Bonizzi, L.//Roncada, P.//Drago, L. 	Draft Genome Sequence of Staphylococcus epidermidis Clinical Strain GOI1153754-03-14 Isolated from an Infected Knee Prosthesis.	Genome Announcements	2017	5		e00378-17			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. 		
@D	Botterman, J.//Zabeau, M. 	High-level production of the EcoRI endonuclease under the control of the pL promoter of bacteriophage lambda.	Gene	1985	37		229-239			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. 		
@D	Botterman, J.//Zabeau, M. 	High-level production of the restriction endonucleases EcoRI and EcoRV in Escherichia coli.	Arch. Int. Physiol. Biochim.	1985	93		S38			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. 		
@D	Bouam, A.//Levasseur, A.//Bonnet, M.//Borand, L.//Van Goethem, C.//Drancourt, M.//Godreuil, S. 	Complete Genome Sequence of Mycobacterium sp. Strain 3519A.	Genome Announcements	2018	6		e01565-17			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. 		
@D	Bouam, A.//Levasseur, A.//Bonnet, M.//Borand, L.//Van Goethem, C.//Drancourt, M.//Godreuil, S. 	Complete Genome Sequence of Mycobacterium sp. Strain 4858.	Genome Announcements	2018	6		e01604-17			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. 		
@D	Bouam, A.//Levasseur, A.//Drancourt, M. 	Draft Genome Sequence of Mycobacterium porcinum CSURP1564.	Genome Announcements	2018	6		e00291-18			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. 		
@D	Bouam, A.//Levasseur, A.//Drancourt, M. 	Draft Genome Sequence of Mycobacterium setense CSUR47.	Genome Announcements	2018	6		e01415-17			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. 		
@D	Bouam, A.//Robert, C.//Croce, O.//Levasseur, A.//Drancourt, M. 	Draft Genome Sequence of Mycobacterium boenickei CIP 107829.	Genome Announcements	2017	5		e00292-17			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. 		
@D	Bouam, A.//Robert, C.//Levasseur, A.//Drancourt, M. 	Draft Genome Sequence of Mycobacterium colombiense.	Genome Announcements	2017	5		e00119-17			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. 		
@D	Bouchard, D.//Peton, V.//Almeida, S.//Le Marechal, C.//Miyoshi, A.//Azevedo, V.//Berkova, N.//Rault, L.//Francois, P.//Schrenzel, J.//Even, S.//Hernandez, D.//Le Loir, Y. 	Genome Sequence of Staphylococcus aureus Newbould 305, a Strain Associated with Mild Bovine Mastitis.	J. Bacteriol.	2012	194		6292-6293			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. 		
@D	Bouche, J.P.C. 	Isolation and in vitro restriction of unmethylated DNA from Escherichia coli K.	Biochim. Biophys. Acta	1974	366		135-142			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. 		
@D	Boucher, I.//Emond, E.//Parrot, M.//Moineau, S. 	DNA sequence analysis of three Lactococcus lactis plasmids encoding phage resistance mechanisms.	J. Dairy Sci.	2001	84		1610-1620			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. 		
@D	Boucher, Y.//Nesbo, C.L.//Joss, M.J.//Robinson, A.//Mabbutt, B.C.//Gillings, M.R.//Doolittle, W.F.//Stokes, H.W. 	Recovery and evolutionary analysis of complete integron gene cassette arrays from Vibrio.	BMC Evol. Biol.	2006	6		3			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. 		
@D	Bougueleret, L.//Schwarzstein, M.//Tsugita, A.//Zabeau, M. 	Characterization of the genes coding for the EcoRV restriction and modification system of Escherichia coli.	Nucleic Acids Res.	1984	12		3659-3677			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. 		
@D	Bougueleret, L.//Tenchini, M.L.//Botterman, J.//Zabeau, M. 	Overproduction of the EcoRV endonuclease and methylase.	Nucleic Acids Res.	1985	13		3823-3839			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. 		
@D	Boujelben, I.//Yarza, P.//Almansa, C.//Villamor, J.//Maalej, S.//Anton, J.//Santos, F. 	Virioplankton community structure in Tunisian solar salterns.	Appl. Environ. Microbiol.	2012	78		7429-7437			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. 		
@D	Boukerb, A.M.//Marti, R.//Cournoyer, B. 	Genome Sequences of Three Strains of the Pseudomonas aeruginosa PA7 Clade.	Genome Announcements	2015	3		e01366-15			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. 		
@D	Bourbonniere, M.//Nalbantoglu, J. 	The restriction enzyme AlwNI is blocked by overlapping methylation.	Nucleic Acids Res.	1991	19		4774			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. 		
@D	Bourchis, D.//Bestor, T.H. 	Meiotic catastrophe and retrotransposon reactivation in male germ cells lacking Dnmt3L.	Nature	2004	431		96-99			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. 		
@D	Bourchis, D.//Xu, G.-L.//Lin, C.-S.//Bollman, B.//Bestor, T.H. 	Dnmt3L and the establishment of maternal genomic imprints.	Science	2001	294		2536-2539			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. 		
@D	Bourges, A.C.//Torres, M.O.E.//Ghosh, A.//Tadesse, W.M.//Declerck, N.//Aertsen, A.//Royer, C.A. 	High pressure activation of the Mrr restriction endonuclease in Escherichia coli  involves tetramer dissociation.	Nucleic Acids Res.	2017	45		5323-5332			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. 		
@D	Bourgogne, A. et al. 	Large scale variation in Enterococcus faecalis illustrated by the genome analysis of strain OG1RF.	Genome Biology	2008	9		R110			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. 		
@D	Bouriotis, V.//Zafeiropoulos, A.//Clonis, Y.D. 	High-performance liquid chromatography for the purification of restriction endonucleases, application to BanII, SacI, and SphI.	Anal. Biochem.	1987	160		127-134			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. 		
@D	Bourniquel, A.A.//Bickle, T.A. 	Complex restriction enzymes: NTP-driven molecular motors.	Biochimie	2002	84		1047-1059			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. 		
@D	Bourniquel, A.A.//Casey, M.G.//Mollet, B.//Pridmore, R.D. 	DNA sequence and functional analysis of Lactobacillus delbrueckii subsp. lactis plasmids pN42 and pJBL2.	Plasmid	2002	47		153-157			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. 		
@D	Bourniquel, A.A.//Mollet, B.//Bickle, T.A. 	Type I restriction-modification systems from Lactobacillus delbrueckii subsp. lactis.	Abstr. Gen. Meet. Am. Soc. Microbiol.	2002	102		238			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. 		
@D	Boussemaer, J.P.//Schrauwen, P.P.//Sourrouille, J.L.//Guy, P. 	Multiple modification/restriction systems in lactic streptococci and their significance in defining a phage-typing system.	J. Dairy Res.	1980	47		401-409			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. 		
@D	Boutibonnes, P. 	Cell death in bacterial populations: caused or programmed?  Accepted or deliberate?	Med. Sci. (Paris)	1997	13		73-80			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. 		
@D	Bowden, K.E.//Weigand, M.R.//Peng, Y.//Cassiday, P.K.//Sammons, S.//Knipe, K.//Rowe, L.A.//Loparev, V.//Sheth, M.//Weening, K.//Tondella, M.L.//Williams, M.M. 	Genome Structural Diversity among 31 Bordetella pertussis Isolates from Two Recent U.S. Whooping Cough Statewide Epidemics.	mSphere	2016	1		e00036-16			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. 		
@D	Bowen, L.M.//Dupureur, C.M. 	Investigation of restriction enzyme cofactor requirements: A relationship between metal ion properties and sequence specificity.	Biochemistry	2003	42		12643-12653			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. 		
@D	Bowen, L.M.//Muller, G.//Riehl, J.P.//Dupureur, C.M. 	Lanthanide spectroscopic studies of the dinuclear and Mg(II)-dependent PvuII restriction endonuclease.	Biochemistry	2004	43		15286-15295			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. 		
@D	Bower, E.K.M.//Cooper, L.P.//Roberts, G.A.//White, J.H.//Luyten, Y.//Morgan, R.D.//Dryden, D.T.F. 	A model for the evolution of prokaryotic DNA restriction-modification systems based upon the structural malleability of Type I restriction-modification  enzymes.	Nucleic Acids Res.	2018	46		9067-9080			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. 		
@D	Bowman, J.P. 	Draft Genome Sequence of the Psychrophilic Gliding Species Gelidibacter algens ACAM 536.	Genome Announcements	2016	4		e00908-16			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. 		
@D	Bown, L.//Bignell, D.R.D. 	Draft Genome Sequence of the Plant Pathogen Streptomyces sp. Strain 11-1-2.	Genome Announcements	2017	5		e00968-17			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. 		
@D	Boybek, A.//Ray, T.D.//Evans, M.C.//Dyson, P.J. 	Novel site-specific DNA modification in Streptomyces: analysis of preferred intragenic modification sites present in a 5.7 kb amplified DNA sequence.	Nucleic Acids Res.	1998	26		3364-3371			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. 		
@D	Boyd, A.C.//Charles, I.G.//Keyte, J.W.//Brammar, W.J. 	Isolation and computer-aided characterization of MmeI, a Type II restriction endonuclease from Methylophilus methylotrophus.	Nucleic Acids Res.	1986	14		5255-5274			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. 		
@D	Boyd, D.A.//Mataseje, L.F.//Pelude, L.//Mitchell, R.//Bryce, E.//Roscoe, D.//Embree, J.//Katz, K.//Kibsey, P.//Lavallee, C.//Simor, A.E.//Taylor, G.//Turgeon, N.//Langley, J.M.//Amaratunga, K.//Mulvey, M.R. 	Results from the Canadian Nosocomial Infection Surveillance Program for detection of carbapenemase-producing Acinetobacter spp. in Canadian hospitals, 2010-16.	J. Antimicrob. Chemother.	2018	0		0			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. 		
@D	Boye, E.//Lobner-Olesen, A. 	The role of dam methyltransferase in the control of DNA replication in E. coli.	Cell	1990	62		981-989			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. 		
@D	Boye, E.//Marinus, M.G.//Lobner-Olesen, A. 	Quantitation of Dam methyltransferase in Escherichia coli.	J. Bacteriol.	1992	174		1682-1685			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. 		
@D	Boyer, H. 	Genetic control of restriction and modification in Escherichia coli.	J. Bacteriol.	1964	88		1652-1660			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. 		
@D	Boyer, H.//Scibienski, E.//Slocum, H.//Roulland-Dussoix, D. 	The in vitro restriction of the replicative form of W.T. and mutant fd phage DNA.	Virology	1971	46		703-710			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. 		
@D	Boyer, H.W. 	DNA restriction and modification mechanisms in bacteria.	Annu. Rev. Microbiol.	1971	25		153-176			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. 		
@D	Boyer, H.W. 	Restriction and modification of DNA: enzymes and substrates.	Fed. Proc.	1974	33		1125-1127			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. 		
@D	Boyer, H.W.//Chow, L.T.//Dugaiczyk, A.//Hedgpeth, J.//Goodman, H.M. 	DNA substrate site for the EcoRII restriction endonuclease and modification methylase.	Nature New Biol.	1973	244		40-43			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. 		
@A	Boyer, H.W.//Greene, P.J.//Meagher, R.B.//Betlach, M.C.//Russel, D.//Goodman, H.M. 		The methylation of DNA as the biochemical basis of host controlled modification of DNA in bacteria.			Antoni, F.//Farago, A. 		FEBS J.				New York	Elsevier	1975		34		23-37									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). 		
@D	Boyer, H.W.//Roulland-Dussoix, D. 	A complementation analysis of the restriction and modification of DNA in Escherichia coli.	J. Mol. Biol.	1969	41		459-472			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. 		
@D	Boyer, M.//Yutin, N.//Pagnier, I.//Barrassi, L.//Fournous, G.//Espinosa, L.//Robert, C.//Azza, S.//Sun, S.//Rossmann, M.G.//Suzan-Monti, M.//La Scola, B.//Koonin, E.V.//Raoult, D. 	Giant Marseillevirus highlights the role of amoebae as a melting pot in emergence of chimeric microorganisms.	Proc. Natl. Acad. Sci. U. S. A.	2009	106		21848-21853			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. 		
@D	Boyle, B.//Fernandez, L.//Laroche, J.//Kukavica-Ibrulj, I.//Mendes, C.M.//Hancock, R.W.//Levesque, R.C. 	Complete Genome Sequences of Three Pseudomonas aeruginosa Isolates with Phenotypes of Polymyxin B Adaptation and Inducible Resistance.	J. Bacteriol.	2012	194		529-530			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). 		
@D	Boyle, B.//Vaillancourt, K.//Bonifait, L.//Charette, S.J.//Gottschalk, M.//Grenier, D. 	Genome Sequence of the Swine Pathogen Streptococcus suis Serotype 2 Strain S735.	J. Bacteriol.	2012	194		6343-6344			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. 		
@D	Bozic, D.//Grazulis, S.//Siksnys, V.//Huber, R. 	Crystal structure of Citrobacter freundii restriction endonuclease Cfr10I at 2.15 A resolution.	J. Mol. Biol.	1996	255		176-186			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. 		
@D	Braasch, J.L.//Lapin, C.N.//Dowd, S.E.//McLaughlin, R.W. 	Draft Genome Sequence of Robinsoniella peoriensis Strain WTD, Isolated from the Fecal Material of a Wood Turtle.	Genome Announcements	2015	3		e01444-14			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. 		
@D	Brabec, V.//Balcarova, Z. 	Restriction-enzyme cleavage of DNA modified by platinum (II) complexes.	Eur. J. Biochem.	1993	216		183-187			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. 		
@D	Brack, C.//Eberle, H.//Bickle, T.A.//Yuan, R. 	Mapping of recognition sites for the restriction endonuclease from Escherichia coli K12 on bacteriophage PM2 DNA.	J. Mol. Biol.	1976	108		583-593			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. 		
@D	Bradbury, M.//Greenfield, P.//Midgley, D.//Li, D.//Tran-Dinh, N.//Vriesekoop, F.//Brown, J.L. 	Draft Genome Sequence of Clostridium sporogenes PA 3679, the Common Nontoxigenic  Surrogate for Proteolytic Clostridium botulinum.	J. Bacteriol.	2012	194		1631-1632			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. 		
@D	Braesel, J.//Crnkovic, C.M.//Kunstman, K.J.//Green, S.J.//Maienschein-Cline, M.//Orjala, J.//Murphy, B.T.//Eustaquio, A.S. 	Complete Genome of Micromonospora sp. Strain B006 Reveals Biosynthetic Potential of a Lake Michigan Actinomycete.	J. Nat. Prod.	2018	81		2057-2068			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. 		
@D	Braga, E.A.//Nosikov, V.V.//Polyanovsky, O.L. 	The use of antibiotics actinomycin D and distamycin A for mapping of phage lambda HindIII fragments.	FEBS Lett.	1976	70		91-95			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. 		
@D	Braga, E.A.//Nosikov, V.V.//Tanyashin, V.I.//Zhuze, A.L.//Polyanovskii, O.L. 	Limitation of the action of restriction endonucleases by antibiotics bound to DNA.	Dokl. Akad. Nauk.	1975	225		707-710			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. 		
@D	Bragin, E.Y.//Shtratnikova, V.Y.//Dovbnya, D.V.//Schelkunov, M.I.//Pekov, Y.A.//Malakho, S.G.//Egorova, O.V.//Ivashina, T.V.//Sokolov, S.L.//Ashapkin, V.V.//Donova, M.V. 	Comparative analysis of genes encoding key steroid core oxidation enzymes in fast-growing Mycobacterium spp. strains.	J. Steroid Biochem. Mol. Biol.	2013	138		41-53			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. 		
@D	Brahmachari, S.K.//Shouche, Y.S.//Cantor, C.R.//McClelland, M. 	Sequences that adopt non-B-DNA conformation in form V DNA as probed by enzymic methylation.	J. Mol. Biol.	1987	193		201-211			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. 		
@D	Braid, M.D.//Silhavy, J.L.//Kitts, C.L.//Cano, R.J.//Howe, M.M. 	Complete Genomic Sequence of Bacteriophage B3, a Mu-Like Phage of Pseudomonas aeruginosa.	J. Bacteriol.	2004	186		6560-6574			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. 		
@D	Brambila-Tapia, A.J.//Poot-Hernandez, A.C.//Perez-Rueda, E.//Rodriguez-Vazquez, K. 	Identification of DNA Methyltransferase Genes in Human Pathogenic Bacteria by Comparative Genomics.	Indian J. Microbiol.	2016	56		134-141			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. 		
@D	Brambilla, E. et al. 	Complete genome sequence of Methanoplanus petrolearius type strain (SEBR 4847).	Standards in Genomic Sciences	2010	3		203-211			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. 		
@D	Brammar, W.J.//Murray, N.E.//Winton, S. 	Restriction of lambda trp bacteriophages by Escherichia coli K.	J. Mol. Biol.	1974	90		633-647			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. 		
@D	Brancaccio, V.F.//Zhurina, D.S.//Riedel, C.U. 	Tough nuts to crack Site-directed mutagenesis of bifidobacteria remains a challenge.	Bioengineered	2013	4		197-202			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. 		
@D	Brandt, J.U.//Jakob, F.//Behr, J.//Geissler, A.J.//Vogel, R.F. 	Dissection of exopolysaccharide biosynthesis in Kozakia baliensis.	Microb. Cell Fact.	2016	15		170			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. 		
@D	Brandt, J.U.//Jakob, F.//Geissler, A.J.//Behr, J.//Vogel, R.F. 	Multiple Genome Sequences of Heteropolysaccharide-Forming Acetic Acid Bacteria.	Genome Announcements	2017	5		e00185-17			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. 		
@D	Branger, M.//Hauer, A.//Michelet, L.//Karoui, C.//Cochard, T.//De Cruz, K.//Henault, S.//Boschiroli, M.L.//Biet, F. 	Draft Genome Sequence of Mycobacterium bovis Strain D-10-02315 Isolated from Wild Boar.	Genome Announcements	2016	4		e01268-16			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. 		
@D	Branger, M.//Hauer, A.//Michelet, L.//Karoui, C.//Cochard, T.//De Cruz, K.//Henault, S.//Boschiroli, M.L.//Biet, F. 	Draft Genome Sequences of Three Mycobacterium bovis Strains Identified in Cattle  and Wildlife in France.	Genome Announcements	2017	5		e00410-17			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. 		
@D	Brank, A.S. 	Development and characterization of DNA methyltransferase inhibitors.	Diss. Abstr.	2001	61		5291-B			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. 		
@D	Brank, A.S.//Eritja, R.//Garcia, R.//Marquez, V.//Christman, J. 	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.	J. Mol. Biol.	2002	323		53-67			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. 		
@D	Brank, A.S.//Van Bemmel, D.M.//Christman, J.K. 	Optimization of baculovirus-mediated expression and purification of  hexahistidine-tagged murine DNA (cytosine-C5)-methyltransferase-1 in   Spodoptera frugiperda 9 cells.	Protein Expr. Purif.	2002	25		31-40			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. 		
@D	Brankatschk, K.//Blom, J.//Goesmann, A.//Smits, T.H.//Duffy, B. 	Genome of a European Fresh-Vegetable Food Safety Outbreak Strain of Salmonella enterica subsp. enterica Serovar Weltevreden.	J. Bacteriol.	2011	193		2066			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. 		
@D	Brassard, S.//Paquet, H.//Roy, P.H. 	A transposon-like sequence adjacent to the AccI restriction-modification operon.	Gene	1995	157		69-72			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. 		
@D	Brathwaite, K.J.//Siringan, P.//Moreton, J.//Wilson, R.//Connerton, I.F. 	Complete Genome Sequence of Universal Bacteriophage Host Strain Campylobacter jejuni subsp. jejuni PT14.	Genome Announcements	2013	1		e00969-13			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. 		
@D	Braun, B.//Kunzel, S.//Schroder, J.//Szewzyk, U. 	Draft Genome Sequence of Actinobacterial Strain Kineosporia sp. R_H_3, a Neutrophilic Iron-Depositing Bacterium.	Genome Announcements	2018	6		e00335-18			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. 		
@D	Braun, B.//Kunzel, S.//Schroder, J.//Szewzyk, U. 	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.	Genome Announcements	2017	5		e00864-17			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. 		
@D	Braun, B.//Kunzel, S.//Szewzyk, U. 	Draft Genome Sequence of the Gram-Positive Neutrophilic Iron-Precipitating Kineosporia sp. Strain A_224.	Genome Announcements	2017	5		e00763-17			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. 		
@D	Braun, B.//Kunzel, S.//Szewzyk, U. 	Draft Genome Sequence of Strain B 225, an Iron-Depositing Isolate of the Genus Novosphingobium.	Genome Announcements	2018	6		e00325-18			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. 		
@D	Braun, B.//Kunzel, S.//Szewzyk, U. 	Draft Genome Sequence of Ideonella sp. Strain A 288, Isolated from an Iron-Precipitating Biofilm.	Genome Announcements	2017	5		e00803-17			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. 		
@D	Braun, B.//Szewzyk, U. 	Complete Genome Sequence of 'Candidatus Viadribacter manganicus' Isolated from a  German Floodplain Area.	Genome Announcements	2016	4		e00897-16			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. 		
@D	Braun, D.R.//Chevrette, M.G.//Acharya, D.//Currie, C.R.//Rajski, S.R.//Ritchie, K.B.//Bugni, T.S. 	Complete Genome Sequence of Dietzia sp. Strain WMMA184, a Marine Coral-Associated Bacterium.	Genome Announcements	2018	6		e01582-17			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. 		
@D	Braun, D.R.//Chevrette, M.G.//Acharya, D.D.//Currie, C.R.//Rajski, S.R.//Bugni, T.S. 	Draft Genome Sequence of Micromonospora sp. Strain WMMA1996, a Marine Sponge-Associated Bacterium.	Genome Announcements	2018	6		e00077-18			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. 		
@D	Braun, J. 	Structural study of the inhibition of DNA (cytosine-5) methyltransferases by original non-nucleoside inhibitors.	Chim. Nouv.	2010	28		20-22					
@D	Bravo, J.I.//Lozano, G.L.//Handelsman, J. 	Draft Genome Sequence of Flavobacterium johnsoniae CI04, an Isolate from the Soybean Rhizosphere.	Genome Announcements	2017	5		e01535-16			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. 		
@D	Brawand, S.G.//Rychener, L.//Schwendener, S.//Pantucek, R.//Perreten, V. 	Complete Genome Sequence of the Type Strain of Macrococcus canis.	Genome Announcements	2018	6		e01507-17			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). 		
@D	Brawer, R.//Batista, F.D.//Burrone, O.//Sordelli, D.O.//Cerquetti, M.C. 	The dam methyltransferase of a Salmonella typhimurium insertion mutant.	Abstr. Gen. Meet. Am. Soc. Microbiol.	1996	96		500			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. 		
@D	Brawer, R.//Batista, F.D.//Burrone, O.R.//Sordelli, D.O.//Cerquetti, M.C. 	A temperature-sensitive DNA adenine methyltransferase mutant of Salmonella typhimurium.	Arch. Microbiol.	1998	169		530-533			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. 		
@D	Breakwell, D.P.//Barrus, E.Z.//Benedict, A.B.//Brighton, A.K.//Fisher, J.N.//Gardner, A.V.//Kartchner, B.J.//Ladle, K.C.//Lunt, B.L.//Merrill, B.D.//Morrell, J.D.//Burnett, S.H.//Grose, J.H. 	Genome Sequences of Five B1 Subcluster Mycobacteriophages.	Genome Announcements	2013	1		e00968-13			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. 		
@D	Brede, D.A.//Snipen, L.G.//Ussery, D.W.//Nederbragt, A.J.//Nes, I.F. 	Complete genome sequence of the commensal Enterococcus faecalis 62 isolated from a healthy Norwegian infant.	J. Bacteriol.	2011	193		2377-2378			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. 		
@D	Breider, S. et al. 	Genome sequence and emended description of Leisingera nanhaiensis strain DSM 24252(T) isolated from marine sediment.	Standards in Genomic Sciences	2014	9		687-703			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. 		
@D	Breitbart, M.//Haynes, M.//Kelley, S.//Angly, F.//Edwards, R.A.//Felts, B.//Mahaffy, J.M.//Mueller, J.//Nulton, J.//Rayhawk, S.//Rodriguez-Brito, B.//Salamon, P.//Rohwer, F. 	Viral diversity and dynamics in an infant gut.	Res. Microbiol.	2008	159		367-373			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. 		
@D	Breitbart, M.//Hewson, I.//Felts, B.//Mahaffy, J.M.//Nulton, J.//Salamon, P.//Rohwer, F. 	Metagenomic analyses of an uncultured viral community from human feces.	J. Bacteriol.	2003	185		6220-6223			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. 		
@D	Breitbart, M.//Salamon, P.//Andresen, B.//Mahaffy, J.M.//Segall, A.M.//Mead, D.//Azam, F.//Rohwer, F. 	Genomic analysis of uncultured marine viral communities.	Proc. Natl. Acad. Sci. U. S. A.	2002	99		14250-14255			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. 		
@D	Bremer, M.C.D.//Gimble, F.S.//Thorner, J.//Smith, C.L. 	VDE endonuclease cleaves Saccharomyces cerevisiae genomic DNA at a single site: physical mapping of the VMA1 gene.	Nucleic Acids Res.	1992	20		5484			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. 		
@D	Brendler, T.//Austin, S. 	Binding of SeqA protein to DNA requires interaction between two or more complexes bound to separate hemimethylated GATC sequences.	EMBO J.	1999	18		2304-2310			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. 		
@D	Brennan, C.A.//Gumport, R.I. 	T4 RNA ligase catalyzed synthesis of base analogue-containing oligodeoxyribonucleotides and a characterization of their thermal stabilities.	Nucleic Acids Res.	1985	13		8665-8684			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. 		
@D	Brennan, C.A.//Van Cleve, M.D.//Gumport, R.I. 	The effects of base analogue substitutions on the methylation by the EcoRI modification methylase of octadeoxyribonucleotides containing modified EcoRI recognition sequences.	J. Biol. Chem.	1986	261		7279-7286			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. 		
@D	Brennan, C.A.//Van Cleve, M.D.//Gumport, R.I. 	The effects of base analogue substitutions on the cleavage by the EcoRI restriction endonuclease of octadeoxyribonucleotides containing modified EcoRI recognition sequences.	J. Biol. Chem.	1986	261		7270-7278			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. 		
@D	Brennan, M.A.//Trachtenberg, A.M.//McClelland, W.D.//MacLea, K.S. 	Genome Sequence of Oceanimonas doudoroffii ATCC 27123T.	Genome Announcements	2017	5		e00996-17			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. 		
@D	Brenneman, M.//Gimble, F.S.//Wilson, J.H. 	Stimulation of intrachromosomal homologous recombination in human cells by electroporation with site-specific endonucleases.	Proc. Natl. Acad. Sci. U. S. A.	1996	93		3608-3612			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. 		
@D	Brenner, C.//Fuks, F. 	DNA methyltransferases: Facts, clues, mysteries.	Curr. Top. Microbiol. Immunol.	2006	301		45-66			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. 		
@D	Brenner, E.V.//Brouchkov, A.V.//Kurilshikov, A.M.//Griva, G.I.//Kashuba, E.//Kashuba, V.I.//Melefors, O.//Repin, V.E.//Melnikov, V.P.//Vlassov, V.V. 	Draft Genome Sequence of Bacillus cereus Strain F, Isolated from Ancient Permafrost.	Genome Announcements	2013	1		e00561-13			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. 		
@D	Brenner, V.//Focht, D.D. 	Cloning of the Type II methyltransferase from chlorobenzoate degrader Pseudomonas putida P111.	Abstr. Gen. Meet. Am. Soc. Microbiol.	1994	94		459			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. 		
@D	Brenner, V.//Venetianer, P.//Kiss, A. 	Cloning and nucleotide sequence of the gene encoding the EcaI DNA methyltransferase.	Nucleic Acids Res.	1990	18		355-359			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. 		
@D	Brenot, A.//Werts, C.//Ottone, C.//Sertour, N.//Charon, N.W.//Postic, D.//Baranton, G.//Saint, G.I. 	First evidence for a restriction-modification system in Leptospira sp.	FEMS Microbiol. Lett.	2001	201		139-143			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. 		
@D	Brensing-Kuppers, J.//Reischl, U.//Schmitz, G.S.//Kaluza, K.//Jarsch, M.//Kessler, C. 	McrI:  a novel class-II restriction endonuclease from Micrococcus cryophilus recognizing 5'-CGRY/CG-3'.	FEBS Lett.	1990	264		218-222			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. 		
@D	Brevnov, M.G.//Gritsenko, O.M.//Mikhailov, S.N.//Efimtseva, E.V.//Ermolinsky, B.S.//Van Aeroschot, A.//Herdewijn, P.//Repyk, A.V.//Gromova, E.S. 	DNA duplexes with reactive dialdehyde groups as novel reagents for cross-linking to restriction-modification enzymes.	Nucleic Acids Res.	1997	25		3302-3309			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. 		
@D	Brevnov, M.G.//Kubareva, E.A.//Romanova, E.A.//Volkov, E.M.//Karyagina, A.S.//Nikolskaya, I.I.//Gromova, E.S. 	Interaction of the MvaI and SsoII methyltransferases with DNAs altered at the central base pair of the recognition sequence.	Gene	1995	157		149-152			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. 		
@D	Brevnov, M.G.//Kubareva, E.A.//Volkov, E.M.//Romanova, E.A.//Oretskaya, T.S.//Gromova, E.S.//Shabarova, Z.A. 	Influence of a single modification of the DNA sugar-phosphate backbone on the functioning of restriction endonucleases EcoRII, MvaI, and BstNI.	Mol. Biol. (Mosk)	1995	29		1294-1300			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. 		
@D	Brewer, R.J.M.//Haskett, T.L.//Ramsay, J.P.//O'Hara, G.W.//Terpolilli, J.J. 	Complete Genome Sequence of Mesorhizobium ciceri bv. biserrulae WSM1497, an Efficient Nitrogen-Fixing Microsymbiont of the Forage Legume Biserrula pelecinus.	Genome Announcements	2017	5		e00902-17			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). 		
@D	Brezellec, P.//Hoebeke, M.//Hiet, M.S.//Pasek, S.//Ferat, J.L. 	DomainSieve: a protein domain-based screen that led to the identification of dam-associated genes with potential link to DNA maintenance.	Bioinformatics	2006	22		1935-1941			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. 		
@D	Brickner, M.//Chmielewski, J. 	Inhibiting the dimeric restriction endonuclease EcoRI using interfacial helical peptides.	Chem. Biol.	1998	5		339-343			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. 		
@D	Bridger, S.L.//Lancaster, W.A.//Poole, F.L.I.I.//Schut, G.J.//Adams, M.W. 	Genome Sequencing of a Genetically Tractable Pyrococcus furiosus Strain Reveals a Highly Dynamic Genome.	J. Bacteriol.	2012	194		4097-4106			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. 		
@D	Briers, Y.//Klumpp, J.//Schuppler, M.//Loessner, M.J. 	Genome Sequence of Listeria monocytogenes Scott A, a Clinical Isolate from a Food-Borne Listeriosis Outbreak.	J. Bacteriol.	2011	193		4284-4285			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. 		
@D	Briggs, R.E.//Tatum, F.M. 	Generation and molecular characterization of new temperature-sensitive plasmids intended for genetic engineering of Pasteurellaceae.	Appl. Environ. Microbiol.	2005	71		7187-7195			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. 		
@A	Briggs, R.E.//Tatum, F.M. 		Characterization of a restriction endonuclease from Pasteurella haemolytica serotype A1 and construction of a gene-replacement Aroa mutant.			Donachie, W.//Lainson, F.A.//Hodgson, J.C. 		Haemophilus, Actinobacillus and Pasteurella				New York	Plenum Press	1995		0		221-222									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. 		
@D	Briggs, R.E.//Tatum, F.M.//Casey, T.A.//Frank, G.H. 	Characterization of a restriction endonuclease, PhaI, from Pasteurella haemolytica Serotype A1 and protection of heterologous DNA by a cloned PhaI methyltransferase gene.	Appl. Environ. Microbiol.	1994	60		2006-2010			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. 		
@D	Briggs, R.E.//Tatum, F.M.//Casey, T.A.//Frank, G.H. 	Characterization of a restriction endonuclease, PhaI, from Pasteurella haemolytica serotype A1 and protection of heterologous DNA by cloned PhaI methyltransferase.	Abstr. Gen. Meet. Am. Soc. Microbiol.	1994	94		132			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. 		
@D	Bringel, F. et al. 	Genome Sequence of the Dichloromethane-Degrading Bacterium Hyphomicrobium sp. Strain GJ21.	Genome Announcements	2017	5		e00622-17			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. 		
@D	Brinkley, C.//Burland, V.//Keller, R.//Rose, D.J.//Boutin, A.T.//Klink, S.A.//Blattner, F.R.//Kaper, J.B. 	Nucleotide Sequence Analysis of the Enteropathogenic Escherichia coli Adherence Factor Plasmid pMAR7.	Infect. Immun.	2006	74		5408-5413			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. 		
@D	Brinkley, P.//Bautista, D.S.//Graham, F.L. 	The cleavage site of restriction endonuclease MnlI.	Gene	1991	100		267-268			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. 		
@D	Brinkrolf, K.//Schneider, J.//Knecht, M.//Ruckert, C.//Tauch, A. 	Draft Genome Sequence of Turicella otitidis ATCC 51513, Isolated from Middle Ear  Fluid from a Child with Otitis Media.	J. Bacteriol.	2012	194		5968-5969			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. 		
@D	Brizendine, A.M.//Rousseau, S.//Hernandez, A.C.//Kuty, E.G.F. 	Complete Genome Sequence of Bacillus megaterium Siphophage Stahl.	Genome Announcements	2015	3		e00857-15			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. 		
@D	Brnakova, Z.//Farkasovska, J.//Godany, A. 	The use of bacteriophages in eliminating polyresistant strains of Staphylococcus aureus and Streptococcus agalactiae.	Folia Microbiol. (Praha)	2005	50		187-194			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. 		
@D	Broadbent, J.R.//Hughes, J.E.//Welker, D.L.//Tompkins, T.A.//Steele, J.L. 	Complete Genome Sequence for Lactobacillus helveticus CNRZ 32, an Industrial Cheese Starter and Cheese Flavor Adjunct.	Genome Announcements	2013	1		e00590-13			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. 		
@D	Broadbent, J.R.//Neeno-Eckwall, E.C.//Stahl, B.//Tandee, K.//Cai, H.//Morovic, W.//Horvath, P.//Heidenreich, J.//Perna, N.T.//Barrangou, R.//Steele, J.L. 	Analysis of the Lactobacillus casei supragenome and its influence in species evolution and lifestyle adaptation.	BMC Genomics	2012	13		533			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. 		
@D	Broadbent, S.E.//Balbontin, R.//Casadesus, J.//Marinus, M.G.//van der Woude, M. 	YhdJ, a Nonessential CcrM-Like DNA Methyltransferase of Escherichia coli and Salmonella enterica.	J. Bacteriol.	2007	189		4325-4327			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. 		
@D	Broberg, C.A.//Palacios, M.//Miller, V.L. 	Whole-Genome Draft Sequences of Three Multidrug-Resistant Klebsiella pneumoniae Strains Available from the American Type Culture Collection.	Genome Announcements	2013	1		e00312-13			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. 		
@D	Broberg, C.A.//Wu, W.//Cavalcoli, J.D.//Miller, V.L.//Bachman, M.A. 	Complete Genome Sequence of Klebsiella pneumoniae Strain ATCC 43816 KPPR1, a Rifampin-Resistant Mutant Commonly Used in Animal, Genetic, and Molecular Biology  Studies.	Genome Announcements	2014	2		e00924-14			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. 		
@D	Brocchi, M.//de Vasconcelos, A.T.R.//Zaha, A. 	Restriction-modification systems in Mycoplasma spp.	Genet. Mol. Biol.	2007	30		236-244			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. 		
@D	Brockes, J.P. 	Nucleotide sequences at the sites of action of the deoxyribonucleic acid modification enzyme of bacteriophage P1.	J. Mol. Biol.	1974	88		437-443			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. 		
@D	Brockes, J.P. 	The deoxyribonucleic acid-modification enzyme of bacteriophage P1. Subunit structure.	Biochem. J.	1973	133		629-633			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. 		
@D	Brockes, J.P.//Brown, P.R.//Murray, K. 	The deoxyribonucleic acid modification enzyme of bacteriophage P1: Purification and properties.	Biochem. J.	1972	127		1-10			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. 		
@D	Brok-Volchanskaya, V.S.//Kadyrov, F.A.//Sivogrivov, D.E.//Kolosov, P.M.//Sokolov, A.S.//Shlyapnikov, M.G.//Kryukov, V.M.//Granovsky, I.E. 	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.	Nucleic Acids Res.	2008	36		2094-2105			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. 		
@D	Brolund, A.//Franzen, O.//Melefors, O.//Tegmark-Wisell, K.//Sandegren, L. 	Plasmidome-Analysis of ESBL-Producing Escherichia coli Using Conventional Typing and High-Throughput Sequencing.	PLoS ONE	2013	8		E65793			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. 		
@D	Bromberg, S.//Pratt, K.//Hattman, S. 	Sequence specificity of DNA adenine methylase in the protozoan Tetrahymena thermophila.	J. Bacteriol.	1982	150		993-996			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. 		
@D	Bromfield, E.S.P.//Cloutier, S.//Tambong, J.T.//Tran-Thi, T.V. 	Soybeans inoculated with root zone soils of Canadian native legumes harbour diverse and novel Bradyrhizobium spp. that possess agricultural potential.	Syst. Appl. Microbiol.	2017	40		440-447			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. 		
@D	Bron, P.A.//Lee, I.C.//Backus, L.//van Hijum, S.A.//Wels, M.//Kleerebezem, M. 	Draft Genome Sequence of Lactobacillus plantarum SF2A35B.	Genome Announcements	2016	4		e01638-15			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. 		
@D	Bron, S.//Horz, W. 	Purification and properties of the Bsu endonuclease.	Methods Enzymol.	1980	65		112-132			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. 		
@D	Bron, S.//Janniere, L.//Ehrlich, S.D. 	Restriction and modification in Bacillus subtilis Marburg 168:  Target sites and effects on plasmid transformation.	Mol. Gen. Genet.	1988	211		186-189			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. 		
@D	Bron, S.//Luxen, E.//Trautner, T.A. 	Restriction and modification in B. subtilis:  the role of homology between donor and recipient DNA in transformation and transfection.	Mol. Gen. Genet.	1980	179		111-117			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. 		
@D	Bron, S.//Luxen, E.//Venema, G. 	Resistance of bacteriophage H1 to restriction and modification by Bacillus subtilis R.	J. Virol.	1983	46		703-708			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. 		
@D	Bron, S.//Luxen, E.//Venema, G. 	Restriction and modification in Bacillus subtilis: Effects on transfection under marker rescue conditions.	J. Virol.	1982	42		357-364			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. 		
@D	Bron, S.//Luxen, E.//Venema, G. 	Restriction of hemimethylated DNA by the Bacillus subtilis R system.	Mol. Gen. Genet.	1984	195		370-373			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. 		
@D	Bron, S.//Luxen, E.//Venema, G.//Trautner, T. 	Restriction and modification in B. subtilis:  Effects on transformation and transfection with native and single-stranded DNA.	Mol. Gen. Genet.	1980	179		103-110			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. 		
@D	Bron, S.//Murray, K. 	Restriction and modification in B. subtilis: Nucleotide sequence recognized by restriction endonuclease R.BsuR from strain R.	Mol. Gen. Genet.	1975	143		25-33			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. 		
@D	Bron, S.//Murray, K.//Trautner, T.A. 	Restriction and Modification in B. subtilis:  Purification and General Properties of a Restriction Endonuclease from Strain R.	Mol. Gen. Genet.	1975	143		13-23			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. 		
@D	Bronnec, V.//Haddad, N.//Cruveiller, S.//Hernould, M.//Tresse, O.//Zagorec, M. 	Draft Genome Sequence of Campylobacter jejuni Bf, an Atypical Strain Able To Grow under Aerobiosis.	Genome Announcements	2016	4		e00120-16			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. 		
@D	Brooks, J.//Hattman, S. 	Location of the DNA-adenine methylase gene on the genetic map of phage T2.	Virology	1973	55		285-288			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. 		
@D	Brooks, J.//Masurekar, M.//Hattman, S. 	In vitro methylation of phage lambda.	Abstr. Gen. Meet. Am. Soc. Microbiol.	1975	75		225			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. 		
@D	Brooks, J.E. 	Properties and uses of restriction endonucleases.	Methods Enzymol.	1987	152		113-129			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. 		
@D	Brooks, J.E. 	A comparative study of the wild type and mutant forms of phage T2 DNA-adenine methylase.	Ph.D. Thesis, University of Rochester	1977			1-188			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. 		
@D	Brooks, J.E.//Benner, J.S.//Heiter, D.F.//Silber, K.R.//Sznyter, L.A.//Jager-Quinton, T.//Moran, L.S.//Slatko, B.E.//Wilson, G.G.//Nwankwo, D.O. 	Cloning the BamHI restriction modification system.	Nucleic Acids Res.	1989	17		979-997			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. 		
@D	Brooks, J.E.//Benner, J.S.//Silber, K.R.//Heiter, D.F.//Sznyter, L.A.//Jager-Quinton, T.//Wilson, G.G.//Moran, L.S.//Slatko, B.E.//Nwankwo, D.O. 	Cloning and characterization of the BamHI restriction modification system.	Gene	1988	74		13			Meeting Abstract 		
@D	Brooks, J.E.//Blumenthal, R.M.//Gingeras, T.R. 	The isolation and characterization of the Escherichia coli DNA adenine methylase (dam) gene.	Nucleic Acids Res.	1983	11		837-851			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. 		
@D	Brooks, J.E.//Hattman, S. 	In vitro methylation of bacteriophage lambda DNA by wild type (dam+) mutant (damh) forms of the phage T2 DNA adenine methylase.	J. Mol. Biol.	1978	126		381-394			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. 		
@D	Brooks, J.E.//Nathan, P.D.//Landry, D.//Sznyter, L.A.//Waite-Rees, P.//Ives, C.L.//Moran, L.S.//Slatko, B.E.//Benner, J.S. 	Characterization of the cloned BamHI restriction modification system:  its nucleotide sequence, properties of the methylase, and expression in heterologous hosts.	Nucleic Acids Res.	1991	19		841-850			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. 		
@D	Brooks, J.E.//Nwankwo, D.//Sznyter, L.//Jager, T.//Wilson, G.//Heiter, D.//Slatko, B.//Benner, J. 	Cloning of the BamHI restriction-modification system.	Abstr. Gen. Meet. Am. Soc. Microbiol.	1987	87		154			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. 		
@D	Brooks, J.E.//Roberts, R.J. 	Modification profiles of bacterial genomes.	Nucleic Acids Res.	1982	10		913-934			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. 		
@D	Brooks, J.E.//Sznyter, L.//Vaccaro, C.//Arnaud, M.//Jager-Quinton, T.//Wilson, G.//Moran, L.//Slatko, B.//Bernan, V. 	Cloning and characterization of the SphI restriction modification system from Streptomyces phaeochromogenes.	J. Cell Biochem. Suppl.	1990	14A		106			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. 		
@D	Brooks, S.L.//Van Hamme, J.D. 	Whole-Genome Shotgun Sequence of Rhodococcus Species Strain JVH1.	J. Bacteriol.	2012	194		5492-5493			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. 		
@D	Brouwer, M.S.//Allan, E.//Mullany, P.//Roberts, A.P. 	Draft Genome Sequence of the Nontoxigenic Clostridium difficile Strain CD37.	J. Bacteriol.	2012	194		2125-2126			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. 		
@D	Brovedan, M.//Marchiaro, P.M.//Moran-Barrio, J.//Revale, S.//Cameranesi, M.//Brambilla, L.//Viale, A.M.//Limansky, A.S. 	Draft Genome Sequence of Acinetobacter bereziniae HPC229, a Carbapenem-Resistant  Clinical Strain from Argentina Harboring blaNDM-1.	Genome Announcements	2016	4		e00117-16			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. 		
@D	Brown, C.J.//Sen, D.//Yano, H.//Bauer, M.L.//Rogers, L.M.//Van der Auwera, G.A.//Top, E.M. 	Diverse broad-host-range plasmids from freshwater carry few accessory genes.	Appl. Environ. Microbiol.	2013	79		7684-7695			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. 		
@D	Brown, C.T.//Hug, L.A.//Thomas, B.C.//Sharon, I.//Castelle, C.J.//Singh, A.//Wilkins, M.J.//Williams, K.H.//Banfield, J.F. 	rRNA introns, odd ribosomes, and small enigmatic genomes across a large radiation of phyla.	Nature	2015	523		208			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. 		
@D	Brown, D.R.//May, M.//Michaels, D.L.//Barbet, A.F. 	Genome Annotation of Five Mycoplasma canis Strains.	J. Bacteriol.	2012	194		4138-4139			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. 		
@D	Brown, F.L.//Musich, P.R.//Maio, J. 	Cae I: an endonuclease isolated from the African green monkey with properties indicating site-specific cleavage of homologous and heterologous mammalian DNA.	Nucleic Acids Res.	1978	5		1093-1107			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. 		
@D	Brown, L.M.//Gunasekera, T.S.//Bowen, L.L.//Ruiz, O.N. 	Draft Genome Sequence of Rhodovulum sp. Strain NI22, a Naphthalene-Degrading Marine Bacterium.	Genome Announcements	2015	3		e01475-14			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. 		
@D	Brown, L.M.//Gunasekera, T.S.//Ruiz, O.N. 	Draft Genome Sequence of Pseudomonas stutzeri Strain 19, an Isolate Capable of Efficient Degradation of Aromatic Hydrocarbons.	Genome Announcements	2017	5		e01373-17			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. 		
@D	Brown, L.M.//Gunasekera, T.S.//Ruiz, O.N. 	Draft Genome Sequence of Nocardioides luteus Strain BAFB, an Alkane-Degrading Bacterium Isolated from JP-7-Polluted Soil.	Genome Announcements	2017	5		e01529-16			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. 		
@D	Brown, L.M.//Gunasekera, T.S.//Ruiz, O.N. 	Draft Genome Sequence of Pseudomonas aeruginosa ATCC 33988, a Bacterium Highly Adapted to Fuel-Polluted Environments.	Genome Announcements	2014	2		e01113-14			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. 		
@D	Brown, L.M.//Gunasekera, T.S.//Striebich, R.C.//Ruiz, O.N. 	Draft Genome Sequence of Gordonia sihwensis Strain 9, a Branched Alkane-Degrading Bacterium.	Genome Announcements	2016	4		e00622-16			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. 		
@D	Brown, N.L. 	Sequence determination of restriction-endonuclease recognition sites.	Biochem. Soc. Trans.	1980	8		398-399			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. 		
@D	Brown, N.L.//Hutchison, C.A. III//Smith, M. 	The specific non-symmetrical sequence recognized by restriction endonuclease MboII.	J. Mol. Biol.	1980	140		143-148			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. 		
@D	Brown, N.L.//McClelland, M.//Whitehead, P.R. 	HgiAI: A restriction endonuclease from Herpetosiphon giganteus HP1023.	Gene	1980	9		49-68			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. 		
@D	Brown, N.L.//Smith, M. 	A general method for defining restriction enzyme cleavage and recognition sites.	Methods Enzymol.	1980	65		391-404			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. 		
@D	Brown, N.L.//Smith, M. 	The mapping and sequence determination of the single site in PhiX174am3 replicative form DNA cleaved by restriction endonuclease PstI.	FEBS Lett.	1976	65		284-287			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. 		
@D	Brown, N.L.//Smith, M. 	Cleavage specificity of the restriction endonuclease isolated from Haemophilus gallinarum (HgaI).	Proc. Natl. Acad. Sci. U. S. A.	1977	74		3213-3216			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. 		
@D	Brown, N.P.//Sander, C.//Bork, P. 	Frame: detection of genomic sequencing errors.	Bioinformatics	1998	14		367-371			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. 		
@D	Brown, S.D. et al. 	Genome Sequence of the Mercury-Methylating Strain Desulfovibrio desulfuricans ND132.	J. Bacteriol.	2011	193		2078-2079			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. 		
@D	Brown, S.D.//Begemann, M.B.//Mormile, M.R.//Wall, J.D.//Han, C.S.//Goodwin, L.A.//Pitluck, S.//Land, M.L.//Hauser, L.J.//Elias, D.A. 	Complete Genome Sequence of the Haloalkaliphilic, Hydrogen-Producing bacterium Halanaerobium hydrogenoformans.	J. Bacteriol.	2011	193		3682-3683			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. 		
@D	Brown, S.D.//Hurt, R.A. Jr.//Gilmour, C.C.//Elias, D.A. 	Draft genome sequences for three mercury-methylating, sulfate-reducing bacteria.	Genome Announcements	2013	1		e00618-13			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. 		
@D	Brown, S.D.//Jun, S. 	Complete Genome Sequence of Escherichia coli NCM3722.	Genome Announcements	2015	3		e00879-15			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. 		
@D	Brown, S.D.//Klingeman, D.M.//Lu, T.Y.//Johnson, C.M.//Utturkar, S.M.//Land, M.L.//Schadt, C.W.//Doktycz, M.J.//Pelletier, D.A. 	Draft Genome Sequence of Rhizobium sp. Strain PDO1-076, a Bacterium Isolated from Populus deltoides.	J. Bacteriol.	2012	194		2383-2384			Rhizobium sp. strain PDO1-076 is a plant-associated bacterium isolated from Populus deltoides, and its draft genome sequence is reported. 		
@D	Brown, S.D.//Lamed, R.//Morag, E.//Borovok, I.//Shoham, Y.//Klingeman, D.M.//Johnson, C.M.//Yang, Z.//Land, M.L.//Utturkar, S.M.//Keller, M.//Bayer, E.A. 	Draft Genome Sequences for Clostridium thermocellum Wild-Type Strain YS and Derived Cellulose Adhesion-Defective Mutant Strain AD2.	J. Bacteriol.	2012	194		3290-3291			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. 		
@D	Brown, S.D.//Palumbo, A.V.//Panikov, N.//Ariyawansa, T.//Klingeman, D.M.//Johnson, C.M.//Land, M.L.//Utturkar, S.M.//Epstein, S.S. 	Draft Genome Sequence for Microbacterium laevaniformans Strain OR221, a Bacterium Tolerant to Metals, Nitrate, and Low pH.	J. Bacteriol.	2012	194		3279-3280			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. 		
@D	Brown, S.D.//Podar, M.//Klingeman, D.M.//Johnson, C.M.//Yang, Z.K.//Utturkar, S.M.//Land, M.L.//Mosher, J.J.//Hurt, R.A. Jr.//Phelps, T.J.//Palumbo, A.V.//Arkin, A.P.//Hazen, T.C.//Elias, D.A. 	Draft Genome Sequences for Two Metal-Reducing Pelosinus fermentans Strains Isolated from a Cr(VI)-Contaminated Site and for Type Strain R7.	J. Bacteriol.	2012	194		5147-5148			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. 		
@D	Brown, S.D.//Utturkar, S.M.//Arkin, A.P.//Deutschbauer, A.M.//Elias, D.A.//Hazen, T.C.//Chakraborty, R. 	Draft Genome Sequence for Desulfovibrio africanus Strain PCS.	Genome Announcements	2013	1		e00144-13			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. 		
@D	Brown, S.D.//Utturkar, S.M.//Klingeman, D.M.//Johnson, C.M.//Martin, S.L.//Land, M.L.//Lu, T.Y.//Schadt, C.W.//Doktycz, M.J.//Pelletier, D.A. 	Twenty-One Genome Sequences from Pseudomonas Species and 19 Genome Sequences from Diverse Bacteria Isolated from the Rhizosphere and Endosphere of Populus  deltoides.	J. Bacteriol.	2012	194		5991-5993			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. 		
@D	Brown, S.D.//Utturkar, S.M.//Magnuson, T.S.//Ray, A.E.//Poole, F.L.//Lancaster, W.A.//Thorgersen, M.P.//Adams, M.W.//Elias, D.A. 	Complete Genome Sequence of Pelosinus sp. Strain UFO1 Assembled Using Single-Molecule Real-Time DNA Sequencing Technology.	Genome Announcements	2014	2		e00881-14			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. 		
@D	Brown, S.D.//Wall, J.D.//Kucken, A.M.//Gilmour, C.C.//Podar, M.//Brandt, C.C.//Teshima, H.//Detter, J.C.//Han, C.S.//Land, M.L.//Lucas, S.//Han, J.//Pennacchio, L.//Nolan, M.//Pitluck, S.//Woyke, T.//Goodwin, L.//Palumbo, A.V.//Elias, D.A. 	Genome Sequence of the Mercury-Methylating and Pleomorphic Desulfovibrio africanus strain Walvis Bay.	J. Bacteriol.	2011	193		4037-4038			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. 		
@D	Brown, T.A. 	Restriction and modification.	Essential Molecular Biology	1991	2		260-284			*
 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.
 
 		
@D	Brown, W.M.//Vinograd, J. 	Restriction endonuclease cleavage maps of animal mitochondrial DNAs.	Proc. Natl. Acad. Sci. U. S. A.	1974	71		4617-4621			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. 		
@D	Browne, A.S.//Biggs, P.J.//Elliott, A.//Jaros, P.//French, N.P.//Midwinter, A.C. 	Draft Whole-Genome Sequences of Three Diarrheagenic Escherichia coli Strains Isolated from Farmed Deer in New Zealand.	Genome Announcements	2018	6		e00300-18			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. 		
@D	Brownlee, C. 	Danna and Nathans: Restriction enzymes and the boon to modern molecular biology.	Proc. Natl. Acad. Sci. U. S. A.	2005	102		5909			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. 		
@D	Bruce, T.//Leite, F.G.//Tschoeke, D.A.//Miranda, M.//Pereira, N. Jr.//Valle, R.//Thompson, C.C.//Thompson, F.L. 	Exploring the Genome of a Butyric Acid Producer, Clostridium butyricum INCQS635.	Genome Announcements	2014	2		e01169-14			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. 		
@D	Brueckner, B.//Kuck, D.//Lyko, F. 	DNA methyltransferase inhibitors for cancer therapy.	Cancer J.	2007	13		17-22			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. 		
@D	Bruffaerts, N.//Vluggen, C.//Duytschaever, L.//Mathys, V.//Saegerman, C.//Chapeira, O.//Huygen, K. 	Genome Sequences of Four Strains of Mycobacterium avium subsp. hominissuis, Isolated from Swine and Humans, Differing in Virulence in a Murine Intranasal  Infection Model.	Genome Announcements	2016	4		e00533-16			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. 		
@D	Bruggemann, H.//Baumer, S.//Fricke, W.F.//Wiezer, A.//Liesegang, H.//Decker, I.//Herzberg, C.//Martinez-Arias, R.//Merkl, R.//Henne, A.//Gottschalk, G. 	The genome sequence of Clostridium tetani, the causative agent of tetanus disease.	Proc. Natl. Acad. Sci. U. S. A.	2003	100		1316-1321			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. 		
@D	Bruggemann, H.//Henne, A.//Hoster, F.//Liesegang, H.//Wiezer, A.//Strittmatter, A.//Hujer, S.//Durre, P.//Gottschalk, G. 	The Complete Genome Sequence of Propionibacterium Acnes, a Commensal of Human Skin.	Science	2004	305		671-673			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. 		
@D	Brumm, P.//Land, M.L.//Hauser, L.J.//Jeffries, C.D.//Chang, Y.J.//Mead, D.A. 	Complete genome sequences of Geobacillus sp. Y412MC52, a xylan-degrading strain isolated from obsidian hot spring in Yellowstone National Park.	Standards in Genomic Sciences	2015	10		81			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. 		
@D	Brumm, P.J.//Land, M.L.//Mead, D.A. 	Complete genome sequences of Geobacillus sp. WCH70, a thermophilic strain isolated from wood compost.	Standards in Genomic Sciences	2016	11		33			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. 		
@D	Brumm, P.J.//Land, M.L.//Mead, D.A. 	Complete genome sequence of Geobacillus thermoglucosidasius C56-YS93, a novel biomass degrader isolated from obsidian hot spring in Yellowstone National Park.	Standards in Genomic Sciences	2015	10		73			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. 		
@D	Brumm, P.J.//Monsma, S.//Keough, B.//Jasinovica, S.//Ferguson, E.//Schoenfeld, T.//Lodes, M.//Mead, D.A. 	Complete Genome Sequence of Thermus aquaticus Y51MC23.	PLoS ONE	2015	10		e0138674			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. 		
@D	Bruna, R.E.//Revale, S.//Garcia, V.E.//Mariscotti, J.F. 	Draft Whole-Genome Sequence of Serratia marcescens Strain RM66262, Isolated from  a Patient with a Urinary Tract Infection.	Genome Announcements	2015	3		e01423-15			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. 		
@D	Brunder, W.//Karch, H.//Schmidt, H. 	Complete sequence of the large virulence plasmid pSFO157 of the sorbitol-fermenting enterohemorrhagic Escherichia coli O157:H(-) strain 3072/96.	Int. J. Med. Microbiol.	2006	296		467-474			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. 		
@D	Brunet-Galmes, I.//Busquets, A.//Pena, A.//Gomila, M.//Nogales, B.//Garcia-Valdes, E.//Lalucat, J.//Bennasar, A.//Bosch, R. 	Complete Genome Sequence of the Naphthalene-Degrading Bacterium Pseudomonas stutzeri AN10 (CCUG 29243).	J. Bacteriol.	2012	194		6642-6643			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. 		
@D	Bruno, D.D.C.F.//Bartelli, T.F.//Briones, M.R.S. 	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.	Genome Announcements	2018	6		e00533-18			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. 		
@D	Bruno-Barcena, J.M.//Chinn, M.S.//Grunden, A.M. 	Genome Sequence of the Autotrophic Acetogen Clostridium autoethanogenum JA1-1 Strain DSM 10061, a Producer of Ethanol from Carbon Monoxide.	Genome Announcements	2013	1		e00628-13			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. 		
@D	Bryanskaya, A.V.//Rozanov, A.S.//Logacheva, M.D.//Kotenko, A.V.//Peltek, S.E. 	Draft Genome Sequence of Geobacillus icigianus Strain G1w1T Isolated from Hot Springs in the Valley of Geysers, Kamchatka (Russian Federation).	Genome Announcements	2014	2		e01098-14			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. 		
@D	Bryant, D.A.//Costas, A.M.//Maresca, J.A.//Chew, A.G.//Klatt, C.G.//Bateson, M.M.//Tallon, L.J.//Hostetler, J.//Nelson, W.C.//Heidelberg, J.F.//Ward, D.M. 	Candidatus Chloracidobacterium thermophilum: an aerobic phototrophic Acidobacterium.	Science	2007	317		523-526			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. 		
@D	Bryk, M.//Belisle, M.//Mueller, J.E.//Belfort, M. 	Selection of a remote cleavage site by I-TevI, the td intron-encoded endonuclease.	J. Mol. Biol.	1995	247		197-210			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. 		
@D	Bryk, M.//Quirk, S.M.//Mueller, J.E.//Loizos, N.//Lawrence, C.//Belfort, M. 	The td intron endonuclease I-TevI makes extensive sequence-tolerant contacts across the minor groove of its DNA target.	EMBO J.	1993	12		2141-2149			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. 		
@D	Brzezinski, R.//Piekarowicz, A. 	Steps in the reaction mechanism of the Haemophilus influenzae Rf restriction endonuclease.	J. Mol. Biol.	1982	154		615-627			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. 		
@D	Brzuszkiewicz, E.//Bruggemann, H.//Liesegang, H.//Emmerth, M.//Olschlager, T.//Nagy, G.//Albermann, K.//Wagner, C.//Buchrieser, C.//Emody, L.//Gottschalk, G.//Hacker, J.//Dobrindt, U. 	How to become a uropathogen: Comparative genomic analysis of extraintestinal pathogenic Escherichia coli strains.	Proc. Natl. Acad. Sci. U. S. A.	2006	103		12879-12884			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. 		
@D	Brzuszkiewicz, E.//Schulz, T.//Rydzewski, K.//Daniel, R.//Gillmaier, N.//Dittmann, C.//Holland, G.//Schunder, E.//Lautner, M.//Eisenreich, W.//Luck, C.//Heuner, K. 	Legionella oakridgensis ATCC 33761 genome sequence and phenotypic characterization reveals its replication capacity in amoebae.	Int. J. Med. Microbiol.	2013	303		514-528			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. 		
@D	Brzuszkiewicz, E.//Waschkowitz, T.//Wiezer, A.//Daniel, R. 	Complete Genome Sequence of the B12-Producing Shimwellia blattae Strain DSM 4481, Isolated from a Cockroach.	J. Bacteriol.	2012	194		4436			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. 		
@D	Bucci, C.//Lavitola, A.//Salvatore, P.//Del Giudice, L.//Massardo, D.R.//Bruni, C.B.//Alifano, P. 	Hypermutation in pathogenic bacteria: frequent phase variation in meningococci is a phenotypic trait of a specialized mutator biotype.	Mol. Cell	1999	3		435-445			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. 		
@D	Buchmann, A.//Eitel, M.//Koch, P.//Schwarz, P.N.//Stegmann, E.//Wohlleben, W.//Wolanski, M.//Krawiec, M.//Zakrzewska-Czerwinska, J.//Mendez, C.//Botas, A.//Nunez, L.E.//Moris, F.//Cortes, J.//Gross, H. 	High-Quality Draft Genome Sequence of the Actinobacterium Nocardia terpenica IFM  0406, Producer of the Immunosuppressant Brasilicardins, Using Illumina and PacBio  Technologies.	Genome Announcements	2016	4		e01391-16			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. 		
@D	Buchrieser, C.//Glaser, P.//Rusniok, C.//Nedjari, H.//D'Hauteville, H.//Kunst, F.//Sansonetti, P.//Parsot, C. 	The virulence plasmid pWR100 and the repertoire of proteins secreted by the type III secretion apparatus of Shigella flexneri.	Mol. Microbiol.	2000	38		760-771			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. 		
@D	Buddruhs, N.//Chertkov, O.//Petersen, J.//Fiebig, A.//Chen, A.//Pati, A.//Ivanova, N.//Lapidus, A.//Goodwin, L.A.//Chain, P.//Detter, J.C.//Gronow, S.//Kyrpides, N.C.//Woyke, T.//Goker, M.//Brinkhoff, T.//Klenk, H.P. 	Complete genome sequence of the marine methyl-halide oxidizing Leisingera methylohalidivorans type strain (DSM 14336(T)), a representative of the  Roseobacter clade.	Standards in Genomic Sciences	2013	9		128-141			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. 		
@D	Budiharjo, A.//Jeong, H.//Wulandari, D.//Lee, S.//Ryu, C.M. 	Complete Genome Sequence of Bacillus altitudinis P-10, a Potential Bioprotectant  against Xanthomonas oryzae pv. oryzae, Isolated from Rice Rhizosphere in Java,  Indonesia.	Genome Announcements	2017	5		e01388-17			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. 		
@D	Budker, V.G.//Degtyarev, S.K.//Sokolov, A.V. 	Cleavage of DNA adsorbed on the surface of phospholipid membranes by Type II restriction endonucleases.	Biokhimiia	1986	51		1496-1498			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. 		
@D	Budroni, S.//Siena, E.//Dunning, H.J.C.//Seib, K.L.//Serruto, D.//Nofroni, C.//Comanducci, M.//Riley, D.R.//Daugherty, S.C.//Angiuoli, S.V.//Covacci, A.//Pizza, M.//Rappuoli, R.//Moxon, E.R.//Tettelin, H.//Medini, D. 	Neisseria meningitidis is structured in clades associated with restriction modification systems that modulate homologous recombination.	Proc. Natl. Acad. Sci. U. S. A.	2011	108		4494-4499			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. 		
@D	Buell, C.R. et al. 	The complete genome sequence of the Arabidopsis and tomato pathogen Pseudomonas syringae pv. tomato DC3000.	Proc. Natl. Acad. Sci. U. S. A.	2003	100		10181-10186			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. 		
@D	Buera, M.P.//Rossi, S.//Moreno, S.//Chirife, J. 	DSC confirmation that vitrification is not necessary for stabilization of the restriction enzyme EcoRI dried with saccharides.	Biotechnol. Prog.	1999	15		577-579			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. 		
@D	Bugarel, M.//den Bakker, H.C.//Nightingale, K.K.//Brichta-Harhay, D.M.//Edrington, T.S.//Loneragan, G.H. 	Two Draft Genome Sequences of a New Serovar of Salmonella enterica, Serovar Lubbock.	Genome Announcements	2015	3		e00215-15			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. 		
@D	Bugreev, D.V.//Nevinsky, G.A. 	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.	Biokhimiia	1999	64		291-305			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. 		
@D	Bugrysheva, J.V.//Cherney, B.//Sue, D.//Conley, A.B.//Rowe, L.A.//Knipe, K.M.//Frace, M.A.//Loparev, V.N.//Avila, J.R.//Anderson, K.//Hodge, D.R.//Pillai, S.P.//Weigel, L.M. 	Complete Genome Sequences for Three Chromosomes of the Burkholderia stabilis Type Strain (ATCC BAA-67).	Genome Announcements	2016	4		e01294-16			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. 		
@D	Bugrysheva, J.V.//Sue, D.//Hakovirta, J.//Loparev, V.N.//Knipe, K.//Sammons, S.A.//Ranganathan-Ganakammal, S.//Changayil, S.//Srinivasamoorthy, G.//Weil, M.R.//Tatusov, R.L.//Gee, J.E.//Elrod, M.G.//Hoffmaster, A.R.//Weigel, L.M. 	Finished Annotated Genome Sequence of Burkholderia pseudomallei Strain Bp1651, a  Multidrug-Resistant Clinical Isolate.	Genome Announcements	2015	3		e01427-15			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. 		
@D	Buhk, H.-J.//Behrens, B.//Tailor, R.//Wilke, K.//Prada, J.J.//Gunthert, U.//Noyer-Weidner, M.//Jentsch, S.//Trautner, T.A. 	Restriction and modification in Bacillus subtilis: nucleotide sequence, functional organization and product of the DNA methyltransferase gene of bacteriophage SPR.	Gene	1984	29		51-61			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. 		
@D	Buhler, R.//Yuan, R. 	Characterization of a restriction enzyme from Escherichia coli K carrying a mutation in the modification subunit.	J. Biol. Chem.	1978	253		6756-6760			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. 		
@D	Buhnik-Rosenblau, K.//Danin-Poleg, Y.//Elgavish, S.//Kashi, Y. 	Draft Genome Sequence of Lactobacillus johnsonii Strain 16, Isolated from Mice.	Genome Announcements	2015	3		e01141-15			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. 		
@D	Bui, L.M.G.//Kidd, S.P. 	A full genomic characterization of the development of a stable Small Colony Variant cell-type by a clinical Staphylococcus aureus strain.	Infect. Genet. Evol.	2015	36		345-355			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. 		
@D	Bujan, N.//Lasa, A.//E-Toranzo, A.//Magarinos, B. 	Draft Genome Sequence of the Fish Strain Edwardsiella tarda NCIMB 2034.	Genome Announcements	2017	5		e00359-17			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. 		
@D	Bujan, N.//Toranzo, A.E.//Magarinos, B. 	Draft Genome Sequence of Edwardsiellapiscicida Strain ACC35.1 Isolated from Diseased Turbot (Scophthalmus maximus) in Europe.	Genome Announcements	2017	5		e01626-16			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. 		
@D	Bujnicki, J.M. 	Phylogeny of the restriction endonuclease-like superfamily inferred from comparison of protein structures.	J. Mol. Evol.	2000	50		39-44			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. 		
@D	Bujnicki, J.M. 	A model of structure and action of Sau3AI restriction endonuclease that comprises two MutH-like endonuclease domains within a single polypeptide.	Acta Microbiol. Pol.	2001	50		219-231			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. 		
@D	Bujnicki, J.M. 	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.	In Silico Biology	1999	1		175-182			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. 		
@D	Bujnicki, J.M. 	Sequence permutations in the molecular evolution of DNA methyltransferases.	BMC Evol. Biol.	2002	2		3			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. 		
@D	Bujnicki, J.M. 	Crystallographic and bioinformatic studies on restriction endonucleases: Inference of evolutionary relationships in the 'midnight zone' of homology.	Curr. Protein Pept. Sci.	2003	4		327-337			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. 		
@D	Bujnicki, J.M. 	Homology modelling of the DNA 5mC methyltransferase M.BssHII. Is permutation of functional subdomains common to all subfamilies of DNA methyltransferases?	Int. J. Biol. Macromol.	2000	27		195-204			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. 		
@D	Bujnicki, J.M. 	Understanding the evolution of restriction-modification systems: Clues from sequence and structure comparisons.	Acta Biochim. Pol.	2001	48		935-967			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. 		
@A	Bujnicki, J.M. 		Molecular phylogenetics of restriction endonucleaseses.			Pingoud, A. 		Nucleic Acids Mol. Biol.				Berlin Heidelberg	Springer-Verlag	2004		14		63-93									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. 		
@D	Bujnicki, J.M.//Feder, M.//Ayres, C.L.//Redman, K.L. 	Sequence-structure-function studies of tRNA:m5C methyltransferase Trm4p and its relationship to DNA:m5C and RNA:m5U methyltransferases.	Nucleic Acids Res.	2004	32		2453-2463			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. 		
@D	Bujnicki, J.M.//Feder, M.//Radlinska, M.//Blumenthal, R.M. 	Structure prediction and phylogenetic analysis of a functionally diverse family of proteins homologous to the MT-A70 subunit of the  human mRNA:m6A methyltransferase.	J. Mol. Evol.	2002	55		431-444			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. 		
@D	Bujnicki, J.M.//Radlinska, M. 	Molecular phylogenetics of DNA 5mC-methyltransferases.	Acta Microbiol. Pol.	1999	48		19-30			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. 		
@D	Bujnicki, J.M.//Radlinska, M. 	Molecular evolution of DNA-(cytosine-N4) methyltransferases: evidence for their polyphyletic origin.	Nucleic Acids Res.	1999	27		4501-4509			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. 		
@D	Bujnicki, J.M.//Radlinska, M. 	Cloning and characterization of M.LmoA118I, a novel DNA:m4C methyltransferase from the Listeria  monocytogenes Phage A118, a close homolog of M.NgoMXV.	Acta Microbiol. Pol.	2001	50		155-160			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. 		
@D	Bujnicki, J.M.//Radlinska, M. 	Is the HemK family of putative S-adenosylmethionine-dependent methyltransferases a "missing" zeta subfamily of adenine methyltransferases?  A hypothesis.	Life	1999	48		247-249			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. 		
@D	Bujnicki, J.M.//Radlinska, M.//Rychlewski, L. 	Atomic model of the 5-methylcytosine-specific restriction enzyme McrA reveals an atypical zinc finger and structural similarity to beta beta alpha-Me endonucleases.	Mol. Microbiol.	2000	37		1280-1281			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. 		
@D	Bujnicki, J.M.//Radlinska, M.//Zaleski, P.//Piekarowicz, A. 	Cloning of the Haemophilus influenzae Dam methyltransferase and analysis of its relationship to the Dam methyltransferase encoded by the HP1 phage.	Acta Biochim. Pol.	2001	48		969-983			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. 		
@D	Bujnicki, J.M.//Rotkiewicz, P.//Kolinski, A.//Rychlewski, L. 	Three-dimensional modeling of the I-TevI homing endonuclease catalytic domain, a GIY-YIG superfamily member, using NMR restraints and Monte Carlo dynamics.	Protein Eng.	2001	14		717-721			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. 		
@D	Bujnicki, J.M.//Rychlewski, L. 	The herpesvirus alkaline exonuclease belongs to the restriction endonuclease PD-(D/E)XK superfamily: Insight from molecular modeling and phylogenetic analysis.	Virus Genes	2001	22		219-230			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. 		
@D	Bujnicki, J.M.//Rychlewski, L. 	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.	Gene	2001	267		183-191			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. 		
@D	Bujnicki, J.M.//Rychlewski, L. 	Unusual evolutionary history of the tRNA splicing endonuclease EndA: Relationship to the LAGLIDADG and PD-(D/E)XK deoxyribonucleases.	Protein Sci.	2001	10		656-660			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. 		
@D	Bujnicki, J.M.//Rychlewski, L.//Radlinska, M. 	Polyphyletic evolution of type II restriction enzymes revisited: two independent sources of second-hand folds revealed.	Trends Biochem. Sci.	2001	26		9-11			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. 		
@D	Bulach, D.M.//Zuerner, R.L.//Wilson, P.//Seemann, T.//McGrath, A.//Cullen, P.A.//Davis, J.//Johnson, M.//Kuczek, E.//Alt, D.P.//Peterson-Burch, B.//Coppel, R.L.//Rood, J.I.//Davies, J.K.//Adler, B. 	Genome reduction in Leptospira borgpetersenii reflects limited transmission potential.	Proc. Natl. Acad. Sci. U. S. A.	2006	103		14560-14565			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. 		
@D	Bulanenkova, S.//Kotova, E.//Snezhkov, E.//Akopov, S.//Nikolaev, L.//Sverdlov, E. 	Dam methylase accessibility as an instrument for analysis of mammalian chromatin structure.	FEBS J.	2012	279		493			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. 		
@D	Bulgari, D.//Minio, A.//Casati, P.//Quaglino, F.//Delledonne, M.//Bianco, P.A. 	Curtobacterium sp. Genome Sequencing Underlines Plant Growth Promotion-Related Traits.	Genome Announcements	2014	2		e00592-14			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. 		
@D	Bulkacz, J.//Roulland-Dussoix, D.//Boyer, H.W. 	Deoxyribonucleic acid modification by intermediate-type modification mutants of Escherichia coli K-12 and B.	J. Bacteriol.	1975	124		1395-1402			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. 		
@D	Bulkowska, U.//Ishikawa, T.//Kurlandzka, A.//Trzcinska-Danielewicz, J.//Derlacz, R.//Fronk, J. 	Expression and of murine DNA methyltransferases Dnmt1 and Dnmt3a in the yeast Saccharomyces cerevisiae.	Yeast	2007	24		871-882			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. 		
@D	Bull, J.J.//Vimr, E.R.//Molineux, I.J. 	A tale of tails: Sialidase is key to success in a model of phage therapy against K1-capsulated Escherichia coli.	Virology	2010	398		79-86			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. 		
@D	Bull, L.N.//Hewitt, J.E.//Cox, D.R.//Myers, R.M. 	Sensitivity of HincII to CpG methylation.	Nucleic Acids Res.	1993	21		2021			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. 		
@D	Bullas, L.R. 	Cloning of the SA system for the restriction and modification of DNA from Salmonella typhimurium into phage lambda.	Abstr. Gen. Meet. Am. Soc. Microbiol.	1994	94		224			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. 		
@D	Bullas, L.R.//Colson, C. 	DNA restriction and modification systems in Salmonella.  III.  SP, a Salmonella potsdam system allelic to the SB system in Salmonella typhimurium.	Mol. Gen. Genet.	1975	139		177-188			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. 		
@D	Bullas, L.R.//Colson, C.//Neufeld, B. 	Deoxyribonucleic acid restriction and modification systems in Salmonella:  chromosomally located systems of different serotypes.	J. Bacteriol.	1980	141		275-292			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. 		
@D	Bullas, L.R.//Colson, C.//van Pel, A. 	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.	J. Gen. Microbiol.	1976	95		166-172			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. 		
@D	Bullas, L.R.//Harding, G. 	Cryptic genes for the restriction and modification of DNA in Salmonella typhi and Salmonella gallinarum.	Abstr. Gen. Meet. Am. Soc. Microbiol.	1996	96		258			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. 		
@D	Bullas, L.R.//Nutter, R.L. 	Host-induced modification of Salmonella potsdam bacteriophage P3 by growth in E. coli.	Bacteriol. Proc.	1969	69		157			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. 		
@D	Bullas, L.R.//Rajadas, P.T. 	Evidence of additional families of TypeI hsd genes concerned with the restriction and modification of DNA in Salmonella.	Abstr. Gen. Meet. Am. Soc. Microbiol.	1987	87		154			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. 		
@D	Bullas, L.R.//Ryu, J.-I. 	Salmonella typhimurium LT2 strains which are r- m+ for all three chromosomally located systems of DNA restriction and modification.	J. Bacteriol.	1983	156		471-474			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. 		
@D	Bult, C.J. et al. 	Complete genome sequence of the Methanogenic archaeon, Methanococcus jannaschii.	Science	1996	273		1058-1073			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. 		
@D	Buluwela, L.//Malcolm, A.D.B.//Coleman, D.V.//Gardner, S.D. 	The use of the restriction endonuclease DdeI for mapping related DNAs.	Biosci. Rep.	1981	1		223-228			Restriction endonuclease mapping of BK virus strain GS using DdeI has allowed us to correct and extend the previously published map. 		
@D	Bulyk, M.L.//Gentalen, E.//Lockhart, D.J.//Church, G.M. 	Quantifying DNA-protein interactions by double-stranded DNA arrays.	Nat. Biotechnol.	1999	17		573-577			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. 		
@D	Bumgardner, E.//Bey, R.F.//Kittichotirat, W.//Bumgarner, R.E.//Lawrence, P.K. 	Genome Sequences of Seven Mycoplasma hyosynoviae Strains Isolated from the Joint  Tissue of Infected Swine (Sus scrofa).	Genome Announcements	2014	2		e00552-14			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. 		
@D	Bunina, Z.F.//Kramarov, V.M.//Mazanov, A.L.//Pachkunov, D.M.//Smolianinov, V.V.//Matvienko, N.N. 	BbvII:  A new site-specific endonuclease from Bacillus brevis 80.	Bioorg. Khim.	1983	9		1578-1580			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. 		
@D	Bunina, Z.F.//Kramarov, V.M.//Smolyaninov, V.V.//Tolstova, L.A. 	XphI - A new sequence-specific endonuclease from Xanthomonas phaseoli.	Bioorg. Khim.	1984	10		1333-1335			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. 		
@D	Bunina, Z.F.//Smolyaninov, V.V. 	Dynamics of site-specific endonuclease accumulation in Caryophanon latum L. cells.	Biotekhnologiya	1988	4		621-623			None 		
@D	Bunting, K.A.//Roe, S.M.//Headley, A.//Brown, T.//Savva, R.//Pearl, L.H. 	Crystal structure of the Escherichia coli dcm very-short-patch DNA repair endonuclease bound to its reaction product-site in a DNA superhelix.	Nucleic Acids Res.	2003	31		1633-1639			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. 		
@D	Buongiorno, J.//Bird, J.T.//Krivushin, K.//Oshurkova, V.//Shcherbakova, V.//Rivkina, E.M.//Lloyd, K.G.//Vishnivetskaya, T.A. 	Draft Genome Sequence of Antarctic Methanogen Enriched from Dry Valley Permafrost.	Genome Announcements	2016	4		e01362-16			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. 		
@D	Burall, L.S.//Grim, C.//Gopinath, G.//Laksanalamai, P.//Datta, A.R. 	Whole-Genome Sequencing Identifies an Atypical Listeria monocytogenes Strain Isolated from Pet Foods.	Genome Announcements	2014	2		e01243-14			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. 		
@D	Burbank, D.E.//Shields, S.L.//Schuster, A.M.//Van Etten, J.L. 	5-Azacytidine-resistant mutants of Chlorella Virus IL-3A.	Virology	1990	176		311-315			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. 		
@D	Burckhardt, J.//Weisemann, J.//Hamilton, D.L.//Yuan, R. 	Complexes formed between the restriction endonuclease EcoK and heteroduplex DNA.	J. Mol. Biol.	1981	153		425-440			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. 		
@D	Burckhardt, J.//Weisemann, J.//Yuan, R. 	Characterization of the DNA methylase activity of the restriction enzyme from Escherichia coli K.	J. Biol. Chem.	1981	256		4024-4032			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. 		
@D	Burenina, O.Y.//Fedotova, E.A.//Ryazanova, A.Y.//Protsenko, A.S.//Zakharova, M.V.//Karyagina, A.S.//Solonin, A.S.//Oretskaya, T.S.//Kubareva, E.A. 	Peculiarities of the Regulation of Gene Expression in the Ecl18kI RestrictionModification System.	Acta Naturae	2013	5		70-80			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. 		
@D	Burger, K.J.//Schinzel, R. 	Restriction endonuclease BglI as a tool for in vitro reconstruction and recombination of plasmid and bacteriophage genomes.	Mol. Gen. Genet.	1983	189		269-274			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. 		
@D	Burgers, W.A.//Blanchon, L.//Pradhan, S.//de Launoit, Y.//Kouzarides, T.//Fuks, F. 	Viral oncoproteins target the DNA methyltransferases.	Oncogene	2007	26		1650-1655			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. 		
@D	Burgess, S.A.//Cox, M.P.//Flint, S.H.//Lindsay, D.//Biggs, P.J. 	Draft Genome Sequences of Three Strains of Geobacillus stearothermophilus Isolated from a Milk Powder Manufacturing Plant.	Genome Announcements	2015	3		e00939-15			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. 		
@D	Burghartz, M.//Bunk, B.//Sproer, C.//Voget, S.//Daniel, R.//Overmann, J.//Jahn, M. 	Complete Genome Sequence of the Urethral Catheter Isolate Myroides sp. A21.	Genome Announcements	2015	3		e00068-15			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. 		
@D	Burguener, G.F.//Maldonado, M.J.//Revale, S.//Fernandez, Do.P.D.//Rascovan, N.//Vazquez, M.//Farias, M.E.//Marti, M.A.//Turjanski, A.G. 	Draft Genome Sequence of the Polyextremophilic Halorubrum sp. Strain AJ67, Isolated from Hyperarsenic Lakes in the Argentinian Puna.	Genome Announcements	2014	2		e01096-13			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. 		
@D	Burkhart, J.G.//Burkhart, B.A.//Sampson, K.//Malling, H.V. 	Evidence for a previously undetected CpG methyl-directed restriction system in E.coli.	Nucleic Acids Res.	1992	20		4368					
@D	Burks, J.N.//Wujick, C.T.//Marshall, L.M.//Kozarov, E.V.//Progulske-Fox, A. 	Function of the porphyromonas gingivalis DNA adenine methylase in the expression of virulence.	J. Dent. Res.	2002	81		A-497			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. 		
@D	Burland, V.//Plunkett, G. III//Sofia, H.J.//Daniels, D.L.//Blattner, F.R. 	Analysis of the Escherichia coli genome VI: DNA sequence of the region from 92.8 through 100 minutes.	Nucleic Acids Res.	1995	23		2105-2119			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. 		
@D	Burland, V.//Shao, Y.//Perna, N.T.//Plunkett, G.//Sofia, H.J.//Blattner, F.R. 	The complete DNA sequence and analysis of the large virulence plasmid of Escherichia coli O157:H7.	Nucleic Acids Res.	1998	26		4196-4204			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. 		
@D	Burns, B.P.//Gudhka, R.K.//Neilan, B.A. 	Genome Sequence of the Halophilic Archaeon Halococcus hamelinensis.	J. Bacteriol.	2012	194		2100-2101			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. 		
@D	Burrus, V.//Bontemps, C.//Decaris, B.//Guedon, G. 	Characterization of a novel type II restriction-modification system, Sth368I, encoded by the integrative element ICESt1 of Streptococcus thermophilus CNRZ368.	Appl. Environ. Microbiol.	2001	67		1522-1528			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. 		
@D	Burrus, V.//Quezada-Calvillo, R.//Marrero, J.//Waldor, M.K. 	SXT-Related Integrating Conjugative Element in New World Vibrio cholerae.	Appl. Environ. Microbiol.	2006	72		3054-3057			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. 		
@D	Burstein, D.//Amaro, F.//Zusman, T.//Lifshitz, Z.//Cohen, O.//Gilbert, J.A.//Pupko, T.//Shuman, H.A.//Segal, G. 	Genomic analysis of 38 Legionella species identifies large and diverse effector repertoires.	Nat. Genet.	2016	48		167-175			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. 		
@D	Burt, A.//Koufopanou, V. 	Homing endonuclease genes: the rise and fall and rise again of a selfish element.	Curr. Opin. Genet. Dev.	2004	14		609-615			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. 		
@D	Bury, C.//Garman, E.F.//Ginn, H.M.//Ravelli, R.B.//Carmichael, I.//Kneale, G.//McGeehan, J.E. 	Radiation damage to nucleoprotein complexes in macromolecular crystallography.	J. Synchrotron. Radiat.	2015	22		213-224			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. 		
@D	Buryanov, Y.//Shevchuk, T. 	The use of prokaryotic DNA methyltransferases as experimental and analytical tools in modern biology.	Anal. Biochem.	2005	338		1-11			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. 		
@D	Buryanov, Y.I.//Baryshev, M.M.//Kosykh, V.G.//Bayev, A.A. 	The purification and characterization of BstNI modification methylase.	J. Cell Biochem. Suppl.	1989	13D		211			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. 		
@D	Buryanov, Y.I.//Bogdarina, I.G.//Bayev, A.A. 	Site specificity and chromatographic properties of E. coli K12 and EcoRII DNA-cytosine methylases.	FEBS Lett.	1978	88		251-254			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). 		
@D	Buryanov, Y.I.//Bogdarina, I.G.//Vagabova, L.M. 	DNA-cytosine methylation in Escherichia coli MRE 600 cells.	Dokl. Akad. Nauk.	1976	230		976-978					
@D	Buryanov, Y.I.//Bogdarina, I.T.//Baev, A.A. 	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.	Dokl. Akad. Nauk.	1977	237		465-468					
@D	Buryanov, Y.I.//Kholodkov, O.A.//Bogdarina, I.G.//Neserenko, V.F.//Zakharchenko, V.N.//Chernov, A.P. 	On the ability of E. coli DNA methylases to modify denatured DNA's.	Biokhimiia	1983	48		1752-1754			Adenine and cytosine DNA methylases from different strains of E. coli are able to methylate denaturated and single-stranded DNA's. 		
@D	Buryanov, Y.I.//Nesterenko, V.F.//Dyacheniko, G.P.//Korunskii, O.F.//Skryabin, G.K. 	Specificity of different fractions of DNA-cytosine-methylase from Escherichia coli MRE 600.	Dokl. Akad. Nauk.	1976	227		228-231					
@D	Buryanov, Y.I.//Nesterenko, V.F.//Kosykh, V.G.//Baev, A.A. 	Different molecular structure of DNA methylases EcoRII and Eco MRE600 dcmII.	Dokl. Akad. Nauk.	1981	257		495-497			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. 		
@D	Buryanov, Y.I.//Nesterenko, V.F.//Vagabova, L.M. 	The presence of two DNA-cytosine methylases in cells of Escherichia coli MRE600.	Dokl. Akad. Nauk.	1976	227		1472-1475			None 		
@D	Buryanov, Y.I.//Shevchuk, T.V. 	DNA methyltransferases and structural-functional specificity of eukaryotic DNA modification.	Biochemistry	2005	70		730-742			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. 		
@D	Buryanov, Y.I.//Zakharchenko, N.S.//Shevchuk, T.V.//Bogdarina, I.G. 	Effect of the M.EcoRII methyltransferase-encoding gene on the phenotype of Nicotiana tabacum transgenic cells.	Gene	1995	157		283-287			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. 		
@D	Buryanov, Y.I.//Zakharenko, V.N.//Baev, A.A. 	Isolation, purification and properties of adenine DNA methylase Eco dam.	Dokl. Akad. Nauk.	1981	259		1492-1495					
@D	Buryanov, Y.I.//Zinovev, V.V.//Gorbunov, Y.A.//Tuzikov, F.V.//Rechkunova, N.I.//Malygin, E.G.//Bayev, A.A. 	Interaction of the Eco Dam methyltransferase with synthetic oligodeoxyribonucleotides.	Gene	1988	74		67-69			Meeting Abstract 		
@D	Buryanov, Y.I.//Zinoviev, V.V.//Vienozhinskis, M.T.//Malygin, E.G.//Nesterenko, V.F.//Popov, S.G.//Gorbunov, Y.A. 	Does the DNA methylase Eco dam pair nucleotide sequences to form site-specific duplexes?	FEBS Lett.	1984	168		166-168			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. 		
@D	Busch, A.//Ryll, M.//Immel, A.//Kornell, S.//Krause-Kyora, B.//Tomaso, H.//Hotzel, H. 	Draft Genome Sequence of Riemerella anatipestifer Isolate 17CS0503.	Genome Announcements	2018	6		e00274-18			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. 		
@D	Busch, A.//Thomas, P.//Myrtennas, K.//Forsman, M.//Braune, S.//Runge, M.//Tomaso, H. 	High-Quality Draft Genome Sequence of Francisella tularensis subsp. holarctica Strain 08T0073 Isolated from a Wild European Hare.	Genome Announcements	2017	5		e01577-16			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. 		
@D	Busche, T.//Novakova, R.//Al'Dilaimi, A.//Homerova, D.//Feckova, L.//Rezuchova, B.//Mingyar, E.//Csolleiova, D.//Bekeova, C.//Winkler, A.//Sevcikova, B.//Kalinowski, J.//Kormanec, J.//Ruckert, C. 	Complete Genome Sequence of Streptomyces lavendulae subsp. lavendulae CCM 3239 (Formerly 'Streptomyces aureofaciens CCM 3239'), a Producer of the Angucycline-Type Antibiotic Auricin.	Genome Announcements	2018	6		e00103-18			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. 		
@D	Busquets, A. et al. 	Draft Genome Sequence of Pseudomonas azotifigens Strain DSM 17556T (6H33bT), a Nitrogen Fixer Strain Isolated from a Compost Pile.	Genome Announcements	2013	1		e00893-13			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. 		
@D	Busquets, A.//Pena, A.//Gomila, M.//Bosch, R.//Nogales, B.//Garcia-Valdes, E.//Lalucat, J.//Bennasar, A. 	Genome Sequence of Pseudomonas stutzeri Strain JM300 (DSM 10701), a Soil Isolate  and Model Organism for Natural Transformation.	J. Bacteriol.	2012	194		5477-5478			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. 		
@D	Busquets, A.//Pena, A.//Gomila, M.//Mayol, J.//Bosch, R.//Nogales, B.//Garcia-Valdes, E.//Bennasar, A.//Lalucat, J. 	Draft Genome Sequence of Pseudomonas stutzeri Strain B1SMN1, a Nitrogen-Fixing and Naphthalene-Degrading Strain Isolated from Wastewater.	Genome Announcements	2013	1		e00584-13			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. 		
@D	Busslinger, M.//deBoer, E.//Wright, S.//Grosveld, F.G.//Flavell, R.A. 	The sequence GGCmCGG is resistant to MspI cleavage.	Nucleic Acids Res.	1983	11		3559-3569			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. 		
@D	Bustos, P.//Santamaria, R.I.//Perez-Carrascal, O.M.//Acosta, J.L.//Lozano, L.//Juarez, S.//Martinez-Flores, I.//Martinez-Romero, E.//Cevallos, M.A.//Romero, D.//Davila, G.//Vinuesa, P.//Miranda, F.//Ormeno, E.//Gonzalez, V. 	Complete Genome Sequences of Three Rhizobium gallicum Symbionts Associated with Common Bean (Phaseolus vulgaris).	Genome Announcements	2017	5		e00030-17			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. 		
@D	Butkus, V.//Bitinaite, J.//Kersulyte, D.//Janulaitis, A. 	A new restriction endonuclease Eco31I recognizing a non-palindromic sequence.	Biochim. Biophys. Acta	1985	826		208-212			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/. 		
@D	Butkus, V.//Kazlauskiene, R.//Gilvonauskaite, R.//Petrusyte, M.//Janulaitis, A. 	Determination of substrate specificity of restriction endonuclease Eco78I.	Bioorg. Khim.	1985	11		1572-1573			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. 		
@D	Butkus, V.//Klimasauskas, S.//Kersulyte, D.//Vaitkevicius, D.//Lebionka, A.//Janulaitis, A. 	Investigation of restriction-modification enzymes from M. varians RFL19 with a new type of specificity toward modification of substrate.	Nucleic Acids Res.	1985	13		5727-5746			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. 		
@A	Butkus, V.//Klimasauskas, S.//Petrauskiene, L.//Maneliene, Z. 		The effects of N4- and C5-methylation of cytosine on DNA physical properties and restriction endonuclease action.			Zelinka, J.//Balan, J. 		Metabolism and Enzymology of Nucleic Acids				Bratislava	Publishing House of the Slovak Akademy of Science	1987		6		119-127									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. 		
@D	Butkus, V.//Klimasauskas, S.//Petrauskiene, L.//Maneliene, Z.//Janulaitis, A.//Minchenkova, L.E.//Schyolkina, A.K. 	Synthesis and physical characterization of DNA fragments containing N4-methylcytosine and 5-methylcytosine.	Nucleic Acids Res.	1987	15		8467-8478			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. 		
@D	Butkus, V.//Klimasauskas, S.//Petrauskiene, L.//Maneliene, Z.//Lebionka, A.//Janulaitis, A. 	Interaction of AluI, Cfr6I and PvuII restriction-modification enzymes with substrates containing either N4-methylcytosine or 5-methylcytosine.	Biochim. Biophys. Acta	1987	909		201-207			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. 		
@A	Butkus, V.//Klimasauskas, S.//Petrauskiene, L.//Maneliene, Z.//Minchenkova, L.E.//Schyolkina, A.K.//Janulaitis, A. 		The effects of N4- and C5-methylation of cytosine on DNA physical properties and restriction endonuclease action.			Zelinka, J.//Balan, J. 		Metabolism and Enzymology of Nucleic Acids				New York	Plenum	1988		7		73-78									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. 		
@D	Butkus, V.//Petrauskiene, L.//Maneliene, Z.//Klimasauskas, S.//Laucys, V.//Janulaitis, A. 	Cleavage of methylated CCCGGG sequences containing either N4-methylcytosine or 5-methylcytosine with MspI, HpaII, SmaI, XmaI and Cfr9I restriction endonucleases.	Nucleic Acids Res.	1987	15		7091-7102			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. 		
@D	Butkus, V.V.//Klimasauskas, S.J.//Janulaitis, A. 	Analysis of products of DNA modification by methylases:  A procedure for the determination of 5- and N4-methylcytosines in DNA.	Anal. Biochem.	1985	148		194-198			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. 		
@D	Butkus, V.V.//Petrusyte, M.P.//Janulaitis, A. 	Determination of substrate specificity of Eco47I and Eco52I restriction endonucleases.	Bioorg. Khim.	1985	11		987-988			Cleavage sites for Eco47I and Eco52I restriction endonucleases, which are isoschizomers of AvaII and XmaIII, respectively, have been structurally elucidated. 		
@D	Butler, C.A.//Gotschlich, E.C. 	High-frequency mobilization of broad-host-range plasmids into Neisseria gonorrhoeae requires methylation in the donor.	J. Bacteriol.	1991	173		5793-5799			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. 		
@D	Butler, D.//Fitzgerald, G.F. 	Transcriptional analysis and regulation of expression of the ScrFI restriction-modification system of Lactococcus lactis subsp. cremoris UC503.	J. Bacteriol.	2001	183		4668-4673			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. 		
@D	Butler, M.I.//Stockwell, P.A.//Black, M.A.//Day, R.C.//Lamont, I.L.//Poulter, R.T.M. 	Pseudomonas syringae pv. actinidiae from Recent Outbreaks of Kiwifruit Bacterial Canker Belong to Different Clones that Originated in China.	PLoS ONE	2013	8		e57464			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. 		
@D	Butler, R.R.I.I.I.//Soomer-James, J.T.A.//Frenette, M.//Pombert, J.F. 	Complete Genome Sequences of Two Human Oral Microbiome Commensals, Streptococcus  salivarius ATCC 25975 and S. salivarius ATCC 27945.	Genome Announcements	2017	5		e00536-17			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. 		
@D	Butler, R.R.I.I.I.//Wang, J.//Stark, B.C.//Pombert, J.F. 	Complete Genome Sequences of Two Interactive Moderate Thermophiles, Paenibacillus napthalenovorans 32O-Y and Paenibacillus sp. 32O-W.	Genome Announcements	2016	4		e01717-15			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. 		
@D	Butler-Wu, S.M.//Sengupta, D.J.//Kittichotirat, W.//Matsen, F.A.//Bumgarner, R.E. 	Genome sequence of a novel species, Propionibacterium humerusii.	J. Bacteriol.	2011	193		3678			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. 		
@D	Butterer, A.//Pernstich, C.//Smith, R.M.//Sobott, F.//Szczelkun, M.D.//Toth, J. 	Type III restriction endonucleases are heterotrimeric: comprising one helicase-nuclease subunit and a dimeric methyltransferase that binds only one  specific DNA.	Nucleic Acids Res.	2014	42		5139-5150			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. 		
@D	Byrne-Bailey, K.G.//Coates, J.D. 	Complete Genome Sequence of the Anaerobic Perchlorate-Reducing Bacterium Azospira suillum Strain PS.	J. Bacteriol.	2012	194		2767-2768			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. 		
@D	Byrne-Bailey, K.G.//Weber, K.A.//Chair, A.H.//Bose, S.//Knox, T.//Spanbauer, T.L.//Chertkov, O.//Coates, J.D. 	Completed genome sequence of the anaerobic iron oxidizing bacterium Acidovorax ebreus strain TPSY.	J. Bacteriol.	2009	192		1475-1476			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. 		
@D	Byrne-Bailey, K.G.//Weber, K.A.//Coates, J.D. 	Draft Genome Sequence of the Anaerobic, Nitrate-Dependent, Fe(II)-Oxidizing Bacterium Pseudogulbenkiania ferrooxidans Strain 2002.	J. Bacteriol.	2012	194		2400-2401			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. 		
@D	Byrne-Bailey, K.G.//Wrighton, K.C.//Melnyk, R.A.//Agbo, P.//Hazen, T.C.//Coates, J.D. 	Complete genome sequence of the electricity-producing Thermincola potens strain JR.	J. Bacteriol.	2010	192		4078-4079			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. 		
@D	Cab-Barrera, E.L.//Barrera-Saldana, H.A. 	A general method to optimize the amount of enzyme in restriction and DNA modification reactions using the beta galactosidase blue-white plaques assay.	Biotechniques	1989	7		132-135			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. 		
@D	Caballero, J.I.//Zerillo, M.M.//Snelling, J.//Boucher, C.//Tisserat, N. 	Genome Sequence of Xanthomonas arboricola pv. Corylina, Isolated from Turkish Filbert in Colorado.	Genome Announcements	2013	1		e00246-13			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. 		
@D	Cabria, G.L.//Argayosa, V.B.//Lazaro, J.E.//Argayosa, A.M.//Arcilla, C.A. 	Draft Genome Sequence of Haloalkaliphilic Exiguobacterium sp. Strain AB2 from Manleluag Ophiolitic Spring, Philippines.	Genome Announcements	2014	2		e00840-14			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. 		
@D	Caceres, O.//Montenegro, J.//Padilla, C.//Tarazona, D.//Bailon, H.//Garcia, P.//Cespedes, M.//Valencia, P.//Guio, H. 	Whole-Genome Sequencing and Comparative Analysis of Yersinia pestis, the Causative Agent of a Plague Outbreak in Northern Peru.	Genome Announcements	2013	1		e00249-12			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. 		
@D	Cadillo-Quiroz, H.//Browne, P.//Kyrpides, N.//Woyke, T.//Goodwin, L.//Detter, C.//Yavitt, J.B.//Zinder, S.H. 	Complete Genome Sequence of Methanosphaerula palustris E1-9CT, a Hydrogenotrophic Methanogen Isolated from a Minerotrophic Fen Peatland.	Genome Announcements	2015	3		e01280-15			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. 		
@D	Cadillo-Quiroz, H.//Didelot, X.//Held, N.L.//Herrera, A.//Darling, A.//Reno, M.L.//Krause, D.J.//Whitaker, R.J. 	Patterns of gene flow define species of thermophilic archaea.	PLoS Biology	2012	10		E1001265			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. 		
@D	Cai, H.//Chen, F. 	Genome Sequence of the Proteorhodopsin-Containing Bacterium Flavobacterium sp. Strain TH167, Isolated from Cyanobacterial Aggregates in a Eutrophic Lake.	Genome Announcements	2018	6		e00217-18			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. 		
@D	Cai, H.//Zeng, Y. 	High-quality draft genome sequence of Aquidulcibacter paucihalophilus TH1-2(T) isolated from cyanobacterial aggregates in a eutrophic lake.	Standards in Genomic Sciences	2017	12		69			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. 		
@D	Cai, L.//Shao, M.F.//Zhang, T. 	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.	Standards in Genomic Sciences	2014	9		1302-1310			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. 		
@D	Cai, L.//Tan, D.//Aibaidula, G.//Dong, X.R.//Chen, J.C.//Tian, W.D.//Chen, G.Q. 	Comparative genomics study of polyhydroxyalkanoates (PHA) and ectoine relevant genes from Halomonas sp. TD01 revealed extensive horizontal gene transfer events and co-evolutionary relationships.	Microb. Cell Fact.	2011	10		88			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. 		
@D	Cai, L.//Zhang, T. 	Genome of Bacillus macauensis ZFHKF-1, a Long-Chain-Forming Bacterium.	J. Bacteriol.	2012	194		4780			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). 		
@D	Cai, L.//Zheng, S.W.//Shen, Y.J.//Zheng, G.D.//Liu, H.T.//Wu, Z.Y. 	Complete genome sequence provides insights into the biodrying-related microbial function of Bacillus thermoamylovorans isolated from sewage sludge biodrying material.	Bioresource Technology	2018	260		141-149			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. 		
@D	Cai, M.//Chen, W.M.//Nie, Y.//Chi, C.Q.//Wang, Y.N.//Tang, Y.Q.//Li, G.Y.//Wu, X.L. 	Complete Genome Sequence of Amycolicicoccus subflavus DQS3-9A1T, an actinomycete isolated from crude oil-polluted soil.	J. Bacteriol.	2011	193		4538-4539			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. 		
@D	Cai, Q.//Ye, X.//Chen, B.//Zhang, B. 	Complete Genome Sequence of Exiguobacterium sp. Strain N4-1P, a Psychrophilic Bioemulsifier Producer Isolated from a Cold Marine Environment in North Atlantic   Canada.	Genome Announcements	2017	5		e01248-17			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. 		
@D	Cai, W.//Srivastava, S.K.//Stulberg, M.J.//Nakhla, M.K.//Rascoe, J. 	Draft Genome Sequences of Two Dickeya dianthicola Isolates from Potato.	Genome Announcements	2018	6		e00115-18			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. 		
@D	Cai, W.//Yan, Z.//Rascoe, J.//Stulberg, M.J. 	Draft Whole-Genome Sequence of 'Candidatus Liberibacter asiaticus' Strain TX1712  from Citrus in Texas.	Genome Announcements	2018	6		e00554-18			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. 		
@D	Cai, X.//Kang, X.//Xi, H.//Liu, C.//Xue, Y. 	Complete Genome Sequence of the Endophytic Biocontrol Strain Bacillus velezensis  CC09.	Genome Announcements	2016	4		e01048-16			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. 		
@D	Cailliez-Grimal, C.//Chaillou, S.//Anba-Mondoloni, J.//Loux, V.//Afzal, M.I.//Rahman, A.//Kergourlay, G.//Champomier-Verges, M.C.//Zagorec, M.//Dalgaard, P.//Leisner, J.J.//Prevost, H.//Revol-Junelles, A.M.//Borges, F. 	Complete Chromosome Sequence of Carnobacterium maltaromaticum LMA 28.	Genome Announcements	2013	1		e00115-12			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. 		
@D	Cajo, G.C.//Brcic-Kostic, K.//Ivancic, I.//Trgovcevic, Z.//Salaj-Smic, E. 	Inactivation of the EcoKI restriction in UV-irradiated Escherichia coli: The role of RecBCD enzyme.	Periodicum Biologorum	2001	103		157-161			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. 		
@D	Cajthamlova, K.//Sisakova, E.//Weiser, J.//Weiserova, M. 	Phosphorylation of type IA restriction-modification complex enzyme EcoKI on the HsdR subunit.	FEMS Microbiol. Lett.	2007	270		171-177			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. 		
@D	Cal, S.//Connolly, B.A. 	DNA distortion and base flipping by the EcoRV DNA methyltransferase.	J. Biol. Chem.	1997	272		490-496			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. 		
@D	Cal, S.//Connolly, B.A. 	The EcoRV modification methylase causes considerable bending of DNA upon binding to its recognition sequence GATATC.	J. Biol. Chem.	1996	271		1008-1015			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. 		
@D	Calarco, J.P.//Martienssen, R.A. 	Imprinting: DNA Methyltransferases Illuminate Reprogramming.	Curr. Biol.	2012	22		R929-R931					
@D	Calcutt, M.J.//Foecking, M.F. 	Complete Genome Sequence of Kocuria palustris MU14/1.	Genome Announcements	2015	3		e01195-15			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. 		
@D	Calcutt, M.J.//Foecking, M.F. 	Genome Sequence of Mycoplasma putrefaciens Type Strain KS1.	J. Bacteriol.	2011	193		6094			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. 		
@D	Calcutt, M.J.//Foecking, M.F. 	Complete Genome Sequence of Mycoplasma bovoculi Strain M165/69T (ATCC 29104).	Genome Announcements	2014	2		e00115-14			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. 		
@D	Calcutt, M.J.//Foecking, M.F. 	Complete Genome Sequence of Mycoplasma hominis Strain Sprott (ATCC 33131), Isolated from a Patient with Nongonococcal Urethritis.	Genome Announcements	2015	3		e00771-15			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. 		
@D	Calcutt, M.J.//Foecking, M.F. 	Analysis of the Complete Mycoplasma hominis LBD-4 Genome Sequence Reveals Strain-Variable Prophage Insertion and Distinctive Repeat-Containing Surface Protein Arrangements.	Genome Announcements	2015	3		e01582-14			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. 		
@D	Calcutt, M.J.//Foecking, M.F.//Fox, L.K. 	Complete Genome Sequence of the Bovine Mastitis Pathogen Mycoplasma californicum  Strain ST-6T (ATCC 33461T).	Genome Announcements	2014	2		e00648-14			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. 		
@D	Calcutt, M.J.//Foecking, M.F.//Fry, P.R.//Hsieh, H.Y.//Perry, J.//Stewart, G.C.//Scholl, D.T.//Messier, S.//Middleton, J.R. 	Draft Genome Sequence of Bovine Mastitis Isolate Staphylococcus agnetis CBMRN 20813338.	Genome Announcements	2014	2		e00883-14			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. 		
@D	Calcutt, M.J.//Foecking, M.F.//Heidari, M.B.//McIntosh, M.A. 	Complete Genome Sequence of Mycoplasma flocculare Strain Ms42T (ATCC 27399T).	Genome Announcements	2015	3		e00124-15			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. 		
@D	Calcutt, M.J.//Foecking, M.F.//Hsieh, H.Y.//Adkins, P.R.//Stewart, G.C.//Middleton, J.R. 	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.	Genome Announcements	2015	3		e01525-14			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. 		
@D	Calcutt, M.J.//Foecking, M.F.//Hsieh, H.Y.//Perry, J.//Stewart, G.C.//Middleton, J.R. 	Draft Genome Sequence of Staphylococcus simulans UMC-CNS-990, Isolated from a Case of Chronic Bovine Mastitis.	Genome Announcements	2013	1		e01037-13			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. 		
@D	Calcutt, M.J.//Foecking, M.F.//Hsieh, H.Y.//Perry, J.//Stewart, G.C.//Middleton, J.R. 	Genome Sequence Analysis of Staphylococcus equorum Bovine Mastitis Isolate UMC-CNS-924.	Genome Announcements	2013	1		e00840-13			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. 		
@D	Calcutt, M.J.//Foecking, M.F.//Martin, N.T.//Mhlanga-Mutangadura, T.//Reilly, T.J. 	Draft Genome Sequence of Moraxella bovoculi Strain 237T (ATCC BAA-1259T) Isolated from a Calf with Infectious Bovine Keratoconjunctivitis.	Genome Announcements	2014	2		e00612-14			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. 		
@D	Calcutt, M.J.//Foecking, M.F.//Mhlanga-Mutangadura, T.//Reilly, T.J. 	Genome Sequence of Actinobacillus suis Type Strain ATCC 33415T.	Genome Announcements	2014	2		e00926-14			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. 		
@D	Calcutt, M.J.//Foecking, M.F.//Nagaraja, T.G.//Stewart, G.C. 	Draft Genome Sequence of Fusobacterium necrophorum subsp. funduliforme Bovine Liver Abscess Isolate B35.	Genome Announcements	2014	2		e00412-14			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. 		
@D	Calcutt, M.J.//Foecking, M.F.//Rosales, R.S.//Ellis, R.J.//Nicholas, R.A. 	Genome Sequence of Mycoplasma hyorhinis Strain GDL-1.	J. Bacteriol.	2012	194		1848			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. 		
@D	Calcutt, M.J.//Kent, B.N.//Foecking, M.F. 	Complete Genome Sequence of Mycoplasma yeatsii Strain GM274B (ATCC 43094).	Genome Announcements	2015	3		e00328-15			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. 		
@D	Calcutt, M.J.//Szikriszt, B.//Poti, A.//Molnar, J.//Gervai, J.Z.//Tusnady, G.E.//Foecking, M.F.//Szuts, D. 	Genome Sequence Analysis of Mycoplasma sp. HU2014, Isolated from Tissue Culture.	Genome Announcements	2015	3		e01086-15			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. 		
@D	Caldelari, I.//Chane-Woon-Ming, B.//Noirot, C.//Moreau, K.//Romby, P.//Gaspin, C.//Marzi, S. 	Complete Genome Sequence and Annotation of the Staphylococcus aureus Strain HG001.	Genome Announcements	2017	5		e00783-17			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). 		
@D	Calderon, C.E.//Ramos, C.//de Vicente, A.//Cazorla, F.M. 	Comparative Genomic Analysis of Pseudomonas chlororaphis PCL1606 Reveals New Insight into Antifungal Compounds Involved in Biocontrol.	Mol. Plant Microbe Interact.	2015	28		249-260			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. 		
@D	Calero-Delgado, B.//Martin-Platero, A.M.//Perez-Pulido, A.J.//Benitez-Cabello, A.//Casimiro-Soriguer, C.S.//Martinez-Bueno, M.//Arroyo-Lopez, F.N.//Rodriguez-Gomez, F.//Bautista-Gallego, J.//Garrido-Fernandez, A.//Jimenez-Diaz, R. 	Draft Genome Sequences of Six Lactobacillus pentosus Strains Isolated from Brines of Traditionally Fermented Spanish-Style Green Table Olives.	Genome Announcements	2018	6		e00379-18			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. 		
@D	Califano, G.//Franco, T.//Goncalves, A.C.//Castanho, S.//Soares, F.//Ribeiro, L.//Mata, L.//Costa, R. 	Draft Genome Sequence of Aliivibrio fischeri Strain 5LC, a Bacterium Retrieved from Gilthead Sea Bream (Sparus aurata) Larvae Reared in Aquaculture.	Genome Announcements	2015	3		e00593-15			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. 		
@D	Calisto, R.M.//Pich, O.Q.//Pinol, J.//Fita, I.//Querol, E.//Carpena, X. 	Crystal structure of a putative type I restriction-modification S subunit from Mycoplasma genitalium.	J. Mol. Biol.	2005	351		749-762			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. 		
@D	Callahan, S.J.//Luyten, Y.A.//Gupta, Y.K.//Wilson, G.G.//Roberts, R.J.//Morgan, R.D.//Aggarwal, A.K. 	Structure of Type IIL Restriction-Modification Enzyme MmeI in Complex with DNA Has Implications for Engineering New Specificities.	PLoS Biology	2016	14		e1002442			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. 		
@D	Callahan, S.J.//Morgan, R.D.//Jain, R.//Townson, S.A.//Wilson, G.G.//Roberts, R.J.//Aggarwal, A.K. 	Crystallization and preliminary crystallographic analysis of the type IIL restriction enzyme MmeI in complex with DNA.	Acta Crystallogr. F Struct. Biol. Cryst. Commun.	2011	67		1262-1265			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. 		
@D	Callanan, M.//Kaleta, P.//O'Callaghan, J.//O'Sullivan, O.//Jordan, K.//McAuliffe, O.//Sangrador-Vegas, A.//Slattery, L.//Fitzgerald, G.F.//Beresford, T.//Ross, R.P. 	Genome sequence of Lactobacillus helveticus: an organism distinguished by selective gene loss and IS element expansion.	J. Bacteriol.	2008	190		727-735			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. 		
@D	Calleja, F.//Dekker, B.M.M.//Coursin, T.//de Waard, A. 	A new sequence specific endonuclease EspI, of cyanobacterial origin.	FEBS Lett.	1984	178		69-72			The isolation of a new sequence-specific endonuclease from a unicellular cyanobacterium is described.  This enzyme specifically cleaves the nucleotide sequence GC^TNAGC. 		
@D	Calleja, F.//Tandeau de Marsac, N.//Coursin, T.//van Ormondt, H.//de Waard, A. 	A new endonuclease recognizing the deoxynucleotide sequence C^CNNGG from the cyanobacterium Synechocystis 6701.	Nucleic Acids Res.	1985	13		6745-6751			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. 		
@D	Callow, P.//Sukhodub, A.//Taylor, J.E.//Kneale, G.G. 	Shape and Subunit Organisation of the DNA Methyltransferase M.AhdI by Small-angle Neutron Scattering.	J. Mol. Biol.	2007	369		177-185			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. 		
@D	Callow, P.//Timmins, P.//Kneale, G. 	Preliminary neutron scattering studies of the Type I restriction-modification enzyme M.Ahdl.	Phys. Rev., B Condens. Matter	2006	385-386		853-855			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. 		
@D	Calmann, M.A.//Marinus, M.G. 	Regulated expression of the Escherichia coli dam gene.	J. Bacteriol.	2003	185		5012-5014			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. 		
@D	Calva, E.//Silva, C.//Zaidi, M.B.//Sanchez-Flores, A.//Estrada, K.//Silva, G.G.//Soto-Jimenez, L.M.//Wiesner, M.//Fernandez-Mora, M.//Edwards, R.A.//Vinuesa, P. 	Complete Genome Sequencing of a Multidrug-Resistant and Human-Invasive Salmonella enterica Serovar Typhimurium Strain of the Emerging Sequence Type 213 Genotype.	Genome Announcements	2015	3		e00663-15			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. 		
@D	Calvin-Koons, M.D.//Blumenthal, R.M. 	Characterization of pPvu1, the autonomous plasmid from Proteus vulgaris that carries the genes of the PvuII restriction-modification system.	Gene	1995	157		73-79			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. 		
@D	Cameron, D.R.//Jiang, J.H.//Abbott, I.J.//Spelman, D.W.//Peleg, A.Y. 	Draft Genome Sequences of Clinical Daptomycin-Nonsusceptible Methicillin-Resistant Staphylococcus aureus Strain APS211 and Its  Daptomycin-Susceptible Progenitor APS210.	Genome Announcements	2015	3		e00568-15			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. 		
@D	Cameron, D.R.//Jiang, J.H.//Hassan, K.A.//Elbourne, L.D.//Tuck, K.L.//Paulsen, I.T.//Peleg, A.Y. 	Insights on virulence from the complete genome of Staphylococcus capitis.	Front. Microbiol.	2015	6		980			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. 		
@D	Camiolo, S.//Porceddu, A.//Ruiu, L. 	Genome Sequence of Brevibacillus laterosporus UNISS 18, a Pathogen of Mosquitoes  and Flies.	Genome Announcements	2017	5		e00419-17			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. 		
@D	Campbell, B.J.//Smith, J.L.//Hanson, T.E.//Klotz, M.G.//Stein, L.Y.//Lee, C.K.//Wu, D.//Robinson, J.M.//Khouri, H.M.//Eisen, J.A.//Cary, S.C. 	Adaptations to submarine hydrothermal environments exemplified by the genome of Nautilia profundicola.	PLoS Genet.	2009	5		e1000362			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. 		
@D	Campedelli, I.//Florez, A.B.//Salvetti, E.//Delgado, S.//Orru, L.//Cattivelli, L.//Alegria, A.//Felis, G.E.//Torriani, S.//Mayo, B. 	Draft Genome Sequence of Three Antibiotic-Resistant Leuconostoc mesenteroides Strains of Dairy Origin.	Genome Announcements	2015	3		e01018-15			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. 		
@D	Campellone, K.G.//Roe, A.J.//Lobner-Olesen, A.//Murphy, K.C.//Magoun, L.//Brady, M.J.//Donohue-Rolfe, A.//Tzipori, S.//Gally, D.L.//Leong, J.M.//Marinus, M.G. 	Increased adherence and actin pedestal formation by dam-deficient enterohaemorrhagic Escherichia coli O157 : H7.	Mol. Microbiol.	2007	63		1468-1481			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. 		
@D	Campione-Piccardo, J.//Moro, R. 	Modification of DNA ends and detection of restriction enzyme recognition sequences in their ligated junctions.	Comput. Appl. Biosci.	1988	4		215-216			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. 		
@D	Campioni, F.//Cao, G.//Kastanis, G.//Sanchez, L.M.//Bergamini, A.M.M.//Rodrigues, D.D.P.//Allard, M.W.//Falcao, J.P. 	Draft Genome Sequences of 256 Salmonella enterica subsp. enterica Serovar Enteritidis Strains Isolated from Humans, Food, Chickens, and Farm Environments  in Brazil.	Genome Announcements	2017	5		e00399-17			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. 		
@D	Campioni, F.//Vilela, F.P.//Cao, G.//Kastanis, G.//Miller, D.//Sanchez, L.M.//Tiba-Casas, M.R.//Fernandes, S.A.//Rodrigues, D.D.P.//Costa, R.G.//Allard, M.W.//Falcao, J.P. 	Draft Genome Sequences of 112 Salmonella enterica Serovar Dublin Strains Isolated from Humans and Animals in Brazil.	Genome Announcements	2018	6		e00405-18			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. 		
@D	Campos, F.S.//Santos, G.R.//Nascimento, V.L.//Correia, R.F.T.//Cangussu, A.S.R.//Hoffmann, K.//Oliveira, E.E.//Ribeiro, B.M.//Aguiar, R.W.S. 	Genome Sequence of a New Siphoviridae Phage Found in a Brazilian Bacillus thuringiensis Serovar israelensis Strain.	Genome Announcements	2018	6		e01606-17			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. 		
@D	Campos-Guillen, J.//Caballero, P.J.//Cruz, M.J.A.//Molina, V.C.//Salas, R.L.M.//Limpens, G.C.//Garcia, S.I.//Hernandez, R.M.R.//Soto, A.G.//Cruz, H.A.//Saldana, G.C.//Romero, G.S.//Pastrana, M.X.//Alvarez, H.E.//Gosar, M.//Dizdarevic, T. 	Draft Genome Sequence of the Mercury-Resistant Bacterium Acinetobacter idrijaensis Strain MII, Isolated from a Mine-Impacted Area, Idrija, Slovenia.	Genome Announcements	2014	2		e01177-14			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. 		
@D	Campoy, S.//Aranda, J.//Alvarez, G.//Barbe, J.//Llagostera, M. 	Isolation and Sequencing of a Temperate Transducing Phage for Pasteurella multocida.	Appl. Environ. Microbiol.	2006	72		3154-3160			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. 		
@D	Campoy, S.//Mazon, G.//de Henestrosa, A.R.F.//Llagostera, M.//Monteiro, P.B.//Barbe, J. 	A new regulatory DNA motif of the gamma subclass proteobacteria: identification of the LexA protein binding site of the plant pathogen  Xylella fastidiiosa.	Microbiology	2002	148		3583-3597			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. 		
@D	Camus, J.C.//Pryor, M.J.//Medigue, C.//Cole, S.T. 	Re-annotation of the genome sequence of Mycobacterium tuberculosis H37Rv.	Microbiology	2002	148		2967-2973			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. 		
@D	Canevari, C.A.B.//Nishibe, C.//Moura, A.//de Alencar, A.P.//de Azevedo, I.M.//Hodon, M.A.//Mota, P.M.//Sales, E.B.//Fonseca, J.A.A.//Almeida, N.F.//Araujo, F.R. 	Draft Genome Sequence of Mycobacterium bovis Strain AN5, Used for Production of Purified Protein Derivative.	Genome Announcements	2014	2		e00277-14			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. 		
@A	Canosi, U.//Luder, G.//Trautner, T.A.//Bron, S. 		Restriction and modification in B. subtilis:  effects on plasmid transformation.			 		Transformation 1980:  Proceedings of the Fifth European Meeting on Bacterial Transformation and Transfection				Oxford	Cotswold Press	1981		0		179-187									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. 		
@D	Cantalupo, G.//Bucci, C.//Salvatore, P.//Pagliarulo, C.//Roberti, V.//Lavitola, A.//Bruni, C.B.//Alifano, P. 	Evolution and function of the Neisserial dam-replacing gene.	FEBS Lett.	2001	495		178-183			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. 		
@D	Cao, B.//Chen, C.//DeMott, M.S.//Cheng, Q.//Clark, T.A.//Xiong, X.//Zheng, X.//Butty, V.//Levine, S.S.//Yuan, G.//Boitano, M.//Khai, L.//Song, Yi.//Zhou, X.//Deng, Z.//Turner, S.W.//Korlach, J.//You, D.//Wang, L.//Chen, S.//Dedon, P.C. 	Genomic mapping of phosphorothioates reveals partial modification of short consensus sequences.	Nat. Commun.	2014	5		3951			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. 		
@D	Cao, B.//Ma, T.//Ren, Y.//Ren, Y.//Li, G.//Li, P.//Guo, X.//Ding, P.//Feng, L. 	Complete Genome Sequence of Pusillimonas sp. T7-7, a cold-tolerate diesel oil-degrading bacterium isolated from the Bohai Sea in China.	J. Bacteriol.	2011	193		4021-4022			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. 		
@D	Cao, Bo.//Cheng, Q.//Gu, C.//Yao, F.//DeMott, M.S.//Zheng, X.//Deng, Z.//Dedon, P.C.//You, D. 	Pathological phenotypes and in vivo DNA cleavage by unrestrained activity of a phosphorothioate- based restriction system in Salmonella.	Mol. Microbiol.	2014	93		776-785			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. 		
@D	Cao, D. 	Cosolute effects as probes of the role of water in DNA binding and catalysis by three restriction endonucleases.	Ph.D. Thesis, University of Pittsburgh	2002			283			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. 		
@D	Cao, D.//Ju, Z.//Gao, C.//Mei, X.//Fu, D.//Zhu, H.//Luo, Y.//Zhu, B. 	Genome-wide identification of cytosine-5 DNA methyltransferases and demethylases in Solanum lycopersicum.	Gene	2014	550		230-237			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. 		
@D	Cao, G.//Allard, M.W.//Hoffmann, M.//Monday, S.R.//Muruvanda, T.//Luo, Y.//Payne, J.//Rump, L.//Meng, K.//Zhao, S.//McDermott, P.F.//Brown, E.W.//Meng, J. 	Complete Sequences of Six IncA/C Plasmids of Multidrug-Resistant Salmonella enterica subsp. enterica Serotype Newport.	Genome Announcements	2015	3		e00027-15			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. 		
@D	Cao, G.//Ju, W.//Rump, L.//Zhao, S.//Zou, L.//Wang, C.//Strain, E.//Luo, Y.//Timme, R.//Allard, M.//Brown, E.//Meng, J. 	Genome Sequences of Two Emerging Non-O157 Shiga Toxin-Producing Escherichia coli  Strains.	Genome Announcements	2013	1		e00200-13			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. 		
@D	Cao, G.//Liu, Y.//Liu, G.//Wang, J.//Wang, G. 	Draft genome sequence of pseudomonas strain p818, isolated from glyphosate-polluted soil.	Genome Announcements	2013	1		e01079-13			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. 		
@D	Cao, G.//Zhang, J.//Xu, X.//Jin, H.//Yang, X.//Pan, H.//Allard, M.//Brown, E.//Meng, J. 	Whole-Genome Sequences of 12 Clinical Strains of Listeria monocytogenes.	Genome Announcements	2015	3		e01203-14			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. 		
@D	Cao, G.//Zhao, S.//Strain, E.//Luo, Y.//Timme, R.//Wang, C.//Brown, E.//Meng, J.//Allard, M. 	Draft Genome Sequences of Eight Salmonella enterica Serotype Newport Strains from Diverse Hosts and Locations.	J. Bacteriol.	2012	194		5146			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. 		
@D	Cao, G.//Zhong, C.//Zong, G.//Fu, J.//Liu, Z.//Zhang, G.//Qin, R. 	Complete Genome Sequence of Streptomyces clavuligerus F613-1, an Industrial Producer of Clavulanic Acid.	Genome Announcements	2016	4		e01020-16			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. 		
@D	Cao, H.//Shimura, Y.//Masanobu, K.//Yin, Y. 	Draft Genome Sequence of the Toxic Bloom-Forming Cyanobacterium Aphanizomenon flos-aquae NIES-81.	Genome Announcements	2014	2		e00044-14			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%. 		
@D	Cao, J.//Maignien, L.//Shao, Z.//Alain, K.//Jebbar, M. 	Genome Sequence of the Piezophilic, Mesophilic Sulfate-Reducing Bacterium Desulfovibrio indicus J2T.	Genome Announcements	2016	4		e00214-16			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. 		
@D	Cao, W. 	Binding kinetics and footprinting of TaqI endonuclease: Effects of metal cofactors on sequence-specific interactions.	Biochemistry	1999	38		8080-8087			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. 		
@D	Cao, W.//Barany, F. 	Identification of TaqI endonuclease active site residues by Fe2+-mediated oxidative cleavage.	J. Biol. Chem.	1998	273		33002-33010			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. 		
@D	Cao, W.//Lu, J. 	Exploring the catalytic center of TaqI endonuclease: rescuing catalytic activity by double mutations and Mn(2+).	Biochim. Biophys. Acta	2001	1546		253-260			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. 		
@D	Cao, W.//Lu, J.//Barany, F. 	Nucleotide sequences and gene organization of TaqI endonuclease isoschizomers from Thermus sp. SM32 and Thermus filiformis Tok6AI.	Gene	1997	197		205-214			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. 		
@D	Cao, W.//Lu, J.//Welch, S.G.//Williams, R.A.D.//Barany, F. 	Cloning and thermostability of TaqI endonuclease isoschizomers from Thermus species SM32 and Thermus filiformis Tok6A1.	Biochem. J.	1998	333		425-431			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. 		
@D	Cao, W.//Mayer, A.N.//Barany, F. 	Stringent and relaxed specificities of TaqI endonuclease: interactions with metal cofactors and DNA sequences.	Biochemistry	1995	34		2276-2283			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. 		
@D	Cao, X.//Li, Z.//Lou, Z.//Fu, B.//Liu, Y.//Shang, Y.//Jing, Z.//Zhou, J. 	Whole-Genome Sequences of Brucella melitensis Strain QY1, Isolated from Sheep in  Gansu, China.	Genome Announcements	2017	5		e00896-17			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. 		
@D	Cao, X.//Li, Z.//Lou, Z.//Fu, B.//Liu, Y.//Shang, Y.//Zhou, J.//Jing, Z. 	Whole-Genome Sequences of Brucella melitensis Strain QH61, Isolated from Yak in Qinghai, China.	Genome Announcements	2018	6		e01422-17			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. 		
@D	Cao, X.//Springer, N.M.//Muszynski, M.G.//Phillips, R.L.//Kaeppler, S.//Jacobsen, S.E. 	Conserved plant genes with similarity to mammalian de novo DNA methyltransferases.	Proc. Natl. Acad. Sci. U. S. A.	2000	97		4979-4984			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. 		
@D	Cao, X.F.//Aufsatz, W.//Zilberman, D.//Mette, M.F.//Huang, M.S.//Matzke, M.//Jacobsen, S.E. 	Role of the DRM and CMT3 Methyltransferases in RNA-directed DNA methylation.	Curr. Biol.	2003	13		2212-2217			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. 		
@D	Cao, X.F.//Jacobsen, S.E. 	Role of the Arabidopsis DRM methyltransferases in de novo DNA methylation and gene silencing.	Curr. Biol.	2002	12		1138-1144			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. 		
@D	Cao, X.F.//Jacobsen, S.E. 	Locus-specific control of asymmetric and CpNpG methylation by the DRM and CMT3 methyltransferase genes.	Proc. Natl. Acad. Sci. U. S. A.	2002	99		16491-16498			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. 		
@D	Cao, X.M.//Chen, T.//Xu, L.Z.//Yao, L.S.//Qi, J.//Zhang, X.L.//Yan, Q.L.//Deng, Y.H.//Guo, T.Y.//Wang, J.//Hu, K.X.//Xu, B.L. 	Complete Genome Sequence of Wohlfahrtiimonas chitiniclastica Strain SH04, Isolated from Chrysomya megacephala Collected from Pudong International Airport  in China.	Genome Announcements	2013	1		e0011913			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. 		
@D	Cao, Y.//Liu, X.F.//Zhang, H.L.//Chen, Y.J.//Hu, C.J. 	Draft Genome Sequence of the Human-Pathogenic Bacterium Vibrio alginolyticus E0666.	Genome Announcements	2013	1		e00686-13			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. 		
@D	Cao, Y.//Tian, B.//Liu, Y.//Cai, L.//Wang, H.//Lu, N.//Wang, M.//Shang, S.//Luo, Z.//Shi, J. 	Genome Sequencing of Ralstonia solanacearum FQY_4, Isolated from a Bacterial Wilt Nursery Used for Breeding Crop Resistance.	Genome Announcements	2013	1		e00125-13			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. 		
@D	Capowski, E.E.//Wells, J.M.//Karrer, K.M. 	Maintenance of methylation patterns in Tetrahymena thermophila.	Gene	1988	74		103-104			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. 		
@D	Capozzi, V.//Russo, P.//Lamontanara, A.//Orru, L.//Cattivelli, L.//Spano, G. 	Genome Sequences of Five Oenococcus oeni Strains Isolated from Nero Di Troia Wine from the Same Terroir in Apulia, Southern Italy.	Genome Announcements	2014	2		e01077-14			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. 		
@D	Cappelletti, M.//Di Gennaro, P.//D'Ursi, P.//Orro, A.//Mezzelani, A.//Landini, M.//Fedi, S.//Frascari, D.//Presentato, A.//Zannoni, D.//Milanesi, L. 	Genome Sequence of Rhodococcus sp. Strain BCP1, a Biodegrader of Alkanes and Chlorinated Compounds.	Genome Announcements	2013	1		e00657-13			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. 		
@D	Carasso, E.//Salmon-Divon, M.//Carmeli, Y.//Banin, E.//Navon-Venezia, S. 	Draft Genome Sequences of Two Multidrug-Resistant Extended-Spectrum-beta-Lactamase-Producing Klebsiella pneumoniae Strains Causing   Bloodstream Infections.	Genome Announcements	2016	4		e01533-15			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. 		
@D	Carattoli, A.//Villa, L.//Poirel, L.//Bonnin, R.A.//Nordmann, P. 	Evolution of IncA/C blaCMY-2-Carrying Plasmids by Acquisition of the blaNDM-1 Carbapenemase Gene.	Antimicrob. Agents Chemother.	2012	56		783-786			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. 		
@D	Carballeira, N.//Jorge, Y.//Guerra, M.//Madrazo, J.J.//Lleonart, R.//Silva, A.//Garcia, O.//De La Fuente, J.//Herrera, L. 	Cloning and characterization of the PvuII restriction-modification system in Proteus vulgaris.  Purification of recombinant restrictase.	Biotecnol. Apl.	1990	7		167-175			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. 		
@D	Carbonari, C.C.//Fittipaldi, N.//Teatero, S.//Athey, T.B.//Pianciola, L.//Masana, M.//Melano, R.G.//Rivas, M.//Chinen, I. 	Whole-Genome Sequencing Applied to the Molecular Epidemiology of Shiga Toxin-Producing Escherichia coli O157:H7 in Argentina.	Genome Announcements	2016	4		e01341-16			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. 		
@D	Carbone, I.//Anderson, J.B.//Kohn, L.M. 	A group-I intron in the mitochondrial small subunit ribosomal RNA gene of Sclerotinia sclerotiorum.	Curr. Genet.	1995	27		166-176			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. 		
@D	Card, C.O.//Wilson, G.G.//Weule, K.//Hasapes, J.//Kiss, A.//Roberts, R.J. 	Cloning and characterization of the HpaII methylase gene.	Nucleic Acids Res.	1990	18		1377-1383			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. 		
@D	Cardenas, J.P.//Lazcano, M.//Ossandon, F.J.//Corbett, M.//Holmes, D.S.//Watkin, E. 	Draft Genome Sequence of the Iron-Oxidizing Acidophile Leptospirillum ferriphilum Type Strain DSM 14647.	Genome Announcements	2014	2		e01153-14			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. 		
@D	Cardinali-Rezende, J.//Alexandrino, P.M.//Nahat, R.A.//Sant'Ana, D.P.//Silva, L.F.//Gomez, J.G.//Taciro, M.K. 	Draft Genome Sequence of Pseudomonas sp. Strain LFM046, a Producer of Medium-Chain-Length Polyhydroxyalkanoate.	Genome Announcements	2015	3		e00966-15			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%. 		
@D	Cardinali-Rezende, J.//Nahat, R.A.//Guzman, M.C.W.//Carreno, F.C.R.//Silva, L.F.//Taciro, M.K.//Gomez, J.G. 	Draft Genome Sequence of Halomonas sp. HG01, a Polyhydroxyalkanoate-Accumulating  Strain Isolated from Peru.	Genome Announcements	2016	4		e01598-15			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%. 		
@D	Cardoso, M.C.//Leonhardt, H. 	DNA methyltransferase is actively retained in the cytoplasm during early development.	J. Cell Biol.	1999	147		25-32			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. 		
@D	Cardozo, F.A.//Alfonso, V.N.C.//Zimpel, C.K.//Pessoa, A.//Rivera, I.N. 	Draft Genome Sequence of Aeromonas caviae CH129, a Marine-Derived Bacterium Isolated from the Coast of Sao Paulo State, Brazil.	Genome Announcements	2016	4		e01336-16			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. 		
@D	Cardozo, F.A.//Zimpel, C.K.//Guimaraes, A.M.//Pessoa, A.//Rivera, I.N. 	Draft Genome Sequence of Marine-Derived Aeromonas caviae CHZ306, a Potential Chitinase Producer Strain.	Genome Announcements	2016	4		e01293-16			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. 		
@D	Carignani, G.//Groudinsky, O.//Frezza, D.//Schiavon, E.//Bergantino, E.//Slonimski, P.P. 	An mRNA maturase is encoded by the first intron of the mitochondrial gene for the subunit I of cytochrome oxidase in S. cerevisiae.	Cell	1983	35		733-742			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. 		
@D	Carkaci, D.//Dargis, R.//Nielsen, X.C.//Skovgaard, O.//Fuursted, K.//Christensen, J.J. 	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.	Genome Announcements	2016	4		e00302-16			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. 		
@D	Carl, G.//Jackel, C.//Grutzke, J.//Hertwig, S.//Grobbel, M.//Malorny, B.//Rau, J.//Kasbohrer, A.//Hammerl, J.A. 	Complete Genome Sequence of the Temperate Klebsiella pneumoniae Phage KPP5665-2.	Genome Announcements	2017	5		e01118-17			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. 		
@D	Carle, P.//Saillard, C.//Carrere, N.//Carrere, S.//Duret, S.//Eveillard, S.//Gaurivaud, P.//Gourgues, G.//Gouzy, J.//Salar, P.//Verdin, E.//Breton, M.//Blanchard, A.//Laigret, F.//Bove, J.M.//Renaudin, J.//Foissac, X. 	Partial chromosome sequence of Spiroplasma citri reveals extensive viral invasion and important gene decay.	Appl. Environ. Microbiol.	2010	76		3420-3426			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. 		
@D	Carlier, A.//Agnoli, K.//Pessi, G.//Suppiger, A.//Jenul, C.//Schmid, N.//Tummler, B.//Pinto-Carbo, M.//Eberl, L. 	Genome Sequence of Burkholderia cenocepacia H111, a Cystic Fibrosis Airway Isolate.	Genome Announcements	2014	2		e00298-14			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. 		
@D	Carlson, K.//Kosturko, L.D. 	Endonuclease II of coliphage T4: a recombinase disguised as a restriction endonuclease?	Mol. Microbiol.	1998	27		671-676			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. 		
@D	Carlson, K.//Krabbe, M.//Nystrom, A.C.//Kosturko, L.D. 	DNA determinants of restriction.	J. Biol. Chem.	1993	268		8908-8918			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. 		
@A	Carlson, K.//Raleigh, E.A.//Hattman, S. 		Restriction and Modification.			Karam, J.D.//Karam, J.D. 		Molecular Biology of Bacteriophage T4				Washington, D.C.	American Society for Microbiology	1994				369-381									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. 		
@D	Carlson, K.//Wiberg, J.S. 	In vivo cleavage of cytosine-containing bacteriophage T4 DNA to genetically distinct, discretely sized fragments.	J. Virol.	1983	48		18-30			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. 		
@D	Carlson, L.L.//Page, A.W.//Bestor, T.H. 	Properties and localization of DNA methyltransferase in preimplantation mouse embryos: implications for genomic imprinting.	Genes Dev.	1992	6		2536-2541			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. 		
@D	Carneiro, A.R. et al. 	Genome Sequence of Exiguobacterium antarcticum B7, Isolated from a Biofilm in Ginger Lake, King George Island, Antarctica.	J. Bacteriol.	2012	194		6689-6690			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. 		
@D	Carneiro, A.R.//Juca, R.R.T.//Barauna, R.A.//de Sa, P.H.//Marinho, A.D.//Barbosa, S.//Pereira, A.//Alves, A.//Egas, C.//Correia, A.//Henriques, I.//Silva, A. 	Draft Genome Sequence of Serratia fonticola LMG 7882T Isolated from Freshwater.	Genome Announcements	2013	1		e00971-13			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. 		
@D	Carney, J.G.//Trachtenberg, A.M.//Rheaume, B.A.//Linnane, J.D.//Pitts, N.L.//Mykles, D.L.//MacLea, K.S. 	Genome Sequence of a Marine Spirillum, Oceanospirillum multiglobuliferum ATCC 33336T, Isolated from Japan.	Genome Announcements	2017	5		e00396-17			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. 		
@D	Carnilli, R.//Del Grosso, M.//Lannelli, F.//Pantostil, A. 	New genetic element carrying the erythromycin resistance determinant erm (TR) in Streptococcus pneumoniae.	Antimicrob. Agents Chemother.	2008	52		619-625			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. 		
@D	Caro-Quintero, A.//Auchtung, J.//Deng, J.//Brettar, I.//Hofle, M.//Tiedje, J.M.//Konstantinidis, K.T. 	Genome Sequencing of Five Shewanella baltica Strains Recovered from the Oxic-Anoxic Interface of the Baltic Sea.	J. Bacteriol.	2012	194		1236			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. 		
@D	Carotti, D.//Funiciello, S.//Lavia, P.//Caiafa, P.//Strom, R. 	Different effects of histone H1 on de novo DNA methylation in vitro depend on both the DNA base composition and the DNA methyltransferase.	Biochemistry	1996	35		11660-11667			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. 		
@D	Carotti, D.//Funiciello, S.//Palitti, F.//Strom, R. 	Influence of pre-existing methylation on the de novo activity of eukaryotic DNA methyltransferase.	Biochemistry	1998	37		1101-1108			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. 		
@D	Carpenter, M.//Divvela, P.//Pingoud, V.//Bujnicki, J.//Bhagwat, A.S. 	Sequence-dependent enhancement of hydrolytic deamination of cytosines in DNA by the restriction enzyme PspGI.	Nucleic Acids Res.	2006	34		3762-3770			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. 		
@D	Carpenter, M.A. 	Studies of base flipping by the Pyrococcus species GI-H restriction-modification system.	Ph.D. Thesis, Wayne State Univ., Detroit, MI, USA	2008						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. 		
@D	Carpenter, M.A.//Bhagwat, A.S. 	DNA base flipping by both members of the PspGI restriction-modification system.	Nucleic Acids Res.	2008	36		5417-5425			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. 		
@D	Carpenter, S.//Mishra, P.//Ghoshal, C.//Dash, P.//Wang, L.//Midha, S.//Laha, G.S.//Lore, J.//Kositratana, W.//Singh, N.//Singh, K.//Patil, P.//Oliva, R.//Patarapuwadol, S.//Bogdanove, A.J.//Rai, R. 	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.	bioRxiv	2018	0		0			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 		
@D	Carraro, N.//Sauve, M.//Matteau, D.//Lauzon, G.//Rodrigue, S.//Burrus, V. 	Development of pVCR94DeltaX from Vibrio cholerae, a prototype for studying multidrug resistant IncA/C conjugative plasmids.	Front. Microbiol.	2014	5		44			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. 		
@D	Carrasco, G.//Monzon, S.//Jimenez, P.//Cuesta, I.//Bartolome-Alvarez, J.//Valdezate, S. 	First Draft Genome Sequence of a Clinical Strain of Nocardia cerradoensis.	Genome Announcements	2017	5		e00551-17			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. 		
@D	Carraway, M.//Youderian, P.//Marinus, M.G. 	Spontaneous mutations occur near dam recognition sites in a dam- Escherichia coli host.	Genetics	1987	116		343-347			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. 		
@D	Carrias, A.//Welch, T.J.//Waldbieser, G.C.//Mead, D.A.//Terhune, J.S.//Liles, M.R. 	Comparative genomic analysis of bacteriophages specific to the channel catfish pathogen Edwardsiella ictaluri.	Virol. J.	2011	8		6			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. 		
@D	Carrick, K.L.//Topal, M.D. 	Amino Acid Substitutions at Position 43 of NaeI Endonuclease - Evidence for Changes in NaeI Structure.	J. Biol. Chem.	2003	278		9733-9739			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. 		
@D	Carrington, M.//Doro, E.//Forlenza, M.//Wiegertjes, G.F.//Kelly, S. 	Transcriptome Sequence of the Bloodstream Form of Trypanoplasma borreli, a Hematozoic Parasite of Fish Transmitted by Leeches.	Genome Announcements	2017	5		e01712-16			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. 		
@D	Carrion, V.J.//Cordovez, V.//Tyc, O.//Etalo, D.W.//de Bruijn, I.//de Jager, V.C.//Medema, M.H.//Eberl, L.//Raaijmakers, J.M. 	Involvement of Burkholderiaceae and sulfurous volatiles in disease-suppressive soils.	ISME J.	2018	12		23072321			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. 		
@D	Carroll, R.K.//Burda, W.N.//Roberts, J.C.//Peak, K.K.//Cannons, A.C.//Shaw, L.N. 	Draft Genome Sequence of Strain CBD-635, a Methicillin-Resistant Staphylococcus aureus USA100 Isolate.	Genome Announcements	2013	1		e00491-13			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. 		
@D	Carruthers, M.D.//Harding, C.M.//Baker, B.D.//Bonomo, R.A.//Hujer, K.M.//Rather, P.N.//Munson, R.S. Jr. 	Draft Genome Sequence of the Clinical Isolate Acinetobacter nosocomialis Strain M2.	Genome Announcements	2013	1		e00906-13			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). 		
@D	Carter, A.T.//Pearson, B.M.//Crossman, L.C.//Drou, N.//Heavens, D.//Baker, D.//Febrer, M.//Caccamo, M.//Grant, K.A.//Peck, M.W. 	Complete Genome Sequence of proteolytic Clostridium botulinum type A5 (B3') Strain H04402 065.	J. Bacteriol.	2011	193		2351-2352			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. 		
@D	Carter, J.A.//Chater, K.F.//Bruton, C.J.//Brown, N.L. 	A comparison of DNA cleavage by the restriction enzymes SalPI and PstI.	Nucleic Acids Res.	1980	8		4943-4954			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. 		
@D	Carter, J.M.//Friedrich, N.C.//Kleinstiver, B.//Edgell, D.R. 	Strand-specific Contacts and Divalent Metal Ion Regulate Double-strand Break Formation by the GIY-YIG Homing Endonuclease I-BmoI.	J. Mol. Biol.	2007	374		306-321			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. 		
@D	Carter, L.//Chase, H.R.//Choi, H.//Jun, S.//Park, J.//Jeong, S.//Kim, M.//Han, K.//Lee, C.//Jeong, H.//Finkelstein, S.//Negrete, F.//Cinar, H.N.//Tall, B.D.//Gopinath, G.R. 	Draft Genome Sequences of Enterotoxigenic Bacillus cereus Strains Obtained from Powdered Infant Formula.	Genome Announcements	2017	5		e01644-16			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%. 		
@D	Carter, M.Q.//Pham, A. 	Complete Genome Sequence of a Natural Escherichia coli O145:H11 Isolate That Belongs to Phylogroup A.	Genome Announcements	2018	6		e00349-18			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. 		
@D	Carter, M.Q.//Pham, A. 	Complete Genome Sequences of Two Atypical Enteropathogenic Escherichia coli O145  Environmental Strains.	Genome Announcements	2018	6		e00418-18			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. 		
@D	Carter, M.Q.//Pham, A.//Huynh, S.//He, X. 	Complete Genome Sequence of a Shiga Toxin-Producing Enterobacter cloacae Clinical Isolate.	Genome Announcements	2017	5		e00883-17			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. 		
@D	Carvin, C.D.//Dhasarathy, A.//Friesenhahn, L.B.//Jessen, W.J.//Kladde, M.P. 	Targeted cytosine methylation for in vivo detection of protein-DNA interactions.	Proc. Natl. Acad. Sci. U. S. A.	2003	100		7743-7748			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. 		
@D	Carvin, C.D.//Parr, R.D.//Kladde, M.P. 	Site-selective in vivo targeting of cytosine-5 DNA methylation by zinc-finger proteins.	Nucleic Acids Res.	2003	31		6493-6501			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. 		
@D	Casadesus, J.//Low, D. 	Epigenetic gene regulation in the bacterial world.	Microbiol. Mol. Biol. Rev.	2006	70		830-856			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. 		
@A	Casadesus, J.//Torreblanca, J. 		Methylation-related epigenetic signals in bacterial DNA.			V.E.A. Russo//R.A. Martiensson//A.D. Riggs 		Epigenetic Mechanisms of Gene Regulation				Cold Spring Harbor, NY	Cold Spring Harbor Laboratory Press	1996				141-153									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. 		
@D	Casale, A.//Clark, S.//Grasso, M.//Kryschuk, M.//Ritzer, L.//Trudeau, M.//Williams, L.E. 	Complete Genome Sequence of Escherichia coli ML35.	Genome Announcements	2018	6		e00034-18			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. 		
@D	Cascales, D.//Guijarro, J.A.//Reimundo, P.//Garcia-Torrico, A.I.//Mendez, J. 	Genome Sequence of the Fish Pathogen Yersinia ruckeri Strain 150, Isolated from Diseased Rainbow Trout.	Genome Announcements	2016	4		e01331-16			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. 		
@D	Caserta, M.//Zacharias, W.//Nwankwo, D.//Wilson, G.G.//Wells, R.D. 	Cloning, sequencing, in vivo promoter mapping, and expression in Escherichia coli of the gene for the HhaI methyltransferase.	J. Biol. Chem.	1987	262		4770-4777			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. 		
@D	Casey, A.//McAuliffe, O.//Coffey, A.//Hunt, K.//Fanning, S.//Fox, E.//Jordan, K. 	Complete Genome Sequence of Listeria monocytogenes Strain DPC6895, a Serotype 1/2b Isolate from Bovine Raw Milk.	Genome Announcements	2015	3		e00629-15			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. 		
@D	Casey, A.//McAuliffe, O.//Fox, E.M.//Leong, D.//Gahan, C.G.//Jordan, K. 	Draft Genome Sequences of Listeria monocytogenes Serotype 4b Strains 944 and 2993 and Serotype 1/2c Strains 198 and 2932.	Genome Announcements	2016	4		e00482-16			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. 		
@D	Casjens, S.//Hayden, M.//Jackson, E.//Deans, R. 	Additional restriction endonuclease cleavage sites on the bacteriophage P22 genome.	J. Virol.	1983	45		864-867			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. 		
@D	Casjens, S.//Palmer, N.//van Vugt, R.//Huang, W.M.//Stevenson, B.//Rosa, P.//Lathigra, R.//Sutton, G.//Peterson, J.//Dodson, R.J.//Haft, D.//Hickey, E.//Gwinn, M.//White, O.//Fraser, C.M. 	A bacterial genome in flux: the twelve linear and nine circular extrachromosomal DNAs in an infectious isolate of the Lyme disease spirochete Borrelia burgdorferi.	Mol. Microbiol.	2000	35		490-516			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. 		
@D	Casjens, S.//Winn-Stapley, D.A.//Gilcrease, E.B.//Morona, R.//Kuhlewein, C.//Chua, J.E.//Manning, P.A.//Inwood, W.//Clark, A.J. 	The chromosome of Shigella flexneri bacteriophage Sf6: complete nucleotide sequence, genetic mosaicism, and DNA packaging.	J. Mol. Biol.	2004	339		379-394			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. 		
@D	Casjens, S.R.//Fraser-Liggett, C.M.//Mongodin, E.F.//Qiu, W.G.//Dunn, J.J.//Luft, B.J.//Schutzer, S.E. 	Whole Genome Sequence of an Unusual Borrelia burgdorferi Sensu Lato Isolate.	J. Bacteriol.	2011	193		1489-1490			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.' 		
@D	Casjens, S.R.//Gilcrease, E.B.//Huang, W.M.//Bunny, K.L.//Pedulla, M.L.//Ford, M.E.//Houtz, J.M.//Hatfull, G.F.//Hendrix, R.W. 	The pKO2 Linear Plasmid Prophage of Klebsiella oxytoca.	J. Bacteriol.	2004	186		1818-1832			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. 		
@D	Casjens, S.R.//Mongodin, E.F.//Qiu, W.G.//Dunn, J.J.//Luft, B.J.//Fraser-Liggett, C.M.//Schutzer, S.E. 	Whole-Genome Sequences of Two Borrelia afzelii and Two Borrelia garinii Lyme Disease Agent Isolates.	J. Bacteriol.	2011	193		6995-6996			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. 		
@D	Caspers, M.P.//Boekhorst, J.//Abee, T.//Siezen, R.J.//Kort, R. 	Complete Genome Sequence of Anoxybacillus flavithermus TNO-09.006, a Thermophilic Sporeformer Associated with a Dairy-Processing Environment.	Genome Announcements	2013	1		e00010-13			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. 		
@D	Caspers, M.P.//Boekhorst, J.//de Jong, A.//Kort, R.//Nierop, G.M.//Abee, T. 	Draft Genome Sequences of Four Thermophilic Spore Formers Isolated from a Dairy-Processing Environment.	Genome Announcements	2016	4		e00757-16			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). 		
@D	Casselli, T.//Tourand, Y.//Scheidegger, A.//Arnold, W.K.//Proulx, A.//Stevenson, B.//Brissette, C.A. 	DNA Methylation by Restriction Modification Systems Affects the Global Transcriptome Profile in Borrelia burgdorferi.	J. Bacteriol.	2018	200		e00395-18			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. 		
@D	Cassir, N.//Croce, O.//Pagnier, I.//Benamar, S.//Couderc, C.//Robert, C.//Raoult, D.//La Scola, B. 	Non-contiguous finished genome sequence and description of Bacteroides neonati sp. nov., a new species of anaerobic bacterium.	Standards in Genomic Sciences	2014	9		794-806			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. 		
@D	Castel, A.L.//Nakamori, M.//Thornton, C.A.//Pearson, C.E. 	Identification of restriction endonucleases sensitive to 5-cytosine methylation at non-CpG sites, including expanded (CAG)n/(CTG)n repeats.	EPIGENETICS	2011	6		417-421			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. 		
@D	Castelan-Vega, J.A.//Jimenez-Alberto, A.//Ribas-Aparicio, R.M. 	Homology modeling and molecular dynamics simulations of HgiDII methyltransferase in complex with DNA and S-adenosyl-methionine: Catalytic mechanism and interactions with DNA.	J. Mol. Model.	2010	16		1213-1222			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. 		
@D	Castellano, S.//Kuck, D.//Sala, M.//Novellino, E.//Lyko, F.//Sbardella, G. 	Constrained analogues of procaine as novel small molecule inhibitors of DNA methyltransferase-1.	J. Med. Chem.	2008	51		2321-2325			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. 		
@D	Casteneda-Ruelas, G.M.//Carreon-Gaxiola, C.//Castelan-Sanchez, H.G.//Acatzi-Silva, A.//Romero-Martinez, S.//Garcia-Molina, A.//Jimenez-Edeza, M. 	Draft Genome Sequences of 18 Salmonella enterica subsp. enterica Serovar Oranienburg Strains Isolated from Rivers in Northwestern Mexico.	Genome Announcements	2017	5		e01585-16			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. 		
@D	Castignetti, D.//Polley, N.//Putonti, C. 	Draft Genome Sequence of the Siderophore-Degrading Soil Bacterium Mesorhizobium loti Strain LU.	Genome Announcements	2018	6		e00029-18			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. 		
@D	Castillo, A.//Peterson, S. 	The role of GATC flanking sequences in the methylation efficiency of Escherichia coli DNA adenine methyltransferase.	FASEB J.	2009	23		482.3			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. 		
@D	Castillo, D.//D'Alvise, P.//Kalatzis, P.G.//Kokkari, C.//Middelboe, M.//Gram, L.//Liu, S.//Katharios, P. 	Draft Genome Sequences of Vibrio alginolyticus Strains V1 and V2, Opportunistic Marine Pathogens.	Genome Announcements	2015	3		e00729-15			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. 		
@D	Castillo, D.//D'Alvise, P.//Middelboe, M.//Gram, L.//Liu, S.//Kalatzis, P.G.//Kokkari, C.//Katharios, P. 	Draft Genome Sequences of the Fish Pathogen Vibrio harveyi Strains VH2 and VH5.	Genome Announcements	2015	3		e01062-15			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. 		
@D	Castillo, D.//Gram, L.//Dailey, F.E. 	Genome Sequences of Shewanella baltica and Shewanella morhuae Strains Isolated from the Gastrointestinal Tract of Freshwater Fish.	Genome Announcements	2018	6		e00541-18			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. 		
@D	Castillo, D.//Gram, L.//Dailey, F.E. 	Complete Genome Sequence of Shewanella sp. WE21, a Rare Isolate with Multiple Novel Large Genomic Islands.	Genome Announcements	2018	6		e00277-18			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. 		
@D	Castillo, D.//Jun, J.W.//D'Alvise, P.//Middelboe, M.//Gram, L.//Liu, S.//Katharios, P. 	Draft Genome Sequence of Vibrio parahaemolyticus VH3, Isolated from an Aquaculture Environment in Greece.	Genome Announcements	2015	3		e00731-15			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. 		
@D	Castillo, D.//Vandieken, V.//Engelen, B.//Engelhardt, T.//Middelboe, M. 	Draft Genome Sequences of Six Vibrio diazotrophicus Strains Isolated from Deep Subsurface Sediments of the Baltic Sea.	Genome Announcements	2018	6		e00081-18			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. 		
@D	Castillo, V.G.A.//Poehlein, A. 	Genome Sequence of the Acetogenic Bacterium Moorella mulderi DSM 14980T.	Genome Announcements	2016	4		e00444-16			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). 		
@D	Castrillo, M.L.//Bich, G.A.//Modenutti, C.//Turjanski, A.//Zapata, P.D.//Villalba, L.L. 	First Whole-Genome Shotgun Sequence of a Promising Cellulase Secretor, Trichoderma koningiopsis Strain POS7.	Genome Announcements	2017	5		e00823-17			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. 		
@D	Castro, M.//Moya-Beltran, A.//Covarrubias, P.C.//Gonzalez, M.//Cardenas, J.P.//Issotta, F.//Nunez, H.//Acuna, L.G.//Encina, G.//Holmes, D.S.//Johnson, D.B.//Quatrini, R. 	Draft genome sequence of the type strain of the sulfur-oxidizing acidophile, Acidithiobacillus albertensis (DSM 14366).	Standards in Genomic Sciences	2017	12		77			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. 		
@D	Castro, W.O.//Lima, A.R.//Moraes, P.H.//Siqueira, A.S.//Aguiar, D.C.//Barauna, A.R.//Martins, L.C.//Fuzii, H.T.//de Lima, C.P.//Vianez-Junior, J.L.//Nunes, M.R.//Dall'Agnol, L.T.//Goncalves, E.C. 	Draft Genome Sequence of Microcystis aeruginosa CACIAM 03, a Cyanobacterium Isolated from an Amazonian Freshwater Environment.	Genome Announcements	2016	4		e01299-16			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. 		
@D	Castro, W.O.//Torres-Ballesteros, A.M.//Nakayama, C.R.//Melo, I.S.//Pellizari, V.H.//Silva, A.//Ramos, R.T. 	Draft Genome Sequence of Haloferax sp. Strain ATB1, Isolated from a Semi-Arid Region in the Brazilian Caatinga.	Genome Announcements	2014	2		e00812-14			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. 		
@D	Castro-Jaimes, S.//Salgado-Camargo, A.D.//Grana-Miraglia, L.//Lozano, L.//Bocanegra-Ibarias, P.//Volkow-Fernandez, P.//Silva-Sanchez, J.//Castillo-Ramirez, S.//Cevallos, M.A. 	Complete Genome Sequence of a Multidrug-Resistant Acinetobacter baumannii Isolate Obtained from a Mexican Hospital (Sequence Type 422).	Genome Announcements	2016	4		e00583-16			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. 		
@D	Castro-Nallar, E.//Valenzuela, S.L.//Baquedano, S.//Sanchez, C.//Fernandez, F.//Trombert, A.N. 	Draft Genome Sequences of Five Enterococcus Species Isolated from the Gut of Patients with Suspected Clostridium difficile Infection.	Genome Announcements	2017	5		e00379-17			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. 		
@D	Castronovo, M.//Radovic, S.//Grunwald, C.//Casalis, L.//Morgante, M.//Scoles, G. 	Control of Steric Hindrance on Restriction Enzyme Reactions with Surface-Bound DNA Nanostructures.	Nano Lett.	2008	8		4140-4145			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. 		
@D	Catania, J.//Keenan, B.C.//Margison, G.P.//Fairweather, D.S. 	Determination of 5-methylcytosine by acid hydrolysis of DNA with hydrofluoric acid.	Anal. Biochem.	1987	167		347-351			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. 		
@D	Catcheside, D.E.A. 	A restriction and modification model for the initiation and control of recombination in Neurospora.	Genet. Res.	1986	47		157-165			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. 		
@A	Catterall, J.F.//Lees, N.D.//Welker, N.E. 		Restriction and modification in Thermophilic bacilli.			Schlessinger, D. 		Microbiology-1976				Washington	American Society for Microbiology	1976		0		358-366									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. 		
@D	Catterall, J.F.//Welker, N.E. 	Purification and Properties of the Bst1503 Endonuclease.	Methods Enzymol.	1980	65		167-170			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. 		
@D	Catterall, J.F.//Welker, N.E. 	Reduced efficiency of transfection in Bacillus stearothermophilus with modified phage DNA.	Mol. Genetics Bulletin	1974	37		9-10			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. 		
@D	Catterall, J.F.//Welker, N.E. 	Isolation and properties of a thermostable restriction endonuclease (Endo R.Bst1503) .	J. Bacteriol.	1977	129		1110-1120			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. 		
@D	Catto, L.E.//Bellamy, S.R.//Retter, S.E.//Halford, S.E. 	Dynamics and consequences of DNA looping by the FokI restriction endonuclease.	Nucleic Acids Res.	2008	36		2073-2081			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. 		
@D	Catto, L.E.//Ganguly, S.//Milsom, S.E.//Welsh, A.J.//Halford, S.E. 	Protein assembly and DNA looping by the FokI restriction endonuclease.	Nucleic Acids Res.	2006	34		1711			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. 		
@D	Caulfield, T.//Medina-Franco, J.L. 	Molecular dynamics simulations of human DNA methyltransferase 3B with selective inhibitor nanaomycin A.	J. Struct. Biol.	2011	176		185-191			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. 		
@D	Cavalca, L.//Corsini, A.//Andreoni, V.//Muyzer, G. 	Draft Genome Sequence of the Arsenite-Oxidizing Strain Aliihoeflea sp. 2WW, Isolated from Arsenic-Contaminated Groundwater.	Genome Announcements	2013	1		e01072-13			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. 		
@D	Cavalcante, A.L.//Dias, L.M.//Alves, J.T.//Veras, A.A.//Guimaraes, L.C.//Rocha, F.S.//Gala-Garcia, A.//Retamal, P.//Ramos, R.T.//Azevedo, V.//Silva, A.//Carneiro, A.R. 	Complete Genome Sequence of Corynebacterium pseudotuberculosis Strain E19, Isolated from a Horse in Chile.	Genome Announcements	2015	3		e01385-15			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. 		
@D	Caverly, L.J.//Spilker, T.//LiPuma, J.J. 	Complete Genome Sequences of 17 Rapidly Growing Nontuberculous Mycobacterial Strains.	Genome Announcements	2016	4		e01009-16			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. 		
@D	Caverly, L.J.//Spilker, T.//LiPuma, J.J. 	Complete Genome Sequence of Mycobacterium abscessus subsp. bolletii.	Genome Announcements	2016	4		e00543-16			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. 		
@D	Cayley, S.//Record, M.T. 	Anions affect the in vitro function of endonuclease EcoRI.	J. Cell Biochem. Suppl.	1987	11C		204			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. 		
@D	Cazalet, C.//Gomez-Valero, L.//Rusniok, C.//Lomma, M.//Dervins-Ravault, D.//Newton, H.J.//Sansom, F.M.//Jarraud, S.//Zidane, N.//Ma, L.//Bouchier, C.//Etienne, J.//Hartland, E.L.//Buchrieser, C. 	Analysis of the Legionella longbeachae genome and transcriptome uncovers unique strategies to cause Legionnaires' disease.	PLoS Genet.	2010	6		e1000851			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. 		
@D	Cazalet, C.//Rusniok, C.//Bruggemann, H.//Zidane, N.//Magnier, A.//Ma, L.//Tichit, M.//Jarraud, S.//Bouchier, C.//Vandenesch, F.//Kunst, F.//Etienne, J.//Glaser, P.//Buchrieser, C. 	Evidence in the Legionella pneumophila genome for exploitation of host cell functions and high genome plasticity.	Nat. Genet.	2004	36		1165-1173			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. 		
@D	Ccorahua-Santo, R.//Cervantes, M.//Duran, Y.//Aguirre, M.//Marin, C.//Ramirez, P. 	Draft Genome Sequence of Klebsiella michiganensis 3T412C, Harboring an Arsenic Resistance Genomic Island, Isolated from Mine Tailings in Peru.	Genome Announcements	2017	5		e00611-17			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. 		
@D	Ceccaldi, A.//Rajavelu, A.//Champion, C.//Rampon, C.//Jurkowska, R.//Jankevicius, G.//Senamaud-Beaufort, C.//Ponger, L.//Gagey, N.//Ali, H.D.//Tost, J.//Vriz, S.//Ros, S.//Dauzonne, D.//Jeltsch, A.//Guianvarc'h, D.//Arimondo, P.B. 	C5-DNA Methyltransferase Inhibitors: From Screening to Effects on Zebrafish Embryo Development.	Chembiochem	2011	12		1337-1345			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. 		
@D	Ceccaldi, A.//Rajavelu, A.//Ragozin, S.//Senamaud-Beaufort, C.//Bashtrykov, P.//Testa, N.//Dali-Ali, H.//Maulay-Bailly, C.//Amand, S.//Guianvarc'h, D.//Jeltsch, A.//Arimondo, P.B. 	Identification of Novel Inhibitors of DNA Methylation by Screening of a Chemical Library.	ACS Chem. Biol.	2013	8		543-548			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. 		
@D	Cecchini, D.//Laville, E.//Laguerre, S.//Robe, P.//Leclerc, M.//Dore, J.//Henrissat, B.//Remaud-Simeon, M.//Monsan, P.//Potocki-Veronese, G. 	Functional metagenomics reveals novel pathways of prebiotic breakdown by human gut bacteria.	PLoS ONE	2013	8		e72766			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. 		
@D	Cech, D.//Pein, C.-D. 	The influence of modifications on the cleavage of oligonucleotide duplexes by EcoRII and MvaI endonucleases.	Nucleosides and Nucleotides	1988	7		585-588			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. 		
@D	Cedar, H.//Solage, A.//Glaser, G.//Razin, A. 	Direct detection of methylated cytosine in DNA by use of the restriction enzyme MspI.	Nucleic Acids Res.	1979	6		2125-2132			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. 		
@D	Cedar, H.//Verdine, G.L. 	The amazing demethylase.	Nature	1999	397		568-569			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. 		
@D	Centeno-Leija, S.//Vinuesa, P.//Rodriguez-Pena, K.//Trenado-Uribe, M.//Cardenas-Conejo, Y.//Serrano-Posada, H.//Rodriguez-Sanoja, R.//Sanchez, S. 	Draft Genome Sequence of an Endophytic Actinoplanes Species, Encoding Uncommon trans-Acyltransferase Polyketide Synthases.	Genome Announcements	2016	4		e00164-16			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. 		
@D	Centorame, P.//Acciari, V.A.//Orsini, M.//Torresi, M.//Iannetti, L.//Angius, A.//Di Giammartino, D.//Prencipe, V.A.//Migliorati, G. 	Whole-Genome Sequence of Listeria monocytogenes Serovar 4b Strain IZSAM_Lm_hs2008, Isolated from a Human Infection in Italy.	Genome Announcements	2015	3		e00053-15			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. 		
@D	Cerdeira, L.//Fernandes, M.R.//Francisco, G.R.//Bueno, M.F.//Ienne, S.//Souza, T.A.//de Oliveira, G.D.//Lincopan, N. 	Draft Genome Sequence of a Hospital-Associated Clone of Klebsiella pneumoniae ST340/CC258 Coproducing RmtG and KPC-2 Isolated from a Pediatric Patient.	Genome Announcements	2016	4		e01130-16			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. 		
@D	Cerdeira, L.T. et al. 	Complete genome sequence of Corynebacterium pseudotuberculosis strain CIP 52.97, isolated from a horse in Kenya.	J. Bacteriol.	2011	193		7025-7026			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. 		
@D	Cerdeira, L.T. et al. 	Whole-Genome Sequence of Corynebacterium pseudotuberculosis PAT10 Strain Isolated from Sheep in Patagonia, Argentina.	J. Bacteriol.	2011	193		6420-6421			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. 		
@D	Cerdeno-Tarraga, A.M. et al. 	The complete genome sequence and analysis of Corynebacterium diphtheriae NCTC13129.	Nucleic Acids Res.	2003	31		6516-6523			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. 		
@D	Cerdeno-Tarraga, A.M. et al. 	Extensive DNA inversions in the B. fragilis genome control variable gene expression.	Science	2005	307		1463-1465			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. 		
@D	Cermak, T.//Doyle, E.L.//Christian, M.//Wang, L.//Zhang, Y.//Schmidt, C.//Baller, J.A.//Somia, N.V.//Bogdanove, A.J.//Voytas, D.F. 	Efficient design and assembly of custom TALEN and other TAL effector-based constructs for DNA targeting.	Nucleic Acids Res.	2011	39		E82			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. 		
@D	Cerquetti, M.C.//Brawer, R.//Gherardi, M.M.//Sordelli, D.O. 	Location of aroB and dam genes in the Salmonella typhimurium chromosome.	Abstr. Gen. Meet. Am. Soc. Microbiol.	1997	97		318			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. 		
@D	Cerquetti, M.C.//Brawer, R.//Gherardi, M.M.//Sordelli, D.O. 	Map position of the dam gene in Salmonella typhimurium.	Abstr. Gen. Meet. Am. Soc. Microbiol.	1996	96		491			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. 		
@D	Cerra, J.//Donohue, H.//Kral, A.//Oser, M.//Rostkowski, L.//Zappia, L.//Williams, L.E. 	Complete Genome Sequence of Pseudomonas sp. Strain NC02, Isolated from Soil.	Genome Announcements	2018	6		e00033-18			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. 		
@D	Cerritelli, S.//Springhorn, S.S.//Lacks, S.A. 	DpnA, a methylase for single-strand DNA in the DpnII restriction system, and its biological function.	Proc. Natl. Acad. Sci. U. S. A.	1989	86		9223-9227			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. 		
@D	Cerritelli, S.//White, S.W.//Lacks, S.A. 	Crystallization of the DpnM methylase from the DpnII restriction system of Streptococcus pneumoniae.	J. Mol. Biol.	1989	207		841-842			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. 		
@D	Cerritelli, S.//White, S.W.//Springhorn, S.S.//Lacks, S.A. 	Two DNA methylases in the DpnII restriction system of Streptococcus pneumoniae.	FASEB J.	1990	4		A2295			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. 		
@D	Cerveny, J.//Sinetova, M.A.//Zavrel, T.//Los, D.A. 	Mechanisms of High Temperature Resistance of Synechocystis sp. PCC 6803: An Impact of Histidine Kinase 34.	Life	2015	5		676-699			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. 		
@D	Cervoni, N.//Bhattacharya, S.//Szyf, M. 	DNA demethylase is a processive enzyme.	J. Biol. Chem.	1999	274		8363-8366			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. 		
@D	Cervoni, N.//Szyf, M. 	Demethylase activity is directed by histone acetylation.	J. Biol. Chem.	2001	276		40778-40787			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. 		
@D	Cesnaviciene, E.//Mitkaite, G.//Stankevicius, K.//Janulaitis, A.//Lubys, A. 	Esp1396I restriction-modification system: Structural organization and mode of regulation.	Nucleic Acids Res.	2003	31		743-749			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. 		
@D	Cesnaviciene, E.E.//Petrusyte, M.M.//Kazlauskiene, R.R.//Maneliene, Z.//Timinskas, A.//Lubys, A.//Janulaitis, A. 	Characterization of AloI, a Restriction-modification System of a New Type.	J. Mol. Biol.	2001	314		205-216			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. 		
@D	Cha, I.T.//Lee, M.H.//Kim, B.Y.//Cho, Y.J.//Kim, D.W.//Yim, K.J.//Song, H.S.//Seo, M.J.//Rhee, J.K.//Choi, J.S.//Choi, H.J.//Yoon, C.//Roh, S.W.//Nam, Y.D. 	Genome sequence of the haloarchaeon Haloterrigena jeotgali type strain A29(T) isolated from salt-fermented food.	Standards in Genomic Sciences	2015	10		49			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. 		
@D	Chaboki, K.M. 	Characterization of a restriction endonuclease isolated from Bacillus subtilis F2.	Biophys. J.	2001	80		282A			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. 		
@D	Chacon-Vargas, K.//Chirino, A.A.//Davis, M.M.//Debler, S.A.//Haimer, W.R.//Wilbur, J.J.//Mo, X.//Worthing, B.W.//Wainblat, E.G.//Zhao, S.//Gibbons, J.G. 	Genome Sequence of Zymomonas mobilis subsp. mobilis NRRL B-1960.	Genome Announcements	2017	5		e00562-17			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. 		
@D	Chagas, F.O.//Ruzzini, A.C.//Bacha, L.V.//Samborskyy, M.//Conti, R.//Pessotti, R.C.//de Oliveira, L.G.//Clardy, J.//Pupo, M.T. 	Genome Sequence of Streptomyces sp. Strain RTd22, an Endophyte of the Mexican Sunflower.	Genome Announcements	2016	4		e00693-16			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. 		
@D	Chahar, S.//Elsawy, H.//Ragozin, S.//Jeltsch, A. 	Changing the DNA Recognition Specificity of the EcoDam DNA-(Adenine-N6)-Methyltransferase by Directed Evolution.	J. Mol. Biol.	2010	395		79-88			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. 		
@D	Chai, B.//Wang, H.//Chen, X. 	Draft Genome Sequence of High-Melanin-Yielding Aeromonas media Strain WS.	J. Bacteriol.	2012	194		6693-6694			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. 		
@D	Chaillet, R.//Cirio, C.//Navara, C. 	The somatic form of the mouse Dnmt1 maintenance methyltransferase is expressed throughout preimplantation development.	Biol. Reprod.	2007	SI		90			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. 		
@D	Chain, P.//Lamerdin, J.//Larimer, F.//Regala, W.//Lao, V.//Land, M.//Hauser, L.//Hooper, A.//Klotz, M.//Norton, J.//Sayavedra-Soto, L.//Arciero, D.//Hommes, N.//Whittaker, M.//Arp, D. 	Complete genome sequence of the ammonia-oxidizing bacterium and obligate chemolithoautotroph Nitrosomonas europaea.	J. Bacteriol.	2003	185		2759-2773			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. 		
@D	Chain, P.S. et al. 	Inaugural Article: Burkholderia xenovorans LB400 harbors a multi-replicon, 9.73-Mbp genome shaped for versatility.	Proc. Natl. Acad. Sci. U. S. A.	2006	103		15280-15287			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. 		
@D	Chain, P.S.//Comerci, D.J.//Tolmasky, M.E.//Larimer, F.W.//Malfatti, S.A.//Vergez, L.M.//Aguero, F.//Land, M.L.//Ugalde, R.A.//Garcia, E. 	Whole-genome analyses of speciation events in pathogenic Brucellae.	Infect. Immun.	2005	73		8353-8361			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. 		
@D	Chain, P.S.//Hu, P.//Malfatti, S.A.//Radnedge, L.//Larimer, F.//Vergez, L.M.//Worsham, P.//Chu, M.C.//Andersen, G.L. 	Complete Genome Sequence of Yersinia pestis Strains Antiqua and Nepal516: Evidence of Gene Reduction in an Emerging Pathogen.	J. Bacteriol.	2006	188		4453-4463			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. 		
@D	Chain, P.S.//Lang, D.M.//Comerci, D.J.//Malfatti, S.A.//Vergez, L.M.//Shin, M.//Ugalde, R.A.//Garcia, E.//Tolmasky, M.E. 	Genome of Ochrobactrum anthropi ATCC 49188T, a Versatile Opportunistic Pathogen and Symbiont of Several Eukaryotic Hosts.	J. Bacteriol.	2011	193		4274-4275			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. 		
@D	Chain, P.S.G. et al. 	Insights into the evolution of Yersinia pestis through whole-genome comparison with Yersinia pseudotuberculosis.	Proc. Natl. Acad. Sci. U. S. A.	2004	101		13826-13831			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. 		
@D	Chakrabortti, A.//Li, J.//Liang, Z.X. 	Draft Genome Sequence of Nocardia jinanensis, an Opportunistic Bacterial Pathogen That Causes Cellulitis.	Genome Announcements	2016	4		e00593-16			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. 		
@D	Chakraborty, R.//Woo, H.//Dehal, P.//Walker, R.//Zemla, M.//Auer, M.//Goodwin, L.A.//Kazakov, A.//Novichkov, P.//Arkin, A.P.//Hazen, T.C. 	Complete genome sequence of Pseudomonas stutzeri strain RCH2 isolated from a Hexavalent Chromium [Cr(VI)] contaminated site.	Standards in Genomic Sciences	2017	12		23			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. 		
@D	Challacombe, J.F. et al. 	Complete genome sequence of Halorhodospira halophila SL1.	Standards in Genomic Sciences	2013	8		206-214			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. 		
@D	Challacombe, J.F.//Duncan, A.J.//Brettin, T.S.//Bruce, D.//Chertkov, O.//Detter, J.C.//Han, C.S.//Misra, M.//Richardson, P.//Tapia, R.//Thayer, N.//Xie, G.//Inzana, T.J. 	Complete Genome Sequence of Haemophilus somnus (Histophilus somni) Strain 129Pt and Comparison to Haemophilus ducreyi 35000HP and Haemophilus  influenzae Rd.	J. Bacteriol.	2007	189		1890-1898			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. 		
@D	Challacombe, J.F.//Petersen, J.M.//Gallegos-Graves, V.//Hodge, D.//Pillai, S.//Kuske, C.R. 	Whole genome relationships among Francisella bacteria of diverse origin define new species and provide specific regions for detection.	Appl. Environ. Microbiol.	2017	83		e02589-16			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. 		
@D	Chambaud, I.//Heilig, R.//Ferris, S.//Barbe, V.//Samson, D.//Galisson, F.//Moszer, I.//Dybvig, K.//Wroblewski, H.//Viari, A.//Rocha, E.P.C.//Blanchard, A. 	The complete genome sequence of the murine respiratory pathogen  Mycoplasma pulmonis.	Nucleic Acids Res.	2001	29		2145-2153			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. 		
@D	Chames, P.//Epinat, J.C.//Guillier, S.//Patin, A.//Lacroix, E.//Paques, F. 	In vivo selection of engineered homing endonucleases using double-strand break induced homologous recombination.	Nucleic Acids Res.	2005	33		e178			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. 		
@D	Champion, C.//Guianvarc'h, D.//Senamaud-Beaufort, C.//Jurkowska, R.Z.//Jeltsch, A.//Ponger, L.//Arimondo, P.B.//Guieysse-Peugeot, A.L. 	Mechanistic Insights on the Inhibition of C5 DNA Methyltransferases by Zebularine.	PLoS ONE	2010	5		e12388			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. 		
@D	Champion, M.D. et al. 	Comparative Genomic Characterization of Francisella tularensis Strains Belonging to Low and High Virulence Subspecies.	PLoS Pathog.	2009	5		e1000459			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. 		
@D	Chan, G.F.//Gan, H.M.//Rashid, N.A. 	Genome Sequence of Citrobacter sp. Strain A1, a Dye-Degrading Bacterium.	J. Bacteriol.	2012	194		5485-5486			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. 		
@D	Chan, G.F.//Gan, H.M.//Rashid, N.A. 	Genome Sequence of Enterococcus sp. Strain C1, an Azo Dye Decolorizer.	J. Bacteriol.	2012	194		5716-5717			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. 		
@D	Chan, H.-Y.//Chan, Y.-C.//Kam, K.-M.//Shaw, P.-C. 	Isolation and characterization of restriction endonuclease EclHKI from an Enterobacter cloacae strain.	World J. Microbiol. Biotechnol.	1994	10		30-32			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. 		
@D	Chan, J.//Halachev, M.//Yates, E.//Smith, G.//Pallen, M. 	Whole-Genome Sequence of the Emerging Pathogen Mycobacterium abscessus Strain 47J26.	J. Bacteriol.	2012	194		549			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. 		
@D	Chan, K.G.//Chen, J.W.//Chang, C.Y.//Yin, W.F.//Chan, X.Y. 	Draft Genome Sequence of Lysinibacillus sp. Strain A1, Isolated from Malaysian Tropical Soil.	Genome Announcements	2015	3		e00095-15			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. 		
@D	Chan, K.G.//Chen, J.W.//Tee, K.K.//Chang, C.Y.//Yin, W.F.//Chan, X.Y. 	Whole-Genome Analysis of Quorum-Sensing Burkholderia sp. Strain A9.	Genome Announcements	2015	3		e00063-15			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. 		
@D	Chan, K.G.//Chin, P.S.//Tee, K.K.//Chang, C.Y.//Yin, W.F.//Sheng, K.Y. 	Draft Genome Sequence of Aeromonas caviae Strain L12, a Quorum-Sensing Strain Isolated from a Freshwater Lake in Malaysia.	Genome Announcements	2015	3		e00079-15			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. 		
@D	Chan, K.G.//Chong, T.M.//Adrian, T.G.//Kher, H.L.//Hong, K.W.//Grandclement, C.//Faure, D.//Yin, W.F.//Dessaux, Y. 	Whole-Genome Sequence of Stenotrophomonas maltophilia ZBG7B Reveals Its Biotechnological Potential.	Genome Announcements	2015	3		e01442-15			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. 		
@D	Chan, K.G.//Kher, H.L.//Chang, C.Y.//Yin, W.F.//Tan, K.H. 	Analysis of Pectate Lyase Genes in Dickeya chrysanthemi Strain L11, Isolated from a Recreational Lake in Malaysia: a Draft Genome Sequence Perspective.	Genome Announcements	2015	3		e00145-15			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. 		
@D	Chan, K.G.//Ng, K.T.//Pang, Y.K.//Chong, T.M.//Kamarulzaman, A.//Yin, W.F.//Tee, K.K. 	Genome Anatomy of Streptococcus parasanguinis Strain C1A, Isolated from a Patient with Acute Exacerbation of Chronic Obstructive Pulmonary Disease, Reveals Unusual  Genomic Features.	Genome Announcements	2015	3		e00541-15			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. 		
@D	Chan, K.G.//Sulaiman, J.//Yong, D.A.//Tee, K.K.//Yin, W.F.//Priya, K. 	Draft Genome Perspective of Staphylococcus saprophyticus Strain SU8, an N-Acyl Homoserine Lactone-Degrading Bacterium.	Genome Announcements	2015	3		e01097-15			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. 		
@D	Chan, K.G.//Tan, K.H.//Yin, W.F.//Tan, J.Y. 	Complete Genome Sequence of Cedecea neteri Strain SSMD04, a Bacterium Isolated from Pickled Mackerel Sashimi.	Genome Announcements	2014	2		e01339-14			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. 		
@D	Chan, K.G.//Tan, W.S. 	Genomic Insights of Pectobacterium carotovorum Strain M022 Quorum-Sensing Activity through Whole-Genome Sequencing.	Genome Announcements	2015	3		e01554-14			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. 		
@D	Chan, K.G.//Tan, W.S. 	Insights into Cedecea neteri strain M006 through complete genome sequence, a rare bacterium from aquatic environment.	Standards in Genomic Sciences	2017	12		40			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. 		
@D	Chan, K.G.//Tan, W.S.//Chang, C.Y.//Yin, W.F.//Mumahad, Y.N.Y. 	Genome Sequence Analysis Reveals Evidence of Quorum-Sensing Genes Present in Aeromonas hydrophila Strain M062, Isolated from Freshwater.	Genome Announcements	2015	3		e00100-15			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. 		
@D	Chan, K.G.//Tee, K.K.//Yin, W.F.//Tan, J.Y. 	Complete Genome Sequence of Pluralibacter gergoviae FB2, an N-Acyl Homoserine Lactone-Degrading Strain Isolated from Packed Fish Paste.	Genome Announcements	2014	2		e01276-14			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. 		
@D	Chan, K.G.//Wong, C.S.//Yin, W.F.//Chan, X.Y. 	Draft Genome Sequence of Quorum-Sensing and Quorum-Quenching Pseudomonas aeruginosa Strain MW3a.	Genome Announcements	2014	2		e00258-14			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. 		
@D	Chan, K.G.//Yin, W.F.//Goh, S.Y. 	Complete Genome Sequence of Pandoraea pnomenusa 3kgm, a Quorum-Sensing Strain Isolated from a Former Landfill Site.	Genome Announcements	2014	2		e00427-14			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. 		
@D	Chan, K.G.//Yin, W.F.//Lim, Y.L. 	Complete Genome Sequence of Pseudomonas aeruginosa Strain YL84, a Quorum-Sensing  Strain Isolated from Compost.	Genome Announcements	2014	2		e00246-14			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. 		
@D	Chan, K.G.//Yin, W.F.//Tee, K.K.//Chang, C.Y.//Priya, K. 	Pandoraea sp. Strain E26: Discovery of Its Quorum-Sensing Properties via Whole-Genome Sequence Analysis.	Genome Announcements	2015	3		e00565-15			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. 		
@D	Chan, K.G.//Yunos, N.Y. 	Whole-Genome Sequencing Analysis of Chromobacterium piscinae Strain ND17, a Quorum-Sensing Bacterium.	Genome Announcements	2016	4		e00081-16			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. 		
@D	Chan, Q.W.//Cornman, R.S.//Birol, I.//Liao, N.Y.//Chan, S.K.//Docking, T.R.//Jackman, S.D.//Taylor, G.A.//Jones, S.J.//de Graaf, D.C.//Evans, J.D.//Foster, L.J. 	Updated genome assembly and annotation of Paenibacillus larvae, the agent of American foulbrood disease of honey bees.	BMC Genomics	2011	12		450			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. 		
@D	Chan, S.-H.//Zhu, Z.//Van Etten, J.L.//Xu, S.-Y. 	Cloning of CviPII nicking and modification system from chlorella virus Nys-1 and application of Nt.CviPII in random DNA amplification.	Nucleic Acids Res.	2004	32		6187-6199			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. 		
@D	Chan, S.H.//Bao, Y.//Ciszak, E.//Laget, S.//Xu, S.Y. 	Catalytic domain of restriction endonuclease BmrI as a cleavage module for engineering endonucleases with novel substrate specificities.	Nucleic Acids Res.	2007	35		6238-6248			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. 		
@D	Chan, S.H.//Opitz, L.//Higgins, L.//O'loane, D.//Xu, S.-Y. 	Cofactor Requirement of HpyAV Restriction Endonuclease.	PLoS ONE	2010	5		e9071			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. 		
@D	Chan, S.H.//Stoddard, B.L.//Xu, S.Y. 	Natural and engineered nicking endonucleases--from cleavage mechanism to engineering of strand-specificity.	Nucleic Acids Res.	2011	39		1-18			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. 		
@D	Chan, S.H.//Zhu, Z.Y.//Dunigan, D.D.//Van Etten, J.L.//Xu, S.Y. 	Cloning of Nt.CviQII nicking endonuclease and its cognate methyltransferase: M.CviQII methylates AG sequences.	Protein Expr. Purif.	2006	49		138-150			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. 		
@D	Chan, S.W.-L.//Zilberman, D.//Xie, Z.//Johansen, L.K.//Carrington, J.C.//Jacobsen, S.E. 	RNA silencing genes control de novo DNA methylation.	Science	2004	303		1336			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. 		
@D	Chan, W.Y.//Dietel, K.//Lapa, S.V.//Avdeeva, L.V.//Borriss, R.//Reva, O.N. 	Draft Genome Sequence of Bacillus atrophaeus UCMB-5137, a Plant Growth-Promoting  Rhizobacterium.	Genome Announcements	2013	1		e00233-13			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. 		
@D	Chan, X.Y.//Chen, J.W.//Adrian, T.G.//Hong, K.W.//Chang, C.Y.//Yin, W.F.//Chan, K.G. 	Whole-Genome Sequence and Fosfomycin Resistance of Bacillus sp. Strain G3(2015) Isolated from Seawater off the Coast of Malaysia.	Genome Announcements	2017	5		e00067-17			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. 		
@D	Chan, X.Y.//Chua, K.H.//Puthucheary, S.D.//Yin, W.F.//Chan, K.G. 	Draft Genome Sequence of an Aeromonas sp. Strain 159 Clinical Isolate That Shows  Quorum-Sensing Activity.	J. Bacteriol.	2012	194		6350			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. 		
@D	Chan, X.Y.//Chua, K.H.//Yin, W.F.//Puthucheary, S.D.//Chan, K.G. 	Whole-Genome Analysis of Aeromonas hydrophila Strain 187, Exhibiting Quorum-Sensing Activity.	Genome Announcements	2014	2		e01360-14			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. 		
@D	Chan, Y.//Ma, A.P.//Lacap-Bugler, D.C.//Huo, Y.B.//Keung, L.W.//Leung, F.C.//Watt, R.M. 	Complete Genome Sequence for Treponema sp. OMZ 838 (ATCC 700772, DSM 16789), Isolated from a Necrotizing Ulcerative Gingivitis Lesion.	Genome Announcements	2014	2		e01333-14			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). 		
@D	Chan, Y.-S.//Takeuchi, R.//Jarjour, J.//Huen, D.S.//Stoddard, B.L.//Russell, S. 	The Design and In Vivo Evaluation of Engineered I-OnuI-Based Enzymes for HEG Gene Drive.	PLoS ONE	2013	8		e74254			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 		
@D	Chand, M.K.//Nirwan, N.//Diffin, F.M.//van Aelst, K.//Kulkarni, M.//Pernstich, C.//Szczelkun, M.D.//Saikrishnan, K. 	Translocation-coupled DNA cleavage by the Type ISP restriction-modification enzymes.	Nat. Chem. Biol.	2015	11		870-877			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. 		
@D	Chander, A.M.//Kaur, G.//Nair, R.G.//Dhawan, D.K.//Kochhar, R.//Mayilraj, S.//Bhadada, S.K. 	Genome Sequencing of Serinicoccus chungangensis Strain CD08_5 Isolated from Duodenal Mucosa of a Celiac Disease Patient.	Genome Announcements	2016	4		e00043-16			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. 		
@D	Chander, A.M.//Kumari, M.//Kochhar, R.//Dhawan, D.K.//Bhadada, S.K.//Mayilraj, S. 	Genome Sequence of Kocuria polaris Strain CD08_4, an Isolate from the Duodenal Mucosa of a Celiac Disease Patient.	Genome Announcements	2017	5		e01158-17			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. 		
@D	Chander, A.M.//Nair, R.G.//Kaur, G.//Kochhar, R.//Mayilraj, S.//Dhawan, D.K.//Bhadada, S.K. 	Genome Sequence of Kocuria palustris Strain CD07_3 Isolated from the Duodenal Mucosa of a Celiac Disease Patient.	Genome Announcements	2016	4		e00210-16			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. 		
@D	Chandrababunaidu, M.M.//Sen, D.//Tripathy, S. 	Draft Genome Sequence of Filamentous Marine Cyanobacterium Lyngbya confervoides Strain BDU141951.	Genome Announcements	2015	3		e00066-15			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. 		
@D	Chandrababunaidu, M.M.//Singh, D.//Sen, D.//Bhan, S.//Das, S.//Gupta, A.//Adhikary, S.P.//Tripathy, S. 	Draft Genome Sequence of Tolypothrix boutellei Strain VB521301.	Genome Announcements	2015	3		e00001-15			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. 		
@D	Chandrasegaran, S.//Carroll, D. 	Origins of Programmable Nucleases for Genome Engineering.	J. Mol. Biol.	2016	428		963-989			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. 		
@D	Chandrasegaran, S.//Lunnen, K.D.//Smith, H.O.//Wilson, G.G. 	Cloning and sequencing the HinfI restriction and modification genes.	Gene	1988	70		387-392			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). 		
@A	Chandrasegaran, S.//Smith, H.O. 		Amino acid sequence homologies among twenty-five restriction endonucleases and methylases.			Sarma, R.H.//Sarma, M.H. 		Structure and Expression. From Proteins to Ribosomes.				New York	Adenine Press	1988		1		149-156									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. 		
@D	Chandrasegaran, S.//Smith, H.O.//Amzel, M.L.//Ysern, X. 	Preliminary x-ray diffraction analysis of HhaII endonuclease-DNA cocrystals.	Proteins	1986	1		263-266			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. 		
@D	Chandrasegaran, S.//Smith, J. 	Chimeric restriction enzymes: What is next?	Biol. Chem.	1999	380		841-848			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. 		
@D	Chandrasegaran, S.//Wu, L.P.//Valda, E.//Smith, H.O. 	Overproduction and purification of the M.HhaII methyltransferase from Haemophilus haemolyticus.	Gene	1988	74		15-21			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. 		
@D	Chandrasekhar, K.//Raman, R. 	Restriction enzyme HincII is sensitive to methylation of cytosine that occurs 5' to the recognition sequence.	Nucleic Acids Res.	1996	24		1045-1046			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. 		
@D	Chandrashekaran, S.//Babu, P.//Nagaraja, V. 	Purification and characterization of restriction endonuclease BasI from Bacillus species.	J. Biochem. Mol. Biol. Biophys.	1999	3		225-229			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. 		
@D	Chandrashekaran, S.//Babu, P.//Nagaraja, V. 	Characterization of DNA binding activities of over-expressed KpnI restriction endonuclease and modification methylase.	J. Biosci.	1999	24		269-277			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. 		
@D	Chandrashekaran, S.//Manjunatha, U.H.//Nagaraja, V. 	KpnI restriction endonuclease and methyltransferase exhibit contrasting mode of sequence recognition.	Nucleic Acids Res.	2004	32		3148-3155			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. 		
@D	Chandrashekaran, S.//Saravanan, M.//Radha, D.R.//Nagaraja, V. 	Ca2+-mediated site-specific DNA cleavage and suppression of promiscuous activity of KpnI restriction endonuclease.	J. Biol. Chem.	2004	279		49736-49740			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. 		
@D	Chandrashekaran, S.//Shankar, A.B.//Babu, P.//Paul, B.D.//Nagaraja, V. 	Identification and characterization of a type II restriction endonuclease, StrI from Streptomyces thermodiastaticus.	Curr. Sci.	1999	77		273-276			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. 		
@D	Chandrashekharan, S.//Paul, B.D.//Nagaraja, V. 	Design of a novel regulatory circuit for expression of restriction endonucleases.	Biol. Chem.	1998	379		579-582			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. 		
@D	Chang, D.//Zhu, Y.//Chen, J.//Fang, X.//Li, T.//Wang, J.//Guo, Y.//Su, L.//Xu, G.//Wang, Y.//Chen, Z.//Liu, C. 	Draft Genome Sequences and Annotation of Enterococcus faecium Strain LCT-EF20.	Genome Announcements	2013	1		e00083-12			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. 		
@D	Chang, D.//Zhu, Y.//Fang, X.//Li, T.//Wang, J.//Guo, Y.//Su, L.//Liu, Y.//Jiang, X.//Wang, L.//Guo, N.//Liu, C. 	Draft Genome Sequences of the Enterococcus faecium Strain LCT-EF258.	Genome Announcements	2013	1		e00147-12			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. 		
@D	Chang, D.//Zhu, Y.//Zou, Y.//Fang, X.//Li, T.//Wang, J.//Guo, Y.//Su, L.//Xia, J.//Yang, R.//Fang, C.//Liu, C. 	Draft Genome Sequence of Enterococcus faecium Strain LCT-EF90.	J. Bacteriol.	2012	194		3556-3557			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. 		
@D	Chang, D.H.//Jin, T.E.//Rhee, M.S.//Jeong, H.//Kim, S.//Kim, B.C. 	Draft Genome Sequence of Bordetella trematum Strain HR18.	Genome Announcements	2015	3		e01357-14			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. 		
@D	Chang, D.H.//Rhee, M.S.//Jeong, H.//Kim, S.//Kim, B.C. 	Draft Genome Sequence of Acinetobacter sp. HR7, Isolated from Hanwoo, Korean Native Cattle.	Genome Announcements	2015	3		e01358-14			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). 		
@D	Chang, H.K.//Zylstra, G.J.//Chae, J.C. 	Genome Sequence of n-Alkane-Degrading Hydrocarboniphaga effusa Strain AP103T (ATCC BAA-332T).	J. Bacteriol.	2012	194		5120			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%. 		
@D	Chang, S.//Cohen, S.N. 	In vivo site-specific genetic recombination promoted by the EcoRI restriction endonuclease.	Proc. Natl. Acad. Sci. U. S. A.	1977	74		4811-4815			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. 		
@D	Chang, S.//Zhang, G.//Chen, X.//Long, H.//Wang, Y.//Chen, T.//Liu, G. 	The complete genome sequence of the cold adapted crude-oil degrader: Pedobacter steynii DX4.	Standards in Genomic Sciences	2017	12		45			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. 		
@D	Chang, S.H.//Cho, S.T.//Chen, C.L.//Yang, J.Y.//Kuo, C.H. 	Draft Genome Sequence of a 16SrII-A Subgroup Phytoplasma Associated with Purple Coneflower (Echinacea purpurea) Witches' Broom Disease in Taiwan.	Genome Announcements	2015	3		e01398-15			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. 		
@D	Chang, Y.C.//Sawada, K.//Kim, E.S.//Jung, K.//Kikuchi, S. 	Whole-Genome Sequence of Aquamicrobium sp. Strain SK-2, a Polychlorinated Biphenyl-Utilizing Bacterium Isolated from Sewage Sludge.	Genome Announcements	2015	3		e00439-15			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. 		
@D	Chang, Y.J. et al. 	Non-contiguous finished genome sequence and contextual data of the filamentous soil bacterium Ktedonobacter racemifer type strain (SOSP1-21).	Standards in Genomic Sciences	2011	5		97-111			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. 		
@D	Chang, Y.J. et al. 	Complete genome sequence of Acidaminococcus fermentans type strain (VR4).	Standards in Genomic Sciences	2010	3		1-14			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. 		
@D	Chanto, G.//Occhialini, A.//Gras, N.//Alm, R.A.//Megraud, F.//Marais, A. 	Identification of strain-specific genes located outside the plasticity zone in nine clinical isolates of Helicobacter pylori.	Microbiology	2002	148		3671-3680			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. 		
@D	Chapartegui-Gonzalez, I.//Lazaro-Diez, M.//Redondo-Salvo, S.//Alted-Perez, L.//Ocejo-Vinyals, J.G.//Navas, J.//Ramos-Vivas, J. 	Whole-Genome Sequence of Acinetobacter pittii HUMV-6483 Isolated from Human Urine.	Genome Announcements	2017	5		e00658-17			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. 		
@D	Chapelais-Baron, M.//Goubet, I.//Duchaud, E.//Rosenfeld, E. 	Draft Genome Sequence of the Iridescent Marine Bacterium Cellulophaga lytica CECT 8139.	Genome Announcements	2017	5		e00811-17			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. 		
@D	Chaplin, A.V.//Efimov, B.A.//Khokhlova, E.V.//Kafarskaia, L.I.//Tupikin, A.E.//Kabilov, M.R.//Shkoporov, A.N. 	Draft Genome Sequence of Coprobacter fastidiosus NSB1T.	Genome Announcements	2014	2		e00122-14			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. 		
@D	Chaplin, A.V.//Shkoporov, A.N.//Efimov, B.A.//Pikina, A.P.//Borisova, O.Y.//Gladko, I.A.//Postnikova, E.A.//Lordkipanidze, A.E.//Kafarskaia, L.I. 	Draft Genome Sequence of Lactobacillus fermentum NB-22.	Genome Announcements	2015	3		e00896-15			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. 		
@D	Chapman, J.A. et al. 	The dynamic genome of Hydra.	Nature	2010	464		592-596			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. 		
@D	Charette, S.J.//Brochu, F.//Boyle, B.//Filion, G.//Tanaka, K.H.//Derome, N. 	Draft Genome Sequence of the Virulent Strain 01-B526 of the Fish Pathogen Aeromonas salmonicida.	J. Bacteriol.	2012	194		722-723			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. 		
@D	Charlop-Powers, Z.//Banik, J.J.//Owen, J.G.//Craig, J.W.//Brady, S.F. 	Selective enrichment of environmental DNA libraries for genes encoding nonribosomal peptides and polyketides by phosphopantetheine transferase-dependent complementation of siderophore biosynthesis.	ACS Chem. Biol.	2013	8		138-143			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. 		
@D	Chase, H.R.//Eberl, L.//Stephan, R.//Jeong, H.//Lee, C.//Finkelstein, S.//Negrete, F.//Gangiredla, J.//Patel, I.//Tall, B.D.//Gopinath, G.R.//Lehner, A. 	Draft Genome Sequence of Cronobacter sakazakii GP1999, Sequence Type 145, an Epiphytic Isolate Obtained from the Tomato's Rhizoplane/Rhizosphere Continuum.	Genome Announcements	2017	5		e00723-17			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%. 		
@D	Chase, H.R.//Gopinath, G.R.//Gangiredla, J.//Patel, I.R.//Kothary, M.H.//Carter, L.//Sathyamoorthy, V.//Lee, B.//Park, E.//Yoo, Y.J.//Chung, T.J.//Choi, H.//Jun, S.//Park, J.//Jeong, S.//Kim, M.//Reich, F.//Klein, G.//Tall, B.D. 	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.	Genome Announcements	2016	4		e01072-16			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. 		
@D	Chastain-Gross, R.P.//Xie, G.//Belanger, M.//Kumar, D.//Whitlock, J.A.//Liu, L.//Raines, S.M.//Farmerie, W.G.//Daligault, H.E.//Han, C.S.//Brettin, T.S.//Progulske-Fox, A. 	Genome Sequence of Porphyromonas gingivalis Strain 381.	Genome Announcements	2017	5		e01467-16			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%. 		
@D	Chater, K.F. 	Actinophage DNA.	Dev. Ind. Microbiol.	1980	21		65-74			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. 		
@D	Chater, K.F. 	A site-specific endodeoxyribonuclease from Streptomyces albus CMI 52766 sharing site-specificity with Providencia stuartii endonuclease PstI.	Nucleic Acids Res.	1977	4		1989-1998			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. 		
@A	Chater, K.F. 		Streptomyces Phages and Their Applications to Streptomyces Genetics.			Queener, S.W.//Day, L.E. 		The Bacteria					Academic Press	1986		9		119-158									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. 		
@A	Chater, K.F. 		Some Recent Developments in Streptomyces Genetics.			Sebek, O.K.//Laskin, A.I. 		Genetics of Industrial Microorganisms				Washington, D.C.	American Society for Microbiology	1979		0		123-133									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. 		
@A	Chater, K.F. 		Restriction in Streptomyces.			Mordarski, M.//Kurytowicz, W. Jeljaszewicz//J. 		Nocardia and Streptomyces. Proceedings of the International Symposium on Nocardia and Streptomyces. Warsaw Oct 4-8 1978				Stuttgart	Gustav Fischer Verlag	1978		0		303-311									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. 		
@D	Chater, K.F.//Carter, A.T. 	A New, Wide Host-range, Temperate Bacteriophage (R4) of Streptomyces and its Interaction with some Restriction-Modification Systems.	J. Gen. Microbiol.	1979	115		431-442			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. 		
@D	Chater, K.F.//Carter, A.T. 	Restriction of a bacteriophage in Streptomyces albus P (CMI 52766) by Endonuclease SalPI.	J. Gen. Microbiol.	1978	109		181-185			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. 		
@D	Chater, K.F.//Wilde, L.C. 	Restriction of a bacteriophage of Streptomyces albus G involving endonuclease SalI.	J. Bacteriol.	1976	128		644-650			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. 		
@D	Chater, K.F.//Wilde, L.C. 	Streptomyces albus G Mutants Defective in the SalGI Restriction-Modification System.	J. Gen. Microbiol.	1980	116		323-334			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. 		
@D	Chatterjee, D.//Thakur, A.R.//Raychaudhuri, S. 	Draft Genome Sequence of Ammonia-Producing Acinetobacter sp. Strain MCC2139 from  Dairy Effluent.	Genome Announcements	2013	1		e00410-13			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%. 		
@D	Chatterjee, D.K.//Hammond, A.W.//Blakesley, R.W.//Adams, S.M.//Gerard, G.F. 	Genetic organization of the KpnI restriction-modification system.	Nucleic Acids Res.	1991	19		6505-6509			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. 		
@D	Chatterjee, P.//Brady, K.L.//Solem, A.//Ho, Y.//Caprara, M.G. 	Functionally distinct nucleic acid binding sites for a group I intron encoded RNA maturase/DNA homing endonuclease.	J. Mol. Biol.	2003	329		239-251			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. 		
@D	Chaturvedi, D.//Chakravorty, M. 	Restriction-modification system in bacteriophage MB78.	Biochem. Biophys. Res. Commun.	2003	303		884-890			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. 		
@D	Chaturvedi, D.//Chakravorty, M. 	Identification of an unusual restriction-modification system in bacteriophage MB78.	Biochem. Soc. Trans.	2000	28		A171			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. 		
@D	Chau, M.L. et al. 	Group B Streptococcus Infections Caused by Improper Sourcing and Handling of Fish for Raw Consumption, Singapore, 2015-2016.	Emerg. Infect. Dis.	2017	23		1982-1990			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. 		
@D	Chaudhuri, P.//Goswami, T.T.K.//Lalsiamthara, J.//Kaur, G.//Vishnu, U.S.//Sankarasubramanian, J.//Gunasekaran, P.//Rajendhran, J. 	Draft Genome Sequence of the Intermediate Rough Vaccine Strain Brucella abortus S19Deltaper Mutant.	Genome Announcements	2015	3		e01336-15			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. 		
@D	Chaudhuri, R.R. et al. 	Complete genome sequence and comparative metabolic profiling of the prototypical enteroaggregative Escherichia coli strain 042.	PLoS ONE	2010	5		e8801			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. 		
@D	Chaudhuri, S.R. 	Draft Genome Sequence of an Industrially Important Bacillus sp. from Mandarmani Coastal Waters in Midnapur District, West Bengal, India.	Genome Announcements	2016	4		e00867-16			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%. 		
@D	Chauhan, A.//Green, S.//Pathak, A.//Thomas, J.//Venkatramanan, R. 	Whole-genome sequences of five oyster-associated bacteria show potential for crude oil hydrocarbon degradation.	Genome Announcements	2013	1		e00802-13			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. 		
@D	Chauhan, A.//Layton, A.C.//Williams, D.//Smartt, A.E.//Ripp, S.//Karpinets, T.V.//Brown, S.D.//Sayler, G.S. 	Draft Genome Sequence of the Polycyclic Aromatic Hydrocarbon-Degrading, Genetically Engineered Bioluminescent Bioreporter Pseudomonas fluorescens  HK44.	J. Bacteriol.	2011	193		5009			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. 		
@D	Chauhan, D.//Srivastava, P.A.//Yennamalli, R.M.//Priyadarshini, R. 	Draft Genome Sequence of Deinococcus indicus DR1, a Novel Strain Isolated from a  Freshwater Wetland.	Genome Announcements	2017	5		e00754-17			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. 		
@D	Chauhan, H.C.//Patel, B.K.//Chandel, B.S.//Patel, K.B.//Patel, A.C.//Shrimali, M.D.//Patel, S.S.//Bhagat, A.G.//Rajgor, M.//Patel, M.A.//Patel, M.//Kala, J.//Patel, B. 	Complete Genome Sequence of Brucella abortus SKN 13 Isolated from Placenta of Aborted Cattle in Gujarat, India.	Genome Announcements	2016	4		e01123-16			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. 		
@D	Chauthaiwale, V.M.//Vyas, P.R.//Deshpande, V.V. 	Genetic transformation of Chainia and heat attenuation of its restriction system.	Can. J. Microbiol.	1991	37		713-715			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. 		
@D	Chavez, S.L.//Pera, R.A.R. 	Identification of the De Novo DNA Methyltransferase, DNMT3A2, as a Novel Regulator of Germ Cell Development.	Reprod. Sci.	2011	18		172A			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. 		
@D	Chavez-Bueno, S.//Day, M.W.//Toby, I.T.//Akins, D.R.//Dyer, D.W. 	Genome Sequence of SCB34, a Sequence Type 131 Multidrug-Resistant Escherichia coli Isolate Causing Neonatal Early-Onset Sepsis.	Genome Announcements	2014	2		e00514-14			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. 		
@D	Che, J.//Liu, B.//Lin, Y.//Tang, W.//Tang, J. 	Draft Genome Sequence of Biocontrol Bacterium Brevibacillus brevis Strain FJAT-0809-GLX.	Genome Announcements	2013	1		e00160-13			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. 		
@D	Che, S.//Song, L.//Song, W.//Yang, M.//Liu, G.//Lin, X. 	Complete Genome Sequence of Antarctic Bacterium Psychrobacter sp. Strain G.	Genome Announcements	2013	1		e00725-13			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. 		
@D	Checinska, S.A.//Singh, N.K.//Allen, J.E.//Thissen, J.//Jaing, C.//Venkateswaran, K. 	Draft Genome Sequences of Biosafety Level 2 Opportunistic Pathogens Isolated from the Environmental Surfaces of the International Space Station.	Genome Announcements	2016	4		e01263-16			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. 		
@D	Chedin, F. 	The DNMT3 Family of Mammalian De Novo DNA Methyltransferases.	Prog. Mol. Biol. Transl. Sci.	2011	101		255-285			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. 		
@D	Chedin, F.//Lieber, M.R.//Hsieh, C.L. 	The DNA methyltransferase-like protein DNMT3L stimulates de novo methylation by Dnmt3a.	Proc. Natl. Acad. Sci. U. S. A.	2002	99		16916-16921			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. 		
@D	Chee, J.L.//Ravins, M.//Hanski, E.//Chen, S.L. 	Complete Genome Sequence of Streptococcus pyogenes emm14 JS95, a Necrotizing Fasciitis Strain Isolated in Israel.	Genome Announcements	2017	5		e00025-17			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. 		
@D	Cheevadhanarak, S. et al. 	Draft genome sequence of Arthrospira platensis C1 (PCC9438).	Standards in Genomic Sciences	2012	6		43-53			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. 		
@D	Chekireb, D.//Crovadore, J.//Brachmann, A.//Chablais, R.//Cochard, B.//Lefort, F. 	Whole-Genome Sequences of 14 Strains of Bradyrhizobium canariense and 1 Strain of Bradyrhizobium japonicum Isolated from Lupinus spp. in Algeria.	Genome Announcements	2017	5		e00676-17			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. 		
@D	Cheleuitte-Nieves, C.//Gulvik, C.A.//Humrighouse, B.W.//Bell, M.E.//Villarma, A.//Westblade, L.F.//Lipman, N.S.//Fischetti, V.A.//McQuiston, J.R. 	Draft Reference Genome Sequence of Corynebacterium mastitidis 16-1433, Isolated from a Mouse.	Genome Announcements	2018	6		e00050-18			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. 		
@D	Chen, A.//Powell, L.M.//Dryden, D.T.F.//Murray, N.E.//Brown, T. 	Tyrosine 27 of the specificity polypeptide of EcoKI can be UV crosslinked to a bromodeoxyuridine-substituted DNA target sequence.	Nucleic Acids Res.	1995	23		1177-1183			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. 		
@D	Chen, B.S.//Otten, L.G.//Resch, V.//Muyzer, G.//Hanefeld, U. 	Draft genome sequence of Rhodococcus rhodochrous strain ATCC 17895.	Standards in Genomic Sciences	2013	9		175-184			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. 		
@D	Chen, Bi.-F.//Chan, W.-Yee. 	The de novo DNA methyltransferase DNMT3A in development and cancer.	EPIGENETICS	2014	9		669-677			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. 		
@D	Chen, C. et al. 	A Glimpse of Streptococcal Toxic Shock Syndrome from Comparative Genomics of S. suis 2 Chinese Isolates.	PLoS ONE	2007	2		e315			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. 		
@D	Chen, C.//Ai, L.//Zhou, F.//Wang, L.//Zhang, H.//Chen, W.//Guo, B. 	Complete genome sequence of the probiotic bacterium Lactobacillus casei LC2W.	J. Bacteriol.	2011	193		3419-3420			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. 		
@D	Chen, C.//Kittichotirat, W.//Chen, W.//Downey, J.S.//Bumgarner, R. 	Genome Sequence of a Serotype b Non-JP2 Aggregatibacter actinomycetemcomitans Strain, ANH9381, from a Periodontally Healthy Individual.	J. Bacteriol.	2012	194		1837			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. 		
@D	Chen, C.//Kittichotirat, W.//Chen, W.//Downey, J.S.//Si, Y.//Bumgarner, R. 	Genome sequence of naturally competent Aggregatibacter actinomycetemcomitans serotype a strain D7S-1.	J. Bacteriol.	2010	192		2643-2644			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. 		
@D	Chen, C.//Kittichotirat, W.//Si, Y.//Bumgarner, R. 	Genome sequence of Aggregatibacter actinomycetemcomitans serotype c strain D11S-1.	J. Bacteriol.	2009	191		7378-7379			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. 		
@D	Chen, C.//Sun, L. 	Draft Genome Sequence of Exiguobacterium sp. HVEsp1, a Thermophilic Bacterium Isolated from a Deep-Sea Hydrothermal Vent in the Okinawa Trough.	Genome Announcements	2017	5		e00253-17			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. 		
@D	Chen, C.//Wang, L.//Chen, S.//Wu, X.//Gu, M.//Chen, X.//Jiang, S.//Wang, Y.//Deng, Z.//Dedon, P.C.//Chen, S. 	Convergence of DNA methylation and phosphorothioation epigenetics in bacterial genomes.	Proc. Natl. Acad. Sci. U. S. A.	2017	114		4501-4506			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. 		
@D	Chen, C.-H.B.//Sigman, D.S. 	Chemical Conversion of a DNA-binding protein into a site-specific nuclease.	Science	1987	237		1197-1201			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. 		
@D	Chen, C.-K.//Boucle, C.M.//Blaschek, H.P. 	Factors involved in the transformation of previously non-transformable Clostridium perfringens type B.	FEMS Microbiol. Lett.	1996	140		185-191			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. 		
@D	Chen, C.C.//Hsia, K.C.//Huang, C.T.//Wong, W.W.//Yen, M.Y.//Li, L.H.//Lin, K.Y.//Chen, K.W.//Li, S.Y. 	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.	J. Bacteriol.	2011	193		1788-1789			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. 		
@D	Chen, C.C.//Lin, Y.C.//Sheng, W.H.//Chen, Y.C.//Chang, S.C.//Hsia, K.C.//Liao, M.H.//Li, S.Y. 	Genome Sequence of a Dominant Multidrug-resistant Acinetobacter baumannii strain TCDC-AB0715.	J. Bacteriol.	2011	193		2361-2362			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. 		
@D	Chen, C.C.//Wang, K.Y.//Shen, C.K.J. 	DNA 5-Methylcytosine Demethylation Activities of the Mammalian DNA Methyltransferases.	J. Biol. Chem.	2013	288		9084-9091			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. 		
@D	Chen, C.C.//Wang, K.Y.//Shen, C.K.J. 	The Mammalian de Novo DNA Methyltransferases DNMT3A and DNMT3B Are Also DNA 5-Hydroxymethylcytosine Dehydroxymethylases.	J. Biol. Chem.	2012	287		33116-33121			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. 		
@D	Chen, C.J.//Unger, C.//Hoffmann, W.//Lindsay, J.A.//Huang, Y.C.//Gotz, F. 	Characterization and Comparison of 2 Distinct Epidemic Community-Associated Methicillin-Resistant Staphylococcus aureus Clones of ST59 Lineage.	PLoS ONE	2013	8		E63210			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. 		
@D	Chen, C.J.//Wu, T.L.//Lu, P.L.//Chen, Y.T.//Fung, C.P.//Chuang, Y.C.//Lin, J.C.//Siu, L.K. 	Closely Related NDM-1-Encoding Plasmids from Escherichia coli and Klebsiella pneumoniae in Taiwan.	PLoS ONE	2014	9		E104899			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. 		
@D	Chen, C.Y.//Wu, K.M.//Chang, Y.C.//Chang, C.H.//Tsai, H.C.//Liao, T.L.//Liu, Y.M.//Chen, H.J.//Shen, A.B.//Li, J.C.//Su, T.L.//Shao, C.P.//Lee, C.T.//Hor, L.I.//Tsai, S.F. 	Comparative genome analysis of Vibrio vulnificus, a marine pathogen.	Genome Res.	2003	13		2577-2587			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. 		
@D	Chen, D. 	Chemical modification of restriction endonuclease Bsp63I and its substrate.	Hunan Jiaoyu Xueyuan Xuebao	1997	15		91-94			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. 		
@D	Chen, D.//Liu, B.//Zhu, Y.//Wang, J.//Chen, Z.//Che, J.//Zheng, X.//Chen, X. 	Complete Genome Sequence of Ralstonia solanacearum FJAT-1458, a Potential Biocontrol Agent for Tomato Wilt.	Genome Announcements	2017	5		e00070-17			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. 		
@D	Chen, D.//Liu, B.//Zhu, Y.//Zhang, H.//Chen, Z.//Zheng, X.//Xiao, R.//Chen, Y. 	Complete Genome Sequence of Ralstonia solanacearum FJAT-91, a High-Virulence Pathogen of Tomato Wilt.	Genome Announcements	2017	5		e00900-17			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%. 		
@D	Chen, D.//Liu, Q.//Chen, X.//Zhao, X.//Chen, Y. 	The inhibition of restriction endonuclease PvuII cleavage activity by methylation outside its recognition sequence.	Nucleic Acids Res.	1991	19		5703-5705			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. 		
@D	Chen, D.//Sun, M.//Liu, Y.//Shi, G.//Chen, Y. 	Molecular mechanism of the inhibitory effect of methylation outside the recognition sequence of restriction endonuclease PvuII on its cleavage activity.	Chinese Sci. Bull.	1998	43		47-53			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. 		
@D	Chen, F.//Wang, H.//Cao, Y.//Li, X.//Wang, G. 	High quality draft genomic sequence of Arenimonas donghaensis DSM 18148(T).	Standards in Genomic Sciences	2015	10		59			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. 		
@D	Chen, F.//Yang, Z.//Yan, M.//Alvarado, J.B.//Wang, G.//Benner, S.A. 	Recognition of an expanded genetic alphabet by type-II restriction endonucleases and their application to analyze polymerase fidelity.	Nucleic Acids Res.	2011	39		3949-3961			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. 		
@D	Chen, F.J.//Lauderdale, T.L.//Wang, L.S.//Huang, I.W. 	Complete Genome Sequence of Staphylococcus aureus Z172, a Vancomycin-Intermediate and Daptomycin-Nonsusceptible Methicillin-Resistant Strain Isolated in Taiwan.	Genome Announcements	2013	1		e01011-13			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. 		
@D	Chen, G.//Murdoch, R.W.//Mack, E.E.//Seger, E.S.//Loffler, F.E. 	Complete Genome Sequence of Dehalobacterium formicoaceticum Strain DMC, a Strictly Anaerobic Dichloromethane-Degrading Bacterium.	Genome Announcements	2017	5		e00897-17			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. 		
@D	Chen, G.C.C.//Brown, A.//Lema, M.W. 	Restriction endonuclease activities in the legionellae.	Can. J. Microbiol.	1986	32		591-593			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. 		
@D	Chen, H.//Brinkac, L.M.//Mishra, P.//Li, N.//Lymperopoulou, D.S.//Dickerson, T.L.//Gordon-Bradley, N.//Williams, H.N.//Badger, J.H. 	Draft genome sequences for the obligate bacterial predators Bacteriovorax spp. of four phylogenetic clusters.	Standards in Genomic Sciences	2015	10		11			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. 		
@D	Chen, H.-P.//Zhu, S.-H.//Casabon, I.//Hallam, S.J.//Crocker, F.H.//Mohn, W.W.//Indest, K.J.//Eltis, L.D. 	Genomic and Transcriptomic Studies of an RDX (Hexahydro-1,3,5-Trinitro-1,3,5-Triazine)-Degrading Actinobacterium.	Appl. Environ. Microbiol.	2012	78		7798-7800			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. 		
@D	Chen, J.//Fang, Q. 	Whole-Genome Sequencing Analysis of Methicillin-Resistant Staphylococcus simulans Causing Surgical Site Infection.	Genome Announcements	2016	4		e00555-16			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. 		
@D	Chen, J.//Herzenberg, L.A.//Herzenberg, L.A. 	Heparin inhibits EcoRI endonuclease cleavage of DNA at certain EcoRI sites.	Nucleic Acids Res.	1990	18		3255			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. 		
@D	Chen, J.//Huang, H.//Chang, C.J.//Stenger, D.C. 	Draft Genome Sequence of Xylella fastidiosa subsp. multiplex Strain Griffin-1 from Quercus rubra in Georgia.	Genome Announcements	2013	1		e00756-13			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. 		
@D	Chen, J.//Li, Y.//Zhang, K.//Wang, H. 	Whole-Genome Sequence of Phage-Resistant Strain Escherichia coli DH5alpha.	Genome Announcements	2018	6		e00097-18			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. 		
@D	Chen, J.//Wang, X.//Zhu, S.//Chen, Y.//Yang, J. 	Complete Genome Sequence of Alteromonas stellipolaris LMG 21856, a Budding Brown  Pigment-Producing Oligotrophic Bacterium Isolated from the Southern Ocean.	Genome Announcements	2016	4		e00137-16			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%. 		
@D	Chen, J.//Wu, F.//Zheng, Z.//Deng, X.//Burbank, L.P.//Stenger, D.C. 	Draft Genome Sequence of Xylella fastidiosa subsp. fastidiosa Strain Stag's Leap.	Genome Announcements	2016	4		e00240-16			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. 		
@D	Chen, J.//Xia, Y.//Cheng, C.//Fang, C.//Shan, Y.//Jin, G.//Fang, W. 	Genome sequence of a non-pathogenic Listeria monocytogenes serovar 4a strain M7.	J. Bacteriol.	2011	193		5019-5020			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. 		
@D	Chen, J.//Xie, G.//Han, S.//Civerolo, E.L. 	Two whole genome sequences of Xylella fastidiosa (strains M12 and M23) causing almond leaf scorch disease in California.	J. Bacteriol.	2010	192		4534			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. 		
@D	Chen, J.H.//Zhang, J.//Yang, H.H.//Fu, F.F.//Chen, G.N. 	A strategy for development of electrochemical DNA biosensor based on site-specific DNA cleavage of restriction endonuclease.	Biosensors and Bioelectronics	2010	26		144-148			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. 		
@D	Chen, J.W.//Chan, K.G. 	Genome Sequence of Dyella japonica Strain A8, a Quorum-Quenching Bacterium That Degrades N-Acylhomoserine Lactones, Isolated from Malaysian Tropical Soil.	J. Bacteriol.	2012	194		6331			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. 		
@D	Chen, J.W.//Gan, H.M.//Yin, W.F.//Chan, K.G. 	Genome Sequence of Roseomonas sp. Strain B5, a Quorum-Quenching N-Acylhomoserine  Lactone-Degrading Bacterium Isolated from Malaysian Tropical Soil.	J. Bacteriol.	2012	194		6681-6682			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. 		
@D	Chen, K.//Reuter, M.//Sanghvi, B.//Roberts, G.A.//Cooper, L.P.//Tilling, M.//Blakely, G.W.//Dryden, D.T.F. 	ArdA proteins from different mobile genetic elements can bind to the EcoKI Type I DNA methyltransferase of E. coli K12.	Biochim. Biophys. Acta	2014	1844		505-511			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. 		
@D	Chen, K.//Roberts, G.A.//Stephanou, A.S.//Cooper, L.P.//White, J.H.//Dryden, D.T.F. 	Fusion of GFP to the M.EcoKI DNA methyltransferase produces a new probe of Type I DNA restriction and modification enzymes.	Biochem. Biophys. Res. Commun.	2010	398		254-259			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. 		
@D	Chen, K.//Stephanou, A.S.//Roberts, G.A.//White, J.H.//Cooper, L.P.//Houston, P.J.//Lindsay, J.A.//Dryden, D.T. 	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.	Adv. Exp. Med. Biol.	2016	915		81-97			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. 		
@D	Chen, L.//Brugger, K.//Skovgaard, M.//Redder, P.//She, Q.//Torarinsson, E.//Greve, B.//Awayez, M.//Zibat, A.//Klenk, H.-P.//Garrett, R.A. 	The genome of Sulfolobus acidocaldarius, a model organism of the Crenarchaeota.	J. Bacteriol.	2005	187		4992-4999			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. 		
@D	Chen, L.//Chavda, K.D.//DeLeo, F.R.//Bryant, K.A.//Jacobs, M.R.//Bonomo, R.A.//Kreiswirth, B.N. 	Genome Sequence of a Klebsiella pneumoniae Sequence Type 258 Isolate with Prophage-Encoded K. pneumoniae Carbapenemase.	Genome Announcements	2015	3		e00659-15			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. 		
@D	Chen, L.//Chavda, K.D.//Fraimow, H.S.//Mediavilla, J.R.//Melano, R.G.//Jacobs, M.R.//Bonomo, R.A.//Kreiswirth, B.N. 	Complete nucleotide sequence of blaKPC-4 and blaKPC-5 harboring IncN and IncX plasmids from Klebsiella pneumoniae strains isolated in New Jersey.	Antimicrob. Agents Chemother.	2013	57		269-276			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. 		
@D	Chen, L.//Chavda, K.D.//Melano, R.G.//Hong, T.//Rojtman, A.D.//Jacobs, M.R.//Bonomo, R.A.//Kreiswirth, B.N. 	Molecular Survey of the Dissemination of Two blaKPC-Harboring IncFIA Plasmids in New Jersey and New York Hospitals.	Antimicrob. Agents Chemother.	2014	58		2289-2294			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. 		
@D	Chen, L.//Chavda, K.D.//Melano, R.G.//Jacobs, M.R.//Koll, B.//Hong, T.//Rojtman, A.D.//Levi, M.H.//Bonomo, R.A.//Kreiswirth, B.N. 	Comparative Genomic Analysis of KPC-Encoding pKpQIL-Like Plasmids and Their Distribution in New Jersey and New York Hospitals.	Antimicrob. Agents Chemother.	2014	58		2871-2877			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. 		
@D	Chen, L.//Hu, H.//Chavda, K.D.//Zhao, S.//Liu, R.//Liang, H.//Zhang, W.//Wang, X.//Jacobs, M.R.//Bonomo, R.A.//Kreiswirth, B.N. 	Complete sequence of a KPC-producing IncN multidrug-resistant plasmid from an epidemic Escherichia coli ST131 strain in China.	Antimicrob. Agents Chemother.	2014	58		2422-2425			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. 		
@D	Chen, L.//Lin, J.//Liu, X.//Pang, X.//Lin, H.//Lin, J. 	Transposition of IS elements induced by electroporation of suicide plasmid in Acidithiobacillus caldus.	Enzyme Microb. Technol.	2013	53		165-169			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. 		
@D	Chen, L.//MacMillan, A.M.//Chang, W.//Ezaz-Nikpay, K.//Lane, W.S.//Verdine, G.L. 	Direct identification of the active-site nucleophile in a DNA (Cytosine-5)-methyltransferase.	Biochemistry	1991	30		11018-11025			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. 		
@D	Chen, L.//MacMillan, A.M.//Verdine, G.L. 	Mutational separation of DNA binding from catalysis in a DNA cytosine methyltransferase.	J. Am. Chem. Soc.	1993	115		5318-5319			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. 		
@D	Chen, L.//Mediavilla, J.R.//Oliveira, D.C.//Willey, B.M.//de Lencastre, H.//Kreiswirth, B.N. 	Multiplex real-time PCR for rapid Staphylococcal cassette chromosome mec typing.	J. Clin. Microbiol.	2009	47		3692-3706			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. 		
@D	Chen, L.//Mediavilla, J.R.//Smyth, D.S.//Chavda, K.D.//Ionescu, R.//Roberts, R.B.//Robinson, D.A.//Kreiswirth, B.N. 	Identification of a novel transposon (Tn6072) and a truncated staphylococcal cassette chromosome mec element in methicillin-resistant Staphylococcus aureus ST239.	Antimicrob. Agents Chemother.	2010	54		3347-3354			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. 		
@D	Chen, L.//Paulsen, D.B.//Scruggs, D.W.//Banes, M.M.//Reeks, B.Y.//Lawrence, M.L. 	Alteration of DNA adenine methylase (Dam) activity in Pasteurella multocida causes increased spontaneous mutation frequency and attenuation in mice.	Microbiology	2003	149		2283-2290			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. 		
@D	Chen, L.//Wu, D.//Cai, X.//Guo, F.//Blackall, P.J.//Xu, X.//Chen, H. 	Electrotransformation of Haemophilus parasuis with in vitro modified DNA based on a novel shuttle vector.	Vet. Microbiol.	2012	155		310-316			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. 		
@D	Chen, L.//Zhang, D.T.//Zhang, J.//Su, Y.A.//Zhang, H. 	Whole-Genome Sequences of Two Clinical Isolates of Extensively Drug-Resistant Mycobacterium tuberculosis from Zunyi, China.	Genome Announcements	2014	2		e00910-14			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. 		
@D	Chen, L.//Zou, G.//Cao, X.//Rufan, Z. 	The synthesis of nine kinds of oligodeoxynucleotide containing the recognition sequence for PstI and their interaction with enzyme.	J. Wuhan Univ.	1996	42		499-506			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. 		
@D	Chen, M.//Lin, L.//Zhang, Y.//Sun, L.//An, Q. 	Genome Sequence of Klebsiella oxytoca SA2, an Endophytic Nitrogen-Fixing Bacterium Isolated from the Pioneer Grass Psammochloa villosa.	Genome Announcements	2013	1		e00601-13			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. 		
@D	Chen, M.//Qin, N.//Pei, W.//Li, Q.//Yang, Q.//Chen, Y.//Huang, D.//Xiang, Y.//Lin, L. 	Draft Whole-Genome Sequences of Zhihengliuella halotolerans La12 and Microbacterium kitamiense Sa12, Strains with Cellulase Activity, Isolated from  the Qinghai-Tibetan Plateau.	Genome Announcements	2018	6		e01531-17			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. 		
@D	Chen, M.//Yan, Y.//Zhang, W.//Lu, W.//Wang, J.//Ping, S.//Lin, M. 	Complete Genome Sequence of the Type Strain Pseudomonas stutzeri CGMCC 1.1803.	J. Bacteriol.	2011	193		6095			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. 		
@D	Chen, M.//Zhu, B.//Lin, L.//Yang, L.//Li, Y.//An, Q. 	Complete genome sequence of Kosakonia sacchari type strain SP1(T.).	Standards in Genomic Sciences	2014	9		1311-1318			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. 		
@D	Chen, M.X.//Li, H.Y.//Ye, X.S.//He, X.Y. 	Draft Genome Sequence of an Extracellular Protease-Producing Bacterium, Stenotrophomonas bentonitica VV6, Isolated from Arctic Seawater.	Genome Announcements	2018	6		e01610-17			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. 		
@D	Chen, P.//den Bakker, H.C.//Korlach, J.//Kong, N.//Storey, D.B.//Paxinos, E.E.//Ashby, M.//Clark, T.//Luong, K.//Wiedmann, M.//Weimer, B.C. 	Comparative Genomics Reveals the Diversity of Restriction-Modification Systems and DNA Methylation Sites in Listeria monocytogenes.	Appl. Environ. Microbiol.	2017	83		e02091-16			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. 		
@D	Chen, P.//Jeannotte, R.//Weimer, B.C. 	Exploring bacterial epigenomics in the next-generation sequencing era: a new approach for an emerging frontier.	Trends Microbiol.	2014	22		292-300			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. 		
@D	Chen, P.//Kong, N.//Huang, B.//Thao, K.//Ng, W.//Storey, D.B.//Arabyan, N.//Foutouhi, A.//Foutouhi, S.//Weimer, B.C. 	100K Pathogen Genome Project: 306 Listeria Draft Genome Sequences for Food Safety and Public Health.	Genome Announcements	2017	5		e00967-16			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. 		
@D	Chen, P.//Li, J.//Zhao, J.//He, L.//Zhang, Z. 	Differential dependence on DNA ligase of type II restriction enzymes: A practical way toward ligase-free DNA automaton.	Biochem. Biophys. Res. Commun.	2007	353		733-737			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. 		
@D	Chen, P.//Li, S.//Yan, L.//Wang, N.//Yan, X.//Li, H. 	Draft Genome Sequence of Bacillus subtilis Type Strain B7-S, Which Converts Ferulic Acid to Vanillin.	Genome Announcements	2014	2		e00025-14			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. 		
@D	Chen, P.C.//Chen, T.W.//Han, Y.A.//Ng, W.V.//Yang, C.S. 	Complete Genome Sequence of a New Halophilic Archaeon, Haloarcula taiwanensis, Isolated from a Solar Saltern in Southern Taiwan.	Genome Announcements	2018	6		e01529-17			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). 		
@D	Chen, Q.//Fischer, J.R.//Benoit, V.M.//Dufour, N.P.//Youderian, P.//Leong, J.M. 	In Vitro CpG Methylation Increases the Transformation Efficiency of Borrelia burgdorferi Strains Harboring the Endogenous Linear Plasmid lp56.	J. Bacteriol.	2008	190		7885-7891			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. 		
@D	Chen, Q.//Wang, C.H.//Deng, S.K.//Wu, Y.D.//Li, Y.//Yao, L.//Jiang, J.D.//Yan, X.//He, J.//Li, S.P. 	Novel three-component Rieske non-heme iron oxygenase system catalyzing the N-dealkylation of chloroacetanilide herbicides in sphingomonads DC-6 and DC-2.	Appl. Environ. Microbiol.	2014	80		5078-5085			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. 		
@D	Chen, Q.//Zhou, J.W.//Wu, S.H.//Meng, X.H.//Yu, D.J.//Wang, X.J. 	Draft Genome Sequence of Carbapenem-Resistant Klebsiella pneumoniae XPY20 Collected from a Bloodstream Infection Patient.	Genome Announcements	2018	6		e00443-18			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. 		
@D	Chen, Q.Q.//Liu, B.//Liu, G.H.//Wang, J.P.//Che, J.M. 	Draft Genome Sequence of Bacillus tequilensis Strain FJAT-14262a.	Genome Announcements	2015	3		e01317-15			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. 		
@D	Chen, S.//Chen, L.//Chen, L.//Ren, X.//Ge, H.//Kang, G.//Sun, S.//Chen, Z.//Sun, Y.//Li, Y. 	Complete Genome Sequence of Lactobacillus reuteri WHH1689, Isolated from Traditional Chinese Highland Barley Wine.	Genome Announcements	2018	6		e00425-18			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). 		
@D	Chen, S.//Hao, H.//Zhao, P.//Gao, P.//He, Y.//Ji, W.//Wang, Z.//Lu, Z.//Liu, Y.//Chu, Y. 	Complete Genome Sequence of Mycoplasma bovis Strain 08M.	Genome Announcements	2017	5		e00324-17			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. 		
@D	Chen, S.//Soehnlen, M.//Downes, F.P.//Walker, E.D. 	Insights from the draft genome into the pathogenicity of a clinical isolate of Elizabethkingia meningoseptica Em3.	Standards in Genomic Sciences	2017	12		56			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. 		
@D	Chen, S.//Soehnlen, M.//Walker, E.D. 	Genome Sequence of Elizabethkingia meningoseptica EM1, Isolated from a Patient with a Bloodstream Infection.	Genome Announcements	2016	4		e01137-16			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. 		
@D	Chen, S.//Wang, C.//Li, H.//Shen, Y. 	Draft Genome Sequence of Haloparvum sedimenti Strain DYS4, the Type Species of the Genus Haloparvum, Isolated from a Salt Mine.	Genome Announcements	2017	5		e00770-17			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. 		
@D	Chen, S.//Wang, C.//Zhao, Z.//Yang, Z.L. 	Genome Sequence of Halorubrum sp. Strain T3, an Extremely Halophilic Archaeon Harboring a Virus-Like Element.	J. Bacteriol.	2012	194		6608-6609			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). 		
@D	Chen, S.C.//Chen, M.F.//Weng, C.Y.//Lai, M.C.//Wu, S.Y. 	Draft Genome Sequence of Methanoculleus sediminis S3FaT, a Hydrogenotrophic Methanogen Isolated from a Submarine Mud Volcano in Taiwan.	Genome Announcements	2016	4		e00308-16			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. 		
@D	Chen, S.L.//Hung, C.S.//Xu, J.//Reigstad, C.S.//Magrini, V.//Sabo, A.//Blasiar, D.//Bieri, T.//Meyer, R.R.//Ozersky, P.//Armstrong, J.R.//Fulton, R.S.//Latreille, J.P.//Spieth, J.//Hooton, T.M.//Mardis, E.R.//Hultgren, S.J.//Gordon, J.I. 	Identification of genes subject to positive selection in uropathogenic strains of Escherichia coli: A comparative genomics approach.	Proc. Natl. Acad. Sci. U. S. A.	2006	103		5977-5982			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. 		
@D	Chen, S.L.//Shapiro, L. 	Identification of long intergenic repeat sequences associated with DNA methylation sites in Caulobacter crescentus and other alpha-proteobacteria.	J. Bacteriol.	2003	185		4997-5002			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. 		
@D	Chen, S.L.//Wu, M.//Henderson, J.P.//Hooton, T.M.//Hibbing, M.E.//Hultgren, S.J.//Gordon, J.I. 	Genomic Diversity and Fitness of E. coli Strains Recovered from the Intestinal and Urinary Tracts of Women with Recurrent Urinary Tract Infection.	Sci. Transl. Med.	2013	5		184RA60			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. 		
@D	Chen, T.//Li, E. 	Structure and function of eukaryotic DNA methyltransferases.	Curr. Top. Dev. Biol.	2004	60		55-89			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. 		
@D	Chen, T.//Ueda, Y.//Dodge, J.E.//Wang, Z.//Li, E. 	Establishment and maintenance of genomic methylation patterns in mouse embryonic stem cells by Dnmt3a and Dnmt3b.	Mol. Cell. Biol.	2003	23		5594-5605			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. 		
@D	Chen, T.//Ueda, Y.//Xie, S.//Li, E. 	A novel Dnmt3a isoform produced from an alternative promoter localizes to euchromatin and its expression correlates with active de novo methylation.	J. Biol. Chem.	2002	277		38746-38754			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. 		
@D	Chen, W.//Wang, Y.//Li, D.//Li, L.//Xiao, Q.//Zhou, Q. 	Draft Genome Sequence of Brevibacillus brevis Strain X23, a Biocontrol Agent against Bacterial Wilt.	J. Bacteriol.	2012	194		6634-6635			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. 		
@D	Chen, X.//E, Z.//Gu, D.//Lv, L.//Li, Y. 	Complete Genome Sequence of Bifidobacterium actinocoloniiforme Type Strain DSM 22766T, Isolated from Bumblebee Digestive Tracts.	Genome Announcements	2015	3		e01084-15			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. 		
@D	Chen, X.//Wang, Z.-C. 	Plant DNA methyltransferase.	Shengming De Huaxue	2009	29		534-538			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. 		
@D	Chen, X.//Zhang, B.//Zhang, W.//Wu, X.//Zhang, M.//Chen, T.//Liu, G.//Dyson, P. 	Genome Sequence of Streptomyces violaceusniger Strain SPC6, a Halotolerant Streptomycete That Exhibits Rapid Growth and Development.	Genome Announcements	2013	1		e00494-13			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. 		
@D	Chen, X.H. et al. 	Comparative analysis of the complete genome sequence of the plant growth-promoting bacterium Bacillus amyloliquefaciens FZB42.	Nat. Biotechnol.	2007	25		1007-1014			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. 		
@D	Chen, X.J.//Han, K.//Feng, J.//Zhuo, L.//Li, Y.J.//Li, Y.Z. 	The complete genome sequence and analysis of a plasmid-bearing myxobacterial strain Myxococcus fulvus 124B02 (M 206081).	Standards in Genomic Sciences	2016	11		1			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. 		
@D	Chen, Y.//Chatterjee, S.S.//Porcella, S.F.//Yu, Y.S.//Otto, M. 	Complete Genome Sequence of a Panton-Valentine Leukocidin-Negative Community-Associated Methicillin-Resistant Staphylococcus aureus Strain of Sequence type 72 from Korea.	PLoS ONE	2013	8		E72803			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. 		
@D	Chen, Y.//Crosby, H.A.//Oosthuysen, W.F.I.I.//Diekema, D.J.//Kelley, S.T.//Horswill, A.R. 	Draft Genome Sequence of USA100 Methicillin-Resistant Staphylococcus aureus Strain 209.	Genome Announcements	2018	6		e01399-17			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. 		
@D	Chen, Y.//Cui, Y.//Pu, F.//Jiang, G.//Zhao, X.//Yuan, Y.//Zhao, W.//Li, D.//Liu, H.//Li, Y.//Liang, T.//Xu, L.//Wang, Y.//Song, Q.//Yang, J.//Liang, L.//Yang, R.//Han, L.//Song, Y. 	Draft genome sequence of an Acinetobacter genomic species 3 strain harboring a blaNDM-1 gene.	J. Bacteriol.	2011	194		204-205			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. 		
@D	Chen, Y.//He, Y.//Zhang, B.//Yang, J.//Li, W.//Dong, Z.//Hu, S. 	Complete Genome Sequence of Alicyclobacillus acidocaldarius Strain Tc-4-1.	J. Bacteriol.	2011	193		5602-5603			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. 		
@D	Chen, Y.//Ji, Y.J.//Roxby, R.//Conrad, C. 	In vivo expression of single-stranded DNA in mammalian cells with DNA enzyme sequences targeted to C-raf.	Antisense Nucleic Acid Drug Dev.	2000	10		415-422			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. 		
@D	Chen, Y.//Mukherjee, S.//Hoffmann, M.//Kotewicz, M.L.//Young, S.//Abbott, J.//Luo, Y.//Davidson, M.K.//Allard, M.//McDermott, P.//Zhao, S. 	Whole Genome Sequencing of a Gentamicin-Resistant Campylobacter coli isolated from United States Retail Meats Reveals Novel Plasmid Mediated Aminoglycoside Resistance Genes.	Antimicrob. Agents Chemother.	2013	57		5398-5405			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. 		
@D	Chen, Y.//Stine, O.C.//Badger, J.H.//Gil, A.I.//Nair, G.B.//Nishibuchi, M.//Fouts, D.E. 	Comparative Genomic Analysis of Vibrio parahaemolyticus: Serotype Conversion and Virulence.	BMC Genomics	2011	12		294			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. 		
@D	Chen, Y.//Strain, E.A.//Allard, M.//Brown, E.W. 	Genome sequences of Listeria monocytogenes strains J1816 and J1-220 associated with human outbreaks.	J. Bacteriol.	2011	193		3424-3425			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. 		
@D	Chen, Y.//Strain, E.A.//Allard, M.//Brown, E.W. 	Genome Sequence of Cronobacter sakazakii E899, a Strain Associated with Human Illness.	J. Bacteriol.	2011	193		5861			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. 		
@D	Chen, Y.//Xiang, Y.//Yuan, R.//Chai, Y. 	A restriction enzyme-powered autonomous DNA walking machine: its application for a highly sensitive electrochemiluminescence assay of DNA.	Nanoscale	2015	7		981-986			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. 		
@D	Chen, Y.H.//Lin, S.S.//Shyu, Y.T. 	Revealing the Saline Adaptation Strategies of the Halophilic Bacterium Halomonas beimenensis through High-throughput Omics and Transposon Mutagenesis Approaches.	Sci. Rep.	2017	7		0			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. 		
@D	Chen, Y.S.//Lin, H.H.//Hsueh, P.T.//Liu, P.J.//Ni, W.F.//Chung, W.C.//Lin, C.P.//Chen, Y.L. 	Whole-Genome Sequence of an Epidemic Strain of Burkholderia pseudomallei vgh07 in Taiwan.	Genome Announcements	2015	3		e00345-15			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. 		
@D	Chen, Y.T.//Lauderdale, T.L.//Liao, T.L.//Shiau, Y.R.//Shu, H.Y.//Wu, K.M.//Yan, J.J.//Su, I.J.//Tsai, S.F. 	Sequencing and comparative genomic analysis of pK29, a 269-kilobase conjugative plasmid encoding CMY-8 and CTX-M-3 beta-lactamases in  Klebsiella pneumoniae.	Antimicrob. Agents Chemother.	2007	51		3004-3007			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. 		
@D	Chen, Y.T.//Liao, T.L.//Liu, Y.M.//Lauderdale, T.L.//Yan, J.J.//Tsai, S.F. 	Mobilization of qnrB2 and ISCR1 in plasmids.	Antimicrob. Agents Chemother.	2009	53		1235-1237			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. 		
@D	Chen, Y.T.//Lin, J.C.//Fung, C.P.//Lu, P.L.//Chuang, Y.C.//Wu, T.L.//Siu, L.K. 	KPC-2-encoding plasmids from Escherichia coli and Klebsiella pneumoniae in Taiwan.	J. Antimicrob. Chemother.	2014	69		628-631			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. 		
@D	Chen, Y.T.//Peng, H.L.//Shia, W.C.//Hsu, F.R.//Ken, C.F.//Tsao, Y.M.//Chen, C.H.//Liu, C.E.//Hsieh, M.F.//Chen, H.C.//Tang, C.Y.//Ku, T.H. 	Whole-genome sequencing and identification of Morganella morganii KT pathogenicity-related genes.	BMC Genomics	2012	13		S4			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. 		
@D	Chen, Y.T.//Shu, H.Y.//Li, L.H.//Liao, T.L.//Wu, K.M.//Shiau, Y.R.//Yan, J.J.//Su, I.J.//Tsai, S.F.//Lauderdale, T.L. 	Complete Nucleotide Sequence of pK245, a 98-Kilobase Plasmid Conferring Quinolone Resistance and Extended-Spectrum-beta-Lactamase Activity in a Clinical Klebsiella pneumoniae Isolate.	Antimicrob. Agents Chemother.	2006	50		3861-3866			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. 		
@D	Chen, Y.Z.//Mohan, V.//Griffey, R.H. 	Spontaneous base flipping in DNA and its possible role in methyltransferase binding.	Phys. Rev. E	2000	62		1133-1137			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. 		
@D	Chen, Z.//Chang, D.//Zou, Y.//Su, L.//Zhu, Y.//Fang, X.//Wang, J.//Guo, Y.//Zhao, J.//Li, D.//Fang, C.//Yang, R.//Liu, C. 	Genome Sequence of Enterococcus faecium Clinical Isolate LCT-EF128.	J. Bacteriol.	2012	194		4765			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. 		
@D	Chen, Z.//Gui, J.//Gao, X.//Pei, C.//Hong, Y.//Zhang, Q. 	Genome architecture changes and major gene variations of Andrias davidianus ranavirus (ADRV).	Vet. Res.	2013	44		101			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. 		
@D	Chen, Z.//Kong, H. 	Isolation and characterization of restriction endonuclease BstYI from Bacillus stearothermophilus Y406.	FEBS Lett.	1988	234		169-171			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). 		
@D	Chen, Z.//Kong, H.//Wang, L. 	Isolation and characterization of restriction endonucleases BstFI and BstSI from Bacillus stearothermophilus.	J. Fudan Univ. (Natural Sci.)	1989	28		363-366			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. 		
@D	Chen, Z.//Lei, X.//Li, Y.//Zhang, J.//Zhang, H.//Yang, L.//Zheng, W.//Xu, H.//Zheng, T. 	Whole-Genome Sequence of Marine Bacterium Phaeodactylibacter xiamenensis Strain KD52, Isolated from the Phycosphere of Microalga Phacodactylum tricornutum.	Genome Announcements	2014	2		e01289-14			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. 		
@D	Chen, Z.//Li, Y.//Chang, D.//An, L.//Guo, Y.//Wang, J.//Li, T.//Wang, Y.//Zhang, X.//Dai, W.//Liu, C. 	Draft Genome Sequence of Enterococcus faecium Strain LCT-EF301, Which Shows Changes in Biochemical Metabolism following Space Flight.	Genome Announcements	2014	2		e00103-14			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. 		
@D	Chen, Z.//Ou, W.//Fan, X.//Cui, G.//Wang, Q.//Li, Q.//Sun, R.//Wu, X.//Qin, W.//Wang, Y. 	Complete Genome Sequences of Two Multidrug-Resistant Mycobacterium tuberculosis Strains Isolated in Guiyang, China.	Genome Announcements	2018	6		e01257-17			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. 		
@D	Chen, Z.//Wen, F.//Sun, N.//Zhao, H. 	Directed evolution of homing endonuclease I-SceI with altered sequence specificity.	Protein Eng. Des. Sel.	2009	22		249-256			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. 		
@D	Chen, Z.//Wilkins, M.R.//Hunter, N.//Nadkarni, M.A. 	Draft Genome Sequences of Two Clinical Isolates of Lactobacillus rhamnosus from Initial Stages of Dental Pulp Infection.	Genome Announcements	2013	1		e00073-12			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. 		
@D	Chen, Z.//Wojcik, S.F.//Welker, N.E. 	Genetic analysis of Bacillus stearothermophilus by protoplast fusion.	J. Bacteriol.	1986	165		994-1001			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. 		
@D	Chen, Z.//Yang, R.//Chen, B.//Li, R. 	Restriction and modification in a gram-negative thermophilic bacterium and isolation of restriction endonuclease TspAI.	J. Fudan Univ. (Natural Sci.)	1989	28		96-101			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. 		
@D	Chen, Z.//Zhao, H. 	A highly sensitive selection method for directed evolution of homing endonucleases.	Nucleic Acids Res.	2005	33		e154			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. 		
@D	Chen, Z.-X.//Riggs, A.D. 	Self-association of human de novo DNA methyltransferases, DNMT3A and DNMT3B.	Biochem. Cell Biol.	2005	83		566			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. 		
@D	Chen, Z.F.//Pan, X.S. 	Identification of a new type-II restriction enzyme BsrGI from Bacillus stearothermophilus GR75.	Chinese Sci. Bull.	1994	39		526-528			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'. 		
@D	Chen, Z.X.//Mann, J.R.//Hsieh, C.L.//Riggs, A.D.//Chedin, F. 	Physical and functional interactions between the human DNMT3L protein and members of the de novo methyltransferase family.	J. Cell. Biochem.	2005	95		902-917			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. 		
@D	Cheng, C.K.//Au, C.H.//Li, L.//Nong, W.//Law, P.T.//Cheung, W.M.//Ling, J.M.//Kwan, H.S. 	Genome Sequences of Salmonella enterica Serotype Typhimurium Blood Clinical Isolate ST4848/06 and Stool Isolate ST1489/06.	Genome Announcements	2013	1		e00823-13			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. 		
@D	Cheng, D.-F.//Liu, Q.//Zhao, X.-L.//Dong, Y.-S.//Li, Q. 	Quantitive study on the inhibitive effect of methylation outside the recognition sequence of restriction endonuclease PvuII on its cleavage activity.	Shengwu Huazue Zazhi	1996	12		36-41			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. 		
@D	Cheng, H.//Fang, M.X.//Jiang, X.W.//Wu, M.//Zhu, X.F.//Zheng, G.//Yang, Z.J. 	Draft Genome Sequence of Amphibacillus jilinensis Y1(T), a Facultatively Anaerobic, Alkaliphilic and Halotolerant Bacterium.	Standards in Genomic Sciences	2013	8		491-499			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. 		
@D	Cheng, H.//Huo, Y.Y.//Hu, J.//Xu, X.W.//Wu, M. 	High quality draft genome sequence of an extremely halophilic archaeon Natrinema  altunense strain AJ2T.	Standards in Genomic Sciences	2017	12		25			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. 		
@D	Cheng, H.//Wu, Y.H.//Huo, Y.Y.//Wang, C.S.//Xu, X.W. 	Draft Genome Sequence of Altererythrobacter marensis DSM 21428T, Isolated from Seawater.	Genome Announcements	2016	4		e01607-15			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. 		
@D	Cheng, J.//Yang, H.//Fang, J.//Ma, L.//Gong, R.//Wang, P.//Li, Z.//Xu, Y. 	Molecular mechanism for USP7-mediated DNMT1 stabilization by acetylation.	Nat. Commun.	2015	6		7023			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. 		
@D	Cheng, S.-C.//Kim, R.//King, K.//Kim, S.-H.//Modrich, P. 	Isolation of gram quantities of EcoRI restriction and modification enzymes from an overproducing strain.	J. Biol. Chem.	1984	259		11571-11575			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. 		
@D	Cheng, S.-C.//Modrich, P. 	Positive-selection cloning vehicle useful for overproduction of hybrid proteins.	J. Bacteriol.	1983	154		1005-1008			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. 		
@D	Cheng, T.//Lin, P.//Jin, S.//Wu, Y.//Fu, B.//Long, R.//Liu, D.//Guo, Y.//Peng, L.//Xia, Q. 	Complete Genome Sequence of Bacillus bombysepticus, a Pathogen Leading to Bombyx  mori Black Chest Septicemia.	Genome Announcements	2014	2		e00312-14			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. 		
@D	Cheng, T.H.//Saidin, J.//Danish-Daniel, M.//Gan, H.M.//Mat, I.M.N.//Abu, B.M.F.//Ismail, N. 	Genome Sequence of Serratia marcescens subsp. sakuensis Strain K27, a Marine Bacterium Isolated from Sponge (Haliclona amboinensis).	Genome Announcements	2018	6		e00022-18			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. 		
@D	Cheng, V.W.//Zhang, G.//Oyedotun, K.S.//Ridgway, D.//Ellison, M.J.//Weiner, J.H. 	Complete Genome of the Solvent-Tolerant Staphylococcus warneri Strain SG1.	Genome Announcements	2013	1		e0003813			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. 		
@D	Cheng, W.//Zhan, G.//Liu, W.//Zhu, R.//Yu, X.//Li, Y.//Li, Y.//Wu, W.//Wang, X. 	Draft Genome Sequence of Endophytic Herbaspirillum sp. Strain WT00C, a Tea Plant  Growth-Promoting Bacterium.	Genome Announcements	2017	5		e01719-16			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. 		
@D	Cheng, X. 	Structure and function of DNA methyltransferases.	Annu. Rev. Biophys. Biomol. Struct.	1995	24		293-318			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 		
@D	Cheng, X. 	DNA modification by methyltransferases.	Curr. Opin. Struct. Biol.	1995	5		4-10			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. 		
@D	Cheng, X.//Balendiran, K.//Schildkraut, I.//Anderson, J.E. 	Structure of PvuII endonuclease with cognate DNA.	EMBO J.	1994	13		3927-3935			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. 		
@D	Cheng, X.//Balendiran, K.//Schildkraut, I.//Anderson, J.E. 	Crystal stucture of the PvuII restriction endonuclease.	Gene	1995	157		139-140			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. 		
@D	Cheng, X.//Blumenthal, R.M. 	Finding a basis for flipping bases.	Structure	1996	4		639-645			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. 		
@D	Cheng, X.//Blumenthal, R.M. 	Mammalian DNA methyltransferases: A structural perspective.	Structure	2008	16		341-350			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. 		
@D	Cheng, X.//Kumar, S.//Klimasauskas, S.//Roberts, R.J. 	Crystal structure of the HhaI DNA methyltransferase.	Cold Spring Harb. Symp. Quant. Biol.	1993	58		331-338			Structures of M.HhaI with AdoMet and M.HhaI, DNA and AdoHcy are described. 		
@D	Cheng, X.//Kumar, S.//Posfai, J.//Pflugrath, J.W.//Roberts, R.J. 	Crystal structure of the HhaI DNA methyltransferase complexed with S-adenosyl-L-methionine.	Cell	1993	74		299-307			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. 		
@D	Cheng, X.//Kumar, S.//Sha, M.//Roberts, R.J. 	Crystal structure of HhaI DNA methyltransferase complexed with S-adenosyl-L-methionine.	Acta Crystallogr. A	1993	SA49		61			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. 		
@D	Cheng, X.//Roberts, R.J. 	AdoMet-dependent methylation, DNA methyltransferases and base flipping.	Nucleic Acids Res.	2001	29		3784-3795			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. 		
@D	Cheng, X.D.//Collins, R.C.//Jia, D.//Khan, S.I.//Horton, J.R.//Qiu, C.//Sawada, K.//Yang, Z.//Zhang, X. 	Structural and functional analysis of methyltransferases.	Cell Res.	2003	13		408			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. 		
@D	Chenoll, E.//Codoner, F.M.//Martinez-Blanch, J.F.//Acevedo-Pierart, M.//Ormeno, M.L.//Ramon, D.//Genoves, S. 	Complete Genome Sequence of the Probiotic Strain Lactobacillus salivarius LPM01.	Genome Announcements	2016	4		e01319-16			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. 		
@D	Chenoll, E.//Codoner, F.M.//Martinez-Blanch, J.F.//Ramon, D.//Genoves, S.//Menabrito, M. 	Complete Genome Sequence of Lactobacillus rhamnosus Strain BPL5 (CECT 8800), a Probiotic for Treatment of Bacterial Vaginosis.	Genome Announcements	2016	4		e00292-16			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. 		
@D	Chenoll, E.//Codoner, F.M.//Silva, A.//Martinez-Blanch, J.F.//Martorell, P.//Ramon, D.//Genoves, S. 	Draft Genome Sequence of Bifidobacterium animalis subsp. lactis Strain CECT 8145, Able To Improve Metabolic Syndrome In Vivo.	Genome Announcements	2014	2		e00183-14			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. 		
@D	Chenoll, E.//Rivero, M.//Codoner, F.M.//Martinez-Blanch, J.F.//Ramon, D.//Genoves, S.//Moreno, M.J.A. 	Complete Genome Sequence of Bifidobacterium longum subsp. infantis Strain CECT 7210, a Probiotic Strain Active against Rotavirus Infections.	Genome Announcements	2015	3		e00105-15			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. 		
@D	Cherepanova, N.A.//Minero, A.S.//Rakhimova, A.R.//Gromova, E.S. 	Mechanism of CpG DNA Methyltransferases M.SssI and Dnmt3a Studied by DNA Containing 2-Aminopurine.	Nucleosides Nucleotides Nucleic Acids	2011	30		619-631			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. 		
@D	Cherepanova, N.A.//Zhuze, A.L.//Gromova, E.S. 	Inhibition of murine DNA methyltransferase Dnmt3a by DNA duplexes containing pyrimidine-2(1H)-one.	Biochemistry	2010	75		1244-1256			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. 		
@D	Chernikova, T.N.//Kyrpides, N.//Bargiela, R.//Woyke, T.//Shapiro, N.//Whitman, W.B.//Golyshin, P.N. 	Draft Genome Sequence of Monaibacterium marinum C7(T), Isolated from Seawater from the Menai Straits, Wales, United Kingdom.	Genome Announcements	2018	6		e01444-17			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%. 		
@D	Chernov, A.P.//Kaliman, A.V. 	Some peculiarities of the antirestriction mechanism of bacteriophage T5.	Mol. Gen. Mikrobiol. Virusol.	1987	1		14-19			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. 		
@D	Chernov, A.V.//Lepikhov, K.A.//Zheleznaya, L.A.//Matvienko, N.I. 	Two site-specific endonucleases from thermophilic strain Bacillus species OV.	Biokhimiia	1996	61		1837-1847			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. 		
@D	Chernov, A.V.//Matvienko, N.N.//Zheleznaya, L.A.//Matvienko, N.I. 	A new site-specific endonuclease-methylase from the thermophilic strain of Bacillus species LU11.	Biokhimiia	1994	59		1714-1729			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. 		
@D	Chernov, A.V.//Matvienko, N.N.//Zheleznaya, L.A.//Matvienko, N.I. 	BspLUII III, a bifunctional restriction and modification enzyme from a thermohilic strain Bacillus species LUII.	Nucleic Acids Res.	1995	23		1213-1214			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. 		
@D	Chernov, A.V.//Vollmayr, P.//Walter, J.//Trautner, T.A. 	Masc2, a C5-DNA-methyltransferase from Ascobolus immersus with similarity to methyltransferases of higher organisms.	Biol. Chem.	1997	378		1467-1473			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. 		
@D	Chernov, A.V.//Zheleznaya, L.A.//Matvienko, N.I. 	Site-specific endonuclease BspKT8 from the Thermophile strain Bacillus species KT8.	Biokhimiia	1995	60		1318-1325			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. 		
@D	Chernuhin, V.A.//Gonchar, D.A.//Abdurashidov, M.A.//Belichenko, O.A.//Dedkov, V.S.//Mihnenkova, N.A.//Lomakovskaja, E.N.//Udal'cova, S.G.//Degterev, S.H. 	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'.	Acta Naturae	2016	8		117-125					
@D	Chernukhin, V.A.//Boltengagen, A.A.//Tarasova, G.V.//Dedkov, V.S.//Degtyarev, S.K. 	New Restriction Endonuclease AluBI from Arthrobacter luteus B - AluI Isoshizomer, nonsensitive to Presence of 5-methylcytosine in the Recognition Sequence AGCT.	Ovchinnikov Bull. Biotechnol. Phys. Chem. Biol.	2007	3		21-27			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. 		
@D	Chernukhin, V.A.//Chmuzh, E.V.//Tomilova, Y.E.//Nayakshina, T.N.//Gonchar, D.A.//Dedkov, V.S.//Degtyarev, S.K. 	A novel site-specific endonuclease GluI recognizes methylated DNA sequence 5'-G(5mC)^NG(5mC)-3'/3'-(5mC)GN^(5mC)G.	Ovchinnikov Bull. Biotechnol. Phys. Chem. Biol.	2007	3		13-17			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. 		
@D	Chernukhin, V.A.//Golikova, L.N.//Gonchar, D.A.//Abdurashitov, M.A.//Kashirina, Y.G.//Netesova, N.A.//Degtyarev, S.K. 	M.BstF5I-2 and M.BstF5I-4 DNA methyltransferases from BstF5I restriction-modification system of Bacillus stearothermophilus F5.	Biokhimiia	2003	68		967-975			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. 		
@D	Chernukhin, V.A.//Gonchar, D.A.//Abdurashitov, M.A.//Belichenko, O.A.//Dedkov, V.S.//Mikhnenkova, N.A.//Lomakovskaya, E.N.//Udalyeva, S.G.//Degtyarev, S.K. 	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'.	Acta Naturae	2016	28		42-51			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. 		
@D	Chernukhin, V.A.//Kashirina, Y.G.//Sukhanova, K.S.//Abdurashitov, M.A.//Gonchar, D.A.//Degtyarev, S.K. 	Isolation and characterization of biochemical properties of DNA methyltransferase FauIA modifying the second cytosine in the  nonpalindromic sequence 5 '-CCCGC-3 '.	Biokhimiia	2005	70		829-837			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. 		
@D	Chernukhin, V.A.//Kashirina, Y.G.//Tomilova, J.E.//Gonchar, D.A.//Dedkov, V.S.//Mikhnenkova, N.A.//Degtyarev, S.K. 	New Eight Bases Cutter AbsI from Arthrobacter species Recognizes Palindromic DNA Sequence 5'-CC^TCGAGG-3'.	Ovchinnikov Bull. Biotechnol. Phys. Chem. Biol.	2006	2		29-34			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. 		
@D	Chernukhin, V.A.//Kileva, E.V.//Sokolova, V.A.//Gonchar, D.A.//Golikova, L.N.//Dedkov, V.S.//Mikhnenkova, N.A.//Degtyarev, S.K. 	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.	Ovchinnikov Bull. Biotechnol. Phys. Chem. Biol.	2012	8		16-26			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. 		
@D	Chernukhin, V.A.//Kuznetsov, V.V.//Gonchar, D.A.//Kashirina, Y.G.//Netesova, N.A.//Degtyarev, S.K. 	Substrate Specificity and Biochemical Properties of M3.BstF5I DNA Methyltransferase from the BstF5I Restriction-Modification System.	Biochemistry	2010	75		63-71			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. 		
@D	Chernukhin, V.A.//Nayakshina, T.N.//Abdurashitov, M.A.//Tomilova, Y.E.//Mezentseva, N.V.//Dedkov, V.S.//Mikhnenkova, N.A.//Gonchar, D.A.//Degtyarev, S.K. 	A novel restriction endonuclease GlaI recognizes the methylated sequence 5'-G(5mC)^GC-3'.	Biotekhnologiya	2006	0		26-30			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. 		
@D	Chernukhin, V.A.//Nayakshina, T.N.//Gonchar, D.A.//Tomilova, J.E.//Tarasova, M.V.//Dedkov, V.S.//Mikhenenkova, N.A.//Degtyarev, S.K. 	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.	Ovchinnikov Bull. Biotechnol. Phys. Chem. Biol.	2011	7		35-42			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. 		
@D	Chernukhin, V.A.//Seggewiss, J.//Kashirina, Y.G.//Gonchar, D.A.//Degtyarev, S.K. 	Purification and properties of recombinant DNA methyltransferase M2.BstSE of the BstSEI nickase-modification system.	Mol. Biol. (Mosk)	2009	43		8-15			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. 		
@D	Chernukhin, V.A.//Tomilova, J.E.//Chmuzh, E.V.//Sokolova, O.O.//Dedkov, V.S.//Degtyarev, S.K. 	Site-specific endonuclease BlsI recognizes DNA sequence 5'-G(5mC)N^GC-3' and cleaves it producing 3' sticky ends.	Ovchinnikov Bull. Biotechnol. Phys. Chem. Biol.	2007	3		28-33			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. 		
@D	Cherny, D.I.//Kurakin, A.V. 	Site-selective targeting of duplex DNA with methyltransferase and biotinylated synthetic reagents.	Electron Microsc.	1994	3A		449-450			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. 		
@D	Cherry, J.L. 	Methylation-Induced Hypermutation in Natural Populations of Bacteria.	J. Bacteriol.	2018	200		e00371-18			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. 		
@D	Chertkov, O. et al. 	Complete genome sequence of Tolumonas auensis type strain (TA 4).	Standards in Genomic Sciences	2011	5		112-120			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. 		
@D	Chertkov, O. et al. 	Complete genome sequence of Aminobacterium colombiense type strain (ALA-1).	Standards in Genomic Sciences	2010	2		280-289			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. 		
@D	Chertkov, O. et al. 	Complete genome sequence of Thermomonospora curvata type strain (B9).	Standards in Genomic Sciences	2011	4		13-22			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. 		
@D	Chertkov, O. et al. 	Complete genome sequence of Hirschia baltica type strain (IFAM 1418T).	Standards in Genomic Sciences	2011	5		287-297			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. 		
@D	Chervaux, C.//Grimaldi, C.//Bolotin, A.//Quinquis, B.//Legrain-Raspaud, S.//van Hylckama, V.J.E.//Denariaz, G.//Smokvina, T. 	Genome Sequence of the Probiotic Strain Bifidobacterium animalis subsp. lactis CNCM I-2494.	J. Bacteriol.	2011	193		5560-5561			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. 		
@A	Chevalier, B.//Monnat, R.J. Jr.//Stoddard, B.L. 		The LAGLIDADG homing endonuclease family.			Belfort, M. 		Nucleic Acids Mol. Biol.				Berlin Heidelberg	Springer-Verlag	2005		16		33-47									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. 		
@D	Chevalier, B.//Sussman, D.//Otis, C.//Noel, A.J.//Turmel, M.//Lemieux, C.//Stephens, K.//Monnat, R.J.//Stoddard, B.L. 	Metal-dependent DNA cleavage mechanism of the I-CreI LAGLIDADG homing endonuclease.	Biochemistry	2004	43		14015-14026			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. 		
@D	Chevalier, B.//Turmel, M.//Lemieux, C.//Monnat, R.J.//Stoddard, B.L. 	Flexible DNA target site recognition by divergent homing endonuclease isoschizomers I-CreI and I-MsoI.	J. Mol. Biol.	2003	329		253-269			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. 		
@D	Chevalier, B.S.//Kortemme, T.//Chadsey, M.S.//Baker, D.//Monnat, R.J.//Stoddard, B.L. 	Design, activity, and structure of a highly specific artificial endonuclease.	Mol. Cell	2002	10		895-905			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. 		
@D	Chevalier, B.S.//Monnat, R.J. Jr.//Stoddard, B.L. 	The homing endonuclease I-CreI uses three metals, one of which is shared between the two active sites.	Nat. Struct. Biol.	2001	8		312-316			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. 		
@D	Chevalier, B.S.//Stoddard, B.L. 	Homing endonucleases: structural and functional insight into the catalysts of intron/intein mobility.	Nucleic Acids Res.	2001	29		3757-3774			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. 		
@D	Chi, M.-G. 	Isolation and purification of EcoRI restriction endonuclease.	Junshi Yixue Kexueyuan Yuankan	1995	19		132-135			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. 		
@D	Chiara, M.//D'Erchia, A.M.//Manzari, C.//Minotto, A.//Montagna, C.//Addante, N.//Santagada, G.//Latorre, L.//Pesole, G.//Horner, D.S.//Parisi, A. 	Draft Genome Sequences of Six Listeria monocytogenes Strains Isolated from Dairy  Products from a Processing Plant in Southern Italy.	Genome Announcements	2014	2		e00282-14			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. 		
@D	Chibani, C.M.//Poehlein, A.//Roth, O.//Liesegang, H.//Wendling, C.C. 	Draft Genome Sequence of Vibrio splendidus DSM 19640.	Genome Announcements	2017	5		e01368-17			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. 		
@D	Chiciudean, I.//Nie, Y.//Tanase, A.M.//Stoica, I.//Wu, X.L. 	Complete genome sequence of Tsukamurella sp. MH1, a wide-chain length alkane-degrading actinomycete.	J. Biotechnol.	2017	268		1-5			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. 		
@D	Chien, H.R. 	Cloning and genetic analysis of restriction and modification systems from Neisseria gonorrhoeae.	Ph.D. Thesis, University of Maryland, USA	1991			1-126			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. ] 		
@D	Chien, M. et al. 	The genomic sequence of the accidental pathogen Legionella pneumophila.	Science	2004	305		1966-1968			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. 		
@D	Chien, R.H.//Stein, D.C.//Seifert, H.S.//Floyd, K.//So, M. 	Cloning and characterization of a restriction and modification system from Neisseria gonorrhoeae strain MS11.	Abstr. Gen. Meet. Am. Soc. Microbiol.	1988	88		213			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. ] 		
@D	Chies, J.M.//de O-Dias, A.C.//Maia, H.M.M.//Astolfi-Filho, S. 	BanAI a new isoschizomer of the type II restriction endonuclease HaeIII discovered in a Bacillus anthracis isolate from Amazon Basin.	FEMS Microbiol. Lett.	2002	215		97-101			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. 		
@D	Chies, J.M.//Dias, A.C.D.O.//Maia, H.M.M.//Braga, L.P.D.S.//Astolfi-Filho, S. 	Isolation and characterization of Bliai, an isoschizomer of CLAI from Bacillus licheniformis.	Braz. J. Microbiol.	2006	37		551-555			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. 		
@A	Chik, J.//Robins, L.//Stoddard, B. 		Expression and purification of Ltr-II: A homing endonuclease for gene targeting.			 		ACS Abstracts				San Diego		2012		243		475									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. 		
@D	Chikaev, N.A.//Baklanov, M.M.//Ryazankin, I.A.//Nechaev, Y.S. 	Purification of restriction endonucleases using aqueous two-phase systems.	Prikl. Biokhim. Mikrobiol.	1987	23		84-92			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. 		
@D	Chilley, P.M.//Wilkins, B.M. 	Distribution of the ardA family of antirestriction genes on conjugative plasmids.	Microbiology	1995	141		2157-2164			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. 		
@D	Chin, V.//Valinluck, V.//Magaki, S.//Ryu, J. 	KpnBI is the prototype of a new family (IE) of bacterial type I restriction-modification system.	Nucleic Acids Res.	2004	32		e138			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. 		
@D	Chin, V.R.//Valinluck, V.//Ryu, J. 	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.	Abstr. Gen. Meet. Am. Soc. Microbiol.	2001	101		404-405			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. 		
@D	Chinen, A.//Naito, Y.//Handa, N.//Kobayashi, I. 	Evolution of sequence recognition by restriction-modification enzymes: Selective pressure for specificity decrease.	Genes Genet. Syst.	2000	75		381			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. 		
@D	Chinen, A.//Naito, Y.//Handa, N.//Kobayashi, I. 	Evolution of sequence recognition by restriction-modification enzymes: selective pressure for specificity decrease.	Mol. Biol. Evol.	2000	17		1610-1619			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. 		
@D	Chinen, A.//Uchiyama, I.//Kobayashi, I. 	Comparison between Pyrococcus horikoshii and Pyrococcus abyssi genome sequences reveals linkage of restriction-modification genes with large genome polymorphisms.	Gene	2000	259		109-121			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. 		
@D	Chinen, A.//Uchiyama, I.//Kobayashi, I. 	Association of putative restriction modification genes with large genome polymorphisms suggested from comparison of Pyrococcus horikoshii and Pyrococcus abyssi genome sequences.	Genome Informatics	2000	11		339-340			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. 		
@D	Chinenova, T.A.//Mkrtumian, N.M.//Lomovskaia, N.D. 	[Genetic characteristics of a new phage resistance trait in Streptomyces coelicolor A3(2)].	Genetika	1982	18		1945-1952			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. 		
@D	Chiou, C.S.//Li, H.Y.//Tung, S.K.//Chen, C.Y.//Teng, C.H.//Shu, J.C.//Tseng, J.T.//Hsu, C.Y.//Chen, C.C. 	Identification of prophage gene z2389 in Escherichia coli EDL933 encoding a DNA cytosine methyltransferase for full protection of Notl sites.	Int. J. Med. Microbiol.	2010	300		296-303			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. 		
@D	Chiou, T.Y.//Oshima, K.//Suda, W.//Hattori, M.//Takahashi, T. 	Draft Genome Sequence of Lactobacillus farciminis NBRC 111452, Isolated from Koso, a Japanese Sugar-Vegetable Fermented Beverage.	Genome Announcements	2016	4		e01514-15			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. 		
@D	Chiriac, C.//Baricz, A.//Coman, C. 	Draft Genome Sequence of Janthinobacterium sp. Strain ROICE36, a Putative Secondary Metabolite-Synthesizing Bacterium Isolated from Antarctic Snow.	Genome Announcements	2018	6		e01553-17			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). 		
@D	Chirikjian, J.G.//George, A.//Smith, L.A. 	Purification of restriction endonucleases including the isolation of a novel activity using affinity chromatography.	Fed. Proc.	1978	37		1415			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. 		
@A	Chirikjian, J.G.//George, J. 		Sequence-specific endonucleases: General properties and specific characteristics.			Chirikjian, J.G. 		Gene Amplif. Anal.					Elsevier North Holland	1981		1		73-99									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 		
@D	Chistoserdova, L.//Lapidus, A.//Han, C.//Goodwin, L.//Saunders, L.//Brettin, T.//Tapia, R.//Gilna, P.//Lucas, S.//Richardson, P.M.//Lidstrom, M.E. 	Genome of Methylobacillus flagellatus, Molecular Basis for Obligate Methylotrophy, and Polyphyletic Origin of Methylotrophy.	J. Bacteriol.	2007	189		4020-4027			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. 		
@D	Chiu, C.H.//Tang, P.//Chu, C.//Hu, S.//Bao, Q.//Yu, J.//Chou, Y.Y.//Wang, H.S.//Lee, Y.S. 	The genome sequence of Salmonella enterica serovar Choleraesuis, a highly invasive and resistant zoonotic pathogen.	Nucleic Acids Res.	2005	33		1690-1698			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. 		
@D	Chiu, C.M.//Chang, C.H.//Pan, S.F.//Wu, H.C.//Li, S.W.//Chang, C.H.//Lee, Y.S.//Chiang, C.M.//Chen, Y.S. 	Draft Genome Sequence of Lactobacillus pobuzihii E100301T.	Genome Announcements	2013	1		e00185-13			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). 		
@D	Chiu, S.H.//Chen, C.C.//Wang, L.T.//Huang, L. 	Whole-Genome Sequencing of Lactobacillus salivarius Strains BCRC 14759 and BCRC 12574.	Genome Announcements	2017	5		e01336-17			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. 		
@D	Chiura, H.//Noro, Y.//Kanayama, S.//Ueda, Y.//Simidu, U.//Takagi, J. 	Site specific deoxyribonuclease produced by a marine bacterium, Flavobacterium I 16-04.	Agric. Biol. Chem.	1988	52		2107-2109			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. 		
@D	Chiura, H.X.//Kamiyama, T.//Hirano, H.//Futagami, M.//Watahiki, M.//Kobayashi, K.//Simidu, U.//Takagi, J. 	Purification and characterization of AspMDI, an isoschizomer of Sau3AI, from a marine bacterium, Alcaligenes sp MD1.	Nucleic Acids Res.	1992	20		1996			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. 		
@D	Chiurillo, M.A.//Moran, Y.//Canas, M.//Valderrama, E.//Granda, N.//Sayegh, M.//Ramirez, J.L. 	Genotyping of virulence-associated genes from biopsy specimens show high genetic diversity of Helicobacter pylori strains infecting patients in Venezuela.	Int. J. Infect. Dis.	2013	17		e750-6			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. 		
@D	Chivian, D. et al. 	Environmental genomics reveals a single-species ecosystem deep within Earth.	Science	2008	322		275-278			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. 		
@D	Chlebowicz, M.A.//Nganou, K.//Kozytska, S.//Arends, J.P.//Engelmann, S.//Grundmann, H.//Ohlsen, K.//van Dijl, J.M.//Buist, G. 	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.	Antimicrob. Agents Chemother.	2010	54		783-791			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. 		
@D	Chmelo, R.//Foltz, L.//Eadie, J.S. 	Determination of restriction enzyme digestion completeness under low target concentration.	FASEB J.	1993	7		A1304			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. 		
@D	Chmiel, A.A.//Bujnicki, J.M.//Skowronek, K.J. 	A homology model of restriction endonuclease SfiI in complex with DNA.	BMC Struct. Biol.	2005	5		2			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. 		
@D	Chmiel, A.A.//Radlinska, M.//Pawlak, S.D.//Krowarsch, D.//Bujnicki, J.M.//Skowronek, K.J. 	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.	Protein Eng. Des. Sel.	2005	18		181-189			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. 		
@D	Chmuzh, E.V.//Kashirina, J.G.//Tomilova, J.E.//Mezentseva, N.V.//Dedkov, V.S.//Gonchar, D.A.//Abdurashitov, M.A.//Degtyarev, S.K. 	A Novel Restriction endonuclease BisI from Bacillus subtilis T30, recognizes a methylated DNA sequence 5'- G(m5C)^NGC-3'.	Biotekhnologiya	2005	3		22-26			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. 		
@D	Chmuzh, E.V.//Kashirina, Y.G.//Tomilova, Y.E.//Chernukhin, V.A.//Okhapkina, S.S.//Gonchar, D.A.//Dedkov, V.S.//Abdurashitov, M.A.//Degtyarev, S.K. 	The Fsp4HI restriction-modification system: Gene cloning, comparison of protein structures, and biochemical properties of recombinant DNA methyltransferase M.Fsp4HI.	Mol. Biol. (Mosk)	2007	41		43-50			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'. 		
@D	Cho, E.//Park, S.N.//Kim, H.K.//Kim, D.S.//Jung, J.//Baek, J.H.//Lim, Y.K.//Jo, E.//Choi, M.H.//Chang, Y.H.//Shin, Y.//Paek, J.//Shin, J.H.//Kim, J.//Choi, S.H.//Park, H.S.//Kim, H.//Kook, J.K. 	Draft Genome Sequence of the Novel Peptoniphilus sp. Strain ChDC B134, Isolated from a Human Periapical Abscess Lesion.	Genome Announcements	2013	1		e00822-13			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. 		
@D	Cho, M.-J.//Park, J.-U.//Jeon, B.S.//Pack, J.-W.//Byun, E.Y.//Lee, S.-K.//Park, Y.-H.//Song, J.-H.//Lee, W.-K.//Baik, S.-C.//Choi, Y.-J.//Jung, S.-A.//Choe, M.-Y.//Choi, S.-H.//Ko, G.-H.//Youn, H.-S.//Rhee, K.-H. 	Characterization of type II restriction endonucleases (Hpy51-I) from Helicobacter pylori strain 51.	J. Bact. Virol.	2001	31		207-215			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. 		
@D	Cho, N.H.//Kim, H.R.//Lee, J.H.//Kim, S.Y.//Kim, J.//Cha, S.//Kim, S.Y.//Darby, A.C.//Fuxelius, H.H.//Yin, J.//Kim, J.H.//Kim, J.//Lee, S.J.//Koh, Y.S.//Jang, W.J.//Park, K.H.//Andersson, S.G.//Choi, M.S.//Kim, I.S. 	The Orientia tsutsugamushi genome reveals massive proliferation of conjugative type IV secretion system and host-cell interaction genes.	Proc. Natl. Acad. Sci. U. S. A.	2007	104		7981-7986			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. 		
@D	Cho, S.-H.//Kang, C. 	DNA sequence-dependent cleavage sites of restriction endonuclease HphI.	Mol. Cells	1990	1		81-86			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. 		
@D	Cho, S.T.//Chen, C.L.//Yang, Y.//Wang, T.F.//Kuo, C.H. 	Draft Genome Sequence of Burkholderia sp. Strain WAC0059, a Bacterium Isolated from the Medicinal Fungus Antrodia cinnamomea.	Genome Announcements	2018	6		e00027-18			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. 		
@D	Cho, S.T.//Haryono, M.//Chang, H.H.//Santos, M.N.M.//Lai, E.M.//Kuo, C.H. 	Complete Genome Sequence of Agrobacterium tumefaciens 1D1609.	Genome Announcements	2018	6		e00253-18			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. 		
@D	Cho, Y.J.//Choi, J.K.//Kim, J.H.//Lim, Y.S.//Ham, J.S.//Kang, D.K.//Chun, J.//Paik, H.D.//Kim, G.B. 	Genome Sequence of Lactobacillus salivarius GJ-24, a probiotic strain isolated from healthy adult intestine.	J. Bacteriol.	2011	193		5021-5022			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. 		
@D	Cho, Y.J.//Jung, Y.J.//Hong, S.G.//Kim, O.S. 	Complete Genome Sequence of a Psychrotolerant Denitrifying Bacterium, Janthinobacterium svalbardensis PAMC 27463.	Genome Announcements	2017	5		e01178-17			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. 		
@D	Choe, W.//Chandrasegaran, S.//Ostermeier, M. 	Protein fragment complementation in M.HhaI DNA methyltransferase.	Biochem. Biophys. Res. Commun.	2005	334		1233-1240			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. 		
@D	Choi, D.H.//Ahn, C.//Jang, G.I.//Lapidus, A.//Han, J.//Reddy, T.B.//Huntemann, M.//Pati, A.//Ivanova, N.//Markowitz, V.//Rohde, M.//Tindall, B.//Goker, M.//Woyke, T.//Klenk, H.P.//Kyrpides, N.C.//Cho, B.C. 	High-quality draft genome sequence of Gracilimonas tropica CL-CB462(T) (DSM 19535(T)), isolated from a Synechococcus culture.	Standards in Genomic Sciences	2015	10		98			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. 		
@D	Choi, D.H.//Jang, G.I.//Lapidus, A.//Copeland, A.//Reddy, T.B.K.//Mukherjee, S.//Huntemann, M.//Varghese, N.//Ivanova, N.//Pillay, M.//Tindall, B.J.//Goker, M.//Woyke, T.//Klenk, H.P.//Kyrpides, N.C.//Cho, B.C. 	Draft genome sequence of Marinobacterium rhizophilum CL-YJ9T (DSM 18822T), isolated from the rhizosphere of the coastal tidal-flat plant Suaeda japonica.	Standards in Genomic Sciences	2017	12		65			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. 		
@D	Choi, D.H.//Kwon, Y.M.//Kwon, K.K.//Kim, S.J. 	Complete genome sequence of US6-1.	Standards in Genomic Sciences	2015	10		107			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. 		
@D	Choi, D.H.//Ryu, J.Y.//Kwon, K.K.//Lee, J.H.//Kim, C.//Lee, C.M.//Noh, J.H. 	Draft genome sequence of Rubidibacter lacunae strain KORDI 51-2(T), a cyanobacterium isolated from seawater of Chuuk lagoon.	Standards in Genomic Sciences	2013	9		197-204			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. 		
@D	Choi, G.-E.//Cho, Y.J.//Koh, W.J.//Chun, J.//Cho, S.N.//Shin, S.J. 	Draft Genome Sequence of Mycobacterium abscessus subsp. bolletii BDT.	J. Bacteriol.	2012	194		2756-2757			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). 		
@D	Choi, H.S.//Kwon, M.G.//Kim, M.S.//Park, M.A.//Kim, D.W.//Park, J.Y.//Kim, J.S.//Na, Y.J.//Kim, M.Y.//Kim, D.S.//Chae, S.H.//Seo, J.S. 	Draft Genome Sequence of Beta-Hemolytic Streptococcus iniae KCTC 11634.	Genome Announcements	2013	1		e00897-13			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. 		
@D	Choi, J.H.//Sugiura, H.//Moriuchi, R.//Kawagishi, H.//Dohra, H. 	High-Quality Draft Genome Sequence of Burkholderia contaminans CH-1, a Gram-Negative Bacterium That Metabolizes 2-Azahypoxanthine, a Plant  Growth-Regulating Compound.	Genome Announcements	2017	5		e01148-17			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. 		
@D	Choi, K.D.//Kim, K.//Yoo, O.J. 	A new restriction endonuclease from Clostridium thermocellum.	Sanop Misaengmul Hakhoe Chi	1987	15		352-355			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. 		
@D	Choi, K.D.//Yoo, O.J. 	A new restriction endonuclease, CthII, from Clostridium thermocellum ATCC 27405.	Korean Biochem. J.	1990	23		418-421			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. 		
@D	Choi, O.//Lim, J.Y.//Seo, Y.S.//Hwang, I.//Kim, J. 	Complete Genome Sequence of the Rice Pathogen Pantoea ananatis Strain PA13.	J. Bacteriol.	2012	194		531			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. 		
@D	Choi, S.-H. 	Restriction-modification systems and genetic variability of Xanthomonas oryzae pv.	Diss. Abstr.	1994	54		5462B-5463B			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.
 
 		
@D	Choi, S.C.//Parker, J.//Richards, V.P.//Ross, K.//Jilly, B.//Chen, J. 	Draft Genome Sequence of an Atypical Strain of Streptococcus pneumoniae Isolated  from a Respiratory Infection.	Genome Announcements	2014	2		e00822-14			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%. 		
@D	Choi, S.H.//Heo, K.//Byun, H.M.//An, W.//Lu, W.//Yang, A.S. 	Identification of preferential target sites for human DNA methyltransferases.	Nucleic Acids Res.	2011	39		104-118			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. 		
@D	Choi, S.H.//Ji, Y.//Park, S.//Mathara, J.//Holzapfel, W.//Kang, J. 	Complete Genome Sequence of Lactobacillus rhamnosus BFE5264, Isolated from Maasai Traditional Fermented Milk.	Genome Announcements	2017	5		e00563-17			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. 		
@D	Choi, S.H.//Leach, J.E. 	Identification of the XorII methyltransferase gene and a vsr homolog from Xanthomonas oryzae pv. oryzae.	Mol. Gen. Genet.	1994	244		383-390			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. 		
@D	Choi, S.H.//Vera Cruz, C.M.//Leach, J.E. 	Distribution of Xanthomonas oryzae pv. oryzae DNA modification systems in Asia.	Appl. Environ. Microbiol.	1998	64		1663-1668			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. 		
@D	Choi, S.K.//Jeong, H.//Kloepper, J.W.//Ryu, C.M. 	Genome Sequence of Bacillus amyloliquefaciens GB03, an Active Ingredient of the First Commercial Biological Control Product.	Genome Announcements	2014	2		e01092-14			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. 		
@D	Choi, W.S.//Kang, S.C.//Seo, J.S.//Yoo, O.J. 	Inhibition of SmaI, AvaI, NaeI and XmaI endonuclease activities by the methylation of DNA with HpaII methylase.	Korean J. Microbiol.	1986	24		86-90			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. 		
@D	Choi, Y.//Shin, H.//Lee, J.H.//Ryu, S. 	Identification and characterization of a novel flagellum-dependent Salmonella-infecting bacteriophage, iEPS5.	Appl. Environ. Microbiol.	2013	79		4829-4837			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. 		
@D	Choi, Y.-J.//Kim, S.-J.//Hwang, H.-Y.//Yim, J.//Kim, J.-C. 	Characterization of restriction endonuclease EagBI from Enterobacter agglomerans CBNU45.	Korean J. Microbiol.	1994	32		91-95			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. 		
@D	Choi, Y.U.//Kwon, Y.K.//Ye, B.R.//Hyun, J.H.//Heo, S.J.//Affan, A.//Yoon, K.T.//Park, H.S.//Oh, C.//Kang, D.H. 	Draft Genome Sequence of Marinobacterium stanieri S30, a Strain Isolated from a Coastal Lagoon in Chuuk State in Micronesia.	J. Bacteriol.	2012	194		1260			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. 		
@D	Chollet, A.//Kawashima, E. 	DNA containing the base analogue 2-aminoadenine:  preparation, use as hybridization probes and cleavage by restriction endonucleases.	Nucleic Acids Res.	1988	16		305-317			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. 		
@D	Chong, S.//Shao, Y.//Paulus, H.//Benner, J.//Perler, F.B.//Xu, M.-Q. 	Protein splicing involving the Saccharomyces cerevisiae VMA intein.	J. Biol. Chem.	1996	271		22159-22168			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. 		
@D	Chong, T.M.//Tung, H.J.//Yin, W.F.//Chan, K.G. 	Insights from the Genome Sequence of Quorum-Quenching Staphylococcus sp. Strain AL1, Isolated from Traditional Chinese Soy Sauce Brine Fermentation.	J. Bacteriol.	2012	194		6611-6612			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. 		
@D	Chong, T.M.//Yin, W.F.//Mondy, S.//Grandclement, C.//Dessaux, Y.//Chan, K.G. 	Heavy-Metal Resistance of a France Vineyard Soil Bacterium, Pseudomonas mendocina Strain S5.2, Revealed by Whole-Genome Sequencing.	J. Bacteriol.	2012	194		6366			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. 		
@D	Choo, S.W.//Wong, Y.L.//Beh, C.Y.//Lokanathan, N.//Leong, M.L.//Ong, C.S.//Ng, K.P.//Ngeow, Y.F. 	Whole-Genome Shotgun Sequencing of Mycobacterium abscessus M156, an Emerging Clinical Pathogen in Malaysia.	Genome Announcements	2013	1		e00063-12			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. 		
@D	Choo, S.W.//Wong, Y.L.//Leong, M.L.//Heydari, H.//Ong, C.S.//Ng, K.P.//Ngeow, Y.F. 	Analysis of the Genome of Mycobacterium abscessus Strain M94 Reveals an Uncommon  Cluster of tRNAs.	J. Bacteriol.	2012	194		5724			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. 		
@D	Choo, S.W.//Wong, Y.L.//Tan, J.L.//Ong, C.S.//Wong, G.J.//Ng, K.P.//Ngeow, Y.F. 	Annotated Genome Sequence of Mycobacterium massiliense Strain M154, Belonging to  the Recently Created Taxon Mycobacterium abscessus subsp. bolletii comb. nov.	J. Bacteriol.	2012	194		4778			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. 		
@D	Choo, S.W.//Wong, Y.L.//Yusoff, A.M.//Leong, M.L.//Wong, G.J.//Ong, C.S.//Ng, K.P.//Ngeow, Y.F. 	Genome Sequence of the Mycobacterium abscessus Strain M93.	J. Bacteriol.	2012	194		3278			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. 		
@D	Choo, S.W.//Yusoff, A.M.//Wong, Y.L.//Wee, W.Y.//Ong, C.S.//Ng, K.P.//Ngeow, Y.F. 	Genome Analysis of Mycobacterium massiliense Strain M172, Which Contains a Putative Mycobacteriophage.	J. Bacteriol.	2012	194		5128			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. 		
@D	Choo, Y. 	Recognition of DNA methylation by zinc fingers.	Nat. Struct. Biol.	1998	5		264-265			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. 		
@D	Choo, Y.//Isalan, M. 	Advances in zinc finger engineering.	Curr. Opin. Struct. Biol.	2000	10		411-416			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. 		
@D	Chopin, A.//Chopin, M.-C.//Moillo-Batt, A.//Langella, P. 	Two plasmid-determined restriction and modification systems in Streptococcus lactis.	Plasmid	1984	11		260-263			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. 		
@D	Chou, L.F.//Chen, Y.T.//Lu, C.W.//Ko, Y.C.//Tang, C.Y.//Pan, M.J.//Tian, Y.C.//Chiu, C.H.//Hung, C.C.//Yang, C.W. 	Sequence of Leptospira santarosai serovar Shermani genome and prediction of virulence-associated genes.	Gene	2012	511		364-370			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. 		
@D	Chouaia, B.//Crotti, E.//Brusetti, L.//Daffonchio, D.//Essoussi, I.//Nouioui, I.//Sbissi, I.//Ghodhbane-Gtari, F.//Gtari, M.//Vacherie, B.//Barbe, V.//Medigue, C.//Gury, J.//Pujic, P.//Normand, P. 	Genome Sequence of Blastococcus saxobsidens DD2, a Stone-Inhabiting Bacterium.	J. Bacteriol.	2012	194		2752-2753			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. 		
@D	Choudhary, M.//Mackenzie, C.//Nereng, K.//Sodergren, E.//Weinstock, G.M.//Kaplan, S. 	Low-resolution sequencing of Rhodobacter sphaeroides 2.4.1T: chromosome II is a true chromosome.	Microbiology	1997	143		3085-3099			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. 		
@D	Choudhary, M.//Zanhua, X.//Fu, Y.X.//Kaplan, S. 	Genome Analyses of Three Strains of Rhodobacter sphaeroides: Evidence of Rapid Evolution of Chromosome II.	J. Bacteriol.	2007	189		1914-1921			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. 		
@D	Choudhry, S. 	Characterization of new type II restriction endonucleases from bacteria.	Proc. Pakistan Acad. Sci.	1999	36		165-171			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. 		
@D	Choudhury, J.D.//Pramanik, A.//Webster, N.S.//Llewellyn, L.E.//Gachhui, R.//Mukherjee, J. 	Draft Genome Sequence of Pseudoalteromonas sp. Strain NW 4327 (MTCC 11073, DSM 25418), a Pathogen of the Great Barrier Reef Sponge Rhopaloeides odorabile.	Genome Announcements	2014	2		e00001-14			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. 		
@D	Choudhury, K.//Leibowitz, M.J. 	Pentamidine-induced Alteration in Restriction Endonuclease Cleavage of Plasmid DNA.	J. Biomol. Struct. Dyn.	2003	21		127-134			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. 		
@D	Choulika, A.//Perrin, A.//Dujon, B.//Nicolas, J.-F. 	Induction of homologous recombination in mammalian chromosomes by using the I-SceI system of Saccharomyces cerevisiae.	Mol. Cell. Biol.	1995	15		1968-1973			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. 		
@D	Choulika, A.//Perrin, A.//Dujon, B.//Nicolas, J.-F. 	The yeast I-SceI meganuclease induces site-directed chromosomal recombination in mammalian cells.	C.R. Acad. Sci. III	1994	317		1013-1019			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. 		
@D	Chovatia, M. et al. 	Complete genome sequence of Thermanaerovibrio acidaminovorans type strain (Su883).	Standards in Genomic Sciences	2009	1		254-261			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. 		
@D	Chow, N.A.//Gade, L.//Batra, D.//Rowe, L.A.//Juieng, P.//Ben-Ami, R.//Loparev, V.N.//Litvintseva, A.P. 	Genome Sequence of a Multidrug-Resistant Candida haemulonii Isolate from a Patient with Chronic Leg Ulcers in Israel.	Genome Announcements	2018	6		e00176-18			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%. 		
@D	Chow, V. et al. 	Complete genome sequence of Paenibacillus sp. strain JDR-2.	Standards in Genomic Sciences	2012	6		1-10			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. 		
@D	Chowdhury, P.R.//Boucher, Y.//Hassan, K.A.//Paulsen, I.T.//Stokes, H.W.//Labbate, M. 	Genome sequence of Vibrio rotiferianus strain DAT722.	J. Bacteriol.	2011	193		3381-3382			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. 		
@D	Chowdhury, P.R.//Ingold, A.//Vanegas, N.//Martinez, E.//Merlino, J.//Merkier, A.K.//Castro, M.//Rocha, G.G.//Borthagaray, G.//Centron, D.//Toledo, H.B.//Marquez, C.M.//Stokes, H.W. 	Dissemination of multiple drug resistance genes by class 1 integrons in Klebsiella pneumoniae isolates from four countries: a comparative study.	Antimicrob. Agents Chemother.	2011	55		3140-3149			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. 		
@D	Christ, C.//Nelson, M. 	DNA modification methylases:  New uses in the manipulation of DNA.	Biotechniques	1984	2		218-221			None 		
@D	Christ, F.//Schoettler, S.//Wende, W.//Steuer, S.//Pingoud, A.//Pingoud, V. 	The monomeric homing endonuclease PI-SceI has two catalytic centres for cleavage of the two strands of its DNA substrate.	EMBO J.	1999	18		6908-6916			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. 		
@D	Christ, F.//Steuer, S.//Thole, H.//Wende, W.//Pingoud, A.//Pingoud, V. 	A model for the PI-SceIxDNA complex based on multiple base and phosphate backbone-specific photocross-links.	J. Mol. Biol.	2000	300		867-875			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. 		
@D	Christensen, L.F.B.//Otzen, D.//Dueholm, M.S. 	High-Quality Draft Genome Sequence of Sphaerisporangium cinnabarinum ATCC 31213.	Genome Announcements	2018	6		e00456-18			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. 		
@D	Christensen, L.L.//Josephsen, J. 	The methyltransferase from the LlaDII restriction-modification system influences the level of expression of its own gene.	J. Bacteriol.	2004	186		287-295			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. 		
@D	Christman, J.K.//Sheikhnejad, G.//Marasco, C.J.//Sufrin, J.R. 	5-methyl-2'-deoxycytidine in single-stranded DNA can act in cis to signal de novo DNA methylation.	Proc. Natl. Acad. Sci. U. S. A.	1995	92		7347-7351			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. 		
@D	Christopher, L.P.//Kapatral, V.//Vaisvil, B.//Emel, G.//Deveaux, L.C. 	Draft Genome Sequence of a New Homofermentative, Lactic Acid-Producing Enterococcus faecalis Isolate, CBRD01.	Genome Announcements	2014	2		e00147-14			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. 		
@D	Chu, F.K.//Maley, F.//Wang, A.-M.//Pedersen-Lane, J.//Maley, G. 	Purification and substrate specificity of a T4 phage intron-encoded endonuclease.	Nucleic Acids Res.	1991	19		6863-6869			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. 		
@D	Chu, F.K.//Maley, G.//Pedersen-Lane, J.//Wang, A.-M.//Maley, F. 	Characterization of the restriction site of a prokaryotic intron-encoded endonuclease.	Proc. Natl. Acad. Sci. U. S. A.	1990	87		3574-3578			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. 		
@D	Chu, F.K.//Maley, G.F.//Maley, F.//Belfort, M. 	Intervening sequence in the thymidylate synthase gene of bacteriophage T4.	Proc. Natl. Acad. Sci. U. S. A.	1984	81		3049-3053			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. 		
@D	Chu, F.K.//Maley, G.F.//West, D.K.//Belfort, M.//Maley, F. 	Characterization of the intron in the phage T4 thymidylate synthase gene and evidence for its self-excision from the primary transcript.	Cell	1986	45		157-166			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. 		
@D	Chu, Y.//Gao, P.//Zhao, P.//He, Y.//Liao, N.//Jackman, S.//Zhao, Y.//Birol, I.//Duan, X.//Lu, Z. 	Genome Sequence of Mycoplasma capricolum subsp. capripneumoniae Strain M1601.	J. Bacteriol.	2011	193		6098-6099			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). 		
@D	Chua, K.//Seemann, T.//Harrison, P.F.//Davies, J.K.//Coutts, S.J.//Chen, H.//Haring, V.//Moore, R.//Howden, B.P.//Stinear, T.P. 	Complete genome sequence of Staphylococcus aureus strain JKD6159, a unique Australian clone of ST93-IV community methicillin-resistant Staphylococcus  aureus.	J. Bacteriol.	2010	192		5556-5557			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. 		
@D	Chua, P.//Yoo, H.S.//Gan, H.M.//Lee, S.M. 	Draft Genome Sequences of Two Cellulolytic Paenibacillus sp. Strains, MAEPY1 and  MAEPY2, from Malaysian Landfill Leachate.	Genome Announcements	2014	2		e00065-14			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. 		
@D	Chuah, L.O.//Yap, K.P.//Thong, K.L.//Liong, M.T.//Ahmad, R.//Shamila-Syuhada, A.K.//Rusul, G. 	Genome Sequence of 'Anthococcus,' a Novel Genus of the Family Streptococcaceae Isolated from Flowers.	Genome Announcements	2016	4		e01410-16			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%. 		
@D	Chuang, L.S.-H.//Ng, H.-H.//Chia, J.-N.//Li, B.F.L. 	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.	J. Mol. Biol.	1996	257		935-948			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. 		
@D	Chuang, L.S.H.//Ian, H.-I.//Koh, T.W.//Ng, H.-H.//Xu, G.//Li, B.F.L. 	Human DNA-(cytosine-5) methyltransferase-PCNA complex as a target for p21WAF1.	Science	1997	277		1996-2000			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. 		
@D	Chuang, L.S.H.//Tan, E.H.H.//Oh, H.K.//Li, B.F.L. 	Selective depletion of human DNA-methyltransferase DNMT1 proteins by sulfonate-derived methylating agents.	Cancer Res.	2002	62		1592-1597			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. 		
@D	Chuea-Nongthon, C.//Rodtong, S.//Yongsawatdigul, J.//Steele, J.L. 	Draft Genome Sequences of Tetragenococcus muriaticus Strains 3MR10-3 and PMC-11-5 Isolated from Thai Fish Sauce during Natural Fermentation.	Genome Announcements	2017	5		e00198-17			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. 		
@D	Chugani, S.//Kim, B.S.//Phattarasukol, S.//Brittnacher, M.J.//Choi, S.H.//Harwood, C.S.//Greenberg, E.P. 	Strain-dependent diversity in the Pseudomonas aeruginosa quorum-sensing regulon.	Proc. Natl. Acad. Sci. U. S. A.	2012	109		E2823-E2831			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. 		
@D	Chuluunbaatar, T.//Ivanenko-Johnston, T.//Fuxreiter, M.//Meleshko, R.//Rasko, T.//Simon, I.//Heitman, J.//Kiss, A. 	An EcoRI-RsrI chimeric restriction endonuclease retains parental sequence specificity.	Biochim. Biophys. Acta	2007	1774		583-594			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. 		
@D	Chun, B.H.//Lee, S.H.//Jeon, H.H.//Kim, D.W.//Jeon, C.O. 	Complete genome sequence of Leuconostoc suionicum DSM 20241T provides insights into its functional and metabolic features.	Standards in Genomic Sciences	2017	12		38			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. 		
@D	Chun, J.H.//Hong, K.J.//Cha, S.H.//Cho, M.H.//Lee, K.J.//Jeong, D.H.//Yoo, C.K.//Rhie, G.E. 	Complete Genome Sequence of Bacillus anthracis H9401, an Isolate from a Korean Patient with Anthrax.	J. Bacteriol.	2012	194		4116-4117			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. 		
@D	Chung, D.//Cha, M.//Farkas, J.//Westpheling, J. 	Construction of a stable replicating shuttle vector for Caldicellulosiruptor species: use for extending genetic methodologies to other members of this genus.	PLoS ONE	2013	8		e62881			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. 		
@D	Chung, D.//Farkas, J.//Huddleston, J.R.//Olivar, E.//Westpheling, J. 	Methylation by a Unique alpha-class N4-Cytosine Methyltransferase Is Required for DNA Transformation of Caldicellulosiruptor bescii DSM6725.	PLoS ONE	2012	7		e43844			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. 		
@D	Chung, D.H.//Huddleston, J.R.//Farkas, J.//Westpheling, J. 	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.	J. Ind. Microbiol. Biotechnol.	2011	38		1867-1877			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. 		
@D	Chung, D.W.//Farkas, J.//Westpheling, J. 	Overcoming restriction as a barrier to DNA transformation in Caldicellulosiruptor species results in efficient marker replacement.	Biotechnol. Biofuels.	2013	6		16187			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. 		
@D	Chung, E.J.//Choi, G.G.//Nam, Y.H.//Choi, A. 	Draft Genome Sequence of Paucibacter aquatile CR182(T), a Strain with Antimicrobial Activity Isolated from Freshwater of Nakdong River in South Korea.	Genome Announcements	2018	6		e00194-18			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. 		
@D	Chung, G.T.//Yoo, J.S.//Oh, H.B.//Lee, Y.S.//Cha, S.H.//Kim, S.J.//Yoo, C.K. 	The Complete Genome Sequence of Neisseria gonorrhoeae NCCP11945.	J. Bacteriol.	2008	190		6035-6036			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. 		
@D	Chung, H.M. et al. 	Complete Genome Sequences of Mycobacteriophages Clautastrophe, Kingsolomon, Krypton555, and Nicholas.	Genome Announcements	2017	5		e01129-17			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. 		
@D	Chung, H.Y.//Kim, Y.T.//Kim, S.//Na, E.J.//Ku, H.J.//Lee, K.H.//Heo, S.T.//Ryu, S.//Kim, H.//Choi, S.H.//Lee, J.H. 	Complete genome sequence of Vibrio vulnificus FORC_017 isolated from a patient with a hemorrhagic rash after consuming raw dotted gizzard shad.	Gut Pathog.	2016	8		22			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. 		
@D	Chung, H.Y.//Lee, K.H.//Ryu, S.//Yoon, H.//Lee, J.H.//Kim, H.B.//Kim, H.//Jeong, H.G.//Choi, S.H.//Kim, B.S. 	Genome Sequence of Bacillus cereus FORC_021, a Food-Borne Pathogen Isolated from a Knife at a Sashimi Restaurant.	J. Microbiol. Biotechnol.	2016	26		2030-2035			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. 		
@D	Chung, J.H.//Jeong, H.//Ryu, C.M. 	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.	Genome Announcements	2018	6		e00044-18			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. 		
@D	Chung, W.C.//Chen, L.L.//Lo, W.S.//Kuo, P.A.//Tu, J.//Kuo, C.H. 	Complete Genome Sequence of Serratia marcescens WW4.	Genome Announcements	2013	1		e0012613			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. 		
@D	Cibulski, S.P.//Siqueira, F.M.//Teixeira, T.F.//Mayer, F.Q.//Almeida, L.G.//Roehe, P.M. 	Genome Sequence of Mycoplasma hyorhinis Isolated from Cell Cultures.	Genome Announcements	2016	4		e01119-16			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. 		
@D	Cigna, J.//Raoul-des-Essarts, Y.//Mondy, S.//Helias, V.//Beury-Cirou, A.//Faure, D. 	Draft Genome Sequences of Pseudomonas fluorescens Strains PA4C2 and PA3G8 and Pseudomonas putida PA14H7, Three Biocontrol Bacteria against Dickeya  Phytopathogens.	Genome Announcements	2015	3		e01503-14			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. 		
@D	Cimdins, A.//Luthje, P.//Li, F.//Ahmad, I.//Brauner, A.//Romling, U. 	Draft Genome Sequences of Semiconstitutive Red, Dry, and Rough Biofilm-Forming Commensal and Uropathogenic Escherichia coli Isolates.	Genome Announcements	2017	5		e01249-16			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. 		
@D	Cimerman, A.//Arnaud, G.//Foissac, X. 	Stolbur phytoplasma genome survey achieved using a suppression subtractive hybridization approach with high specificity.	Appl. Environ. Microbiol.	2006	72		3274-3283			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. 		
@D	Cinelli, T.//Moscetti, I.//Matchi, G. 	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.	Microb. Ecol.	2014	68		842-858			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. 		
@D	Ciranna, A.//Larjo, A.//Kivisto, A.//Santala, V.//Roos, C.//Karp, M. 	Draft Genome Sequence of the Hydrogen- and Ethanol-Producing Anaerobic Alkalithermophilic Bacterium Caloramator celer.	Genome Announcements	2013	1		e00471-13			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. 		
@D	Citron, M.//Velleman, M.//Schuster, H. 	Three additional operators, Op21, Op68, and Op88, of bacteriophage P1.	J. Biol. Chem.	1989	264		3611-3617			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. 		
@D	Claesson, M.J.//Li, Y.//Leahy, S.//Canchaya, C.//van Pijkeren, J.P.//Cerdeno-Tarraga, A.M.//Parkhill, J.//Flynn, S.//O'sullivan, G.C.//Collins, J.K.//Higgins, D.//Shanahan, F.//Fitzgerald, G.F.//van Sinderen, D.//O'toole, P.W. 	Multireplicon genome architecture of Lactobacillus salivarius.	Proc. Natl. Acad. Sci. U. S. A.	2006	103		6718-6723			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. 		
@D	Clancy, C.D.//Forde, B.M.//Moore, S.A.//O'Toole, P.W. 	Draft Genome Sequences of Helicobacter pylori Strains 17874 and P79.	J. Bacteriol.	2012	194		2402			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. 		
@D	Clanton, D.J.//Riggsby, W.S.//Miller, R.V. 	NgoII, a restriction endonuclease from Neisseria gonorrhoeae.	J. Bacteriol.	1979	137		1299-1307			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. ] 		
@D	Clanton, D.J.//Woodward, J.M.//Miller, R.V. 	Identification of a new sequence-specific endonuclease NgoII, from Neisseria gonorrhoeae.	J. Bacteriol.	1978	135		270-273			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. 		
@D	Clark, C.G.//Chong, P.M.//McCorrister, S.J.//Mabon, P.//Walker, M.//Westmacott, G.R. 	DNA Sequence Heterogeneity of Campylobacter jejuni CJIE4 Prophages and Expression of Prophage Genes.	PLoS ONE	2014	9		E95349			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. 		
@D	Clark, C.G.//Ng, L.-K. 	Sequence variability of Campylobacter temperate bacteriophages.	BMC Microbiol.	2008	8		49			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. 		
@D	Clark, J.//Harrison, J.C.//Mdegela, R.H.//March, J.B. 	Extended stability of restriction enzymes at ambient temperatures.	Biotechniques	2000	29		536			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. 		
@D	Clark, J.//Shevchuk, T.//Kho, M.R.//Smith, S.S. 	Methods for the design and analysis of oligodeoxynucleotide-based DNA (cytosine-5) methyltransferase inhibitors.	Anal. Biochem.	2003	321		50-64			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. 		
@D	Clark, N.C.//Zhu, W.//Patel, J.B. 	Missense Mutation of hsdR-Encoded Type I Restriction Enzyme Implicated in Transfer of Vancomycin-Resistance from Enterococcus to Staphylococcus aureus.	Abstr. InterSci. Conf. Antimicrob. Agents Chemother.	2007	47		83-84			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. 		
@D	Clark, S.J.//Harrison, J.//Paul, C.L.//Frommer, M. 	High sensitivity mapping of methylated cytosines.	Nucleic Acids Res.	1994	22		2990-2997			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. 		
@D	Clark, T.A.//Lu, X.//Luong, K.//Dai, Q.//Boitano, M.//Turner, S.W.//He, C.//Korlach, J. 	Enhanced 5-methylcytosine detection in single-molecule, real-time sequencing via  Tet1 oxidation.	BMC Biol.	2013	11		4			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. 		
@D	Clark, T.A.//Murray, I.A.//Morgan, R.D.//Kislyuk, A.O.//Spittle, K.E.//Boitano, M.//Fomenkov, A.//Roberts, R.J.//Korlach, J. 	Characterization of DNA methyltransferase specificities using single-molecule, real-time DNA sequencing.	Nucleic Acids Res.	2012	40		e29			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. 		
@D	Clark, T.R.//Noriea, N.F.//Bublitz, D.C.//Ellison, D.W.//Martens, C.//Lutter, E.I.//Hackstadt, T. 	Comparative Genome Sequencing of Rickettsia rickettsii Strains Differing in Virulence.	Infect. Immun.	2015	83		1568-1576			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. 		
@D	Clarke, C.M.//Hartley, B.S. 	Purification, properties and specificity of the restriction endonuclease from Bacillus stearothermophilus.	Biochem. J.	1979	177		49-62			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'. 		
@D	Clarke, D.J.//Chaudhuri, R.R.//Martin, H.M.//Campbell, B.J.//Rhodes, J.M.//Constantinidou, C.//Pallen, M.J.//Loman, N.J.//Cunningham, A.F.//Browning, D.F.//Henderson, I.R. 	Complete genome sequence of the Crohn's disease-associated adherent-invasive Escherichia coli strain HM605.	J. Bacteriol.	2011	193		4540			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. 		
@D	Clarke, N.D. 	A proposed mechanism for the self-splicing of proteins.	Proc. Natl. Acad. Sci. U. S. A.	1994	91		11084-11088			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. 		
@A	Clarke, S.//Banfield, K. 		S-Adenosylmethionine-dependent methyltransferases.			Carmel, R. and Jacobsen//D.W. 		Homocysteine in Health and Disease					Cambridge University Press	2001				63-78									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. 		
@D	Claus, H.//Friedrich, A.//Frosch, M.//Vogel, U. 	Differential distribution of novel restriction-modification systems in clonal lineages of Neisseria meningitidis.	J. Bacteriol.	2000	182		1296-1303			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. 		
@D	Claus, H.//Stoevesandt, J.//Frosch, M.//Vogel, U. 	Genetic isolation of meningococci of the electrophoretic type 37 complex.	J. Bacteriol.	2001	183		2570-2575			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. 		
@D	Clauwers, C.//Briers, Y.//Lavigne, R.//Michiels, C.W. 	Two Complete and One Draft Genome Sequence of Nonproteolytic Clostridium botulinum Type E Strains NCTC 8266, NCTC 8550, and NCTC 11219.	Genome Announcements	2015	3		e00083-15			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. 		
@D	Cleaver, J.E.//Samson, L.//Thomas, G.H. 	Restriction enzyme cleavage of ultraviolet-damaged DNA.	Biochim. Biophys. Acta	1982	697		255-258			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. 		
@D	Clements, J.B.//Cortini, R.//Wilkie, N.M. 	Analysis of Herpesvirus DNA Substructure by means of Restriction Endonucleases.	J. Gen. Virol.	1976	30		243-256			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. 		
@D	Cleto, S.//Van der Auwera, G.//Almeida, C.//Vieira, M.J.//Vlamakis, H.//Kolter, R. 	Genome Sequence of Serratia plymuthica V4.	Genome Announcements	2014	2		e00340-14			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. 		
@D	Clifford, R.J.//Hang, J.//Riley, M.C.//Onmus-Leone, F.//Kuschner, R.A.//Lesho, E.P.//Waterman, P.E. 	Complete Genome Sequence of Providencia stuartii Clinical Isolate MRSN 2154.	J. Bacteriol.	2012	194		3736-3737			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. 		
@D	Clum, A. et al. 	Complete genome sequence of Acidimicrobium ferrooxidans type strain (ICP).	Standards in Genomic Sciences	2009	1		38-45			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. 		
@D	Clum, A. et al. 	Complete genome sequence of Pirellula staleyi type strain (ATCC 27377).	Standards in Genomic Sciences	2009	1		308-316			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. 		
@D	Clyman, J. 	Some microbes have splicing proteins.	ASM News	1995	61		344-347			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. 		
@D	Clyman, J.//Belfort, M. 	Trans and cis requirements for intron mobility in a prokaryotic system.	Genes Dev.	1992	6		1269-1279			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. 		
@D	Coad, J.E.//Lander, T.A.//Litz, C.E. 	Inhibition of restriction endonucleases by common clinical anticoagulants.	Anal. Biochem.	1992	205		368-369			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. 		
@D	Coates-Brown, R.//Horsburgh, M.J. 	Whole-Genome Sequence of Staphylococcus hominis Strain J31 Isolated from Healthy  Human Skin.	Genome Announcements	2017	5		e01548-16			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. 		
@D	Cocks, B.G.//Finch, L.R. 	Characterization of a restriction endonuclease from Ureaplasma urealyticum 960 and differences in deoxyribonucleic acid modification of human ureaplasmas.	Int. J. Syst. Bacteriol.	1987	37		451-453			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. 		
@D	Coene, M.//Hoet, P.//Cocito, C. 	Physical map of Phage 2 C DNA: Evidence for the existence of large redundant ends.	Eur. J. Biochem.	1983	132		69-75			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. 		
@D	Coetzee, J.N.//Smit, J.A. 	Restriction without modification of phage 34/13 in a strain of Proteus mirabilis.	S. Afr. Med. J.	1969	43		356			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. 		
@D	Coffey, A.//Ross, R.P. 	Bacteriophage-resistance systems in dairy starter strains: molecular analysis to application.	Antonie Van Leeuwenhoek	2002	82		303-321			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. 		
@D	Coffey, A.//Stokes, D.//Fitzgerald, G.F.//Ross, R.P. 	Traditional and molecular approaches to improving bacteriophage resistance of Cheddar and Mozzarella cheese starters.	Irish J. Agr. Food Res.	2001	40		239-270			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. 		
@D	Coffey, B.//Ross, R.P.//O'Flynn, G.//O'Sullivan, O.//Casey, A.//Callanan, M.//Coffey, A.//McAuliffe, O. 	Complete Genome Sequence of vB_EcoM_112, a T-Even-Type Bacteriophage Specific for Escherichia coli O157:H7.	Genome Announcements	2014	2		e00393-14			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. 		
@D	Coffin, S.R.//Reich, N.O. 	Escherichia coli DNA Adenine Methyltransferase THE STRUCTURAL BASIS OF PROCESSIVE CATALYSIS AND INDIRECT READ-OUT.	J. Biol. Chem.	2009	284		18390-18400			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. 		
@D	Coffin, S.R.//Reich, N.O. 	Modulation of Escherichia coli DNA methyltransferase activity by biologically derived GATC-flanking sequences.	J. Biol. Chem.	2008	283		20106-20116			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. 		
@D	Coffin, S.R.//Reich, N.O. 	Escherichia coli DNA Adenine Methyltransferase: Intrasite Processivity and Substrate-Induced Dimerization and Activation.	Biochemistry	2009	48		7399-7410			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. 		
@D	Coffman, G.L.//Gaubatz, J.W.//Yielding, K.L.//Yielding, L.W. 	Demonstration of specific high affinity binding sites in plasmid DNA by photoaffinity labeling with an ethidium analog.	J. Biol. Chem.	1982	257		13205-13207			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. 		
@D	Cohen, H.M.//Griffiths, A.D.//Tawfik, D.S.//Loakes, D. 	Determinants of cofactor binding to DNA methyltransferases: insights from a systematic series of structural variants of  S-adenosylhomocysteine.	Org. Biomol. Chem.	2005	3		152-161			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. 		
@D	Cohen, H.M.//Tawfik, D.S.//Griffiths, A.D. 	Altering the sequence specificity of HaeIII methyltransferase by directed evolution using in vitro compartmentalization.	Protein Eng. Des. Sel.	2004	17		3-11			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. 		
@D	Cohen, H.M.//Tawfik, D.S.//Griffiths, A.D. 	Promiscuous methylation of non-canonical DNA sites by HaeIII methyltransferase.	Nucleic Acids Res.	2002	30		3880-3885			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. 		
@D	Cohen, M.F.//Hu, P.//Nguyen, M.V.//Kamennaya, N.//Brown, N.//Woyke, T.//Kyrpides, N.//Holman, H.Y.//Torok, T. 	Genome Sequence of the Alkaline-Tolerant Cellulomonas sp. Strain FA1.	Genome Announcements	2015	3		e00646-15			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. 		
@D	Cohen, N.R.//Ross, C.A.//Jain, S.//Shapiro, R.S.//Gutierrez, A.//Belenky, P.//Li, H.//Collins, J.J. 	A role for the bacterial GATC methylome in antibiotic stress survival.	Nat. Genet.	2016	48		581-586			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. 		
@D	Cohen-Gihon, I.//Israeli, O.//Beth-Din, A.//Levy, H.//Cohen, O.//Shafferman, A.//Zvi, A.//Chitlaru, T. 	Whole-Genome Sequencing of the Nonproteolytic Bacillus anthracis V770-NP1-R Strain Reveals Multiple Mutations in Peptidase Loci.	Genome Announcements	2014	2		e00075-14			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. 		
@D	Cohen-Karni, D.//Xu, D.//Apone, L.//Fomenkov, A.//Sun, Z.Y.//Davis, P.J.//Kinney, S.R.M.//Yamada-Mabuchi, M.//Xu, S.Y.//Davis, T.//Pradhan, S.//Roberts, R.J.//Zheng, Y. 	The MspJI family of modification-dependent restriction endonucleases for epigenetic studies.	Proc. Natl. Acad. Sci. U. S. A.	2011	108		11040-11045			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. 		
@D	Coil, D.A.//Alexiev, A.//Wallis, C.//O'Flynn, C.//Deusch, O.//Davis, I.//Horsfall, A.//Kirkwood, N.//Jospin, G.//Eisen, J.A.//Harris, S.//Darling, A.E. 	Draft genome sequences of 26 porphyromonas strains isolated from the canine oral  microbiome.	Genome Announcements	2015	3		e00187-15			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. 		
@D	Coil, D.A.//Badger, J.H.//Forberger, H.C.//Riggs, F.//Madupu, R.//Fedorova, N.//Ward, N.//Robb, F.T.//Eisen, J.A. 	Complete Genome Sequence of the Extreme Thermophile Dictyoglomus thermophilum H-6-12.	Genome Announcements	2014	2		e00109-14			Here, we present the complete genome of the extreme thermophile, Dictyoglomus thermophilum H-6-12 (phylum Dictyoglomi), which consists of 1,959,987 bp. 		
@D	Coil, D.A.//Benardini, J.N.//Eisen, J.A. 	Draft Genome Sequence of Bacillus safensis JPL-MERTA-8-2, Isolated from a Mars-Bound Spacecraft.	Genome Announcements	2015	3		e01360-15			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. 		
@D	Coil, D.A.//Doctor, J.I.//Lang, J.M.//Darling, A.E.//Eisen, J.A. 	Draft Genome Sequence of Kocuria sp. Strain UCD-OTCP (Phylum Actinobacteria).	Genome Announcements	2013	1		e00172-13			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. 		
@D	Coil, D.A.//Eisen, J.A. 	Draft Genome Sequence of Porphyrobacter mercurialis (sp. nov.) Strain Coronado.	Genome Announcements	2015	3		e00856-15			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. 		
@D	Coil, D.A.//Jospin, G.//Eisen, J.A.//Adams, J.Y. 	Additional Draft Genome Sequences of Escherichia coli Strains Isolated from Septic Patients.	Genome Announcements	2016	4		e01614-15			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. 		
@D	Coil, D.A.//Lo, J.R.//Chen, R.//Ward, N.//Robb, F.T.//Eisen, J.A. 	Draft Genome Sequence of the Arsenate-Respiring Bacterium Chrysiogenes arsenatis  Strain DSM 11915.	Genome Announcements	2013	1		e00953-13			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. 		
@D	Coker, O.O.//Regmi, S.M.//Suriyaphol, P.//Chininmanu, K.//Prammananan, T.//Chaiprasert, A. 	Whole-Genome Sequence of a Multidrug-Resistant Mycobacterium tuberculosis Beijing Sequence Type 10 Isolate from an Outbreak in Thailand.	Genome Announcements	2014	2		e00803-14			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. 		
@D	Col, B.//Ozkeserli, Z.//Kumar, D.//Ozdag, H.//Alakoc, Y.D. 	Genome Sequence of the Boron-Tolerant and -Requiring Bacterium Bacillus boroniphilus.	Genome Announcements	2014	2		e00935-13			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. 		
@D	Colaco, C.//Sen, S.//Thangavelu, M.//Pinder, S.//Roser, B. 	Extraordinary stability of enzymes dried in trehalose: simplified molecular biology.	Biotechnology	1992	10		1007-1011			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. 		
@D	Colandene, J.D.//Topal, M.D. 	The domain organization of NaeI endonuclease: Separation of binding and catalysis.	Proc. Natl. Acad. Sci. U. S. A.	1998	95		3531-3536			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. 		
@D	Colandene, J.D.//Topal, M.D. 	Evidence for mutations that break communication between the Endo and Topo domains in NaeI endonuclease/topoisomerase.	Biochemistry	2000	2000		13703-13707			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. 		
@D	Colasanti, J.//Sundaresan, V. 	Cytosine methylated DNA synthesized by Taq polymerase used to assay methylation sensitivity of restriction endonuclease HinfI.	Nucleic Acids Res.	1991	19		391-394			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. 		
@D	Colavecchio, A.//Leo, V.//Zaccheo, S.//Jeukens, J.//Emond-Rheault, J.G.//Hamel, J.//Kukavica-Ibrulj, I.//Levesque, R.C.//Goodridge, L. 	Whole-Genome Sequencing of Lactobacillus Species from Two Commercial Probiotic Products.	Genome Announcements	2017	5		e01279-17			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. 		
@D	Cole, S.T. et al. 	Massive gene decay in the leprosy bacillus.	Nature	2001	409		1007-1011			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. 		
@D	Cole, S.T. et al. 	Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence.	Nature	1998	393		537-544			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. 		
@D	Coleman, M.L.//Sullivan, M.B.//Martiny, A.C.//Steglich, C.//Barry, K.//Delong, E.F.//Chisholm, S.W. 	Genomic islands and the ecology and evolution of Prochlorococcus.	Science	2006	311		1768-1770			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. 		
@D	Coleman, N.V. et al. 	Genome sequence of the ethene- and vinyl chloride-oxidizing actinomycete Nocardioides sp. strain JS614.	J. Bacteriol.	2011	193		3399-3400			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. 		
@D	Colleaux, L.//d'Auriol, L.//Betermier, M.//Cottarel, G.//Jacquier, A.//Galibert, F.//Dujon, B. 	Universal code equivalent of a yeast mitochondrial intron reading frame is expressed into E. coli as a specific double strand endonuclease.	Cell	1986	44		521-533			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. 		
@D	Colleaux, L.//D'Auriol, L.//Galibert, F.//Dujon, B. 	Recognition and cleavage site of the intron-encoded omega transposase.	Proc. Natl. Acad. Sci. U. S. A.	1988	85		6022-6026			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. 		
@D	Colleaux, L.//Michel-Wolwertz, M.-R.//Matagne, R.F.//Dujon, B. 	The apocytochrome b gene of Chlamydomonas smithii contains a mobile intron related to both Saccharomyces and Neurospora introns.	Mol. Gen. Genet.	1990	223		288-296			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. 		
@D	Collier, D.A.//Thuong, N.T.//Helene, C. 	Sequence-specific bifunctional DNA ligands based on triple-helix-forming oligonucleotides inhibit restriction enzyme cleavage under physiological conditions.	J. Am. Chem. Soc.	1991	113		1457-1458			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. 		
@D	Collier, G.B. 	Regulation of intracellular S-adenosyl-L-methionine as a strategy for cloning restriction endonucleases.	Diss. Abstr.	1995	56		73B			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. 		
@D	Collier, G.B.//Mattson, T.L.//Connaughton, J.F.//Kalloss, W.D. 	Development of a novel screening system for cloning restriction endonucleases.	FASEB J.	1993	7		A1303			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. 		
@D	Collier, J.//McAdams, H.H.//Shapiro, L. 	A DNA methylation ratchet governs progression through a bacterial cell cycle.	Proc. Natl. Acad. Sci. U. S. A.	2007	104		17111-17116			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. 		
@D	Collin, B.//Pinnell, L.J.//Tallman, J.J.//Turner, J.W. 	Draft Genome Sequences of One Marine and One Clinical Vibrio parahaemolyticus Strain, Both Isolated in Sweden.	Genome Announcements	2016	4		e01196-16			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. 		
@D	Collingro, A.//Kostanjsek, R.//Toenshoff, E.R.//Schulz, F.//Schuster, L.//Domann, D.//Horn, M. 	Draft Genome Sequence of 'Candidatus Hepatoplasma crinochetorum' Ps, a Bacterial  Symbiont in the Hepatopancreas of the Terrestrial Isopod Porcellio scaber.	Genome Announcements	2015	3		e00674-15			'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. 		
@D	Collingro, A.//Tischler, P.//Weinmaier, T.//Penz, T.//Heinz, E.//Brunham, R.C.//Read, T.D.//Bavoil, P.M.//Sachse, K.//Kahane, S.//Friedman, M.G.//Rattei, T.//Myers, G.S.A.//Horn, M. 	Unity in variety -- the pan-genome of the Chlamydiae.	Mol. Biol. Evol.	2011	28		3253-3270			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. 		
@D	Collins, A.J.//Nyholm, S.V. 	Draft genome of Phaeobacter gallaeciensis ANG1, a dominant member of the accessory nidamental gland of Euprymna scolopes.	J. Bacteriol.	2011	193		3397-3398			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. 		
@D	Collins, C.//Kowalski, C.//Zebrowski, J.//Tulchinskaya, Y.//Tai, A.K.//James-Pederson, M.//Hirst, R. 	Draft Genome Sequence of Methylobacterium sp. Strain ARG-1 Isolated from the White-Rot Fungus Armillaria gallica.	Genome Announcements	2016	4		e00398-16			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. 		
@D	Collins, E.B. 	Host-controlled variations in bacteriophages active against lactic Streptococci.	Virology	1956	2		261-271			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. 		
@D	Collins, J.//Mayer, H. 	Restriction endonucleases or the site-specific DNA endonucleases.	Arzneimittelforschung	1980	30		541-547			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. 		
@D	Collins, R.E.//Rocap, G. 	REPK: an analytical web server to select restriction endonucleases for terminal restriction fragment length polymorphism analysis.	Nucleic Acids Res.	2007	35		W58-W62			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. 		
@D	Collyn, F.//Billault, A.//Mullet, C.//Simonet, M.//Marceau, M. 	YAPI, a new Yersinia pseudotuberculosis pathogenicity island.	Infect. Immun.	2004	72		4784-4790			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. 		
@D	Colson, A.M.//Colson, C. 	Expression of the Escherichia coli K, B and Phage P1 DNA host specificities in Salmonella typhimurium.	J. Gen. Microbiol.	1972	70		123-128			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. 		
@D	Colson, A.M.//Colson, C.//Van Pel, A. 	Host-controlled restriction mutants of Salmonella typhimurium.	J. Gen. Microbiol.	1969	58		57-64			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. 		
@D	Colson, C. 	Genetics of R-M systems in Salmonella.	Heredity	1978	41		123			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. 		
@D	Colson, C.//Colson, A.M. 	A new Salmonella typhimurium DNA host specificity.	J. Gen. Microbiol.	1971	69		345-351			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. 		
@D	Colson, C.//Colson, A.M.//van Pel, A. 	Chromosomal location of host specificity in Salmonella typhimurium.	J. Gen. Microbiol.	1970	60		265-271			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. 		
@D	Colson, C.//Glover, S.W.//Symonds, N.//Stacey, K.A. 	The location of the genes for host-controlled modification and restriction in Escherichia coli K-12.	Genetics	1965	52		1043-1050			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. 		
@D	Colson, C.//van Pel, A. 	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.	Mol. Gen. Genet.	1974	129		325-337			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. 		
@A	Colston, M.J.//Davis, E.O. 		Homologous recombination, DNA repair and mycobacterial recA genes.			Bloom, B.R. 		Tuberculosis: Pathogenesis, Protection, and Control				Washington, DC	American Society for Microbiology	1994		0		217-226									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. 		
@D	Colston, S.M.//Ellis, G.A.//Kim, S.//Wijesekera, H.W.//Leary, D.H.//Lin, B.//Kirkup, B.C.//Hervey, W.J. IV//Vora, G.J. 	Complete Genome Sequences of Two Bioluminescent Vibrio campbellii Strains Isolated from Biofouling Communities in the Bay of Bengal.	Genome Announcements	2018	6		e00422-18			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. 		
@D	Colston, S.M.//Navarro, A.//Martinez-Murcia, A.J.//Graf, J. 	Draft Genome Sequence of Aeromonas cavernicola sp. nov. DSM 24474(T), Isolated from a Cavern Brook in the Moravia Region of the Czech Republic.	Genome Announcements	2018	6		e00227-18			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. 		
@D	Colston, S.M.//Navarro, A.//Martinez-Murcia, A.J.//Graf, J. 	Draft Genome Sequence of Aeromonas lusitana sp. nov. Strain DSM 24905(T), Isolated from a Hot Spring in Vila-Real, Portugal.	Genome Announcements	2018	6		e00226-18			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. 		
@D	Comai, L.//Young, K.//Till, B.J.//Reynolds, S.//Greene, E.A.//Codomo, C.A.//Enns, L.//Johnson, J.E.//Burtner, C.//Odden, A.//Henikoff, S. 	Efficient discovery of DNA polymorphisms in natural populations by Ecotilling.	Plant J.	2004	37		778-786			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. 		
@D	Comandatore, F.//Gaibani, P.//Ambretti, S.//Landini, M.P.//Daffonchio, D.//Marone, P.//Sambri, V.//Bandi, C.//Sassera, D. 	Draft Genome of Klebsiella pneumoniae Sequence Type 512, a Multidrug-Resistant Strain Isolated during a Recent KPC Outbreak in Italy.	Genome Announcements	2013	1		e00035-12			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. 		
@D	Comandatore, F.//Sassera, D.//Ambretti, S.//Landini, M.P.//Daffonchio, D.//Marone, P.//Sambri, V.//Bandi, C.//Gaibani, P. 	Draft Genome Sequences of Two Multidrug Resistant Klebsiella pneumoniae ST258 Isolates Resistant to Colistin.	Genome Announcements	2013	1		e00113-12			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. 		
@D	Comstock, L.R.//Rajski, S.R. 	Methyltransferase-directed DNA strand scission.	J. Am. Chem. Soc.	2005	127		14136-14137			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. 		
@D	Comstock, L.R.//Rajski, S.R. 	Conversion of DNA methyltransferases into azidonucleosidyl transferases via synthetic cofactors.	Nucleic Acids Res.	2005	33		1644-1652			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. 		
@D	Conchillo-Sole, O.//Yero, D.//Coves, X.//Huedo, P.//Martinez-Servat, S.//Daura, X.//Gibert, I. 	Draft Genome Sequence of Stenotrophomonas maltophilia Strain UV74 Reveals Extensive Variability within Its Genomic Group.	Genome Announcements	2015	3		e00611-15			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. 		
@D	Conlan, L.H.//Dupureur, C.M. 	Dissecting the metal ion dependence of DNA binding by PvuII endonuclease.	Biochemistry	2002	41		1335-1342			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. 		
@D	Conlan, L.H.//Jose, T.J.//Thornton, K.C.//Dupureur, C.M. 	Modulating restriction endonuclease activities and specificities using neutral detergents.	Biotechniques	1999	27		955-960			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. 		
@D	Conlan, L.M. 	The influence of divalent metal ions on DNA binding and cleavage by the restriction enzyme PvuII endonuclease.	Ph.D. Thesis, Texas A and M Univ., College Station, TX, USA	2002			143			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. 		
@D	Conlan, S. et al. 	Single-molecule sequencing to track plasmid diversity of hospital-associated carbapenemase-producing Enterobacteriaceae.	Sci. Transl. Med.	2014	6		254ra126			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. 		
@D	Conlan, S.//Deming, C.//Tsai, Y.C.//Lau, A.F.//Dekker, J.P.//Korlach, J.//Segre, J.A. 	Complete Genome Sequence of a Klebsiella pneumoniae Isolate with Chromosomally Encoded Carbapenem Resistance and Colibactin Synthesis Loci.	Genome Announcements	2014	2		e01332-14			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. 		
@D	Conlan, S.//Lau, A.F.//Palmore, T.N.//Frank, K.M.//Segre, J.A. 	Complete Genome Sequence of a Klebsiella pneumoniae Strain Carrying blaNDM-1 on a Multidrug Resistance Plasmid.	Genome Announcements	2016	4		e00664-16			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. 		
@D	Conlan, S.//Lawrence, C.//McCue, L.A. 	Rhodopseudomonas palustris regulons detected by cross-species analysis of alphaproteobacterial genomes.	Appl. Environ. Microbiol.	2005	71		7442-7452			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. 		
@D	Connaughton, J.F.//Kaloss, W.D.//Vanek, P.G.//Nardone, G.A.//Chirikjian, J.G. 	The complete sequence of the Bacillus amyloliquefaciens proviral H2, BamHI methylase gene.	Nucleic Acids Res.	1990	18		4002			None 		
@D	Connaughton, J.F.//Vanek, P.G.//Chirikjian, J.G. 	Cloning of the BamHI methyl transferase gene from Bacillus amyloliquefaciens.	J. Cell Biol.	1988	107		535a			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. 		
@D	Connaughton, J.F.//Vanek, P.G.//Lee-Lin, S.-Q.//Chirikjian, J.G. 	Cloning of the BamHI methyltransferase gene from Bacillus amyloliquefaciens.	Gene Anal. Tech.	1988	5		116-124			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. 		
@D	Connolly, B.A. 	Assay of restriction endonucleases using oligonucleotides.	Methods Mol. Biol.	1994	30		371-383			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. 		
@D	Connolly, B.A.//Eckstein, F.//Pingoud, A. 	The Stereochemical Course of the Restriction Endonuclease EcoRI-catalyzed reaction.	J. Biol. Chem.	1984	259		10760-10763			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. 		
@D	Connolly, B.A.//Potter, B.V.L.//Eckstein, F.//Pingoud, A.//Grotjahn, L. 	Synthesis and characterization of an octanucleotide containing the EcoRI recognition sequence with a phosphorothioate group at the cleavage site.	Biochemistry	1984	23		3443-3453			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. 		
@D	Conrad, M.//Topal, M.D. 	Modified DNA fragments activate NaeI cleavage of refractory DNA sites.	Nucleic Acids Res.	1992	20		5127-5130			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. 		
@D	Conrad, M.//Topal, M.D. 	DNA and spermidine provide a switch mechanism to regulate the activity of restriction enzyme NaeI.	Proc. Natl. Acad. Sci. U. S. A.	1989	86		9707-9711			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. 		
@D	Contreras, S.//Sagory-Zalkind, P.//Blanquart, H.//Iltis, A.//Morand, S. 	Complete Genome Sequence of Vitreoscilla filiformis (ATCC 15551), Used as a Cosmetic Ingredient.	Genome Announcements	2017	5		e00913-17			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. 		
@D	Contreras-Castro, L.//Maldonado, L.A.//Quintana, E.T.//Raggi, L.//Sanchez-Flores, A. 	Draft Genome Sequence of Two Marine Plantactinospora spp. from the Gulf of California.	Genome Announcements	2018	6		e00436-18			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. 		
@D	Cook, L.E.//Gang, S.S.//Ihlan, A.//Maune, M.//Tanner, R.S.//McInerney, M.J.//Weinstock, G.//Lobos, E.A.//Gunsalus, R.P. 	Genome Sequence of Acetomicrobium hydrogeniformans OS1.	Genome Announcements	2018	6		e00581-18			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. 		
@D	Cook, L.J.//Cox, J.P.L. 	Methylated DNA labels for marking objects.	Biotechnol. Lett.	2003	25		89-94			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. 		
@D	Cook, S.N.//Jack, W.E.//Xiong, X.//Danley, L.E.//Ellman, J.A.//Schultz, P.G.//Noren, C.J. 	Photochemically initiated protein splicing.	Angew. Chem. Int. Ed. Engl.	1995	34		1629-1630			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. 		
@D	Coolen, J.P.//Sjodin, A.//Maraha, B.//Hajer, G.F.//Forsman, M.//Verspui, E.//Frenay, H.M.//Notermans, D.W.//de Vries, M.C.//Reubsaet, F.A.//Paauw, A.//Roeselers, G. 	Draft genome sequence of Francisella tularensis subsp. holarctica BD11-00177.	Standards in Genomic Sciences	2013	8		539-547			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. 		
@D	Cooney, C.A. 	The restriction enzyme EheI (GGC/GCC) is sensitive to CpG methylation.	Nucleic Acids Res.	1990	18		3667			None 		
@D	Cooney, C.A.//Eykholt, R.L.//Bradbury, E.M. 	Methylation is co-ordinated on the putative replication origins of Physarum ribosomal DNA.	J. Mol. Biol.	1988	204		889-901			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. 		
@D	Cooper, A.//Koziol, A.G.//Carrillo, C.D.//Lambert, D. 	Draft Genome Sequences of Salmonella enterica subsp. enterica Serovar Berta ATCC  8392 and a Nalidixic Acid-Resistant Isolate of This Strain.	Genome Announcements	2016	4		e00186-16			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. 		
@D	Cooper, A.//Lambert, D.//Koziol, A.G.//Seyer, K.//Carrillo, C.D. 	Draft Genome Sequence of Salmonella enterica subsp. enterica Serovar Mishmarhaemek Isolated from Bovine Feces.	Genome Announcements	2015	3		e01210-15			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. 		
@D	Cooper, A.A.//Chen, Y.-J.//Lindorfer, M.A.//Stevens, T.H. 	Protein splicing of the yeast TFP1 intervening protein sequence: a model for self-excision.	EMBO J.	1993	12		2575-2583			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. 		
@D	Cooper, A.A.//Stevens, T.H. 	Protein splicing: self-splicing of genetically mobile elements at the protein level.	Trends Biochem. Sci.	1995	20		351-356			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. 		
@D	Cooper, A.A.//Stevens, T.H. 	Protein splicing: Excision of intervening sequences at the protein level.	Bioessays	1993	15		667-674			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. 		
@D	Cooper, J.E.//Feil, E.J. 	The phylogeny of Staphylococcus aureus - which genes make the best intra-species markers?	Microbiology	2006	152		1297-1305			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. 		
@D	Cooper, K.K.//Cooper, M.A.//Zuccolo, A.//Law, B.//Joens, L.A. 	Complete Genome Sequence of Campylobacter jejuni Strain S3.	J. Bacteriol.	2011	193		1491-1492			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. 		
@D	Cooper, K.K.//Mandrell, R.E.//Louie, J.W.//Korlach, J.//Clark, T.A.//Parker, C.T.//Huynh, S.//Chain, P.S.//Ahmed, S.//Carter, M.Q. 	Comparative genomics of enterohemorrhagic Escherichia coli O145:H28 demonstrates  a common evolutionary lineage with Escherichia coli O157:H7.	BMC Genomics	2014	15		17			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. 		
@D	Cooper, K.K.//Mandrell, R.E.//Louie, J.W.//Korlach, J.//Clark, T.A.//Parker, C.T.//Huynh, S.//Chain, P.S.//Ahmed, S.//Carter, M.Q. 	Complete Genome Sequences of Two Escherichia coli O145:H28 Outbreak Strains of Food Origin.	Genome Announcements	2014	2		e00482-14			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. 		
@D	Cooper, L.P.//Dryden, D.T.F. 	The domains of a type I DNA methyltransferase: interactions and role in recognition of DNA methylation.	J. Mol. Biol.	1994	236		1011-1021			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. 		
@D	Cooper, L.P.//Roberts, G.A.//White, J.H.//Luyten, Y.A.//Bower, E.K.M.//Morgan, R.D.//Roberts, R.J.//Lindsay, J.A.//Dryden, D.T.F. 	DNA target recognition domains in the Type I restriction and modification systems of Staphylococcus aureus.	Nucleic Acids Res.	2017	45		3395-3406			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. 		
@D	Cooper, T.F.//Heinemann, J.A. 	Postsegregational killing does not increase plasmid stability but acts to mediate the exclusion of competing plasmids.	Proc. Natl. Acad. Sci. U. S. A.	2000	97		12643-12648			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. 		
@D	Copeland, A. et al. 	Complete genome sequence of Desulfomicrobium baculatum type strain (X).	Standards in Genomic Sciences	2009	1		29-37			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. 		
@D	Copeland, A. et al. 	Complete genome sequence of Catenulispora acidiphila type strain (ID 139908).	Standards in Genomic Sciences	2009	1		119-125			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. 		
@D	Copeland, A. et al. 	Complete genome sequence of Atopobium parvulum type strain (IPP 1246).	Standards in Genomic Sciences	2009	1		166-173			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. 		
@D	Copeland, A. et al. 	Complete genome sequence of the orange-red pigmented, radioresistant Deinococcus  proteolyticus type strain (MRP(T)).	Standards in Genomic Sciences	2012	6		240-250			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. 		
@D	Copeland, A. et al. 	Complete genome sequence of the aquatic bacterium Runella slithyformis type strain (LSU 4(T)).	Standards in Genomic Sciences	2012	6		145-154			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. 		
@D	Copeland, A. et al. 	Complete genome sequence of the aerobic, heterotrophy Marinithermus hydrothermalis type strain (T1T) from a deep-sea hydrothermal vent chimney.	Standards in Genomic Sciences	2012	6		21-30			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. 		
@D	Copeland, A. et al. 	Complete genome sequence of the halophilic and highly halotolerant Chromohalobacter salexigens type strain (1H11T).	Standards in Genomic Sciences	2011	5		379-388			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. 		
@D	Copeland, J.C.//Bryson, V. 	Restriction in matings of Escherichia coli strain K-12 with strain B.	Genetics	1966	54		441-452			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. 		
@D	Corby-Harris, V.//Anderson, K.E. 	Draft Genome Sequences of Four Parasaccharibacter apium Strains Isolated from Honey Bees.	Genome Announcements	2018	6		e00165-18			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. 		
@D	Corina, L.E. 	Homing endonuclease I-CreII: A novel dual-motif enzyme that catalyzes group I intron homing.	Ph.D. Thesis, Southwestern Medical Center, Univ. of Texas, USA	2005			1-148			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. 		
@D	Corina, L.E.//Qiu, W.//Desai, A.//Herrin, D.L. 	Biochemical and mutagenic analysis of I-CreII reveals distinct but important roles for both the H-N-H and GIY-YIG motifs.	Nucleic Acids Res.	2009	37		5810-5821			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. 		
@D	Cornelius, A.J.//Miller, W.G.//Lastovica, A.J.//On, S.L.W.//French, N.P.//Vandenberg, O.//Biggs, P.J. 	Complete Genome Sequence of Campylobacter concisus ATCC 33237T and Draft Genome Sequences for an Additional Eight Well-Characterized C. concisus Strains.	Genome Announcements	2017	5		e00711-17			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. 		
@D	Cornell, C.R.//Marasini, D.//Fakhr, M.K. 	Draft Genome Sequences of Megaplasmid-Bearing Streptomyces sp. Strains BF-3 and 4F, Isolated from the Great Salt Plains of Oklahoma.	Genome Announcements	2018	6		e00208-18			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. 		
@D	Cornell, J.L.//Breslin, E.//Schuhmacher, Z.//Himelright, M.//Berluti, C.//Boyd, C.//Carson, R.//Del Gallo, E.//Giessler, C.//Gilliam, B.//Heatherly, C.//Nevin, J.//Nguyen, B.//Nguyen, J.//Parada, J.//Sutterfield, B.//Tukruni, M.//Temple, L. 	Complete Genome Sequence of Bacillus thuringiensis Bacteriophage Smudge.	Genome Announcements	2016	4		e00572-16			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. 		
@D	Cornish-Bowden, A. 	Nomenclature for incompletely specified bases in nucleic acid sequences: recommendations 1984.	Nucleic Acids Res.	1985	13		3021-3030			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. 		
@D	Corretto, E.//Antonielli, L.//Sessitsch, A.//Compant, S.//Hofer, C.//Puschenreiter, M.//Brader, G. 	Complete genome sequence of the heavy metal resistant bacterium Agromyces aureus  AR33T and comparison with related Actinobacteria.	Standards in Genomic Sciences	2017	12		2			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. 		
@D	Corretto, E.//Antonielli, L.//Sessitsch, A.//Kidd, P.//Weyens, N.//Brader, G. 	Draft Genome Sequences of 10 Microbacterium spp., with Emphasis on Heavy Metal-Contaminated Environments.	Genome Announcements	2015	3		e00432-15			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. 		
@D	Corsini, G.//Valdes, N.//Pradel, P.//Tello, M.//Cottet, L.//Muino, L.//Karahanian, E.//Castillo, A.//Gonzalez, A.R. 	Draft Genome Sequence of a Copper-Resistant Marine Bacterium, Pantoea agglomerans Strain LMAE-2, a Bacterial Strain with Potential Use in Bioremediation.	Genome Announcements	2016	4		e00525-16			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. 		
@D	Corvaglia, A.R.//Francois, P.//Bertrand, X.//Quentin, R.//Hernandez, D.//van der Mee-Marquet, N. 	Whole-Genome Sequences of Two Staphylococcus aureus ST398 Strains of Human Origin, S94 and S100.	Genome Announcements	2013	1		e00691-13			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. 		
@D	Corvaglia, A.R.//Francois, P.//Hernandez, D.//Perron, K.//Linder, P.//Schrenzel, J. 	A type III-like restriction endonuclease functions as a major barrier to horizontal gene transfer in clinical Staphylococcus aureus strains.	Proc. Natl. Acad. Sci. U. S. A.	2010	107		11954-11958			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. 		
@D	Cosate, M.R.//Soares, S.C.//Mendes, T.A.//Raittz, R.T.//Moreira, E.C.//Leite, R.//Fernandes, G.R.//Haddad, J.P.//Ortega, J.M. 	Whole-Genome Sequence of Leptospira interrogans Serovar Hardjo Subtype Hardjoprajitno Strain Norma, Isolated from Cattle in a Leptospirosis Outbreak in   Brazil.	Genome Announcements	2015	3		e01302-15			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. 		
@D	Cossio-Bayugar, R.//Miranda-Miranda, E.//Arreguin-Perez, C.A.//Lozano, L.//Perez-de-la-Rosa, D.//Rocha-Martinez, M.K.//Bravo-Diaz, M.A.//Sachman-Ruiz, B. 	Draft Genome Sequence of Enterococcus casseliflavus PAVET15 Obtained from the Oviduct Infection of the Cattle Tick (Rhipicephalus microplus) in Jiutepec, Morelos, Mexico.	Genome Announcements	2017	5		e00196-17			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. 		
@D	Cosstick, R.//Li, X.//Tuli, D.K.//Williams, D.M.//Connolly, B.A.//Newman, P.C. 	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.	Nucleic Acids Res.	1990	18		4771-4778			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. 		
@D	Cossu, M.//Badel, C.//Catchpole, R.//Gadelle, D.//Marguet, E.//Barbe, V.//Forterre, P.//Oberto, J. 	Flipping chromosomes in deep-sea archaea.	PLoS Genet.	2017	13		e1006847			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. 		
@D	Costa, M.O.//Beltrame, C.O.//Ferreira, F.A.//Botelho, A.M.//Lima, N.C.//Souza, R.C.//de Almeida, L.G.//Vasconcelos, A.T.//Nicolas, M.F.//Figueiredo, A.M. 	Complete Genome Sequence of a Variant of the Methicillin-Resistant Staphylococcus aureus ST239 Lineage, Strain BMB9393, Displaying Superior Ability To Accumulate  ica-Independent Biofilm.	Genome Announcements	2013	1		e00576-13			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. 		
@D	Costa, N.D.//Thacker, J. 	The Efficiency of Restriction Endonuclease Digests Determined by PCR.	Biotechniques	1992	13		190			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. 		
@D	Costa, P.S.//Tschoeke, D.A.//Silva, B.S.//Thompson, F.//Reis, M.P.//Chartone-Souza, E.//Nascimento, A.M. 	Draft Genome Sequence of Micrococcus sp. Strain MS-AsIII-49, an Arsenate-Reducing Isolate from Tropical Metal-Rich Sediment.	Genome Announcements	2015	3		e00122-15			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. 		
@D	Costa, S.K.//Donegan, N.P.//Corvaglia, A.R.//Francois, P.//Cheung, A.L. 	Bypassing the restriction system to improve transformation of Staphylococcus epidermidis.	J. Bacteriol.	2017	199		e00271-17			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. 		
@D	Costa, W.L.O.//Alves, J.T.C.//Dias, L.M.//Araujo, C.L.A.//Morais, E.//Silva, A.G.M.//Andrade, S.S.//Ramos, R.T.J.//Silva, A.//Folador, A.R.C. 	Whole-Genome Sequence of Corynebacterium pseudotuberculosis PA04, Isolated from the Lymph Node of a Sheep in the Amazon, Brazil.	Genome Announcements	2017	5		e00202-17			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. 		
@D	Costello, E.K.//Sun, C.L.//Carlisle, E.M.//Morowitz, M.J.//Banfield, J.F.//Relman, D.A. 	Candidatus Mycoplasma girerdii replicates, diversifies, and co-occurs with Trichomonas vaginalis in the oral cavity of a premature infant.	Sci. Rep.	2017	7		3764			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. 		
@D	Cote, V.//Mercier, J.P.//Lemieux, C.//Turmel, M. 	The single group-I intron in the chloroplast rrnL gene of Chlamydomonas humicola encodes a site-specific DNA endonuclease (I-ChuI).	Gene	1993	129		69-76			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. 		
@D	Coucheron, D.H. 	Acetobacter strains contain DNA modified at GAATTC and GANTC.	Can. J. Microbiol.	1997	43		456-460			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. 		
@D	Couger, M.B.//Hanafy, R.A.//Edens, C.//Budd, C.//French, D.P.//Hoff, W.D.//Elshahed, M.S.//Youssef, N.H. 	Draft Genome of the Arthrobacter sp. Strain Edens01.	Genome Announcements	2015	3		e01475-15			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. 		
@D	Couger, M.B.//Hanafy, R.A.//Mitacek, R.M.//Budd, C.//French, D.P.//Hoff, W.D.//Elshahed, M.S.//Youssef, N.H. 	The Draft Genome Sequence of Xanthomonas sp. Strain Mitacek01 Expands the Pangenome of a Genus of Plant Pathogens.	Genome Announcements	2015	3		e01450-15			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. 		
@D	Couger, M.B.//Hurlbut, A.//Murphy, C.L.//Budd, C.//French, D.P.//Hoff, W.D.//Elshahed, M.S.//Youssef, N.H. 	Draft Genome Sequence of the Environmental Isolate Chryseobacterium sp. Hurlbut01.	Genome Announcements	2015	3		e01071-15			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. 		
@D	Couger, M.B.//Wright, A.//Lutter, E.I.//Youssef, N. 	Draft Genome Sequences of Five Pseudomonas aeruginosa Clinical Strains Isolated from Sputum Samples from Cystic Fibrosis Patients.	Genome Announcements	2016	4		e01528-15			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. 		
@D	Coulby, J.//Sternberg, N. 	Bacteriophage P1 encodes its own dam methylase.	Plasmid	1987	17		81			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. 		
@D	Coulby, J.N.//Sternberg, N.L. 	Characterization of the phage P1 dam gene.	Gene	1988	74		191			Meeting Abstract 		
@D	Coulson, T.J.//Patten, C.L. 	Complete Genome Sequence of Enterobacter cloacae UW5, a Rhizobacterium Capable of High Levels of Indole-3-Acetic Acid Production.	Genome Announcements	2015	3		e00843-15			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. 		
@D	Coupland, P.//Chandra, T.//Quail, M.//Reik, W.//Swerdlow, H. 	Direct sequencing of small genomes on the Pacific Biosciences RS without library  preparation.	Biotechniques	2012	53		365-372			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. 		
@D	Courties, A.//Riedel, T.//Jarek, M.//Intertaglia, L.//Lebaron, P.//Suzuki, M.T. 	Genome Sequence of Strain MOLA814, a Proteorhodopsin-Containing Representative of the Betaproteobacteria Common in the Ocean.	Genome Announcements	2013	1		e01062-13			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. 		
@D	Courtine, D.//Alain, K.//Georges, M.//Bienvenu, N.//Morrison, H.G.//Eren, A.M.//Maignien, L. 	Complete Genome Sequence of Hyperthermophilic Archaeon Thermococcus sp. EXT12c, Isolated from the East Pacific Rise 9 degrees N.	Genome Announcements	2017	5		e01385-17			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. 		
@D	Cousin, S.//Clermont, D.//Creno, S.//Ma, L.//Loux, V.//Bizet, C.//Bouchier, C. 	Draft Genome Sequence of Lactobacillus pasteurii CRBIP 24.76T.	Genome Announcements	2013	1		e00660-13			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. 		
@D	Cousin, S.//Creno, S.//Ma, L.//Clermont, D.//Loux, V.//Bizet, C.//Bouchier, C. 	Draft Genome Sequence of Lactobacillus hominis Strain CRBIP 24.179T, Isolated from Human Intestine.	Genome Announcements	2013	1		e00662-13			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. 		
@D	Cousin, S.//Loux, V.//Ma, L.//Creno, S.//Clermont, D.//Bizet, C.//Bouchier, C. 	Draft Genome Sequences of Lactobacillus equicursoris CIP 110162T and Lactobacillus sp. Strain CRBIP 24.137, Isolated from Thoroughbred Racehorse Feces  and Human Urine, Respectively.	Genome Announcements	2013	1		e00663-13			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. 		
@D	Cousin, S.//Ma, L.//Creno, S.//Clermont, D.//Loux, V.//Bizet, C.//Bouchier, C. 	Draft Genome Sequence of Lactobacillus gigeriorum CRBIP 24.85T, Isolated from a Chicken Crop.	J. Bacteriol.	2012	194		5973			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). 		
@D	Cousineau, B.//Lawrence, S.//Smith, D.//Belfort, M. 	Retrotransposition of a bacterial group II intron.	Nature	2000	404		1018-1021			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. 		
@D	Cousineau, B.//Smith, D.//Lawrence-Cavanagh, S.//Mueller, J.E.//Yang, J.//Mills, D.//Manias, D.//Dunny, G.//Lambowitz, A.M.//Belfort, M. 	Retrohoming of a bacterial group II intron: Mobility via complete reverse splicing, independent of homologous DNA recombination.	Cell	1998	94		451-462			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. 		
@D	Coutinho, B.G.//Passos-da-Silva, D.//Previato, J.O.//Mendonca-Previato, L.//Venturi, V. 	Draft Genome Sequence of the Rice Endophyte Burkholderia kururiensis M130.	Genome Announcements	2013	1		e0022512			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. 		
@D	Couto, N.//Chlebowicz, M.A.//Raangs, E.C.//Friedrich, A.W.//Rossen, J.W. 	Complete Genome Sequences of Two Methicillin-Resistant Staphylococcus haemolyticus Isolates of Multilocus Sequence Type 25, First Detected by Shotgun  Metagenomics.	Genome Announcements	2018	6		e00036-18			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. 		
@D	Couturier, M.//Lindas, A.C. 	The DNA Methylome of the Hyperthermoacidophilic Crenarchaeon Sulfolobus acidocaldarius.	Front. Microbiol.	2018	9		137			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. 		
@D	Cowan, G.M. 	A new family of type I restriction and modification systems.	Diss. Abstr.	1989	50		441			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. 		
@A	Cowan, G.M. 		New family of Type I restriction and modification systems.			 		Ph.D. Thesis, University of Edinburgh, Edinburgh, Scotland				Edinburgh		1988				1-128									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. 		
@D	Cowan, G.M.//Daniel, A.S.//Gann, A.A.F.//Kelleher, J.E.//Murray, N.E. 	Defining domains in type-I restriction and modification enzymes.	Gene	1988	74		239-241			Meeting Abstract 		
@D	Cowan, G.M.//Gann, A.A.F.//Murray, N.E. 	Conservation of complex DNA recognition domains between families of restriction enzymes.	Cell	1989	56		103-109			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. 		
@D	Cowan, J.A. 	Role of metal ions in promoting DNA binding and cleavage by restriction endonucleases.	Nucleic Acids Mol. Biol.	2004	14		339-360			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. 		
@D	Cowley, L.A.//Petersen, F.C.//Junges, R.//Jimenez, M.J.D.//Morrison, D.A.//Hanage, W.P. 	Evolution via recombination: Cell-to-cell contact facilitates larger recombination events in Streptococcus pneumoniae.	PLoS Genet.	2018	14		e1007410			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. 		
@D	Cox, K.L.//Baltz, R.H. 	Restriction of bacteriophage plaque formation in Streptomyces spp.	J. Bacteriol.	1984	159		499-504			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. 		
@D	Cox, R.//Goorha, S.//Irving, C. 	Acrolein, a metabolite of cyclophosphamide, alters DNA methylase activity in a non-competitive fashion by reacting with -SH groups of the enzyme.	Proc. Amer. Assoc. Cancer Res.	1987	28		86			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. 		
@D	Cox, R.//Goorha, S.//Irving, C.C. 	Inhibition of DNA methylase activity by acrolein.	Carcinogenesis	1988	9		463-465			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. 		
@D	Coyne, M.J.//Zitomersky, N.L.//McGuire, A.M.//Earl, A.M.//Comstock, L.E. 	Evidence of Extensive DNA Transfer between Bacteroidales Species within the Human Gut.	MBio	2014	5		e01305-14			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. 		
@D	Craig, J.W.//Chang, F.Y.//Kim, J.H.//Obiajulu, S.C.//Brady, S.F. 	Expanding Small-Molecule Functional Metagenomics through Parallel Screening of Broad-Host-Range Cosmid Environmental DNA Libraries in Diverse Proteobacteria.	Appl. Environ. Microbiol.	2010	76		1633-1641			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. 		
@D	Craig, R.J.//Arraj, J.A.//Marinus, M.G. 	Induction of damage inducible (SOS) repair in dam mutants of Escherichia coli exposed to 2-aminopurine.	Mol. Gen. Genet.	1984	194		539-540			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. 		
@D	Crampton, N.//Roes, S.//Dryden, D.T.//Rao, D.N.//Edwardson, J.M.//Henderson, R.M. 	DNA looping and translocation provide an optimal cleavage mechanism for the type III restriction enzymes.	EMBO J.	2007	26		3815-3825			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. 		
@D	Crampton, N.//Yokokawa, M.//Dryden, D.T.F.//Edwardson, J.//Michael, R.//Desirazu, N.//Takeyasu, K.//Yoshimura, S.H.//Henderson, R.M. 	Fast-scan atomic force microscopy reveals that the type III restriction enzyme EcoP15I is capable of DNA translocation and looping.	Proc. Natl. Acad. Sci. U. S. A.	2007	104		12755-12760			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. 		
@D	Cranz, S.//Beck, C.//Roth, M.//Jeltsch, A. 	Molecular enzymology of the adenine-N6 DNA methyltransferase M.EcoRV: Site-directed mutagenesis analysis of DNA sequence and target base recognition.	Biochem. Soc. Trans.	2000	28		A309			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. 		
@D	Crasta, O.R.//Folkerts, O.//Fei, Z.//Mane, S.P.//Evans, C.//Martino-Catt, S.//Bricker, B.//Yu, G.//Du, L.//Sobral, B.W. 	Genome sequence of Brucella abortus vaccine strain S19 compared to virulent strains yields candidate virulence genes.	PLoS ONE	2008	3		e2193			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. 		
@D	Crawford, J.T.//Cave, M.D.//Bates, J.H. 	Evidence for plasmid-mediated restriction-modification in Mycobacterium avium intracellulare.	J. Gen. Microbiol.	1981	127		333-338			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. 		
@D	Crawford, M.A. et al. 	Genome Sequences of Multidrug-Resistant, Colistin-Susceptible and -Resistant Klebsiella pneumoniae Clinical Isolates from Pakistan.	Genome Announcements	2016	4		e01419-16			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. 		
@D	Cregg, J.M.//Nguyen, A.H.//Ito, J. 	DNA modification induced during infection of Bacillus subtilis by phage Phi3T.	Gene	1980	12		17-24			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. 		
@D	Cregg, J.M.//Stewart, C.R. 	EcoRI cleavage of DNA from Bacillus subtilis phage SPO1.	Virology	1978	85		601-605			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. 		
@D	Cress, B.F.//Erkert, K.A.//Barquera, B.//Koffas, M.A. 	Draft Genome Sequence of Pseudoalteromonas luteoviolacea Strain B (ATCC 29581).	Genome Announcements	2013	1		e0004813			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. 		
@D	Cress, B.F.//Greene, Z.R.//Linhardt, R.J.//Koffas, M.A. 	Draft Genome Sequence of Escherichia coli Strain ATCC 23506 (Serovar O10:K5:H4).	Genome Announcements	2013	1		e0004913			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. 		
@D	Cress, B.F.//Greene, Z.R.//Linhardt, R.J.//Koffas, M.A. 	Draft Genome Sequence of Escherichia coli Strain ATCC 23502 (Serovar O5:K4:H4).	Genome Announcements	2013	1		e0004613			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. 		
@D	Cress, B.F.//Linhardt, R.J.//Koffas, M.A. 	Draft Genome Sequence of Escherichia coli Strain Nissle 1917 (Serovar O6:K5:H1).	Genome Announcements	2013	1		e0004713			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. 		
@D	Criscuolo, A.//Chesneau, O.//Clermont, D.//Bizet, C. 	Draft Genome Sequence of the Fish Pathogen Flavobacterium columnare Genomovar III Strain PH-97028 (=CIP 109753).	Genome Announcements	2018	6		e00222-18			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. 		
@D	Criscuolo, A.//de la Blanchardiere, A.//Coeuret, S.//Passet, V.//Saguet-Rysanek, V.//Vergnaud, M.//Verdon, R.//Leclercq, A.//Lecuit, M.//Brisse, S. 	Draft Genome Sequence of Campylobacter coli Strain IPSID-1 Isolated from a Patient with Immunoproliferative Small Intestinal Disease.	Genome Announcements	2014	2		e00079-14			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. 		
@D	Croce, O.//Hugon, P.//Lagier, J.C.//Bibi, F.//Robert, C.//Azhar, E.I.//Raoult, D.//Fournier, P.E. 	Genome Sequence of Bacillus simplex Strain P558, Isolated from a Human Fecal Sample.	Genome Announcements	2014	2		e01241-14			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. 		
@D	Croce, O.//Robert, C.//Raoult, D.//Drancourt, M. 	Draft Genome Sequence of Mycobacterium vulneris DSM 45247T.	Genome Announcements	2014	2		e00370-14			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. 		
@D	Croce, O.//Robert, C.//Raoult, D.//Drancourt, M. 	Draft Genome Sequence of Mycobacterium mageritense DSM 44476T.	Genome Announcements	2014	2		e00354-14			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. 		
@D	Croce, O.//Robert, C.//Raoult, D.//Drancourt, M. 	Draft Genome Sequence of Mycobacterium asiaticum Strain DSM 44297.	Genome Announcements	2014	2		e00320-14			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. 		
@D	Croce, O.//Robert, C.//Raoult, D.//Drancourt, M. 	Draft Genome Sequence of Mycobacterium austroafricanum DSM 44191.	Genome Announcements	2014	2		e00317-14			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. 		
@D	Croce, O.//Robert, C.//Raoult, D.//Drancourt, M. 	Draft Genome Sequence of Mycobacterium cosmeticum DSM 44829.	Genome Announcements	2014	2		e00315-14			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. 		
@D	Croce, O.//Robert, C.//Raoult, D.//Drancourt, M. 	Draft Genome Sequence of Mycobacterium farcinogenes NCTC 10955.	Genome Announcements	2014	2		e00523-14			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. 		
@D	Crofts, T.S.//Wang, B.//Spivak, A.//Gianoulis, T.A.//Forsberg, K.J.//Gibson, M.K.//Johnsky, L.A.//Broomall, S.M.//Rosenzweig, C.N.//Skowronski, E.W.//Gibbons, H.S.//Sommer, M.O.A.//Dantas, G. 	Draft Genome Sequences of Three beta-Lactam-Catabolizing Soil Proteobacteria.<jour_book>Genome Announc.		2017	5		e00653-17			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. 		
@D	Crombie, A.T.//Emery, H.//McGenity, T.J.//Murrell, J.C. 	Draft Genome Sequences of Three Terrestrial Isoprene-Degrading Rhodococcus Strains.	Genome Announcements	2017	5		e01256-17			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. 		
@D	Crook, M.B.//Mitra, S.//Ane, J.M.//Sadowsky, M.J.//Gyaneshwar, P. 	Complete Genome Sequence of the Sesbania Symbiont and Rice Growth-Promoting Endophyte Rhizobium sp. Strain IRBG74.	Genome Announcements	2013	1		e00934-13			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. 		
@D	Crooks, C.//Palmer, J.M.//Lindner, D.L. 	Draft Genome Sequence of Burkholderia cepacia ATCC 17759, a Polyhydroxybutyrate-Co-Valerate Copolymer-Producing Bacterium.	Genome Announcements	2018	6		e00348-18			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. 		
@D	Crooks, P.A.//Tribe, M.J.//Pinney, R.J. 	Inhibition of bacterial DNA cytosine-5-methyltransferase by S-adenosyl-L-homocysteine and some related compounds.	J. Pharm. Pharmacol.	1984	36		85-89			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. 		
@D	Cross, K.L.//Chirania, P.//Xiong, W.//Beall, C.J.//Elkins, J.G.//Giannone, R.J.//Griffen, A.L.//Guss, A.M.//Hettich, R.L.//Joshi, S.S.//Mokrzan, E.M.//Martin, R.K.//Zhulin, I.B.//Leys, E.J.//Podar, M. 	Insights into the Evolution of Host Association through the Isolation and Characterization of a Novel Human Periodontal Pathobiont, Desulfobulbus oralis.	MBio	2018	9		e02061-17			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. 		
@D	Cross, S.H.//Meehan, R.R.//Nan, X.//Bird, A. 	A component of the transcriptional repressor MeCP1 shares a motif with DNA methyltransferase and HRX proteins.	Nat. Genet.	1997	16		256-259			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. 		
@D	Crossman, L.C. et al. 	A Commensal Gone Bad: Complete Genome Sequence of the Prototypical Enterotoxigenic Escherichia coli Strain H10407.	J. Bacteriol.	2010	192		5822-5831			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. 		
@D	Crossman, L.C. et al. 	The complete genome, comparative and functional analysis of Stenotrophomonas maltophilia reveals an organism heavily shielded by drug  resistance determinants.	Genome Biol.	2008	9		R74			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. 		
@D	Croucher, N.J. et al. 	Dominant Role of Nucleotide Substitution in the Diversification of Serotype 3 Pneumococci over Decades and during a Single Infection.	PLoS Genet.	2013	9		e1003868-100386			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. 		
@D	Croucher, N.J.//Coupland, P.G.//Stevenson, A.E.//Callendrello, A.//Bentley, S.D.//Hanage, W.P. 	Diversification of bacterial genome content through distinct mechanisms over different timescales.	Nat. Commun.	2014	5		5471			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. 		
@D	Croucher, N.J.//Walker, D.//Romero, P.//Lennard, N.//Paterson, G.K.//Bason, N.C.//Mitchell, A.M.//Quail, M.A.//Andrew, P.W.//Parkhill, J.//Bentley, S.D.//Mitchell, T.J. 	Role of conjugative elements in the evolution of the multidrug-resistant pandemic clone Streptococcus pneumoniaeSpain23F ST81.	J. Bacteriol.	2009	191		1480-1489			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. 		
@D	Crouzier, L.//Dubois, C.//Wengel, J.//Veedu, R.N. 	Cleavage and protection of locked nucleic acid-modified DNA by restriction endonucleases.	Bioorg. Med. Chem. Lett.	2012	22		4836-4838			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. 		
@D	Crovadore, J.//Calmin, G.//Chablais, R.//Cochard, B.//Lefort, F. 	Whole-Genome Sequence of Enteractinococcus helveticum sp. nov. Strain UASWS1574 Isolated from Industrial Used Waters.	Genome Announcements	2016	4		e00756-16			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. 		
@D	Crovadore, J.//Calmin, G.//Chablais, R.//Cochard, B.//Schulz, T.//Lefort, F. 	Whole-Genome Sequence of Pseudomonas graminis Strain UASWS1507, a Potential Biological Control Agent and Biofertilizer Isolated in Switzerland.	Genome Announcements	2016	4		e01096-16			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. 		
@D	Crovadore, J.//Calmin, G.//Chablais, R.//Cochard, B.//Schulz, T.//Lefort, F. 	Whole-Genome Sequence of Bradyrhizobium elkanii Strain UASWS1016, a Potential Symbiotic Biofertilizer for Agriculture.	Genome Announcements	2016	4		e01095-16			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. 		
@D	Crovadore, J.//Calmin, G.//Cochard, B.//Chablais, R.//Grizard, D.//Berthon, J.Y.//Lefort, F. 	Whole-Genome Sequence of Pseudomonas putida Strain UASWS0946, a Highly Ammonia-Tolerant Nitrifying Bacterium Isolated from Sewage Sludge Aerobic Granules.	Genome Announcements	2015	3		e01153-15			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. 		
@D	Crovadore, J.//Calmin, G.//Cochard, B.//Chablais, R.//Lefort, F. 	Whole-Genome Sequence of Bradyrhizobium elkanii Strain UASWS1015, a Highly Ammonia-Tolerant Nitrifying Bacterium.	Genome Announcements	2016	4		e00111-16			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. 		
@D	Crovadore, J.//Calmin, G.//Tonacini, J.//Chablais, R.//Baumgartner, A.//Schnyder, B.//Hodille, E.//Lefort, F. 	Whole-Genome Sequences of 15 Strains of Staphylococcus aureus subsp. aureus Isolated from Foodstuff and Human Clinical Samples.	Genome Announcements	2015	3		e00684-15			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. 		
@D	Crovadore, J.//Calmin, G.//Tonacini, J.//Chablais, R.//Schnyder, B.//Messelhausser, U.//Lefort, F. 	Whole-Genome Sequences of Seven Strains of Bacillus cereus Isolated from Foodstuff or Poisoning Incidents.	Genome Announcements	2016	4		e00435-16			We present here the whole shotgun genome sequences of seven strains of Bacillus cereus isolated from foodstuff samples or food poisoning incidents. 		
@D	Crovadore, J.//Cochard, B.//Calmin, G.//Chablais, R.//Schulz, T.//Lefort, F. 	Whole-Genome Sequence of Mesorhizobium hungaricum sp. nov. Strain UASWS1009, a Potential Resource for Agricultural and Environmental Uses.	Genome Announcements	2016	4		e01158-16			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. 		
@D	Crovadore, J.//Cochard, B.//Calmin, G.//Chablais, R.//Schulz, T.//Lefort, F. 	Whole-Genome Sequence of Pseudomonas xanthomarina Strain UASWS0955, a Potential Biological Agent for Agricultural and Environmental Uses.	Genome Announcements	2016	4		e01136-16			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. 		
@D	Crovadore, J.//Xu, S.//Chablais, R.//Cochard, B.//Lukito, D.//Calmin, G.//Lefort, F. 	Metagenome-Assembled Genome Sequence of Rhodopseudomonas palustris Strain ELI 1980, Commercialized as a Biostimulant.	Genome Announcements	2017	5		e00221-17			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. 		
@D	Crowe, S.A.//Hahn, A.S.//Morgan-Lang, C.//Thompson, K.J.//Simister, R.L.//Lliros, M.//Hirst, M.//Hallam, S.J. 	Draft Genome Sequence of the Pelagic Photoferrotroph Chlorobium phaeoferrooxidans.	Genome Announcements	2017	5		e01584-16			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. 		
@D	Crowley, S.//Bottacini, F.//Mahony, J.//van Sinderen, D. 	Complete Genome Sequence of Lactobacillus plantarum Strain 16, a Broad-Spectrum Antifungal-Producing Lactic Acid Bacterium.	Genome Announcements	2013	1		e00533-13			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. 		
@D	Cruz, A.K.//Kidane, G.//Pires, M.Q.//Rabinovitch, L.//Guaycurus, T.V.//Morel, C.M. 	An Sau3AI restriction endonuclease isoschizomer from Bacillus cereus.	FEBS Lett.	1984	173		99-102			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. 		
@D	Cruz, A.K.//Pires, M.Q.//Lima, V.G.//Morel, C.M. 	Restriction endonucleases from microorganisms isolated in Brazil: an isoschizomer of HaeIII from a thermophilic Bacillus sp.	Braz. J. Med. Biol. Res.	1989	22		1321-1328			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. 		
@D	Cruz-Morales, P.//Vijgenboom, E.//Iruegas-Bocardo, F.//Girard, G.//Yanez-Guerra, L.A.//Ramos-Aboites, H.E.//Pernodet, J.L.//Anne, J.//van Wezel, G.P.//Barona-Gomez, F. 	The genome sequence of Streptomyces lividans 66 reveals a novel tRNA-dependent peptide biosynthetic system within a metal-related genomic island.	Genome Biol. Evol.	2013	5		1165-1175			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. 		
@D	Csepregi, K.//Valasek, A.//Penzes, A.//Toth, Z.//Kiss, E.I.//Kerepesi, I.//Horvath, B.//Nagy, I.//Fekete, C. 	Draft Genome Sequence of an Efficient Antibiotic-Producing Industrial Strain of Saccharomonospora azurea, SZMC 14600.	J. Bacteriol.	2012	194		1263			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. 		
@D	Cserhati, M.//Kriszt, B.//Szoboszlay, S.//Toth, A.//Szabo, I.//Tancsics, A.//Nagy, I.//Horvath, B.//Nagy, I.//Kukolya, J. 	De Novo Genome Project of Cupriavidus basilensis OR16.	J. Bacteriol.	2012	194		2109-2110			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. 		
@D	Csirik, J.//Magyar, J.//Polner, G. 	A computer algorithm to determine the recognition site of restriction enzymes.	Comput. Appl. Biosci.	1987	3		245-246			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. 		
@D	Cuadros-Orellana, S.//Martin-Cuadrado, A.B.//Legault, B.//D'Auria, G.//Zhaxybayeva, O.//Papke, R.T.//Rodriguez-Valera, F. 	Genomic plasticity in prokaryotes: the case of the square haloarchaeon.	ISME J.	2007	1		235-245			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. 		
@D	Cuculich, P.S. 	Overexpression of E. coli EcoRI modification system enzymes.	The Nucleus	1996	75		8-10			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. 		
@D	Cue, D.//Hong, L.//Hanson, R.S.//Flickinger, M.C. 	Characterization of a restriction-modification system of the thermotolerant methylotroph Bacillus methanolicus.	Appl. Environ. Microbiol.	1996	62		1107-1111			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. 		
@D	Cue, D.//Lam, H.//Hanson, R.S.//Flickinger, M. 	Characterization of a Bacillus methanolicus restriction/modification system.	Abstr. Gen. Meet. Am. Soc. Microbiol.	1995	95		525			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. 		
@D	Cui, C.//Li, P.//Liu, G.//Tang, H.//Lin, K.//Luo, Q.//Liu, S.//Xu, P.//Liu, Y. 	Genome Sequence of Martelella sp. Strain AD-3, a Moderately Halophilic Polycyclic Aromatic Hydrocarbon-Degrading Bacterium.	Genome Announcements	2014	2		e01189-13			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. 		
@D	Cui, G.-Z.//Hong, W.//Zhang, J.//Li, W.-L.//Feng, Y.//Liu, Y.-J.//Cui, Q. 	Targeted gene engineering in Clostridium cellulolyticum H10 without methylation.	J. Microbiol. Methods	2012	89		201-208			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. 		
@D	Cui, X.X.//Davis, G. 	Mobile group II intron targeting: applications in prokaryotes and perspectives in eukaryotes.	Front. Biosci.	2007	12		4972-4985			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. 		
@D	Cui, Y.//Cheng, B.//Meng, Y.//Li, C.//Yin, H.//Xu, P.//Yang, C. 	Expression and functional analysis of two NhaD type antiporters from the halotolerant and alkaliphilic Halomonas sp. Y2.	Extremophiles	2016	20		631-639			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. 		
@D	Cui, Z.//Gao, W.//Li, Q.//Xu, G.//Zheng, L. 	Genome Sequence of the Polycyclic Aromatic Hydrocarbon-Degrading Bacterium Strain Marinobacter nanhaiticus D15-8WT.	Genome Announcements	2013	1		e00301-13			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. 		
@D	Cui, Z.//Xu, G.//Li, Q.//Gao, W.//Zheng, L. 	Genome Sequence of the Pyrene- and Fluoranthene-Degrading Bacterium Cycloclasticus sp. Strain PY97M.	Genome Announcements	2013	1		e00536-13			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. 		
@D	Cuiv, P.O.//Klaassens, E.S.//Durkin, A.S.//Harkins, D.M.//Foster, L.//McCorrison, J.//Torralba, M.//Nelson, K.E.//Morrison, M. 	Draft genome sequence of Turicibacter sanguinis PC909 isolated from human faeces.	J. Bacteriol.	2010	193		1288-1289			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. 		
@D	Culley, D.E.//Shi, L.//Reed, S.//Romme, M. 	Genetic and biochemical studies of the transformation barriers present in Shewanella oneidensis MR-1.	Abstr. Gen. Meet. Am. Soc. Microbiol.	2004	104		320			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. 		
@D	Cullik, A.//Pfeifer, Y.//Prager, R.//von Baum, H.//Witte, W. 	A novel IS26 structure surrounds blaCTX-M genes in different plasmids from German clinical Escherichia coli isolates.	J. Med. Microbiol.	2010	59		580-587			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. 		
@D	Cummings, D.J.//McNally, K.L.//Domenico, J.M.//Matsuura, E.T. 	The complete DNA sequence of the mitochondrial genome of Podospora anserina.	Curr. Genet.	1990	17		375-402			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. 		
@D	Cummings, M.//Adams, R.L.P. 	Cloning the pea DNA methylase cDNA.	Biochem. Soc. Trans.	1992	21		7s			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. 		
@D	Cunnac, S.//Bolot, S.//Forero, S.N.//Ortiz, E.//Szurek, B.//Noel, L.D.//Arlat, M.//Jacques, M.A.//Gagnevin, L.//Carrere, S.//Nicole, M.//Koebnik, R. 	High-Quality Draft Genome Sequences of Two Xanthomonas citri pv. malvacearum Strains.	Genome Announcements	2013	1		e00674-13			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. 		
@D	Cuppels, D.A.//Van Etten, J.L.//Lambrecht, P.//Vidaver, A.K. 	Survey of phytopathogenic pseudomonads for a restriction and modification system active on the double-stranded ribonucleic acid phage Phi-6.	Curr. Microbiol.	1981	5		247-249			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. 		
@D	Curcio, M.J.//Belfort, M. 	Retrohoming: cDNA-mediated mobility.	Cell	1996	84		9-12			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. 		
@D	Cusick, K.D.//Dale, J.R.//Little, B.J.//Biffinger, J.C. 	Draft Genome Sequences of Four Alteromonas macleodii Strains Isolated from Copper Coupons and Grown Long-Term at Elevated Copper Levels.	Genome Announcements	2016	4		e01311-16			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. 		
@D	Cymerman, I.A.//Obarska, A.//Skowronek, K.J.//Lubys, A.//Bujnicki, J.M. 	Identification of a new subfamily of HNH nucleases and experimental characterization of a representative member, HphI restriction endonuclease.	Proteins	2006	65		867-876			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. 		
@D	Czajkowski, R.//van der Wolf, J.M. 	Draft Genome Sequence of the Biocontrol Strain Serratia plymuthica A30, Isolated  from Rotting Potato Tuber Tissue.	J. Bacteriol.	2012	194		6999-7000			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. 		
@D	Czank, A.//Hauselmann, R.//Page, A.W.//Leonhardt, H.//Bestor, T.H.//Schafner, W.//Hergersberg, M. 	Expression in mammalian cells of a cloned gene encoding murine DNA methyltransferase.	Gene	1991	109		259-263			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. 		
@D	Czapinska, H.//Kowalska, M.//Zagorskaite, E.//Manakova, E.//Slyvka, A.//Xu, S.Y.//Siksnys, V.//Sasnauskas, G.//Bochtler, M. 	Activity and structure of EcoKMcrA.	Nucleic Acids Res.	2018	46		9829-9841			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. 		
@D	D'Afonseca, V.//Prosdocimi, F.//Dorella, F.A.//Pacheco, L.G.//Moraes, P.M.//Pena, I.//Ortega, J.M.//Teixeira, S.//Oliveira, S.C.//Coser, E.M.//Oliveira, L.M.//Correa-de-Oliveira, G.//Meyer, R.//Miyoshi, A.//Azevedo, V. 	Survey of genome organization and gene content of Corynebacterium pseudotuberculosis.	Microbiol. Res.	2010	165		312-320			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. 		
@D	D'Agostino, N.//Sorrentino, R.//Scotti, R.//Salzano, M.//Aurilia, V.//Zaccardelli, M. 	Draft Genome Sequence of the Plant Growth-Promoting Rhizobacterium Pseudomonas fluorescens Strain CREA-C16 Isolated from Pea (Pisum sativum L.) Rhizosphere.	Genome Announcements	2017	5		e01456-16			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. 		
@D	D'Andrea, M.M.//Giani, T.//Henrici, De.A.L.//Ciacci, N.//Gniadkowski, M.//Miriagou, V.//Torricelli, F.//Rossolini, G.M. 	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.	Genome Announcements	2016	4		e01702-15			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. 		
@D	D'Angelo, T.//Oshone, R.//Abebe-Akele, F.//Simpson, S.//Morris, K.//Thomas, W.K.//Tisa, L.S. 	Permanent Draft Genome Sequence of Frankia sp. Strain BR, a Nitrogen-Fixing Actinobacterium Isolated from the Root Nodules of Casuarina equisetifolia.	Genome Announcements	2016	4		e01000-16			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. 		
@D	D'Angelo, T.//Oshone, R.//Abebe-Akele, F.//Simpson, S.//Morris, K.//Thomas, W.K.//Tisa, L.S. 	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.	Genome Announcements	2016	4		e00660-16			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. 		
@D	D'Arcy, A.//Brown, R.S.//Zabeau, M.//van Resandt, R.W.//Winkler, F.K. 	Purification and crystallization of the EcoRV restriction endonuclease.	J. Biol. Chem.	1985	260		1987-1990			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. 		
@D	D'Argenio, V.//Petrillo, M.//Cantiello, P.//Naso, B.//Cozzuto, L.//Notomista, E.//Paolella, G.//Di Donato, A.//Salvatore, F. 	De Novo Sequencing and Assembly of the Whole Genome of Novosphingobium sp. Strain PP1Y.	J. Bacteriol.	2011	193		4296			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. 		
@D	D'Auria, G.//Dzunkova, M.//Moya, A.//Tomaska, M.//Kolosta, M.//Kmet, V. 	Genome Sequence of Lactobacillus plantarum 19L3, a Strain Proposed as a Starter Culture for Slovenska Bryndza Ovine Cheese.	Genome Announcements	2014	2		e00292-14			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. 		
@D	D'Auria, G.//Galan, J.C.//Rodriguez-Alcayna, M.//Moya, A.//Baquero, F.//Latorre, A. 	Complete Genome Sequence of Acidaminococcus intestini RYC-MR95, a Gram-Negative Bacterium from the Phylum Firmicutes.	J. Bacteriol.	2011	193		7008-7009			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. 		
@D	D'Auria, G.//Torrents, E.//Luquin, M.//Comas, I.//Julian, E. 	Draft Genome Sequence of Mycobacterium brumae ATCC 51384.	Genome Announcements	2016	4		e00237-16			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. 		
@D	D'haeseleer, P.//Johnson, S.L.//Davenport, K.W.//Chain, P.S.//Schoeniger, J.//Ray, D.//Sinha, A.//Williams, K.P.//Pena, J.//Branda, S.S.//El-Etr, S. 	Genome Sequence of the Historical Clinical Isolate Burkholderia pseudomallei PHLS 6.	Genome Announcements	2016	4		e00649-16			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. 		
@D	D'Souza, D.R.//Morgan, R.D.//Parashar, V.//Capalash, N.//Sharma, P. 	Characterization of BflI - a thermostable, Co++-requiring isoschizomer of BsiYI from Anoxybacillus flavithermus.	World J. Microbiol. Biotechnol.	2004	20		593-598			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. 		
@D	da Gama, A.M.//de Almeida, L.G.//Yamane, T.//Spira, B. 	Two Draft Genome Sequences of Chromobacterium violaceum Isolates from the Rio Negro.	Genome Announcements	2018	6		e01348-17			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. 		
@D	da Mota, F.F.//Vollu, R.E.//Jurelevicius, D.//Seldin, L. 	Whole-Genome Sequence of Rummeliibacillus stabekisii Strain PP9 Isolated from Antarctic Soil.	Genome Announcements	2016	4		e00416-16			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). 		
@D	da Piedade, I.//Skive, B.//Christensen, H.//Bojesen, A.M. 	Draft Genome Sequence of Streptococcus equi subsp. zooepidemicus Strain S31A1, Isolated from Equine Infectious Endometritis.	Genome Announcements	2013	1		e00683-13			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. 		
@D	da Silva, A.C.R. et al. 	Comparison of the genomes of two Xanthomonas pathogens with differing host specificities.	Nature	2002	417		459-463			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. 		
@D	da Silva, F.D.//Lima, A.R.//Moraes, P.H.//Siqueira, A.S.//Dall'Agnol, L.T.//Barauna, A.R.//Martins, L.C.//Oliveira, K.G.//de Lima, C.P.//Nunes, M.R.//Vianez-Junior, J.L.//Goncalves, E.C. 	Draft Genome Sequence of Limnobacter sp. Strain CACIAM 66H1, a Heterotrophic Bacterium Associated with Cyanobacteria.	Genome Announcements	2016	4		e00399-16			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. 		
@D	Da Silva, S.A.C.//Rodrigues, J. 	Draft Genome Sequence of Shiga Toxin-Producing Escherichia coli Strain D92/09.	Genome Announcements	2015	3		e00805-15			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. 		
@D	Daas, M.S.//Rosana, A.R.R.//Acedo, J.Z.//Douzane, M.//Nateche, F.//Kebbouche-Gana, S.//Vederas, J.C. 	Insights into the draft genome sequence of bioactives-producing Bacillus thuringiensis DNG9 isolated from Algerian soil-oil slough.	Standards in Genomic Sciences	2018	13		25			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. 		
@D	Daas, M.S.//Rosana, A.R.R.//Acedo, J.Z.//Douzane, M.//Nateche, F.//Kebbouche-Gana, S.//Vederas, J.C. 	Draft Genome Sequence of Bacillus paralicheniformis F47, Isolated from an Algerian Salty Lake.	Genome Announcements	2018	6		e00190-18			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. 		
@D	Daas, M.S.//Rosana, A.R.R.//Acedo, J.Z.//Nateche, F.//Kebbouche-Gana, S.//Vederas, J.C.//Case, R.J. 	Draft Genome Sequences of Bacillus cereus E41 and Bacillus anthracis F34 Isolated from Algerian Salt Lakes.	Genome Announcements	2017	5		e00383-17			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. 		
@D	Dabe, E.C.//Kohn, A.B.//Bobkova, Y.//Kocot, K.//Citarella, M.//Bostwick, C.J.//Winters, G.C.//Swalla, B.J.//Moroz, L.L. 	Epigenomic Signatures in Basal Metazoans: DNA Methyltransferase in Pleurobrachia bachei.	Integr. Comp. Biol.	2013	53		E273			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. 		
@D	Daboussi, F. et al. 	Chromosomal context and epigenetic mechanisms control the efficacy of genome editing by rare-cutting designer endonucleases.	Nucleic Acids Res.	2012	40		6367-6379			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. 		
@D	Dabrazhynetskaya, A.//Soika, V.//Volokhov, D.//Simonyan, V.//Chizhikov, V. 	Genome Sequence of Mycoplasma hyorhinis Strain DBS 1050.	Genome Announcements	2014	2		e00127-14			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. 		
@D	Dabul, A.N.//Kos, V.N.//Gilmore, M.S.//Camargo, I.L. 	Draft Genome Sequence of Methicillin-Resistant Staphylococcus aureus Strain SA16, Representative of an Endemic Clone from a Brazilian Hospital.	Genome Announcements	2013	1		e00754-13			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. 		
@D	Daccord, A.//Ceccarelli, D.//Burrus, V. 	Integrating conjugative elements of the SXT/R391 family trigger the excision and drive the mobilization of a new class of Vibrio genomic islands.	Mol. Microbiol.	2010	78		576-588			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. 		
@D	Daebeler, A.//Herbold, C.W.//Vierheilig, J.//Sedlacek, C.J.//Pjevac, P.//Albertsen, M.//Kirkegaard, R.H.//de la Torre, J.R.//Daims, H.//Wagner, M. 	Cultivation and Genomic Analysis of 'Candidatus Nitrosocaldus islandicus,' an Obligately Thermophilic, Ammonia-Oxidizing Thaumarchaeon from a Hot Spring Biofilm in Graendalur Valley, Iceland.	Front. Microbiol.	2018	9		193			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. 		
@D	Dahai, T.//Ando, S.//Takasaki, Y.//Tadano, J. 	Site-directed mutagenesis of restriction endonuclease HindIII.	Biosci. Biotechnol. Biochem.	1999	63		1703-1707			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. 		
@D	Dahlem, T.J.//Hoshijima, K.//Jurynec, M.J.//Gunther, D.//Starker, C.G.//Locke, A.S.//Weis, A.M.//Voytas, D.F.//Grunwald, D.J. 	Simple Methods for Generating and Detecting Locus-Specific Mutations Induced with TALENs in the Zebrafish Genome.	PLoS Genet.	2012	8		E1002861			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. 		
@D	Dahms, P.A.//Martin, A.L.//Ganz, H.H.//Eisen, J.A.//Coil, D.A. 	Draft Genome Sequence of Propionibacterium avidum Strain UCD-PD2 Isolated from a  Feline Anal Sac.	Genome Announcements	2017	5		e00034-17			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. 		
@D	Dai, J.//Wang, S.//Guerlebeck, D.//Laturnus, C.//Guenther, S.//Shi, Z.//Lu, C.//Ewers, C. 	Suppression subtractive hybridization identifies an autotransporter adhesin gene  of E. coli IMT5155 specifically associated with avian pathogenic Escherichia coli  (APEC).	BMC Microbiol.	2010	10		236			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. 		
@D	Dai, K.//Jin, J.//Wen, Y.//Wen, X.//He, L.//Cao, S.//Huang, X.//Wu, R.//Zhao, Q. 	Complete Genome Sequence of Highly Virulent Haemophilus parasuis Serotype 11 Strain SC1401.	Genome Announcements	2016	4		e00628-16			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. 		
@D	Dai, L.//Chai, D.//Gu, S.Q.//Gabel, J.//Noskov, S.Y.//Blocker, F.J.//Lambowitz, A.M.//Zimmerly, S. 	A Three-Dimensional Model of a Group II Intron RNA and Its Interaction with the Intron-Encoded Reverse Transcriptase.	Mol. Cell	2008	30		472-485			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. 		
@D	Dai, Q.//Restrepo, B.I.//Porcella, S.F.//Raffel, S.J.//Schwan, T.G.//Barbour, A.G. 	Antigenic variation by Borrelia hermsii occurs through recombination between extragenic repetitive elements on linear plasmids.	Mol. Microbiol.	2006	60		1329-1343			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. 		
@D	Dai, W.//Zhu, Y.//Wang, X.//Sakenova, N.//Yang, Z.//Wang, H.//Li, G.//He, J.//Huang, D.//Cai, Y.//Guo, W.//Wang, Q.//Feng, T.//Fan, Q.//Zheng, T.//Han, A. 	Draft Genome Sequence of the Bacterium Comamonas aquatica CJG.	Genome Announcements	2016	4		e01186-16			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. 		
@D	Dai, Y.//Ni, Z.F.//Dai, J.//Zhao, T.//Sun, Q.X. 	Isolation and expression analysis of genes encoding DNA methyltransferase in wheat (Triticum aestivum L.).	Biochim. Biophys. Acta	2005	1729		118-125			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. 		
@D	Daifuku, T.//Yoshida, T.//Kitamura, T.//Kawaichi, S.//Inoue, T.//Nomura, K.//Yoshida, Y.//Kuno, S.//Sako, Y. 	Variation of the Virus-Related Elements within Syntenic Genomes of the Hyperthermophilic Archaeon Aeropyrum.	Appl. Environ. Microbiol.	2013	79		5891-5898			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. 		
@D	Daigle, K.//Shenoy, S.//Ehrlich, K.//Gehrke, C.//Ehrlich, M. 	Restriction at mismatched sites in DNA.	Fed. Proc.	1986	45		1783			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. 		
@D	Daiyasu, H.//Komori, K.//Sakae, S.//Ishino, Y.//Toh, H. 	Hjc resolvase is a distantly related member of the type II restriction endonuclease family.	Nucleic Acids Res.	2000	28		4540-4543			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. 		
@D	Dale, C.J.H.//Moses, E.K.//Ong, C.C.//Morrow, C.J.//Reed, M.B.//Hasse, D.//Strugnell, R.A. 	Identification and sequencing of the groE operon and flanking genes of Lawsonia intracellularis: use in phylogeny.	Microbiology	1998	144		2073-2084			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. 		
@D	Dalgaard, J.Z. 	Mobile introns and inteins: friend or foe?	Trends Genet.	1994	10		306-307			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. 		
@D	Dalgaard, J.Z.//Garrett, R.A. 	Protein-coding introns from the 23S rRNA-encoding gene form stable circles in the hyperthermophilic archaeon Pyrobaculum organotrophum.	Gene	1992	121		103-110			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. 		
@D	Dalgaard, J.Z.//Garrett, R.A.//Belfort, M. 	A site-specific endonuclease encoded by a typical archaeal intron.	Proc. Natl. Acad. Sci. U. S. A.	1993	90		5414-5417			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. 		
@D	Dalgaard, J.Z.//Garrett, R.A.//Belfort, M. 	Purification and characterization of two forms of I-DmoI, a thermophilic site-specific endonuclease encoded by an archaeal intron.	J. Biol. Chem.	1994	269		28885-28892			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. 		
@D	Dalgaard, J.Z.//Klar, A.J.//Moser, M.J.//Holley, W.R.//Chatterjee, A.//Mian, I.S. 	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.	Nucleic Acids Res.	1997	25		4626-4638			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. 		
@D	Dalgaard, J.Z.//Silva, G.H.//Belfort, M.//Van Roey, P. 	Crystallization and preliminary crystallographic analysis of the archaeal intron-encoded endonuclease I-DmoI.	Acta Crystallogr. D Biol. Crystallogr.	1998	54		1435-1436			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. 		
@D	Dalhoff, C.//Lukinavicius, G.//Klimasauskas, S.//Weinhold, E. 	Direct transfer of extended groups from synthetic cofactors by DNA methyltransferases.	Nat. Chem. Biol.	2006	2		31-32			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. 		
@D	Dalhoff, C.//Lukinavicius, G.//Klimasauskas, S.//Weinhold, E. 	Synthesis of S-adenosyl-L-methionine analogs and their use for sequence-specific transalkylation of DNA by methyltransferases.	Nat. Protoc.	2006	1		1879-1886			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. 		
@D	Dalia, A.B.//Lazinski, D.W.//Camilli, A. 	Characterization of Undermethylated Sites in Vibrio cholerae.	J. Bacteriol.	2013	195		2389-2399			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. 		
@D	Daligault, H. et al. 	Complete genome sequence of Haliscomenobacter hydrossis type strain (O).	Standards in Genomic Sciences	2011	4		352-360			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. 		
@D	Daligault, H.E. et al. 	Genome Assembly of Shigella flexneri ATCC 12022, a Quality Control Reference Strain.	Genome Announcements	2014	2		e01052-14			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. 		
@D	Daligault, H.E. et al. 	Twenty Whole-Genome Bacillus sp. Assemblies.	Genome Announcements	2014	2		e00958-14			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. 		
@D	Daligault, H.E. et al. 	Genome Assembly of Methicillin-Resistant Quality Control Strain Staphylococcus aureus CDC73-57501 (ATCC 29247).	Genome Announcements	2014	2		e00961-14			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. 		
@D	Daligault, H.E. et al. 	Draft Genomes for Eight Burkholderia mallei Isolates from Turkey.	Genome Announcements	2016	4		e01234-15			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. 		
@D	Daligault, H.E. et al. 	Whole-Genome Assemblies of 56 Burkholderia Species.	Genome Announcements	2014	2		e01106-14			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. 		
@D	Daligault, H.E. et al. 	Whole-Genome Yersinia sp. Assemblies from 10 Diverse Strains.	Genome Announcements	2014	2		e01055-14			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. 		
@D	Daligault, H.E.//Davenport, K.W.//Minogue, T.D.//Bishop-Lilly, K.A.//Bruce, D.C.//Chain, P.S.//Coyne, S.R.//Frey, K.G.//Jaissle, J.//Koroleva, G.I.//Ladner, J.T.//Li, P.E.//Meincke, L.//Munk, A.C.//Palacios, G.F.//Redden, C.L.//Johnson, S.L. 	Complete Genome Assembly of Corynebacterium sp. Strain ATCC 6931.	Genome Announcements	2014	2		e01074-14			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. 		
@D	Daligault, H.E.//Davenport, K.W.//Minogue, T.D.//Bishop-Lilly, K.A.//Bruce, D.C.//Chain, P.S.//Coyne, S.R.//Frey, K.G.//Jaissle, J.//Koroleva, G.I.//Ladner, J.T.//Lo, C.C.//Meincke, L.//Munk, A.C.//Palacios, G.F.//Redden, C.L.//Johnson, S.L. 	Draft Genome Assembly of Klebsiella pneumoniae Type Strain ATCC 13883.	Genome Announcements	2014	2		e00939-14			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. 		
@D	Daligault, H.E.//Davenport, K.W.//Minogue, T.D.//Bishop-Lilly, K.A.//Bruce, D.C.//Chain, P.S.//Coyne, S.R.//Frey, K.G.//Jaissle, J.//Koroleva, G.I.//Ladner, J.T.//Lo, C.C.//Meincke, L.//Munk, C.//Palacios, G.F.//Redden, C.L.//Johnson, S.L. 	Complete Genome Assembly of a Quality Control Reference Isolate, Moraxella catarrhalis Strain ATCC 25240.	Genome Announcements	2014	2		e00938-14			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. 		
@D	Daligault, H.E.//Davenport, K.W.//Minogue, T.D.//Bishop-Lilly, K.A.//Bruce, D.C.//Chain, P.S.//Coyne, S.R.//Frey, K.G.//Jaissle, J.//Koroleva, G.I.//Ladner, J.T.//Lo, C.C.//Meincke, L.//Munk, C.//Palacios, G.F.//Redden, C.L.//Johnson, S.L. 	Draft Genome Assembly of Bordetella bronchiseptica ATCC 10580, a Historical Canine Clinical Isolate.	Genome Announcements	2014	2		e00916-14			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. 		
@D	Daligault, H.E.//Davenport, K.W.//Minogue, T.D.//Broomall, S.M.//Bruce, D.C.//Chain, P.S.//Coyne, S.R.//Gibbons, H.S.//Jaissle, J.//Lo, C.C.//Meincke, L.//Munk, A.C.//Rosenzweig, C.N.//Johnson, S.L. 	Draft Genome Assembly of Ralstonia pickettii Type Strain K-288 (ATCC 27853).	Genome Announcements	2014	2		e00973-14			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. 		
@D	Daligault, H.E.//Davenport, K.W.//Minogue, T.D.//Broomall, S.M.//Bruce, D.C.//Chain, P.S.//Coyne, S.R.//Gibbons, H.S.//Jaissle, J.//Rosenzweig, C.N.//Scholz, M.//Teshima, H.//Johnson, S.L. 	Genome Assembly of Serratia marcescens Type Strain ATCC 13880.	Genome Announcements	2014	2		e00967-14			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. 		
@D	Dall'Acqua, W.//Carter, P. 	Substrate-assisted catalysis: Molecular basis and biological significance.	Protein Sci.	2000	9		1-9			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. 		
@D	Dall'Agnol, H.//Nancucheo, I.//Johnson, D.B.//Oliveira, R.//Leite, L.//Pylro, V.S.//Holanda, R.//Grail, B.//Carvalho, N.//Nunes, G.L.//Tzotzos, G.//Fernandes, G.R.//Dutra, J.//Orellana, S.C.//Oliveira, G. 	Draft Genome Sequence of 'Acidibacillus ferrooxidans' ITV01, a Novel Acidophilic  Firmicute Isolated from a Chalcopyrite Mine Drainage Site in Brazil.	Genome Announcements	2016	4		e01748-15			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. 		
@D	Dall'Agnol, R.F.//Costa, M.R.//Ribeiro, R.A.//Delamuta, J.R.//Chueire, L.M.//Hungria, M. 	Genome Sequence of Paraburkholderia nodosa Strain CNPSo 1341, a N2-Fixing Symbiont of the Promiscuous Legume Phaseolus vulgaris.	Genome Announcements	2016	4		e01073-16			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. 		
@D	Dalmasso, C.//Oger, P.//Courtine, D.//Georges, M.//Takai, K.//Maignien, L.//Alain, K. 	Complete Genome Sequence of the Hyperthermophilic and Piezophilic Archeon Thermococcus piezophilus CDGST, Able To Grow under Extreme Hydrostatic Pressures.	Genome Announcements	2016	4		e00610-16			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. 		
@A	Daly, C.//Fitzgerald, G. 		Mechanisms of bacteriophage insensitivity in the lactic streptococci.			Ferretti, J.J.//Curtiss, R.//III 		Streptococcal Genetics				Washington, DC	American Society for Microbiology	1987		0		259-268									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. 		
@D	Daly, C.//Fitzgerald, G.F.//Davis, R. 	Biotechnology of lactic acid bacteria with special reference to bacteriophage resistance.	Antonie Van Leeuwenhoek	1996	70		99-110			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. 		
@D	Daly, M.J.//Gaidamakova, E.K.//Matrosova, V.Y.//Vasilenko, A.//Zhai, M.//Leapman, R.D.//Lai, B.//Ravel, B.//Li, S.M.//Kemner, K.M.//Fredrickson, J.K. 	Protein Oxidation Implicated as the Primary Determinant of Bacterial Radioresistance.	PLoS Biology	2007	5		e92			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. 		
@D	Dam, B.//Kube, M.//Dam, S.//Reinhardt, R.//Liesack, W. 	Complete Sequence Analysis of Two Methanotroph-Specific repABC-Containing Plasmids from Methylocystis sp. Strain SC2.	Appl. Environ. Microbiol.	2012	78		4373-4379			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. 		
@D	Damelin, M.//Bestor, T.H. 	Biological functions of DNA methyltransferase 1 require its methyltransferase activity.	Mol. Cell. Biol.	2007	27		3891-3899			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. 		
@D	Danaher, R.//Stein, D.C. 	Characterization of a restriction enzyme isolated from a hydrothermal vent community bacterium, Hyphomonas jannaschiana.	Abstr. Gen. Meet. Am. Soc. Microbiol.	1988	88		213			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. 		
@A	Danaher, R.//Stein, D.C. 		Characterization of a restriction endonuclease and the cloning of its corresponding DNA methylase from the thermal vent bacterium Hyphomonas jannaschiana.			 		Abstr. 1st Intl. Symp. Marine Mol. Biol.				Baltimore, MD	Center Marine Biotechnoogy	1988		0		25									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. 		
@D	Danaher, R.J.//Stein, D.C. 	Expression of cloned restriction and modification genes, hjaIRM from Hyphomonas jannaschiana in Escherichia coli.	Gene	1990	89		129-133			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. 		
@D	Dandare, S.U.//Skvortsov, T.//Arkhipova, K.//Allen, C.C.R. 	Draft Genome Sequence of Rhodococcus sp. Strain NCIMB 12038, a Naphthalene-Degrading Bacterium.	Genome Announcements	2018	6		e01420-17			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. 		
@D	Dandekar, T.//Huynen, M.//Regula, J.T.//Ueberle, B.//Zimmermann, C.U.//Andrade, M.A.//Doerks, T.//Sanchez-Pulido, L.//Snel, B.//Suyama, M.//Yuan, Y.P.//Herrmann, R.//Bork, P. 	Re-annotating the Mycoplasma pneumoniae genome sequence: adding value, function and reading frames.	Nucleic Acids Res.	2000	28		3278-3288			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. 		
@D	Dang, H.T.//Yotsumoto, K.//Enomoto, K. 	Draft Genome Sequence of Violacein-Producing Marine Bacterium Pseudoalteromonas sp. 520P1.	Genome Announcements	2014	2		e01346-14			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. 		
@D	Daniel, A.S.//Fuller-Pace, F.V.//Legge, D.M.//Murray, N.E. 	Distribution and diversity of hsd genes in Escherichia coli and other enteric bacteria.	J. Bacteriol.	1988	170		1775-1782			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. 		
@D	Daniel, D.S.//Gan, H.M.//Lee, S.M.//Dykes, G.A.//Rahman, S. 	Draft Genome Sequences of Six Enterococcus faecalis Strains Isolated from Malaysian Clinical and Environmental Origins.	Genome Announcements	2017	5		e00553-17			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. 		
@D	Daniel, J.J.//Givan, S.A.//Brun, Y.V.//Brown, P.J. 	Draft Genome Sequence of Prosthecomicrobium hirschii ATCC 27832T.	Genome Announcements	2015	3		e01355-15			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. 		
@D	Daniels, J.S.//Gates, K.S. 	Specificity of DNA cleavage by the type IIs restriction enzyme, HphI.	ACS Abstracts	1994	208		66			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. 		
@D	Daniels, L.E.//Wood, K.M.//Scott, D.J.//Halford, S.E. 	Subunit assembly for DNA cleavage by restriction endonuclease SgrAI.	J. Mol. Biol.	2003	327		579-591			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. 		
@D	Daniels, L.L.//Wais, A.C. 	Restriction and modification of halophage S45 in Halobacterium.	Curr. Microbiol.	1984	10		133-136			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. 		
@D	Danilevich, V.N.//Livshits, V.A. 	The plasmid carrying a temperature-sensitive mutation in the DNA-methylase gene of the PstI system: Effect on host cells at nonpermissive temperature.	Genetika	1999	35		574-586			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. 		
@D	Danin-Poleg, Y.//Elgavish, S.//Raz, N.//Efimov, V.//Kashi, Y. 	Genome Sequence of the Pathogenic Bacterium Vibrio vulnificus Biotype 3.	Genome Announcements	2013	1		e00136-13			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. 		
@D	Danin-Poleg, Y.//Raz, N.//Roig, F.J.//Amaro, C.//Kashi, Y. 	Draft Genome Sequence of Environmental Bacterium Vibrio vulnificus CladeA-yb158.	Genome Announcements	2015	3		e00754-15			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. 		
@D	Danish-Daniel, M.//Gan, H.Y.//Gan, H.M.//Saari, N.A.//Usup, G. 	Genome Sequence of Nitratireductor basaltis Strain UMTGB225, a Marine Bacterium Isolated from a Green Barrel Tunicate in Bidong Island, Malaysia.	Genome Announcements	2014	2		e01015-14			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. 		
@D	Danish-Daniel, M.//Ming, G.H.//Mohd, N.M.E.//Sung, Y.Y.//Usup, G. 	Genome Sequence of Bacillus sp. Strain UMTAT18 Isolated from the Dinoflagellate Alexandrium tamiyavanichii Found in the Straits of Malacca.	Genome Announcements	2016	4		e01106-16			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. 		
@D	Danna, K.//Nathans, D. 	Specific cleavage of simian virus 40 DNA by restriction endonuclease of Hemophilus influenzae.	Proc. Natl. Acad. Sci. U. S. A.	1971	68		2913-2917			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. 		
@D	Danna, K.J. 	Daniel Nathans.	Proc. Amer. Phil. Soc.	2010	154		338-354			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." 		
@D	Danna, K.J.//Nathans, D. 	Bidirectional replication of simian virus 40 DNA.	Proc. Natl. Acad. Sci. U. S. A.	1972	69		3097-3100			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. 		
@D	Dannheim, H.//Riedel, T.//Neumann-Schaal, M.//Bunk, B.//Schober, I.//Sproer, C.//Chibani, C.M.//Gronow, S.//Liesegang, H.//Overmann, J.//Schomburg, D. 	Manual curation and reannotation of the genomes of Clostridium difficile 630Deltaerm and C. difficile 630.	J. Med. Microbiol.	2017	66		286-293			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. 		
@D	Dantoft, S.H.//Bielak, E.M.//Seo, J.G.//Chung, M.J.//Jensen, P.R. 	Complete Genome Sequence of Pediococcus pentosaceus Strain SL4.	Genome Announcements	2013	1		e01106-13			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. 		
@D	Danzitz, M.J. 	Analysis of a protein: DNA interface; the effect of altered DNA substrates on EcoRI methylase function.	Diss. Abstr.	1993	53		5180B			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.
 
 		
@D	Danzitz, M.J.//Reich, N.O. 	Investigations of EcoRI methylase contacts with its DNA substrate.	ACS Abstracts	1988	196		95			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). 		
@D	Danzitz, M.J.//Reich, N.O. 	Characterization of a protein-DNA interface:  DNA substrate functionalties important for EcoRI methylase specificity.	J. Cell Biochem. Suppl.	1989	13D		84			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. 		
@D	Dar, M.E.//Bhagwat, A.S. 	Mechanism of expression of DNA repair gene vsr, an Escherichia coli gene that overlaps the DNA cystosine methylase gene, dcm.	Mol. Microbiol.	1993	9		823-833			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. 		
@D	Darii, M.V.//Cherepanova, N.A.//Subach, O.M.//Kirsanova, O.V.//Rasko, T.//Slaska-Kiss, K.//Kiss, A.//Deville-Bonne, D.//Reboud-Ravaux, M.//Gromova, E.S. 	Mutational analysis of the CG recognizing DNA methyltransferase SssI: Insight into enzyme-DNA interactions.	Biochim. Biophys. Acta	2009	1794		1654-1662			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. 		
@D	Darii, M.V.//Kirsanova, O.V.//Drutsa, V.L.//Kochetkov, S.N.//Gromova, E.S. 	Isolation and site-directed mutagenesis of DNA methyltransferase SssI.	Mol. Biol. (Mosk)	2007	41		110-117			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. 		
@D	Darmon, E.//Leach, D.R.F. 	Bacterial Genome Instability.	Microbiol. Mol. Biol. Rev.	2014	78		1-39			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. 		
@D	Darrasse, A.//Bolot, S.//Serres-Giardi, L.//Charbit, E.//Boureau, T.//Fisher-Le, S.M.//Briand, M.//Arlat, M.//Gagnevin, L.//Koebnik, R.//Noel, L.D.//Carrere, S.//Jacques, M.A. 	High-Quality Draft Genome Sequences of Xanthomonas axonopodis pv. glycines Strains CFBP 2526 and CFBP 7119.	Genome Announcements	2013	1		e01036-13			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. 		
@D	Dartois, V.//De Backer, O.//Colson, C. 	Sequence of the Salmonella typhimurium StyLT1 restriction-modification genes: homologies with EcoP1 and EcoP15 type-III R-M systems and presence of helicase domains.	Gene	1993	127		105-110			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. 		
@D	Darzi, Y.//Jiao, Y.//Hasegawa, M.//Moon, H.//Nunez, G.//Inohara, N.//Raes, J. 	The Genomic Sequence of the Oral Pathobiont Strain NI1060 Reveals Unique Strategies for Bacterial Competition and Pathogenicity.	PLoS ONE	2016	11		E0158866			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. 		
@D	Das, A.//Panda, A.//Singh, D.//Chandrababunaidu, M.M.//Mishra, G.P.//Bhan, S.//Adhikary, S.P.//Tripathy, S. 	Deciphering the Genome Sequences of the Hydrophobic Cyanobacterium Scytonema tolypothrichoides VB-61278.	Genome Announcements	2015	3		e00228-15			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. 		
@D	Das, S.//Pettersson, B.M.//Behra, P.R.//Mallick, A.//Cheramie, M.//Ramesh, M.//Shirreff, L.//DuCote, T.//Dasgupta, S.//Ennis, D.G.//Kirsebom, L.A. 	Extensive genomic diversity among Mycobacterium marinum strains revealed by whole genome sequencing.	Sci. Rep.	2018	8		12040			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. 		
@D	Das, S.//Pettersson, B.M.//Behra, P.R.//Ramesh, M.//Dasgupta, S.//Bhattacharya, A.//Kirsebom, L.A. 	The Mycobacterium phlei genome: expectations and surprises.	Genome Biol. Evol.	2016	8		975-985			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. 		
@D	Das, S.//Singh, D.//Madduluri, M.//Chandrababunaidu, M.M.//Gupta, A.//Adhikary, S.P.//Tripathy, S. 	Draft Genome Sequence of Bioactive-Compound-Producing Cyanobacterium Tolypothrix  campylonemoides Strain VB511288.	Genome Announcements	2015	3		e00226-15			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. 		
@A	Dassa, B.//Pietrokovski, S. 		Origin and evolution of inteins and other hint domains.			Belfort, M.//Derbyshire, V.//Stoddard, B.L.//ood, D.W. 		Nucleic Acids Mol. Biol.				Berlin Heidelberg	Springer-Verlag	2005		16		211-231									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. 		
@D	Dassa, B.//Utturkar, S.//Hurt, R.A.//Klingeman, D.M.//Keller, M.//Xu, J.//Reddy, Y.H.//Borovok, I.//Rozman, G.I.//Lamed, R.//Zhivin, O.//Bayer, E.A.//Brown, S.D. 	Near-Complete Genome Sequence of the Cellulolytic Bacterium Bacteroides (Pseudobacteroides) cellulosolvens ATCC 35603.	Genome Announcements	2015	3		e01022-15			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. 		
@D	Datta, J.//Ghoshal, K.//Sharma, S.M.//Tajima, S.//Jacob, S.T. 	Biochemical fractionation reveals association of DNA methyltransferase (Dnmt) 3b With Dnmt1 and that of Dnmt 3a with a histone H3 methyltransferase and Hdac1.	J. Cell. Biochem.	2003	88		855-864			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. 		
@D	Datta, J.//Majumder, S.//Bai, S.M.//Ghoshal, K.//Kutay, H.//Smith, D.S.//Crabb, J.W.//Jacob, S.T. 	Physical and functional interaction of DNA methyltransferase 3A with Mbd3 and Brg1 in mouse lymphosarcoma cells.	Cancer Res.	2005	65		10891-10900			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. 		
@D	Datz, M.//Janetzki-Mittmann, C.//Franke, S.//Gunzer, F.//Schmidt, H.//Karch, H. 	Analysis of the enterohemorrhagic Escherichia coli 0157 DNA region containing lambdoid phage gene p and Shiga-like toxin structural genes.	Appl. Environ. Microbiol.	1996	62		791-797			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. 		
@D	Daujotyte, D.//Liutkeviciute, Z.//Tamulaitis, G.//Klimasauskas, S. 	Chemical mapping of cytosines enzymatically flipped out of the DNA helix.	Nucleic Acids Res.	2008	36		e57			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. 		
@D	Daujotyte, D.//Serva, S.//Vilkaitis, G.//Merkiene, E.//Venclovas, C.//Klimasauskas, S. 	HhaI DNA methyltransferase uses the protruding Gln237 for active flipping of its target cytosine.	Structure	2004	12		1047-1055			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. 		
@D	Daujotyte, D.//Vilkaitis, G.//Manelyte, L.//Skalicky, J.//Szyperski, T.//Klimasauskas, S. 	Solubility engineering of the HhaI methyltransferase.	Protein Eng.	2003	16		295-301			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. 		
@D	Daum, H.A.//White, H.W.//Seidell, C.M.//Johnson, P.A. 	Cloning, restriction digestion and DNA labeling of large DNA fragments (>1 kb) in the presence of remelted SeaPlaque GTG agarose gels.	Biotechniques	1991	11		784-790			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. 		
@D	Daum, L.T.//Bumah, V.V.//Masson-Meyers, D.S.//Khubbar, M.//Rodriguez, J.D.//Fischer, G.W.//Enwemeka, C.S.//Gradus, S.//Bhattacharyya, S. 	Whole-Genome Sequence for Methicillin-Resistant Staphylococcus aureus Strain ATCC BAA-1680.	Genome Announcements	2015	3		e00011-15			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. 		
@D	Davalieva, K.//Ziberovski, J.//Efremov, G.D. 	Bme585I [5'-CCCGC(4/6)-3'], a new isoschizomer of restriction endonuclease FauI, isolated from a strain of Bacillus mesentericus.	Microbiol. Res.	2004	159		129-133			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. 		
@D	Davenport, K.W. et al. 	Whole-genome sequences of nine francisella isolates.	Genome Announcements	2014	2		e00941-14			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. 		
@D	Davenport, K.W.//Daligault, H.E.//Minogue, T.D.//Bishop-Lilly, K.A.//Broomall, S.M.//Bruce, D.C.//Chain, P.S.//Coyne, S.R.//Frey, K.G.//Gibbons, H.S.//Jaissle, J.//Redden, C.L.//Rosenzweig, C.N.//Scholz, M.B.//Teshima, H.//Johnson, S.L. 	Complete Genome Assembly of Staphylococcus epidermidis AmMS 205.	Genome Announcements	2014	2		e01059-14			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. 		
@D	Davenport, K.W.//Daligault, H.E.//Minogue, T.D.//Bishop-Lilly, K.A.//Bruce, D.C.//Chain, P.S.//Coyne, S.R.//Frey, K.G.//Jaissle, J.//Koroleva, G.I.//Ladner, J.T.//Li, P.E.//Palacios, G.F.//Redden, C.L.//Scholz, M.B.//Teshima, H.//Johnson, S.L. 	Whole-Genome Sequence of Listeria monocytogenes Type Strain 53 XXIII.	Genome Announcements	2014	2		e00970-14			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. 		
@D	Davenport, K.W.//Daligault, H.E.//Minogue, T.D.//Bishop-Lilly, K.A.//Bruce, D.C.//Chain, P.S.//Coyne, S.R.//Frey, K.G.//Jaissle, J.//Koroleva, G.I.//Ladner, J.T.//Lo, C.C.//Palacios, G.F.//Redden, C.L.//Scholz, M.B.//Teshima, H.//Johnson, S.L. 	Complete Genome Sequence of Type Strain Pasteurella multocida subsp. multocida ATCC 43137.	Genome Announcements	2014	2		e01070-14			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. 		
@D	Davenport, K.W.//Daligault, H.E.//Minogue, T.D.//Bishop-Lilly, K.A.//Bruce, D.C.//Chain, P.S.//Coyne, S.R.//Frey, K.G.//Jaissle, J.//Koroleva, G.I.//Ladner, J.T.//Palacios, G.F.//Redden, C.L.//Scholz, M.B.//Teshima, H.//Johnson, S.L. 	Draft Genome Assembly of Delftia acidovorans Type Strain 2167.	Genome Announcements	2014	2		e00917-14			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. 		
@D	Davenport, K.W.//Daligault, H.E.//Minogue, T.D.//Broomall, S.M.//Bruce, D.C.//Chain, P.S.//Coyne, S.R.//Gibbons, H.S.//Jaissle, J.//Li, P.E.//Rosenzweig, C.N.//Scholz, M.B.//Johnson, S.L. 	Complete Genome Sequence of Stenotrophomonas maltophilia Type Strain 810-2 (ATCC  13637).	Genome Announcements	2014	2		e00974-14			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. 		
@D	Davenport, K.W.//Daligault, H.E.//Minogue, T.D.//Bruce, D.C.//Chain, P.S.//Coyne, S.R.//Jaissle, J.G.//Koroleva, G.I.//Ladner, J.T.//Li, P.E.//Palacios, G.F.//Scholz, M.B.//Teshima, H.//Johnson, S.L. 	Draft Genome Assembly of Acinetobacter baumannii ATCC 19606.	Genome Announcements	2014	2		e00832-14			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. 		
@D	David, A.//Bleimling, N.//Beuck, C.//Lehn, J.M.//Weinhold, E.//Teulade-Fichou, M.P. 	DNA mismatch-specific base flipping by a bisacridine macrocycle.	Chembiochem	2003	4		1326-1331			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. 		
@D	Davidson, F.W.//Whitney, H.G.//Tahlan, K. 	Genome Sequences of Klebsiella variicola Isolates from Dairy Animals with Bovine  Mastitis from Newfoundland, Canada.	Genome Announcements	2015	3		e00938-15			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. 		
@D	Davidson, R.M.//Reynolds, P.R.//Farias-Hesson, E.//Duarte, R.S.//Jackson, M.//Strong, M. 	Genome Sequence of an Epidemic Isolate of Mycobacterium abscessus subsp. bolletii from Rio de Janeiro, Brazil.	Genome Announcements	2013	1		e00617-13			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. 		
@D	Davidson, Y.Y.//Soper, S.A.//Margolis, S.//Sander, L.C. 	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.	J. Sep. Sci.	2001	24		10-16			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. 		
@D	Davie, J.J.//Earl, J.//de Vries, S.P.//Ahmed, A.//Hu, F.Z.//Bootsma, H.J.//Stol, K.//Hermans, P.W.//Wadowsky, R.M.//Ehrlich, G.D.//Hays, J.P.//Campagnari, A.A. 	Comparative analysis and supragenome modeling of twelve Moraxella catarrhalis clinical isolates.	BMC Genomics	2011	12		70			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. 		
@D	Davies, G.P.//Kemp, P.//Molineux, I.J.//Murray, N.E. 	The DNA translocation and ATPase activities of restriction-deficient mutants of EcoKI.	J. Mol. Biol.	1999	292		787-796			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. 		
@D	Davies, G.P.//Martin, I.//Sturrock, S.S.//Cronshaw, A.//Murray, N.E.//Dryden, D.T.F. 	On the structure and operation of type I DNA restriction enzymes.	J. Mol. Biol.	1999	290		565-579			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. 		
@D	Davies, G.P.//Powell, L.M.//Webb, J.L.//Cooper, L.P.//Murray, N.E. 	EcoKI with an amino acid substitution in any one of seven DEAD-box motifs has impaired ATPase and endonuclease activities.	Nucleic Acids Res.	1998	26		4828-4836			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. 		
@D	Davies, J.K. 	DNA restriction and modification systems in Neisseria gonorrhoeae.	Clin. Microbiol. Rev.	1989	2		S78-S82			A review.  Introduces new nomenclature. 		
@D	Davies, J.K.//Normark, S. 	A relationship between plasmid structure, structural lability, and sensitivity to site-specific endonucleases in Neisseria gonorrhoeae.	Mol. Gen. Genet.	1980	177		251-260			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. 		
@D	Davies, M.R.//Shera, J.//Van Domselaar, G.H.//Sriprakash, K.S.//McMillan, D.J. 	A Novel Integrative Conjugative Element Mediates Genetic Transfer from Group G Streptococcus to Other -Hemolytic Streptococci.	J. Bacteriol.	2009	191		2257-2265			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. 		
@D	Davis, B.M.//Chao, M.C.//Waldor, M.K. 	Entering the era of bacterial epigenomics with single molecule real time DNA sequencing.	Curr. Opin. Microbiol.	2013	16		192-198			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. 		
@D	Davis, E.O.//Jenner, P.J. 	Protein splicing -- the lengths some proteins will go to.	Antonie Van Leeuwenhoek	1995	67		131-137			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. 		
@D	Davis, E.O.//Jenner, P.J.//Brooks, P.C.//Colston, M.J.//Sedgwick, S.G. 	Protein splicing in the maturation of M. tuberculosis RecA protein: a mechanism for tolerating a novel class of intervening sequence.	Cell	1992	71		201-210			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. 		
@D	Davis, E.O.//Sedgwick, S.G.//Colston, M.J. 	Novel structure of the recA locus of Mycobacterium tuberculosis implies processing of the gene product.	J. Bacteriol.	1991	173		5653-5662			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. 		
@D	Davis, E.O.//Thangaraj, H.S.//Brooks, P.C.//Colston, M.J. 	Evidence of selection for protein introns in the recAs of pathogenic mycobacteria.	EMBO J.	1994	13		699-703			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. 		
@D	Davis, J.//Hill, R.T. 	Draft Genome Sequence of Hawaiian Sea Slug Symbiont Vibrio sp. Strain ER1A.	Genome Announcements	2014	2		e00820-14			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. 		
@D	Davis, J.R. et al. 	Genome Sequence of Streptomyces viridosporus Strain T7A ATCC 39115, a Lignin-Degrading Actinomycete.	Genome Announcements	2013	1		e00416-13			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. 		
@D	Davis, J.R.//Goodwin, L.A.//Woyke, T.//Teshima, H.//Bruce, D.//Detter, C.//Tapia, R.//Han, S.//Han, J.//Pitluck, S.//Nolan, M.//Mikhailova, N.//Land, M.L.//Sello, J.K. 	Genome Sequence of Amycolatopsis sp. Strain ATCC 39116, a Plant Biomass-Degrading Actinomycete.	J. Bacteriol.	2012	194		2396-2397			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. 		
@D	Davis, M.//Guorong, X.//Glickman, G.//Reich, N. 	Eludication of sites flanking CpG dinucleotides important in the regulation of mammalian cytosine DNA methyltransferase.	FASEB J.	1993	7		A1291			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. 		
@D	Davis, R.//Hossain, M.J.//Liles, M.R.//Panizzi, P. 	Complete Genome Sequence of Staphylococcus aureus Tager 104, a Sequence Type 49 Ancestor.	Genome Announcements	2013	1		e00706-13			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. 		
@D	Davis, R.//Van der Lelie, D.//Mercenier, A.//Daly, C.//Fitzgerald, G.F. 	ScrFI restriction-modification system of Lactococcus lactis subsp. cremoris UC503: Cloning and Characterization of two ScrFI methylase genes.	Appl. Environ. Microbiol.	1993	59		777-785			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. 		
@D	Davis, R.E.//Shao, J.//Dally, E.L.//Zhao, Y.//Gasparich, G.E.//Gaynor, B.J.//Athey, J.C.//Harrison, N.A.//Donofrio, N. 	Complete Genome Sequence of Spiroplasma kunkelii Strain CR2-3x, Causal Agent of Corn Stunt Disease in Zea mays L.	Genome Announcements	2015	3		e01216-15			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. 		
@D	Davis, R.E.//Shao, J.//Zhao, Y.//Gasparich, G.E.//Gaynor, B.J.//Donofrio, N. 	Complete Genome Sequence of Spiroplasma citri Strain R8-A2T, Causal Agent of Stubborn Disease in Citrus Species.	Genome Announcements	2017	5		e00206-17			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. 		
@D	Davis, R.E.//Shao, J.//Zhao, Y.//Gasparich, G.E.//Gaynor, B.J.//Donofrio, N. 	Complete Genome Sequence of Spiroplasma turonicum Strain Tab4cT, a Parasite of a  Horse Fly, Haematopota sp. (Diptera: Tabanidae).	Genome Announcements	2015	3		e01367-15			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. 		
@D	Davis, R.W. IV//Brannen, A.D.//Hossain, M.J.//Monsma, S.//Bock, P.E.//Nahrendorf, M.//Mead, D.//Lodes, M.//Liles, M.R.//Panizzi, P. 	Complete genome of Staphylococcus aureus Tager 104 provides evidence of its relation to modern systemic hospital-acquired strains.	BMC Genomics	2016	17		179			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. 		
@D	Davis, T.O.//Henderson, I.//Brehm, J.K.//Minton, N.P. 	Development of a transformation and gene reporter system for group II, non-proteolytic Clostridium botulinum type B strains.	J. Mol. Microbiol. Biotechnol.	2000	2		59-69			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. 		
@D	Davison, J.//Brunel, F. 	Restriction insensitivity in bacteriophage T5.  I. Genetic characterization of mutants sensitive to EcoRI restriction.	J. Virol.	1979	29		11-16			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. 		
@D	Dawar, C.//Aggarwal, R.K. 	Draft Genome Sequence of Rhodococcus rhodochrous Strain KG-21, a Soil Isolate from Oil Fields of Krishna-Godavari Basin, India.	Genome Announcements	2015	3		e01201-15			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. 		
@D	Dawar, C.//Aggarwal, R.K. 	Draft Genome Sequence of Hydrocarbon-Degrading Pseudomonas putida Strain KG-4, Isolated from Soil Samples Collected from Krishna-Godavari Basin in India.	Genome Announcements	2015	3		e00590-15			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. 		
@D	Dawoud, T.M.//Jiang, T.//Mandal, R.K.//Ricke, S.C.//Kwon, Y.M. 	Improving the Efficiency of Transposon Mutagenesis in Salmonella Enteritidis by Overcoming Host-Restriction Barriers.	Mol. Biotechnol.	2014	56		1004-1010			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. 		
@D	Day, J.P.//Reich, N.O.//Hager, P.//Rosenberg, J.//McClarin, J.A.//Grable, J.//Boyer, H.W.//Greene, P.J. 	Characterization of three EcoRI endonuclease mutants with altered DNA-Protein contacts designed to change specificity.	J. Cell Biochem. Suppl.	1987	11C		205			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. 		
@D	Day, M.//Ibrahim, M.//Dyer, D.//Bulla, L. Jr. 	Genome Sequence of Bacillus thuringiensis subsp. kurstaki Strain HD-1.	Genome Announcements	2014	2		e00613-14			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. 		
@D	Day, M.W.//Jackson, L.A.//Akins, D.R.//Dyer, D.W.//Chavez-Bueno, S. 	Whole-Genome Sequences of the Archetypal K1 Escherichia coli Neonatal Isolate RS218 and Contemporary Neonatal Bacteremia Clinical Isolates SCB11, SCB12, and SCB15.	Genome Announcements	2015	3		e01598-14			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. 		
@D	Day, R.S. 	UV-induced alleviation of K-specific restriction of bacteriophage lambda.	J. Virol.	1977	21		1249-1251			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. 		
@D	de Aguiar, E.L. et al. 	Complete genome sequence of Streptococcus agalactiae strain GBS85147 serotype of  type Ia isolated from human oropharynx.	Standards in Genomic Sciences	2016	11		39			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 %. 		
@D	de Alencar, S.A.//Costa, F.S.//Rodrigues, G.R.//Barreto, C.C. 	Draft Genome Sequence of a Novel Mucilaginibacter Member Isolated from Brazilian  Amazon Soil.	Genome Announcements	2016	4		e01033-16			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. 		
@D	de Almeida, J.B.//de Carvalho, S.P.//de Freitas, L.M.//Guimaraes, A.M.//do Nascimento, N.C.//Dos Santos, A.P.//Messick, J.B.//Timenetsky, J.//Marques, L.M. 	Draft Genome Sequence of Methicillin-Resistant Staphylococcus aureus Strain LC33  Isolated from Human Breast Milk.	Genome Announcements	2017	5		e00154-17			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. 		
@D	de Almeida, L.M.//Pires, C.//Cerdeira, L.T.//de Oliveira, T.G.//McCulloch, J.A.//Perez-Chaparro, P.J.//Sacramento, A.G.//Brito, A.C.//da Silva, J.L.//de Araujo, M.R.//Lincopan, N.//Martin, M.J.//Gilmore, M.S.//Mamizuka, E.M. 	Complete Genome Sequence of Linezolid-Susceptible Staphylococcus haemolyticus Sh29/312/L2, a Clonal Derivative of a Linezolid-Resistant Clinical Strain.	Genome Announcements	2015	3		e00494-15			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. 		
@D	de Andrade-Barboza, S.//Meygret, A.//Vincent, P.//Moullec, S.//Soriano, N.//Lagente, V.//Minet, J.//Kayal, S.//Faili, A. 	Complete Genome Sequence of Noninvasive Streptococcus pyogenes M/emm28 Strain STAB10015, Isolated from a Child with Perianal Dermatitis in French Brittany.	Genome Announcements	2015	3		e00806-15			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). 		
@D	De Backer, O.//Colson, C. 	Molecular nature of the restriction-modification system LT of Salmonella typhimurium.	J. Cell Biochem. Suppl.	1989	13D		212			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. 		
@D	De Backer, O.//Colson, C. 	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.	J. Bacteriol.	1991	173		1328-1330			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. 		
@D	De Backer, O.//Colson, C. 	Two-step cloning and expression in Escherichia coli of the DNA restriction-modification system StyLTI of Salmonella typhimurium.	J. Bacteriol.	1991	173		1321-1327			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. 		
@D	De Backer, O.//Colson, C. 	Identification of the recognition sequence for the M.StyLTI methyltransferase of Salmonella typhimurium LT7: an asymmetric site typical of type-III enzymes.	Gene	1991	97		103-107			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. 		
@D	de Been, M.//Lanza, V.F.//de Toro, M.//Scharringa, J.//Dohmen, W.//Du, Y.//Hu, J.//Lei, Y.//Li, N.//Tooming-Klunderud, A.//Heederik, D.J.//Fluit, A.C.//Bonten, M.J.//Willems, R.J.//de la Cruz, F.//van Schaik, W. 	Dissemination of cephalosporin resistance genes between Escherichia coli strains  from farm animals and humans by specific plasmid lineages.	PLoS Genet.	2014	10		e1004776			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. 		
@D	De Bolle, X.//Bayliss, C.D.//Field, D.//van de Ven, T.//Saunders, N.J.//Hood, D.W.//Moxon, E.R. 	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.	Mol. Microbiol.	2000	35		211-222			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. 		
@D	De Carli, S.//Graf, T.//Mayer, F.Q.//Cibulski, S.//Lehmann, F.K.//Fonseca, A.S.//Ikuta, N.//Lunge, V.R. 	Draft Genome Sequence of a Salmonella enterica subsp. enterica Serovar Gallinarum bv. Gallinarum Isolate Associated with Fowl Typhoid Outbreaks in Brazil.	Genome Announcements	2016	4		e00019-16			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. 		
@D	de Carvalho, S.P.//de Almeida, J.B.//de Freitas, L.M.//Guimaraes, A.M.//do Nascimento, N.C.//Dos Santos, A.P.//Messick, J.B.//Timenetsky, J.//Marques, L.M. 	Draft Genome Sequences of Two Clinical Methicillin-Resistant Staphylococcus aureus Strains Isolated from Healthy Children in Brazil.	Genome Announcements	2017	5		e00158-17			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. 		
@D	de Diego-Diaz, B.//Treu, L.//Campanaro, S.//da Silva, D.V.//Basaglia, M.//Favaro, L.//Casella, S.//Squartini, A. 	Genome Sequence of Rhizobium sullae HCNT1 Isolated from Hedysarum coronarium Nodules and Featuring Peculiar Denitrification Phenotypes.	Genome Announcements	2018	6		e01518-17			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. 		
@D	de Diego-Diaz, B.//Treu, L.//Campanaro, S.//da Silva, D.V.//Saviane, A.//Cappellozza, S.//Squartini, A. 	Genome Sequence of Enterococcus mundtii EM01, Isolated from Bombyx mori Midgut and Responsible for Flacherie Disease in Silkworms Reared on an Artificial Diet.	Genome Announcements	2018	6		e01495-17			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. 		
@D	De Feyter, R.//Gabriel, D.W. 	Use of cloned DNA methylase genes to increase the frequency of transfer of foreign genes into Xanthomonas campestris pv. malvacearum.	J. Bacteriol.	1991	173		6421-6427			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. 		
@D	de Franca, P.//Camilo, E.//Fantinatti-Garboginni, F. 	Draft Genome Sequence of Marinobacter sp. Strain ANT_B65, Isolated from Antarctic Marine Sponge.	Genome Announcements	2018	6		e01404-17			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. 		
@D	De Groot, A.//Dulermo, R.//Ortet, P.//Blanchard, L.//Guerin, P.//Fernandez, B.//Vacherie, B.//Dossat, C.//Jolivet, E.//Siguier, P.//Chandler, M.//Barakat, M.//Dedieu, A.//Barbe, V.//Heulin, T.//Sommer, S.//Achouak, W.//Jean, A. 	Alliance of Proteomics and Genomics to Unravel the Specificities of Sahara Bacterium.	PLoS Genet.	2009	5		e1000434			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. 		
@D	De Jonckheere, J.F. 	Evidence for the ancestral origin of group I introns in the SSUrDNA of Naegleria spp.	J. Eukaryot. Microbiol.	1994	41		457-463			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. 		
@D	de Jong, A.//van Heel, A.J.//Montalban-Lopez, M.//Krawczyk, A.O.//Berendsen, E.M.//Wells-Bennik, M.//Kuipers, O.P. 	Draft Genome Sequences of Five Spore-Forming Food Isolates of Bacillus pumilus.	Genome Announcements	2015	3		e01539-14			Here, we report the draft genome sequences of five food isolates of Bacillus pumilus, a spore-forming Gram-positive bacterium. 		
@D	de la Campa, A.G.//Kale, P.//Springhorn, S.S.//Lacks, S.A. 	Proteins encoded by the DpnII restriction gene cassette:  Two methylases and an endonuclease.	J. Mol. Biol.	1987	196		457-469			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. 		
@D	de la Campa, A.G.//Springhorn, S.S.//Kale, P.//Lacks, S.A. 	Proteins encoded by the DpnI restriction gene cassette.	J. Biol. Chem.	1988	263		14696-14702			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. 		
@D	de la Fuente, J.//Diez-Delgado, I.//Contreras, M.//Vicente, J.//Cabezas-Cruz, A.//Manrique, M.//Tobes, R.//Lopez, V.//Romero, B.//Dominguez, L.//Garrido, J.M.//Juste, R.//Gortazar, C. 	Complete Genome Sequences of Field Isolates of Mycobacterium bovis and Mycobacterium caprae.	Genome Announcements	2015	3		e00247-15			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. 		
@D	de la Haba, R.R.//Sanchez-Porro, C.//Leon, M.J.//Papke, R.T.//Ventosa, A. 	Draft Genome Sequence of the Moderately Halophilic Bacterium Pseudoalteromonas ruthenica Strain CP76.	Genome Announcements	2013	1		e00268-13			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. 		
@D	De Lencastre, H.//Wu, S.W.//Pinho, M.G.//Ludovice, A.M.//Filipe, S.//Gardete, S.//Sobral, R.//Gill, S.//Chung, M.//Tomasz, A. 	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.	Microb. Drug Resist.	1999	5		163-175			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. 		
@D	De Leon, K.B.//Utturkar, S.M.//Camilleri, L.B.//Elias, D.A.//Arkin, A.P.//Fields, M.W.//Brown, S.D.//Wall, J.D. 	Complete Genome Sequence of Pelosinus fermentans JBW45, a Member of a Remarkably  Competitive Group of Negativicutes in the Firmicutes Phylum.	Genome Announcements	2015	3		e01090-15			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. 		
@D	De Leon, K.B.//Young, M.L.//Camilleri, L.B.//Brown, S.D.//Skerker, J.M.//Deutschbauer, A.M.//Arkin, A.P.//Fields, M.W. 	Draft Genome Sequence of Pelosinus fermentans JBW45, Isolated during In Situ Stimulation for Cr(VI) Reduction.	J. Bacteriol.	2012	194		5456-5457			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. 		
@D	De Leon, M.P.//Park, A.Y.//Montecillo, A.D.//Siringan, M.A.T.//Rosana, A.R.R.//Kim, S.G. 	Near-Complete Genome Sequences of Streptomyces sp. Strains AC1-42T and AC1-42W, Isolated from Bat Guano from Cabalyorisa Cave, Mabini, Pangasinan, Philippines.	Microbiol. Resour. Announc.	2018	7		e00904-18			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. 		
@D	de Lima-Morales, D.//Chaves-Moreno, D.//Jarek, M.//Vilchez-Vargas, R.//Jauregui, R.//Pieper, D.H. 	Draft Genome Sequence of Pseudomonas veronii Strain 1YdBTEX2.	Genome Announcements	2013	1		e00258-13			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. 		
@D	de los Reyes-Gavilan, C.G.//Aparicio, J.F.//Barbes, C.//Hardisson, C.//Sanchez, J. 	An exocytoplasmic endonuclease with restriction function in Streptomyces antibioticus.	J. Bacteriol.	1988	170		1339-1345			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. 		
@D	de los Reyes-Gavilan, C.G.//Limsowtin, G.K.Y.//Sechaud, L.//Veaux, M.//Accolas, J.-P. 	Evidence for a plasmid-linked restriction-modification system in Lactobacillus helveticus.	Appl. Environ. Microbiol.	1990	56		3412-3419			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. 		
@D	De Luca, S.//Nicholson, P.//Magistrali, C.F.//Garcia-Martin, A.B.//Rychener, L.//Zeeh, F.//Frey, J.//Perreten, V. 	Transposon-associated lincosamide resistance lnu(C) gene identified in Brachyspira hyodysenteriae ST83.	Vet. Microbiol.	2018	214		51-55			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. 		
@D	De Maayer, P.//Chan, W.Y.//Rezzonico, F.//Buhlmann, A.//Venter, S.N.//Blom, J.//Goesmann, A.//Frey, J.E.//Smits, T.H.//Duffy, B.//Coutinho, T.A. 	Complete Genome Sequence of Clinical Isolate Pantoea ananatis LMG 5342.	J. Bacteriol.	2012	194		1615-1616			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. 		
@D	De Maayer, P.//Chan, W.Y.//Venter, S.N.//Toth, I.K.//Birch, P.R.//Joubert, F.//Coutinho, T.A. 	Genome sequence of Pantoea ananatis LMG20103, the causative agent of Eucalyptus blight and dieback.	J. Bacteriol.	2010	192		2936-2937			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. 		
@D	De Maayer, P.//Williamson, C.E.//Vennard, C.T.//Danson, M.J.//Cowan, D.A. 	Draft Genome Sequences of Geobacillus sp. Strains CAMR5420 and CAMR12739.	Genome Announcements	2014	2		e00567-14			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. 		
@D	de Man, T.J.//Perry, K.A.//Avillan, J.J.//Rasheed, J.K.//Limbago, B.M. 	Draft Genome Sequence of a New Delhi Metallo-beta-Lactamase-5 (NDM-5)-Producing Multidrug-Resistant Escherichia coli Isolate.	Genome Announcements	2015	3		e00017-15			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. 		
@D	de Man, T.J.//Perry, K.A.//Lawsin, A.//Coulliette, A.D.//Jensen, B.//Toney, N.C.//Limbago, B.M.//Noble-Wang, J. 	Draft Genome Sequence of Mycobacterium wolinskyi, a Rapid-Growing Species of Nontuberculous Mycobacteria.	Genome Announcements	2016	4		e00138-16			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. 		
@D	de Mello, S.S.//Van Tyne, D.//Dabul, A.N.//Gilmore, M.S.//Camargo, I.L. 	High-Quality Draft Genome Sequence of the Multidrug-Resistant Clinical Isolate Enterococcus faecium VRE16.	Genome Announcements	2016	4		e00992-16			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. 		
@D	de Melo, A.G.//Labrie, S.J.//Dumaresq, J.//Roberts, R.J.//Tremblay, D.M.//Moineau, S. 	Complete Genome Sequence of Brevibacterium linens SMQ-1335.	Genome Announcements	2016	4		e01242-16			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. 		
@D	De Meyer, S.E.//Fabiano, E.//Tian, R.//Van Berkum, P.//Seshadri, R.//Reddy, T.//Markowitz, V.//Ivanova, N.//Pati, A.//Woyke, T.//Howieson, J.//Kyrpides, N.//Reeve, W. 	High-quality permanent draft genome sequence of the Parapiptadenia rigida-nodulating Burkholderia sp. strain UYPR1.413.	Standards in Genomic Sciences	2015	10		31			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. 		
@D	De Meyer, S.E.//Fabiano, E.//Tian, R.//Van Berkum, P.//Seshadri, R.//Reddy, T.//Markowitz, V.//Ivanova, N.N.//Pati, A.//Woyke, T.//Howieson, J.//Kyrpides, N.C.//Reeve, W. 	High-quality permanent draft genome sequence of the Parapiptadenia rigida-nodulating Cupriavidus sp. strain UYPR2.512.	Standards in Genomic Sciences	2015	10		13			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. 		
@D	De Meyer, S.E.//Nguyen, D.T.//Wang, P.//Andrews, M. 	Complete Genome Sequence of Mesorhizobium sophorae ICMP 19535T, a Highly Specific, Nitrogen-Fixing Symbiont of New Zealand Endemic Sophora spp.	Genome Announcements	2017	5		e00958-17			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. 		
@D	De Meyer, S.E.//Parker, M.//Van Berkum, P.//Tian, R.//Seshadri, R.//Reddy, T.B.//Markowitz, V.//Ivanova, N.//Pati, A.//Woyke, T.//Kyrpides, N.//Howieson, J.//Reeve, W. 	High-quality permanent draft genome sequence of the Mimosa asperata - nodulating  Cupriavidus sp. strain AMP6.	Standards in Genomic Sciences	2015	10		80			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. 		
@D	De Meyer, S.E.//Tian, R.//Seshadri, R.//Ivanova, N.//Pati, A.//Markowitz, V.//Woyke, T.//Yates, R.//Howieson, J.//Kyrpides, N.//Reeve, W. 	High-quality permanent draft genome sequence of the Lebeckia - nodulating Burkholderia dilworthii strain WSM3556(T).	Standards in Genomic Sciences	2015	10		64			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. 		
@D	De Meyer, S.E.//Tian, R.//Seshadri, R.//Reddy, T.//Markowitz, V.//Ivanova, N.//Pati, A.//Woyke, T.//Kyrpides, N.//Yates, R.//Howieson, J.//Reeve, W. 	High-quality permanent draft genome sequence of the Lebeckia ambigua-nodulating Burkholderia sp. strain WSM4176.	Standards in Genomic Sciences	2015	10		79			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). 		
@D	de Oliveira, L.G.//Tormet, G.G.D.//Samborsky, M.//Marcon, J.//Araujo, W.L.//de Azevedo, J.L. 	Genome Sequence of Streptomyces wadayamensis Strain A23, an Endophytic Actinobacterium from Citrus reticulata.	Genome Announcements	2014	2		e00625-14			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. 		
@D	de Oliveira-Veras, A.A. et al. 	Draft Genome Sequences of Vibrio fluvialis Strains 560 and 539, Isolated from Environmental Samples.	Genome Announcements	2015	3		e01344-14			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. 		
@D	de Padua-Pereira, U. et al. 	Complete genome sequence of Streptococcus agalactiae strain SA20-06, a fish pathogen associated to meningoencephalitis outbreaks.	Standards in Genomic Sciences	2013	8		188-197			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. 		
@D	de Sa, P.C.//Da Silva, M.L.//Carneiro, A.R.//Gomes, J.C.//Dias, L.M.//Alves, J.T.//De Oliveira, V.A.A.//Barauna, R.A.//Das Gracas, D.A.//Matte, M.H.//Sato, M.I.//Hachich, E.M.//Matte, G.R.//Ramos, R.T.//Silva, A. 	Draft Genome Sequence of Non-O1 and Non-O139 Vibrio cholerae Strain VCC19.	Genome Announcements	2014	2		e01094-14			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. 		
@D	de Siqueira, K.A.//Liotti, R.G.//Mendes, T.A.O.//Soares, M.A. 	Draft Genome Sequences of Pseudomonas sp. Strain 382 and Pantoea coffeiphila 342, Endophytic Bacteria Isolated from Brazilian Guarana [Paullinia cupana (Mart.)  Ducke].	Genome Announcements	2018	6		e00287-18			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. 		
@D	de Siqueira, K.A.//Mello, I.S.//Pietro-Souza, W.//Mendes, T.A.O.//Soares, M.A. 	Draft Genome Sequence of the Mercury-Resistant Strain Acinetobacter baumannii I43.	Genome Announcements	2018	6		e00283-18			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. 		
@D	de Souza, J.A.//Tieppo, E.//Magnani, G.S.//Alves, L.M.//Cardoso, R.L.//Cruz, L.M.//de Oliveira, L.F.//Raittz, R.T.//de Souza, E.M.//Pedrosa, F.O.//Lemos, E.G. 	Draft Genome Sequence of the Nitrogen-Fixing Symbiotic Bacterium Bradyrhizobium elkanii 587.	J. Bacteriol.	2012	194		3547-3548			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. 		
@D	de Souza, R.//Sant'Anna, F.H.//Ambrosini, A.//Tadra-Sfeir, M.//Faoro, H.//Pedrosa, F.O.//Souza, E.M.//Passaglia, L.M. 	Genome of Rhizobium sp. UR51a, Isolated from Rice Cropped in Southern Brazilian Fields.	Genome Announcements	2015	3		e00249-15			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. 		
@D	de Souza, R.//Sant'Anna, F.H.//Ambrosini, A.//Tadra-Sfeir, M.//Faoro, H.//Pedrosa, F.O.//Souza, E.M.//Passaglia, L.M. 	Genome of Pseudomonas sp. FeS53a, a Putative Plant Growth-Promoting Bacterium Associated with Rice Grown in Iron-Stressed Soils.	Genome Announcements	2015	3		e00248-15			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. 		
@D	de Souza, V.//Piro, V.C.//Faoro, H.//Tadra-Sfeir, M.Z.//Chicora, V.K.//Guizelini, D.//Weiss, V.//Vialle, R.A.//Monteiro, R.A.//Steffens, M.B.//Marchaukoski, J.N.//Pedrosa, F.O.//Cruz, L.M.//Chubatsu, L.S.//Raittz, R.T. 	Draft Genome Sequence of Herbaspirillum huttiense subsp. putei IAM 15032, a Strain Isolated from Well Water.	Genome Announcements	2013	1		e00252-12			Here we report the one-scaffold draft genome of subsp. strain 7-2 (IAM 15032), which was isolated from well water. 		
@D	de Souza, Y.P.A.//da Mota, F.F.//Rosado, A.S. 	Draft Genome Sequence of Geobacillus sp. LEMMY01, a Thermophilic Bacterium Isolated from the Site of a Burning Grass Pile.	Genome Announcements	2017	5		e00200-17			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. 		
@D	De Vries, D.R.//Martin, A.L.//Ganz, H.H.//Eisen, J.A.//Coil, D.A. 	Draft Genome Sequence of Enterococcus faecalis Strain UCD-PD3.	Genome Announcements	2016	4		e01386-16			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. 		
@D	de Vries, G.E.//Harms, N.//Hoogendijk, J.//Stouthamer, A.H. 	Isolation and characterization of Paracoccus denitrificans mutants with increased conjugation frequencies and pleiotropic loss of a (nGATCn) DNA-modifying property.	Arch. Microbiol.	1989	152		52-57			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. 		
@D	de Vries, H.J.//Marshall, I.P.G.//Schreiber, L.//Plugge, C.M. 	Draft Genome Sequence of Sphingomonas sp. Strain Sph1(2015), Isolated from a Fouled Membrane Filter Used To Produce Drinking Water.	Genome Announcements	2017	5		e00517-17			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. 		
@D	De Vries, N.//Duinsbergen, D.//Kuipers, E.J.//Pot, R.G.J.//Wiesenekker, P.//Penn, C.W.//Van Vliet, A.H.M.//Vandenbroucke-Grauls, C.M.J.E.//Kusters, J.G. 	Transcriptional phase variation of a Type III restriction-modification system in Helicobacter pylori.	J. Bacteriol.	2002	184		6615-6623			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. 		
@D	de Vries, N.//Duinsbergen, D.//Kuipers, E.J.//Wiesenekker, P.//Vandenbroucke-Grauls, C.M.//Kusters, J.G. 	Phase variation in a type III restriction-modification system of Helicobacter pylori.	Gastroenterology	2000	118		A736			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. 		
@D	de Vries, N.//Duinsbergen, D.//Kuipers, E.J.//Wiesenekker, P.//Vandenbroucke-Grauls, C.M.J.//Kusters, J.G. 	Transcriptional phase variation in a type III restriction modification system of Helicobacter pylori.	Gut	2000	47		A17			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. 		
@D	de Waard, A.//Duyvesteyn, M. 	Are sequence-specific deoxyribonucleases of value as taxonomic markers of cyanobacterial species?	Arch. Microbiol.	1980	128		242-247			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. 		
@D	de Waard, A.//Korsuize, J.//van Beveren, C.P.//Maat, J. 	A new sequence-specific endonuclease from Anabaena cylindrica.	FEBS Lett.	1978	96		106-110			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. 		
@D	de Waard, A.//van Beveren, C.P.//Duyvesteyn, M.//van Ormondt, H. 	Two sequence-specific endonucleases from Anabaena oscillarioides.	FEBS Lett.	1979	101		71-76			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. 		
@D	de Wit, C.M.//Dekker, B.M.M.//Neele, A.C.//de Waard, A. 	Purification and characterization of endonucleases DraII and III from Deinococcus radiophilus.	FEBS Lett.	1985	180		219-223			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. 		
@D	Dean, A.B.//Stanger, M.J.//Dansereau, J.T.//Van Roey, P.//Derbyshire, V.//Belfort, M. 	Zinc finger as distance determinant in the flexible linker of intron  endonuclease I-TevI.	Proc. Natl. Acad. Sci. U. S. A.	2002	99		8554-8561			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. 		
@D	Dean, P.D.C.//Walker, J.N.B. 	Recent advances in high-performance liquid affinity chromatography columns.	Biochem. Soc. Trans.	1985	13		1055-1058			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. 		
@D	Dean, S.N.//Vora, G.J.//Walper, S.A. 	Complete Genome Sequence of Lactobacillus acidophilus Strain ATCC 53544.	Genome Announcements	2017	5		e01138-17			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. 		
@D	Deangelis, K.M.//D'Haeseleer, P.//Chivian, D.//Fortney, J.L.//Khudyakov, J.//Simmons, B.//Woo, H.//Arkin, A.P.//Davenport, K.W.//Goodwin, L.//Chen, A.//Ivanova, N.//Kyrpides, N.C.//Mavromatis, K.//Woyke, T.//Hazen, T.C. 	Complete genome sequence of 'Enterobacter lignolyticus' SCF1.	Standards in Genomic Sciences	2011	5		69-85			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. 		
@D	DeBacker, O.//Chomez, P.//DePlaen, E. 	Positive selection of recombinant plasmids based on the EcoK restriction activity of Escherichia coli K-12.	Gene	1994	150		197-198			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. 		
@D	DeBoy, R.T.//Mongodin, E.F.//Fouts, D.E.//Tailford, L.E.//Khouri, H.//Emerson, J.B.//Mohamoud, Y.//Watkins, K.//Henrissat, B.//Gilbert, H.J.//Nelson, K.E. 	Insights into plant cell wall degradation from the genome sequence of the soil bacterium Cellvibrio japonicus.	J. Bacteriol.	2008	190		5455-5463			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. 		
@D	Debroas, D.//Humbert, J.F.//Enault, F.//Bronner, G.//Faubladier, F.//Cornillot, C. 	Metagenomic approach studying the taxonomic and functional diversity of the bacterial community in a mesotrophic lake (Lac du Bourget - France).	Environ. Microbiol.	2009	11		2412-2424			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. 		
@D	Debrouwere, L.//Zabeau, M.//Van Montagu, M.//Schell, J. 	The ral gene of phage lambda.	Mol. Gen. Genet.	1980	179		75-80			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. 		
@D	Debroy, S.//Bhattacharjee, A.//Thakur, A.R.//Raychaudhuri, S. 	Draft Genome Sequence of the Nitrate- and Phosphate-Accumulating Bacillus sp. Strain MCC0008.	Genome Announcements	2013	1		e00189-12			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%. 		
@D	Debroy, S.//Mukherjee, P.//Roy, S.//Thakur, A.R.//Raychaudhuri, S. 	Draft Genome Sequence of a Nitrate- and Phosphate-Removing Bacillus sp., WBUNB009.	Genome Announcements	2013	1		e00254-12			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. 		
@D	Debroy, S.//Mukherjee, P.//Roy, S.//Thakur, A.R.//Raychaudhuri, S. 	Draft Genome Sequence of a Phosphate-Accumulating Bacillus sp., WBUNB004.	Genome Announcements	2013	1		e00251-12			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. 		
@D	Debruyn, J.M.//Radosevich, M.//Wommack, K.E.//Polson, S.W.//Hauser, L.J.//Fawaz, M.N.//Korlach, J.//Tsai, Y.C. 	Genome Sequence and Methylome of Soil Bacterium Gemmatirosa kalamazoonensis KBS708T, a Member of the Rarely Cultivated Gemmatimonadetes Phylum.	Genome Announcements	2014	2		e00226-14			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. 		
@D	Decatur, W.A.//Johansen, S.//Vogt, V.M. 	Expression of the Naegleria intron endonuclease is dependent on a functional group I self-cleaving ribozyme.	RNA	2000	6		616-627			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. 		
@D	Deckert, G.//Warren, P.V.//Gaasterland, T.//Young, W.G.//Lenox, A.L.//Graham, D.E.//Overbeek, R.//Snead, M.A.//Keller, M.//Aujay, M.//Huber, R.//Feldman, R.A.//Short, J.M.//Olson, G.J.//Swanson, R.V. 	The complete genome of the hyperthermophilic bacterium Aquifex aeolicus.	Nature	1998	392		353-358			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. 		
@D	Dedkov, V.S. 	New DNA methyltransferase M.AjnI from the bacterium Acinetobacter johnsonii R2 produces the 5'-m5CCWGG-3' sequence.	Prikl. Biokhim. Mikrobiol.	2010	46		849-853			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. 		
@D	Dedkov, V.S. 	Analysis of specificity of DNA-methyltransferase M.AspS9I in cell lysate by means of restriction endonuclease blocking.	Biotekhnologiya	2009	0		30-39			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. 		
@D	Dedkov, V.S. 	Defining specificity of DNA methyltransferase M.Bsc4I in cellular lysate by blocking restriction endonucleases and computer modeling.	Mol. Gen. Mikrobiol. Virusol.	2009	0		3-8			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. 		
@D	Dedkov, V.S. 	Determining of G+C Content in Bacterial DNA using Restriction Endonucleases.	Biotekhnologiya	2004	4		77-82			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. 		
@D	Dedkov, V.S. 	Novel M.BstC8I methyltransferase forms 5'-G(m5C)NNGC-3'. Investigation of restriction endonuclease sensitivity to M.BstC8I methylation.	Mol. Genet. Microbiol. Virol.	2012	27		40-47			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. 		
@D	Dedkov, V.S. 	New DNA methyltransferase M.AjnI from Acinetobacter johnsonii R2 produces 5'-m5CCWGG-3' sequence.	Biotekhnologiya	2010	0		36-40					
@D	Dedkov, V.S.//Bondar, T.S.//Shevchenco, A.V.//Degtyarev, S.K. 	New rare-cutting restriction endonuclease SmiI from Streptococcus milleri recognizes 5'-ATTT/AAAT-3'.	Mol. Gen. Mikrobiol. Virusol.	2000	1		23-27			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. 		
@D	Dedkov, V.S.//Degtyarev, S.K. 	Actinobacillus and Streptococcus: producers of isoschizomers of the restriction endonucleases R.HphI, R.SauI, R.NheI, R.MboI and R.SwaI.	Biol. Chem.	1998	379		573-574			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. 		
@D	Dedkov, V.S.//Degtyarev, S.K. 	Detection of restriction endonucleases in Streptomyces and Nocardia cells.	Prikl. Biokhim. Mikrobiol.	1992	28		309-313			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. 		
@D	Dedkov, V.S.//Gonchar, D.A.//Abdurashitov, M.A.//Udalyeva, S.G.//Urumceva, L.A.//Chernukhin, V.A.//Mutylo, G.V.//Degtyarev, S.K. 	Cloning and Study of New DNA Methyltransferase M.FatI Modifying Cytosine in a Recognition Site CATG.	Res. J. Pharm. Biol. Chem. Sci.	2015	6		1341-1348			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. 		
@D	Dedkov, V.S.//Gonchar, D.A.//Abdurashitov, M.A.//Udalyeva, S.G.//Urumceva, L.A.//Chernukhin, V.A.//Shiryaeva, E.N.//Degtyarev, S.K. 	Cloning and study of new DNA methyltransferase M.AluBI modifying adenine in a recognition site AGCT.	Biotecnol. Apl.	2015	32		3211-3216			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. 		
@D	Dedkov, V.S.//Gonchar, D.A.//Chernukhin, V.A.//Abdurashitov, M.A.//Udalyeva, S.G.//Urumceva, L.A.//Degtyarev, S.K. 	New DNA methyltransferase M.AgsI produces TTSA(m6A).	Biotechnology: an Indian Journal	2016	12		100-106			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. 		
@D	Dedkov, V.S.//Kileva, E.V.//Popichenko, D.V.//Degtyarev, S.K. 	FatI restriction endonuclease from Flavobacterium aquatile NL3 cleaves DNA at 5'-^CATG-3' site.	Biotekhnologiya	2002	5		3-7					
@D	Dedkov, V.S.//Mikhnenkova, N.A.//Djanobilova, Z.K.//Tarasova, M.V. 	A M.BssECI DNA Methyltransferase Forms 5 '-m4CCNNGG-3 '. Sensitivity of Restriction Endonucleases to the New Methylation.	Biotekhnologiya	2012	2		32-42			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. 		
@D	Dedkov, V.S.//Mikhnenkova, N.A.//Vlasenko, L.P.//Tomilova, J.E.//Kashirina, J.G.//Gonchar, D.A.//Degtyarev, S.K. 	Restriction Endonuclease AjnI from Acinetobacter johnsonii R2, an Isoschizomer of EcoRII, recognizes 5'- CCWGG-3' and cleaves dcm-methylated sites.	Biotekhnologiya	2004	3		19-24			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. 		
@D	Dedkov, V.S.//Nayakshina, T.N.//Popichenko, D.V.//Degtyarev, S.K. 	Restriction endonuclease BmtI from Bacillus megaterium S2 cleaves DNA at 5'-GCTAG^C-3' site.	Biotekhnologiya	2003	1		11-15			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. 		
@D	Dedkov, V.S.//Prihodko, G.G.//Puchkova, L.I.//Serov, G.D.//Rechkunova, N.I.//Degtyarev, S.K. 	SsrI - a Type II restriction endonuclease from Staphylococcus saprophyticus cells.	Mol. Gen. Mikrobiol. Virusol.	1989	11		24-27			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. 		
@D	Dedkov, V.S.//Rechkunova, N.I.//Prihodko, E.A.//Kileva, E.V.//Kusner, Y.S.//Verchozina, V.A.//Degtyarev, S.K. 	CciNI, an isoschizomer of NotI from Curtobacterium citreum recognizes 5'-GC/GGCCGC-3'.	Gene	1995	157		99-100			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. 		
@D	Dedkov, V.S.//Repin, V.E.//Rechkunova, N.I.//Degtyarev, S.K.//Verhosina, V.A.//Vinogradova, T.P. 	Screening of strains producing restriction endonucleases in Lake Baikal.	Izv. Sib. Otd. Akad. Nauk SSSR	1990	1		35-37			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. 		
@D	Dedkov, V.S.//Sinichkina, S.A.//Abdurashitov, M.A.//Popichenko, D.V.//Degtyarev, S.K. 	Restriction endonucleases FalI and FalII from Flavobacterium aquatile Ob10 recognize 5'-(8/13)AAGN5CTT(13/8)-3' and 5'-CG^CG-3',  respectively.	Biotekhnologiya	2003	6		24-29			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. 		
@D	Dedkov, V.S.//Sinichkina, S.A.//Popichenko, D.V.//Degtyarev, S.K. 	Restriction endonuclease ZraI from Zoogloea ramigera 11 recognizes 5'-GAC/GTC-3'.	Biotekhnologiya	2001	6		3-7			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. 		
@D	Dedkov, V.S.//Zernov, Y.P.//Rechkunova, N.I.//Degtyarev, S.K. 	Isolation of aquatic microorganisms producing the restriction endonucleases from the Black Sea.	Mol. Gen. Mikrobiol. Virusol.	1990	0		17-18			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. 		
@D	Dedysh, S.N.//Naumoff, D.G.//Vorobev, A.V.//Kyrpides, N.//Woyke, T.//Shapiro, N.//Crombie, A.T.//Murrell, J.C.//Kalyuzhnaya, M.G.//Smirnova, A.V.//Dunfield, P.F. 	Draft Genome Sequence of Methyloferula stellata AR4, an Obligate Methanotroph Possessing Only a Soluble Methane Monooxygenase.	Genome Announcements	2015	3		e01555-14			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. 		
@D	Deep, K.//Poddar, A.//Whitman, W.B.//Das, S.K. 	Draft Genome Sequence of Anoxybacillus suryakundensis Strain JS1T (DSM 27374T) Isolated from a Hot Spring in Jharkhand, India.	Genome Announcements	2016	4		e00824-16			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. 		
@D	DeFilippes, F.M. 	A simple assay for DNA restriction endonucleases.	Anal. Biochem.	1973	52		637-641			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. 		
@D	DeFilippes, F.M. 	A new method for isolation of a restriction enzyme from Haemophilus parainfluenzae.	Biochem. Biophys. Res. Commun.	1974	58		586-596			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. 		
@D	Defossez, P.-A. 	Ceci n'est pas une DNMT: Recently discovered functions of DNMT2 and their relation to methyltransferase activity (Comment on DOI 10.1002/bies.201300088).	Bioessays	2013	35		1024					
@D	Degnan, P.H.//Yu, Y.//Sisneros, N.//Wing, R.A.//Moran, N.A. 	Hamiltonella defensa, genome evolution of protective bacterial endosymbiont from pathogenic ancestors.	Proc. Natl. Acad. Sci. U. S. A.	2009	106		9063-9068			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. 		
@D	deGraaff, J.//Kreuning, P.C.//van de Putte, P. 	Host controlled restriction and modification of bacteriophage mu and mu-promoted chromosome mobilization in Citrobacter freundii.	Mol. Gen. Genet.	1973	123		283-288			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. 		
@D	Degtyarev, S.K.//Abdurashitov, M.A.//Kolyhalov, A.A.//Rechkunova, N.I. 	AclI, a new restriction endonuclease from Acinetobacter calcoaceticus recognizing 5'-AA^CGTT-3' .	Nucleic Acids Res.	1992	20		3787			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. 		
@D	Degtyarev, S.K.//Belavin, P.A.//Shishkina, I.G.//Zarytova, V.F.//Gavryuchenkova, L.P.//Morozov, S.M. 	Immobilized oligonucleotides as affinity ligands for restriction endonucleases.	Bioorg. Khim.	1989	15		358-362			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. 		
@D	Degtyarev, S.K.//Belichenko, O.A.//Lebedeva, N.A.//Dedkov, V.S.//Abdurashitov, M.A. 	BtrI, a novel restriction endonuclease, recognises the non-palindromic sequence 5'-CACGTC(-3/-3)-3'.	Nucleic Acids Res.	2000	28		e56			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. 		
@D	Degtyarev, S.K.//Kolyhalov, A.A.//Rechkunova, N.I.//Abdurashitov, M.A. 	AcsI, a new restriction endonuclease from Arthrobacter citreus 310 recognizing 5'-Pu^AATTPy-3'.	Nucleic Acids Res.	1992	20		3789			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. 		
@D	Degtyarev, S.K.//Kolyhalov, A.A.//Rechkunova, N.I.//Dedkov, V.S. 	Determination of substrate specificity of restriction endonuclease FauI.	Bioorg. Khim.	1989	15		130-132			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. 		
@D	Degtyarev, S.K.//Kolyhalov, A.A.//Rechkunova, N.T.//Tepavicharova, I.I.//Mechandjiska, L.I.//Builieva, E.I. 	Bsp1720I, an isoschizomer of EspI from Bacillus species 1720 recognizing 5'-GC^TNAGC-3'.	Nucleic Acids Res.	1991	19		2504			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'. 		
@D	Degtyarev, S.K.//Kolykhalov, A.A.//Rechkunova, N.I.//Dedkov, V.S.//Zhilkin, P.A. 	BsiI - A new unusual restriction endonuclease.	Mol. Biol. (Mosk)	1990	24		244-247			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. 		
@D	Degtyarev, S.K.//Netesova, N.A.//Abdurashitov, M.A.//Shevchenko, A.V. 	Primary structure and strand specificity of BstF5I-1 DNA methyltransferase which recognizes 5'-GGATG-3'.	Gene	1997	187		217-219			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'). 		
@D	Degtyarev, S.K.//Netesova, N.A.//Chizhikov, V.E.//Abdurashitov, M.A. 	Cloning and characterization of the gene encoding M.FauI DNA methyltransferase.	Biol. Chem.	1998	379		567-568			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. 		
@D	Degtyarev, S.K.//Prihodko, G.G.//Rechkunova, N.I. 	Determination of the substrate specificity of restriction endonuclease SfeI.	Bioorg. Khim.	1988	14		848-849			The recognition sequence and cleavage site C^TRYAG of a new restriction endonuclease SfeI have been determined. 		
@D	Degtyarev, S.K.//Prikhodko, E.A.//Prikhodko, G.G.//Krasnykh, V.N. 	VspI methylase belongs to m6A-gamma class of adenine methylases.	Nucleic Acids Res.	1993	21		2015			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. 		
@D	Degtyarev, S.K.//Prikhodko, E.A.//Rechkunova, N.I.//Gorbunov, Y.A. 	Interaction of VspI and Tru9I restriction endonucleases with synthetic oligonucleotides.	Biochim. Biophys. Acta	1993	1172		89-94			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. 		
@D	Degtyarev, S.K.//Prikhodko, E.A.//Rechkunova, N.I.//Prikhodko, G.G.//Krasnykh, V.N. 	Biochemical characterization of VspI methyltransferase.	Gene	1995	157		65-66			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'. 		
@D	Degtyarev, S.K.//Rechkunova, N.I. 	Determination of purity of restriction endonucleases.	Izv. Sib. Otd. Akad. Nauk SSSR	1988	14		102-105			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. 		
@D	Degtyarev, S.K.//Rechkunova, N.I.//Grinev, A.A.//Dedkov, V.S. 	Determination of substrate specificity of restriction endonucleases Bme18I and Kzo9I.	Izv. Sib. Otd. Akad. Nauk SSSR	1989	15		25-26			The recognition sequence and cleavage point of restriction endonucleases Bme18I and Kzo9I have been determined as G^G(A/T) CC and ^GATC, respectively. 		
@D	Degtyarev, S.K.//Rechkunova, N.I.//Kolyhalov, A.A.//Dedkov, V.S.//Zhilkin, P.A. 	II-Q restriction endonucleases - new class of type II enzymes.	Nucleic Acids Res.	1990	18		5807-5810			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. 		
@D	Degtyarev, S.K.//Rechkunova, N.I.//Netesova, N.A.//Tchigikov, V.E.//Malygin, E.G.//Kochkin, A.V.//Mikhajlov, V.V.//Rasskazov, V.A. 	Determination of substrate specificity of restriction endonuclease VneI.	Bioorg. Khim.	1987	13		422-423			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. 		
@D	Degtyarev, S.K.//Rechkunova, N.I.//Repin, V.E.//Kolyhalov, A.A.//Netesov, S.V. 	The recognition sequence and cleavage point of restriction endonuclease Bse 21 I.	Izv. Sib. Otd. Akad. Nauk SSSR	1990	1		138-139			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. 		
@D	Degtyarev, S.K.//Rechkunova, N.I.//Zernov, Y.P.//Dedkov, V.S.//Chizikov, V.E.//Van Calligan, M.//Williams, R.//Murray, E. 	Bsp24I, a new unusual restriction endonuclease.	Gene	1993	131		93-95			*
 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.
 
 		
@D	Degtyarev, S.K.//Repin, V.E.//Rechkunova, N.I.//Tchigikov, V.E.//Malygin, E.G.//Mikhajlov, V.V.//Rasskazov, V.A. 	Determination of the substrate specificity of restriction endonuclease VspI.	Bioorg. Khim.	1987	13		420-421			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. 		
@D	Degtyarev, S.K.//Zernov, Y.P. 	Type II restriction enzymes:  Possible evolutionary links between the enzymes and their palindromic tetranucleotide recognition sequences.	Mol. Biol. (Mosk)	1990	24		1393-1398			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. 		
@D	Degtyarev, S.K.//Zilkin, P.A.//Prihodko, G.G.//Repin, V.E.//Rechkunova, N.I. 	Determination of unusual substrate specificity of restriction endonuclease Bpu10I.	Mol. Biol. (Mosk)	1989	23		1051-1056			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. 		
@D	Deibert, M.//Grazulis, S.//Janulaitis, A.//Siksnys, V.//Huber, R. 	Crystal structure of MunI restriction endonuclease in complex with cognate DNA at 1.7 A resolution.	EMBO J.	1999	18		5805-5816			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. 		
@D	Deibert, M.//Grazulis, S.//Sasnauskas, G.//Siksnys, V.//Huber, R. 	Structure of the tetrameric restriction endonuclease NgoMIV in complex with cleaved DNA.	Nat. Struct. Biol.	2000	7		792-799			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. 		
@D	Deissler, H.//Genc, B.//Doerfler, W. 	Restriction endonuclease BsoFI is sensitive to the 5'-methylation of deoxycytidines in its recognition sequence.	Nucleic Acids Res.	1995	23		4227-4228			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. 		
@D	Deitzler, G.E.//Ruiz, M.J.//Lu, W.//Weimer, C.//Park, S.//Robinson, L.S.//Hallsworth-Pepin, K.//Wollam, A.//Mitreva, M.//Lewis, W.G.//Lewis, A.L. 	Genome Sequences of Nine Gram-Negative Vaginal Bacterial Isolates.	Genome Announcements	2016	4		e00889-16			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. 		
@D	Deitzler, G.E.//Ruiz, M.J.//Weimer, C.//Park, S.//Robinson, L.//Hallsworth-Pepin, K.//Wollam, A.//Mitreva, M.//Lewis, A.L.//Lewis, W.G. 	Genome Sequences of 14 Firmicutes Strains Isolated from the Human Vagina.	Genome Announcements	2016	4		e00888-16			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. 		
@D	DeJonckheere, J.F.//Brown, S. 	Three different group I introns in the nuclear large subunit ribosomal DNA of the amoeboflagellate Naegleria.	Nucleic Acids Res.	1998	26		456-461			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. 		
@D	Del Castillo, C.S.//Hikima, J.I.//Jang, H.B.//Nho, S.W.//Jung, T.S.//Wongtavatchai, J.//Kondo, H.//Hirono, I.//Takeyama, H.//Aoki, T. 	Comparative sequence analysis of a multi-drug resistant plasmid from Aeromonas hydrophila.	Antimicrob. Agents Chemother.	2013	57		120-129			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. 		
@D	Del Cerro, C.//Felpeto-Santero, C.//Rojas, A.//Tortajada, M.//Ramon, D.//Garcia, J.L. 	Genome Sequence of the Butanol Hyperproducer Clostridium saccharoperbutylacetonicum N1-4.	Genome Announcements	2013	1		e0007013			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. 		
@D	Del Cerro, C.//Garcia, J.M.//Rojas, A.//Tortajada, M.//Ramon, D.//Galan, B.//Prieto, M.A.//Garcia, J.L. 	Genome Sequence of the Methanotrophic Poly-beta-Hydroxybutyrate Producer Methylocystis parvus OBBP.	J. Bacteriol.	2012	194		5709-5710			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. 		
@D	del Gaudio, R.//Di Giaimo, R.//Potenza, N.//Branno, M.//Aniello, F.//Geraci, G. 	Characterization of a new variant DNA (cytosine-5)-methyltransferase unable to methylate double stranded DNA isolated from the marine annelid worm Chaetopterus variopedatus.	FEBS Lett.	1999	460		380-384			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. 		
@D	Del Giudice, L. 	Method for isolating restriction- and modificationless mutants of Escherichia coli K-12.	J. Bacteriol.	1979	137		673-676			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. 		
@D	Del Rio, T.G. et al. 	Complete genome sequence of Intrasporangium calvum type strain (7 KIP).	Standards in Genomic Sciences	2010	3		294-303			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. 		
@D	Delahodde, A.//Goguel, V.//Becam, A.M.//Creusot, F.//Perea, J.//Banroques, J.//Jacq, C. 	Site-specific DNA endonuclease and RNA maturase activities of two homologous intron-encoded proteins from yeast mitochondria.	Cell	1989	56		431-444			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). 		
@D	Delamuta, J.R.//Gomes, D.F.//Ribeiro, R.A.//Chueire, L.M.//Souza, R.C.//Almeida, L.G.//Vasconcelos, A.T.//Hungria, M. 	Genome Sequence of Bradyrhizobium tropiciagri Strain CNPSo 1112T, Isolated from a Root Nodule of Neonotonia wightii.	Genome Announcements	2015	3		e01482-15			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. 		
@D	Delamuta, J.R.//Ribeiro, R.A.//Gomes, D.F.//Souza, R.C.//Chueire, L.M.//Hungria, M. 	Genome Sequence of Bradyrhizobium stylosanthis Strain BR 446T, a Nitrogen-Fixing  Symbiont of the Legume Pasture Stylosanthes guianensis.	Genome Announcements	2016	4		e00631-16			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. 		
@D	Delamuta, J.R.M.//Ribeiro, R.A.//Gomes, D.F.//Souza, R.C.//Chueire, L.M.//Hungria, M. 	Genome Sequence of Bradyrhizobium pachyrhizi Strain PAC48T, a Nitrogen-Fixing Symbiont of Pachyrhizus erosus (L.) Urb.	Genome Announcements	2015	3		e01074-15			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. 		
@D	Delannoy, C.M.//Zadoks, R.N.//Lainson, F.A.//Ferguson, H.W.//Crumlish, M.//Turnbull, J.F.//Fontaine, M.C. 	Draft Genome Sequence of a Nonhemolytic Fish-Pathogenic Streptococcus agalactiae  Strain.	J. Bacteriol.	2012	194		6341-6342			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. 		
@D	Delannoy, S.//Mariani-Kurkdjian, P.//Bonacorsi, S.//Liguori, S.//Ison, S.A.//Fach, P. 	Draft Genome Sequences of Human-Pathogenic Escherichia coli O26:H11 Strains Carrying the stx2 Gene Only and Circulating in France.	Genome Announcements	2015	3		e00852-15			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. 		
@D	Deleo, F.R.//Chen, L.//Porcella, S.F.//Martens, C.A.//Kobayashi, S.D.//Porter, A.R.//Chavda, K.D.//Jacobs, M.R.//Mathema, B.//Olsen, R.J.//Bonomo, R.A.//Musser, J.M.//Kreiswirth, B.N. 	Molecular dissection of the evolution of carbapenem-resistant multilocus sequence type 258 Klebsiella pneumoniae.	Proc. Natl. Acad. Sci. U. S. A.	2014	111		4988-4993			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. 		
@D	Delestre, C.//Laugraud, A.//Ridgway, H.//Ronson, C.//O'Callaghan, M.//Barrett, B.//Ballard, R.//Griffiths, A.//Young, S.//Blond, C.//Gerard, E.//Wakelin, S. 	Genome sequence of the clover symbiont Rhizobium leguminosarum bv. trifolii strain CC275e.	Standards in Genomic Sciences	2015	10		121			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.). 		
@D	Delhalle, E. 	Restriction and modification of bacteriophages by Escherichia coli K12 involving a cryptic P1 prophage associated with different plasmids.	Ann. Microbiol. (Paris)	1973	124A		173-178			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. 		
@D	Deligios, M.//Bacciu, D.//Deriu, E.//Corti, G.//Bordoni, R.//De Bellis, G.//Leori, G.S.//Rubino, S.//Uzzau, S. 	Draft Genome Sequence of the Host-Restricted Salmonella enterica Serovar Abortusovis Strain SS44.	Genome Announcements	2014	2		e00261-14			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. 		
@D	DeLong, E.F.//Preston, C.M.//Mincer, T.//Rich, V.//Hallam, S.J.//Frigaard, N.U.//Martinez, A.//Sullivan, M.B.//Edwards, R.//Brito, B.R.//Chisholm, S.W.//Karl, D.M. 	Community genomics among stratified microbial assemblages in the ocean's interior.	Science	2006	311		496-503			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. 		
@D	Delorme, C.//Bartholini, C.//Luraschi, M.//Pons, N.//Loux, V.//Almeida, M.//Guedon, E.//Gibrat, J.F.//Renault, P. 	Complete Genome Sequence of the Pigmented Streptococcus thermophilus Strain JIM8232.	J. Bacteriol.	2011	193		5581-5582			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. 		
@D	Delorme, C.//Guedon, E.//Pons, N.//Cruaud, C.//Couloux, A.//Loux, V.//Chiapello, H.//Poyart, C.//Gautier, C.//Sanchez, N.//Almeida, M.//Kennedy, S.//Ehrlich, S.D.//Gibrat, J.F.//Wincker, P.//Renault, P. 	Complete Genome Sequence of the clinical Streptococcus salivarius strain CCHSS3.	J. Bacteriol.	2011	193		5041-5042			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. 		
@D	DelVecchio, V.G. et al. 	The genome sequence of the facultative intracellular pathogen Brucella melitensis.	Proc. Natl. Acad. Sci. U. S. A.	2002	99		443-448			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. 		
@D	Delver, E.P.//Agofanova, O.V.//Tupikova, E.E.//Vorobeva, E.P.//Belogurov, A.A. 	System controlling expression of antirestriction genes ardA and ardB of IncN transmission plasmid pKM101 (R46).	Mol. Biol. (Mosk)	1998	32		208-213			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. 		
@D	Delver, E.P.//Kotova, V.U.//Zavilgelsky, G.B.//Belogurov, A.A. 	Nucleotide sequence of the Gene (ard) encoding the antirestriction protein of plasmid colIb-P9.	J. Bacteriol.	1991	173		5887-5892			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. 		
@D	Demarre, G.//Chattoraj, D.K. 	DNA adenine methylation is required to replicate both Vibrio cholerae chromosomes once per cell cycle.	PLoS Genet.	2010	6		e1000939			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. 		
@D	Dematheis, F.//Antwerpen, M.H.//Grass, G.//Walter, M.C.//Borgmann, S. 	Genome Sequence of Bacillus safensis Strain Ingolstadt Isolated from the Pectoralis Pouch of a Patient with Defibrillator-Related Surgery.	Genome Announcements	2017	5		e01031-17			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. 		
@D	deMayo, J.A.//Maas, K.R.//Klassen, J.L.//Balunas, M.J. 	Draft Genome Sequence of Streptomyces sp. AVP053U2 Isolated from Styela clava, a  Tunicate Collected in Long Island Sound.	Genome Announcements	2016	4		e00874-16			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. 		
@D	Demey, L.M.//Miller, C.R.//Manzella, M.P.//Spurbeck, R.R.//Sandhu, S.K.//Reguera, G.//Kashefi, K. 	The draft genome of the hyperthermophilic archaeon Pyrodictium delaneyi strain hulk, an iron and nitrate reducer, reveals the capacity for sulfate reduction.	Standards in Genomic Sciences	2017	12		47			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. 		
@D	Demidova, G.V.//Goncharov, E.K.//Tynianova, V.I. 	Comparison of specific recognition sites of adenine and cytosine DNA-methyltransferase of Yersinia pestis EV 76C dam and dcm by Escherichia coli methylases.	Biokhimiia	1984	49		1594-1597			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. 		
@D	Dempsey, R.M.//Carroll, D.//Kong, H.M.//Higgins, L.//Keane, C.T.//Coleman, D.C. 	Sau421, a Bcgl-like restriction-modification system encoded by the Staphylococcus aureus quadruple-converting phage phi 42.	Microbiology	2005	151		1301-1311			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. 		
@D	den Bakker, H.C.//Moreno-Switt, A.I.//Govoni, G.//Cummings, C.A.//Ranieri, M.L.//Degoricija, L.//Hoelzer, K.//Rodriguez-Rivera, L.D.//Brown, S.//Bolchacova, E.//Furtado, M.R.//Wiedmann, M. 	Genome sequencing reveals diversification of virulence factor content and possible host adaptation in distinct subpopulations of Salmonella enterica.	BMC Genomics	2011	12		425			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. 		
@D	Denes, T.//Vongkamjan, K.//Ackermann, H.W.//Moreno-Switt, A.I.//Wiedmann, M.//den Bakker, H.C. 	Comparative genomic and morphological analysis of Listeria phages isolated from farm environments.	Appl. Environ. Microbiol.	2014	80		4616-4625			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. 		
@D	Deng, H.//Yang, X.//Yeo, S.P.//Gao, Z. 	Highly Sensitive Electrochemical Methyltransferase Activity Assay.	Anal. Chem.	2014	86		2117-2123			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. 		
@D	Deng, J.//Szyf, M. 	Multiple isoforms of DNA methyltransferase are encoded by the vertebrate cytosine DNA methyltransferase gene.	J. Biol. Chem.	1998	273		22869-22872			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. 		
@D	Deng, P.//Wang, X.//Baird, S.M.//Lu, S.E. 	Complete genome of Pseudomonas chlororaphis strain UFB2, a soil bacterium with antibacterial activity against bacterial canker pathogen of tomato.	Standards in Genomic Sciences	2015	10		117			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. 		
@D	Deng, W. et al. 	Genome sequence of Yersinia pestis KIM.	J. Bacteriol.	2002	184		4601-4611			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. 		
@D	Deng, W.//Liou, S.R.//Plunkett, I.I.I.G.//Mayhew, G.F.//Rose, D.J.//Burland, V.//Kodoyianni, V.//Schwartz, D.C.//Blattner, F.R. 	Comparative Genomics of Salmonella enterica Serovar Typhi Strains Ty2 and CT18.	J. Bacteriol.	2003	185		2330-2337			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. 		
@D	Deng, X.//Dohmae, N.//Nealson, K.H.//Hashimoto, K.//Okamoto, A. 	Multi-heme cytochromes provide a pathway for survival in energy-limited environments.	Sci. Adv.	2018	4		eaao5682			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. 		
@D	Deng, X.//Salazar, J.K.//Frezet, S.//Maccannell, D.//Ribot, E.M.//Fields, P.I.//Fricke, W.F.//Zhang, W. 	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.	Genome Announcements	2013	1		e00260-13			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. 		
@D	Deng, Y.//Chen, C.//Zhao, Z.//Huang, X.//Yang, Y.//Ding, X. 	Complete Genome Sequence of Vibrio alginolyticus ZJ-T.	Genome Announcements	2016	4		e00912-16			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. 		
@D	Deng, Y.//Zhu, Y.//Wang, P.//Zhu, L.//Zheng, J.//Li, R.//Ruan, L.//Peng, D.//Sun, M. 	Complete Genome Sequence of Bacillus subtilis BSn5, an Endophytic Bacterium of Amorphophallus konjac with Antimicrobial Activity for the  Plant Pathogen Erwinia carotovora subsp. carotovora.	J. Bacteriol.	2011	193		2070-2071			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. 		
@D	Deng, Y.M.//Liu, C.Q.//Dunn, N.W. 	LldI, a plasmid-encoded type I restriction and modification system in Lactococcus lactis.	DNA Seq.	2000	11		239-245			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. 		
@D	Denjmuchametov, M.M.//Ruban, N.M.//Zakharova, M.V.//Beletzkaja, I.V.//Kravetz, A.N.//Solonin, A.S. 	Eco27kI, a new isoschizomer of AvaI from Escherichia coli.	Nucleic Acids Res.	1992	20		1992			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'. 		
@D	Denjmukhametov, M.M.//Brevnov, M.G.//Zakharova, M.V.//Repyk, A.V.//Solonin, A.S.//Petrauskene, O.V.//Gromova, E.S. 	The Ecl18kI restriction-modification system: cloning, expression, properties of the purified enzymes.	FEBS Lett.	1998	433		233-236			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. 		
@D	Denjmukhametov, M.M.//Zakharova, M.V.//Kravets, A.N.//Pertsev, A.V.//Sineva, E.V.//Repik, A.V.//Beletskaya, I.V.//Gromova, E.S.//Solonin, A.S. 	Characterization of plasmids encoding type II restriction-modification systems, isoschizomers of SsoII.	Mol. Biol. (Mosk)	1997	31		831-838			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. 		
@D	Dennison, N.J.//Saraiva, R.G.//Cirimotich, C.M.//Mlambo, G.//Mongodin, E.F.//Dimopoulos, G. 	Functional genomic analyses of Enterobacter, Anopheles and Plasmodium reciprocal interactions that impact vector competence.	Malar. J.	2016	15		425			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. 		
@D	Denny, A.L.//Arruda, S.E. 	Draft Genome Sequences of Escherichia coli Strains FP2 and FP3, Isolated from the Canada Goose (Branta canadensis).	Microbiol. Resour. Announc.	2018	7		e01079-18			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). 		
@D	Denou, E.//Bruttin, A.//Barretto, C.//Ngom-Bru, C.//Brussow, H.//Zuber, S. 	T4 phages against Escherichia coli diarrhea: potential and problems.	Virology	2009	388		21-30			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. 		
@D	Denovan-Wright, E.M.//Nedelcu, A.M.//Lee, R.W. 	Complete sequence of the mitochondrial DNA of Chlamydomonas eugametos.	Plant Mol. Biol.	1998	36		285-295			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. 		
@D	deOliveira-Cunha, C.//Goda-Zuleta, L.F.//Paula-deAlmeida, L.G.//Prioli-Ciapina, L.//Lustrino-Borges, W.//Pitard, R.M.//Baldani, J.I.//Straliotto, R.//deFaria, S.M.//Hungria, M.//Sousa-Cavada, B.//Mercante, F.M.//Ribeiro-deVasconcelos, A.T. 	Complete Genome Sequence of Burkholderia phenoliruptrix BR3459a (CLA1), a Heat-Tolerant, Nitrogen-Fixing Symbiont of Mimosa flocculosa.	J. Bacteriol.	2012	194		6675-6676			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. 		
@D	DePaoli-Roach, A.//Roach, P.J.//Zucker, K.E.//Smith, S.S. 	Selective phosphorylation of human DNA methyltransferase by protein kinase C.	FEBS Lett.	1986	197		149-153			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. 		
@D	Deplus, R.//Brenner, C.//Burgers, W.A.//Putmans, P.//Kouzarides, T.//de Launoit, Y.//Fuks, F. 	Dnmt3L is a transcriptional repressor that recruits histone deacetylase.	Nucleic Acids Res.	2002	30		3831-3838			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. 		
@D	Deppenmeier, U. et al. 	The genome of Methanosarcina mazei: evidence for lateral gene transfer between bacteria and archaea.	J. Mol. Microbiol. Biotechnol.	2002	4		453-461			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. 		
@D	Deptula, P.//Laine, P.K.//Roberts, R.J.//Smolander, O.P.//Vihinen, H.//Piironen, V.//Paulin, L.//Jokitalo, E.//Savijoki, K.//Auvinen, P.//Varmanen, P. 	De novo assembly of genomes from long sequence reads reveals uncharted territories of Propionibacterium freudenreichii.	BMC Genomics	2017	18		790			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. 		
@D	Deraspe, M.//Alexander, D.C.//Xiong, J.//Ma, J.H.//Low, D.E.//Jamieson, F.B.//Roy, P.H. 	Genomic analysis of Pseudomonas aeruginosa PA96, the host of carbapenem resistance plasmid pOZ176.	FEMS Microbiol. Lett.	2014	356		212-216			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. 		
@D	Derbise, A.//Chenal-Francisque, V.//Huon, C.//Fayolle, C.//Demeure, C.E.//Chane-Woon-Ming, B.//Medigue, C.//Hinnebusch, B.J.//Carniel, E. 	Delineation and Analysis of Chromosomal Regions Specifying Yersinia pestis.	Infect. Immun.	2010	78		3930-3941			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. 		
@D	Derbyshire, V.//Kowalski, J.C.//Dansereau, J.T.//Hauer, C.R.//Belfort, M. 	Two-domain structure of the td intron-encoded endonuclease I-TevI correlates with the two-domain configuration of the homing site.	J. Mol. Biol.	1997	265		494-506			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. 		
@D	Dertli, E.//Skory, C.D.//Simsek, O. 	Genome Sequences of Five Lactobacillus sp. Isolates from Traditional Turkish Sourdough.	Genome Announcements	2018	6		e00616-18			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. 		
@D	Desai, D.//Li, J.H.//van Zijll-de-Jong, E.//Braun, R.//Pitman, A.//Visnovsky, S.//Hampton, J.//Christey, M. 	Draft Genome Sequences of Two New Zealand Xanthomonas campestris pv. campestris Isolates, ICMP 4013 and ICMP 21080.	Genome Announcements	2015	3		e01247-15			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. 		
@D	Desai, H.P.//Morrison, S.S.//Diaz, M.H.//Benitez, A.J.//Wolff, B.J.//Winchell, J.M. 	Complete Genome Sequence of Mycoplasma pneumoniae Type 2 Reference Strain FH Using Single-Molecule Real-Time Sequencing Technology.	Genome Announcements	2017	5		e01629-16			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. 		
@D	Desai, P.T.//Porwollik, S.//Long, F.//Cheng, P.//Wollam, A.//Bhonagiri-Palsikar, V.//Hallsworth-Pepin, K.//Clifton, S.W.//Weinstock, G.M.//McClelland, M. 	Evolutionary Genomics of Salmonella enterica Subspecies.	MBio	2013	4		e00198-13			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. 		
@D	Deschamps, P.//Zivanovic, Y.//Moreira, D.//Rodriguez-Valera, F.//Lopez-Garcia, P. 	Pangenome evidence for extensive interdomain horizontal transfer affecting lineage core and shell genes in uncultured planktonic thaumarchaeota and euryarchaeota.	Genome Biol. Evol.	2014	6		1549-1563			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. 		
@D	Deschavanne, P.//Radman, M. 	Counterselection of GATC sequences in enterobacteriophages by the components of the methyl-directed mismatch repair system.	J. Mol. Evol.	1991	33		125-132			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.
 
 		
@D	Descloux, S.//Rossano, A.//Perreten, V. 	Characterization of new Staphylococcal Cassette Chromosome mec (SCCmec) and topoisomerase genes in fluoroquinolone and methicillin-resistant Staphylococcus pseudintermedius.	J. Clin. Microbiol.	2008	46		1818-1823			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. 		
@D	Deshpande, N.P.//Wong, Y.K.//Manefield, M.//Wilkins, M.R.//Lee, M. 	Genome Sequence of Dehalobacter UNSWDHB, a Chloroform-Dechlorinating Bacterium.	Genome Announcements	2013	1		e00720-13			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. 		
@D	Deshuillers, P.L.//Santos, A.P.//do Nascimento, N.C.//Hampel, J.A.//Bergin, I.L.//Dyson, M.C.//Messick, J.B. 	Complete Genome Sequence of Mycoplasma ovis Strain Michigan, a Hemoplasma of Sheep with Two Distinct 16S rRNA Genes.	Genome Announcements	2014	2		e01235-13			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. 		
@D	Desiere, F.//McShan, W.M.//van Sinderen, D.//Ferretti, J.J.//Brussow, H. 	Comparative Genomics Reveals Close Genetic Relationships between Phages from Dairy Bacteria and Pathogenic Streptococci: Evolutionary Implications for Prophage-Host Interactions.	Virology	2001	288		325-341			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. 		
@D	Desiniotis, A.//Kouvelis, V.N.//Davenport, K.//Bruce, D.//Detter, C.//Tapia, R.//Han, C.//Goodwin, L.A.//Woyke, T.//Kyrpides, N.C.//Typas, M.A.//Pappas, K.M. 	Complete Genome Sequence of the Ethanol-Producing Zymomonas mobilis subsp. mobilis Centrotype ATCC 29191.	J. Bacteriol.	2012	194		5966-5967			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. 		
@D	Desirazu, N.R.//Reddy, Y.V. 	Targetted DNA distortion by EcoP15I DNA methyltransferase.	Biochem. Soc. Trans.	2000	28		A309			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. 		
@D	Detich, N.//Hamm, S.//Just, G.//Knox, J.D.//Szyf, M. 	The methyl donor S-adenosylmethionine inhibits active demethylation of DNA: a candidate novel mechanism for the pharmacological effects of s-adenosylmethionine.	J. Biol. Chem.	2003	278		20812-20820			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. 		
@D	Detich, N.//Ramchandani, S.//Szyf, M. 	A conserved 3'-untranslated element mediates growth regulation of DNA methyltransferase 1 and inhibits its transforming activity.	J. Biol. Chem.	2001	276		24881-24890			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. 		
@D	Detich, N.//Theberge, J.//Szyf, M. 	Promoter-specific activation and demethylation by MBD2/demethylase.	J. Biol. Chem.	2002	277		35791-35794			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. 		
@D	Deutsch, J.//Razin, A.//Sedat, J. 	Analysis of 5-methylcytosine in DNA.	Anal. Biochem.	1976	72		586-592			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. 		
@D	Devajyothi, C.//Brahmachari, V. 	Detection of a CpA methylase in an insect system: Characterization and substrate specificity.	Mol. Cell. Biochem.	1992	110		103-111			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. 		
@D	Deveau, A.//Gross, H.//Morin, E.//Karpinets, T.//Utturkar, S.//Mehnaz, S.//Martin, F.//Frey-Klett, P.//Labbe, J. 	Genome Sequence of the Mycorrhizal Helper Bacterium Pseudomonas fluorescens BBc6R8.	Genome Announcements	2014	2		e01152-13			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. 		
@D	Devers-Lamrani, M.//Spor, A.//Mounier, A.//Martin-Laurent, F. 	Draft Genome Sequence of Pseudomonas sp. Strain ADP, a Bacterial Model for Studying the Degradation of the Herbicide Atrazine.	Genome Announcements	2016	4		e01733-15			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. 		
@D	Devi, S.H.//Taylor, T.D.//Avasthi, T.S.//Kondo, S.//Suzuki, Y.//Megraud, F.//Ahmed, N. 	Genome of Helicobacter pylori Strain 908.	J. Bacteriol.	2010	192		6488-6489			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. 		
@D	Devi, U.//Khatri, I.//Kumar, N.//Kumar, L.//Sharma, D.//Subramanian, S.//Saini, A.K. 	Draft Genome Sequence of a Plant Growth-Promoting Rhizobacterium, Serratia fonticola Strain AU-P3(3).	Genome Announcements	2013	1		e00946-13			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. 		
@D	Devi, U.//Khatri, I.//Kumar, N.//Sharma, D.//Subramanian, S.//Saini, A.K. 	Draft Genome Sequence of Plant-Growth-Promoting Rhizobacterium Serratia fonticola Strain AU-AP2C, Isolated from the Pea Rhizosphere.	Genome Announcements	2013	1		e01022-13			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. 		
@D	Devitt, N.P.//Herman, B.//Luchterhand, R.A.//Costa, M.A.//Jacobi, J.L.//Davin, L.B.//Lewis, N.G.//Bell, C.J. 	Draft Genome Sequence of a Gordonia sp. Isolated from the Soil of a Red Alder Plant.	Genome Announcements	2017	5		e01039-17			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. 		
@D	Devor, E.J. 	The relative efficiency of restriction enzymes:  an update.	Am. J. Hum. Genet.	1988	42		179-182			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. 		
@D	Dey, R.//Pal, K.K.//Sherathia, D.//Dalsania, T.//Savsani, K.//Patel, I.//Sukhadiya, B.//Mandaliya, M.//Thomas, M.//Ghorai, S.//Vanpariya, S.//Rupapara, R.//Rawal, P.//Saxena, A.K. 	Draft Genome Sequence of Bacillus sp. Strain NSP2.1, a Nonhalophilic Bacterium Isolated from the Salt Marsh of the Great Rann of Kutch, India.	Genome Announcements	2013	1		e00909-13			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. 		
@D	Dey, R.//Pal, K.K.//Sherathia, D.//Dalsania, T.//Savsani, K.//Patel, I.//Thomas, M.//Ghorai, S.//Vanpariya, S.//Rupapara, R.//Rawal, P.//Sukhadiya, B.//Mandaliya, M.//Saxena, A.K. 	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.	Genome Announcements	2013	1		e00835-13			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. 		
@D	Dey, R.//Pal, K.K.//Sherathia, D.//Sukhadiya, B.//Dalsania, T.//Patel, I.//Savsani, K.//Thomas, M.//Vanpariya, S.//Mandaliya, M.//Rupapara, R.//Rawal, P.//Ghorai, S.//Bhayani, S.//Shah, A.//Saxena, A.K. 	Insight into the First Draft Genome Sequence of the Genus Sediminibacillus, Sediminibacillus halophilus Strain NSP9.3.	Genome Announcements	2014	2		e01133-13			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. 		
@D	Dey, R.//Pal, K.K.//Sherathia, D.//Vanpariya, S.//Patel, I.//Dalsania, T.//Savsani, K.//Sukhadiya, B.//Mandaliya, M.//Thomas, M.//Ghorai, S.//Rupapara, R.//Rawal, P. 	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.	Genome Announcements	2013	1		e01104-13			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. 		
@D	Dhakal, R.//Seale, R.//Brent, D.//Hilton, C.//Craven, H.//Turner, M.S. 	Draft Genome Comparison of Representatives of the Three Dominant Genotype Groups of Dairy Bacillus licheniformis Strains.	Appl. Environ. Microbiol.	2014	80		3453-3462			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. 		
@D	Dhakan, D.B.//Saxena, R.//Chaudhary, N.//Sharma, V.K. 	Draft Genome Sequence of Tepidimonas taiwanensis Strain MB2, a Chemolithotrophic  Thermophile Isolated from a Hot Spring in Central India.	Genome Announcements	2016	4		e01723-15			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. 		
@D	Dhar, H.//Swarnkar, M.K.//Gulati, A.//Singh, A.K.//Kasana, R.C. 	Draft Genome Sequence of a Cellulase-Producing Psychrotrophic Paenibacillus Strain, IHB B 3415, Isolated from the Cold Environment of the Western Himalayas,  India.	Genome Announcements	2015	3		e01581-14			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. 		
@D	Dharmalingam, K.//Goldberg, E.B. 	Restriction in vivo.  IV. Effect of restriction of parental DNA on the expression of restriction alleviation systems in phage T4.	Virology	1979	96		404-411			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. 		
@D	Dharmalingam, K.//Goldberg, E.B. 	Mechanism localisation and control of restriction cleavage of phage T4 and lambda chromosomes in vivo.	Nature	1976	260		406-410			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. 		
@D	Dharmalingam, K.//Goldberg, E.B. 	Restriction in vivo.  V. Induction of SOS functions in Escherichia coli by restricted T4 phage DNA and alleviation of restriction by SOS functions.	Mol. Gen. Genet.	1980	178		51-58			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. 		
@D	Dharmalingam, K.//Goldberg, E.B. 	Phage-coded protein prevents restriction of unmodified progeny T4 DNA.	Nature	1976	260		454-455			None 		
@D	Dharmalingam, K.//Revel, H.R.//Goldberg, E.B. 	Physical mapping and cloning of bacteriophage T4 anti-restriction ednonuclease gene.	J. Bacteriol.	1982	149		694-699			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. 		
@D	Dharmaprakash, A.//Reghunathan, D.//Sivakumar, K.C.//Prasannakumar, M.//Thomas, S. 	Insights into the Genome Sequences of an N-Acyl Homoserine Lactone Molecule Producing Two Pseudomonas spp. Isolated from the Arctic.	Genome Announcements	2016	4		e00767-16			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. 		
@D	Dherbecourt, J.//Falentin, H.//Canaan, S.//Thierry, A. 	A genomic search approach to identify esterases in Propionibacterium freudenreichii involved in the formation of flavour in Emmental cheese.	Microb. Cell Fact.	2008	7		16			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. 		
@D	Dhillon, B.//Cavaletto, J.R.//Wood, K.V.//Goodwin, S.B. 	Accidental Amplification and Inactivation of a Methyltransferase Gene Eliminates Cytosine Methylation in Mycosphaerella graminicola.	Genetics	2010	186		67			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. 		
@D	Di Bonaventura, M.P.//Desalle, R.//Pop, M.//Nagarajan, N.//Figurski, D.H.//Fine, D.H.//Kaplan, J.B.//Planet, P.J. 	Complete Genome Sequence of Aggregatibacter (Haemophilus) aphrophilus NJ8700.	J. Bacteriol.	2009	191		4693-4694			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. 		
@D	Di Cagno, R.//De Angelis, M.//Cattonaro, F.//Gobbetti, M. 	Draft Genome Sequence of Lactobacillus rossiae DSM 15814T.	J. Bacteriol.	2012	194		5460-5461			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. 		
@D	Di Gennaro, P.//Zampolli, J.//Presti, I.//Cappelletti, M.//D'Ursi, P.//Orro, A.//Mezzelani, A.//Milanesi, L. 	Genome Sequence of Rhodococcus opacus Strain R7, a Biodegrader of Mono- and Polycyclic Aromatic Hydrocarbons.	Genome Announcements	2014	2		e00827-14			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. 		
@D	Di Giaimo, R.//Locascio, A.//Aniello, F.//Branno, M.//del Gaudio, R.//Potenza, N.//Geraci, G. 	DNA (cytosine-5) methyltransferase turnover and cellular localization in developing Paracentrotus lividus sea urchin embryo.	Gene	2001	272		199-208			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. 		
@D	Di Lallo, G.//Evangelisti, M.//Mancuso, F.//Ferrante, P.//Marcelletti, S.//Tinari, A.//Superti, F.//Migliore, L.//D'Addabbo, P.//Frezza, D.//Scortichini, M.//Thaller, M.C. 	Isolation and partial characterization of bacteriophages infecting Pseudomonas syringae pv. actinidiae, causal agent of kiwifruit bacterial canker.	J. Basic Microbiol.	2014	54		1-12			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. 		
@D	Di Pilato, V.//Chiarelli, A.//Boinett, C.J.//Riccobono, E.//Harris, S.R.//D'Andrea, M.M.//Thomson, N.R.//Rossolini, G.M.//Giani, T. 	Complete Genome Sequence of the First KPC-Type Carbapenemase-Positive Proteus mirabilis Strain from a Bloodstream Infection.	Genome Announcements	2016	4		e00607-16			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. 		
@D	Di Pilato, V.//Pollini, S.//Rossolini, G.M. 	Characterization of plasmid pAX22, encoding VIM-1 metallo-beta-lactamase, reveals a new putative mechanism of In70 integron mobilization.	J. Antimicrob. Chemother.	2014	69		67-71			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. 		
@D	Di, D.Y.//Jang, J.//Unno, T.//Hur, H.G. 	Emergence of Klebsiella variicola positive for NDM-9, a variant of New Delhi metallo-beta-lactamase, in an urban river in South Korea.	J. Antimicrob. Chemother.	2017	72		1063-1067			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. 		
@D	Diagne, N.//Swanson, E.//Pesce, C.//Fall, F.//Diouf, F.//Bakhoum, N.//Fall, D.//Faye, M.N.//Oshone, R.//Simpson, S.//Morris, K.//Thomas, W.K.//Moulin, L.//Diouf, D.//Tisa, L.S. 	Permanent Draft Genome Sequences for Mesorhizobium sp. Strains LCM 4576, LCM 4577, and ORS3428, Salt-Tolerant, Nitrogen-Fixing Bacteria Isolated from  Senegalese Soils.	Genome Announcements	2017	5		e01154-17			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. 		
@D	Diagne, N.//Swanson, E.//Pesce, C.//Fall, F.//Diouf, F.//Bakhoum, N.//Fall, D.//Ndigue, F.M.//Oshone, R.//Simpson, S.//Morris, K.//Thomas, W.K.//Moulin, L.//Diouf, D.//Tisa, L.S. 	Permanent Draft Genome Sequence of Ensifer sp. Strain LCM 4579, a Salt-Tolerant,  Nitrogen-Fixing Bacterium Isolated from Senegalese Soil.	Genome Announcements	2017	5		e00117-17			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. 		
@D	Diagne, N.//Swanson, E.//Pesce, C.//Fall, F.//Diouf, F.//Bakhoum, N.//Fall, D.//Ndigue, F.M.//Oshone, R.//Simpson, S.//Morris, K.//Thomas, W.K.//Moulin, L.//Diouf, D.//Tisa, L.S. 	Permanent Draft Genome Sequence of Rhizobium sp. Strain LCM 4573, a Salt-Tolerant, Nitrogen-Fixing Bacterium Isolated from Senegalese Soils.	Genome Announcements	2017	5		e00285-17			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. 		
@D	Dias, G.M.//Thompson, C.C.//Fishman, B.//Naka, H.//Haygood, M.G.//Crosa, J.H.//Thompson, F.L. 	Genome Sequence of the Marine Bacterium Vibrio campbellii DS40M4, Isolated from Open Ocean Water.	J. Bacteriol.	2012	194		904			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. 		
@D	Dias, L.M.//Alves, J.T.//Veras, A.A.//Barauna, R.A.//Sa, P.H.//Spier, S.//Edman, J.M.//Guimaraes, L.C.//Rocha, F.S.//Ramos, R.T.//Azevedo, V.//Silva, A.//Carneiro, A.R. 	Whole-Genome Sequence of Corynebacterium pseudotuberculosis Strain 226, Isolated  from the Abscess of a Goat in California.	Genome Announcements	2016	4		e00038-16			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. 		
@D	Diaz, L.A.//Hardisson, C.//Rodicio, M.R. 	Isolation and characterization of actinophages infecting Streptomyces species and their interaction with host restriction-modification systems.	J. Gen. Microbiol.	1989	135		1847-1856			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. 		
@D	Diaz, M.//Wegmann, U.//Akinyemi, N.//Oguntoyinbo, F.A.//Sayavedra, L.//Mayer, M.J.//Narbad, A. 	Complete Genome Sequence of Ochrobactrum haematophilum FI11154, Isolated from Kunu-Zaki, a Nigerian Millet-Based Fermented Food.	Genome Announcements	2018	6		e00428-18			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. 		
@D	Diaz, M.H.//Desai, H.P.//Morrison, S.S.//Benitez, A.J.//Wolff, B.J.//Caravas, J.//Read, T.D.//Dean, D.//Winchell, J.M. 	Comprehensive bioinformatics analysis of Mycoplasma pneumoniae genomes to investigate underlying population structure and type-specific determinants.	PLoS ONE	2017	12		E0174701			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. 		
@D	Diaz-Cardenas, C.//Lopez, G.//Alzate-Ocampo, J.D.//Gonzalez, L.N.//Shapiro, N.//Woyke, T.//Kyrpides, N.C.//Restrepo, S.//Baena, S. 	Draft genome sequence of Dethiosulfovibrio salsuginis DSM 21565(T) an anaerobic,  slightly halophilic bacterium isolated from a Colombian saline spring.	Standards in Genomic Sciences	2017	12		86			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. 		
@D	Diaz-Quinonez, J.A.//Hernandez-Monroy, I.//Lopez-Martinez, I.//Ortiz-Alcantara, J.//Gonzalez-Duran, E.//Ruiz-Matus, C.//Kuri-Morales, P.//Ramirez-Gonzalez, J.E. 	Genome Sequence of Vibrio cholerae Strain O1 Ogawa El Tor, Isolated in Mexico, 2013.	Genome Announcements	2014	2		e01123-14			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. 		
@D	Diaz-Sanchez, S.//Hernandez-Jarguin, A.//Fernandez-de-Mera, I.G.//Alberdi, P.//Zweygarth, E.//Gortazar, C.//de la Fuente, J. 	Draft Genome Sequences of Anaplasma phagocytophilum, A. marginale, and A. ovis Isolates from Different Hosts.	Genome Announcements	2018	6		e01503-17			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. 		
@D	Dib, J.R.//Angelov, A.//Liebl, W.//Dobber, J.//Voget, S.//Schuldes, J.//Gorriti, M.//Farias, M.E.//Meinhardt, F.//Daniel, R. 	Complete Genome Sequence of the Linear Plasmid pJD12 Hosted by Micrococcus sp. D12, Isolated from a High-Altitude Volcanic Lake in Argentina.	Genome Announcements	2015	3		e00627-15			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. 		
@D	Dichosa, A.E. et al. 	Draft Genome Sequence of Thauera sp. Strain SWB20, Isolated from a Singapore Wastewater Treatment Facility Using Gel Microdroplets.	Genome Announcements	2015	3		e00132-15			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. 		
@D	Dick, G.J.//Andersson, A.F.//Baker, B.J.//Simmons, S.L.//Thomas, B.C.//Yelton, A.P.//Banfield, J.F. 	Community-wide analysis of microbial genome sequence signatures.	Genome Biology	2009	10		R85			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. 		
@D	Dick, G.J.//Podell, S.//Johnson, H.A.//Rivera-Espinoza, Y.//Bernier-Latmani, R.//McCarthy, J.K.//Torpey, J.W.//Clement, B.G.//Gaasterland, T.//Tebo, B.M. 	Genomic insights into Mn(II) oxidation by the marine alphaproteobacterium Aurantimonas sp. strain SI85-9A1.	Appl. Environ. Microbiol.	2008	74		2646-2658			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. 		
@D	Dickerson, R.E.//Drew, H.R. 	Structure of a B-DNA dodecamer  II.  Influence of base sequence on helix structure.	J. Mol. Biol.	1981	149		761-786			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. 		
@D	Dickman, S. 	Lithuanian biochemist builds enzyme empire.	Science	1992	257		1473-1474			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. 		
@D	Didelot, X.//Pang, B.//Zhou, Z.//McCann, A.//Ni, P.//Li, D.//Achtman, M.//Kan, B. 	The role of china in the global spread of the current cholera pandemic.	PLoS Genet.	2015	11		E1005072			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. 		
@D	Didier, S.//Lazzaroni, J.C.//Portalier, R. 	Cell localization of EcoRI endonuclease in Escherichia coli K-12.	Appl. Microbiol. Biotechnol.	1988	28		468-470			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. 		
@D	Didovyk, A. 	The structural basis of DNA recognition and base extrusion by a DNA cytosine-5 methyltransferase M.HaeIII.	Ph.D. Thesis, Harvard University, USA	2010						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. 		
@D	Didovyk, A.//Verdine, G.L. 	Structural Origins of DNA Target Selection and Nucleobase Extrusion by a DNA Cytosine Methyltransferase.	J. Biol. Chem.	2012	287		40099-40105			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. 		
@D	Dieguez, A.L.//Romalde, J.L. 	Complete Genome Sequence of Arcobacter sp. Strain LFT 1.7 Isolated from Great Scallop (Pecten maximus) Larvae.	Genome Announcements	2017	5		e01617-16			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. 		
@D	Dieguez, A.L.//Romalde, J.L. 	Draft Genome Sequences of Neptuniibacter sp. Strains LFT 1.8 and ATR 1.1.	Genome Announcements	2017	5		e01541-16			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. 		
@D	Diekmann, S.//McLaughlin, L.W. 	DNA curvature in native and modified EcoRI recognition sites and possible influence upon the endonuclease cleavage reaction.	J. Mol. Biol.	1988	202		823-834			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. 		
@D	Diene, S.M.//Merhej, V.//Henry, M.//El Filali, A.//Roux, V.//Robert, C.//Azza, S.//Gavory, F.//Barbe, V.//La Scola, B.//Raoult, D.//Rolain, J.M. 	The Rhizome of the Multidrug-Resistant Enterobacter aerogenes Genome Reveals How New 'Killer Bugs' Are Created because of a Sympatric Lifestyle.	Mol. Biol. Evol.	2013	30		369-383			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. 		
@D	Diep, A.L.//Lang, J.M.//Darling, A.E.//Eisen, J.A.//Coil, D.A. 	Draft Genome Sequence of Dietzia sp. Strain UCD-THP (Phylum Actinobacteria).	Genome Announcements	2013	1		e00197-13			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. 		
@D	Diep, B.A.//Gill, S.R.//Chang, R.F.//Phan, T.H.//Chen, J.H.//Davidson, M.G.//Lin, F.//Lin, J.//Carleton, H.A.//Mongodin, E.F.//Sensabaugh, G.F.//Perdreau-Remington, F. 	Complete genome sequence of USA300, an epidemic clone of community-acquired meticillin-resistant Staphylococcus aureus.	Lancet	2006	367		731-739			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. 		
@D	Dikic, J.//Menges, C.//Clarke, S.//Kokkinidis, M.//Pingoud, A.//Wende, W.//Desbiolles, P. 	The rotation-coupled sliding of EcoRV.	Nucleic Acids Res.	2012	40		4064-4070			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. 		
@D	Dila, D.//Raleigh, E.A. 	Genetic dissection of the methylcytosine-specific restriction system mcrB of Escherichia coli K-12.	Gene	1988	74		23-24			Meeting Abstract 		
@D	Dila, D.//Sutherland, E.//Moran, L.//Slatko, B.//Raleigh, E.A. 	Genetic and sequence organization of the mcrBC locus of Escherichia coli K-12.	J. Bacteriol.	1990	172		4888-4900			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. 		
@D	Dimitrova, D.//Engelbrecht, K.C.//Putonti, C.//Koenig, D.W.//Wolfe, A.J. 	Draft Genome Sequence of Escherichia coli K-12 (ATCC 10798).	Genome Announcements	2017	5		e00573-17			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. 		
@D	Dinakaran, V.//Shankar, M.//Jayashree, S.//Rathinavel, A.//Gunasekaran, P.//Rajendhran, J. 	Genome Sequence of Staphylococcus arlettae Strain CVD059, Isolated from the Blood of a Cardiovascular Disease Patient.	J. Bacteriol.	2012	194		6615-6616			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%. 		
@D	Ding, F.//Chaillet, J.R. 	In vivo stabilization of the Dnmt1 (cytosine-5)-methyltransferase protein.	Proc. Natl. Acad. Sci. U. S. A.	2002	99		14861-14866			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. 		
@D	Ding, F.//Patel, C.//Ratnam, S.//McCarrey, J.R.//Chaillet, J.R. 	Conservation of Dnmt1o Cytosine methyltransferase in the marsupial Monodelphis domestica.	Genesis	2003	36		209-213			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. 		
@D	Ding, H.//Moksa, M.M.//Hirst, M.//Beatty, J.T. 	Draft Genome Sequences of Six Rhodobacter capsulatus Strains, YW1, YW2, B6, Y262, R121, and DE442.	Genome Announcements	2014	2		e00050-14			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. 		
@D	Ding, H.//Niu, B.//Fan, H.//Li, Y.//Wang, Q. 	Draft Genome Sequence of Bacillus cereus 905, a Plant Growth-Promoting Rhizobacterium of Wheat.	Genome Announcements	2016	4		e00489-16			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. 		
@D	Ding, J.//Dou, Y.//Wang, Y.//Chang, Y. 	Draft Genome Sequence of Vibrio fortis Dalian14 Isolated from Diseased Sea Urchin (Strongylocentrotus intermedius).	Genome Announcements	2014	2		e00409-14			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. 		
@D	Ding, J.//Pan, Y.//Jiang, H.//Cheng, J.//Liu, T.//Qin, N.//Yang, Y.//Cui, B.//Chen, C.//Liu, C.//Mao, K.//Zhu, B. 	Whole genome sequences of four Brucella strains.	J. Bacteriol.	2011	193		3674-3675			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. 		
@D	Ding, J.-Y.//Shiu, J.-H.//Chen, W.-M.//Chiang, Y.-R.//Tang, S.-L. 	Genomic Insight into the Host Endosymbiont Relationship of Endozoicomonas montiporae CL-33T with its Coral Host.	Front. Microbiol.	2016	7		251			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. 		
@D	Ding, J.Y.//Chiang, P.W.//Hong, M.J.//Dyall-Smith, M.//Tang, S.L. 	Complete Genome Sequence of the Extremely Halophilic Archaeon Haloarcula hispanica Strain N601.	Genome Announcements	2014	2		e00178-14			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. 		
@D	Ding, R.//Li, Y.//Qian, C.//Wu, X. 	Draft Genome Sequence of Paenibacillus elgii B69, a Strain with Broad Antimicrobial Activity.	J. Bacteriol.	2011	193		4537			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. 		
@D	Dingman, D.W. 	Presence of N6-methyladenine in GATC sequences of Bacillus popilliae and Bacillus lentimorbus KLN2.	J. Bacteriol.	1990	172		6156-6159			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. 		
@D	Dingman, D.W. 	Four Complete Paenibacillus larvae Genome Sequences.	Genome Announcements	2017	5		e00407-17			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. 		
@D	Dinsmore, P.K.//Klaenhammer, T.R. 	Bacteriophage resistance in Lactococcus.	Mol. Biotechnol.	1995	4		297-314			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. 		
@D	Diop, A.//Diop, K.//Tomei, E.//Raoult, D.//Fenollar, F.//Fournier, P.E. 	Draft Genome Sequence of Ezakiella peruensis Strain M6.X2, a Human Gut Gram-Positive Anaerobic Coccus.	Genome Announcements	2018	6		e01487-17			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. 		
@D	Divyashri, G.//Rajagopal, K.//Prapulla, S.G. 	Draft Genome Sequence of Lactobacillus plantarum Kanjika 2007, Isolated from Kanjika, a South Indian Traditional Food.	Genome Announcements	2016	4		e00924-16			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). 		
@D	Dix, T.I.//Kieronska, D.H. 	Errors between sites in restriction site mapping.	Comput. Appl. Biosci.	1988	4		117-123			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. 		
@D	Djao, O.D. et al. 	Complete genome sequence of Syntrophothermus lipocalidus type strain (TGB-C1).	Standards in Genomic Sciences	2010	3		268-275			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. 		
@D	Djordjevic, G.M. 	Development of a triggered suicide system for bacteriophage defense.	Diss. Abstr.	1997	58		1095B			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. 		
@D	Djordjevic, G.M.//Klaenhammer, T.R. 	Positive selection, insertion cloning vectors for lactic acid bacteria based on a restriction endonuclease cassette.	Abstr. Gen. Meet. Am. Soc. Microbiol.	1995	95		527			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. 		
@D	Djordjevic, G.M.//Klaenhammer, T.R. 	Positive selection, cloning vectors for gram-positive bacteria based on a restriction endonuclease cassette.	Plasmid	1996	35		37-45			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. 		
@D	Djordjevic, G.M.//O'Sullivan, D.J.//Walker, S.A.//Conkling, M.A.//Klaenhammer, T.R. 	A triggered-suicide system designed as a defense against bacteriophages.	J. Bacteriol.	1997	179		6741-6748			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. 		
@D	Djordjevic, M. 	Modeling bacterial immune systems: Strategies for expression of toxic - but useful - molecules.	Biosystems	2013	112		139-144			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. 		
@D	Djukic, M.//Becker, D.//Poehlein, A.//Voget, S.//Daniel, R. 	Genome Sequence of Paenibacillus alvei DSM 29, a Secondary Invader during European Foulbrood Outbreaks.	J. Bacteriol.	2012	194		6365			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. 		
@D	Djukic, M.//Daniel, R.//Poehlein, A. 	First Insights into the Genome of Fructobacillus sp. EFB-N1, Isolated from Honey  Bee Larva Infected with European Foulbrood.	Genome Announcements	2015	3		e00868-15			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. 		
@D	Djukic, M.//Poehlein, A.//Strauss, J.//Tann, F.J.//Leimbach, A.//Hoppert, M.//Daniel, R. 	High quality draft genome of Lactobacillus kunkeei EFB6, isolated from a German European foulbrood outbreak of honeybees.	Standards in Genomic Sciences	2015	10		16			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. 		
@D	Djukic, M.//Poehlein, A.//Thurmer, A.//Daniel, R. 	Genome Sequence of Brevibacillus laterosporus LMG 15441, a Pathogen of Invertebrates.	J. Bacteriol.	2011	193		5535-5536			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. 		
@D	Dmitrenko, O.A.//Sidorenko, S.V.//Zhukhovitsky, V.G.//Terekhova, R.V.//Karabak, V.I.//Tarasevich, N.N.//Vasilyeva, E.I.//Prokhorov, V.Y. 	Comparative effectiveness of typing Staphylococcus aureus methicillin-resistant strains, isolated in Moscow hospitals, with the use of three collections of bacteriophages.	Zh. Mikrobiol. Epidemiol. Immunobiol.	2003	1		3-9			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. 		
@D	do Nascimento, N.C.//Dos Santos, A.P.//Chu, Y.//Guimaraes, A.M.//Pagliaro, A.//Messick, J.B. 	Genome Sequence of Mycoplasma parvum (Formerly Eperythrozoon parvum), a Diminutive Hemoplasma of the Pig.	Genome Announcements	2013	1		e00986-13			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. 		
@D	do Nascimento, N.C.//Guimaraes, A.M.//Santos, A.P.//Sanmiguel, P.J.//Messick, J.B. 	Complete Genome Sequence of Mycoplasma haemocanis Strain Illinois.	J. Bacteriol.	2012	194		1605-1606			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. 		
@D	Do, J.W.//Moon, C.H.//Kim, H.J.//Ko, M.S.//Kim, S.B.//Son, J.H.//Kim, J.S.//An, E.J.//Kim, M.K.//Lee, S.K.//Han, M.S.//Cha, S.J.//Park, M.S.//Park, M.A.//Lee, J.S.//Kim, Y.C.//Choi, D.L.//Kim, J.W.//Park, J.W. 	Complete genomic DNA sequence of rock bream iridovirus.	Virology	2004	325		351-363			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. 		
@D	Doan, D.P.//Lessor, L.E.//Hernandez, A.C.//Kuty, E.G.F. 	Complete Genome Sequence of Enterotoxigenic Escherichia coli Siphophage Seurat.	Genome Announcements	2015	3		e00044-15			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. 		
@D	Doberenz, S.//Eckweiler, D.//Reichert, O.//Jensen, V.//Bunk, B.//Sproer, C.//Kordes, A.//Frangipani, E.//Luong, K.//Korlach, J.//Heeb, S.//Overmann, J.//Kaever, V.//Haussler, S. 	Identification of a Pseudomonas aeruginosa PAO1 DNA Methyltransferase, Its Targets, and Physiological Roles.	MBio	2017	8		e02312-16			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. 		
@D	Doberva, M.//Sanchez-Ferandin, S.//Ferandin, Y.//Intertaglia, L.//Croue, J.//Suzuki, M.//Lebaron, P.//Lami, R. 	Genome Sequence of the Sponge-Associated Ruegeria halocynthiae Strain MOLA R1/13b, a Marine Roseobacter with Two Quorum-Sensing-Based Communication Systems.	Genome Announcements	2014	2		e00998-14			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. 		
@D	Doberva, M.//Sanchez-Ferandin, S.//Ferandin, Y.//Intertaglia, L.//Joux, F.//Lebaron, P.//Lami, R. 	Genome Sequence of Maribius sp. Strain MOLA 401, a Marine Roseobacter with a Quorum-Sensing Cell-Dependent Physiology.	Genome Announcements	2014	2		e00997-14			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. 		
@D	Dobkin, C.//Ferrando, C.//Brown, W.T. 	PFGE of human DNA: 5-azacytidine improves restriction.	Nucleic Acids Res.	1987	15		3183			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. 		
@D	Dobrindt, U.//Blum-Oehler, G.//Nagy, G.//Schneider, G.//Johann, A.//Gottschalk, G.//Hacker, J. 	Genetic structure and distribution of four pathogenicity islands (PAI I(536) to PAI IV(536)) of uropathogenic Escherichia coli strain 536.	Infect. Immun.	2002	70		6365-6372			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. 		
@D	Dobritsa, A.P.//Dobritsa, S.V. 	DNA protection with the DNA methylase M.BbvI from Bacillus brevis var. GB against cleavage by the restriction endonucleases PstI and PvuII.	Gene	1980	10		105-112			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. 		
@D	Dobritsa, A.P.//Mikhailov, A.A.//Vanyushin, B.F. 	Methylation of phage 1P+f DNA of Bacillus brevis var. G-B.	Biokhimiia	1975	40		1269-1274			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. 		
@D	Dodd, A.//Swanevelder, D.//Featherston, J.//Rumbold, K. 	Draft Genome Sequence of Streptomyces albulus Strain CCRC 11814, an {varepsilon}-Poly-L-Lysine-Producing Actinomycete.	Genome Announcements	2013	1		e00696-13			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. 		
@D	Dodge, A.G.//Wackett, L.P.//Sadowsky, M.J. 	Plasmid Localization and Organization of Melamine Degradation Genes in Rhodococcus sp. Strain Mel.	Appl. Environ. Microbiol.	2012	78		1397-1403			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. 		
@D	Doerfler, W. 	Patterns of DNA methylation-evolutionary vestiges of foreign DNA inactivation as a host defense mechanism.	Biol. Chem. Hoppe Seyler	1991	372		557-564			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. 		
@D	Doggett, N.A.//Stubben, C.J.//Chertkov, O.//Bruce, D.C.//Detter, J.C.//Johnson, S.L.//Han, C.S. 	Complete Genome Sequence of Bacillus thuringiensis Serovar Israelensis Strain HD-789.	Genome Announcements	2013	1		e01023-13			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. 		
@D	Dogs, M. et al. 	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.	Standards in Genomic Sciences	2013	9		334-350			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. 		
@D	Dogs, M. et al. 	Genome sequence of Phaeobacter daeponensis type strain (DSM 23529(T)), a facultatively anaerobic bacterium isolated from marine sediment, and emendation  of Phaeobacter daeponensis.	Standards in Genomic Sciences	2013	9		142-159			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. 		
@D	Doherty, J.P.//Lindeman, R.//Trent, R.J.//Graham, M.W.//Woodcock, D.M. 	Escherichia coli host strains SURE and SRB fail to preserve a palindrome cloned in lambda phage: improved alternate host strains.	Gene	1993	124		29-35			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. 		
@D	Dohra, H.//Miyake, Y.//Kodani, S. 	Draft Genome Sequence of Streptomyces olivochromogenes NBRC 3561, a Bioactive Peptide-Producing Actinobacterium.	Genome Announcements	2017	5		e01048-17			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. 		
@D	Dohra, H.//Suzuki, H.//Suzuki, T.//Tanaka, K.//Fujishima, M. 	Draft Genome Sequence of Holospora undulata Strain HU1, a Micronucleus-Specific Symbiont of the Ciliate Paramecium caudatum.	Genome Announcements	2013	1		e00664-13			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. 		
@D	Dohra, H.//Suzuki, T.//Inoue, Y.//Kodani, S. 	Draft Genome Sequence of Planomonospora sphaerica JCM9374, a Rare Actinomycete.	Genome Announcements	2016	4		e00779-16			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. 		
@D	Doi, A.//Pack, S.P.//Kodaki, T.//Makino, K. 	Reinvestigation of the Molecular Influence of Hypoxanthine on the DNA Cleavage Efficiency of Restriction Endonucleases BglII, EcoRI and BamHI.	J. Biochem. (Tokyo)	2009	146		201-208			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. 		
@D	Doi, K.//Fujino, Y.//Nagayoshi, Y.//Ohshima, T.//Ogata, S. 	Complete Genome Sequence of Thiostrepton-Producing Streptomyces laurentii ATCC 31255.	Genome Announcements	2016	4		e00360-16			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%. 		
@D	Doi, K.//Mori, K.//Martono, H.//Nagayoshi, Y.//Fujino, Y.//Tashiro, K.//Kuhara, S.//Ohshima, T. 	Draft Genome Sequence of Geobacillus kaustophilus GBlys, a Lysogenic Strain with  Bacteriophage OH2.	Genome Announcements	2013	1		e00634-13			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%. 		
@D	Doi, K.//Mori, K.//Mutaguchi, Y.//Tashiro, K.//Fujino, Y.//Ohmori, T.//Kuhara, S.//Ohshima, T. 	Draft Genome Sequence of D-Branched-Chain Amino Acid Producer Lactobacillus otakiensis JCM 15040T, Isolated from a Traditional Japanese Pickle.	Genome Announcements	2013	1		e00546-13			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%. 		
@D	Doi, K.//Mori, K.//Tashiro, K.//Fujino, Y.//Nagayoshi, Y.//Hayashi, Y.//Kuhara, S.//Ohshima, T. 	Draft Genome Sequence of Pediococcus lolii NGRI 0510Q(T) Isolated from Ryegrass Silage.	Genome Announcements	2013	1		e00156-12			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%. 		
@D	Doi, N.//Kumadaki, S.//Oishi, Y.//Matsumura, N.//Yanagawa, H. 	In vitro selection of restriction endonucleases by in vitro compartmentalization.	Nucleic Acids Res.	2004	32		e95			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. 		
@D	Doi, N.//Yanagawa, H. 	In vitro selection of restriction enzyme and receptor ligands by microcapsulated cell free protein synthesis system.	Baiotekunoroji Janaru	2005	5		84-86					
@D	Doi, Y.//Hazen, T.H.//Boitano, M.//Tsai, Y.C.//Clark, T.A.//Korlach, J.//Rasko, D.A. 	Whole-genome assembly of Klebsiella pneumoniae coproducing NDM-1 and OXA-232 carbapenemases using single-molecule, real-time sequencing.	Antimicrob. Agents Chemother.	2014	58		5947-5953			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. 		
@D	Doi, Y.//Takizawa, N. 	Complete Genome Sequence of Enterococcus faecalis Strain W11 Isolated from an Algal Food Product.	Genome Announcements	2016	4		e01037-16			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. 		
@D	Doing, G.//Perron, G.G.//Jude, B.A. 	Draft Genome Sequence of a Violacein-Producing Iodobacter sp. from the Hudson Valley Watershed.	Genome Announcements	2018	6		e01428-17			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. 		
@D	Doiron, K.M.//Lavigne-Nicolas, J.//Cupples, C.G. 	Effect of interaction between 5-azacytidine and DNA (cytosine-5) methyltransferase on C-to-G and C-to-T mutations in Escherichia coli.	Mutat. Res.	1999	429		37-44			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. 		
@D	Doiron, K.M.J.//Viau, S.//Koutroumanis, M.//Cupples, C.G. 	Overexpression of vsr in Escherichia coli is mutagenic.	J. Bacteriol.	1996	178		4294-4296			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. 		
@D	Dolka, B.//Boyen, F.//Butaye, P.//Heidemann, O.R.//Naundrup, T.I.C.//Christensen, J.P. 	Draft Genome Sequences of Two Commensal Enterococcus cecorum Strains Isolated from Chickens in Belgium.	Genome Announcements	2015	3		e01108-15			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. 		
@D	Dolka, B.//Heidemann, O.R.//Naundrup, T.I.C.//Christensen, J.P. 	Draft Genome Sequences of Five Clinical Enterococcus cecorum Strains Isolated from Different Poultry Species in Poland.	Genome Announcements	2015	3		e01082-15			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. 		
@D	Domann, E.//Fischer, F.//Glowatzki, F.//Fritzenwanker, M.//Hain, T.//Zechel-Gran, S.//Giffhorn-Katz, S.//Neubauer, B.A. 	Draft Genome Sequence of Lactobacillus delbrueckii Strain #22 Isolated from a Patient with Short Bowel Syndrome and Previous d-Lactic Acidosis and  Encephalopathy.	Genome Announcements	2016	4		e00747-16			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. 		
@D	Dombroski, D.F.//Morgan, A.R. 	Restriction nuclease digestions driven to completion by Escherichia coli RNA polymerase and T4 gene 32 protein.	J. Biol. Chem.	1985	260		415-417			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. 		
@D	Domingo, M.C.//Fournier, E.//Masse, C.//Charest, H.//Bernard, K.//Cote, J.C.//Tremblay, C. 	Draft Genome Sequences of Two Toxigenic Corynebacterium ulcerans Strains.	Genome Announcements	2015	3		e00699-15			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. 		
@D	Domingos, D.F.//Dellagnezze, B.M.//Greenfield, P.//Reyes, L.R.//Melo, I.S.//Midgley, D.J.//Oliveira, V.M. 	Draft Genome Sequence of Bacillus pumilus CCMA-560, Isolated from an Oil-Contaminated Mangrove Swamp.	Genome Announcements	2013	1		e00707-13			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. 		
@D	Domingos, D.F.//Dellagnezze, B.M.//Greenfield, P.//Reyes, L.R.//Melo, I.S.//Midgley, D.J.//Oliveira, V.M. 	Draft Genome Sequence of the Biosurfactant-Producing Bacterium Gordonia amicalis  Strain CCMA-559, Isolated from Petroleum-Impacted Sediment.	Genome Announcements	2013	1		e00894-13			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. 		
@D	Dominguez, M.A. Jr.//Thornton, K.C.//Melendez, M.G.//Dupureur, C.M. 	Differential effects of isomeric incorporation of fluorophenylalanines into PvuII endonuclease.	Proteins	2001	45		55-61			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. 		
@D	Dominguez-Bello, M.G.//Maldonado, A.L. 	Population dynamics and Restriction-Modification (RM) systems in Helicobacter pylori.	Zoonoses Public Health	2007	54		114			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. 		
@D	Dominova, I.N.//Kublanov, I.V.//Podosokorskaya, O.A.//Derbikova, K.S.//Patrushev, M.V.//Toshchakov, S.V. 	Complete Genomic Sequence of 'Thermofilum adornatus' Strain 1910bT, a Hyperthermophilic Anaerobic Organotrophic Crenarchaeon.	Genome Announcements	2013	1		e00726-13			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). 		
@D	Dominova, I.N.//Sorokin, D.Y.//Kublanov, I.V.//Patrushev, M.V.//Toshchakov, S.V. 	Complete Genome Sequence of Salinarchaeum sp. Strain HArcht-Bsk1T, Isolated from  Hypersaline Lake Baskunchak, Russia.	Genome Announcements	2013	1		e00505-13			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. 		
@D	Domotor, D.//Becsagh, P.//Rakhely, G.//Schneider, G.//Kovacs, T. 	Complete Genomic Sequence of Erwinia amylovora Phage PhiEaH2.	J. Virol.	2012	86		10899			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. 		
@D	Donado-Godoy, P.//Bernal, J.F.//Rodriguez, F.//Gomez, Y.//Agarwala, R.//Landsman, D.//Marino-Ramirez, L. 	Genome Sequences of Multidrug-Resistant Salmonella enterica Serovar Paratyphi B (dT+) and Heidelberg Strains from the Colombian Poultry Chain.	Genome Announcements	2015	3		e01265-15			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. 		
@D	Donahue, J.P.//Israel, D.A.//Peek, R.M.//Blaser, M.J.//Miller, G.G. 	Overcoming the restriction barrier to plasmid transformation of Helicobacter pylori.	Mol. Microbiol.	2000	37		1066-1074			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. 		
@D	Donahue, J.P.//Israel, D.A.//Torres, V.J.//Necheva, A.S.//Miller, G.G. 	Inactivation of a Helicobacter pylori DNA methyltransferase alters dnaK operon expression following host-cell adherence.	FEMS Microbiol. Lett.	2002	208		295-301			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. 		
@A	Donahue, J.P.//Peek, R.M. Jr. 		Restriction and modification systems.			Mobley, H.L.T.//Mendz, G.L.//Hazell, S.L. 		Helicobacter pylori: Physiology and Genetics				Washington, DC	ASM Press	2001				269-276									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. 		
@D	Donati, C. et al. 	Structure and dynamics of the pan-genome of Streptococcus pneumoniae and closely related species.	Genome Biol.	2010	11		R107			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. 		
@D	Dong, A.//Yoder, J.A.//Zhang, X.//Zhou, L.//Bestor, T.H.//Cheng, X. 	Structure of human DNMT2, an enigmatic DNA methyltransferase homolog that displays denaturant-resistant binding to DNA.	Nucleic Acids Res.	2001	29		439-448			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. 		
@D	Dong, A.P.//Zhou, L.//Zhang, X.//Stickel, S.//Roberts, R.J.//Cheng, X.D. 	Structure of the Q237W mutant of HhaI DNA methyltransferase: an insight into protein-protein interactions.	Biol. Chem.	2004	385		373-379			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. 		
@D	Dong, C.//Bai, X.//Lai, Q.//Xie, Y.//Chen, X.//Shao, Z. 	Draft Genome Sequence of Sphingobium sp. Strain C100, a Polycyclic Aromatic Hydrocarbon-Degrading Bacterium from the Deep-Sea Sediment of the Arctic Ocean.	Genome Announcements	2014	2		e01210-13			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%. 		
@D	Dong, C.//Bai, X.//Lai, Q.//Xie, Y.//Chen, X.//Shao, Z. 	Draft Genome Sequence of Marinomonas sp. Strain D104, a Polycyclic Aromatic Hydrocarbon-Degrading Bacterium from the Deep-Sea Sediment of the Arctic Ocean.	Genome Announcements	2014	2		e01211-13			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%. 		
@D	Dong, C.//Chen, X.//Xie, Y.//Lai, Q.//Shao, Z. 	Complete genome sequence of Thalassolituus oleivorans R6-15, an obligate hydrocarbonoclastic marine bacterium from the Arctic Ocean.	Standards in Genomic Sciences	2014	9		893-901			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. 		
@D	Dong, H.//Chang, J.//He, X.//Hou, Q.//Long, W. 	Complete Genome Sequence of Bacillus subtilis Strain CGMCC 12426, an Efficient Poly-gamma-Glutamate Producer.	Genome Announcements	2017	5		e01163-17			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. 		
@D	Dong, H.J. et al. 	Engineering Clostridium Strain to Accept Unmethylated DNA.	PLoS ONE	2010	5		e9038			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. 		
@D	Dong, N.//Zhang, R.//Liu, L.//Li, R.//Lin, D.//Chan, E.W.//Chen, S. 	Genome analysis of clinical multilocus sequence Type 11 Klebsiella pneumoniae from China.	Microbial Genomics	2018	4		e000149			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. 		
@D	Dong, Q.//Cao, X.//Zou, G.//Zhu, R. 	A simple and practical quantitative method for measuring the activity of restriction endonucleases.	Yichuan	1987	9		34-36			None 		
@D	Dong, Q.//Ruan, L.//Shi, H. 	Genome sequence of a high agarase-producing strain Flammeovirga sp. SJP92.	Standards in Genomic Sciences	2017	12		13			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. 		
@D	Dong, Q.//Zou, G.//Cao, X.//Zhu, R. 	Chemical modification and inhibition kinetics of restriction endonuclease Bsp63I.	Wuhan Daxue Xuebao	1996	42		237-240			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. *> 		
@D	Dong, Q.Q.//Hu, H.J.//Luo, X.G.//Wang, Q.T.//Gu, X.C.//Zhou, H.//Zhou, W.J.//Ni, X.M.//Zhang, T.C. 	Complete Genome Sequence of Lactobacillus plantarum CGMCC 8198.	Genome Announcements	2017	5		e01559-16			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. 		
@D	Dong, X.//Bi, D.//Wang, H.//Zou, P.//Xie, G.//Wan, X.//Yang, Q.//Zhu, Y.//Chen, M.//Guo, C.//Liu, Z.//Wang, W.//Huang, J. 	pirAB(vp) -Bearing Vibrio parahaemolyticus and Vibrio campbellii Pathogens Isolated from the Same AHPND-Affected Pond Possess Highly Similar Pathogenic Plasmids.	Front. Microbiol.	2017	8		1859			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. 		
@D	Dong, X.//El Karkouri, K.//Robert, C.//Gavory, F.//Raoult, D.//Fournier, P.E. 	Genomic Comparison of Rickettsia helvetica and Other Rickettsia Species.	J. Bacteriol.	2012	194		2751			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. 		
@D	Dong, X.//El Karkouri, K.//Robert, C.//Raoult, D.//Fournier, P.E. 	Genome Sequence of Rickettsia australis, the Agent of Queensland Tick Typhus.	J. Bacteriol.	2012	194		5129			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. 		
@D	Dong, X.//El-Karkouri, K.//Robert, C.//Raoult, D.//Fournier, P.E. 	Genomic Analysis of Rickettsia japonica Strain YHT.	J. Bacteriol.	2012	194		6992			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. 		
@D	Dong, Y.//Chang, Y.J.//Sanford, R.A.//Fouke, B.W. 	Draft Genome Sequence of Tepidibacillus decaturensis Strain Z9, an Anaerobic, Moderately Thermophilic, and Heterotrophic Bacterium from the Deep Subsurface of   the Illinois Basin, USA.	Genome Announcements	2016	4		e00190-16			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. 		
@D	Dong, Z.//Hsiang, T.//Luo, M.//Xiang, M. 	Draft Genome Sequence of an Isolate of Fusarium oxysporum f. sp. melongenae, the  Causal Agent of Fusarium Wilt of Eggplant.	Genome Announcements	2017	5		e01597-16			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. 		
@D	Donner, J.//Bunk, B.//Schober, I.//Sproer, C.//Bergmann, S.//Jarek, M.//Overmann, J.//Wagner-Dobler, I. 	Complete Genome Sequences of Three Multidrug-Resistant Clinical Isolates of Streptococcus pneumoniae Serotype 19A with Different Susceptibilities to the  Myxobacterial Metabolite Carolacton.	Genome Announcements	2017	5		e01641-16			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. 		
@D	Doolitle, M.M.//Sirotkin, K. 	Bacteriophage T2 and T4, dam+ and damh and Eco dam+ methylation: preference at different sites.	Biochim. Biophys. Acta	1988	949		240-246			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. 		
@D	Doolittle, R.F. 	The comings and goings of homing endonucleases and mobile introns.	Proc. Natl. Acad. Sci. U. S. A.	1993	90		5379-5381			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. 		
@D	Dopazo, J.//Mendoza, A.//Herrero, J.//Caldara, F.//Humbert, Y.//Friedli, L.//Guerrier, M.//Grand-Schenk, E.//Gandin, C.//DeFrancesco, M.//Polissi, A.//Buell, G.//Feger, G.//Garcia, E.//Peitsch, M.//Garcia-Bustos, J.F. 	Annotated draft genomic sequence from a Streptococcus pneumoniae type 19F clinical isolate.	Microb. Drug Resist.	2001	7		99-125			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. 		
@D	Dordet-Frisoni, E. et al. 	Draft Genome Sequences of Mycoplasma auris and Mycoplasma yeatsii, Two Species of the Ear Canal of Caprinae.	Genome Announcements	2013	1		e00280-13			We report here the draft genome sequences of Mycoplasma auris and Mycoplasma yeatsii, two species commonly isolated from the external ear canal of Caprinae. 		
@D	Dornberger, U.//Leijon, M.//Fritzsche, H. 	High base pair opening rates in tracts of GC base pairs.	J. Biol. Chem.	1999	274		6957-6962			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. 		
@D	Dorner, L.F.//Bitinaite, J.//Whitaker, R.D.//Schildkraut, I. 	Genetic analysis of the base-specific contacts of BamHI restriction endonuclease.	J. Mol. Biol.	1999	285		1515-1523			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. 		
@D	Dorner, L.F.//Schildkraut, I. 	Direct selection of binding proficient/catalytic deficient variants of BamHI endonuclease.	Nucleic Acids Res.	1994	22		1068-1074			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. 		
@D	Doroghazi, J.R.//Ju, K.S.//Brown, D.W.//Labeda, D.P.//Deng, Z.//Metcalf, W.W.//Chen, W.//Price, N.P. 	Genome Sequences of Three Tunicamycin-Producing Streptomyces Strains, S. chartreusis NRRL 12338, S. chartreusis NRRL 3882, and S. lysosuperificus  ATCC 31396.	J. Bacteriol.	2011	193		7021-7022			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. 		
@D	Doron, S.//Melamed, S.//Ofir, G.//Leavitt, A.//Lopatina, A.//Keren, M.//Amitai, G.//Sorek, R. 	Systematic discovery of antiphage defense systems in the microbial pangenome.	Science	2018	359		eaar4120			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. 		
@D	Doronina, V.A.//Murray, N.E. 	Proteolytic control of restriction by the type I restriction enzyme EcoKI.	Biochem. Soc. Trans.	2000	2000		A177			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. 		
@D	Doronina, V.A.//Murray, N.E. 	The proteolytic control of restriction activity in Escherichia coli K-12.	Mol. Microbiol.	2001	39		416-428			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. 		
@D	Dorr-de-Quadros, P.//Fulthorpe, R.//Saati, R.//Cerqueira, V.//Bento, F.M. 	Draft Genome Sequence of Bacillus sp. Strain UFRGS-B20, a Hydrocarbon Degrader.	Genome Announcements	2018	6		e00052-18			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. 		
@D	Dorscht, J.//Klumpp, J.//Bielmann, R.//Schmelcher, M.//Born, Y.//Zimmer, M.//Calendar, R.//Loessner, M.J. 	Comparative genome analysis of Listeria bacteriophages reveals extensive mosaicism, programmed translational frameshifting, and a novel prophage insertion site.	J. Bacteriol.	2009	191		7206-7215			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. 		
@D	Dortet, L.//Bonnin, R.A.//Girlich, D.//Imanci, D.//Bernabeu, S.//Fortineau, N.//Naas, T. 	Whole-Genome Sequence of a European Clone II and OXA-72-Producing Acinetobacter baumannii Strain from Serbia.	Genome Announcements	2015	3		e01390-15			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%. 		
@D	Dorvel, B.//Sigalov, G.//Zhao, Q.//Comer, J.//Dimitrov, V.//Mirsaidov, U.//Aksimentiev, A.//Timp, G. 	Analyzing the forces binding a restriction endonuclease to DNA using a synthetic nanopore.	Nucleic Acids Res.	2009	37		4170-4179			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. 		
@D	Dos Santos, A.P.//Guimaraes, A.M.//do Nascimento, N.C.//Sanmiguel, P.J.//Messick, J.B. 	Complete Genome Sequence of Mycoplasma wenyonii Strain Massachusetts.	J. Bacteriol.	2012	194		5458-5459			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. 		
@D	Dos Santos, R.A.//Berretta, A.A.//Barud, H.S.//Ribeiro, S.J.//Gonzalez-Garcia, L.N.//Zucchi, T.D.//Goldman, G.H.//Riano-Pachon, D.M. 	Draft Genome Sequence of Komagataeibacter rhaeticus Strain AF1, a High Producer of Cellulose, Isolated from Kombucha Tea.	Genome Announcements	2014	2		e00731-14			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. 		
@D	Dos Santos, R.A.//Berretta, A.A.//Barud, H.S.//Ribeiro, S.J.//Gonzalez-Garcia, L.N.//Zucchi, T.D.//Goldman, G.H.//Riano-Pachon, D.M. 	Draft Genome Sequence of Komagataeibacter intermedius Strain AF2, a Producer of Cellulose, Isolated from Kombucha Tea.	Genome Announcements	2015	3		e01404-15			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. 		
@D	Doskar, J. 	Determination of the restriction-modification system of the polyvalent bacteriophage 821 in the cells of Staphylococcus-aureus strains.	Scripta Fac. Sci. Nat. Univ. Purk. Brun.	1988	18		421			None 		
@D	Doskar, J. 	Characteristics of restriction-modification system of the polyvalent phage 812 in strains of staphylococcus aureus.	Scripta Fac. Sci. Nat. Univ. Purk. Brun.	1989	19		391-401			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. 		
@D	Dotson, G.A.//Dekker, J.P.//Palmore, T.N.//Segre, J.A.//Conlan, S. 	Draft Genome Sequence of a Klebsiella pneumoniae Carbapenemase-Positive Sequence  Type 111 Pseudomonas aeruginosa Strain.	Genome Announcements	2016	4		e01663-15			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. 		
@D	Dou, D.//Inagaki, K.//Kita, K.//Ohshima, A.//Hiraoka, N.//Kishimoto, N.//Sugio, T.//Tano, T. 	Restriction endonuclease AfaI from Acidiphilium facilis, a new isoschizomer of RsaI: purification and properties.	Biochim. Biophys. Acta	1989	1009		83-86			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. 		
@D	Douc-Rasy, S.//Kolb, A.//Prunell, A. 	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.	Nucleic Acids Res.	1989	17		5173-5189			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. 		
@D	Doughty, B.//Kazer, S.W.//Eisenthal, K.B. 	Binding and cleavage of DNA with the restriction enzyme EcoR1 using time-resolved second harmonic generation.	Proc. Natl. Acad. Sci. U. S. A.	2011	108		19979-19984			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. 		
@D	Downing, M.E.//Brady, K.L.//Caprara, M.G. 	A C-terminal fragment of an intron-encoded maturase is sufficient for promoting group I intron splicing.	RNA	2005	11		437-446			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. 		
@D	Doyle, L.E.//Williams, R.B.H.//Rice, S.A.//Marsili, E.//Lauro, F.M. 	Draft Genome Sequence of Enterobacter sp. Strain EA-1, an Electrochemically Active Microorganism Isolated from Tropical Sediment.	Genome Announcements	2018	6		e00111-18			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. 		
@D	Doyon, J.B.//Pattanayak, V.//Meyer, C.B.//Liu, D.R. 	Directed evolution and substrate specificity profile of homing endonuclease I-SceI.	J. Am. Chem. Soc.	2006	128		2477-2484			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. 		
@D	Drace, K.//Giangiuli, S.//LeSar, C.//Kiefer, A.M. 	Draft Genome Sequence of Mercury-Resistant Pseudomonas putida Strain DRA525.	Genome Announcements	2018	6		e00370-18			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. 		
@D	Draghi, W.O.//Mancini, V.U.M.//Wall, L.G.//Zorreguieta, A. 	Draft Genome Sequence of Burkholderia cordobensis Type Strain LMG 27620, Isolated from Agricultural Soils in Argentina.	Genome Announcements	2015	3		e01238-15			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. 		
@D	Draper, J.L.//Hansen, L.M.//Bernick, D.//Abedrabbo, S.//Underwood, J.G.//Kong, N.//Huang, C.B.//Weis, A.M.//Weimer, B.C.//van Vliet, A.H.M.//Pourmand, N.//Solnick, J.V.//Karplus, K. 	Fallacy of the unique genome: Sequence diversity within single Helicobacter pylori strains.	MBio	2017	8		0					
@D	Draper, J.L.//Hansen, L.M.//Bernick, D.L.//Abedrabbo, S.//Underwood, J.G.//Kong, N.//Huang, B.C.//Weis, A.M.//Weimer, B.C.//van Vliet, A.H.//Pourmand, N.//Solnick, J.V.//Karplus, K.//Ottemann, K.M. 	Fallacy of the Unique Genome: Sequence Diversity within Single Helicobacter pylori Strains.	MBio	2017	8		e02321-16			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. 		
@D	Dreier, J.//Bickle, T.A. 	ATPase activity of the type IC restriction-modification system EcoR124II.	J. Mol. Biol.	1996	257		960-969			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. 		
@D	Dreier, J.//MacWilliams, M.P.//Bickle, T.A. 	DNA cleavage by the type IC restriction-modification enzyme EcoR124II.	J. Mol. Biol.	1996	264		722-733			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. 		
@D	Dreiseikelmann, B.//Eichenlaub, R.//Wackernagel, W. 	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.	Biochim. Biophys. Acta	1979	562		418-428			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. 		
@D	Dreiseikelmann, B.//Wackernagel, W. 	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.	J. Bacteriol.	1981	147		259-261			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. 		
@D	Drew, H.R.//Travers, A. 	Structural junctions in DNA: the influence of flanking sequence on nuclease digestion specificities.	Nucleic Acids Res.	1985	13		4445-4467			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. 		
@D	Drexler, H.//Christensen, J.R. 	Genetic crosses between restricted and unrestricted phage T1 in lysogenic and nonlysogenic hosts.	Virology	1961	13		31-39			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. 		
@D	Dreyer, K.//Schulte-Holthausen, H. 	Casein is a potent enhancer for restriction enzyme activity.	Nucleic Acids Res.	1991	19		4295			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. 		
@D	Dreyfus-Fourcade, M.//Sebald, M.//Zavadova, M. 	Host-controlled restriction and modification of phage r in Clostridium perfringens NCTC 8798 and some of its sporulation mutants.	Ann. Inst. Pasteur Microbiol.	1972	122		1117-1127			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. 		
@D	Driscoll, C.B.//Otten, T.G.//Brown, N.M.//Dreher, T.W. 	Towards long-read metagenomics: complete assembly of three novel genomes from bacteria dependent on a diazotrophic cyanobacterium in a freshwater lake  co-culture.	Standards in Genomic Sciences	2017	12		9			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. 		
@D	Drissi, F.//Labas, N.//Merhej, V.//Raoult, D. 	Draft Genome Sequence of the Lactobacillus agilis Strain Marseille.	Genome Announcements	2015	3		e00840-15			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. 		
@D	Drissi, F.//Merhej, V.//Blanc-Tailleur, C.//Raoult, D. 	Draft Genome Sequence of the Lactobacillus mucosae Strain Marseille.	Genome Announcements	2015	3		e00841-15			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. 		
@D	Droge, M.//Puhler, A.//Selbitschka, W. 	Phenotypic and molecular characterization of conjugative antibiotic resistance plasmids isolated from bacterial communities of activated sludge.	Mol. Gen. Genet.	2000	263		471-482			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. 		
@D	Drotschmann, K.//Aronshtam, A.//Fritz, H.-J.//Marinus, M.G. 	The Escherichia coli MutL protein stimulates binding of Vsr and MutS to heteroduplex DNA.	Nucleic Acids Res.	1998	26		948-953			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. 		
@D	Drouin, M.//Lucas, P.//Otis, C.//Lemieux, C.//Turmel, M. 	Biochemical characterization of I-CmoeI reveals that this H-N-H homing endonuclease shares functional similarities with H-N-H colicins.	Nucleic Acids Res.	2000	28		4566-4572			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. 		
@D	Drozdz, M.//Piekarowicz, A.//Bujnicki, J.M.//Radlinska, M. 	Novel non-specific DNA adenine methyltransferases.	Nucleic Acids Res.	2012	40		2119-2130			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. 		
@D	Dryden, D.T. 	Reeling in the bases.	Nat. Struct. Mol. Biol.	2004	11		804-806			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. 		
@D	Dryden, D.T.//Davies, G.D.//Martin, I.//Powell, L.M.//Murray, N.E.//Ellis, D.J.//Berge, T.//Edwardson, J.M.//Henderson, R.M. 	The assembly of the EcoKI type I DNA restriction/modification enzyme and its interaction with DNA.	Biochem. Soc. Trans.	1999	27		691-696					
@D	Dryden, D.T.//Edwardson, J.M.//Henderson, R.M. 	DNA translocation by type III restriction enzymes: a comparison of current models of their operation derived from ensemble and single-molecule  measurements.	Nucleic Acids Res.	2011	39		4525-4531			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. 		
@D	Dryden, D.T.//Murray, N.E.//Rao, D.N. 	Nucleoside triphosphate-dependent restriction enzymes.	Nucleic Acids Res.	2001	29		3728-3741			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. 		
@D	Dryden, D.T.F. 	Structures of the type I DNA restriction enzymes.	Proc. Natl. Acad. Sci. U. S. A.	2017	114		E10261-E10262			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. 		
@D	Dryden, D.T.F. 	The Architecture of Restriction Enzymes.	Structure	2013	21		1720-1721			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. 		
@A	Dryden, D.T.F. 		Bacterial DNA methyltransferases.			Cheng, X.//Blumenthal, R.M. 		S-Adenosylmethionine-dependent Methyltransferases: Structures and Functions.				Singapore	World Scientific Publishing	1999				283-340									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. 		
@D	Dryden, D.T.F.//Cooper, L.P.//Murray, N.E. 	Purification and characterization of the methyltransferase from the Type I restriction and modification system of Escherichia coli K12.	J. Biol. Chem.	1993	268		13228-13236			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. 		
@D	Dryden, D.T.F.//Cooper, L.P.//Murray, N.E. 	Assembly of the multifunctional EcoKI DNA restriction enzyme in vitro.	Tech. Prot. Chem.	1997	8		593-601			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. 		
@D	Dryden, D.T.F.//Cooper, L.P.//Thorpe, P.H.//Byron, O. 	The in vitro assembly of the EcoKI type I DNA restriction/modification enzyme and its in vivo implications.	Biochemistry	1997	36		1065-1076			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. 		
@D	Dryden, D.T.F.//Davies, G.D.//Powell, L.M.//Murray, N.E.//Ellis, D.J.//Berge, T.//Edwardson, J.M.//Henderson, R.M. 	The assembly of the EcoKI type I DNA restriction/modification enzyme and its interaction with DNA.	Biochem. Soc. Trans.	1999	27		A87			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. 		
@D	Dryden, D.T.F.//Sturrock, S.S.//Winter, M. 	Structural modelling of a type I DNA methyltransferase.	Nat. Struct. Biol.	1995	2		632-635			Amino-acid sequence comparison and tertiary structure modelling suggest a structure for type I DNA methyltransferases and an evolutionary link to type II methyltransferases. 		
@D	Dryden, D.T.F.//Willcock, D.F.//Murray, N.E. 	Mutational analysis of conserved amino-acid motifs in EcoKI adenine methyltransferase.	Gene	1995	157		123-124			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. 		
@D	du Plessis, M. et al. 	Molecular Characterization of Corynebacterium diphtheriae Outbreak Isolates, South Africa, March-June 2015.	Emerg. Infect. Dis.	2017	23		1308-1315			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. 		
@D	Du, J.//Zhong, X.//Bernatavichute, Y.V.//Stroud, H.//Feng, S.//Caro, E.//Vashisht, A.A.//Terragni, J.//Chin, H.G.//Tu, A.//Hetzel, J.//Wohlschlegel, J.A.//Pradhan, S.//Patel, D.J.//Jacobsen, S.E. 	Dual binding of chromomethylase domains to H3K9me2-containing nucleosomes directs DNA methylation in plants.	Cell	2012	151		167-180			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. 		
@D	Du, L.//Zhang, M.//Burton, R.//Spielberger, K.//Mollova, E.//Gilmanshin, R. 	Rapid mapping of large DNA molecules using fluorescent labeled restriction enzyme.	Biophys. J.	2007	S		331A			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. 		
@D	Du, Q.//Wang, Z.//Schramm, V.L. 	Human DNMT1 transition state structure.	Proc. Natl. Acad. Sci. U. S. A.	2016	113		2916-2921			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. 		
@D	Du, X.J.//Jia, S.R.//Yang, Y.//Wang, S. 	Genome Sequence of Gluconacetobacter sp. Strain SXCC-1, Isolated from Chinese Vinegar Fermentation Starter.	J. Bacteriol.	2011	193		3395-3396			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. 		
@D	Du, Y.//Song, L.//Feng, W.//Pei, G.//Zheng, P.//Yu, Z.//Sun, J.//Qiao, J. 	Draft Genome Sequence of Lactococcus lactis subsp. lactis Strain YF11.	Genome Announcements	2013	1		e00599-13			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%). 		
@D	Du, Y.//Yuan, B.//Zeng, Y.//Meng, J.//Li, H.//Wang, R.//Li, G.//Feng, F. 	Draft Genome Sequence of the Cellulolytic Bacterium Clavibacter sp. CF11, a Strain Producing Cold-Active Cellulase.	Genome Announcements	2015	3		e01304-14			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. 		
@D	Du, Z.//Zhang, Z.//Miao, T.//Wu, J.//Lu, G.//Yu, J.//Xiao, J.//Chen, G. 	Draft Genome Sequence of the Novel Agar-Digesting Marine Bacterium HQM9.	J. Bacteriol.	2011	193		4557			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. 		
@D	Dua, A.//Sangwan, N.//Kaur, J.//Saxena, A.//Kohli, P.//Gupta, A.K.//Lal, R. 	Draft Genome Sequence of Agrobacterium sp. Strain UHFBA-218, Isolated from Rhizosphere Soil of Crown Gall-Infected Cherry Rootstock Colt.	Genome Announcements	2013	1		e00302-13			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%. 		
@D	Duan, C.//Tong, Y.//Huang, Y.//Wang, X.//Xiong, X.//Wen, B. 	Complete Genome Sequence of Rickettsia heilongjiangensis, an Emerging Tick-Transmitted Human Pathogen.	J. Bacteriol.	2011	193		5564-5565			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). 		
@D	Duan, C.G.//Zhang, H.//Tang, K.//Zhu, X.//Qian, W.//Hou, Y.J.//Wang, B.//Lang, Z.//Zhao, Y.//Wang, X.//Wang, P.//Zhou, J.//Liang, G.//Liu, N.//Wang, C.//Zhu, J.K. 	Specific but interdependent functions for Arabidopsis AGO4 and AGO6 in RNA-directed DNA methylation.	EMBO J.	2015	34		581-592			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. 		
@D	Duan, X.//Gimble, F.S.//Quiocho, F.A. 	Crystal structure of PI-SceI, a homing endonuclease with protein splicing activity.	Cell	1997	89		555-564			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. 		
@D	Duan, Y.//Wilkosz, P.//Rosenberg, J.M. 	Dynamic contributions to the DNA binding entropy of the EcoRI and EcoRV restriction endonucleases.	J. Mol. Biol.	1996	264		546-555			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. 		
@D	Duarte, V.D.S.//Treu, L.//Campanaro, S.//Dias, R.S.//Silva, C.C.D.//Giacomini, A.//Corich, V.//de Paula, S.O. 	The Complete Genome Sequence of Trueperella pyogenes UFV1 Reveals a Processing System Involved in the Quorum-Sensing Signal Response.	Genome Announcements	2017	5		e00639-17			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. 		
@D	Dubert, J.//Spinard, E.J.//Nelson, D.R.//Gomez-Chiarri, M.//Romalde, J.L.//Barja, J.L. 	Draft Genome Sequence of the New Pathogen for Bivalve Larvae Vibrio bivalvicida.	Genome Announcements	2016	4		e00216-16			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. 		
@D	Dubey, A.K.//Bhattacharya, S.K. 	Angle and locus of the bend induced by the MspI DNA methyltransferase in a sequence-specific complex with DNA.	Nucleic Acids Res.	1997	25		2025-2029			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. 		
@D	Dubey, A.K.//Bisaria, V.S.//Mukhopadhyay, S.N.//Ghose, T.K. 	Stabilization of restriction endonuclease BamHI by cross-linking reagents.	Biotechnol. Bioeng.	1989	33		1311-1316			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. 		
@D	Dubey, A.K.//Mollet, B.//Roberts, R.J. 	Purification and characteriation of the MspI DNA methyltransferase cloned and overexpressed in E. coli.	Nucleic Acids Res.	1992	20		1579-1585			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. 		
@D	Dubey, A.K.//Mukhopadhyay, S.N.//Bisaria, V.S.//Ghose, T.K. 	Sources, production, and purification of restriction enzymes.	Process. Biochem.	1987	22		25-34			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. 		
@D	Dubey, A.K.//Roberts, R.J. 	Sequence-specific DNA binding by the MspI DNA methyltransferase.	Nucleic Acids Res.	1992	20		3167-3173			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. 		
@D	Dubinina, G.//Grabovich, M.//Leshcheva, N.//Rainey, F.A.//Gavrish, E. 	Spirochaeta perfilievii sp. nov., an oxygen-tolerant, sulfide-oxidizing, sulfur-  and thiosulfate-reducing spirochaete isolated from a saline spring.	Int. J. Syst. Evol. Microbiol.	2011	61		110-117			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)). 		
@D	Duceppe, M.O.//Carrillo, C.//Huang, H. 	Draft Genome Sequence of Listeria monocytogenes Strain ATCC 7644.	Genome Announcements	2017	5		e00970-17			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). 		
@D	Duchateau, P.//Grizot, S.//Paques, F. 	Meganuclease engineering.	BIOFUTUR	2008	0		38-42					
@D	Duchaud, E. et al. 	The genome sequence of the entomopathogenic bacterium Photorhabdus luminescens.	Nat. Biotechnol.	2003	21		1307-1313			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. 		
@D	Duchaud, E.//Boussaha, M.//Loux, V.//Bernardet, J.F.//Michel, C.//Kerouault, B.//Mondot, S.//Nicolas, P.//Bossy, R.//Caron, C.//Bessieres, P.//Gibrat, J.F.//Claverol, S.//Dumetz, F.//Henaff, M.L.//Benmansour, A. 	Complete genome sequence of the fish pathogen Flavobacterium psychrophilum.	Nat. Biotechnol.	2007	25		763-769			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. 		
@D	Duda, E.G.//Izsvak, Z.//Orosz, A. 	Isolation and purification of CeqI endonuclease, an isoschizomer of EcoRV.	Nucleic Acids Res.	1987	15		1334			None 		
@D	Dudnik, A.//Dudler, R. 	Non contiguous-finished genome sequence of Pseudomonas syringae pathovar syringae strain B64 isolated from wheat.	Standards in Genomic Sciences	2013	8		420-429			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. 		
@D	Dudnik, A.//Dudler, R. 	High-Quality Draft Genome Sequence of Pseudomonas syringae pv. Syringae Strain SM, Isolated from Wheat.	Genome Announcements	2013	1		e00610-13			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. 		
@D	Dudnik, A.//Dudler, R. 	Genome and Transcriptome Sequences of Pseudomonas syringae pv. syringae B301D-R.	Genome Announcements	2014	2		e00306-14			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. 		
@D	Dueger, E.L.//House, J.K.//Heithoff, D.M.//Mahan, M.J. 	Salmonella DNA adenine methylase mutants prevent colonization of newly hatched chickens by homologous and heterologous serovars.	Int. J. Food Microbiol.	2003	80		153-159			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. 		
@D	Dueger, E.L.//House, J.K.//Heithoff, D.M.//Mahan, M.J. 	Salmonella DNA adenine methylase mutants elicit protective immune responses to homologous and heterologous serovars in chickens.	Infect. Immun.	2001	69		7950-7954			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. 		
@D	Dueger, E.L.//House, J.K.//Heithoff, D.M.//Mahan, M.J. 	Salmonella DNA adenine methylase mutants elicit early and late onset protective immune responses in calves.	Vaccine	2003	21		3249-3258			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. 		
@D	Dueholm, M.S.//Albertsen, M.//D'Imperio, S.//Tale, V.P.//Lewis, D.//Nielsen, P.H.//Nielsen, J.L. 	Complete Genome of Rhodococcus pyridinivorans SB3094, a Methyl-Ethyl-Ketone-Degrading Bacterium Used for Bioaugmentation.	Genome Announcements	2014	2		e00525-14			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. 		
@D	Dueholm, M.S.//Albertsen, M.//Stokholm-Bjerregaard, M.//McIlroy, S.J.//Karst, S.M.//Nielsen, P.H. 	Complete Genome Sequence of the Bacterium Aalborg_AAW-1, Representing a Novel Family within the Candidate Phylum SR1.	Genome Announcements	2015	3		e00624-15			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. 		
@D	Dueholm, M.S.//Danielsen, H.N.//Nielsen, P.H. 	Complete Genome Sequence of Pseudomonas sp. UK4, a Model Organism for Studies of  Functional Amyloids in Pseudomonas.	Genome Announcements	2014	2		e00898-14			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). 		
@D	Duff, M.K.//Davies, J.K. 	Multiple restriction-modification systems in Neisseria gonorrhoeae.	Gene	1988	74		227-228			Meeting Abstract 		
@A	Duff, M.K.//Davies, J.K. 		DNA enzymes of Neisseria gonorrhoeae.			Poolman, J.T.//Zanen, H.C.//Meyer, T.F.//Heckels, J.E.//Makela, P.R.H. 		Gonococci and Meningococci				Dordrecht, The Netherlands	Kluwer Academic Publishers	1988				251-256									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.] 		
@D	Dufresne, A. et al. 	Genome sequence of the cyanobacterium Prochlorococcus marinus SS120, a nearly minimal oxyphototrophic genome.	Proc. Natl. Acad. Sci. U. S. A.	2003	100		10020-10025			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. 		
@D	Dugaiczyk, A.//Boyer, H.W.//Goodman, H.M. 	Ligation of EcoRI endonuclease-generated DNA fragments into linear and circular structures.	J. Mol. Biol.	1975	96		171-184			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. 		
@D	Dugaiczyk, A.//Hedgpeth, J.//Boyer, H.W.//Goodman, H.M. 	Physical identity of the SV40 deoxyribonucleic acid sequence recognized by the EcoRI restriction endonuclease and modification methylase.	Biochemistry	1974	13		503-512			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. 		
@D	Dugaiczyk, A.//Kimball, M.//Linn, S.//Goodman, H.M. 	Location and nucleotide sequence of the site on SV40 DNA methylated by the EcoB modification methylase.	Biochem. Biophys. Res. Commun.	1974	61		1133-1140			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. 		
@D	Dugat, T.//Rossignol, M.N.//Rue, O.//Loux, V.//Marthey, S.//Moroldo, M.//Silaghi, C.//Hoper, D.//Frohlich, J.//Pfeffer, M.//Zweygarth, E.//Lagree, A.C.//Boulouis, H.J.//Haddad, N. 	Draft Anaplasma phagocytophilum Genome Sequences from Five Cows, Two Horses, and  One Roe Deer Collected in Europe.	Genome Announcements	2016	4		e00950-16			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. 		
@D	Dugat-Bony, E.//Sarthou, A.S.//Loux, V.//Vidal, M.//Bonnarme, P.//Irlinger, F.//Layec, S. 	Draft Genome Sequence of Corynebacterium variabile Mu292, Isolated from Munster,  a French Smear-Ripened Cheese.	Genome Announcements	2016	4		e00669-16			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. 		
@D	Duggett, N.A.//Kay, G.L.//Sergeant, M.J.//Bedford, M.//Constantinidou, C.I.//Penn, C.W.//Millard, A.D.//Pallen, M.J. 	Draft Genome Sequences of Six Novel Bacterial Isolates from Chicken Ceca.	Genome Announcements	2016	4		e00448-16			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. 		
@D	Duhaime, M.B.//Wichels, A.//Sullivan, M.B. 	Six Pseudoalteromonas Strains Isolated from Surface Waters of Kabeltonne, Offshore Helgoland, North Sea.	Genome Announcements	2016	4		e01697-15			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. 		
@D	Duhaime, M.B.//Wichels, A.//Waldmann, J.//Teeling, H.//Glockner, F.O. 	Ecogenomics and genome landscapes of marine Pseudoalteromonas phage H105/1.	ISME J.	2011	5		107-121			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. 		
@D	Dujardin, G.//Jacq, C.//Slonimski, P.P. 	Single base substitution in an intron of oxidase gene compensates splicing defects of the cytochrome b gene.	Nature	1982	298		628-632			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. 		
@D	Dujon, B. 	Group I introns as mobile genetic elements: facts and mechanistic speculations--a review.	Gene	1989	82		91-114			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. 		
@D	Dujon, B. 	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.	Cell	1980	20		185-197			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. 		
@A	Dujon, B. 		Homing endonucleases and the yeast mitochondrial omega locus - A historical perspective.			Belfort, M. 		Nucleic Acids Mol. Biol.				Berlin Heidelberg	Springer-Verlag	2005		16		11-31									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. 		
@D	Dujon, B.//Colleaux, L.//Jacquier, A.//Michel, F.//Monteilhet, C. 	Mitochondrial introns as mobile genetic elements: the role of intron-encoded proteins.	Basic Life Sci.	1986	40		5-27			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. 		
@A	Dujon, B.//Colleaux, L.//Jacquier, A.//Michel, F.//Monteilhet, C. 		Mitochondrial introns as mobile genetic elements: The role of intron-encoded proteins.			Wickner, R.B.//Hinnebush, A.//Lambowitz, A.M.//Gunsalus, I.C.//Hollaender, A. 		Extrachromosomal elements in lower eukaryotes				NY	Plenum	1986		0		5-27									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. 		
@A	Dujon, B.//Cottarel, G.//Colleaux, L.//Betermier, M.//Jacquier, A.//D'Auriol, L.//Galibert, F. 		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.			Quagliariello, E. 		Achievements and Perspectives of Mitochondrial Research. Volume II: Biogenesis.				Amsterdam	Elsevier Science Publishers B.V.	1985		0		215-225									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. 		
@D	Dumigan, C.R.//Perry, G.E.//Pauls, K.P.//Raizada, M.N. 	Draft Genome Sequence of Enterobacter cloacae 3F11 (Phylum Proteobacteria).	Microbiol. Resour. Announc.	2018	7		e00846-18			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. 		
@D	Dumonceaux, T.J.//Town, J.//Links, M.G.//Boyetchko, S. 	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.	Genome Announcements	2014	2		e00995-14			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. 		
@D	Duncan, C.H.//Wilson, G.A.//Young, F.E. 	Biochemical and genetic properties of site-specific restriction endonucleases in Bacillus globigii.	J. Bacteriol.	1978	134		338-344			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. 		
@D	Duncan, S.S.//Bertoli, M.T.//Kersulyte, D.//Valk, P.L.//Tamma, S.//Segal, I.//McClain, M.S.//Cover, T.L.//Berg, D.E. 	Genome Sequences of Three hpAfrica2 Strains of Helicobacter pylori.	Genome Announcements	2013	1		e00729-13			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. 		
@D	Dunin-Horkawicz, S.//Feder, M.//Bujnicki, J.M. 	Phylogenomic analysis of the GIY-YIG nuclease superfamily.	BMC Genomics	2006	7		98			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. 		
@D	Dunitz, M.I.//Coil, D.A.//Jospin, G.//Eisen, J.A.//Adams, J.Y. 	Draft Genome Sequences of Escherichia coli Strains Isolated from Septic Patients.	Genome Announcements	2014	2		e01278-14			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. 		
@D	Dunitz, M.I.//James, P.M.//Jospin, G.//Eisen, J.A.//Coil, D.A.//Chandler, J.A. 	Draft Genome Sequence of Tatumella sp. Strain UCD-D_suzukii (Phylum Proteobacteria) Isolated from Drosophila suzukii Larvae.	Genome Announcements	2014	2		e00349-14			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. 		
@D	Dunlap, C.A.//Bowman, M.J.//Schisler, D.A. 	Genomic analysis and secondary metabolite production in Bacillus amyloliquefaciens AS 43.3: a biocontrol antagonist of Fusarium Head Blight.	Biol. Control	2013	64		166-175			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. 		
@A	Dunn, N.W.//Holloway, B.W. 		Transduction and host controlled modification.  The role of the phage.			Ledoux, L. 		Informative molecules in biological systems.				Amsterdam	North Holland	1971		0		223-233									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. 		
@D	Dunny, G.M.//McKay, L.L. 	Group II introns and expression of conjugative transfer functions in lactic acid bacteria.	Antonie Van Leeuwenhoek	1999	76		77-88			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. 		
@D	Dunten, P.W.//Little, E.J.//Gregory, M.T.//Manohar, V.M.//Dalton, M.//Hough, D.//Bitinaite, J.//Horton, N.C. 	The structure of SgrAI bound to DNA; recognition of an 8 base pair target.	Nucleic Acids Res.	2008	36		5405-5416			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. 		
@D	Dunten, P.W.//Little, E.J.//Horton, N.C. 	The restriction enzyme SgrAI: structure solution via combination of poor MIRAS and MR phases.	Acta Crystallogr. D Biol. Crystallogr.	2009	65		393-398			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. 		
@D	Duong, D.A.//Stevens, A.M.//Jensen, R.V. 	Complete Genome Assembly of Pantoea stewartii subsp. stewartii DC283, a Corn Pathogen.	Genome Announcements	2017	5		e00435-17			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. 		
@D	Dupuis, M.-E.//Villion, M.//Magadan, A.H.//Moineau, S. 	CRISPR-Cas and restriction-modification systems are compatible and increase phage resistance.	Nat. Commun.	2013	4		2087			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. 		
@D	Dupureur, C.M. 	Unique P-31 spectral response to the formation of a specific restriction enzyme-DNA complex.	Nucleosides Nucleotides Nucleic Acids	2006	25		747-764			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. 		
@D	Dupureur, C.M. 	Metal ion-dependent DNA-induced conformational changes in PvuII restriction endonucleases.	SAAS Bulletin: Biochem. and Biotech.	1999	12		43-47			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. 		
@D	Dupureur, C.M. 	NMR studies of restriction enzyme-DNA interactions: Role of conformation in sequence specificity.	Biochemistry	2005	44		5065-5074			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. 		
@D	Dupureur, C.M.//Conlan, L.H. 	A catalytically deficient active site variant of PvuII endonuclease binds Mg(II) ions.	Biochemistry	2000	39		10921-10927			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. 		
@D	Dupureur, C.M.//Dominguez, M.A. 	The PD ... (D/E)XK motif in restriction enzymes: A link between function and conformation.	Biochemistry	2001	40		387-394			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. 		
@D	Dupureur, C.M.//Hallman, L.M. 	Effects of divalent metal ions on the activity and conformation of native and 3-fluorotyrosine-PvuII endonucleases.	Eur. J. Biochem.	1999	261		261-268			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. 		
@D	Dupuy, V. et al. 	Complete Genome Sequence of Mycoplasma putrefaciens Strain 9231, One of the Agents of Contagious Agalactia in Goats.	Genome Announcements	2013	1		e00354-13			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. 		
@D	Dupuy, V.//Thiaucourt, F. 	Complete Genome Sequence of Mycoplasma capricolum subsp. capripneumoniae Strain 9231-Abomsa.	Genome Announcements	2014	2		e01067-14			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. 		
@D	Duquesne, K.//Prima, V.//Ji, B.//Rouy, Z.//Medigue, C.//Talla, E.//Sturgis, J.N. 	Draft Genome Sequence of the Purple Photosynthetic Bacterium Phaeospirillum molischianum DSM120, a Particularly Versatile Bacterium.	J. Bacteriol.	2012	194		3559-3560			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. 		
@D	Duquesne, K.//Sturgis, J.N. 	Shotgun Genome Sequence of the Large Purple Photosynthetic Bacterium Rhodospirillum photometricum DSM122.	J. Bacteriol.	2012	194		2380			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. 		
@D	Durai, S.//Mani, M.//Kandavelou, K.//Wu, J.//Porteus, M.H.//Chandrasegaran, S. 	Zinc finger nucleases: custom-designed molecular scissors for genome engineering of plant and mammalian cells.	Nucleic Acids Res.	2005	33		5978-5990			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. 		
@D	Duran, E.//Ramsauer, V.P.//Ballester, M.//Torrenegra, R.D.//Rodriguez, O.E.//Winkle, S.A. 	Qualitative analysis of sequence specific binding of flavones to DNA using restriction endonuclease activity assays.	Biopolymers	2013	99		530-537			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. 		
@D	Duranti, S.//Turroni, F.//Lugli, G.A.//Milani, C.//Viappiani, A.//Mangifesta, M.//Gioiosa, L.//Palanza, P.//van Sinderen, D.//Ventura, M. 	Genomic Characterization and Transcriptional Studies of the Starch-Utilizing Strain Bifidobacterium adolescentis 22L.	Appl. Environ. Microbiol.	2014	80		6080-6090			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. 		
@D	Durfee, T.//Nelson, R.//Baldwin, S.//Plunkett, G. III//Burland, V.//Mau, B.//Petrosino, J.F.//Qin, X.//Muzny, D.M.//Ayele, M.//Gibbs, R.A.//Csorgo, B.//Posfai, G.//Weinstock, G.M.//Blattner, F.R. 	The complete genome sequence of Escherichia coli DH10B: insights into the biology of a laboratory workhorse.	J. Bacteriol.	2008	190		2597-2606			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. 		
@D	Durham, B.P. et al. 	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.	Standards in Genomic Sciences	2014	9		632-645			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. 		
@D	Durmaz, E.//Higgins, D.L.//Klaenhammer, T.R. 	Molecular characterization of a second abortive phage resistance gene present in Lactococcus lactis subsp. lactis ME2.	J. Bacteriol.	1992	174		7463-7469			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. 		
@D	Durmaz, E.//Klaenhammer, T.R. 	Abortive phage resistance mechanism AbiZ speeds the lysis clock to cause premature lysis of phage-infected Lactococcus lactis.	J. Bacteriol.	2007	189		1417-1425			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. 		
@D	Durmaz, E.//Klaenhammer, T.R. 	A starter culture rotation strategy incorporating paired restriction/modification and abortive infection bacteriophage defenses in a single lactococcus lactis strain.	Appl. Environ. Microbiol.	1995	61		1266-1273			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. 		
@D	Durmaz, E.//Miller, M.J.//Azcarate-Peril, M.A.//Toon, S.P.//Klaenhammer, T.R. 	Genome sequence and characteristics of Lrm1, a prophage from industrial Lactobacillus rhamnosus strain M1.	Appl. Environ. Microbiol.	2008	74		4601-4609			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. 		
@D	Durrell, K.//Prins, A.//Le Roes-Hill, M. 	Draft Genome Sequence of Gordonia lacunae BS2T.	Genome Announcements	2017	5		e00959-17			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. 		
@D	Durrenberger, F.//Rochaix, J.-D. 	Characterization of the cleavage site and the recognition sequence of the I-CreI DNA endonuclease encoded by the chloroplast ribosomal intron of Chlamydomonas reinhardtii.	Mol. Gen. Genet.	1993	236		409-414			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. 		
@D	Durrenberger, F.//Rochaix, J.-D. 	Chloroplast ribosomal intron of Chlamydomonas reinhardtii: in vitro self-splicing, DNA endonuclease activity and in vivo mobility.	EMBO J.	1991	10		3495-3501			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. 		
@D	Durrett, R.//Miras, M.//Mirouze, N.//Narechania, A.//Mandic-Mulec, I.//Dubnau, D. 	Genome Sequence of the Bacillus subtilis Biofilm-Forming Transformable Strain PS216.	Genome Announcements	2013	1		e00288-13			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. 		
@D	Dussoix, D.//Arber, W. 	Host Specificity of DNA Produced by Escherichia Coli:  II. Control over acceptance of DNA from infecting phage lambda.	J. Mol. Biol.	1962	5		37-49			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. 		
@D	Dussoix, D.//Arber, W. 	Host specificity of DNA produced by Escherichia coli IV.  Host specificity of infectious DNA from bacteriophage lambda.	J. Mol. Biol.	1965	11		238-246			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. 		
@D	Dusterhoft, A. 	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.	Ph.D. Thesis, Justus-Liebig University, Geissen, W. Germany	1990			1-160			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. 		
@D	Dusterhoft, A.//Erdmann, D.//Kroger, M. 	Stepwise cloning and molecular characterization of the HgiDI restriction-modification system from Herpetosiphon giganteus Hpa2.	Nucleic Acids Res.	1991	19		1049-1056			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. 		
@D	Dusterhoft, A.//Erdmann, D.//Kroger, M. 	Isolation and genetic structure of the AvaII isoschizomeric restriction-modification system HgiBI from Herpetosiphon giganteus Hpg5:  M.HgiBI reveals high homology to M.BanI.	Nucleic Acids Res.	1991	19		3207-3211			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. 		
@D	Dusterhoft, A.//Kroger, M. 	Site directed mutagenesis on the restriction endonuclease EcoRI using mixed oligonucleotides.	Nucl. Nucl.	1988	7		737-740			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. 		
@D	Dusterhoft, A.//Kroger, M. 	Cloning, sequence and characterization of m5C-methyltransferase-encoding gene, hgiDIIM (GTCGAC), from Herpetosiphon giganteus strain Hpa2.	Gene	1991	106		87-92			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. 		
@D	Dutta, V.//Altermann, E.//Olson, J.//Wray, G.A.//Siletzky, R.M.//Kathariou, S. 	Whole-Genome Sequences of Agricultural, Host-Associated Campylobacter coli and Campylobacter jejuni Strains.	Genome Announcements	2016	4		e00833-16			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. 		
@D	Dutta, V.//Lee, S.//Ward, T.J.//Orwig, N.//Altermann, E.//Jima, D.//Parsons, C.//Kathariou, S. 	Draft Genome Sequences of Two Historical Listeria monocytogenes Strains from Human Listeriosis Cases in 1933.	Genome Announcements	2016	4		e01364-16			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. 		
@D	Dutta, V.//Lee, S.//Ward, T.J.//Orwig, N.//Altermann, E.//Jima, D.D.//Parsons, C.//Kathariou, S. 	Genome Sequences of Listeria monocytogenes Strains with Resistance to Arsenic.	Genome Announcements	2017	5		e00327-17			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. 		
@D	Duvnjak, S.//Spicic, S.//Kusar, D.//Papic, B.//Reil, I.//Zdelar-Tuk, M.//Pavlinec, Z.//Duras, M.//Gomercic, T.//Hendriksen, R.S.//Cvetnic, Z. 	Whole-Genome Sequence of the First Sequence Type 27 Brucella ceti Strain Isolated from European Waters.	Genome Announcements	2017	5		e00988-17			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. 		
@D	Duyvesteyn, M.G.C.//de Waard, A. 	A new sequence-specific endonuclease from a thermophilic cyanobacterium, Mastigocladus laminosus.	FEBS Lett.	1980	111		423-426			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. 		
@D	Duyvesteyn, M.G.C.//de Waard, A.//van Ormondt, H. 	Two sequence-specific deoxyribonucleases from Rhodospirillum rubrum.	FEBS Lett.	1980	117		241-246			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). 		
@D	Duyvesteyn, M.G.C.//Korsuize, J.//de Waard, A. 	Isolation and characterization of a sequence-specific deoxyriboendonuclease from Calothrix scopulorum.	Plant Mol. Biol.	1981	1		75-79			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. 		
@D	Duyvesteyn, M.G.C.//Korsuize, J.//de Waard, A.//Vonshak, A.//Wolk, C.P. 	Sequence-specific endonucleases in strains of Anabaena and Nostoc.	Arch. Microbiol.	1983	134		276-281			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. 		
@D	Dwivedi, G.R.//Sharma, E.//Rao, D.N. 	Helicobacter pylori DprA alleviates restriction barrier for incoming DNA.	Nucleic Acids Res.	2013	41		3274-3288			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. 		
@D	Dwivedi, V.//Sangwan, N.//Nigam, A.//Garg, N.//Niharika, N.//Khurana, P.//Khurana, J.P.//Lal, R. 	Draft Genome Sequence of Thermus sp. Strain RL, Isolated from a Hot Water Spring  Located atop the Himalayan Ranges at Manikaran, India.	J. Bacteriol.	2012	194		3534			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%. 		
@D	Dwyer, P.A.//Riftina, F.//Agarwal, K.L. 	Interaction of HpaI endonuclease with chemically synthesized oligonucleotides.	Fed. Proc.	1979	38		294			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. 		
@D	Dwyer-Hallquist, P.//Kezdy, F.J.//Agarwal, K.L. 	Interaction of the HpaI endonuclease with synthetic oligonucleotides.	Biochemistry	1982	21		4693-4700			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. 		
@D	Dy, L.//Chalasani, S.//Essani, K. 	Isolaton of Escherichia coli mutants lacking methylcytosine-dependent restriction systems for cloning extensively methylated frog virus 3 DNA.	Gene	1993	131		87-91			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. 		
@D	Dyachenko, O.V.//Tarlachkov, S.V.//Marinitch, D.V.//Shevchuk, T.V.//Buryanov, Y.I. 	Expression of exogenous DNA methyltransferases: Application in molecular and cell biology.	Biokhimiia	2014	79		77-87			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. 		
@D	Dyachkova, M.S.//Klimina, K.M.//Kovtun, A.S.//Zakharevich, N.V.//Nezametdinova, V.Z.//Averina, O.V.//Danilenko, V.N. 	Draft Genome Sequences of Bifidobacterium angulatum GT102 and Bifidobacterium adolescentis 150: Focusing on the Genes Potentially Involved in the Gut-Brain  Axis.	Genome Announcements	2015	3		e00709-15			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. 		
@D	Dyall-Smith, M.//Pfeiffer, F.//Klee, K.//Palm, P.//Gross, K.//Schuster, S.C.//Rampp, M.//Oesterhelt, D. 	Haloquadratum walsbyi: limited diversity in a global pond.	PLoS ONE	2011	6		e20968			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. 		
@D	Dyall-Smith, M.L.//Liu, Y.//Billman-Jacobe, H. 	Genome Sequence of an Australian Monophasic Salmonella enterica subsp. enterica Typhimurium Isolate (TW-Stm6) Carrying a Large Plasmid with Multiple  Antimicrobial Resistance Genes.	Genome Announcements	2017	5		e00793-17			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. 		
@D	Dyall-Smith, M.L.//Pfeiffer, F.//Oberwinkler, T.//Klee, K.//Rampp, M.//Palm, P.//Gross, K.//Schuster, S.C.//Oesterhelt, D. 	Genome of the Haloarchaeon Natronomonas moolapensis, a Neutrophilic Member of a Previously Haloalkaliphilic Genus.	Genome Announcements	2013	1		e0009513			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. 		
@D	Dybvig, K.//Cao, Z.//French, C.T.//Yu, H. 	Evidence for type III restriction and modification systems in Mycoplasma pulmonis.	J. Bacteriol.	2007	189		2197-2202			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. 		
@D	Dybvig, K.//Sitaraman, R.//French, C.T. 	A family of phase-variable restriction enzymes with differing specificities generated by high-frequency gene rearrangements.	Proc. Natl. Acad. Sci. U. S. A.	1998	95		13923-13928			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. 		
@D	Dybvig, K.//Swinton, D.//Maniloff, J.//Hattman, S. 	Cytosine methylation of the sequence GATC in a mycoplasma.	J. Bacteriol.	1982	151		1420-1424			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. 		
@D	Dybvig, K.//Voelker, L.L. 	Molecular biology of mycoplasmas.	Annu. Rev. Microbiol.	1996	50		25-57			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. 		
@D	Dybvig, K.//Yu, H. 	Regulation of a restriction and modification system via DNA inversion in Mycoplasma pulmonis.	Mol. Microbiol.	1994	12		547-560			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. 		
@D	Dybwad, M.//Aarskaug, T.//Fykse, E.M.//Henie, M.E.//Blatny, J.M. 	Complete Genome Sequences of Six Legionella pneumophila Isolates from Two Collocated Outbreaks of Legionnaires' Disease in 2005 and 2008 in  Sarpsborg/Fredrikstad, Norway.	Genome Announcements	2016	4		e01367-16			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. 		
@D	Dymova, M.A.//Alkhovik, O.I.//Evdokimova, L.S.//Cherednichenko, A.G.//Petrenko, T.I. 	Complete Genome Sequence of a Novel Clinical Isolate, Mycobacterium abscessus Strain NOV0213.	Genome Announcements	2016	4		e01407-15			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. 		
@D	Dynan, W.//Fox, K.//Stoddard, B. 	Editorial: NAR Surveys the Past, Present and Future of Restriction Endonucleases.	Nucleic Acids Res.	2014	42		1-2			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). 		
@D	Dyson, P.//Evans, M. 	Novel post-replicative DNA modification in Streptomyces: analysis of the preferred modification site of plasmid pIJ101.	Nucleic Acids Res.	1998	26		1248-1253			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. 		
@D	Dziewit, L.//Adamczuk, M.//Szuplewska, M.//Bartosik, D. 	DIY series of genetic cassettes useful in construction of versatile = vectors specific for Alphaproteobacteria.	J. Microbiol. Methods	2011	86		166-174			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. 		
@D	Dziewit, L.//Bartosik, D. 	Plasmids of psychrophilic and psychrotolerant bacteria and their role in adaptation to cold environments.	Front. Microbiol.	2014	5		596			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. 		
@D	Dziewit, L.//Cegielski, A.//Romaniuk, K.//Uhrynowski, W.//Szych, A.//Niesiobedzki, P.//Zmuda-Baranowska, M.J.//Zdanowski, M.K.//Bartosik, D. 	Plasmid diversity in arctic strains of Psychrobacter spp.	Extremophiles	2013	17		433-444			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. 		
@D	Dziewit, L.//Kuczkowska, K.//Adamczuk, M.//Radlinska, M.//Bartosik, D. 	Functional characterization of the type II PamI restriction-modification system derived from plasmid pAMI7 of Paracoccus aminophilus JCM 7686.	FEMS Microbiol. Lett.	2011	324		56-63			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. 		
@D	Dziewit, L.//Oscik, K.//Bartosik, D.//Radlinska, M. 	Molecular Characterization of a Novel Temperate Sinorhizobium Bacteriophage, Phi LM21, Encoding DNA Methyltransferase with CcrM-Like Specificity.	J. Virol.	2014	88		13111-13124			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. 		
@D	Earl, A.M.//Desjardins, C.A.//Fitzgerald, M.G.//Arachchi, H.M.//Zeng, Q.//Mehta, T.//Griggs, A.//Birren, B.W.//Toney, N.C.//Carr, J.//Posey, J.//Butler, W.R. 	High quality draft genome sequence of Segniliparus rugosus CDC 945(T)= (ATCC BAA-974(T)).	Standards in Genomic Sciences	2011	5		389-397			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. 		
@D	Earl, A.M.//Eppinger, M.//Fricke, W.F.//Rosovitz, M.J.//Rasko, D.A.//Daugherty, S.//Losick, R.//Kolter, R.//Ravel, J. 	Whole-Genome Sequences of Bacillus subtilis and Close Relatives.	J. Bacteriol.	2012	194		2378-2379			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). 		
@D	Eastberg, J.H.//Eklund, J.//Monnat, R.//Stoddard, B.L. 	Mutability of an HNH nuclease imidazole general base and exchange of a deprotonation mechanism.	Biochemistry	2007	46		7215-7225			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. 		
@D	Eastberg, J.H.//Smith, A.M.//Zhao, L.//Ashworth, J.//Shen, B.W.//Stoddard, B.L. 	Thermodynamics of DNA target site recognition by homing endonucleases.	Nucleic Acids Res.	2007	35		7209-7221			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). 		
@D	Eastman, A.W.//Weselowski, B.//Nathoo, N.//Yuan, Z.C. 	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.	Genome Announcements	2014	2		e01218-13			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. 		
@D	Eberhard, J.//Oza, J.//Reich, N.O. 	Cloning, sequence analysis and heterologous expression of the DNA adenine-(N-6) methyltransferase from the human pathogen Actinobacillus actinomycetemcomitans.	FEMS Microbiol. Lett.	2001	195		223-229			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. 		
@D	Eberhart, L.//Deringer, J.R.//Brayton, K.A.//Sawant, A.//Besser, T.E.//Call, D.R. 	Characterization of a novel microcin that kills enterohemorrhagic E. coli O157:H7 and O26.	Appl. Environ. Microbiol.	2012	78		6592-6599			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. 		
@D	Eby, J.C.//Turner, L.//Nguyen, B.//Kang, J.//Neville, C.//Temple, L. 	Complete Genome Sequence of Bordetella pertussis Strain VA-190 Isolated from a Vaccinated 10-Year-Old Patient with Whooping Cough.	Genome Announcements	2016	4		e00972-16			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. 		
@D	Eckstein, F. 	Action of restriction endonucleases on phosphorothioate DNA.	Biochem. Soc. Trans.	1986	14		204-205			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. 		
@D	Eckstein, F. 	Interaction of DNA containing phosphorothioate groups with restriction enzymes.	Ann. NY Acad. Sci.	1986	471		217-225			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. 		
@D	Eckstein, F. 	Phosphorothioation of DNA in bacteria.	Nat. Chem. Biol.	2007	3		689-690			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. 		
@D	Eckstein, F.//Connolly, B.A.//Potter, V.V.L. 	Cleavage of phosphorothioate-containing oligonucleotides and DNA by restriction endonucleases.	Abteil. Chem.	1987	8		23-27			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. 		
@D	Eckweiler, D.//Bunk, B.//Sproer, C.//Overmann, J.//Haussler, S. 	Complete Genome Sequence of Highly Adherent Pseudomonas aeruginosa Small-Colony Variant SCV20265.	Genome Announcements	2014	2		e01232-13			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. 		
@D	Eddy, S.R.//Gold, L. 	The phage T4 nrdB intron: a deletion mutant of a version found in the wild.	Genes Dev.	1991	5		1032-1041			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. 		
@D	Eddy, S.R.//Gold, L. 	Artificial mobile DNA element constructed from the EcoRI endonuclease gene.	Proc. Natl. Acad. Sci. U. S. A.	1992	89		1544-1547			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. 		
@D	Edgell, D.//Kleinstiver, B.//Wolfs, J.M.//Wang, L.//Kolaczyk, T.//McDowell, B.//Bogdanove, A. 	Genome engineering nucleases derived from GIY-YIG homing endonucleases.	J. Biomol. Struct. Dyn.	2013	31		64-65			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. 		
@D	Edgell, D.R. 	Selfish DNA: Homing Endonucleases Find a Home.	Curr. Biol.	2009	19		R115-R117			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. 		
@A	Edgell, D.R. 		Free-standing homing endonucleases of T-even phage: Freeloaders or functionaries?			Belfort, M. 		Nucleic Acids Mol. Biol.				Berlin Heidelberg	Springer-Verlag	2005		16		147-160									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. 		
@D	Edgell, D.R.//Belfort, M.//Shub, D.A. 	Barriers to intron promiscuity in bacteria.	J. Bacteriol.	2000	182		5281-5289			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? 		
@D	Edgell, D.R.//Derbyshire, V.//Van Roey, P.//LaBonne, S.//Stanger, M.J.//Li, Z.//Boyd, T.M.//Shub, D.A.//Belfort, M. 	Intron-encoded homing endonuclease I-TevI also functions as a transcriptional autorepressor.	Nat. Struct. Mol. Biol.	2004	11		936-944			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. 		
@D	Edgell, D.R.//Fast, N.M.//Doolittle, W.F. 	Selfish DNA: The best defense is a good offense.	Curr. Biol.	1996	6		385-388			The recent discovery of novel biochemical activities of intron-encoded endonucleases emphasizes the selfish nature of mobile genetic elements. 		
@D	Edgell, D.R.//Gibb, E.A.//Belfort, M. 	Mobile DNA elements in T4 and related phages.	Virol. J.	2010	7		290			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. 		
@D	Edgell, D.R.//Shub, D.A. 	Related homing endonucleases I-BmoI and I-TevI use different strategies to cleave homologous recognition sites.	Proc. Natl. Acad. Sci. U. S. A.	2001	98		7898-7903			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. 		
@D	Edgell, D.R.//Stanger, M.J.//Belfort, M. 	Coincidence of cleavage sites of intron endonuclease I-TevI and critical sequences of the host thymidylate synthase gene.	J. Mol. Biol.	2004	343		1231-1241			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. 		
@D	Edgell, D.R.//Stanger, M.J.//Belfort, M. 	Importance of a single base pair for discrimination between intron-containing and intronless alleles by endonuclease I-Bmol.	Curr. Biol.	2003	13		973-978			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. 		
@D	Edgell, M.H.//Hutchison, C.A. III//Sclair, M. 	Specific endonuclease R fragments of bacteriophage PhiX174 deoxyribonucleic acid.	J. Virol.	1972	9		574-582			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. 		
@D	Edlund, A.//Liu, Q.//Watling, M.//To, T.T.//Bumgarner, R.E.//He, X.//Shi, W.//McLean, J.S. 	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.	Genome Announcements	2016	4		e01684-15			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. 		
@D	Edmonds, P.//Hall, B.M.//Edwards, W.R.//Hartline, K.M. 	Presence of methylated adenine in GATC Sequences in chromosomal DNAs from Campylobacter species.	J. Bacteriol.	1992	174		8156-8157			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. 		
@D	Edouard, S.//Bibi, F.//Dhamodharan, R.//Lagier, J.C.//Azhar, E.I.//Robert, C.//Caputo, A.//Yasir, M.//Jiman-Fatani, A.A.//Alawi, M.//Fournier, P.E.//Raoult, D. 	Non-contiguous finished genome sequence and description of Corynebacterium jeddahense sp. nov.	Standards in Genomic Sciences	2014	9		987-1002			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. 		
@D	Edouard, S.//Sankar, S.//Dangui, N.P.//Lagier, J.C.//Michelle, C.//Raoult, D.//Fournier, P.E. 	Genome sequence and description of Nesterenkonia massiliensis sp. nov. strain NP1(T.).	Standards in Genomic Sciences	2014	9		866-882			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. 		
@D	Edwards, C.R.//Onstott, T.C.//Miller, J.M.//Wiggins, J.B.//Wang, W.//Lee, C.K.//Cary, S.C.//Pointing, S.B.//Lau, M.C.Y. 	Draft Genome Sequence of Uncultured Upland Soil Cluster Gammaproteobacteria Gives Molecular Insights into High-Affinity Methanotrophy.	Genome Announcements	2017	5		e00047-17			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. 		
@D	Edwards, R.A.//Helm, R.A.//Maloy, S.R. 	Increasing DNA transfer efficiency by temporary inactivation of host restriction.	Biotechniques	1999	26		892-900			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. 		
@D	Ee, R.//Ambrose, M.//Lazenby, J.//Williams, P.//Chan, K.G.//Roddam, L. 	Genome Sequences of Two Pandoraea pnomenusa Isolates Recovered 11 Months Apart from a Cystic Fibrosis Patient.	Genome Announcements	2015	3		e01389-14			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. 		
@D	Ee, R.//Lim, Y.-L.//Yin, W.-F.//See-Too, W.-S.//Roberts, R.J.//Chan, K.-G. 	Novel methyltransferase recognition motif identified in Chania multitudinisentens RB-25T gen. nov., sp. nov.	Front. Microbiol.	2016	7		1362			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). 		
@D	Ee, R.//Lim, Y.L.//Yin, W.F.//Chan, K.G. 	De Novo Assembly of the Quorum-Sensing Pandoraea sp. Strain RB-44 Complete Genome Sequence Using PacBio Single-Molecule Real-Time Sequencing Technology.	Genome Announcements	2014	2		e00245-14			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. 		
@D	Eevers, N.//Van Hamme, J.D.//Bottos, E.M.//Weyens, N.//Vangronsveld, J. 	Draft Genome Sequence of Enterobacter aerogenes, a DDE-Degrading and Plant Growth-Promoting Strain Isolated from Cucurbita pepo.	Genome Announcements	2015	3		e00317-15			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. 		
@D	Eevers, N.//Van Hamme, J.D.//Bottos, E.M.//Weyens, N.//Vangronsveld, J. 	Sphingomonas taxi, Isolated from Cucurbita pepo, Proves to Be a DDE-Degrading and Plant Growth-Promoting Strain.	Genome Announcements	2015	3		e00489-15			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. 		
@D	Eevers, N.//Van Hamme, J.D.//Bottos, E.M.//Weyens, N.//Vangronsveld, J. 	Draft Genome Sequence of Methylobacterium radiotolerans, a DDE-Degrading and Plant Growth-Promoting Strain Isolated from Cucurbita pepo.	Genome Announcements	2015	3		e00488-15			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. 		
@D	Efendi, Y.S.//Susanti, D.//Tritama, E.//Pasier, M.L.//Niwan, P.G.N.//Raharso, S.//Iskandar, A.P.//Giri-Rachman, E.A.//Mukhopadhyay, B.//Purwantini, E. 	Complete Genome Sequence of Bordetella pertussis Pelita III, the Production Strain for an Indonesian Whole-Cell Pertussis Vaccine.	Genome Announcements	2017	5		e00235-17			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. 		
@D	Efimov, V.//Danin-Poleg, Y.//Green, S.J.//Elgavish, S.//Kashi, Y. 	Draft Genome Sequence of the Pathogenic Bacterium Vibrio vulnificus V252 Biotype  1, Isolated in Israel.	Genome Announcements	2015	3		e01182-15			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. 		
@D	Efimova, E.P.//Delver, E.P.//Belogurov, A.A. 	Alleviation of type I restriction in adenine methylase (dam) mutants of Escherichia coli.	Mol. Gen. Genet.	1988	214		313-316			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. 		
@D	Efimova, E.P.//Delver, E.P.//Belogurov, A.A. 	2-aminopurine and 5-bromouracil induce alleviation of type I restriction in Escherichia coli:  Mismatches function as inducing signals?	Mol. Gen. Genet.	1988	214		317-320			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. 		
@D	Egan, K.//Kelleher, P.//Field, D.//Rea, M.C.//Ross, R.P.//Cotter, P.D.//Hill, C. 	Genome Sequence of Geobacillus stearothermophilus DSM 458, an Antimicrobial-Producing Thermophilic Bacterium, Isolated from a Sugar Beet  Factory.	Genome Announcements	2017	5		e01172-17			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. 		
@D	Egas, C.//Barroso, C.//Froufe, H.J.//Pacheco, J.//Albuquerque, L.//da Costa, M.S. 	Complete genome sequence of the Radiation-Resistant bacterium Rubrobacter radiotolerans RSPS-4.	Standards in Genomic Sciences	2014	9		1062-1075			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. 		
@D	Egidi, E.//Wood, J.L.//Aracic, S.//Kannan, R.//McDonald, L.//Bell, C.A.//Fox, E.M.//Liu, W.//Franks, A.E. 	Draft Genome Sequence of Enterobacter ludwigii NCR3, a Heavy Metal-Resistant Rhizobacterium.	Genome Announcements	2016	4		e01076-16			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. 		
@D	Egidi, E.//Wood, J.L.//Fox, E.M.//Liu, W.//Franks, A.E. 	Draft Genome Sequence of Leifsonia sp. Strain NCR5, a Rhizobacterium Isolated from Cadmium-Contaminated Soil.	Genome Announcements	2017	5		e00520-17			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. 		
@D	Egidi, E.//Wood, J.L.//Fox, E.M.//Liu, W.//Franks, A.E. 	Draft Genome Sequence of Rhodococcus erythropolis NSX2, an Actinobacterium Isolated from a Cadmium-Contaminated Environment.	Genome Announcements	2016	4		e01147-16			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. 		
@D	Egidi, E.//Wood, J.L.//Mathews, E.//Fox, E.//Liu, W.//Franks, A.E. 	Draft Genome Sequence of Bacillus cereus LCR12, a Plant Growth-Promoting Rhizobacterium Isolated from a Heavy Metal-Contaminated Environment.	Genome Announcements	2016	4		e01041-16			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. 		
@D	Ehara, A.//Suzuki, H.//Amachi, S. 	Draft Genome Sequence of Geobacter sp. Strain OR-1, an Arsenate-Respiring Bacterium Isolated from Japanese Paddy Soil.	Genome Announcements	2015	3		e01478-14			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. 		
@D	Ehara, A.//Suzuki, H.//Kanesaki, Y.//Yoshikawa, H.//Amachi, S. 	Draft genome sequence of strain q-1, an iodide-oxidizing alphaproteobacterium isolated from natural gas brine water.	Genome Announcements	2014	2		e00659-14			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. 		
@D	Ehbrecht, H.-J.//Pingoud, A.//Urbanke, C.//Maass, G.//Gualerzi, C. 	Linear diffusion of restriction endonucleases on DNA.	J. Biol. Chem.	1985	260		6160-6166			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. 		
@D	Ehrlich, M.//Ehrlich, K.//Mayo, J.A. 	Unusual properties of the DNA from Xanthomonas phage XP-12 in which 5-methylcytosine completely replaces cytosine.	Biochim. Biophys. Acta	1975	395		109-119			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. 		
@D	Ehrlich, M.//Gama-Sosa, M.A.//Carreira, L.H.//Ljungdahl, L.G.//Kuo, K.C.//Gehrke, C.W. 	DNA methylation in thermophilic bacteria: N4-methylcytosine, 5-methylcytosine, and N6-methyladenine.	Nucleic Acids Res.	1985	13		1399-1412			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. 		
@D	Ehrlich, M.//Norris, K.F.//Wang, R.Y.//Kuo, K.C.//Gehrke, C.W. 	DNA cytosine methylation and heat-induced deamination.	Biosci. Rep.	1986	6		387-393			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. 		
@D	Ehrlich, M.//Wang, R.Y.-H. 	5-Methylcytosine in eukaryotic DNA.	Science	1981	212		1350-1357			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. 		
@D	Ehrlich, M.//Wilson, G.G.//Kenneth, C.K.//Gehrke, C.W. 	N4-Methylcytosine as a minor base in bacterial DNA.	J. Bacteriol.	1987	169		939-943			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. 		
@D	Ehsani, E.//Barrantes, I.//Vandermaesen, J.//Geffers, R.//Jarek, M.//Boon, N.//Springael, D.//Pieper, D.H.//Vilchez-Vargas, R. 	Draft Genome Sequence of Aeromonas sp. Strain EERV15.	Genome Announcements	2016	4		e00811-16			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. 		
@D	Ehsani, E.//Jauregui, R.//Geffers, R.//Jareck, M.//Boon, N.//Pieper, D.H.//Vilchez-Vargas, R. 	Draft Genome Sequence of Rhodococcus sp. Strain 311R.	Genome Announcements	2015	3		e00378-15			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. 		
@D	Ehsani, E.//Jauregui, R.//Geffers, R.//Jarek, M.//Boon, N.//Pieper, D.H.//Vilchez-Vargas, R. 	First Draft Genome Sequence of the Acidovorax caeni sp. nov. Type Strain R-24608  (DSM 19327).	Genome Announcements	2015	3		e01378-15			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. 		
@D	Eichhorn, I.//Tedin, K.//Fulde, M. 	Draft Genome Sequence of Salmonella enterica subsp. enterica Serovar Typhimurium  Q1.	Genome Announcements	2017	5		e01151-17			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. 		
@D	Eichhorn, I.//van der Linden, M.//Jarek, M.//Fulde, M. 	Draft Genome Sequence of Zoonotic Streptococcus canis Isolate G361.	Genome Announcements	2017	5		e00967-17			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. 		
@D	Eickbush, T.H. 	Mobile introns: Retrohoming by complete reverse splicing.	Curr. Biol.	1999	9		R11-R14			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. 		
@D	Eidam, C.//Poehlein, A.//Brenner, M.G.//Kadlec, K.//Liesegang, H.//Brzuszkiewicz, E.//Daniel, R.//Sweeney, M.T.//Murray, R.W.//Watts, J.L.//Schwarz, S. 	Complete Genome Sequence of Mannheimia haemolytica Strain 42548 from a Case of Bovine Respiratory Disease.	Genome Announcements	2013	1		e00318-13			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. 		
@D	Eigner, J.//Block, S. 	Host-controlled restriction of T-even bacteriophages:  relation of four bacterial deoxyribonucleases to restriction.	J. Virol.	1968	2		320-326			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. 		
@D	Eijkelkamp, B.A.//Stroeher, U.H.//Hassan, K.A.//Papadimitrious, M.S.//Paulsen, I.T.//Brown, M.H. 	Adherence and motility characteristics of clinical Acinetobacter baumannii isolates.	FEMS Microbiol. Lett.	2011	323		44-51			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. 		
@D	Eikmeyer, F.//Hadiati, A.//Szczepanowski, R.//Wibberg, D.//Schneiker-Bekel, S.//Rogers, L.M.//Brown, C.J.//Top, E.M.//Puhler, A.//Schluter, A. 	The complete genome sequences of four new IncN plasmids from wastewater treatment plant effluent provide new insights into IncN plasmid diversity and evolution.	Plasmid	2012	68		13-24			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. 		
@D	Einvik, C.//Decatur, W.A.//Embley, T.M.//Vogt, V.M.//Johansen, S. 	Naegleria nucleolar introns contain two group I ribozymes with different functions in RNA splicing and processing.	RNA	1997	3		710-720			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. 		
@D	Eisen, J.A. et al. 	The complete genome sequence of Chlorobium tepidum TLS, a photosynthetic, anaerobic, green-sulfur bacterium.	Proc. Natl. Acad. Sci. U. S. A.	2002	99		9509-9514			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. 		
@D	Eisen, S.//Poehlein, A.//Johnson, D.B.//Daniel, R.//Schlomann, M.//Muhling, M. 	Genome Sequence of the Acidophilic Iron Oxidizer Ferrimicrobium acidiphilum Strain T23T.	Genome Announcements	2015	3		e00383-15			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. 		
@D	Eisen, S.//Poehlein, A.//Johnson, D.B.//Daniel, R.//Schlomann, M.//Muhling, M. 	Genome Sequence of the Acidophilic Ferrous Iron-Oxidizing Isolate Acidithrix ferrooxidans Strain Py-F3, the Proposed Type Strain of the Novel Actinobacterial   Genus Acidithrix.	Genome Announcements	2015	3		e00382-15			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. 		
@D	Eisenschmidt, K. 	Development of a programmable restriction enzyme.	Ph.D. Thesis, Germany	2005			1-116					
@D	Eisenschmidt, K.//Lanio, T.//Jeltsch, A.//Pingoud, A. 	A fluorimetric assay for on-line detection of DNA cleavage by restriction endonucleases.	J. Biotechnol.	2002	96		185-191			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. 		
@D	Eisenschmidt, K.//Lanio, T.//Simoncsits, A.//Jeltsch, A.//Pingoud, V.//Wende, W.//Pingoud, A. 	Developing a programmed restriction endonuclease for highly specific DNA cleavage.	Nucleic Acids Res.	2005	33		7039-7047			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. 		
@D	Ekino, K.//Kwon, I.//Goto, M.//Yoshino, S.//Furukawa, K. 	Functional analysis of HO gene in delayed homothallism in Saccharomyces cerevisiae wy2.	Yeast	1999	15		451-458			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. 		
@D	Eklund, J.L. 	Design and characterization of homing endonuclease I-PpoI variants with novel DNA sequence specificity.	Ph.D. Thesis, University of Washington, Seattle, USA	2005			1-115			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. 		
@D	Eklund, J.L.//Ulge, U.Y.//Eastberg, J.//Monnat, R.J. Jr. 	Altered target site specificity variants of the I-PpoI His-Cys box homing endonuclease.	Nucleic Acids Res.	2007	35		5839-5850			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. 		
@D	El Aamri, F.//Acosta, F.//Real, F.//Padilla, D. 	Whole-Genome Sequence of the Fish Virulent Strain Streptococcus iniae IUSA-1, Isolated from Gilthead Sea Bream (Sparus aurata) and Red Porgy (Pagrus pagrus).	Genome Announcements	2013	1		e0002513			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. 		
@D	El Halfawy, N.M.//El-Naggar, M.Y.//Andrews, S.C. 	Complete Genome Sequence of Lactobacillus plantarum 10CH, a Potential Probiotic Lactic Acid Bacterium with Potent Antimicrobial Activity.	Genome Announcements	2017	5		e01398-17			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. 		
@D	El Houmami, N.//Schrenzel, J.//Yagupsky, P.//Robert, C.//Ceroni, D.//Raoult, D.//Fournier, P.E. 	Draft Genome Sequence of Kingella negevensis SW7208426, the First European Strain of K. negevensis Isolated from a Healthy Child in Switzerland.	Genome Announcements	2017	5		e00571-17			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. 		
@D	El Kafsi, H.//Binesse, J.//Loux, V.//Buratti, J.//Boudebbouze, S.//Dervyn, R.//Hammani, A.//Maguin, E.//van de Guchte, M. 	Genome Sequence of Lactobacillus delbrueckii subsp. lactis CNRZ327, a Dairy Bacterium with Anti-Inflammatory Properties.	Genome Announcements	2014	2		e00328-14			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. 		
@D	El Karkouri, K.//Mediannikov, O.//Robert, C.//Raoult, D.//Fournier, P.E. 	Genome Sequence of the Tick-Borne Pathogen Rickettsia raoultii.	Genome Announcements	2016	4		e00157-16			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. 		
@D	El-Arabi, T.F.//Griffiths, M.W.//She, Y.M.//Villegas, A.//Lingohr, E.J.//Kropinski, A.M. 	Genome sequence and analysis of a broad-host range lytic bacteriophage that infects the Bacillus cereus group.	Virol. J.	2013	10		48			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. 		
@D	El-Deiry, W.S.//Nelkin, B.D.//Celano, P.//Yen, R.-W.C.//Falco, J.P.//Hamilton, S.R.//Baylin, S.B. 	High expression of the DNA methyltransferase gene characterizes human neoplastic cells and progression stages of colon cancer.	Proc. Natl. Acad. Sci. U. S. A.	1991	88		3470-3474			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. 		
@D	El-Said, M.M.//Garcia, J.L.//Martinez, I.//Del Cerro, C.//Nogales, J.//Diaz, E. 	Genome Sequence of Pseudomonas azelaica Strain Aramco J.	Genome Announcements	2015	3		e00037-15			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. 		
@D	El-Sayed, E.S.A.//El-Didamony, G.//Mansour, K. 	Isolation and characterization of two types of actinophage infecting Streptomyces scabies.	Folia Microbiol. (Praha)	2001	46		519-526			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. 		
@D	Elbir, H.//Gimenez, G.//Robert, C.//Bergstrom, S.//Cutler, S.//Raoult, D.//Drancourt, M. 	Complete Genome Sequence of Borrelia crocidurae.	J. Bacteriol.	2012	194		3723-3724			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. 		
@D	Elbir, H.//Larsson, P.//Normark, J.//Upreti, M.//Korenberg, E.//Larsson, C.//Bergstrom, S. 	Genome Sequence of the Asiatic Species Borrelia persica.	Genome Announcements	2014	2		e01127-13			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. 		
@D	Elbir, H.//Larsson, P.//Upreti, M.//Normark, J.//Bergstrom, S. 	Genome Sequence of the Relapsing Fever Borreliosis Species Borrelia hispanica.	Genome Announcements	2014	2		e01171-13			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. 		
@D	Elbir, H.//Robert, C.//Nguyen, T.T.//Gimenez, G.//El Sanousi, S.M.//Flock, J.I.//Raoult, D.//Drancourt, M. 	Staphylococcus aureus subsp. anaerobius strain ST1464 genome sequence.	Standards in Genomic Sciences	2013	9		1-13			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. 		
@D	Elbir, H.//Sitlani, P.//Bergstrom, S.//Barbour, A.G. 	Chromosome and Megaplasmid Sequences of Borrelia anserina (Sakharoff 1891), the Agent of Avian Spirochetosis and Type Species of the Genus.	Genome Announcements	2017	5		e00018-17			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. 		
@D	Elcheninov, A.G.//Menzel, P.//Gudbergsdottir, S.R.//Slesarev, A.I.//Kadnikov, V.V.//Krogh, A.//Bonch-Osmolovskaya, E.A.//Peng, X.//Kublanov, I.V. 	Sugar Metabolism of the First Thermophilic Planctomycete Thermogutta terrifontis: Comparative Genomic and Transcriptomic Approaches.	Front. Microbiol.	2017	8		2140			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. 		
@D	Eldarov, M.A.//Karpichev, I.V.//Samko, O.T.//Anikeitcheva, N.V.//Kalugin, A.A.//Khoroshoutina, E.B.//Sokolov, N.N. 	Isolation and characterization of restriction endonuclease BcuAI from Bacillus cereus A.	Nucleic Acids Res.	1992	20		2898			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. 		
@D	Eldarov, M.A.//Karpichev, I.V.//Samko, O.T.//Anikeitcheva, N.V.//Kalugin, A.A.//Khoroshoutina, E.B.//Sokolov, N.N. 	Characterization of BciBII, an isoschizomer of BstNI from a strain of Bacillus circulans B.	Nucleic Acids Res.	1992	20		2896			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. 		
@D	Elde, M.//Haugen, P.//Willassen, N.P.//Johansen, S. 	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.	Eur. J. Biochem.	1999	259		281-288			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. 		
@D	Elde, M.//Willassen, N.P.//Johansen, S. 	Functional characterization of isoschizomeric His-Cys box homing endonucleases from Naegleria.	Eur. J. Biochem.	2000	267		7257-7266			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. 		
@D	Elfadl, A.K.//Lee, S.W.//Kim, J.H.//Lee, K.L.//Arif-Ullah, H.M.//Chung, M.J.//Ghim, S.G.//Lee, E.J.//Kim, Y.D.//Kim, S.M.//Jeon, S.G.//Lim, J.H.//Choi, H.J.//Park, J.K.//Jeong, K.S. 	Fatal fibrino-hemorrhagic bronchopneumonia associated with Morganella morganii in a bottlenose dolphin: a case report.	Dis. Aquat. Org.	2017	127		41-47			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. 		
@D	Elhai, J. 	Highly Iterated Palindromic Sequences (HIPs) and Their Relationship to DNA Methyltransferases.	Life	2015	5		921-948			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. 		
@D	Elhai, J. 	Determination of bias in the relative abundance of oligonucleotides in DNA sequences.	J. Comput. Biol.	2001	8		151-175			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. 		
@D	Elhai, J.//Cai, Y.//Wolk, C.P. 	Conduction of pEC22, a plasmid coding for MR.EcoT22I, mediated by a resident Tn3-like transposon, Tn5396.	J. Bacteriol.	1994	176		5059-5067			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. 		
@D	Elhai, J.//Vepritskiy, A.//Muro-Pastor, A.M.//Flores, E.//Wolk, C.P. 	Reduction of conjugal transfer efficiency by three restriction activities of Anabaena sp. strain PCC 7120.	J. Bacteriol.	1997	179		1998-2005			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. 		
@D	Elkins, J.G. et al. 	Complete Genome Sequence of the Cellulolytic Thermophile Caldicellulosiruptor obsidiansis OB47T.	J. Bacteriol.	2010	192		6099-6100			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. 		
@D	Elkins, J.G. et al. 	A korarchaeal genome reveals insights into the evolution of the Archaea.	Proc. Natl. Acad. Sci. U. S. A.	2008	105		8102-8107			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. 		
@D	Elkins, J.G. et al. 	Complete Genome Sequence of the Hyperthermophilic Sulfate-Reducing Bacterium Thermodesulfobacterium geofontis OPF15T.	Genome Announcements	2013	1		e00162-13			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. 		
@D	Ellegaard, K.M.//Klasson, L.//Naslund, K.//Bourtzis, K.//Andersson, S.G. 	Comparative genomics of wolbachia and the bacterial species concept.	PLoS Genet.	2013	9		E1003381			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. 		
@D	Elliott, A.G.//Ganesamoorthy, D.//Coin, L.//Cooper, M.A.//Cao, M.D. 	Complete Genome Sequence of Klebsiella quasipneumoniae subsp. similipneumoniae Strain ATCC 700603.	Genome Announcements	2016	4		e00438-16			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. 		
@D	Elliott, S.L.//Brazier, J.//Cosstick, R.//Connolly, B.A. 	Mechanism of the Escherichia coli DNA T:G-mismatch endonuclease (Vsr protein) probed with thiophosphate-containing oligodeoxynucleotides.	J. Mol. Biol.	2005	353		692-703			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. 		
@D	Elliott, T. 	Cloning, genetic characterization, and nucleotide sequence of the hemA-prfA operon of Salmonella typhimurium.	J. Bacteriol.	1989	171		3948-3960			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. 		
@D	Ellis, D.J.//Dryden, D.T.//Berge, T.//Edwardson, J.M.//Henderson, R.M. 	Direct observation of DNA translocation and cleavage by the EcoKI endonuclease using atomic force microscopy.	Nat. Struct. Biol.	1999	6		15-17			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. 		
@D	Ellison, D.W.//Clark, T.R.//Sturdevant, D.E.//Virtaneva, K.//Porcella, S.F.//Hackstadt, T. 	Genomic comparison of virulent Rickettsia rickettsii Sheila Smith and avirulent Rickettsia rickettsii Iowa.	Infect. Immun.	2008	76		542-550			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. 		
@D	Ellison, E.L.//Muscarella, D.E.//Vogt, V.M. 	Characterization of I-PpoI, an intron-encoded endonuclease from Physarum polycephalum.	J. Cell Biochem. Suppl.	1993	17C		177			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. 		
@D	Ellison, E.L.//Vogt, V.M. 	Interaction of the intron-encoded mobility endonuclease I-PpoI with its target site.	Mol. Cell. Biol.	1993	13		7531-7539			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. 		
@D	Ellrott, K.P.//Kasarjian, J.K.A.//Jiang, T.//Ryu, J. 	Restriction enzyme recognition sequence search program.	Biotechniques	2002	33		1322-1326			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. 		
@D	Elnahas, M.O.//De Leon, K.B.//Amin, M.A.//Hussein, M.M.D.//Ali, A.E.//Wall, J.D. 	Complete Genome Sequencing of Streptomyces sp. Strain MOE7, Which Produces an Extracellular Polysaccharide with Antioxidant and Antitumor Activities.	Genome Announcements	2017	5		e00442-17			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. 		
@D	Elsawy, H.//Chahar, S. 	Increasing DNA substrate specificity of the EcoDam DNA-(adenine N-6)-methyltransferase by site-directed mutagenesis.	Biokhimiia	2014	79		1262-1266			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. 		
@D	Elsawy, H.//Chahar, S. 	Increasing DNA substrate specificity of the EcoDam DNA-(adenine N-6)-methyltransferase by site-directed mutagenesis.	Biochemistry	2014	79		1262-1266			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. 		
@D	Elschner, M.C.//Busch, A.//Schliephake, A.//Gaede, W.//Zuchantke, E.//Tomaso, H. 	High-Quality Genome Sequence of Bacillus anthracis Strain 14RA5914 Isolated during an Outbreak in Germany in 2014.	Genome Announcements	2017	5		e01002-17			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. 		
@D	Elschner, M.C.//Thomas, P.//El-Adawy, H.//Mertens, K.//Melzer, F.//Hnizdo, J.//Stamm, I. 	Complete Genome Sequence of a Burkholderia pseudomallei Strain Isolated from a Pet Green Iguana in Prague, Czech Republic.	Genome Announcements	2017	5		e01761-16			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. 		
@D	Elschner, M.C.//Thomas, P.//Melzer, F. 	Complete Genome Sequence of a Burkholderia mallei Isolate Originating from a Glanderous Horse from the Kingdom of Bahrain.	Genome Announcements	2016	4		e01296-16			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. 		
@D	Embleton, M.L.//Siksnys, V.//Halford, S.E. 	DNA cleavage reactions by type II restriction enzymes that require two copies of their recognition sites.	J. Mol. Biol.	2001	311		503-514			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. 		
@D	Embleton, M.L.//Vologodskii, A.V.//Halford, S.E. 	Dynamics of DNA loop capture by the Sfil restriction endonuclease on supercoiled and relaxed DNA.	J. Mol. Biol.	2004	339		53-66			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. 		
@D	Embleton, M.L.//Williams, S.A.//Watson, M.A.//Halford, S.E. 	Specificity from the synapsis of DNA elements by the SfiI endonuclease.	J. Mol. Biol.	1999	289		785-797			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. 		
@D	Embley, T.M.//Dyal, P.//Kilvington, S. 	A group I intron in the small subunit ribosomal RNA gene from Naegleria andersoni ssp. andersoni strain PPMFB-6.	Nucleic Acids Res.	1992	20		6411			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. 		
@D	Emond, E.//Ee, E.L.//Drolet, G.//Moineau, S.//LaPointe, G. 	Molecular characterization of a theta replication plasmid and its use for development of a two-component food-grade cloning system for Lactococcus lactis.	Appl. Environ. Microbiol.	2001	67		1700-1709			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. 		
@D	Emond, E.//Holler, B.J.//Boucher, I.//Vandenbergh, P.A.//Vedamuthu, E.R.//Kondo, J.K.//Moineau, S. 	Phenotypic and genetic characterization of the bacteriophage abortive infection mechanism AbiK from Lactococcus lactis.	Appl. Environ. Microbiol.	1997	63		1274-1283			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. 		
@D	Emond-Rheault, J.G.//Vincent, A.T.//Trudel, M.V.//Brochu, F.//Boyle, B.//Tanaka, K.H.//Attere, S.A.//Jubinville, E.//Loch, T.P.//Winters, A.D.//Faisal, M.//Frenette, M.//Derome, N.//Charette, S.J. 	Variants of a genomic island in Aeromonas salmonicida subsp. salmonicida link isolates with their geographical origins.	Vet. Microbiol.	2014	175		68-76			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. 		
@D	Emperle, M.//Rajavelu, A.//Kunert, S.//Arimondo, P.B.//Reinhardt, R.//Jurkowska, R.Z.//Jeltsch, A. 	The DNMT3A R882H mutant displays altered flanking sequence preferences.	Nucleic Acids Res.	2018	46		3130-3139			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. 		
@D	Encinas, F.//Marin, M.A.//Ramos, J.N.//Vieira, V.V.//Mattos-Guaraldi, A.L.//Vicente, A.C. 	Genomic analysis of a nontoxigenic, invasive Corynebacterium diphtheriae strain from Brazil.	Memorias do Instituto Oswaldo Cruz	2015	110		817-819			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. 		
@D	Endlich, B.//Linn, S. 	The DNA restriction endonuclease of Escherichia coli B.  I. Studies of the DNA translocation and the ATPase activities.	J. Biol. Chem.	1985	260		5720-5728			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. 		
@D	Endlich, B.//Linn, S. 	The DNA restriction endonuclease of Escherichia coli B.  II.  Further studies of the structure of DNA intermediates and products.	J. Biol. Chem.	1985	260		5729-5738			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. 		
@A	Endlich, B.//Linn, S. 		Type I restriction enzymes.			Boyer, P. 		The Enzymes					Academic Press	1981		14		137-156									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. 		
@D	Endo, M.//Nakayama, K.//Majima, T. 	Design and synthesis of photochemically controllable restriction endonuclease BamHI by manipulating the salt-bridge network in the dimer  interface.	J. Org. Chem.	2004	69		4292-4298			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. 		
@D	Endow, S.A. 	Analysis of Drosophila melanogaster Satellite IV with restriction endonuclease MboII.	J. Mol. Biol.	1977	114		441-449			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. 		
@D	Endow, S.A.//Roberts, R.J. 	Two restriction-like enzymes from Xanthomonas malvacearum.	J. Mol. Biol.	1977	112		521-529			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. 		
@D	Eng, C.//Blouin, Y.//Ding, N.//Larigauderie, G.//Ramisse, V.//Pujol, C. 	Draft Genome Sequence of the Biowarfare Simulant Bacillus atrophaeus Strain 930029.	Genome Announcements	2015	3		e00491-15			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. 		
@D	Eng, W.W.//Gan, H.M.//Gan, H.Y.//Hudson, A.O.//Savka, M.A. 	Whole-Genome Sequence and Annotation of Octopine-Utilizing Pseudomonas kilonensis (Previously P. fluorescens) Strain 1855-344.	Genome Announcements	2015	3		e00463-15			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. 		
@D	Engel, P. 	Plasmid transformation of Streptomyces tendae after heat attenuation of restriction.	Appl. Environ. Microbiol.	1987	53		1-3			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. 		
@D	Engel, P.//Vizcaino, M.I.//Crawford, J.M. 	Gut symbionts from distinct hosts exhibit genotoxic activity via divergent colibactin biosynthetic pathways.	Appl. Environ. Microbiol.	2015	81		1502-1512			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. 		
@D	Engelbrecht, K.C.//Putonti, C.//Koenig, D.W.//Wolfe, A.J. 	Draft Genome Sequence of Escherichia coli K-12 (ATCC 29425).	Genome Announcements	2017	5		e00574-17			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. 		
@D	Engin, D.//Hascelik, G. 	iceA genotypes may play a role in acquiring metronidazole resistance in Helicobacter pylori.	Helicobacter	2003	8		356			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. 		
@D	Engler, L.E.//Sapienza, P.//Dorner, L.F.//Kucera, R.//Schildkraut, I.//Jen-Jacobson, L. 	The energetics of the interaction of BamHI endonuclease with its recognition site GGATCC.	J. Mol. Biol.	2001	307		619-636			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. 		
@D	Engler, L.E.//Welch, K.K.//Jen-Jacobson, L. 	Specific binding by EcoRV endonuclease to its DNA recognition site GATATC.	J. Mol. Biol.	1997	269		82-101			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. 		
@D	Enikeeva, F.N.//Severinov, K.V.//Gelfand, M.S. 	Restriction-modification systems and bacteriophage invasion: Who wins?	J. Theor. Biol.	2010	266		550-559			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. 		
@D	Epinat, J.C.//Arnould, S.//Chames, P.//Rochaix, P.//Desfontaines, D.//Puzin, C.//Patin, A.//Zanghellini, A.//Paques, F.//Lacroix, E. 	A novel engineered meganuclease induces homologous recombination in yeast and mammalian cells.	Nucleic Acids Res.	2003	31		2952-2962			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. 		
@D	Eppinger, M. et al. 	Genome Sequences of the Biotechnologically Important Bacillus megaterium Strains QM B1551 and DSM319.	J. Bacteriol.	2011	193		4199-4213			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. 		
@D	Eppinger, M.//Baar, C.//Linz, B.//Raddatz, G.//Lanz, C.//Keller, H.//Morelli, G.//Gressmann, H.//Achtman, M.//Schuster, S.C. 	Who ate whom? Adaptive Helicobacter genomic changes that accompanied a host jump from early humans to large felines.	PLoS Genet.	2006	2		e120			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. 		
@D	Eppinger, M.//Daugherty, S.//Agrawal, S.//Galens, K.//Sengamalay, N.//Sadzewicz, L.//Tallon, L.//Cebula, T.A.//Mammel, M.K.//Feng, P.//Soderlund, R.//Tarr, P.I.//Debroy, C.//Dudley, E.G.//Fraser, C.M.//Ravel, J. 	Whole-Genome Draft Sequences of 26 Enterohemorrhagic Escherichia coli O157:H7 Strains.	Genome Announcements	2013	1		e0013412			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. 		
@D	Eppinger, M.//Guo, Z.//Sebastian, Y.//Song, Y.//Lindler, L.E.//Yang, R.//Ravel, J. 	Draft Genome Sequences of Yersinia pestis Isolates From Natural Foci of Endemic Plague in China.	J. Bacteriol.	2009	191		7628-7629			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. 		
@D	Eppinger, M.//Mammel, M.K.//Leclerc, J.E.//Ravel, J.//Cebula, T.A. 	Genome Signatures of Escherichia coli O157:H7 Isolates from the Bovine Host Reservoir.	Appl. Environ. Microbiol.	2011	77		2916-2925			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. 		
@D	Eppinger, M.//McNair, K.//Zogaj, X.//Dinsdale, E.A.//Edwards, R.A.//Klose, K.E. 	Draft Genome Sequence of the Fish Pathogen Piscirickettsia salmonis.	Genome Announcements	2013	1		e00926-13			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. 		
@D	Erdmann, D. 	Cloning of restriction-modification systems from Herpetosiphon giganteus Hpg9 and Hpg24 in E. coli - Characterization and comparative analysis of the genetic organization and structure.	Ph.D. Thesis, Justus-Liebig University, Geissen, W. Germany	1991			1-204			None 		
@D	Erdmann, D.//Dusterhoft, A.//Kroger, M. 	Cloning and molecular characterization of the HgiCI restriction/modification system from Herpetosiphon giganteus Hpg9 reveals high similarity to BanI.	Eur. J. Biochem.	1991	202		1247-1256			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. 		
@D	Erdmann, D.//Horst, G.//Dusterhoft, A.//Kroger, M. 	Stepwise cloning and genetic organization of the seemingly unclonable HgiCII restriction-modification system from Herpetosiphon giganteus strain Hpg9, using PCR technique.	Gene	1992	117		15-22			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. 		
@D	Erickson, K.E.//Madinger, N.E.//Chatterjee, A. 	Draft Genome Sequence for a Clinical Isolate of Vancomycin-Resistant Enterococcus faecalis.	Genome Announcements	2016	4		e00584-16			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. 		
@D	Erickson, K.E.//Madinger, N.E.//Chatterjee, A. 	Draft Genome Sequences of Clinical Isolates of Multidrug-Resistant Acinetobacter  baumannii.	Genome Announcements	2017	5		e01547-16			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. 		
@D	Erikstad, H.A.//Birkeland, N.K. 	Draft Genome Sequence of 'Candidatus Methylacidiphilum kamchatkense' Strain Kam1, a Thermoacidophilic Methanotrophic Verrucomicrobium.	Genome Announcements	2015	3		e00065-15			'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. 		
@D	Erill, I.//Puigvert, M.//Legrand, L.//Guarischi-Sousa, R.//Vandecasteele, C.//Setubal, J.C.//Genin, S.//Guidot, A.//Valls, M. 	Comparative Analysis of Ralstonia solanacearum Methylomes.	Front. Plant Sci.	2017	8		504			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. 		
@D	Erkel, C.//Kube, M.//Reinhardt, R.//Liesack, W. 	Genome of Rice Cluster I archaea--the key methane producers in the rice rhizosphere.	Science	2006	313		370-372			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. 		
@D	Erlanson, D.A.//Chen, L.//Verdine, G.L. 	DNA methylation through a locally upaired intermediate.	J. Am. Chem. Soc.	1993	115		12583-12584			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. 		
@D	Erlanson, D.A.//Wolfe, S.A.//Chen, L.//Verdine, G.L. 	Selective base-pair destabilization enhances binding of a DNA methyltransferase.	Tetrahedron	1997	53		12041-12056			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. 		
@D	Erova, T.//Sha, J.//Fadl, A.//Khajanchi, B.//Chopra, A. 	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.	Abstr. Gen. Meet. Am. Soc. Microbiol.	2006	106		76			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. 		
@D	Erova, T.E.//Fadl, A.A.//Sha, J.//Khajanchi, B.K.//Pillai, L.L.//Kozlova, E.V.C.A.K. 	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.	Infect. Immun.	2006	74		5763-5772			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. 		
@D	Erova, T.E.//Kosykh, V.G.//Sha, J.//Chopra, A.K. 	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).	Gene	2012	498		280-287			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. 		
@D	Erova, T.E.//Pillai, L.//Fadl, A.A.//Sha, J.//Wang, S.F.//Galindo, C.L.//Chopra, A.K. 	DNA adenine methyltransferase influences the virulence of Aeromonas hydrophila.	Infect. Immun.	2005	74		410-424			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. 		
@D	Ershova, A.//Rusinov, I.//Vasiliev, M.//Spirin, S.//Karyagina, A. 	Restriction-Modification systems interplay causes avoidance of GATC site in prokaryotic genomes.	J. Bioinform. Comput. Biol.	2016	14		1641003			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. 		
@D	Ershova, A.S.//Karyagina, A.S.//Vasiliev, M.O.//Lyashchuk, A.M.//Lunin, V.G.//Spirin, S.A.//Alexeevski, A.V. 	Solitary restriction endonucleases in prokaryotic genomes.	Nucleic Acids Res.	2012	40		10107-10115			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. 		
@D	Ershova, A.S.//Rusinov, I.S.//Spirin, S.A.//Karyagina, A.S.//Alexeevski, A.V. 	Role of Restriction-Modification Systems in Prokaryotic Evolution and Ecology.	Biokhimiia	2015	80		1373-1386			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. 		
@D	Erskine, S.G.//Baldwin, G.S.//Halford, S.E. 	Rapid-reaction analysis of plasmid DNA cleavage by the EcoRV restriction endonuclease.	Biochemistry	1997	36		7567-7576			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. 		
@D	Erskine, S.G.//Halford, S.E. 	Fluorescent substrates for the EcoRV restriction endonuclease.	Biochem. Soc. Trans.	1994	22		299s			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. 		
@D	Erskine, S.G.//Halford, S.E. 	Reactions of the EcoRV restriction endonuclease with fluorescent oligodeoxynucleotides: identical equilibrium constants for binding to specific and non-specific DNA.	J. Mol. Biol.	1998	275		759-772			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. 		
@D	Erskine, S.G.//Halford, S.E. 	Interactions of the EcoRV restriction endonuclease with fluorescent oligodeoxynucleotides.	Gene	1995	157		153-156			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. 		
@D	Eruslanov, B.V.//Kramarov, V.M.//Smolyanivov, V.V.//Borovik, R.V. 	Isolation of the site-specific endonuclease EcoRI with the aid of an immunoabsorbent.	Bioorg. Khim.	1980	6		1361-1369			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). 		
@D	Erwin, A.L.//Gotschlich, E.C. 	Cloning of a Neisseria meningitidis gene for L-lactate dehydrogenase (L-LDH): evidence for a second meningococcal L-LDH with different   regulation.	J. Bacteriol.	1996	178		4807-4813			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. 		
@D	Erwin, A.L.//Sandstedt, S.A.//Bonthuis, P.J.//Geelhood, J.L.//Nelson, K.L.//Unrath, W.C.//Diggle, M.A.//Theodore, M.J.//Pleatman, C.R.//Mothershed, E.A.//Sacchi, C.T.//Mayer, L.W.//Gilsdorf, J.R.//Smith, A.L. 	Analysis of genetic relatedness of Haemophilus influenzae isolates by multilocus sequence typing.	J. Bacteriol.	2008	190		1473-1483			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. 		
@D	Erxleben, A.//Wunsch-Palasis, J.//Gruning, B.A.//Luzhetska, M.//Bechthold, A.//Gunther, S. 	Genome Sequence of Streptomyces sp. Strain Tu6071.	J. Bacteriol.	2011	193		4278-4279			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. 		
@D	Esani, S.//Constable, J.V.//Van Laar, T.A. 	Draft Genome Sequence of a Multidrug-Resistant Strain of Enterococcus faecalis, PM01, Isolated from the Nest of an American Bushtit, Psaltriparius minimus.	Genome Announcements	2017	5		e00017-17			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. 		
@D	Escano, J.//Deng, P.//Lu, S.E.//Smith, L. 	Draft Genome Sequence of Oral Bacterium Streptococcus mutans JH1140.	Genome Announcements	2016	4		e00472-16			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. 		
@D	Eshaghi, A.//Soares, D.//Tsang, R.//Richardson, D.//Kus, J.V.//Patel, S.N. 	Draft Genome Sequences of Two 'Haemophilus quentini' Isolates Recovered from Two  Different Patients' Blood Cultures.	Genome Announcements	2016	4		e01321-16			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. 		
@D	Eshraghi, L.//De Meyer, S.E.//Tian, R.//Seshadri, R.//Ivanova, N.//Pati, A.//Markowitz, V.//Woyke, T.//Kyrpides, N.C.//Tiwari, R.//Yates, R.//Howieson, J.//Reeve, W. 	High-quality permanent draft genome sequence of Bradyrhizobium sp. strain WSM1743 - an effective microsymbiont of an Indigofera sp. growing in Australia.	Standards in Genomic Sciences	2015	10		87			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. 		
@D	Eskes, R.//Liu, L.//Ma, H.//Chao, M.Y.//Dickson, L.//Lambowitz, A.M.//Perlman, P.S. 	Multiple homing pathways used by yeast mitochondrial group II introns.	Mol. Cell. Biol.	2000	20		8432-8446			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. 		
@D	Eskes, R.//Yang, J.//Lambowitz, A.M.//Perlman, P.S. 	Mobility of yeast mitochondrial group II introns: Engineering a new site specificity and retrohoming via full reverse splicing.	Cell	1997	88		865-874			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. 		
@D	Eskin, B. 	The host-controlled restriction enzyme of Escherichia coli B.	Ph.D. Thesis, University of California, Berkeley, USA	1973			1-191			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. 		
@D	Eskin, B.//Lautenberger, J.A.//Linn, S. 	Host-controlled modification and restriction of bacteriophage T7 by Escherichia coli B.	J. Virol.	1973	11		1020-1023			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. 		
@D	Eskin, B.//Linn, S. 	The deoxyribonucleic acid modification and restriction enzymes of Escherichia coli B. III.  Studies of the restriction adenosine triphosphatase.	J. Biol. Chem.	1972	247		6192-6196			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. 		
@D	Eskin, B.//Linn, S. 	The deoxyribonucleic acid modification and restriction enzymes of Escherichia coli B. II. Purification, subunit structure, and catalytic properties of the restriction endonuclease.	J. Biol. Chem.	1972	247		6183-6191			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. 		
@D	Eskridge, R.W.//Weinfeld, H.//Paigen, K. 	Susceptibility of different coliphage genomes to host-controlled variation.	J. Bacteriol.	1967	93		835-844			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. 		
@D	Esmaeel, Q.//Sanchez, L.//Robineau, M.//Dorey, S.//Clement, C.//Jacquard, C.//Barka, E.A. 	Draft Genome Sequence of Plant Growth-Promoting Burkholderia sp. Strain BE12, Isolated from the Rhizosphere of Maize.	Genome Announcements	2018	6		e00299-18			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. 		
@D	Espada, J.//Ballestar, E.//Fraga, M.F.//Garea, A.V.//Juarranz, A.//Stockert, J.C.//Robertson, K.D.//Fuks, F.O.//Esteller, M. 	Human DNA methyltransferase 1 is required for maintenance of the histone H3 modification pattern.	J. Biol. Chem.	2004	279		37175-37184			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. 		
@D	Espedido, B.A.//Steen, J.A.//Barbagiannakos, T.//Mercer, J.//Paterson, D.L.//Grimmond, S.M.//Cooper, M.A.//Gosbell, I.B.//van Hal, S.J.//Jensen, S.O. 	Carriage of an ACME II Variant may have contributed to MRSA ST239-like Strain Replacement in Liverpool Hospital, Sydney, Australia.	Antimicrob. Agents Chemother.	2012	56		3380-3383			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. 		
@D	Esperito-Santo, C.//Lin, Y.//Hao, X.//Wei, G.//Rensing, C.//Grass, G. 	Draft Genome Sequence of Pseudomonas psychrotolerans L19, Isolated from Copper Alloy Coins.	J. Bacteriol.	2012	194		1623-1624			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. 		
@D	Espinosa-Camacho, L.F.//Delgado, G.//Miranda-Novales, G.//Soberon-Chavez, G.//Alcaraz, L.D.//Morales-Espinosa, R. 	Complete Genome Sequences of Two Pseudomonas aeruginosa Strains Isolated from Children with Bacteremia.	Genome Announcements	2017	5		e00927-17			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. 		
@D	Espinosa-Camacho, L.F.//Delgado, G.//Soberon-Chavez, G.//Alcaraz, L.D.//Castanon, J.//Morales-Espinosa, R. 	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.	Genome Announcements	2017	5		e00925-17			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). 		
@D	Espinoza-Miranda, S.S.//Gomez-Rodriguez, J.A.//Huete-Perez, J.A. 	Mining for restriction endonucleases in Nicaragua.	Encuentro	2012	93		49-62			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. 		
@D	Espinoza-Valles, I.//Soto-Rodriguez, S.//Edwards, R.A.//Wang, Z.//Vora, G.J.//Gomez-Gil, B. 	Draft Genome Sequence of the Shrimp Pathogen Vibrio harveyi CAIM 1792.	J. Bacteriol.	2012	194		2104			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. 		
@D	Esposito, D.//Fitzmaurice, W.P.//Benjamin, R.C.//Goodman, S.D.//Waldman, A.S.//Socca, J.J. 	The complete nucleotide sequence of bacteriophage HP1 DNA.	Nucleic Acids Res.	1996	24		2360-2368			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. 		
@D	Essani, K.//Goorha, R.//Granoff, A. 	An animal virus-induced DNA-methyltransferase.	J. Cell Biochem. Suppl.	1989	13D		222			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. 		
@D	Essani, K.//Goorha, R.//Granoff, A. 	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.	Virology	1987	161		211-217			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. 		
@D	Estabrook, R.A.//Lipson, R.//Hopkins, B.//Reich, N. 	The coupling of tight DNA binding and base flipping: identification of a conserved structural motif in base flipping enzymes.	J. Biol. Chem.	2004	279		31419-31428			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. 		
@D	Estabrook, R.A.//Reich, N. 	Observing an induced-fit mechanism during sequence-specific DNA methylation.	J. Biol. Chem.	2006	281		37205-37214			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. 		
@D	Estes, A.M.//Hearn, D.J.//Nadendla, S.//Pierson, E.A.//Dunning, H.J.C. 	Draft Genome Sequence of Enterobacter sp. Strain OLF, a Colonizer of Olive Flies.	Microbiol. Resour. Announc.	2018	7		e01068-18			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. 		
@D	Estrada-Acosta, M.//Medrano-Felix, A.//Jimenez, M.//Gomez-Gil, B.//Leon-Felix, J.//Amarillas, L.//Chaidez, C. 	Draft Genome Sequence of Salmonella enterica subsp. enterica Serotype Saintpaul Strain S-70, Isolated from an Aquatic Environment.	Genome Announcements	2013	1		e01016-13			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. 		
@D	Etienne-Mesmin, L.//Chassaing, B.//Adekunle, O.//Mattei, L.M.//Edwards, A.N.//McBride, S.M.//Bushman, F.D.//Gewirtz, A.T. 	Genome Sequence of a Toxin-Positive Clostridium difficile Strain Isolated from Murine Feces.	Genome Announcements	2017	5		e00088-17			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. 		
@D	Etson, C.M.//Todorov, P.//Walt, D.R. 	Elucidating Restriction Endonucleases Reaction Mechanisms via Dwell-Time Distribution Analysis.	Biophys. J.	2014	106		22A			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. 		
@D	Etson, C.M.//Wilburn, F.//Moody, T.//Fashakin, V.//Walt, D.R. 	Single-Molecule Studies of Restriction Endonuclease Kinetics.	Biophys. J.	2012	102		486A			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. 		
@D	Ettinger, C.L.//Mousa, W.M.//Raizada, M.N.//Eisen, J.A. 	Draft Genome Sequence of Enterobacter sp. Strain UCD-UG_FMILLET (Phylum Proteobacteria).	Genome Announcements	2015	3		e01461-14			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. 		
@D	Ettinger, C.L.//Shehata, H.R.//Johnston-Monje, D.//Raizada, M.N.//Eisen, J.A. 	Draft Genome Sequence of Burkholderia gladioli Strain UCD-UG_CHAPALOTE (Phylum Proteobacteria).	Genome Announcements	2015	3		e01462-14			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. 		
@D	Etzkorn, C.//Horton, N.C. 	Mechanistic insights from the structures of HincII bound to cognate DNA cleaved from addition of Mg2+ and Mn2+.	J. Mol. Biol.	2004	343		833-849			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. 		
@D	Etzkorn, C.//Horton, N.C. 	Ca2+ binding in the active site of HincII: implications for the catalytic mechanism.	Biochemistry	2004	43		13256-13270			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. 		
@D	Euler, C.W.//Ryan, P.A.//Martin, J.M.//Fischetti, V.A. 	M.SpyI, a DNA methyltransferase encoded on a mefA chimeric element, modifies the genome of Streptococcus pyogenes.	J. Bacteriol.	2007	189		1044-1054			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. 		
@D	Eutsey, R.A.//Powell, E.//Dordel, J.//Salter, S.J.//Clark, T.A.//Korlach, J.//Ehrlich, G.D.//Hiller, N.L. 	Genetic Stabilization of the Drug-Resistant PMEN1 Pneumococcus Lineage by Its Distinctive DpnIII Restriction-Modification System.	MBio	2015	6		e00173-15			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. 		
@D	Evans, D.A.//Bronowska, A.K. 	Implications of fast-time scale dynamics of human DNA/RNA cytosine methyltransferases (DNMTs) for protein function.	Theor. Chem. Acc.	2010	125		407-418			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. 		
@D	Evans, M.//Kaczmarek, F.S.//Stutzman-Engwall, K.//Dyson, P. 	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.	Microbiology	1994	140		1367-1371			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. 		
@D	Evans, P.S.//Luo, Y.//Muruvanda, T.//Ayers, S.//Hiatt, B.//Hoffman, M.//Zhao, S.//Allard, M.W.//Brown, E.W. 	Complete Genome Sequences of Salmonella enterica Serovar Heidelberg Strains Associated with a Multistate Food-Borne Illness Investigation.	Genome Announcements	2014	2		e01154-13			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. 		
@D	Evans, T.C. Jr.//Benner, J.//Xu, M.Q. 	Semisynthesis of cytotoxic proteins using a modified protein splicing element.	Protein Sci.	1998	7		2256-2264			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. 		
@D	Evdokimov, A.A.//Sclavi, B.//Zinoviev, V.V.//Malygin, E.G.//Hattman, S.//Buckle, M. 	Study of bacteriophage T4-encoded dam DNA (Adenine-N-6)-methyltransferase binding with substrates by rapid laser  UV cross-linking.	J. Biol. Chem.	2007	282		26067-26076			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. 		
@D	Evdokimov, A.A.//Zinoviev, V.V.//Kuznetsov, V.V.//Netesova, N.A.//Malygin, E.G. 	Design of oligonucleotide inhibitors for human DNA methyltransferase 1.	Mol. Biol. (Mosk)	2009	43		418-425			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. 		
@D	Evdokimov, A.A.//Zinoviev, V.V.//Malygin, E.G. 	The Kinetic Mechanism of Phage T4 DNA-[N6-Adenine]-Methyltransferase.	Mol. Biol. (Mosk)	2002	36		849-861			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. 		
@D	Evdokimov, A.A.//Zinoviev, V.V.//Malygin, E.G. 	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.	Bioorg. Khim.	2000	26		797-800			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. 		
@D	Evdokimov, A.A.//Zinoviev, V.V.//Malygin, E.G.//Schlagman, S.L.//Hattman, S. 	Bacteriophage T4 Dam DNA-[N6-adenine]Methyltransferase. Kinetic evidence for a catalytically essential conformational change in the ternary complex.	J. Biol. Chem.	2002	277		279-286			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. 		
@D	Evdokimova, N.M.//Aleshkin, G.I.//Skavronskaya, A.G. 	Inheritance and phenotypic expression of plasmids coding EcoRI restriction endonuclease in Vibrio cholerae cells.	Biull. Eksp. Biol. Med.	1985	100		472-474			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. 		
@D	Evenhuis, J.P.//LaPatra, S.E.//Graf, J. 	Draft Genome Sequence of the Fish Pathogen Flavobacterium columnare Strain CSF-298-10.	Genome Announcements	2017	5		e00173-17			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. 		
@A	Everett, E.A. 		Structure-function analysis of the EcoRI DNA Methylase.			 		Ph.D. Thesis, Univ. of California, Santa Barbara				Ann Arbor	UMI	1990				1-190									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. 		
@D	Everett, E.A.//Falick, A.M.//Reich, N.O. 	Identification of a critical cysteine in EcoRI DNA methyltransferase by mass spectrometry.	J. Biol. Chem.	1990	265		17713-17719			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. 		
@D	Everett, E.A.//Reich, N.O. 	Determination of the EcoRI methylase Adomet binding region.	J. Cell Biol.	1988	107		854a			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. 		
@D	Everett, E.A.//Reich, N.O. 	Determination of the EcoRI methylase Adomet binding region.	ACS Abstracts	1988	196		94			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. 		
@D	Everett, E.A.//Reich, N.O. 	EcoRI DNA methylase activity is eliminated upon histidine residue modification.	Biochem. Biophys. Res. Commun.	1989	164		233-237			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. 		
@D	Everett, K.D.//Kahane, S.//Bush, R.M.//Friedman, M.G. 	An unspliced group I intron in 23S rRNA links chlamydiales, chloroplasts, and mitochondria.	J. Bacteriol.	1999	181		4734-4740			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. 		
@D	Everroad, R.C.//Stuart, R.K.//Bebout, B.M.//Detweiler, A.M.//Lee, J.Z.//Woebken, D.//Prufert-Bebout, L.//Pett-Ridge, J. 	Permanent draft genome of strain ESFC-1: ecological genomics of a newly discovered lineage of filamentous diazotrophic cyanobacteria.	Standards in Genomic Sciences	2016	11		53			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. 		
@D	Everroad, R.C.//Woebken, D.//Singer, S.W.//Burow, L.C.//Kyrpides, N.//Woyke, T.//Goodwin, L.//Detweiler, A.//Prufert-Bebout, L.//Pett-Ridge, J. 	Draft Genome Sequence of an Oscillatorian Cyanobacterium, Strain ESFC-1.	Genome Announcements	2013	1		e00527-13			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%. 		
@D	Evers, C.//Patel, K.//Petrosyan, V.//Morrison, C.//Varghese, V.//Chu, R.A.//Baig, A.//Thompson, E.J.//Chase, M.//Hu, P.C.//Kalia, A. 	Draft Genome Sequences of Four Genetically Distinct Human Isolates of Streptococcus dysgalactiae subsp. equisimilis.	Genome Announcements	2015	3		e01139-15			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. 		
@D	Ewens, W.J. 	Inference problems in population genetics:  DNA sequences, restriction endonucleases and ascertainment sampling.	Proc. R. Soc. Lond. B Biol. Sci.	1983	219		223-239			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. 		
@D	Ewers, C.//Gottig, S.//Bulte, M.//Fiedler, S.//Tietgen, M.//Leidner, U.//Heydel, C.//Bauerfeind, R.//Semmler, T. 	Genome Sequence of Avian Escherichia coli Strain IHIT25637, an Extraintestinal Pathogenic E. coli Strain of ST131 Encoding Colistin Resistance Determinant  MCR-1.	Genome Announcements	2016	4		e00863-16			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. 		
@D	Ezekiel, U.R.//Zassenhaus, P. 	Evidence for a site-specific endonuclease in yeast mitochondria which recognizes the sequence 5'GCCCGGC.	Biochem. Biophys. Res. Commun.	1994	201		208-214			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. 		
@D	Fabbri, M.//Garzon, R.//Cimmino, A.//Liu, Z.//Zanesi, N.//Callegari, E.//Liu, S.//Alder, H.//Costinean, S.//Fernandez-Cymering, C.//Volinia, S.//Guler, G.//Morrison, C.D.//Chan, K.K.//Marcucci, G.//Calin, G.A.//Huebner, K.//Croce, C.M. 	MicroRNA-29 family reverts aberrant methylation in lung cancer by targeting DNA methyltransferases 3A and 3B.	Proc. Natl. Acad. Sci. U. S. A.	2007	104		15805-15810			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. 		
@D	Fabian, J.S.//Mattson, T.//Bazar, L.S.//Chirikjian, J.G. 	Characterization of the Bacillus amyloliquefaciens HI methyltransferase.	FASEB J.	1998	12		A1446			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. 		
@D	Fabian, J.S.//Mattson, T.//Chirikjian, J.G. 	Characterization of the Bacillus amyloliquefaciens HI methyltransferase.	FASEB J.	1997	11		A900			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. 		
@D	Fabian, J.S.//Mattson, T.//Chirikjian, J.G. 	Comparative study of the biochemical properties of cellular and viral DNA-methyltransferases from Bacillus amyloliquefaciens H1.	FASEB J.	1996	10		A1103			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. 		
@D	Facimoto, C.T.//Chideroli, R.T.//Goncalves, D.D.//Carmo, A.O.D.//Kalaphotakis, E.//Pereira, U.P. 	Whole-Genome Sequence of Streptococcus agalactiae Strain S13, Isolated from a Fish Eye from a Nile Tilapia Farm in Southern Brazil.	Genome Announcements	2017	5		e00917-17			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. 		
@D	Fadeev, E.//De Pascale, F.//Vezzi, A.//Hubner, S.//Aharonovich, D.//Sher, D. 	Why close a bacterial genome? The plasmid of Alteromonas macleodii HOT1A3 is a vector for inter-specific transfer of a flexible genomic island.	Front. Microbiol.	2016	7		248			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. 		
@D	Faelker, S.//Schilling, J.//Schmidt, M.A.//Heusipp, G. 	Overproduction of DNA adenine methyltransferase alters motility, invasion, and the lipopolysaccharide O-antigen composition of Yersinia enterocolitica.	Infect. Immun.	2007	75		4990-4997			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. 		
@D	Faelker, S.//Schmidt, M.A.//Heusipp, G. 	DNA methylation in Yersinia enterocolitica: Role of the DNA adenine methyltransferase in mismatch repair and regulation of virulence factors.	Microbiology	2005	151		2291-2299			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. 		
@D	Fagerlund, A.//Langsrud, S.//Moen, B.//Heir, E.//Moretro, T. 	Complete Genome Sequences of Six Listeria monocytogenes Sequence Type 9 Isolates  from Meat Processing Plants in Norway.	Genome Announcements	2018	6		e00016-18			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. 		
@D	Fajardo-Sanchez, E.//Stricher, F.//Paques, F.//Isalan, M.//Serrano, L. 	Computer design of obligate heterodimer meganucleases allows efficient cutting of custom DNA sequences.	Nucleic Acids Res.	2008	36		2163-2173			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. 		
@D	Falb, M.//Pfeiffer, F.//Palm, P.//Rodewald, K.//Hickmann, V.//Tittor, J.//Oesterhelt, D. 	Living with two extremes: conclusions from the genome sequence of Natronomonas pharaonis.	Genome Res.	2005	15		1336-1343			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. 		
@D	Faldu, P.R.//Kothari, V.V.//Kothari, C.R.//Rawal, C.M.//Domadia, K.K.//Patel, P.A.//Bhimani, H.D.//Raval, V.H.//Parmar, N.R.//Nathani, N.M.//Koringa, P.G.//Joshi, C.G.//Kothari, R.K. 	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.	Genome Announcements	2014	2		e00019-14			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. 		
@D	Falentin, H.//Cousin, S.//Clermont, D.//Creno, S.//Ma, L.//Chuat, V.//Loux, V.//Rudiger, P.//Bizet, C.//Bouchier, C. 	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.	Genome Announcements	2013	1		e00658-13			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. 		
@D	Falentin, H.//Deutsch, S.M.//Jan, G.//Loux, V.//Thierry, A.//Parayre, S.//Maillard, M.B.//Dherbecourt, J.//Cousin, F.J.//Jardin, J.//Siguier, P.//Couloux, A.//Barbe, V.//Vacherie, B.//Wincker, P.//Gibrat, J.F.//Gaillardin, C.//Lortal, S. 	The complete genome of Propionibacterium freudenreichii CIRM-BIA1, a hardy actinobacterium with food and probiotic applications.	PLoS ONE	2010	5		e11748			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. 		
@D	Falentin, H.//Deutsch, S.M.//Loux, V.//Hammani, A.//Buratti, J.//Parayre, S.//Chuat, V.//Barbe, V.//Aury, J.M.//Jan, G.//Le Loir, Y. 	Permanent draft genome sequence of the probiotic strain Propionibacterium freudenreichii CIRM-BIA 129 (ITG P20).	Standards in Genomic Sciences	2016	11		6			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. 		
@D	Falentin, H.//Naquin, D.//Loux, V.//Barloy-Hubler, F.//Loubiere, P.//Nouaille, S.//Lavenier, D.//Le Bourgeois, P.//Francois, P.//Schrenzel, J.//Hernandez, D.//Even, S.//Le Loir, Y. 	Genome Sequence of Lactococcus lactis subsp. lactis bv. diacetylactis LD61.	Genome Announcements	2014	2		e01176-13			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. 		
@D	Falgenhauer, L.//Yao, Y.//Fritzenwanker, M.//Schmiedel, J.//Imirzalioglu, C.//Chakraborty, T. 	Complete Genome Sequence of Phage-Like Plasmid pECOH89, Encoding CTX-M-15.	Genome Announcements	2014	2		e00356-14			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. 		
@D	Falkow, S.//Formal, S.B. 	Restriction in genetic crosses between Escherichia coli and Shigella flexneri.	J. Bacteriol.	1969	100		540-541			Shigella flexneri restricts Escherichia coli deoxyribonucleic acid (DNA) and can modify phage DNA so that it is restricted in E. coli. 		
@D	Fallico, V.//Ross, R.P.//Fitzgerald, G.F.//McAuliffe, O. 	Novel conjugative plasmids from the natural isolate Lactococcus lactis subspecies cremoris DPC3758: A repository of genes for the potential improvement of dairy starters.	J. Dairy Sci.	2012	95		3593-3608			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. 		
@D	Falquet, L.//Calderon-Copete, S.P.//Frey, J. 	Draft Genome Sequence of the Virulent Clostridium chauvoei Reference Strain JF4335.	Genome Announcements	2013	1		e00593-13			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. 		
@D	Falquet, L.//Liljander, A.//Schieck, E.//Gluecks, I.//Frey, J.//Jores, J. 	Complete Genome Sequences of Virulent Mycoplasma capricolum subsp. capripneumoniae Strains F38 and ILRI181.	Genome Announcements	2014	2		e01041-14			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. 		
@D	Falsafi, S.//Reich, N. 	Molecular dynamic-based prediction of DNA structure changes in DNA sequence and correlation to substrate specificity in EcoRI DNA methyltransferase.	FASEB J.	1992	6		A221			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. 		
@D	Fan, L.//Bo, S.//Chen, H.//Ye, W.//Kleinschmidt, K.//Baumann, H.I.//Imhoff, J.F.//Kleine, M.//Cai, D. 	Genome sequence of Bacillus subtilis subsp. spizizenii gtP20b isolated from the Indian Ocean.	J. Bacteriol.	2010	193		1276			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. 		
@D	Fan, L.//Liu, Y.//Li, Z.//Baumann, H.I.//Kleinschmidt, K.//Ye, W.//Imhoff, J.F.//Kleine, M.//Cai, D. 	Draft genome sequence of a marine Streptomyces sp. strain PP-C42, isolated from the Baltic Sea.	J. Bacteriol.	2011	193		3691-3692			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. 		
@D	Fan, X.//Tang, J.//Nie, L.//Huang, J.//Wang, G. 	High-quality-draft genome sequence of the heavy metal resistant and exopolysaccharides producing bacterium Mucilaginibacter pedocola TBZ30(T).	Standards in Genomic Sciences	2018	13		34			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. 		
@D	Fanelli, F.//Liuzzi, V.C.//Quintieri, L.//Mule, G.//Baruzzi, F.//Logrieco, A.F.//Caputo, L. 	Draft Genome Sequence of Pseudomonas fluorescens Strain ITEM 17298, Associated with Cheese Spoilage.	Genome Announcements	2017	5		e01141-17			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. 		
@D	Fang, G. et al. 	Genome-wide mapping of methylated adenine residues in pathogenic Escherichia coli using single-molecule real-time sequencing.  LID - 10.1038/nbt.2432 [doi].	Nat. Biotechnol.	2012	30		1232			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. 		
@D	Fang, X.//Fang, Z.//Zhao, J.//Zou, Y.//Li, T.//Wang, J.//Guo, Y.//Chang, D.//Su, L.//Ni, P.//Liu, C. 	Draft Genome Sequence of Pseudomonas aeruginosa Strain ATCC 27853.	J. Bacteriol.	2012	194		3755			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. 		
@D	Fang, Y.//Huang, Y.//Li, Q.//Chen, H.//Yao, Z.//Pan, J.//Gu, J.//Tang, B.//Wang, H.G.//Yu, B.//Tong, Y.G.//Zou, Q.M.//Mao, X.H. 	First Genome Sequence of a Burkholderia pseudomallei Isolate in China, Strain BPC006, Obtained from a Melioidosis Patient in Hainan.	J. Bacteriol.	2012	194		6604-6605			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. 		
@D	Fanning, T.G.//Kreutzfeldt, H.-J.//Davies, R.W.//Schreier, P.H. 	Detection of restriction endonucleases with a lac repressor-lac operator filter binding assay.	FEBS Lett.	1976	61		237-239			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). 		
@D	Farah, N.//Mehdi, A.//Soomro, S.I.//Soomro, N.I.//Tareb, R.//Desmasures, N.//Vernoux, J.P.//Bakhtiar, S.M.//Imran, M. 	Draft Genome Sequence of Enterococcus mundtii QAUEM2808, Isolated from Dahi, a Fermented Milk Product.	Genome Announcements	2016	4		e00995-16			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%. 		
@D	Farfan, M.//Spataro, N.//Sanglas, A.//Albarral, V.//Loren, J.G.//Bosch, E.//Fuste, M.C. 	Draft Genome Sequence of the Aeromonas diversa Type Strain.	Genome Announcements	2013	1		e00330-13			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. 		
@D	Farias, M.E.//Revale, S.//Mancini, E.//Ordonez, O.//Turjanski, A.//Cortez, N.//Vazquez, M.P. 	Genome sequence of Sphingomonas sp. S17, isolated from an alkaline, hyperarsenic and hypersaline volcanic-associated lake at high altitude in the Argentinean Puna.	J. Bacteriol.	2011	193		3686-3687			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. 		
@D	Farlow, J.//Filippov, A.A.//Sergueev, K.V.//Hang, J.//Kotorashvili, A.//Nikolich, M.P. 	Comparative whole genome analysis of six diagnostic brucellaphages.	Gene	2014	541		115-122			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. 		
@D	Farlow, J.//Kotorashvili, A. 	Genome Sequence of the Soviet/Russian Bacillus anthracis Vaccine Strain 55-VNIIVViM.	Genome Announcements	2016	4		e01401-16			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. 		
@D	Farrance, I.K.//Eadie, J.S.//Ivarie, R. 	Improved chemistry for oligodeoxyribonucleotide synthesis substantially improves restriction enzyme cleavage of a synthetic 35-mer.	Nucleic Acids Res.	1989	17		1231-1245			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. 		
@D	Farrell, S.O. 	A fast restriction enzyme experiment for the undergraduate biochemistry lab.	J. Chem. Educ.	1994	71		1095-1096			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. 		
@D	Farrugia, D.N.//Elbourne, L.D.H.//Hassan, K.A.//Eijkelkamp, B.A.//Tetu, S.G.//Brown, M.H.//Shah, B.S.//Peleg, A.Y.//Mabbutt, B.C.//Paulsen, I.T. 	The Complete Genome and Phenome of a Community-Acquired Acinetobacter baumannii.	PLoS ONE	2013	8		e58628			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. 		
@D	Faruqi, A.F.//Ahmed, N. 	Isolation and partial purification of a restriction endonuclease from Pseudomonas ovalis.	Pak. J. Sci. Ind. Res.	1987	30		390-392			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. 		
@D	Fasanella, A.//Braun, P.//Grass, G.//Hanczaruk, M.//Aceti, A.//Serrecchia, L.//Leonzio, G.//Tolve, F.//Georgi, E.//Antwerpen, M. 	Genome Sequence of Bacillus anthracis Isolated from an Anthrax Burial Site in Pollino National Park, Basilicata Region (Southern Italy).	Genome Announcements	2015	3		e00141-15			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. 		
@D	Fatemi, M.//Hermann, A.//Gowher, H.//Jeltsch, A. 	Dnmt3a and Dnmt1 functionally cooperate during de novo methylation of DNA.	Eur. J. Biochem.	2002	269		4981-4984			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. 		
@D	Fatemi, M.//Hermann, A.//Pradhan, S.//Jeltsch, A. 	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.	J. Mol. Biol.	2001	309		1189-1199			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. 		
@A	Fauman, E.B.//Blumenthal, R.M.//Cheng, X. 		Structure and evolution of AdoMet-dependent methyltransferases.			Cheng, X.//Blumenthal, R.M. 		S-Adenosylmethionine-dependent Methyltransferases: Structures and Functions.				Singapore	World Scientific Publishing	1999				1-38									A review of many different types of SAM-sependent Mtases, including DNA methyltransferases, RNA methyltransferases and many others. 		
@D	Fauvart, M.//Sanchez-Rodriguez, A.//Beullens, S.//Marchal, K.//Michiels, J. 	Genome sequence of Rhizobium etli CNPAF512, a nitrogen-fixing symbiont isolated from bean root nodules in Brazil.	J. Bacteriol.	2011	193		3158-3159			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. 		
@D	Faye, P.//Bertrand, C.//Pedron, J.//Barny, M.A. 	Draft genomes of 'Pectobacterium peruviense' strains isolated from fresh water in France.	Standards in Genomic Sciences	2018	13		27			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. 		
@D	Fazakerley, G.V.//Gabarro-Arpa, J.//Lebret, M.//Guy, A.//Guschlbauer, W. 	The GTm6AC sequence is overwound and bent.	Nucleic Acids Res.	1989	17		2541-2556			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. 		
@D	Fazakerley, G.V.//Quignard, E.//Teoule, R.//Guy, A.//Guschlbauer, W. 	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.	Eur. J. Biochem.	1987	167		397-404			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. 		
@D	Fazal, M.A.//Alexander, S.//Burnett, E.//Deheer-Graham, A.//Oliver, K.//Holroyd, N.//Parkhill, J.//Russell, J.E. 	Complete Whole-Genome Sequence of Salmonella enterica subsp. enterica Serovar Java NCTC5706.	Genome Announcements	2016	4		e01219-16			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. 		
@D	Federici, F.//Manna, L.//Rizzi, E.//Galantini, E.//Marini, U. 	Draft Genome Sequence of Lactobacillus salivarius SGL 03, a Novel Potential Probiotic Strain.	Genome Announcements	2017	5		e01340-17			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. 		
@D	Fedoreyeva, L.I.//Vanyushin, B.F. 	N6-Adenine DNA-methyltransferase in wheat seedlings.	FEBS Lett.	2002	514		305-308			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. 		
@D	Fedotova, E.A.//Protsenko, A.S.//Zakharova, M.V.//Lavrova, N.V.//Alekseevsky, A.V.//Oretskaya, T.S.//Karyagina, A.S.//Solonin, A.S.//Kubareva, E.A. 	SsoII-like DNA-methyltransferase Ecl18kI: Interaction between regulatory and methylating functions.	Biochemistry	2009	74		85-91			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. 		
@D	Feher, Z.//Kiss, A.//Venetianer, P. 	Expression of a bacterial modification methylase gene in yeast.	Nature	1983	302		266-268			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. 		
@D	Feher, Z.//Schlagman, S.L.//Miner, Z.//Hattman, S. 	In vivo methylation of yeast DNA by prokaryotic DNA methyltransferases.	Gene	1988	74		193-195			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). 		
@D	Feher, Z.//Schlagman, S.L.//Miner, Z.//Hattman, S. 	The UV excision-repair system of Saccharomyces cerevisiae is involved in the removal of methylcytosines formed in vivo by a cloned prokaryotic DNA methyltransferase.	Curr. Genet.	1989	16		461-464			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. 		
@D	Feher, Z.//Schlagman, S.L.//Miner, Z.//Hattman, S. 	Expression of prokaryotic DNA methyltransferase genes in yeast.	Zentralbl. Mikrobiol.	1990	145		343			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. 		
@D	Feil, H. et al. 	Comparison of the complete genome sequences of Pseudomonas syringae pv. syringae B728a and pv. tomato DC3000.	Proc. Natl. Acad. Sci. U. S. A.	2005	102		11064-11069			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. 		
@D	Feingersch, R.//Suzuki, M.T.//Shmoish, M.//Sharon, I.//Sabehi, G.//Partensky, F.//Beja, O. 	Microbial community genomics in eastern Mediterranean Sea surface waters.	ISME J.	2010	4		78-87			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. 		
@D	Fekete, P.Z.//Brzuszkiewicz, E.//Blum-Oehler, G.//Olasz, F.//Szabo, M.//Gottschalk, G.//Hacker, J.//Nagy, B. 	DNA sequence analysis of the composite plasmid pTC conferring virulence and antimicrobial resistance for porcine enterotoxigenic Escherichia coli.	Int. J. Med. Microbiol.	2012	302		4-9			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. 		
@D	Fellag, M.//Levasseur, A.//Delerce, J.//Bittar, F.//Marie, J.L.//Davoust, B.//Drancourt, M. 	Draft Genome Sequence of 'Nocardia suismassiliense' Strain S-137 (CSUR P4007).	Genome Announcements	2018	6		e00212-18			'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. 		
@D	Felle, M.//Joppien, S.//Nemeth, A.//Diermeier, S.//Thalhammer, V.//Dobner, T.//Kremmer, E.//Kappler, R.//Langst, G. 	The USP7/Dnmt1 complex stimulates the DNA methylation activity of Dnmt1 and regulates the stability of UHRF1.	Nucleic Acids Res.	2011	39		8355-8365			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. 		
@D	Felley-Bosco, E.//Pourzand, C.//Zijlstra, J.//Amstad, P.//Cerutti, P. 	A genotypic mutation system measuring mutations in restriction recognition sequences.	Nucleic Acids Res.	1991	19		2913-2919			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. 		
@D	Fellinger, K.//Rothbauer, U.//Felle, M.//Laengst, G.//Leonhardt, H. 	Dimerization of DNA methyltransferase 1 is mediated by its regulatory domain.	J. Cell. Biochem.	2009	106		521-528			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. 		
@D	Fellner, L.//Huptas, C.//Simon, S.//Muhlig, A.//Scherer, S.//Neuhaus, K. 	Draft Genome Sequences of Three European Laboratory Derivatives from Enterohemorrhagic Escherichia coli O157:H7 Strain EDL933, Including Two Plasmids.	Genome Announcements	2016	4		e01331-15			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. 		
@D	Felux, A.K.//Franchini, P.//Schleheck, D. 	Permanent draft genome sequence of sulfoquinovose-degrading Pseudomonas putida strain SQ1.	Standards in Genomic Sciences	2015	10		42			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. 		
@D	Feng, H.//Zhi, Y.//Sun, Y.//Wei, X.//Luo, Y.//Zhou, P. 	Draft Genome Sequence of a Novel Streptomyces griseorubens Strain, JSD-1, Active  in Carbon and Nitrogen Recycling.	Genome Announcements	2014	2		e00650-14			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. 		
@D	Feng, K.//Li, R.//Chen, Y.//Zhao, B.//Yin, T. 	Sequencing and Analysis of the Pseudomonas fluorescens GcM5-1A Genome: A Pathogen Living in the Surface Coat of Bursaphelenchus xylophilus.	PLoS ONE	2015	10		E0141515			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. 		
@D	Feng, L.//Ma, T.//Zhang, J.//Xu, F.//Shi, L. 	Draft Genome Sequence of Bacillus subtilis QH-1, a Chromium-Reducing Bacterial Strain Isolated in Qinghai Province, China.	Genome Announcements	2014	2		e00182-14			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. 		
@D	Feng, L.//Reeves, P.R.//Lan, R.//Ren, Y.//Gao, C.//Zhou, Z.//Ren, Y.//Cheng, J.//Wang, W.//Wang, J.//Qian, W.//Li, D.//Wang, L. 	A recalibrated molecular clock and independent origins for the cholera pandemic clones.	PLoS ONE	2008	3		E4053			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. 		
@D	Feng, L.//Wang, W.//Cheng, J.//Ren, Y.//Zhao, G.//Gao, C.//Tang, Y.//Liu, X.//Han, W.//Peng, X.//Liu, R.//Wang, L. 	Genome and proteome of long-chain alkane degrading Geobacillus thermodenitrificans NG80-2 isolated from a deep-subsurface oil reservoir.	Proc. Natl. Acad. Sci. U. S. A.	2007	104		5602-5607			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. 		
@D	Feng, Y.//Xu, H.F.//Li, Q.H.//Zhang, S.Y.//Wang, C.X.//Zhu, D.L.//Cao, F.L.//Li, Y.G.//Johnston, R.N.//Zhou, J.//Liu, G.R.//Liu, S.L. 	Complete Genome Sequence of Salmonella enterica Serovar Pullorum RKS5078.	J. Bacteriol.	2012	194		744			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. 		
@D	Feng, Z.//Fang, G.//Korlach, J.//Clark, T.//Luong, K.//Zhang, X.//Wong, W.//Schadt, E. 	Detecting DNA modifications from SMRT sequencing data by modeling sequence context dependence of polymerase kinetic.	PLOS Comp. Biol.	2013	9		e1002935			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. 		
@D	Feng, Z.//Li, J.//Zhang, J.R.//Zhang, X. 	qDNAmod: a statistical model-based tool to reveal intercellular heterogeneity of  DNA modification from SMRT sequencing data.	Nucleic Acids Res.	2014	42		13488-13499			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. 		
@D	Ferat, J.-L.//Michel, F. 	Group II self-splicing introns in bacteria.	Nature	1993	364		358-361			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. 		
@D	Ferdous, A.//Akaike, T.//Maruyama, A. 	Inhibition of sequence-specific protein-DNA interaction and restriction endonuclease cleavage via triplex stabilization by poly(L-lysine)-graft-dextran copolymer.	Biomacromolecules	2000	1		186-193			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. 		
@D	Ferenci, T.//Zhou, Z.//Betteridge, T.//Ren, Y.//Liu, Y.//Feng, L.//Reeves, P.R.//Wang, L. 	Genomic sequencing reveals regulatory mutations and recombinational events in the widely used MC4100 lineage of Escherichia coli K-12.	J. Bacteriol.	2009	191		4025-4029			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. 		
@D	Fernandez, A.//Gil, E.//Cartelle, M.//Perez, A.//Beceiro, A.//Mallo, S.//Tomas, M.M.//Perez-Llarena, F.J.//Villanueva, R.//Bou, G. 	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.	J. Antimicrob. Chemother.	2007	59		841-847			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. 		
@D	Fernandez, M.//Olek, A.//Walter, J.//Sanchez, J. 	Analysis of DNA methylation processes related to the inhibition of DNA synthesis by 5-azacytidine in Streptomyces antibioticus ETH 7451.	Biol. Chem.	1998	379		559-562			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. 		
@D	Fernandez, M.//Soliveri, J.//Novella, I.S.//Yebra, M.J.//Barbes, C.//Sanchez, J. 	Effect of  5-azacytidine and sinefungin on Streptomyces development.	Gene	1995	157		221-223			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. 		
@D	Fernandez-de-Las-Heras, L.//Alonso, S.//de la Vega-de-Leon, A.//Xavier, D.//Perera, J.//Navarro-Llorens, J.M. 	Draft Genome Sequence of the Steroid Degrader Rhodococcus ruber Strain Chol-4.	Genome Announcements	2013	1		e00215-13			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. 		
@D	Fernandez-Gonzalez, A.J.//Lasa, A.V.//Fernandez-Lopez, M. 	Whole-Genome Sequences of Two Arthrobacter Strains Isolated from a Holm Oak Rhizosphere Affected by Wildfire.	Genome Announcements	2018	6		e00071-18			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. 		
@D	Fernandez-Natal, M.I.//Soriano, F.//Acedo, A.//Hernandez, M.//Tauch, A.//Rodriguez-Lazaro, D. 	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.	Genome Announcements	2015	3		e00765-15			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. 		
@D	Fernandez-Natal, M.I.//Soriano, F.//Ariza-Miguel, J.//Marrodan-Ciordia, T.//Acedo, A.//Hernandez, M.//Tauch, A.//Rodriguez-Lazaro, D. 	Draft Genome Sequences of Corynebacterium kroppenstedtii CNM633/14 and CNM632/14, Multidrug-Resistant and Antibiotic-Sensitive Isolates from Nodules of  Granulomatous Mastitis Patients.	Genome Announcements	2015	3		e00525-15			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. 		
@D	Fernandez-Orth, D.//Cosgaya, C.//Telli, M.//Mosqueda, N.//Mari-Almirall, M.//Roca, I.//Vila, J. 	Draft Genome Sequence of JVAP01T, the Type Strain of the Novel Species Acinetobacter dijkshoorniae.	Genome Announcements	2017	5		e01480-16			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. 		
@D	Fernandez-Ramirez, M.D.//Boekhorst, J.//de Jong, A.//Kuipers, O.P.//Abee, T.//Nierop-Groot, M.N. 	Draft Whole-Genome Sequences of Three Lactobacillus plantarum Food Isolates.	Genome Announcements	2016	4		e00560-16			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. 		
@D	Fernando, D.M.//Chong, P.//Singh, M.//Spicer, V.//Unger, M.//Loewen, P.C.//Westmacott, G.//Kumar, A. 	Multi-omics approach to study global changes in a triclosan-resistant mutant strain of Acinetobacter baumannii ATCC 17978.	Int. J. Antimicrob. Agents	2017	49		74-80			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. 		
@D	Fernando, D.M.//Xu, W.//Loewen, P.C.//Zhanel, G.G.//Kumar, A. 	Triclosan can select for an AdeIJK-overexpressing mutant of Acinetobacter baumannii ATCC 17978 that displays reduced susceptibility to multiple antibiotics.	Antimicrob. Agents Chemother.	2014	58		6424-6431			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. 		
@D	Ferreira, A.C.//Tenreiro, R.//Correa-de-Sa, M.I.//Dias, R. 	Complete Genome Sequences of Two Central European Brucella suis bv. 2 Haplotype 2c Strains Isolated from Wild Boars.	Genome Announcements	2014	2		e00686-14			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. 		
@D	Ferreira, A.C.//Tenreiro, R.//Correa-de-Sa, M.I.//Dias, R. 	Complete Genome Sequences of Three Iberian Brucella suis Biovar 2 Strains Isolated from Wild Boars.	Genome Announcements	2014	2		e00618-14			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). 		
@D	Ferreira, V.//Magalhaes, R.//Almeida, G.//Cabanes, D.//Fritzenwanker, M.//Chakraborty, T.//Hain, T.//Teixeira, P. 	Genome Sequence of Listeria monocytogenes 2542, a Serotype 4b Strain from a Cheese-Related Outbreak in Portugal.	Genome Announcements	2018	6		e00540-18			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. 		
@D	Ferreras, E.R.//De Maayer, P.//Makhalanyane, T.P.//Guerrero, L.D.//Aislabie, J.M.//Cowan, D.A. 	Draft Genome Sequence of Microbacterium sp. Strain CH12i, Isolated from Shallow Groundwater in Cape Hallett, Antarctica.	Genome Announcements	2014	2		e00789-14			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. 		
@D	Ferretti, J.J. et al. 	Complete genome sequence of an M1 strain of Streptococcus pyogenes.	Proc. Natl. Acad. Sci. U. S. A.	2001	98		4658-4663			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. 		
@D	Ferrin, L.J.//Camerini-Otero, R.D. 	Selective cleavage of human DNA: RecA-assisted restriction endonuclease (RARE) cleavage.	Science	1991	254		1494-1497			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. 		
@D	Ferris, P.J.//Vogt, V.M. 	Structure of the central spacer region of extrachromosomal ribosomal DNA in Physarum polycephalum.	J. Mol. Biol.	1982	159		359-381			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. 		
@D	Ferrucci, L.//Rossino, R.//Mezzanotee, R. 	Factors affecting the digestion of restriction endonucleases in situ.	Cytobios	1991	68		45-51			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. 		
@D	Fettweis, J.M.//Serrano, M.G.//Huang, B.//Brooks, J.P.//Glascock, A.L.//Sheth, N.U.//Strauss, J.F. III//Jefferson, K.K.//Buck, G.A. 	An emerging Mycoplasma associated with trichomoniasis, vaginal infection and disease.	PLoS ONE	2014	9		E110943			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. 		
@D	Fevre, C.//Passet, V.//Deletoile, A.//Barbe, V.//Frangeul, L.//Almeida, A.S.//Sansonetti, P.//Tournebize, R.//Brisse, S. 	PCR-based identification of Klebsiella pneumoniae subsp. rhinoscleromatis, the agent of rhinoscleroma.	PLoS Neglected Trop. Dis.	2011	5		E1052			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. 		
@D	Ffrench-Constant, R.H.//Waterfield, N.//Burland, V.//Perna, N.T.//Daborn, P.J.//Bowen, D.//Blattner, F.R. 	A genomic sample sequence of the entomopathogenic bacterium Photorhabdus luminescens W14: Potential implications for virulence.	Appl. Environ. Microbiol.	2000	66		3310-3329			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. 		
@D	Fiala, E.S.//Staretz, M.E.//Pandya, G.//El-Bayoumy, K.//Hamilton, S.R. 	Inhibition of DNA (cytosine-5) methyltransferase (Mtase) by selenium compounds, determined by an improved method for Mtase and global DNA methylation.	Proc. Amer. Assoc. Cancer Res.	1998	39		88			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. 		
@D	Fiala, E.S.//Staretz, M.E.//Pandya, G.A.//El-Bayoumy, K.//Hamilton, S.R. 	Inhibition of DNA cytosine methyltransferase by chemopreventive selenium compounds, determined by an improved assay for DNA cytosine methyltransferase and DNA cytosine methylation.	Carcinogenesis	1998	19		597-604			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. 		
@D	Fiebig, A.//Pradella, S.//Petersen, J.//Michael, V.//Pauker, O.//Rohde, M.//Goker, M.//Klenk, H.P.//Wagner-Dobler, I. 	Genome of the marine alphaproteobacterium Hoeflea phototrophica type strain (DFL-43(T)).	Standards in Genomic Sciences	2013	7		440-448			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. 		
@D	Fiebig, A.//Pradella, S.//Petersen, J.//Pauker, O.//Michael, V.//Lunsdorf, H.//Goker, M.//Klenk, H.P.//Wagner-Dobler, I. 	Genome of the R-body producing marine alphaproteobacterium Labrenzia alexandrii type strain (DFL-11(T)).	Standards in Genomic Sciences	2013	7		413-426			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. 		
@D	Fiebig, A.//Riedel, T.//Gronow, S.//Petersen, J.//Klenk, H.P.//Goker, M. 	Genome sequence of the reddish-pigmented Rubellimicrobium thermophilum type strain (DSM 16684(T)), a member of the Roseobacter clade.	Standards in Genomic Sciences	2013	8		480-490			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. 		
@D	Fiedler, G.//Brinks, E.//Bohnlein, C.//Cho, G.S.//Koberg, S.//Kabisch, J.//Franz, C.M.A.P. 	Draft Genome Sequence of the Intimin-Positive Enteropathogenic Escherichia albertii Strain MBT-EA1, Isolated from Lettuce.	Genome Announcements	2018	6		e00255-18			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. 		
@D	Fiedler, S.//Bender, J.K.//Klare, I.//Halbedel, S.//Grohmann, E.//Szewzyk, U.//Werner, G. 	Tigecycline resistance in clinical isolates of Enterococcus faecium is mediated by an upregulation of plasmid-encoded tetracycline determinants tet(L) and tet(M).	J. Antimicrob. Chemother.	2015	71		871-881			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. 		
@D	Fiedoruk, K.//Daniluk, T.//Swiecicka, I.//Murawska, E.//Sciepuk, M.//Leszczynska, K. 	First Complete Genome Sequence of Escherichia albertii Strain KF1, a New Potential Human Enteric Pathogen.	Genome Announcements	2014	2		e00004-14			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. 		
@D	Field, D. et al. 	The minimum information about a genome sequence (MIGS) specification.	Nat. Biotechnol.	2008	26		541-547			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. 		
@D	Fierer, N.//Breitbart, M.//Nulton, J.//Salamon, P.//Lozupone, C.//Jones, R.//Robeson, M.//Edwards, R.A.//Felts, B.//Rayhawk, S.//Knight, R.//Rohwer, F.//Jackson, R.B. 	Metagenomic and small-subunit rRNA analyses reveal the genetic diversity of bacteria, archaea, fungi, and viruses in soil.	Appl. Environ. Microbiol.	2007	73		7059-7066			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. 		
@D	Fierst, J.L.//Murdock, D.A.//Thanthiriwatte, C.//Willis, J.H.//Phillips, P.C. 	Metagenome-Assembled Draft Genome Sequence of a Novel Microbial Stenotrophomonas  maltophilia Strain Isolated from Caenorhabditisremanei Tissue.	Genome Announcements	2017	5		e01646-16			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. 		
@D	Figueiredo, C.//Quint, W.G.//Sanna, R.//Sablon, E.//Donahue, J.P.//Xu, Q.//Miller, G.G.//Peek, R.M.//Blaser, M.J.//van Doorn, L. 	Genetic organization and heterogeneity of the iceA locus of Helicobacter pylori.	Gene	2000	246		59-68			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. 		
@D	Figueiredo, H.C.//Leal, C.A.//Dorella, F.A.//Carvalho, A.F.//Soares, S.C.//Pereira, F.L.//Azevedo, V.A. 	Complete Genome Sequences of Fish Pathogenic Weissella ceti Strains WS74 and WS105.	Genome Announcements	2014	2		e01014-14			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%. 		
@D	Figueiredo, H.C.//Leal, C.A.//Pereira, F.L.//Soares, S.C.//Goncalves, L.A.//Dorella, F.A.//Carvalho, A.F.//Azevedo, V.A. 	Whole-Genome Sequence of Francisella noatunensis subsp. orientalis Strain FNO01 Isolated from Diseased Nile Tilapia in Brazil.	Genome Announcements	2016	4		e01603-15			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%. 		
@D	Figueiredo, H.C.//Leal, G.//Pereira, F.L.//Soares, S.C.//Dorella, F.A.//Carvalho, A.F.//Pereira, U.P.//Azevedo, V.A. 	Whole-Genome Sequence of Weissella ceti Strain WS08, Isolated from Diseased Rainbow Trout in Brazil.	Genome Announcements	2014	2		e00851-14			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%. 		
@D	Figueiredo, S.C.//Neves-Borges, A.C.//Coelho, A. 	The neuraminidase gene is present in the non-toxigenic Vibrio cholerae Amazonia strain: a different allele in comparison to the pandemic strains.	Memorias do Instituto Oswaldo Cruz	2005	100		563-569			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. 		
@D	Figueiredo, T.A.//Aguiar, S.I.//Melo-Cristino, J.//Ramirez, M. 	DNA methylase activity as a marker for the presence of a family of phage-like elements conferring efflux-mediated macrolide resistance in  streptococci.	Antimicrob. Agents Chemother.	2006	50		3689-3694			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. 		
@D	Filippidou, S.//Jaussi, M.//Junier, T.//Wunderlin, T.//Jeanneret, N.//Regenspurg, S.//Li, P.E.//Lo, C.C.//Johnson, S.//McMurry, K.//Gleasner, C.D.//Vuyisich, M.//Chain, P.S.//Junier, P. 	Genome Sequence of Aeribacillus pallidus Strain GS3372, an Endospore-Forming Bacterium Isolated in a Deep Geothermal Reservoir.	Genome Announcements	2015	3		e00981-15			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. 		
@D	Filippidou, S.//Jaussi, M.//Junier, T.//Wunderlin, T.//Roussel-Delif, L.//Jeanneret, N.//Vieth-Hillebrand, A.//Vetter, A.//Regenspurg, S.//Johnson, S.L.//McMurry, K.//Gleasner, C.D.//Lo, C.C.//Li, P.//Vuyisich, M.//Chain, P.S.//Junier, P. 	Genome Sequence of Anoxybacillus geothermalis Strain GSsed3, a Novel Thermophilic Endospore-Forming Species.	Genome Announcements	2015	3		e00575-15			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. 		
@D	Filippidou, S.//Wunderlin, T.//Junier, T.//Jeanneret, N.//Johnson, S.//McMurry, K.//Gleasner, C.D.//Lo, C.C.//Li, P.E.//Vuyisich, M.//Chain, P.S.//Junier, P. 	Genome Sequence of Bacillus alveayuensis Strain 24KAM51, a Halotolerant Thermophile Isolated from a Hydrothermal Vent.	Genome Announcements	2015	3		e00982-15			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. 		
@D	Filippini, M.//Qi, W.//Blom, J.//Goesmann, A.//Smits, T.H.//Bagheri, H.C. 	Genome Sequence of Fibrella aestuarina BUZ 2T, a Filamentous Marine Bacterium.	J. Bacteriol.	2012	194		3555			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. 		
@D	Filippini, M.//Qi, W.//Jaenicke, S.//Goesmann, A.//Smits, T.H.//Bagheri, H.C. 	Genome Sequence of the Filamentous Bacterium Fibrisoma limi BUZ 3T.	J. Bacteriol.	2012	194		4445			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. 		
@D	Fillo, S.//Giordani, F.//Anselmo, A.//Fortunato, A.//Palozzi, A.M.//De Santis, R.//Ciammaruconi, A.//Spagnolo, F.//Anniballi, F.//Fiore, A.//Auricchio, B.//De Medici, D.//Lista, F. 	Draft Genome Sequence of Clostridium botulinum B2 450 Strain from Wound Botulism  in a Drug User in Italy.	Genome Announcements	2015	3		e00238-15			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. 		
@D	Fillo, S.//Mancini, F.//Anselmo, A.//Fortunato, A.//Rezza, G.//Lista, F.//Ciervo, A. 	Draft Genome Sequence of Streptococcus suis Strain SsRC-1, a Human Isolate from a Fatal Case of Toxic Shock Syndrome.	Genome Announcements	2018	6		e00447-18			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. 		
@D	Finan, T.M.//Weidner, S.//Wong, K.//Buhrmester, J.//Chain, P.//Vorholter, F.J.//Hernandez-Lucas, I.//Becker, A.//Cowie, A.//Gouzy, J.//Golding, B.//Puhler, A. 	The complete sequence of the 1,683-kb pSymB megaplasmid from the N2-fixing endosymbiont Sinorhizobium meliloti.	Proc. Natl. Acad. Sci. U. S. A.	2001	98		9889-9894			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. 		
@D	Fineran, P.C.//Iglesias, C.M.C.//Ramsay, J.P.//Wilf, N.M.//Cossyleon, D.//McNeil, M.B.//Williamson, N.R.//Monson, R.E.//Becher, S.A.//Stanton, J.A.//Brugger, K.//Brown, S.D.//Salmond, G.P. 	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.	Genome Announcements	2013	1		e01039-13			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. 		
@D	Finkbeiner, S.R.//Allred, A.F.//Tarr, P.I.//Klein, E.J.//Kirkwood, C.D.//Wang, D. 	Metagenomic analysis of human diarrhea: viral detection and discovery.	PLoS Pathog.	2008	4		e1000011			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. 		
@D	Finnegan, E.J.//Dennis, E.S. 	Isolation and identification by sequence homology of a putative cytosine methyltransferase from Arabidopsis thaliana.	Nucleic Acids Res.	1993	21		2383-2388			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. 		
@D	Finnegan, E.J.//Genger, R.K.//Peacock, W.J.//Dennis, E.S. 	DNA methylation in plants.	Annu. Rev. Plant Physiol. Plant Mol. Biol.	1998	49		223-247			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. 		
@D	Finnegan, E.J.//Kovac, K.A. 	Plant DNA methyltransferases.	Plant Mol. Biol.	2000	43		189-201			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. 		
@D	Finnegan, E.J.//Peacock, W.J.//Dennis, E.S. 	Reduced DNA methylation in Arabidopsis thaliana results in abnormal plant development.	Proc. Natl. Acad. Sci. U. S. A.	1996	93		8449-8454			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. 		
@D	Finster, K.W.//Kjeldsen, K.U.//Kube, M.//Reinhardt, R.//Mussmann, M.//Amann, R.//Schreiber, L. 	Complete genome sequence of Desulfocapsa sulfexigens, a marine deltaproteobacterium specialized in disproportionating inorganic sulfur  compounds.	Standards in Genomic Sciences	2013	8		58-68			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. 		
@D	Finta, C.//Kiss, A. 	Footprint analysis of the BspRI DNA methyltransferase -- DNA interaction.	Nucleic Acids Res.	1997	25		2841-2846			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. 		
@D	Finta, C.//Sulima, U.//Venetianer, P.//Kiss, A. 	Purification of the KpnI DNA methyltransferase and photolabeling of the enzyme with S-adenosyl-L-methionine.	Gene	1995	164		65-69			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). 		
@D	Fiore, M.F.//Alvarenga, D.O.//Varani, A.M.//Hoff-Risseti, C.//Crespim, E.//Ramos, R.T.//Silva, A.//Schaker, P.D.//Heck, K.//Rigonato, J.//Schneider, M.P.//Jeong, H.//Sim, Y.M.//Kim, H.J.//Lee, Y.J.//Lee, D.W.//Lim, S.K.//Lee, S.J. 	Draft Genome Sequence of the Brazilian Toxic Bloom-Forming Cyanobacterium Microcystis aeruginosa Strain SPC777.	Genome Announcements	2013	1		e00547-13			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. 		
@D	Firczuk, M.//Wojciechowski, M.//Czapinska, H.//Bochtler, M. 	DNA intercalation without flipping in the specific ThaI-DNA complex.	Nucleic Acids Res.	2011	39		744-754			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. 		
@D	Firman, K.//Creasey, W.A.//Watson, G.//Price, C.//Glover, S.W. 	Genetic and physical studies of restriction-deficient mutants of the Inc FIV plasmids R124 and R124/3.	Mol. Gen. Genet.	1983	191		145-153			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. 		
@D	Firman, K.//Dutta, C.//Weiserova, M.//Janscak, P. 	The role of subunit assembly in the functional control of Type I restriction-modification enzymes.	Mol. Biol. Today	2000	1		35-41			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. 		
@D	Firman, K.//Price, C.//Glover, S.W. 	The EcoR124 and EcoR124/3 restriction and modification systems:  cloning the genes.	Plasmid	1985	14		224-234			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. 		
@D	Firman, K.//Szczelkun, M.D. 	Measuring motion on DNA by the type I restriction endonuclease EcoR124I using triplex displacement.	EMBO J.	2000	19		2094-2102			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. 		
@D	Firnhaber, C.//Gerber, M.//Tooley, K.//Scoggin, C. 	DNA Contamination in Commercial Restriction Endonucleases.	Am. J. Hum. Genet.	1986	39		145			None 		
@D	Fisch, K.M.//Silva, P.C.//Genilloud, O.//Almeida, C.//Schaberle, T.F. 	Draft Genome Sequence of Burkholderia contaminans 293K04B, an Endosymbiont of the Sponge-Derived Fungus Stachylidium bicolor.	Genome Announcements	2017	5		e01142-17			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. 		
@D	Fischer, A.//Harrison, K.S.//Ramirez, Y.//Auer, D.//Chowdhury, S.R.//Prusty, B.K.//Sauer, F.//Dimond, Z.//Kisker, C.//Scott-Hefty, P.//Rudel, T. 	Chlamydia trachomatis-containing vacuole serves as deubiquitination platform to stabilize Mcl-1 and to interfere with host defense.	eLife	2017	6		e21465			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. 		
@D	Fischer, A.//Santana-Cruz, I.//Giglio, M.//Nadendla, S.//Drabek, E.//Vilei, E.M.//Frey, J.//Jores, J. 	Genome Sequence of Mycoplasma feriruminatoris sp. nov., a Fast-Growing Mycoplasma Species.	Genome Announcements	2013	1		e00216-12			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. 		
@D	Fischer, A.//Santana-Cruz, I.//Hegerman, J.//Gourle, H.//Schieck, E.//Lambert, M.//Nadendla, S.//Wesonga, H.//Miller, R.A.//Vashee, S.//Weber, J.//Meens, J.//Frey, J.//Jores, J. 	High quality draft genomes of the Mycoplasma mycoides subsp. mycoides challenge strains Afade and B237.	Standards in Genomic Sciences	2015	10		89			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. 		
@D	Fischer, A.//Santana-Cruz, I.//Wambua, L.//Olds, C.//Midega, C.//Dickinson, M.//Kawicha, P.//Khan, Z.//Masiga, D.//Jores, J.//Schneider, B. 	Draft Genome Sequence of 'Candidatus Phytoplasma oryzae' Strain Mbita1, the Causative Agent of Napier Grass Stunt Disease in Kenya.	Genome Announcements	2016	4		e00297-16			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. 		
@D	Fischer, M.G.//Allen, M.J.//Wilson, W.H.//Suttle, C.A. 	Giant virus with a remarkable complement of genes infects marine zooplankton.	Proc. Natl. Acad. Sci. U. S. A.	2010	107		19508-19513			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. 		
@D	Fischer, W.//Breithaupt, U.//Kern, B.//Smith, S.I.//Spicher, C.//Haas, R. 	A comprehensive analysis of Helicobacter pylori plasticity zones reveals that they are integrating conjugative elements with intermediate integration specificity.	BMC Genomics	2014	15		310			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. 		
@D	Fisher, E.W.//Yang, M.-T.//Jeng, S.-T.//Gardner, J.F.//Gumport, R.I. 	Selection of mutations altering specificity in restriction-modification enzymes using the bacteriophage P22 challenge-phage system.	Gene	1995	157		119-121			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. 		
@D	Fisher, E.W.//Yang, M.T.//Gardner, J.F.//Gumport, R.I. 	Isolation of a mutant EcoRI endonuclease with enhanced affinity for duplex methylated d(GAATTC).	FASEB J.	1993	7		A1290			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. 		
@D	Fisher, O.//Siman-Tov, R.//Ankri, S. 	Characterization of cytosine methylated regions and 5-cytosine DNA methyltransferase (Ehmeth) in the protozoan parasite Entamoeba histolytica.	Nucleic Acids Res.	2004	32		287-297			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. 		
@D	Fisunov, G.Y.//Alexeev, D.G.//Bazaleev, N.A.//Ladygina, V.G.//Galyamina, M.A.//Kondratov, I.G.//Zhukova, N.A.//Serebryakova, M.V.//Demina, I.A.//Govorun, V.M. 	Core proteome of the minimal cell: comparative proteomics of three mollicute species.	PLoS ONE	2011	6		E21964			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. 		
@D	Fittipaldi, N.//Beres, S.B.//Olsen, R.J.//Kapur, V.//Shea, P.R.//Watkins, M.E.//Cantu, C.C.//Laucirica, D.R.//Jenkins, L.//Flores, A.R.//Lovgren, M.//Ardanuy, C.//Linares, J.//Low, D.E.//Tyrrell, G.J.//Musser, J.M. 	Full-Genome Dissection of an Epidemic of Severe Invasive Disease Caused by a Hypervirulent, Recently Emerged Clone of Group A Streptococcus.	Am. J. Pathol.	2012	180		1522-1534			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. 		
@D	Fitz-Gibbon, S.//Tomida, S.//Chiu, B.H.//Nguyen, L.//Du, C.//Liu, M.//Elashoff, D.//Erfe, M.C.//Loncaric, A.//Kim, J.//Modlin, R.L.//Miller, J.F.//Sodergren, E.//Craft, N.//Weinstock, G.M.//Li, H. 	Propionibacterium acnes Strain Populations in the Human Skin Microbiome Associated with Acne.	J. Invest. Dermatol.	2013	133		2152-2160			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. 		
@D	Fitz-Gibbon, S.T.//Ladner, H.//Kim, U.-J.//Stetter, K.O.//Simon, M.I.//Miller, J.H. 	Genome sequence of the hyperthermophilic crenarchaeon Pyrobaculum aerophilum.	Proc. Natl. Acad. Sci. U. S. A.	2002	99		984-989			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. 		
@A	Fitzgerald, G.F.//Twomey, D.P.//Daly, C.//Coffey, A.G. 		Bacteriophage resistance in Lactococcus: Molecular characterization of the ScrFI restriction/modification system from Lactococcus lactis subsp. cremoris UC503.			Ferretti, J.J.//Gilmore, M.S.//Klaenhammer, T.R.//Brown, F. 		Genetics and Molecular Biology of Streptococci, Lactococci, and Enterococci				Basel	Karger	1995		85		581-590									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. 		
@D	Fitzgerald, L.A.//Graves, M.V.//Li, X.//Feldblyum, T.//Hartigan, J.//Van Etten, J.L. 	Sequence and annotation of the 314-kb MT325 and the 321-kb FR483 viruses that infect Chlorella Pbi.	Virology	2007	358		459-471			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. 		
@D	Fitzgerald, L.A.//Graves, M.V.//Li, X.//Feldblyum, T.//Nierman, W.C.//Van Etten, J.L. 	Sequence and annotation of the 369-kb NY-2A and the 345-kb AR158 viruses that infect Chlorella NC64A.	Virology	2007	358		472-484			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. 		
@D	Fitzgerald, M.C.//Skowron, P.//Van Etten, J.L.//Smith, L.M.//Mead, D.A. 	Rapid shotgun cloning utilizing the two base recognition endonuclease CviJI.	Nucleic Acids Res.	1992	20		3753-3762			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). 		
@D	Fitzgerald, S.//Dillon, S.C.//Chao, T.C.//Wiencko, H.L.//Hokamp, K.//Cameron, A.D.//Dorman, C.J. 	Re-engineering cellular physiology by rewiring high-level global regulatory genes.	Sci. Rep.	2015	5		17653			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. 		
@D	Fitzgerlad, G.F.//Daly, C.//Brown, L.R.//Gingeras, T.R. 	ScrFI: a new sequence-specific endonuclease from Streptococcus cremoris.	Nucleic Acids Res.	1982	10		8171-8179			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. 		
@D	Fixen, K.R.//Starkenburg, S.R.//Hovde, B.T.//Johnson, S.L.//Deodato, C.R.//Daligault, H.E.//Davenport, K.W.//Harwood, C.S.//Cattolico, R.A. 	Genome Sequences of Eight Bacterial Species Found in Coculture with the Haptophyte Chrysochromulina tobin.	Genome Announcements	2016	4		e01162-16			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. 		
@D	Flanagan, J.C.//Lang, J.M.//Darling, A.E.//Eisen, J.A.//Coil, D.A. 	Draft Genome Sequence of Curtobacterium flaccumfaciens Strain UCD-AKU (Phylum Actinobacteria).	Genome Announcements	2013	1		e00244-13			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. 		
@D	Fleischman, R.A.//Campbell, J.L.//Richardson, C.C. 	Modification and restriction of T-even bacteriophages.	J. Biol. Chem.	1976	251		1561-1570			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. 		
@D	Fleischman, R.A.//Richardson, C.C. 	Analysis of host range restriction in Escherichia coli treated with toluene.	Proc. Natl. Acad. Sci. U. S. A.	1971	68		2527-2531			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. 		
@D	Fleischmann, R.D. et al. 	Whole-genome random sequencing and assembly of Haemophilus influenzae Rd.	Science	1995	269		496-512			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. 		
@D	Fletcher, B.S. 	Development and validation of an approach to produce large-scale quantities of CpG-methylated plasmid DNA.	Micro. Biotech.	2008	1		62-67			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. 		
@D	Flett, F.//Mersinias, V.//Smith, C.P. 	High efficiency intergeneric conjugal transfer of plasmid DNA from Escherichia coli to methyl DNA-restricting streptomycetes.	FEMS Microbiol. Lett.	1997	155		223-229			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. 		
@D	Flett, F.//Wotton, S.F.//Kirby, R. 	A common host specificity in the restriction and modification of a bacteriophage by three distinct Streptomyces species.	J. Gen. Microbiol.	1979	110		465-467			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. 		
@D	Flick, K.E.//Jurica, M.S.//Monnat, R.J. Jr.//Stoddard, B.L. 	DNA binding and cleavage by the nuclear intron-encoded homing endonuclease I-PpoI.	Nature	1998	394		96-101			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. 		
@D	Flick, K.E.//McHugh, D.//Heath, J.D.//Stephens, K.M.//Monnat, R.J. Jr.//Stoddard, B.L. 	Crystallization and preliminary X-ray studies of I-PpoI: A nuclear, intron-encoded homing endonuclease from Physarum polycephalum.	Protein Sci.	1997	6		2677-2680			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. 		
@D	Fliess, A.//Wolfes, H.//Rosenthal, A.//Schwellnus, K.//Blocker, H.//Frank, R.//Pingoud, A. 	Role of thymidine residues in DNA recognition by the EcoRI and EcoRV restriction endonucleases.	Nucleic Acids Res.	1986	14		3463-3474			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. 		
@D	Fliess, A.//Wolfes, H.//Seela, F.//Pingoud, A. 	Analysis of the recognition mechanism involved in the EcoRV catalyzed cleavage of DNA using modified oligodeoxynucleotides.	Nucleic Acids Res.	1988	16		11781-11793			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. 		
@D	Flinspach, K.//Ruckert, C.//Kalinowski, J.//Heide, L.//Apel, A.K. 	Draft Genome Sequence of Streptomyces niveus NCIMB 11891, Producer of the Aminocoumarin Antibiotic Novobiocin.	Genome Announcements	2014	2		e01146-13			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. 		
@D	Flood, B.E.//Jones, D.S.//Bailey, J.V. 	Complete Genome Sequence of Sedimenticola thiotaurini Strain SIP-G1, a Polyphosphate- and Polyhydroxyalkanoate-Accumulating Sulfur-Oxidizing  Gammaproteobacterium Isolated from Salt Marsh Sediments.	Genome Announcements	2015	3		e00671-15			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. 		
@D	Flood, B.E.//Leprich, D.//Bailey, J.V. 	Complete Genome Sequence of Celeribacter baekdonensis Strain LH4, a Thiosulfate-Oxidizing Alphaproteobacterial Isolate from Gulf of Mexico  Continental Slope Sediments.	Genome Announcements	2018	6		e00434-18			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. 		
@D	Flores, A.R. et al. 	Sequence type 1 group B Streptococcus, an emerging cause of invasive disease in adults, evolves by small genetic changes.	Proc. Natl. Acad. Sci. U. S. A.	2015	112		6431-6436			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. 		
@D	Flores, H.//Osuna, J.//Heitman, J.//Soberon, X. 	Saturation mutagenesis of His114 of EcoRI reveals relaxed-specificity mutants.	Gene	1995	157		295-301			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. 		
@D	Flores, V.//Lopez-Merino, A.//Mendoza-Hernandez, G.//Guarneros, G. 	Comparative genomic analysis of two brucellaphages of distant origins.	Genomics	2012	99		233-240			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. 		
@D	Florez, A.B.//Reimundo, P.//Delgado, S.//Fernandez, E.//Alegria, A.//Guijarro, J.A.//Mayo, B. 	Genome Sequence of Lactococcus garvieae IPLA 31405, a Bacteriocin-Producing, Tetracycline-Resistant Strain Isolated from a Raw-Milk Cheese.	J. Bacteriol.	2012	194		5118-5119			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. 		
@D	Floriano, A.M.//Castelli, M.//Krenek, S.//Berendonk, T.U.//Bazzocchi, C.//Petroni, G.//Sassera, D. 	The Genome Sequence of 'Candidatus Fokinia solitaria': Insights on Reductive Evolution in Rickettsiales.	Genome Biol. Evol.	2018	10		1120-1126			"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. 		
@D	Fluchter, S.//Poehlein, A.//Schiel-Bengelsdorf, B.//Daniel, R.//Durre, P. 	Genome Sequence of the Poly-3-Hydroxybutyrate Producer Clostridium acetireducens  DSM 10703.	Genome Announcements	2016	4		e01399-16			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. 		
@D	Flusberg, B.A.//Webster, D.R.//Lee, J.H.//Travers, K.J.//Olivares, E.C.//Clark, T.A.//Korlach, J.//Turner, S.W. 	Direct detection of DNA methylation during single-molecule, real-time sequencing.	Nat. Methods	2010	7		461-465			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. 		
@D	Flynn, J. 	Murine DNA cytosine C-5 methyltransferase: Insights into epigenetic control. from enzymological studies.	Diss. Abstr.	1998	58		3614B			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. 		
@D	Flynn, J.//Azzam, R.//Reich, N. 	DNA binding discrimination of the murine DNA cytosine-C5 methyltransferase.	J. Mol. Biol.	1998	279		101-116			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. 		
@D	Flynn, J.//Fang, J.Y.//Mikovits, J.A.//Reich, N.O. 	A potent cell-active allosteric inhibitor of murine DNA cytosine C5 methyltransferase.	J. Biol. Chem.	2003	278		8238-8243			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. 		
@D	Flynn, J.//Glickman, J.F.//Reich, N.O. 	Murine DNA cytosine-C5 methyltransferase: pre-steady- and steady-state kinetic analysis with regulatory DNA sequences.	Biochemistry	1996	35		7308-7315			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. 		
@D	Flynn, J.//Reich, N. 	Murine DNA (cytosine-5-)-methyltransferase: Steady-state and substrate trapping analyses of the kinetic mechanism.	Biochemistry	1998	37		15162-15169			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. 		
@D	Flynn, J.//Reich, N.O. 	Identification of flanking sequence dependence of DNA recognition for mammalian DNA cytosine methyltransferase.	FASEB J.	1993	7		A1219			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. 		
@D	Flynn, J.D. et al. 	Draft Genome Sequences of Gammaproteobacterial Methanotrophs Isolated from Marine Ecosystems.	Genome Announcements	2016	4		e01629-15			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. 		
@D	Foerg, E.//Saporito, L.//Huang, S.//Yang, J.//Allen, M.M. 	Isolation and characterization of two sequence-specific endonucleases from the cyanobacterium Synechocystis sp. PCC 6308.	FEMS Microbiol. Lett.	1990	69		105-108			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'. 		
@D	Folaranmi, T.A. et al. 	Increased Risk for Meningococcal Disease Among Men Who Have Sex With Men in the United States, 2012-2015.	Clin. Infect. Dis.	2017	65		756-763			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. 		
@D	Foley, S.//Bruttin, A.//Brussow, H. 	Widespread distribution of a group I intron and its three deletion derivatives in the lysin gene of streptococcus thermophilus bacteriophages.	J. Virol.	2000	74		611-618			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. 		
@A	Follman, H.//Balzer, H.-J.//Schleicher, R. 		Biosynthesis and distribution of methylcytosine in wheat DNA.  How different are plant DNA methyltransferases?			Clawson, G.A.//Willis, D.B.//Weissbach, A.//Jones, P.A. 		Nucleic Acid Methylation				New York	Wiley-Liss	1990		0		199-210									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. 		
@D	Fomenkov, A.//Akimov, V.N.//Vasilyeva, L.V.//Andersen, D.T.//Vincze, T.//Roberts, R.J. 	Complete Genome and Methylome Analysis of Psychrotrophic Bacterial Isolates from  Lake Untersee in Antarctica.	Genome Announcements	2017	5		e01753-16			This paper describes the complete genome sequences and methylome analysis of six psychrotrophic strains isolated from perennially ice-covered Lake Untersee in Antarctica. 		
@D	Fomenkov, A.//Clark, T.//Spittle, K.//Anton, B.M.//Vincze, T.//Korlach, J.//Roberts, R.J. 	Molecular dissection of the methylome of Burkholderia cenocepacia J2315.	FEBS J.	2013	280		72-73			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. 		
@D	Fomenkov, A.//Lunnen, K.D.//Zhu, Z.//Anton, B.P.//Wilson, G.G.//Vincze, T.//Roberts, R.J. 	Complete genome sequence and methylome analysis of Bacillus strain X1.	Genome Announcements	2015	3		e01593-14			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. 		
@D	Fomenkov, A.//Sun, Z.//Dila, D.K.//Anton, B.P.//Roberts, R.J.//Raleigh, E.A. 	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.	PLoS ONE	2017	12		e0179853			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. 		
@D	Fomenkov, A.//Sun, Z.//Vincze, T.//Dubinina, G.//Orlova, M.//Tarlachkov, S.V.//Anton, B.P.//Grabovich, M.Y.//Roberts, R.J. 	Complete Genome Sequence of the Freshwater Bacterium Beggiatoa leptomitoformis Strain D-401.	Genome Announcements	2018	6		e00311-18			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. 		
@D	Fomenkov, A.//Vincze, T.//Degtyarev, S.K.//Roberts, R.J. 	Complete Genome Sequence and Methylome Analysis of Acinetobacter calcoaceticus 65.	Genome Announcements	2017	5		e00060-17			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. 		
@D	Fomenkov, A.//Vincze, T.//Grabovich, M.//Anton, B.P.//Dubinina, G.//Orlova, M.//Belousova, E.//Roberts, R.J. 	Complete Genome Sequence of a Strain of Azospirillum thiophilum Isolated from a Sulfide Spring.	Genome Announcements	2016	4		e01521-15			We report the complete, closed genome sequence and complete methylome of Azospirillum thiophilum strain BV-S(T). 		
@D	Fomenkov, A.//Vincze, T.//Grabovich, M.Y.//Dubinina, G.//Orlova, M.//Belousova, E.//Roberts, R.J. 	Complete Genome Sequence of the Freshwater Colorless Sulfur Bacterium Beggiatoa leptomitiformis Neotype Strain D-402T.	Genome Announcements	2015	3		e01436-15			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). 		
@D	Fomenkov, A.//Vincze, T.//Grabovich, M.Y.//Dubinina, G.//Orlova, M.//Belousova, E.//Roberts, R.J. 	Whole-Genome Sequence and Methylome Analysis of the Freshwater Colorless Sulfur Bacterium Thioflexothrix psekupsii D3.	Genome Announcements	2017	5		e00904-17			In this report, we announce the availability of a whole-genome sequence and methylome analysis of Thioflexothrix psekupsii strain D3. 		
@D	Fomenkov, A.//Vincze, T.//Mersha, F.//Roberts, R.J. 	Complete Genome Sequence and Methylome Analysis of Bacillus caldolyticus NEB414.	Genome Announcements	2018	6		e01605-17			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. 		
@D	Fomenkov, A.//Xiao, J.-P.//Dila, D.//Raleigh, E.//Xu, S.-Y. 	The 'endo-blue method' for direct cloning of restriction endonuclease genes in E. coli.	Nucleic Acids Res.	1994	22		2399-2403			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. 		
@D	Fomenkov, A.//Xu, S.-Y. 	Isolation of temperature-sensitive mutants of the BamHI restriction endonuclease.	Gene	1995	157		303-310			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. 		
@D	Fomenkov, A.I.//Kramarov, V.M.//Andreev, L.V.//Mochalov, V.V.//Smolyaninov, V.V.//Matvienko, N.I. 	Isolation and properties of a new site specific endonuclease Bme142I from Bacillus megaterium 142.	Nucleic Acids Res.	1988	16		10399			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'. 		
@D	Fondi, M.//Orlandini, V.//Emiliani, G.//Papaleo, M.C.//Maida, I.//Perrin, E.//Vaneechoutte, M.//Dijkshoorn, L.//Fani, R. 	Draft Genome Sequence of the Hydrocarbon-Degrading and Emulsan-Producing Strain Acinetobacter venetianus RAG-1T.	J. Bacteriol.	2012	194		4771-4772			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. 		
@D	Fondi, M.//Orlandini, V.//Maida, I.//Perrin, E.//Papaleo, M.C.//Emiliani, G.//de Pascale, D.//Parrilli, E.//Tutino, M.L.//Michaud, L.//Lo, G.A.//Fani, R. 	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.	J. Bacteriol.	2012	194		6334-6335			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. 		
@D	Fonfara, I.//Curth, U.//Pingoud, A.//Wende, W. 	Creating highly specific nucleases by fusion of active restriction endonucleases and catalytically inactive homing endonucleases.	Nucleic Acids Res.	2012	40		847-860			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. 		
@D	Fontana, C.A.//Salazar, S.M.//Bassi, D.//Puglisi, E.//Lovaisa, N.//Toffoli, L.M.//Pedraza, R.//Cocconcelli, P.S. 	Genome Sequence of Azospirillum brasilense REC3, Isolated from Strawberry Plants.	Genome Announcements	2018	6		e00089-18			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%. 		
@D	Fontana, P.D.//Fontana, C.A.//Bassi, D.//Puglisi, E.//Salazar, S.M.//Vignolo, G.M.//Coccocelli, P.S. 	Genome Sequence of Acidovorax avenae Strain T10_61 Associated with Sugarcane Red  Stripe in Argentina.	Genome Announcements	2016	4		e01669-15			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%. 		
@D	Fontes-Perez, H.//Olvera-Garcia, M.//Chavez-Martinez, A.//Rodriguez-Almeida, F.A.//Arzola-Alvarez, C.A.//Sanchez-Flores, A.//Corral-Luna, A. 	Genome Sequence of Citrobacter sp. CtB7.12, Isolated from the Gut of the Desert Subterranean Termite Heterotermes aureus.	Genome Announcements	2015	3		e01290-15			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. 		
@D	Foo, S.M.//Eng, W.W.H.//Lee, Y.P.//Gui, K.//Gan, H.M. 	New Sequence Types of Vibrio parahaemolyticus Isolated from a Malaysian Aquaculture Pond, as Revealed by Whole-Genome Sequencing.	Genome Announcements	2017	5		e00302-17			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. 		
@D	Fookes, M.//Yu, J.//De Majumdar, S.//Thomson, N.//Schneiders, T. 	Genome Sequence of Klebsiella pneumoniae Ecl8, a Reference Strain for Targeted Genetic Manipulation.	Genome Announcements	2013	1		e00027-12			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. 		
@D	Foray, V.//Grigorescu, A.S.//Sabri, A.//Haubruge, E.//Lognay, G.//Francis, F.//Fauconnier, M.L.//Hance, T.//Thonart, P. 	Whole-Genome Sequence of Serratia symbiotica Strain CWBI-2.3T, a Free-Living Symbiont of the Black Bean Aphid Aphis fabae.	Genome Announcements	2014	2		e00767-14			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. 		
@D	Ford, E.//Boyer, H.W. 	Degradation of enteric bacterial deoxyribonucleic acid by the Escherichia coli B restriction endonuclease.	J. Bacteriol.	1970	104		594-595			the deoxyribonucleic acid of five different genera of enteric microorganisms was shown to be degraded by the Escherichia coli B restriction endonuclease. 		
@D	Ford, K.//Taylor, C.//Connolly, B.//Hornby, D.P. 	Effects of co-factor and deoxycytidine substituted oligonucleotides upon sequence-specific interations between MspI DNA methyltransferase and DNA.	J. Mol. Biol.	1993	230		779-786			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. 		
@D	Forde, A.//Daly, C.//Fitzgerald, G.F. 	Identification of four phage resistance plasmids from Lactococcus lactis subsp. cremoris HO2.	Appl. Environ. Microbiol.	1999	65		1540-1547			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. 		
@D	Forde, A.//Fitzgerald, G.F. 	Bacteriophage defence systems in lactic acid bacteria.	Antonie Van Leeuwenhoek	1999	76		89-113			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. 		
@D	Forde, B.M.//Ben Zakour, N.L.//Stanton-Cook, M.//Phan, M.D.//Totsika, M.//Peters, K.M.//Chan, K.G.//Schembri, M.A.//Upton, M.//Beatson, S.A. 	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.	PLoS ONE	2014	9		E104400			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. 		
@D	Forde, B.M.//Neville, B.A.//O'Donnell, M.M.//Riboulet-Bisson, E.//Claesson, M.J.//Coughlan, A.//Ross, R.P.//O'Toole, P.W. 	Genome sequences and comparative genomics of two Lactobacillus ruminis strains from the bovine and human intestinal tracts.	Microb. Cell Fact.	2011	10		S13			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. 		
@D	Forde, B.M.//Phan, M.D.//Gawthorne, J.A.//Ashcroft, M.M.//Stanton-Cook, M.//Sarkar, S.//Peters, K.M.//Chan, K.G.//Chong, T.M.//Yin, W.F.//Upton, M.//Schembri, M.A.//Beatson, S.A. 	Lineage-Specific Methyltransferases Define the Methylome of the Globally Disseminated Escherichia coli ST131 Clone.	MBio	2015	6		e01602-15			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. 		
@D	Forde, G.K.//Kedzierski, P.//Sokalski, W.A.//Forde, A.E.//Hill, G.A.//Leszczynski, J. 	Physical nature of interactions within the active site of cytosine-5-methyltransferase.	J. Phys. Chem. A	2006	110		2308-2313			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. 		
@D	Foret, S.//Kucharski, R.//Pellegrini, M.//Feng, S.//Jacobsen, S.E.//Robinson, G.E.//Maleszka, R. 	DNA methylation dynamics, metabolic fluxes, gene splicing, and alternative phenotypes in honey bees.	Proc. Natl. Acad. Sci. U. S. A.	2012	109		4968-4973			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. 		
@D	Formighieri, E.F. et al. 	The mitochondrial genome of the phytopathogenic basidiomycete Moniliophthora perniciosa is 109 kb in size and contains a stable integrated plasmid.	Mycol. Res.	2008	112		1136-1152			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. 		
@D	Formusa, P.A.//Hsiang, T.//Habash, M.B.//Lee, H.//Trevors, J.T. 	Genome Sequence of Pseudomonas mandelii PD30.	Genome Announcements	2014	2		e00713-14			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. 		
@D	Forn-Cuni, G.//Tomas, J.M.//Merino, S. 	Whole-Genome Sequence of Aeromonas hydrophila Strain AH-1 (Serotype O11).	Genome Announcements	2016	4		e00920-16			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. 		
@D	Forn-Cuni, G.//Tomas, J.M.//Merino, S. 	Genome Sequence of Aeromonas hydrophila Strain AH-3 (Serotype O34).	Genome Announcements	2016	4		e00919-16			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. 		
@D	Forrow, S.//Lee, M.//Souhami, R.L.//Hartley, J.A. 	The effect of AT and GC sequence specific minor groove binding agents on restriction endonuclease activity.	ACS Abstracts	1994	208		97			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. 		
@D	Forrow, S.M.//Lee, M.//Souhami, R.L.//Hartley, J.A. 	The effect of AT and GC sequence specific minor groove-binding agents on restriction endonuclease activity.	Chem. Biol. Interact.	1995	96		125-142			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. 		
@D	Forsberg, K.J.//Patel, S.//Gibson, M.K.//Lauber, C.L.//Knight, R.//Fierer, N.//Dantas, G. 	Bacterial phylogeny structures soil resistomes across habitats.	Nature	2014	509		612-616			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. 		
@D	Forsblom, S.//Rigler, R.//Ehrenberg, M.//Pettersson, U.//Philipson, L. 	Kinetic studies on the cleavage of adenovirus DNA by restriction endonuclease EcoRI.	Nucleic Acids Res.	1976	3		3255-3269			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. 		
@D	Fortuna, A.//Ramnarine, R.//Li, A.//Fittipaldi, N.//Frantz, C.//Mallo, G.V. 	Draft Genome Sequences of Four Clinical Legionella pneumophila Isolates from Ontario, Canada.	Genome Announcements	2018	6		e00295-18			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. 		
@D	Foss, H.M.//Roberts, C.J.//Claeys, K.M.//Selker, E.U. 	Abnormal chromosome behavior in Neurospora mutants defective in DNA methylation.	Science	1993	262		1737-1741			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. 		
@D	Foster, B. et al. 	Complete genome sequence of Xylanimonas cellulosilytica type strain (XIL07T).	Standards in Genomic Sciences	2010	2		1-8			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. 		
@D	Foster, J. et al. 	The Wolbachia genome of Brugia malayi: endosymbiont evolution within a human pathogenic nematode.	PLoS Biology	2005	3		E121			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. 		
@D	Foster, P.L.//Rosche, W.A. 	Levels of the Vsr endonuclease do not regulate stationary-phase reversion of a Lac- frameshift allele in Escherichia coli.	J. Bacteriol.	1998	180		1944-1946			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. 		
@D	Fotso, F.A.//Mediannikov, O.//Padmanabhan, R.//Robert, C.//Fournier, P.E.//Raoult, D.//Drancourt, M. 	Genome Sequence of Borrelia crocidurae Strain 03-02, a Clinical Isolate from Senegal.	Genome Announcements	2014	2		e01150-14			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. 		
@D	Fougy, L.//Coeuret, G.//Champomier-Verges, M.C.//Chaillou, S. 	Draft Genome Sequence of Serratia proteamaculans MFPA44A14-05, a Model Organism for the Study of Meat and Seafood Spoilage.	Genome Announcements	2017	5		e00491-17			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. 		
@D	Foulks, J.M.//Parnell, K.M.//Chau, S.//Swierczek, K.//Saunders, M.//Wright, K.//Hendrickson, T.F.//McCullar, M.V.//Kanner, S.B. 	Epigenetic Drug Discovery: Targeting DNA Methyltransferases (vol 17, pg 2, 2012).	J. Biomol. Screen.	2012	17		700			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). 		
@D	Fournier, P.E.//El Karkouri, K.//Leroy, Q.//Robert, C.//Giumelli, B.//Renesto, P.//Socolovschi, C.//Parola, P.//Audic, S.//Raoult, D. 	Analysis of the Rickettsia africae genome reveals that virulence acquisition in Rickettsia species may be explained by genome reduction.	BMC Genomics	2009	10		166			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. 		
@D	Fournier, P.E.//El Karkouri, K.//Robert, C.//Medigue, C.//Raoult, D. 	Complete Genome Sequence of Rickettsia slovaca, the Agent of Tick-Borne Lymphadenitis.	J. Bacteriol.	2012	194		1612			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. 		
@D	Fournier, P.E.//Rouli, L.//El Karkouri, K.//Nguyen, T.T.//Yagupsky, P.//Raoult, D. 	Genomic Comparison of Kingella kingae Strains.	J. Bacteriol.	2012	194		5972			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. 		
@D	Fournier, P.E.//Vallenet, D.//Barbe, V.//Audic, S.//Ogata, H.//Poirel, L.//Richet, H.//Robert, C.//Mangenot, S.//Abergel, C.//Nordmann, P.//Weissenbach, J.//Raoult, D.//Claverie, J.M. 	Comparative genomics of multidrug resistance in Acinetobacter baumannii.	PLoS Genet.	2006	2		e7			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. 		
@D	Foury, F.//Roganti, T.//Lecrenier, N.//Purnelle, B. 	The complete sequence of the mitochondrial genome of Saccharomyces cerevisiae.	FEBS Lett.	1998	440		325-331			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. 		
@D	Fouteau, S.//Guerin, T.//Magdelenat, G.//Roumagnac, M.//Bartoli, M.//Ollivier, B.//Dolla, A.//Barbe, V.//Pradel, N. 	Genome Sequence of Piezophilic Bacterium Desulfovibrio profundus Strain 500-1, Isolated from a Deep Sediment Layer in the Japan Sea.	Genome Announcements	2017	5		e01181-17			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. 		
@D	Fouts, D.E. et al. 	Major structural differences and novel potential virulence mechanisms from the genomes in multiple Campylobacter species.	PLoS Biology	2005	3		e15			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. 		
@D	Fouts, D.E.//Tyler, H.L.//DeBoy, R.T.//Daugherty, S.//Ren, Q.//Badger, J.H.//Durkin, A.S.//Huot, H.//Shrivastava, S.//Kothari, S.//Dodson, R.J.//Mohamoud, Y.//Khouri, H.//Roesch, L.F.//Krogfelt, K.A.//Struve, C.//Triplett, E.W.//Methe, B.A. 	Complete genome sequence of the N2-fixing broad host range endophyte Klebsiella pneumoniae 342 and virulence predictions verified in mice.	PLoS Genet.	2008	4		E1000141			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. 		
@D	Fox, K.L.//Dowideit, S.J.//Erwin, A.L.//Srikhanta, Y.N.//Smith, A.L.//Jennings, M.P. 	Haemophilus influenzae phasevarions have evolved from type III DNA restriction systems into epigenetic regulators of gene expression.	Nucleic Acids Res.	2007	35		5242-5252			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. 		
@D	Fox, K.L.//Srikhanta, Y.N.//Jennings, M.P. 	Phase variable type III restriction-modification systems of host-adapted bacterial pathogens.	Mol. Microbiol.	2007	65		1375-1379			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. 		
@D	Fox, K.R. 	DNAse I footprinting of restriction enzymes.	Biochem. Biophys. Res. Commun.	1988	155		779-785			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. 		
@D	Fox, K.R.//Allinson, S.L.//Sahagun-Krause, H.//Brown, T. 	Recognition of GT mismatches by Vsr mismatch endonuclease.	Nucleic Acids Res.	2000	28		2535-2540			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. 		
@D	Fraga, M.F.//Ballestar, E.//Montoya, G.//Taysavang, P.//Wade, P.A.//Esteller, M. 	The affinity of different MBD proteins for a specific methylated locus depends on their intrinsic binding properties.	Nucleic Acids Res.	2003	31		1765-1774			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. 		
@D	Frampton, R.A.//Thompson, S.M.//Kalamorz, F.//David, C.//Addison, S.M.//Smith, G.R. 	Draft Genome Sequence of a 'Candidatus Liberibacter europaeus' Strain Assembled from Broom Psyllids (Arytainilla spartiophila) from New Zealand.	Genome Announcements	2018	6		e00430-18			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%. 		
@D	Franchina, M.//Hooper, J.//Kay, P.H. 	Five novel alternatively spliced transcripts of DNA (cytosine-5) methyltransferase 2 in human peripheral blood leukocytes.	Int. J. Biochem. Cell Biol.	2001	33		1104-1115			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. 		
@D	Franchina, M.//Kay, P.H. 	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.	DNA Cell Biol.	2000	19		521-526			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. 		
@D	Franchina, M.//Kay, P.H. 	Allele-specific variation in the gene copy number of human cytosine 5-methyltransferase.	Hum. Hered.	2000	50		112-117			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. 		
@D	Francisco, M.S.//Farias, F.M.//Santos, I.N.S.//Marques-Bastos, S.L.S.//Albano, R.M.//Bastos, M.D.C.F. 	Draft Genome Sequence of Staphylococcus aureus 4185, a Strain That Produces Aureocyclicin 4185.	Genome Announcements	2017	5		e01249-17			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. 		
@D	Franco, C.M.//Araujo, R.//Adetutu, E.//Tobe, S.S.//Mallya, S.//Paul, B.//Satyamoorthy, K. 	Complete Genome Sequences of the Endophytic Streptomyces Strains EN16, EN23, and  EN27, Isolated from Wheat Plants.	Genome Announcements	2016	4		e01342-16			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. 		
@D	Franco, C.M.M.//Adetutu, E.M.//Le, H.X.//Ballard, R.A.//Araujo, R.//Tobe, S.S.//Paul, B.//Mallya, S.//Satyamoorthy, K. 	Complete Genome Sequences of the Endophytic Streptomyces sp. Strains LUP30 and LUP47B, Isolated from Lucerne Plants.	Genome Announcements	2017	5		e00556-17			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. 		
@D	Franco, J.A.V.//Collier, R.//Wang, Y.//Huo, N.//Gu, Y.//Thilmony, R.//Thomson, J.G. 	Draft Genome Sequence of Agrobacterium rhizogenes Strain NCPPB2659.	Genome Announcements	2016	4		e00746-16			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. 		
@D	Franco, M.E.//Lopez, S.//Medina, R.//Saparrat, M.C.//Balatti, P. 	Draft Genome Sequence and Gene Annotation of Stemphylium lycopersici Strain CIDEFI-216.	Genome Announcements	2015	3		e01069-15			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. 		
@D	Franco, T.//Califano, G.//Goncalves, A.C.//Cucio, C.//Costa, R. 	Draft Genome Sequence of Vibrio sp. Strain Evh12, a Bacterium Retrieved from the  Gorgonian Coral Eunicella verrucosa.	Genome Announcements	2016	4		e01729-15			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. 		
@D	Francois, J.-C.//Saison-Behmoaras, T.//Barbier, C.//Chassignol, M.//Thuong, N.T.//Helene, C. 	Sequence-specific recognition and cleavage of duplex DNA via triple-helix formation by oligonucleotides covalently linked to a phenanthroline-copper chelate.	Proc. Natl. Acad. Sci. U. S. A.	1989	86		9702-9706			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. 		
@D	Francois, J.-C.//Saison-Behmoaras, T.//Thuong, N.T.//Helene, C. 	Inhibition of restriction endonuclease cleavage via triple helix formation by homopyrimidine oligonucleotides.	Biochemistry	1989	28		9617-9619			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. 		
@D	Frank, J.//Dingemanse, C.//Schmitz, A.M.//Vossen, R.H.//van Ommen, G.J.//den Dunnen, J.T.//Robanus-Maandag, E.C.//Anvar, S.Y. 	The Complete Genome Sequence of the Murine Pathobiont Helicobacter typhlonius.	Front. Microbiol.	2015	6		1549			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. 		
@D	Frank, O.//Goker, M.//Pradella, S.//Petersen, J. 	Ocean's twelve: Flagellar and biofilm chromids in the multipartite genome of Marinovum algicola DG898 exemplify functional compartmentalization.	Environ. Microbiol.	2015	17		4019-4034			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. 		
@D	Frank, O.//Pradella, S.//Rohde, M.//Scheuner, C.//Klenk, H.P.//Goker, M.//Petersen, J. 	Complete genome sequence of the Phaeobacter gallaeciensis type strain CIP 105210(T) (= DSM 26640(T) = BS107(T)).	Standards in Genomic Sciences	2014	9		914-932			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. 		
@D	Frank, S.A. 	Polymorphism of bacterial restriction-modification systems: the advantage of diversity.	Evolution	1994	48		1470-1477			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. 		
@D	Frankel, A.D. 	Sequence-specific recognition of DNA by the HinfI restriction endonuclease.	Ph.D. Thesis, Johns Hopkins University, USA	1983			1-92			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. 		
@D	Frankel, A.D.//Ackers, G.K.//Smith, H.O. 	Measurement of DNA-protein equilibria using gel chromatography:  application to the HinfI restriction endonuclease.	Biochemistry	1985	24		3049-3054			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. 		
@D	Frankel, A.D.//Smith, H.O. 	Restriction and modification enzymes detect no allosteric changes in DNA with bound lac repressor or RNA polymerase.	J. Mol. Biol.	1981	146		611-619			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. 		
@D	Franklin, N.C.//Dove, W.F. 	Genetic evidence for restriction targets in the DNA of phages lambda and Phi80.	Genet. Res.	1969	14		151-157			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. 		
@D	Franzon, V.L.//Barker, A.//Manning, P.A. 	Nucleotide sequence encoding the mannose-fucose-resistant hemagglutinin of Vibrio cholerae O1 and construction of a mutant.	Infect. Immun.	1993	61		3032-3037			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. 		
@D	Fraser, C.M. et al. 	The minimal gene complement of Mycoplasma genitalium.	Science	1995	270		397-403			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. 		
@D	Fraser, C.M. et al. 	Genomic sequence of a Lyme disease spirochaete, Borrelia burgdorferi.	Nature	1997	390		580-586			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. 		
@D	Fraser, C.M. et al. 	Complete genome sequence of Treponema pallidum, the syphilis spirochete.	Science	1998	281		375-388			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. 		
@D	Frauer, C.//Leonhardt, H. 	Twists and turns of DNA methylation.	Proc. Natl. Acad. Sci. U. S. A.	2011	108		8919-8920			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. 		
@D	Frauer, C.//Leonhardt, H. 	A versatile non-radioactive assay for DNA methyltransferase activity and DNA binding.	Nucleic Acids Res.	2009	37		e22			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. 		
@D	Fraunhofer, M.E.//Geissler, A.J.//Jakob, F.//Vogel, R.F. 	Multiple Genome Sequences of Exopolysaccharide-Producing, Brewery-Associated Lactobacillus brevis Strains.	Genome Announcements	2017	5		e00585-17			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. 		
@D	Fraunholz, M.//Bernhardt, J.//Schuldes, J.//Daniel, R.//Hecker, M.//Sinha, B. 	Complete Genome Sequence of Staphylococcus aureus 6850, a Highly Cytotoxic and Clinically Virulent Methicillin-Sensitive Strain with Distant Relatedness to  Prototype Strains.	Genome Announcements	2013	1		e00775-13			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. 		
@D	Frazao, M.R.//Cao, G.//Medeiros, M.I.C.//Duque, S.D.S.//Leon, M.S.//Allard, M.W.//Falcao, J.P. 	Draft Genome Sequences of 116 Campylobacter jejuni Strains Isolated from Humans,  Animals, Food, and the Environment in Brazil.	Genome Announcements	2018	6		e00250-18			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. 		
@D	Frederick, C.A.//Grable, J.//Melia, M.//Samudzi, C.//Jen-Jacobson, L.//Wang, B.-C.//Greene, P.//Boyer, H.W.//Rosenberg, J.M. 	Kinked DNA in crystalline complex with EcoRI endonuclease.	Nature	1984	309		327-331			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. 		
@D	Frederick, C.A.//Quigley, G.J.//van der Marel, G.A.//van Boom, J.H.//Wang, A.H.-J.//Rich, A. 	Methylation of the EcoRI recognition site does not alter DNA conformation:  The crystal structure of d(CGCGAm6ATTCGCG) at 2.0-A resolution.	J. Biol. Chem.	1988	263		17872-17879			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. 		
@D	Free, A.//Wakefield, R.I.//Smith, B.O.//Dryden, D.T.//Barlow, P.N.//Bird, A.P. 	DNA recognition by the methyl-CpG binding domain of MeCP2.	J. Biol. Chem.	2001	276		3353-3360			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. 		
@D	Freese, H.M. et al. 	Genome sequence of the phage-gene rich marine Phaeobacter arcticus type strain DSM 23566(T.).	Standards in Genomic Sciences	2013	8		450-464			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. 		
@D	Freese, H.M.//Methner, A.//Overmann, J. 	Adaptation of Surface-Associated Bacteria to the Open Ocean: A Genomically Distinct Subpopulation of Phaeobacter gallaeciensis Colonizes Pacific Mesozooplankton.	Front. Microbiol.	2017	8		1659			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. 		
@D	Freese, H.M.//Sikorski, J.//Bunk, B.//Scheuner, C.//Meier-Kolthoff, J.P.//Sproer, C.//Gram, L.//Overmann, J. 	Trajectories and Drivers of Genome Evolution in Surface-Associated Marine Phaeobacter.	Genome Biol. Evol.	2017	9		3297-3311			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. 		
@D	Freitag, M.//Selker, E.U. 	Controlling DNA methylation: many roads to one modification.	Curr. Opin. Genet. Dev.	2005	15		191-199			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? 		
@D	Freitag, M.//Williams, R.L.//Kothe, G.O.//Selker, E.U. 	A cytosine methyltransferase homologue is essential for repeat-induced point mutation in Neurospora crassa.	Proc. Natl. Acad. Sci. U. S. A.	2002	99		8802-8807			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. 		
@D	Freitas, A.C.//Hill, J.E. 	Draft Genome Sequences of Bifidobacterium Strains N4G05 and N5G01, Isolated from  the Human Vaginal Microbiome.	Genome Announcements	2018	6		e01433-17			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. 		
@D	French, C.T.//Sitaraman, R.//Dybvig, K. 	DNA inversions regulate a family of phase-variable restriction and modification enzymes in Mycoplasma pulmonis.	Abstr. Gen. Meet. Am. Soc. Microbiol.	1998	0		274-275			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. 		
@D	Fresco-Taboada, A.//Del Cerro, C.//Fernandez-Lucas, J.//Arroyo, M.//Acebal, C.//Garcia, J.L.//de la Mata, I. 	Genome of the Psychrophilic Bacterium Bacillus psychrosaccharolyticus, a Potential Source of 2'-Deoxyribosyltransferase for Industrial Nucleoside  Synthesis.	Genome Announcements	2013	1		e00309-13			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. 		
@D	Frey, B.//Kahle, C.//Zolch, C.//Kaluza, K.//Herz, G.//Lechner, M.//Auer, J.//Schmitz, G. 	Screening for novel class-II restriction endonucleases.	Fresenius Z. Anal. Chem.	1992	343		123-124			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. 		
@D	Frey, B.//Kaluza, K.//Auer, J.//Stratidakis, I.//Rina, M.//Bouriotis, V.//Schmitz, G. 	AspEI, a novel Eam11051 isoschizomer from Aureobacterium species recognizing 5'-GACnnn/nnGTC-3' .	Nucleic Acids Res.	1992	20		3782			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. 		
@D	Frey, K.G.//Bishop-Lilly, K.A.//Daligault, H.E.//Davenport, K.W.//Bruce, D.C.//Chain, P.S.//Coyne, S.R.//Chertkov, O.//Freitas, T.//Jaissle, J.//Koroleva, G.I.//Ladner, J.T.//Minogue, T.D.//Palacios, G.F.//Redden, C.L.//Xu, Y.//Johnson, S.L. 	Full-Genome Assembly of Reference Strain Providencia stuartii ATCC 33672.	Genome Announcements	2014	2		e01082-14			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. 		
@D	Freylikhman, O.//Kiselev, A.//Kazakov, S.//Sergushichev, A.//Panferova, Y.//Tokarevich, N.//Kostareva, A. 	Draft Genome Sequence of Coxiella burnetii Historical Strain Leningrad-2, Isolated from Blood of a Patient with Acute Q Fever in Saint Petersburg, Russia.	Genome Announcements	2018	6		e01464-17			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. 		
@D	Fricke, W.F.//Mammel, M.K.//McDermott, P.F.//Tartera, C.//White, D.G.//Leclerc, J.E.//Ravel, J.//Cebula, T.A. 	Comparative genomics of 28 Salmonella enterica isolates: evidence for CRISPR-mediated adaptive sublineage evolution.	J. Bacteriol.	2011	193		3556-3568			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. 		
@D	Fricke, W.F.//McDermott, P.F.//Mammel, M.K.//Zhao, S.//Johnson, T.J.//Rasko, D.A.//Fedorka-Cray, P.J.//Pedroso, A.//Whichard, J.M.//Leclerc, J.E.//White, D.G.//Cebula, T.A.//Ravel, J. 	Antimicrobial resistance-conferring plasmids with similarity to virulence plasmids from avian pathogenic Escherichia coli strains in Salmonella enterica serovar Kentucky isolates from poultry.	Appl. Environ. Microbiol.	2009	75		5963-5971			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. 		
@D	Fricke, W.F.//Seedorf, H.//Henne, A.//Kruer, M.//Liesegang, H.//Hedderich, R.//Gottschalk, G.//Thauer, R.K. 	The genome sequence of Methanosphaera stadtmanae reveals why this human intestinal archaeon is restricted to methanol and H2 for methane formation and ATP synthesis.	J. Bacteriol.	2006	188		642-658			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. 		
@D	Fridman, O.//Goldberg, A.//Ronin, I.//Shoresh, N.//Balaban, N.Q. 	Optimization of lag time underlies antibiotic tolerance in evolved bacterial populations.	Nature	2014	513		418-421			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. 		
@D	Friedhoff, P.//Franke, I.//Krause, K.L.//Pingoud, A. 	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.	FEBS Lett.	1999	443		209-214			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. 		
@D	Friedhoff, P.//Lurz, R.//Lueder, G.//Pingoud, A. 	Sau3AI, a monomeric type II restriction endonuclease that dimerizes on the DNA and thereby induces DNA loops.	J. Biol. Chem.	2001	276		23581-23588			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. 		
@D	Friedman, J.//Friedmann, A.//Razin, A. 	Studies on the biological role of DNA methylation:  III.  Role in excision of one-genome long single-stranded Phi X174 DNA.	Nucleic Acids Res.	1977	4		3483-3496			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. 		
@D	Friedman, J.//Razin, A. 	Studies on the biological role of DNA methylation.  II.  Role of Phi X174 DNA methylation in the process of viral progeny DNA synthesis.	Nucleic Acids Res.	1976	3		2665-2675			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. 		
@D	Friedman, S. 	The irreversible binding of Azacytosine-containing DNA fragments to bacterial DNA (cytosine-5)methyltransferases.	J. Biol. Chem.	1985	260		5698-5705			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. 		
@D	Friedman, S. 	The effect of 5-azacytidine on E. coli DNA methylase.	Biochem. Biophys. Res. Commun.	1979	89		1328-1333			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%. 		
@D	Friedman, S. 	The inhibition of DNA(Cytosine-5)methylases by 5-azacytidine:  The effect of azacytosine-containing DNA.	Mol. Pharmacol.	1981	19		314-320			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. 		
@D	Friedman, S. 	Adducts of the EcoRII methylase and 5-fluorocytosine-containing DNA.	Abstr. Gen. Meet. Am. Soc. Microbiol.	1991	91		A436			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. 		
@D	Friedman, S. 	Binding of the EcoRII methylase to azacytosine-containing DNA.	Nucleic Acids Res.	1986	14		4543-4556			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. 		
@D	Friedman, S.//Ansari, N. 	Binding of the EcoRII methyltransferase to 5-fluorocytosine-containing DNA.  Isolation of a bound peptide.	Nucleic Acids Res.	1992	20		3241-3248			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. 		
@D	Friedman, S.//Cheong, L.C. 	Effect of 5-azacytidine on deoxyribonucleic acid methylation in Escherichia coli K12.	Biochem. Pharmacol.	1984	33		2675-2679			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. 		
@D	Friedman, S.//Som, S. 	Induction of EcoRII methyltranserase:  Evidence for autogenous control.	J. Bacteriol.	1993	175		6293-6298			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. 		
@D	Friedman, S.//Som, S.//Yang, L.-F. 	The core element of the EcoRII methylase as defined by protease digestion and deletion analysis.	Nucleic Acids Res.	1991	19		5403-5408			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. 		
@D	Friedrich, T.//Fatemi, M.//Gowhar, H.//Leismann, O.//Jeltsch, A. 	Specificity of DNA binding and methylation by the M.FokI DNA methyltransferase.	Biochim. Biophys. Acta	2000	1480		145-159			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. 		
@D	Friedrich, T.//Roth, M.//Helm-Kruse, S.//Jeltsch, A. 	Functional mapping of the EcoRV DNA methyltransferase by random mutagenesis and screening for catalytically inactive mutants.	Biol. Chem.	1998	379		475-480			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. 		
@D	Friedrich, V.//Pabinger, S.//Chen, T.//Messner, P.//Dewhirst, F.E.//Schaffer, C. 	Draft Genome Sequence of Tannerella forsythia Type Strain ATCC 43037.	Genome Announcements	2015	3		e00660-15			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). 		
@D	Friend, P.L. 	Association of chloramphenicol resistance of group A streptococci with host-controlled restriction and modification of bacteriophages.	Can. J. Microbiol.	1971	17		1573-1576			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. 		
@D	Friis, C.//Wassenaar, T.M.//Javed, M.A.//Snipen, L.//Lagesen, K.//Hallin, P.F.//Newell, D.G.//Toszeghy, M.//Ridley, A.//Manning, G.//Ussery, D.W. 	Genomic Characterization of Campylobacter jejuni Strain M1.	PLoS ONE	2010	5		e12253			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. 		
@D	Frindte, K. et al. 	Draft Genome Sequences of Two Gammaproteobacterial Methanotrophs Isolated from Rice Ecosystems.	Genome Announcements	2017	5		e00526-17			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. 		
@D	Frink, S.//Morales, C.//Kiang, D. 	Draft Whole-Genome Sequences of Salmonella enterica subsp. enterica Serovars Enteritidis, Veneziana, and Salford, Isolated from Herbs.	Genome Announcements	2016	4		e00134-16			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. 		
@D	Fritsch, A.//Tiollais, P.//Buc, H. 	Preparative purification of lambda-DNA fragments obtained after EcoRI digestion.	FEBS Lett.	1975	52		121-126			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. 		
@D	Fritsche, P.//Alves, J. 	A monomeric mutant of restriction endonuclease EcoRI nicks DNA without sequence specificity.	Biol. Chem.	2004	385		975-985			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. 		
@D	Fritz, A.//Kuster, W.//Alves, J. 	Asn141 is essential for DNA recognition by EcoRI restriction endonuclease.	FEBS Lett.	1998	438		66-70			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. 		
@D	Fritz, E.//Miller, M.J. 	Draft Genome Sequence of the Murine Bacterial Isolate Lactobacillus murinus EF-1.	Genome Announcements	2017	5		e00077-17			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. 		
@D	Fritzenwanker, M.//Chakraborty, A.//Hain, T.//Zimmermann, K.//Domann, E. 	Draft Genome Sequences of the Probiotic Enterococcus faecalis Symbioflor 1 Clones DSM16430 and DSM16434.	Genome Announcements	2016	4		e01061-16			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. 		
@D	Fritzenwanker, M.//Hain, T.//Kesper, D.A.//Harb, H.//Renz, H.//Domann, E. 	Draft Genome Sequence and Complete Plasmid Sequence of Acinetobacter lwoffii F78, an Isolate with Strong Allergy-Protective Properties.	Genome Announcements	2016	4		e00685-16			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. 		
@D	Fritzenwanker, M.//Kuenne, C.//Billion, A.//Hain, T.//Zimmermann, K.//Goesmann, A.//Chakraborty, T.//Domann, E. 	Complete Genome Sequence of the Probiotic Enterococcus faecalis Symbioflor 1 Clone DSM 16431.	Genome Announcements	2013	1		e00165-12			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. 		
@D	Froman, B.E.//Tait, R.C.//Kado, C.I.//Rodriguez, R.L. 	Purification of restriction endonuclease XcyI from Xanthomonas cyanopsidis.	Gene	1984	28		331-335			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. 		
@D	Frommer, M.//McDonald, L.E.//Millar, D.S.//Collis, C.M.//Watt, F.//Grigg, G.W.//Molloy, P.L.//Paul, C.L. 	A genomic sequencing protocol that yields a positive display of 5-methylcytosine residues in individual DNA strands.	Proc. Natl. Acad. Sci. U. S. A.	1992	89		1827-1831			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. 		
@D	Froseth, B.R.//Harlander, S.K.//McKay, L.L. 	Plasmid-mediated reduced phage sensitivity in Streptococcus lactis KR5.	J. Dairy Sci.	1988	71		275-284			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. 		
@D	Frostesjo, L.//Holm, I.//Grahn, B.//Page, A.W.//Bestor, T.H.//Heby, O. 	Interference with DNA methyltransferase activity and genome methylation during F9 teratocarcinoma stem cell differentiation induced by polyamine depletion.	J. Biol. Chem.	1997	272		4359-4366			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. 		
@D	Fry, P.R.//Calcutt, M.J.//Foecking, M.F.//Hsieh, H.Y.//Suntrup, D.G.//Perry, J.//Stewart, G.C.//Middleton, J.R. 	Draft Genome Sequence of Staphylococcus chromogenes Strain MU 970, Isolated from  a Case of Chronic Bovine Mastitis.	Genome Announcements	2014	2		e00835-14			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. 		
@D	Fsihi, H.//Vincent, V.//Cole, S.T. 	Homing events in the gyrA gene of some mycobacteria.	Proc. Natl. Acad. Sci. U. S. A.	1996	93		3410-3415			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. 		
@D	Fu, A.Q.//Genereux, D.P.//Stoger, R.//Burden, A.F.//Laird, C.D.//Stephens, M. 	Statistical Inference of In Vivo Properties of Human DNA Methyltransferases from Double-Stranded Methylation Patterns.	PLoS ONE	2012	7		e32225			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. 		
@D	Fu, B.//Chen, Q.//Wei, M.//Zhu, J.//Zou, L.//Li, G.//Wang, L. 	Complete Genome Sequence of Xanthomonas arboricola pv. juglandis Strain DW3F3, Isolated from a Juglans regia L. Bacterial Blighted Fruitlet.	Genome Announcements	2018	6		e00023-18			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). 		
@D	Fu, Y.//Wang, R.//Zhang, Z.//Jiao, N. 	Complete Genome Sequence of the d-Amino Acid Catabolism Bacterium Phaeobacter sp. Strain JL2886, Isolated from Deep Seawater of the South China Sea.	Genome Announcements	2016	4		e00913-16			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. 		
@D	Fu, Y.//Wu, Y.//Yuan, Y.//Gao, M. 	Complete Genome Sequence of Bacillus thuringiensis Serovar rongseni Reference Strain SCG04-02, a Strain Toxic to Plutella xylostella.	Genome Announcements	2017	5		e00691-17			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. 		
@D	Fu, Z.//Xiao, R.//Luo, R.//Hu, Z.//Yang, H.//Guo, Z.//Lei, P.//Shan, S. 	Draft Genome Sequence of Bacillus thuringiensis subsp. aizawai HD133.	Genome Announcements	2017	5		e00909-17			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. 		
@D	Fuchs, B.M.//Spring, S.//Teeling, H.//Quast, C.//Wulf, J.//Schattenhofer, M.//Yan, S.//Ferriera, S.//Johnson, J.//Glockner, F.O.//Amann, R. 	Characterization of a marine gammaproteobacterium capable of aerobic anoxygenic photosynthesis.	Proc. Natl. Acad. Sci. U. S. A.	2007	104		2891-2896			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. 		
@D	Fuchs, C.//Rosenvold, E.//Honigman, A.//Szybalski, W. 	Identification of palindromic sequences recognized by restriction endonucleases, as based on the tabularized sequencing data for seven viral and plasmid DNAs.	Gene	1980	10		357-370			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. 		
@D	Fuchs, C.//Rosenvold, E.C.//Honigman, A.//Szybalski, W. 	A simple method for identifying the palindromic sequences recognized by restriction endonucleases: the nucleotide sequence of the AvaII site.	Gene	1978	4		1-23			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. 		
@D	Fuchs, L.Y.//Covarrubias, L.//Escalante, L.//Sanchez, S.//Bolivar, F. 	Characterization of a site-specific restriction endonuclease SphI from Streptomyces phaeochromogenes.	Gene	1980	10		39-46			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. 		
@D	Fuchs, R.//Blakesley, R. 	Guide to the Use of Type II Restriction  Endonucleases.	Methods Enzymol.	1983	100		3-38			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. 		
@A	Fuchs, R.//Kane, J.F. 		Expression of the genes for the Pst restriction-modification enzymes after cloning into a temperature-sensitive replication plasmid.			Ahmad, F.//Schultz, J.//Smith, E.E.//Whelan, W.J. 		Miami BioTechnology Winter Symposium					Academic Press	1982		19		523									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. 		
@D	Fuchu, G.//Ohtsubo, Y.//Ito, M.//Miyazaki, R.//Ono, A.//Nagata, Y.//Tsuda, M. 	Insertion sequence-based cassette PCR: cultivation-independent isolation of gamma-hexachlorocyclohexane-degrading genes from soil DNA.	Appl. Microbiol. Biotechnol.	2008	79		627-632			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. 		
@D	Fucik, V.//Grunnerova, H.//Zadrazil, S. 	Restriction and modification in Bacillus subtilis 168: Regulation of hsrM(nonB) expression in spoOA mutants and effects on permissiveness for Phi15 and Phi105 phages.	Mol. Gen. Genet.	1982	186		118-121			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. 		
@D	Fuentes-Valdes, J.J.//Plominsky, A.M.//Allen, E.E.//Tamames, J.//Vasquez, M. 	Complete Genome Sequence of a Cylindrospermopsin-Producing Cyanobacterium, Cylindrospermopsis raciborskii CS505, Containing a Circular Chromosome and a  Single Extrachromosomal Element.	Genome Announcements	2016	4		e00823-16			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. 		
@D	Fuentes-Valdes, J.J.//Soto-Liebe, K.//Perez-Pantoja, D.//Tamames, J.//Belmar, L.//Pedros-Alio, C.//Garrido, D.//Vasquez, M. 	Draft genome sequences of Cylindrospermopsis raciborskii strains CS-508 and MVCC14, isolated from freshwater bloom events in Australia and Uruguay.	Standards in Genomic Sciences	2018	13		26			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. 		
@D	Fuerst, C.R. 	Plating efficiencies of modified lambda-bio particles on temperature-sensitive hsd mutants of Escherichia coli K12.	Virology	1985	143		352-356			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. 		
@D	Fuglsang, A. 	Distribution of potential type II restriction sites (palindromes) in prokaryotes.	Biochem. Biophys. Res. Commun.	2003	310		280-285			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. 		
@D	Fujihara, H.//Yamazoe, A.//Hosoyama, A.//Suenaga, H.//Kimura, N.//Hirose, J.//Watanabe, T.//Futagami, T.//Goto, M.//Furukawa, K. 	Draft Genome Sequence of Pseudomonas aeruginosa KF702 (NBRC 110665), a Polychlorinated Biphenyl-Degrading Bacterium Isolated from Biphenyl-Contaminated   Soil.	Genome Announcements	2015	3		e00517-15			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. 		
@D	Fujihara, H.//Yamazoe, A.//Hosoyama, A.//Suenaga, H.//Kimura, N.//Hirose, J.//Watanabe, T.//Futagami, T.//Goto, M.//Furukawa, K. 	Draft Genome Sequence of Pseudomonas abietaniphila KF701 (NBRC110664), a Polychlorinated Biphenyl-Degrading Bacterium Isolated from Biphenyl-Contaminated   Soil.	Genome Announcements	2015	3		e00473-15			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. 		
@D	Fujihara, Y.//Miyasako, H.//Kato, K.//Hayashi, T.//Toraya, T. 	Molecular Cloning, Expression, and Characterization of Starfish DNA (Cytosine-5)-methyltransferases.	Biosci. Biotechnol. Biochem.	2012	76		1661-1671			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. 		
@D	Fujii, T.//Koike, H.//Sawayama, S.//Yano, S.//Inoue, H. 	Draft Genome Sequence of Talaromyces cellulolyticus Strain Y-94, a Source of Lignocellulosic Biomass-Degrading Enzymes.	Genome Announcements	2015	3		e00014-15			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. 		
@D	Fujii, T.//Tomita, Y.//Ikushima, S.//Horie, A.//Fujiwara, D. 	Draft Genome Sequence of Lactococcus lactis subsp. lactis JCM 5805T, a Strain That Induces Plasmacytoid Dendritic Cell Activation.	Genome Announcements	2015	3		e00113-15			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. 		
@D	Fujii, Y.//Toh, H.//Matsubara, T.//Tomida, S.//Nguyen, C.T.//Mimura, I.//Nakamura, S.//Morita, H. 	Draft Genome Sequence of Probiotic Lactobacillus acidophilus Strain L-55 Isolated from a Healthy Human Gut.	Genome Announcements	2016	4		e01357-16			Probiotic Lactobacillus acidophilus L-55 was isolated from a healthy human gut. Here, we report the draft genome sequence of this organism. 		
@D	Fujimoto, D.//Srinivasan, P.R.//Borek, E. 	On the nature of the deoxyribonucleic acid methylases.  Biological evidence for the multiple nature of the enzymes.	Biochemistry	1965	4		2849-2855			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. 		
@D	Fujimoto, K.//Iida, H.//Kawakami, M.//Bando, T.//Tao, Z.-F.//Sugiyama, H. 	Sequence-specific protection of plasmid DNA from restriction endonuclease hydrolysis by pyrrole-imidazole-cyclopropapyrroloindole conjugates.	Nucleic Acids Res.	2002	30		3748-3753			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. 		
@D	Fujimoto, R.//Sasaki, T.//Nishio, T. 	Characterization of DNA methyltransferase genes in Brassica rapa.	Genes Genet. Syst.	2006	81		235-242			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. 		
@D	Fujimoto, R.//Sasaki, T.//Nishio, T. 	Characterization of DNA methyltransferase genes in Brassica rapa.	Plant Cell Physiol.	2006	47		S238			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. 		
@D	Fujinami, S.//Oikawa, Y.//Araki, T.//Shinmura, Y.//Midorikawa, R.//Ishizaka, H.//Kato, C.//Horikoshi, K.//Ito, M.//Tamegai, H. 	Genome Sequence of the Deep-Sea Denitrifier Pseudomonas sp. Strain MT-1, Isolated from the Mariana Trench.	Genome Announcements	2014	2		e01313-14			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. 		
@D	Fujinami, S.//Takarada, H.//Kasai, H.//Sekine, M.//Omata, S.//Harada, T.//Fukai, R.//Hosoyama, A.//Horikawa, H.//Kato, Y.//Nakazawa, H.//Fujita, N. 	Complete genome sequence of Ilumatobacter coccineum YM16-304(T.).	Standards in Genomic Sciences	2013	8		430-440			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. 		
@D	Fujinami, S.//Takeda, K.//Onodera, T.//Satoh, K.//Sano, M.//Narumi, I.//Ito, M. 	Draft Genome Sequence of Potassium-Dependent Alkaliphilic Bacillus sp. Strain TS-2, Isolated from a Jumping Spider.	Genome Announcements	2014	2		e00458-14			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. 		
@D	Fujinami, S.//Takeda, K.//Onodera, T.//Satoh, K.//Sano, M.//Narumi, I.//Ito, M. 	Draft Genome Sequence of Sodium-Independent Alkaliphilic Microbacterium sp. Strain TS-1.	Genome Announcements	2013	1		e01043-13			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. 		
@D	Fujinami, S.//Takeda-Yano, K.//Onodera, T.//Satoh, K.//Sano, M.//Takahashi, Y.//Narumi, I.//Ito, M. 	Draft Genome Sequence of Calcium-Dependent Paenibacillus sp. Strain TCA20, Isolated from a Hot Spring Containing a High Concentration of Calcium Ions.	Genome Announcements	2014	2		e00866-14			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. 		
@D	Fujinami, S.//Takeda-Yano, K.//Onodera, T.//Satoh, K.//Shimizu, T.//Wakabayashi, Y.//Narumi, I.//Nakamura, A.//Ito, M. 	Draft Genome Sequence of Methylobacterium sp. ME121, Isolated from Soil as a Mixed Single Colony with Kaistia sp. 32K.	Genome Announcements	2015	3		e01005-15			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. 		
@D	Fujino, Y.//Nagayoshi, Y.//Ohshima, T.//Ogata, S.//Doi, K. 	Complete Genome Sequence of Thermus thermophilus TMY, Isolated from a Geothermal  Power Plant.	Genome Announcements	2017	5		e01596-16			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. 		
@D	Fujisawa, H.//Yonesaki, T.//Minagawa, T. 	Sequence of the T4 recombination gene, uvsX, and its comparison with that of the recA gene of Escherichia coli.	Nucleic Acids Res.	1985	13		7473-7481			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. 		
@D	Fujisawa, T. et al. 	Genomic Structure of an Economically Important Cyanobacterium, Arthrospira (Spirulina) platensis NIES-39.	DNA Res.	2010	17		85-103			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. 		
@D	Fujiwara, Y.//Takai, K.//Uematsu, K.//Tsuchida, S.//Hunt, J.C.//Hashimoto, J. 	Phylogenetic characterization of endosymbionts in three hydrothermal vent mussels: influence on host distributions.	Mar. Ecol. Prog. Ser.	2000	208		147-155					
@D	Fukano, H.//Yoshida, M.//Katayama, Y.//Omatsu, T.//Mizutani, T.//Kurata, O.//Wada, S.//Hoshino, Y. 	Complete Genome Sequence of Mycobacterium stephanolepidis.	Genome Announcements	2017	5		e00810-17			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. 		
@D	Fukano, H.//Yoshida, M.//Shimizu, A.//Iwao, H.//Katayama, Y.//Omatsu, T.//Mizutani, T.//Kurata, O.//Wada, S.//Hoshino, Y. 	Draft Genome Sequence of Mycobacterium montefiorense Isolated from Japanese Black Salamander (Hynobius nigrescens).	Genome Announcements	2018	6		e00448-18			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. 		
@D	Fukao, M.//Oshima, K.//Morita, H.//Toh, H.//Suda, W.//Kim, S.W.//Suzuki, S.//Yakabe, T.//Hattori, M.//Yajima, N. 	Genomic Analysis by Deep Sequencing of the Probiotic Lactobacillus brevis KB290 Harboring Nine Plasmids Reveals Genomic Stability.	PLoS ONE	2013	8		e60521			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. 		
@D	Fuks, F.//Burgers, W.A.//Brehm, A.//Hughes-Davies, L.//Kouzarides, T. 	DNA methyltransferase Dnmt1 associates with histone deacetylase activity.	Nat. Genet.	2000	24		88-91			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. 		
@D	Fuks, F.//Burgers, W.A.//Godin, N.//Kasai, M.//Kouzarides, T. 	Dnmt3a binds deacetylases and is recruited by a sequence-specific repressor to silence transcription.	EMBO J.	2001	20		2536-2544			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. 		
@D	Fukuda, E.//Kaminska, K.H.//Bujnicki, J.M.//Kobayashi, I. 	Cell death upon epigenetic genome methylation: a novel function of methyl-specific deoxyribonucleases.	Genome Biology	2008	9		R163			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. 		
@D	Fukuda, E.//Kobayashi, I. 	Suicidal defense against an epigenetic system: a role for a Type IV methyl-dependent restriction enzyme.	Genes Genet. Syst.	2006	81		408			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. 		
@D	Fukuda, K.//Hosoyama, A.//Tsuchikane, K.//Ohji, S.//Yamazoe, A.//Fujita, N.//Shintani, M.//Kimbara, K. 	Complete Genome Sequence of Polychlorinated Biphenyl Degrader Comamonas testosteroni TK102 (NBRC 109938).	Genome Announcements	2014	2		e00865-14			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. 		
@D	Fukuda, S.//Toh, H.//Hase, K.//Oshima, K.//Nakanishi, Y.//Yoshimura, K.//Tobe, T.//Clarke, J.M.//Topping, D.L.//Suzuki, T.//Taylor, T.D.//Itoh, K.//Kikuchi, J.//Morita, H.//Hattori, M.//Ohno, H. 	Bifidobacteria can protect from enteropathogenic infection through production of acetate.	Nature	2011	469		543-547			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. 		
@D	Fukuda, T.//Nogami, S.//Ohya, Y. 	VDE-initiated intein homing in Saccharomyces cerevisiae proceeds in a meiotic recombination-like manner.	Genes Cells	2003	8		587-602			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. 		
@D	Fukuda, T.//Ohta, K.//Ohya, Y. 	Investigation of the mechanism of meiotic DNA cleavage by VMA1-derived endonuclease uncovers a meiotic alteration in chromatin structure  around the target site.	Euk. Cell	2006	5		981-990			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. 		
@D	Fukuda, T.//Ohta, K.//Ohya, Y. 	Strategies of VDE for propagation in yeast nuclear genome.	Genes Genet. Syst.	2005	80		438			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. 		
@D	Fukui, T.//Atomi, H.//Kanai, T.//Matsumi, R.//Fujiwara, S.//Imanaka, T. 	Complete genome sequence of the hyperthermophilic archaeon Thermococcus kodakaraensis KOD1 and comparison with Pyrococcus genomes.	Genome Res.	2005	15		352-363			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. 		
@D	Fukushima, J.//Tojo, F.//Asano, R.//Kobayashi, Y.//Shimura, Y.//Okano, K.//Miyata, N. 	Complete Genome Sequence of the Unclassified Iron-Oxidizing, Chemolithoautotrophic Burkholderiales Bacterium GJ-E10, Isolated from an Acidic  River.	Genome Announcements	2015	3		e01455-14			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. 		
@D	Fukuyama, Y.//Oguro, T.//Omae, K.//Yoneda, Y.//Yoshida, T.//Sako, Y. 	Draft Genome Sequences of Two Hydrogenogenic Carboxydotrophic Bacteria, Carboxydocella sp. Strains JDF658 and ULO1, Isolated from Two Distinct Volcanic  Fronts in Japan.	Genome Announcements	2017	5		e00242-17			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%). 		
@D	Fukuyama, Y.//Omae, K.//Yoneda, Y.//Yoshida, T.//Sako, Y. 	Draft Genome Sequences of Carboxydothermus pertinax and C. islandicus, Hydrogenogenic Carboxydotrophic Bacteria.	Genome Announcements	2017	5		e01648-16			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%). 		
@D	Fukuyo, M.//Nakano, T.//Zhang, Y.//Furuta, Y.//Ishikawa, K.//Watanabe-Matsui, M.//Yano, H.//Hamakawa, T.//Ide, H.//Kobayashi, I. 	Restriction-modification system with methyl-inhibited base excision and abasic-site cleavage activities.	Nucleic Acids Res.	2015	43		2841-2852			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. 		
@D	Fuller-Pace, F.V.//Bullas, L.R.//Delius, H.//Murray, N.E. 	Genetic recombination can generate altered restriction specificity.	Proc. Natl. Acad. Sci. U. S. A.	1984	81		6095-6099			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. 		
@D	Fuller-Pace, F.V.//Cowan, G.M.//Murray, N.E. 	EcoA and EcoE:  Alternatives to the EcoK Family of Type I Restriction and Modification Systems of Escherichia coli.	J. Mol. Biol.	1985	186		65-75			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. 		
@D	Fuller-Pace, F.V.//Murray, N.E. 	Two DNA recognition domains of the specificity polypeptides of a family of type I restriction enzymes.	Proc. Natl. Acad. Sci. U. S. A.	1986	83		9368-9372			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. 		
@D	Fullerton, H.//Hager, K.W.//Moyer, C.L. 	Draft Genome Sequence of Mariprofundus ferrooxydans Strain JV-1, Isolated from Loihi Seamount, Hawaii.	Genome Announcements	2015	3		e01118-15			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. 		
@D	Fung, W.T. 	Functional analysis of the two subunits of DNA methyltransferase EcoHK31I.	Ph.D. Thesis, Chinese Univ. of Hong Kong, China	2006			1-224			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. 		
@D	Fung, W.T.//Sze, K.H.//Lee, K.F.//Shaw, P.C. 	Functional studies of the small subunit of EcoHK31I DNA methyltransferase.	Biol. Chem.	2006	387		507-513			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. 		
@D	Funo, K.//Kitagawa, W.//Tanaka, M.//Sone, T.//Asano, K.//Kamagata, Y. 	Draft Genome Sequence of Tomitella biformata AHU 1821T, Isolated from a Permafrost Ice Wedge in Alaska.	Genome Announcements	2014	2		e00066-14			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. 		
@D	Furmanczyk, E.M.//Kaminski, M.A.//Dziembowski, A.//Lipinski, L.//Sobczak, A. 	Draft Genome Sequence of the Type Strain Pseudomonas umsongensis DSM 16611.	Genome Announcements	2017	5		e01038-17			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%. 		
@D	Furmanczyk, E.M.//Kaminski, M.A.//Dziembowski, A.//Lipinski, L.//Sobczak, A. 	Draft Genome Sequence of the Type Strain Pseudomonas jessenii DSM 17150.	Genome Announcements	2017	5		e01035-17			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%. 		
@D	Furmanek, B.//Gromek, K.//Sektas, M.//Kaczorowski, T. 	Isolation and characterization of type IIS restriction endonuclease from Neisseria cuniculi ATCC 14688.	FEMS Microbiol. Lett.	2001	196		171-176			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. 		
@D	Furmanek, B.//Sektas, M.//Wons, E.//Kaczorowski, T. 	Molecular characterization of the DNA methyltransferase M1.NcuI from Neisseria cuniculi ATCC 14688.	Res. Microbiol.	2007	158		164-174			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. 		
@D	Furmanek-Blaszk, B. 	Phenotypic and molecular characteristics of an Aeromonas hydrophila strain isolated from the River Nile.	Microbiol. Res.	2014	169		547-552			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. 		
@D	Furmanek-Blaszk, B.//Boratynski, R.//Zolcinska, N.//Sektas, M. 	M1.Mboll and M2.Mboll type IIS methyltransferases: different specificities, the same target.	Microbiology	2009	155		1111-1121			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. 		
@D	Furmanek-Blaszk, B.//Sektas, M. 	The SfaNI restriction-modification system from Enterococcus faecalis NEB215 is located on a putative mobile genetic element.	FEMS Microbiol. Lett.	2015	362		fnv028			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. 		
@D	Fursova, K.K.//Artem'eva, O.A.//Nikanova, D.A.//Larin, A.K.//Zinovieva, N.A.//Brovko, F.A. 	Draft Genome Sequences of Five Staphylococcus aureus Strains Isolated from Clinically Healthy Cows in the Russian Federation.	Genome Announcements	2018	6		e00275-18			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. 		
@D	Furuta, Y. 	[Diversity in genome and epigenome of Helicobacter pylori].	Nihon Saikingaku Zasshi	2015	70		383-389			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. 		
@D	Furuta, Y.//Abe, K.//Kobayashi, I. 	Genome comparison and context analysis reveals putative mobile forms of restriction-modification systems and related rearrangements.	Nucleic Acids Res.	2010	38		2428-2443			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. 		
@D	Furuta, Y.//Abe, K.//Kobayashi, I. 	Search for genomic rearrangements related to restriction-modification systems through genome comparison.	Genes Genet. Syst.	2009	84		441			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. 		
@D	Furuta, Y.//Kawai, M.//Uchiyama, I.//Kobayashi, I. 	Domain Movement within a Gene: A Novel Evolutionary Mechanism for Protein Diversification.	PLoS ONE	2011	6		e18819			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. 		
@D	Furuta, Y.//Kobayashi, I. 	Movement of DNA sequence recognition domains between non-orthologous proteins.	Nucleic Acids Res.	2012	40		9218-9232			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. 		
@D	Furuta, Y.//Kobayashi, I. 	Mobility of DNA sequence recognition domains in DNA methyltransferases suggests epigenetics-driven adaptive evolution.	Mobile Genet. Elements	2012	2		292-296			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. 		
@A	Furuta, Y.//Kobayashi, I. 		Restriction-modification systems as mobile epigenetic elements.			Roberts, A.P.//Mullany, P. 		Bacterial Integrative Mobile Genetic Elements				Austin, TX	Landes Bioscience	2011				85-103									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. 		
@D	Furuta, Y.//Konno, M.//Osaki, T.//Yonezawa, H.//Ishige, T.//Imai, M.//Shiwa, Y.//Shibata-Hatta, M.//Kanesaki, Y.//Yoshikawa, H.//Kamiya, S.//Kobayashi, I. 	Microevolution of Virulence-Related Genes in Helicobacter pylori Familial Infection.	PLoS ONE	2015	10		e0127197			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. 		
@D	Furuta, Y.//Namba, H.//Shibata, T.//Nishiyama, T.//Shigenobu, S.//Suzuki, Y.//Sugano, S.//Hasebe, M.//Kobayashi, I. 	Methylome diversification through changes in the sequence specificity of DNA methyltransferases.	Genes Genet. Syst.	2013	88		347			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. 		
@D	Furuta, Y.//Namba-Fukuyo, H.//Shibata, T.F.//Nishiyama, T.//Shigenobu, S.//Suzuki, Y.//Sugano, S.//Hasebe, M.//Kobayashi, I. 	Methylome Diversification through Changes in DNA Methyltransferase Sequence Specificity.	PLoS Genet.	2014	10		e1004272			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. 		
@D	Futterer, O.//Angelov, A.//Liesegang, H.//Gottschalk, G.//Schleper, C.//Schepers, B.//Dock, C.//Antranikian, G.//Liebl, W. 	Genome sequence of Picrophilus torridus and its implications for life around pH 0.	Proc. Natl. Acad. Sci. U. S. A.	2004	101		9091-9096			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. 		
@D	Fuxreiter, M.//Osman, R. 	Probing the general base catalysis in the first step of BamHI action by computer simulations.	Biochemistry	2001	40		15017-15023			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. 		
@D	Fuxreiter, M.//Osman, R.//Simon, I. 	Computational approaches to restriction endonucleases.	Theochem.	2003	666-7		469-479			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. 		
@D	Fuxreiter, M.//Simon, I. 	Protein stability indicates divergent evolution of PD-(D/E)XK type II restriction endonucleases.	Protein Sci.	2002	11		1978-1983			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. 		
@D	Gaba, S.//Singh, R.N.//Abrol, S.//Yadav, A.N.//Saxena, A.K.//Kaushik, R. 	Draft Genome Sequence of Halolamina pelagica CDK2 Isolated from Natural Salterns  from Rann of Kutch, Gujarat, India.	Genome Announcements	2017	5		e01593-16			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. 		
@D	Gabbara, S.//Bhagwat, A.S. 	The mechanism of inhibition of DNA (cytosine-5-)-methyltransferases by 5-azacytosine is likely to involve methyl transfer to the inhibitor.	Biochem. J.	1995	307		87-92			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. 		
@D	Gabbara, S.//Bhagwat, A.S. 	Interaction of EcoRII endonuclease with DNA substrates containing single recognition sites.	J. Biol. Chem.	1992	267		18623-18630			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. 		
@D	Gabbara, S.//Sheluho, D.//Bhagwat, A.S. 	Cytosine methyltransferase from Escherichia coli in which active site cysteine is replaced with serine is partially active.	Biochemistry	1995	34		8914-8923			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. 		
@D	Gabbara, S.//Wyszynski, M.//Bhagwat, A.S. 	A DNA repair process in Escherichia coli corrects U:G and T:G mismatches to C:G at sites of cytosine methylation.	Mol. Gen. Genet.	1994	243		244-248			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. 		
@D	Gabbara, S.S. 	Molecular mechanism and mutagenic effects of DNA 5-cytosine methyltransferases.	Diss. Abstr.	1994	55		403B-404B			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. 		
@D	Gabed, N.//Yang, M.//Bey, B.H.M.//Drici, H.//Gross, R.//Dandekar, T.//Liang, C. 	Draft Genome Sequence of the Moderately Heat-Tolerant Lactococcus lactis subsp. lactis bv. diacetylactis Strain GL2 from Algerian Dromedary Milk.	Genome Announcements	2015	3		e01334-15			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. 		
@D	Gaboyer, F.//Maignien, L.//Jebbar, M.//Alain, K. 	Draft Genome of Halomonas lionensis RHS90T, a Stress-Tolerant Gammaproteobacterium Isolated from Mediterranean Sea Sediments.	Genome Announcements	2017	5		e00311-17			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. 		
@D	Gaboyer, F.//Maignien, L.//Jebbar, M.//Alain, K. 	Draft Genome Sequence of Phaeobacter leonis Type Strain 306, an Alphaproteobacterium Isolated from Mediterranean Sea Sediments.	Genome Announcements	2017	5		e00312-17			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. 		
@D	Gabrielsen, C.//Brede, D.A.//Hernandez, P.E.//Nes, I.F.//Diep, D.B. 	Genome Sequence of the Bacteriocin-Producing Strain Lactococcus garvieae DCC43.	J. Bacteriol.	2012	194		6976-6977			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. 		
@D	Gabrielsen, C.//Drablos, F.//Afset, J.E. 	Genome Sequences of 11 Shiga Toxin-Producing Escherichia coli Strains.	Genome Announcements	2015	3		e00418-15			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. 		
@D	Gabris, C.//Poehlein, A.//Bengelsdorf, F.R.//Daniel, R.//Durre, P. 	Genome Sequence of Enterococcus faecalis Strain CG_E.	Genome Announcements	2017	5		e01488-16			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. 		
@D	Gabris, C.//Poehlein, A.//Bengelsdorf, F.R.//Daniel, R.//Durre, P. 	Genome Sequence of Lactobacillus sunkii Strain CG_D.	Genome Announcements	2017	5		e01487-16			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. 		
@D	Gabs, S.//Josephsen, J. 	Improvement of phage defence in Lactococcus lactis by introduction of the plasmid encoded restriction and modification system LlaAI.	Lett. Appl. Microbiol.	2003	36		332-336			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. 		
@D	Gabsalilow, L.//Schierling, B.//Friedhoff, P.//Pingoud, A.//Wende, W. 	Site- and strand-specific nicking of DNA by fusion proteins derived from MutH and I-SceI or TALE repeats.	Nucleic Acids Res.	2013	41		e83			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. 		
@D	Gachechiladze, K.K.//Balardshishvili, N.S.//Adamia, R.S.//Chanishvili, T.G.//Kruger, D.H. 	Host-controlled modification and restriction as a criterion of evaluating the therapeutical potential of Pseudomonas phage.	J. Basic Microbiol.	1991	31		101-106			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. 		
@D	Gado, I.//Laszlo, V.G.//Negy, B.//Milch, H.//Drin, I.//Awad-Masalmeh, M.//Horvath, J. 	Phage restriction and the presence of small plasmids in Salmonella enteritidis.	Zentralbl. Bakteriol.	1998	287		509-519			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). 		
@D	Gaechter, T.//Wunderlin, C.//Schmidheini, T.//Solioz, M. 	Genome Sequence of Enterococcus hirae (Streptococcus faecalis) ATCC 9790, a Model Organism for the Study of Ion Transport, Bioenergetics, and Copper Homeostasis.	J. Bacteriol.	2012	194		5126-5127			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. 		
@D	Gagnevin, L.//Bolot, S.//Gordon, J.L.//Pruvost, O.//Verniere, C.//Robene, I.//Arlat, M.//Noel, L.D.//Carrere, S.//Jacques, M.A.//Koebnik, R. 	Draft Genome Sequence of Xanthomonas axonopodis pv. allii Strain CFBP 6369.	Genome Announcements	2014	2		e00727-14			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%. 		
@D	Gai, Z.//Wang, X.//Liu, X.//Tai, C.//Tang, H.//He, X.//Wu, G.//Deng, Z.//Xu, P. 	The genes coding for the conversion of carbazole to catechol are flanked by IS6100 elements in Sphingomonas sp. strain XLDN2-5.	PLoS ONE	2010	5		E10018			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. 		
@D	Gai, Z.//Wang, X.//Tang, H.//Tai, C.//Tao, F.//Wu, G.//Xu, P. 	Genome Sequence of Sphingobium yanoikuyae XLDN2-5, an Efficient Carbazole-Degrading Strain.	J. Bacteriol.	2011	193		6404-6405			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. 		
@D	Gai, Z.//Wang, X.//Zhang, X.//Su, F.//Wang, X.//Tang, H.//Tai, C.//Tao, F.//Ma, C.//Xu, P. 	Genome Sequence of Sphingomonas elodea ATCC 31461, a Highly Productive Industrial Strain of Gellan Gum.	J. Bacteriol.	2011	193		7015-7016			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. 		
@D	Gai, Z.//Zhang, Z.//Wang, X.//Tao, F.//Tang, H.//Xu, P. 	Genome Sequence of Pseudomonas aeruginosa DQ8, an Efficient Degrader of n-Alkanes and Polycyclic Aromatic Hydrocarbons.	J. Bacteriol.	2012	194		6304-6305			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. 		
@D	Gaido, M.L. 	Purification of BsuE methylase to investigate the role of DNA methylation in rat growth hormone gene expression.	Diss. Abstr.	1988	48		2876B			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. 		
@D	Gaido, M.L.//Prostko, C.R.//Strobl, J.S. 	Isolation and characterization of BsuE methyltransferase, a CGCG specific DNA methyltransferase from Bacillus subtilis.	J. Biol. Chem.	1988	263		4832-4836			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. 		
@D	Gaido, M.L.//Strobl, J.S. 	Methylation sensitivity of the restriction enzymes FnuDII and AccII.	Arch. Microbiol.	1987	46		338-340			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. 		
@D	Gaiero, J.R.//Formusa, P.A.//Hsiang, T.//Nicol, R.W.//Habash, M. 	Draft Genome Sequence of Ureolytic Environmental Isolate Bacillus galactosidilyticus PL133.	Genome Announcements	2016	4		e01067-16			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. 		
@D	Gaiero, J.R.//Hsiang, T.//Nicol, R.W.//Habash, M. 	Draft Genome Sequence of Ureolytic Environmental Isolate Staphylococcus sp. NA309.	Genome Announcements	2016	4		e01066-16			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. 		
@D	Gaigalas, M.//Maneliene, Z.//Kazlauskiene, R.//Petrusyte, M.//Janulaitis, A. 	PfoI, a unique type II restriction endonuclease that recognizes the sequence 5'-T/CCNGGA-3'.	Nucleic Acids Res.	2002	30		e98			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. 		
@D	Gaiser, R.A.//Medema, M.H.//Kleerebezem, M.//van Baarlen, P.//Wells, J.M. 	Draft Genome Sequence of a Porcine Commensal, Rothia nasimurium, Encoding a Nonribosomal Peptide Synthetase Predicted To Produce the Ionophore Antibiotic  Valinomycin.	Genome Announcements	2017	5		e00453-17			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. 		
@D	Gaisin, V.A.//Ivanov, T.M.//Kuznetsov, B.B.//Gorlenko, V.M.//Grouzdev, D.S. 	Draft Genome Sequence of Chloroflexus sp. Strain isl-2, a Thermophilic Filamentous Anoxygenic Phototrophic Bacterium Isolated from the Strokkur Geyser,   Iceland.	Genome Announcements	2016	4		e00714-16			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. 		
@A	Gal, S.//Monteith, N.//Shkalim, S.//Huang, H.//Head, T. 		Methylation of dna may be useful as a computational tool: Experimental evidence.			Mahdavi, K.//Culshaw, R.//Boucher, J. 		Current Developments in Mathematical Biology						2007		38		1-14									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. 		
@D	Galac, M.R.//Stam, J.//Maybank, R.//Hinkle, M.//Mack, D.//Rohde, H.//Roth, A.L.//Fey, P.D. 	Complete Genome Sequence of Staphylococcus epidermidis 1457.	Genome Announcements	2017	5		e00450-17			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. 		
@D	Galagan, J.E. et al. 	The genome sequence of the filamentous fungus Neurospora crassa.	Nature	2003	422		859-868			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. 		
@D	Galagan, J.E. et al. 	The genome of Methanosarcina acetivorans reveals extensive metabolic and physiological diversity.	Genome Res.	2002	12		532-542			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. 		
@D	Galardini, M. et al. 	Permanent draft genome sequences of the symbiotic nitrogen fixing Ensifer meliloti strains BO21CC and AK58.	Standards in Genomic Sciences	2013	9		325-333			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. 		
@D	Galarza, M.//Tarazona, D.//Borda, V.//Agapito, J.C.//Guio, H. 	Evidence of Clonal Expansion in the Genome of a Multidrug-Resistant Mycobacterium tuberculosis Clinical Isolate from Peru.	Genome Announcements	2014	2		e00089-14			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. 		
@D	Galburt, E.A.//Chadsey, M.S.//Jurica, M.S.//Chevalier, B.S.//Erho, D.//Tang, W.//Monnat, R.J. Jr.//Stoddard, B.L. 	Conformational changes and cleavage by the homing endonuclease I-PpoI: A critical role for a leucine residue in the active site.	J. Mol. Biol.	2000	300		877-887			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. 		
@D	Galburt, E.A.//Chevalier, B.//Tang, W.//Jurica, M.S.//Flick, K.E.//Monnat, R.J. Jr.//Stoddard, B.L. 	A novel endonuclease mechanism directly visualized for I-PpoI.	Nat. Struct. Biol.	1999	6		1096-1099			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. 		
@A	Galburt, E.A.//Jurica, M.S. 		His-Cys box homing endonuclease.			Belfort, M.//Derbyshire, V.//Stoddard, B.L.//Wood, D.W. 		Nucleic Acids Mol. Biol.				Berlin Heidelberg	Springer-Verlag	2005		16		85-102									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. 		
@D	Galburt, E.A.//Stoddard, B.L. 	Restriction endonucleases: one of these things is not like the others.	Nat. Struct. Biol.	2000	7		89-91			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. 		
@D	Galburt, E.A.//Stoddard, B.L. 	Catalytic mechanisms of restriction and homing endonucleases.	Biochemistry	2002	41		13851-13860			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. 		
@D	Galia, W.//Mariani-Kurkdjian, P.//Loukiadis, E.//Blanquet-Diot, S.//Leriche, F.//Brugere, H.//Shima, A.//Oswald, E.//Cournoyer, B.//Thevenot-Sergentet, D. 	Genome Sequence and Annotation of a Human Infection Isolate of Escherichia coli O26:H11 Involved in a Raw Milk Cheese Outbreak.	Genome Announcements	2015	3		e01568-14			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). 		
@D	Galibert, F. et al. 	The composite genome of the legume symbiont Sinorhizobium meliloti.	Science	2001	293		668-672			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. 		
@D	Gallagher, L.A.//McKevitt, M.//Ramage, E.R.//Manoil, C. 	Genetic dissection of the Francisella novicida restriction barrier.	J. Bacteriol.	2008	190		7830-7837			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. 		
@D	Gallagher, M.L.//Burke, W.F. 	Sequence-specific endonuclease from the transformable cyanobacterium Anacystis nidulans R2.	FEMS Microbiol. Lett.	1985	26		317-321			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. 		
@D	Gallagher, M.L.//Burke, W.F. 	Unique cyanobacterial recognition sequence for the restriction endonuclease AniI.	Abstr. Gen. Meet. Am. Soc. Microbiol.	1987	87		224			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. 		
@D	Gallegos-Monterrosa, R.//Maroti, G.//Balint, B.//Kovacs, A.T. 	Draft Genome Sequence of the Soil Isolate Lysinibacillus fusiformis M5, a Potential Hypoxanthine Producer.	Genome Announcements	2016	4		e01272-16			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. 		
@D	Galli, D.M.//Kerr, M.S.//Fair, A.D.//Permpanich, P.//LeBlanc, D.J. 	Parameters associated with cloning in Actinobacillus actinomycetemcomitans.	Plasmid	2002	47		138-147			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. 		
@D	Gallien, S.//Perrodou, E.//Carapito, C.//Deshayes, C.//Reyrat, J.M.//Van Dorsselaer, A.//Poch, O.//Schaeffer, C.//Lecompte, O. 	Ortho-proteogenomics: multiple proteomes investigation through orthology and a new MS-based protocol.	Genome Res.	2009	19		128-135			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. 		
@D	Gallo, K.A.//Shao, K.L.//Phillips, L.R.//Regan, J.B.//Koziolkiewicz, M.//Uznanski, B.//Stec, W.J.//Zon, G. 	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].	Nucleic Acids Res.	1986	14		7405-7420			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. 		
@D	Galloway-Pena, J.//DebRoy, S.//Brumlow, C.//Li, X.//Tran, T.//Horstmann, N.//Yao, H.//Chen, K.//Wang, F.//Pan, B.-F.//Hawke, D.//Thompson, E.//Arias, C.//Fowler, V.G.//Bhatti, M.//Kalia, A.//Flores, A.R.//Shelburne, S.A. 	Hypervirulent Group A Streptococcus Emergence in an Acaspular Background is Associated with Marked Remodeling of the Bacterial Cell Surface.	PLoS ONE	2019	13		e0207897			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. 		
@D	Galvez, E.J.//Carrillo-Castro, K.//Zarate, L.//Guiza, L.//Pieper, D.H.//Garcia-Bonilla, E.//Salazar, M.//Junca, H. 	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.	Genome Announcements	2016	4		e00321-16			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. 		
@D	Gamez, R.M.//Rodriguez, F.//Bernal, J.F.//Agarwala, R.//Landsman, D.//Marino-Ramirez, L. 	Genome Sequence of the Banana Plant Growth-Promoting Rhizobacterium Bacillus amyloliquefaciens BS006.	Genome Announcements	2015	3		e01391-15			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. 		
@D	Gamez, R.M.//Rodriguez, F.//Ramirez, S.//Gomez, Y.//Agarwala, R.//Landsman, D.//Marino-Ramirez, L. 	Genome Sequence of the Banana Plant Growth-Promoting Rhizobacterium Pseudomonas fluorescens PS006.	Genome Announcements	2016	4		e00329-16			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. 		
@D	Gan, H.M.//Chew, T.H.//Hudson, A.O.//Savka, M.A. 	Genome Sequence of Novosphingobium sp. Strain Rr 2-17, a Nopaline Crown Gall-Associated Bacterium Isolated from Vitis vinifera L. Grapevine.	J. Bacteriol.	2012	194		5137-5138			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. 		
@D	Gan, H.M.//Chew, T.H.//Hudson, A.O.//Savka, M.A. 	Genome Sequence of Methylobacterium sp. Strain GXF4, a Xylem-Associated Bacterium Isolated from Vitis vinifera L. Grapevine.	J. Bacteriol.	2012	194		5157-5158			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. 		
@D	Gan, H.M.//Chew, T.H.//Tay, Y.L.//Lye, S.F.//Yahya, A. 	Genome Sequence of Hydrogenophaga sp. Strain PBC, a 4-Aminobenzenesulfonate-Degrading Bacterium.	J. Bacteriol.	2012	194		4759-4760			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. 		
@D	Gan, H.M.//Chew, T.H.//Tay, Y.L.//Lye, S.F.//Yahya, A. 	Genome Sequence of Ralstonia sp. Strain PBA, a Bacterium Involved in the Biodegradation of 4-Aminobenzenesulfonate.	J. Bacteriol.	2012	194		5139-5140			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. 		
@D	Gan, H.M.//Eng, W.W.H.//Barton, M.K.//Adams, L.E.//Samsudin, N.A.//Bartl, A.J.//Hudson, A.O.//Savka, M.A.//Thomas, J.A. 	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.	Genome Announcements	2017	5		e00857-17			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. 		
@D	Gan, H.M.//Lean, S.S.//Suhaili, Z.//Thong, K.L.//Yeo, C.C. 	Genome Sequence of Acinetobacter baumannii AC12, a Polymyxin-Resistant Strain Isolated from Terengganu, Malaysia.	J. Bacteriol.	2012	194		5979-5980			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. 		
@D	Gan, H.M.//Lee, M.V.J.//Savka, M.A. 	High-Quality Draft Genome Sequence of the Type Strain of Allorhizobium vitis, the Primary Causal Agent of Grapevine Crown Gall.	Microbiol. Resour. Announc.	2018	7		e01045-18			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. 		
@D	Gan, H.M.//McGroty, S.E.//Chew, T.H.//Chan, K.G.//Buckley, L.J.//Savka, M.A.//Hudson, A.O. 	Whole-Genome Sequence of Enterobacter sp. Strain SST3, an Endophyte Isolated from Jamaican Sugarcane (Saccharum sp.) Stalk Tissue.	J. Bacteriol.	2012	194		5981-5982			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. 		
@D	Gan, H.M.//Rajasekaram, G.//Eng, W.W.H.//Kaniappan, P.//Dhanoa, A. 	Whole-Genome Sequences of Two Carbapenem-Resistant Klebsiella quasipneumoniae Strains Isolated from a Tertiary Hospital in Johor, Malaysia.	Genome Announcements	2017	5		e00768-17			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. 		
@D	Gan, H.M.//Triassi, A.J.//Wheatley, M.S.//Savka, M.A.//Hudson, A.O. 	High-Quality Draft Whole-Genome Sequences of Three Strains of Enterobacter Isolated from Jamaican Dioscorea cayenensis (Yellow Yam).	Genome Announcements	2014	2		e00170-14			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. 		
@D	Gan, H.Y. et al. 	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.	Genome Announcements	2015	3		e00288-15			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. 		
@D	Gan, H.Y.//Gan, H.M.//Savka, M.A.//Triassi, A.J.//Wheatley, M.S.//Smart, L.B.//Fabio, E.S.//Hudson, A.O. 	Whole-genome sequences of 13 endophytic bacteria isolated from shrub willow (salix) grown in geneva, new york.	Genome Announcements	2014	2		e00288-14			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. 		
@D	Gan, H.Y.//Gan, H.M.//Tarasco, A.M.//Busairi, N.I.//Barton, H.A.//Hudson, A.O.//Savka, M.A. 	Whole-Genome Sequences of Five Oligotrophic Bacteria Isolated from Deep within Lechuguilla Cave, New Mexico.	Genome Announcements	2014	2		e01133-14			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. 		
@D	Gan, H.Y.//Noor, M.E.//Saari, N.A.//Musa, N.//Mustapha, B.//Usup, G.//Danish-Daniel, M. 	Genome Sequence of Vibrio campbellii Strain UMTGB204, a Marine Bacterium Isolated from a Green Barrel Tunicate.	Genome Announcements	2015	3		e00210-15			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. 		
@D	Ganesan, A.T. 	Genetic recombination during transformation in Bacillus subtilis:  appearance of a deoxyribonucleic acid methylase.	J. Bacteriol.	1979	139		270-279			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. 		
@A	Ganesan, A.T. 		Uptake, restriction, modification and recombination of DNA molecules during transformation in B. subtilis.			Ganesan, A.T.//Chang, S.//Hoch, J.A. 		Molecular Cloning and Gene Regulation in Bacilli					Academic Press	1982		0		261-268									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. 		
@D	Gangaiah, D.//Marinov, G.K.//Roberts, S.A.//Robson, J.//Spinola, S.M. 	Draft Whole-Genome Sequence of Haemophilus ducreyi Strain AUSPNG1, Isolated from  a Cutaneous Ulcer of a Child from Papua New Guinea.	Genome Announcements	2016	4		e01661-15			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. 		
@D	Gangaiah, D.//Webb, K.M.//Humphreys, T.L.//Fortney, K.R.//Toh, E.//Tai, A.//Katz, S.S.//Pillay, A.//Chen, C.Y.//Roberts, S.A.//Munson, R.S. Jr.//Spinola, S.M. 	Haemophilus ducreyi Cutaneous Ulcer Strains Are Nearly Identical to Class I Genital Ulcer Strains.	PLoS Neglected Trop. Dis.	2015	9		E0003918			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. 		
@D	Gangiredla, J.//Barnaba, T.J.//Mammel, M.K.//Lacher, D.W.//Elkins, C.A.//Lampel, K.A.//Whitehouse, C.A.//Tartera, C. 	Fifty-Six Draft Genome Sequences of 10 Lactobacillus Species from 22 Commercial Dietary Supplements.	Genome Announcements	2018	6		e00621-18			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. 		
@D	Gangiredla, J.//Mammel, M.K.//Barnaba, T.J.//Tartera, C.//Gebru, S.T.//Patel, I.R.//Leonard, S.R.//Kotewicz, M.L.//Lampel, K.A.//Elkins, C.A.//Lacher, D.W. 	Species-Wide Collection of Escherichia coli Isolates for Examination of Genomic Diversity.	Genome Announcements	2017	5		e01321-17			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. 		
@D	Gangiredla, J.//Mammel, M.K.//Barnaba, T.J.//Tartera, C.//Gebru, S.T.//Patel, I.R.//Leonard, S.R.//Kotewicz, M.L.//Lampel, K.A.//Elkins, C.A.//Lacher, D.W. 	Draft Genome Sequences of Escherichia albertii, Escherichia fergusonii, and Strains Belonging to Six Cryptic Lineages of Escherichia spp.	Genome Announcements	2018	6		e00271-18			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. 		
@D	Gangoiti, J.//Meng, X.//Lammerts-van-Bueren, A.//Dijkhuizen, L. 	Draft Genome Sequence of Lactobacillus reuteri 121, a Source of alpha-Glucan and  beta-Fructan Exopolysaccharides.	Genome Announcements	2017	5		e01691-16			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. 		
@D	Ganguly, S.//Jimenez-Galisteo, G.//Pletzer, D.//Winterhalter, M.//Benz, R.//Vinas, M. 	Draft Genome Sequence of Dietzia maris DSM 43672, a Gram-Positive Bacterium of the Mycolata Group.	Genome Announcements	2016	4		e00542-16			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. 		
@D	Ganji, R. et al. 	High-Quality Draft Genome Sequence of Thermocrinis jamiesonii GBS1T Isolated from Great Boiling Spring, Nevada.	Genome Announcements	2016	4		e01112-16			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. 		
@D	Gann, A.A.F. 	Recognition domains of type I restriction enzymes.	Diss. Abstr.	1990	50		4377B			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. 		
@A	Gann, A.A.F. 		Recognition domains of Type I restriction enzymes.			 		Ph.D. Thesis				Edinburgh		1988													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. 		
@D	Gann, A.A.F.//Campbell, A.J.B.//Collins, J.F.//Coulson, A.F.W.//Murray, N.E. 	Reassortment of DNA recognition domains and the evolution of new specificities.	Mol. Microbiol.	1987	1		13-22			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. 		
@D	Gao, C.//Hu, C.//Ma, C.//Su, F.//Yu, H.//Jiang, T.//Dou, P.//Wang, Y.//Qin, T.//Lv, M.//Xu, P. 	Genome Sequence of the Lactate-Utilizing Pseudomonas aeruginosa Strain XMG.	J. Bacteriol.	2012	194		4751-4752			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. 		
@D	Gao, E.B.//Gui, J.F.//Zhang, Q.Y. 	A Novel Cyanophage with a Cyanobacterial Nonbleaching Protein A Gene in the Genome.	J. Virol.	2012	86		236-245			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. 		
@D	Gao, F.//Wang, Y.//Liu, Y.J.//Wu, X.M.//Lv, X.//Gan, Y.R.//Song, S.D.//Huang, H. 	Genome sequence of Acinetobacter baumannii MDR-TJ.	J. Bacteriol.	2011	193		2365-2366			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. 		
@D	Gao, G.//Li, J.//Li, T.//Zhang, Z.//Wang, L.//Yuan, X.//Wang, Y.//Xu, J.//Ke, Y.//Huang, L.//Wang, D.//Chen, Z.//Xu, X. 	Complete Genome Sequence of Brucella canis Strain 118, a Strain Isolated from Canine.	J. Bacteriol.	2012	194		6680			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. 		
@D	Gao, H.//Ma, Y.//Shao, Q.//Hong, Q.//Zheng, G.//Li, Z. 	Genome Sequence of Corynebacterium pseudotuberculosis Strain KM01, Isolated from  the Abscess of a Goat in Kunming, China.	Genome Announcements	2018	6		e00013-18			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. 		
@D	Gao, J.//Yu, X.//Xie, Z. 	Draft Genome Sequence of High-Siderophore-Yielding Pseudomonas sp. Strain HYS.	J. Bacteriol.	2012	194		4121			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. 		
@D	Gao, L.//Zhou, J.//Liu, J.//Du, G.//Chen, J. 	Draft Genome Sequence of Gluconobacter oxydans WSH-003, a Strain That Is Extremely Tolerant of Saccharides and Alditols.	J. Bacteriol.	2012	194		4455-4456			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. 		
@D	Gao, P.//Tang, Q.//An, X.M.//Yan, X.X.//Liang, D.C. 	Structure of HsdS Subunit from Thermoanaerobacter tengcongensis Sheds Lights on Mechanism of Dynamic Opening and Closing of Type I Methyltransferase.	PLoS ONE	2011	6		e17346			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. 		
@D	Gao, Q.//Thorson, J.S. 	The biosynthetic genes encoding for the production of the dynemicin enediyne core in Micromonospora chersina ATCC53710.	FEMS Microbiol. Lett.	2008	282		105-114			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. 		
@D	Gao, X.//Liu, K.//Qiu, B.-S. 	An investigation on the genetic background of  Nostoc flagelliforme by similarity analysis of its partial genomic DNA and  phylogenetic comparison of deduced related species.	Acta Physiol. Plant.	2011	33		1301-1318			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. 		
@D	Gao, X.Y.//Zhi, X.Y.//Li, H.W.//Zhou, Y.//Lapidus, A.//Han, J.//Haynes, M.//Lobos, E.//Huntemann, M.//Pati, A.//Ivanova, N.N.//Mavromatis, K.//Tindall, B.J.//Markowitz, V.//Woyke, T.//Klenk, H.P.//Kyrpides, N.C.//Li, W.J. 	Draft genome sequence of Halomonas lutea strain YIM 91125(T) (DSM 23508(T)) isolated from the alkaline Lake Ebinur in Northwest China.	Standards in Genomic Sciences	2015	10		1			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. 		
@D	Gao, Y.H.//Guo, R.J.//Li, S.D. 	Draft Genome Sequence of Bacillus velezensis B6, a Rhizobacterium That Can Control Plant Diseases.	Genome Announcements	2018	6		e00182-18			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. 		
@D	Gao, Y.X.//Zhou, Y.Y.//Xie, Y.//Wang, M.//Wang, S.J.//Shen, S.G. 	Complete Genome Sequence of Actinomyces hongkongensis HKU8T Isolated from Human Blood.	Genome Announcements	2017	5		e01650-16			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. 		
@D	Gao, Z.//Liu, X.//Ruan, L. 	Genome Sequence of Anaerophaga sp. Strain HS1, a Novel, Moderately Thermophilic, Strictly Anaerobic Bacterium Isolated from Hot Spring  Sediment.	J. Bacteriol.	2011	193		5572			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. 		
@D	Garau, G.//Terpolilli, J.//Hill, Y.//Tian, R.//Howieson, J.//Brau, L.//Goodwin, L.//Han, J.//Reddy, T.//Huntemann, M.//Pati, A.//Woyke, T.//Mavromatis, K.//Markowitz, V.//Ivanova, N.//Kyrpides, N.//Reeve, W. 	Genome sequence of Ensifer medicae Di28; an effective N2-fixing microsymbiont of  Medicago murex and M. polymorpha.	Standards in Genomic Sciences	2014	9		4			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. 		
@D	Garbeva, P.//van Elsas, J.D.//de Boer, W. 	Draft Genome Sequence of the Antagonistic Rhizosphere Bacterium Serratia plymuthica Strain PRI-2C.	J. Bacteriol.	2012	194		4119-4120			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. 		
@D	Garcia, B.G.//Ooka, T.//Gotoh, Y.//Vieira, M.A.M.//Yamamoto, D.//Ogura, Y.//Girao, D.M.//Sampaio, S.C.F.//Melo, A.B.//Irino, K.//Hayashi, T.//Gomes, T.A.T. 	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.	Int. J. Med. Microbiol.	2016	306		152-164			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. 		
@D	Garcia, J.C.//Urakawa, H.//Le, V.Q.//Stein, L.Y.//Klotz, M.G.//Nielsen, J.L. 	Draft Genome Sequence of Nitrosospira sp. Strain APG3, a Psychrotolerant Ammonia-Oxidizing Bacterium Isolated from Sandy Lake Sediment.	Genome Announcements	2013	1		e00930-13			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. 		
@D	Garcia, J.L.//Rozas, D.//Del Cerro, C.//Nogales, J.//El-Said, M.M.//Diaz, E. 	Genome Sequence of Pseudomonas azelaica HBP1, Which Catabolizes 2-Hydroxybiphenyl Fungicide.	Genome Announcements	2014	2		e01248-13			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. 		
@D	Garcia, L.R.//Molineux, I.J. 	Translocation and specific cleavage of bacteriophage T7 DNA in vivo by EcoKI.	Proc. Natl. Acad. Sci. U. S. A.	1999	96		12430-12435			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. 		
@D	Garcia, N.S.//Yung, C.M.//Davis, K.M.//Rynearson, T.//Hunt, D.E. 	Draft Genome Sequences of Three Bacterial Isolates from Cultures of the Marine Diatom Thalassiosira rotula.	Genome Announcements	2017	5		e00316-17			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. 		
@D	Garcia, P.//Monjardin, C.//Martin, R.//Madera, C.//Soberon, N.//Garcia, E.//Meana, A.//Suarez, J.E. 	Isolation of new Stenotrophomonas bacteriophages and genomic characterization of temperate phage S1.	Appl. Environ. Microbiol.	2008	74		7552-7560			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. 		
@D	Garcia, R.A.//Bustamante, C.J.//Reich, N.O. 	Sequence-specific recognition by cytosine C5 and adenine N6 DNA methyltransferases requires different deformations of DNA.	Proc. Natl. Acad. Sci. U. S. A.	1996	93		7618-7622			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. 		
@D	Garcia, R.G.//Brank, A.S.//Christman, J.K.//Marquez, V.E.//Eritja, R. 	Synthesis of oligonucleotide inhibitors of DNA (cytosine-C5) methyltransferase containing 5-azacytosine residues at specific sites.	Antisense Nucleic Acid Drug Dev.	2001	11		369-378			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. 		
@D	Garcia-Alvarez, L. et al. 	Meticillin-resistant Staphylococcus aureus with a novel mecA homologue in human and bovine populations in the UK and Denmark: a descriptive study.	Lancet Infect Dis	2011	11		595-603			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. 		
@D	Garcia-Fernandez, A.//Villa, L.//Carta, C.//Venditti, C.//Giordano, A.//Venditti, M.//Mancini, C.//Carattoli, A. 	Klebsiella pneumoniae ST258 Producing KPC-3 Identified in Italy Carries Novel Plasmids and OmpK36/OmpK35 Porin Variants.	Antimicrob. Agents Chemother.	2012	56		2143-2145			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. 		
@D	Garcia-Heredia, I.//Martin-Cuadrado, A.-B.//Mojica, F.J.//Santos, F.//Mira, A.//Anton, J.//Rodriguez-Valera, F. 	Reconstructing viral genomes from the environment using fosmid clones: the case of haloviruses.	PLoS ONE	2012	7		e33802			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. 		
@D	Garcia-Ramon, D.C.//Palma, L.//Berry, C.//Osuna, A.//Vilchez, S. 	Draft Genome Sequence of the Entomopathogenic Bacterium Bacillus pumilus 15.1, a  Strain Highly Toxic to the Mediterranean Fruit Fly Ceratitis capitata.	Genome Announcements	2015	3		e01019-15			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. 		
@D	Garcia-Romero, I.//Perez-Pulido, A.J.//Gonzalez-Flores, Y.E.//Reyes-Ramirez, F.//Santero, E.//Floriano, B. 	Genomic analysis of the nitrate-respiring Sphingopyxis granuli (formerly Sphingomonas macrogoltabida) strain TFA.	BMC Genomics	2016	17		93			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. 		
@D	Garcia-Solache, M.//Rice, L.B. 	Draft Genome Sequence of Vancomycin-Susceptible, Ampicillin-Intermediate Enterococcus faecium Strain D344RRF.	Genome Announcements	2016	4		e01720-15			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. 		
@D	Garcia-Solache, M.//Rice, L.B. 	Genome Sequence of the Multiantibiotic-Resistant Enterococcus faecium Strain C68  and Insights on the pLRM23 Colonization Plasmid.	Genome Announcements	2016	4		e01719-15			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. 		
@D	Garcia-Valdes, E.//Gomila, M.//Mulet, M.//Lalucat, J. 	Draft Genome Sequence of Pseudomonas oceani DSM 100277(T), a Deep-Sea Bacterium.	Genome Announcements	2018	6		e00254-18			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%. 		
@D	Gardes, A.//Kaeppel, E.//Shehzad, A.//Seebah, S.//Teeling, H.//Yarza, P.//Glockner, F.O.//Grossart, H.P.//Ullrich, M.S. 	Complete genome sequence of Marinobacter adhaerens type strain (HP15), a diatom-interacting marine microorganism.	Standards in Genomic Sciences	2010	3		97-107			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. 		
@D	Gardiner, D.M.//Stiller, J.//Covarelli, L.//Lindeberg, M.//Shivas, R.G.//Manners, J.M. 	Genome Sequences of Pseudomonas spp. Isolated from Cereal Crops.	Genome Announcements	2013	1		e00209-13			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. 		
@D	Gardiner, D.M.//Stiller, J.//Kazan, K. 	Genome Sequence of Fusarium graminearum Isolate CS3005.	Genome Announcements	2014	2		e00227-14			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. 		
@D	Gardner, A.F.//Kumar, S.//Perler, F.B. 	Genome Sequence of the Model Hyperthermophilic Archaeon Thermococcus litoralis NS-C.	J. Bacteriol.	2012	194		2375-2376			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. 		
@D	Gardner, R.C.//Howarth, A.J.//Messing, J.//Shepherd, R.J. 	Cloning and sequencing of restriction fragments generated by EcoRI*.	DNA	1982	1		109-115			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. 		
@D	Gardner, S.P.//Kendall, K.J.//Taveirne, M.E.//Olson, J.W. 	Complete Genome Sequence of Campylobacter jejuni subsp. jejuni ATCC 35925.	Genome Announcements	2017	5		e00743-17			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. 		
@D	Gardner, S.P.//Olson, J.W. 	Barriers to Horizontal Gene Transfer in Campylobacter jejuni.	Adv. Appl. Microbiol.	2012	79		19-42			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. 		
@D	Garfin, D.E.//Boyer, H.W.//Goodman, H.M. 	Sequences spanning the EcoRI substrate site.	Nucleic Acids Res.	1975	2		1851-1865			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-. 		
@D	Garfin, D.E.//Goodman, H.M. 	Nucleotide sequences at the cleavage sites of two restriction endonucleases from Hemophilus parainfluenzae.	Biochem. Biophys. Res. Commun.	1974	59		108-116			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. 		
@D	Garg, R.//Kumari, R.//Tiwari, S.//Goyal, S. 	Genomic Survey, Gene Expression Analysis and Structural Modeling Suggest Diverse Roles of DNA Methyltransferases in Legumes.	PLoS ONE	2014	9		14			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. 		
@D	Garita-Cambronero, J.//Palacio-Bielsa, A.//Lopez, M.M.//Cubero, J. 	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.	Genome Announcements	2016	4		e00974-16			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. 		
@D	Garita-Cambronero, J.//Palacio-Bielsa, A.//Lopez, M.M.//Cubero, J. 	Draft genome sequence for virulent and avirulent strains of Xanthomonas arboricola isolated from Prunus spp. in Spain.	Standards in Genomic Sciences	2016	11		12			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. 		
@D	Garita-Cambronero, J.//Sena-Velez, M.//Palacio-Bielsa, A.//Cubero, J. 	Draft Genome Sequence of Xanthomonas arboricola pv. pruni Strain Xap33, Causal Agent of Bacterial Spot Disease on Almond.	Genome Announcements	2014	2		e00440-14			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. 		
@D	Garnett, J.//Halford, S.E. 	Properties and subunit structure of EcoRV methyltransferase.	Gene	1988	74		73-76			Meeting Abstract 		
@D	Garnier, F.//Taourit, S.//Glaser, P.//Courvalin, P.//Galimand, M. 	Characterization of transposon Tn1549, conferring VanB-type resistance in Enterococcus spp.	Microbiology	2000	146		1481-1489			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. 		
@D	Garnier, T. et al. 	The complete genome sequence of Mycobacterium bovis.	Proc. Natl. Acad. Sci. U. S. A.	2003	100		7877-7882			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. 		
@D	Garofolo, G.//Foster, J.T.//Drees, K.//Zilli, K.//Platone, I.//Ancora, M.//Camma, C.//De Massis, F.//Calistri, P.//Di Giannatale, E. 	Genome Sequences of 11 Brucella abortus Isolates from Persistently Infected Italian Regions.	Genome Announcements	2015	3		e01402-15			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. 		
@D	Garrett, M.//Parker, J.//Stephens, C.M. 	Draft Genome Sequences of Antibiotic-Resistant Commensal Escherichia coli.	Genome Announcements	2014	2		e00873-14			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. 		
@D	Garrett, R.A.//Prangishvili, D.//Shah, S.A.//Reuter, M.//Stetter, K.O.//Peng, X. 	Metagenomic analyses of novel viruses and plasmids from a cultured environmental sample of hyperthermophilic neutrophiles.	Environ. Microbiol.	2010	12		2918-2930			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. 		
@D	Garrido, L.M.//Alves, J.M.//Oliveira, L.S.//Gruber, A.//Padilla, G.//Araujo, W.L. 	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.	Genome Announcements	2016	4		e01264-16			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. 		
@D	Garrigues, C.//Johansen, E.//Pedersen, M.B. 	Complete genome sequence of Bifidobacterium animalis subsp. lactis BB-12, a widely consumed probiotic strain.	J. Bacteriol.	2010	192		2467-2468			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. 		
@D	Garvey, P.//van Sinderen, D.//Twomey, D.P.//Hill, C.//Fitzgerald, G.F. 	Molecular genetics of bacteriophage and natural phage defense systems in the genus Lactococcus.	Int. Dairy Journal	1995	5		905-947			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. 		
@D	Garza-Ramos, U.//Silva-Sanchez, J.//Barrios, H.//Rodriguez-Medina, N.//Martinez-Barnetche, J.//Andrade, V. 	Draft Genome Sequence of the First Hypermucoviscous Klebsiella variicola Clinical Isolate.	Genome Announcements	2015	3		e01352-14			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%. 		
@D	Garza-Ramos, U.//Silva-Sanchez, J.//Catalan-Najera, J.//Barrios, H.//Rodriguez-Medina, N.//Garza-Gonzalez, E.//Cevallos, M.A.//Lozano, L. 	Draft Genome Sequence of a Hypermucoviscous Extended-Spectrum-beta-Lactamase-Producing Klebsiella quasipneumoniae subsp.  similipneumoniae Clinical Isolate.	Genome Announcements	2016	4		e00475-16			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. 		
@D	Garza-Ramos, U.//Tamayo-Legorreta, E.//Arellano-Quintanilla, D.M.//Rodriguez-Medina, N.//Silva-Sanchez, J.//Catalan-Najera, J.//Rocha-Martinez, M.K.//Bravo-Diaz, M.A.//Alpuche-Aranda, C. 	Draft Genome Sequence of a Multidrug- and Colistin-Resistant mcr-1-Producing Escherichia coli Isolate from a Swine Farm in Mexico.	Genome Announcements	2018	6		e00102-18			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. 		
@D	Garzetti, D.//Brugiroux, S.//Bunk, B.//Pukall, R.//McCoy, K.D.//Macpherson, A.J.//Stecher, B. 	High-Quality Whole-Genome Sequences of the Oligo-Mouse-Microbiota Bacterial Community.	Genome Announcements	2017	5		e00758-17			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. 		
@D	Garzetti, D.//Eberl, C.//Stecher, B. 	Complete Genome Sequencing of the Mouse Intestinal Isolate Escherichia coli Mt1B1.	Genome Announcements	2018	6		e00426-18			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. 		
@D	Garzetti, D.//Heesemann, J.//Rakin, A. 	Genome Sequences of Four Yersinia enterocolitica Bioserotype 4/O:3 Isolates from  Mammals.	Genome Announcements	2013	1		e00466-13			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. 		
@D	Gasc, C.//Richard, J.Y.//Peyret, P. 	Genome Sequence of Pseudomonas sp. HUK17, Isolated from Hexachlorocyclohexane-Contaminated Soil.	Genome Announcements	2016	4		e00275-16			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. 		
@D	Gasc, C.//Richard, J.Y.//Peyret, P. 	Genome Sequence of Staphylococcus aureus Strain HUK16, Isolated from Hexachlorocyclohexane-Contaminated Soil.	Genome Announcements	2016	4		e00274-16			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. 		
@D	Gasc, C.//Richard, J.Y.//Peyret, P. 	Genome Sequence of Bacillus subtilis Strain HUK15, Isolated from Hexachlorocyclohexane-Contaminated Soil.	Genome Announcements	2016	4		e00273-16			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. 		
@D	Gasiunas, G.//Sasnaukas, G.//Tamulaitis, G.//Siksnys, V. 	Tetrameric restriction enzyme Cfr42I belongs to the GIY-YIG nuclease family.	FEBS J.	2009	276		140-141			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. 		
@D	Gasiunas, G.//Sasnauskas, G.//Tamulaitis, G.//Urbanke, C.//Razaniene, D.//Siksnys, V. 	Tetrameric restriction enzymes: expansion to the GIY-YIG nuclease family.	Nucleic Acids Res.	2008	36		938-949			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. 		
@D	Gasperik, J.//Godany, A.//Hostinova, E.//Zelinka, J. 	Specific endonuclease Sau3239I from Streptomyces aureofaciens CCM 3239.	Biologia (Bratisl)	1983	38		315-319			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). 		
@D	Gasperotti, A.F.//Studdert, C.A.//Revale, S.//Herrera, S.M.K. 	Draft Genome Sequence of Halomonas sp. KHS3, a Polyaromatic Hydrocarbon-Chemotactic Strain.	Genome Announcements	2015	3		e00020-15			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. 		
@D	Gassner, C.//Schneider-Scherzer, E.S.//Lottspeich, F.//Schweiger, M.//Auer, B. 	Escherichia coli bacteriophage T1 DNA methyltransferase appears to interact with Escherichia coli enolase.	Biol. Chem.	1998	379		621-623			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. 		
@D	Gast, F.U.//Brinkmann, T.//Pieper, U.//Kruger, T.//Noyer-Weidner, M.//Pingoud, A. 	The recognition of methylated DNA by the GTP-dependent restriction endonuclease McrBC resides in the N-terminal domain of McrB.	Biol. Chem.	1997	378		975-982			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. 		
@D	Gato, E.//Alvarez-Fraga, L.//Vallejo, J.A.//Rumbo-Feal, S.//Martinez-Guitian, M.//Beceiro, A.//Poza, M.//Bou, G.//Perez, A. 	Draft Genome Sequences of Two Epidemic OXA-48-Producing Klebsiella pneumoniae Clinical Strains Isolated during a Large Outbreak in Spain.	Genome Announcements	2018	6		e00026-18			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%. 		
@D	Gaudet, F.//Talbot, D.//Leonhardt, H.//Jaenisch, R. 	A short DNA methyltransferase isoform restores methylation in vivo.	J. Biol. Chem.	1998	273		32725-32729			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. 		
@D	Gaultier, N.E. et al. 	Complete Genome Sequence of the Bacterium Serratia marcescens SGAir0764, Isolated from Singapore Air.	Genome Announcements	2018	6		e00637-18			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. 		
@D	Gaultier, N.E. et al. 	Genome Sequence of Geobacillus thermoleovorans SGAir0734, Isolated from Singapore Air.	Genome Announcements	2018	6		e00636-18			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. 		
@D	Gaulton, T.//Misra, R.//Rose, G.//Baybayan, P.//Hall, R.//Freeman, J.//Turton, J.//Picton, S.//Korlach, J.//Gharbia, S.//Shah, H. 	Complete Genome Sequence of the Hypervirulent Bacterium Clostridium difficile Strain G46, Ribotype 027.	Genome Announcements	2015	3		e00073-15			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. 		
@D	Gauntlett, J.C.//Nilsson, H.-O.//Fulurija, A.//Marshall, B.J.//Benghezal, M. 	Phase-variable restriction/modification systems are required for Helicobacter pylori colonization.	Gut Pathog.	2014	6		35			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. 		
@D	Gautam, S.S.//Mac Aogain, M.//O'Toole, R.F. 	Draft Genome Sequence of the First Confirmed Isolate of Multidrug-Resistant Mycobacterium tuberculosis in Tasmania.	Genome Announcements	2017	5		e01230-17			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. 		
@D	Gauthier, A.//Turmel, M.//Lemieux, C. 	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.	Curr. Genet.	1991	19		43-47			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. 		
@D	Gauthier, J.//Charette, S.J.//Derome, N. 	Draft Genome Sequence of Pseudomonas fluorescens ML11A, an Endogenous Strain from Brook Charr with Antagonistic Properties against Aeromonas salmonicida subsp.  salmonicida.	Genome Announcements	2017	5		e01716-16			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. 		
@D	Gautier, F.//Bunemann, H.//Grotjahn, L. 	Analysis of calif-thymus satellite DNA:  evidence for specific methylation of cytosine in C-G sequences.	Eur. J. Biochem.	1977	80		175-183			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. 		
@D	Gautier, M.//Chopin, M.-C. 	Plasmid-determined systems for restriction and modification activity and abortive infection in Streptococcus cremoris.	Appl. Environ. Microbiol.	1987	53		923-927			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). 		
@D	Gautier, M.//Veaux, M.//Chopin, M.-C. 	Cloning of three plasmid-determined systems for restriction/modification and abortive infection.	FEMS Microbiol. Rev.	1987	46		44			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. 		
@D	Gawthorne, J.A.//Beatson, S.A.//Srikhanta, Y.N.//Fox, K.L.//Jennings, M.P. 	Origin of the Diversity in DNA Recognition Domains in Phasevarion Associated modA Genes of Pathogenic Neisseria and Haemophilus influenzae.	PLoS ONE	2012	7		e32337			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. 		
@D	Gay, N.R.//Fleming, E.//Oh, J. 	Draft Genome Sequence of Cloacibacterium normanense NRS-1 Isolated from Municipal Wastewater.	Genome Announcements	2016	4		e01397-16			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. 		
@A	Gayle, R.//Bennett, G. 		Synthesis of a specific sequence of DNA using restriction enzymes.			Ahmad, F.//Schultz, J.//Smith, E.E.//Whelan, W.J. 		Miami BioTechnology Winter Symposium					Academic Press	1982		19		526									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. 		
@D	Gayle, R.B.//Auger, E.A.//Gough, G.R.//Gilham, P.T.//Bennett, G.N. 	Formation of MboII vectors and cassettes using asymmetric MboII linkers.	Gene	1987	54		221-228			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. 		
@D	Gazzola, S.//Pietta, E.//Bassi, D.//Fontana, C.//Puglisi, E.//Cappa, F.//Cocconcelli, P.S. 	Draft Genome Sequence of Vancomycin-Heteroresistant Staphylococcus epidermidis Strain UC7032, Isolated from Food.	Genome Announcements	2013	1		e00709-13			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. 		
@D	Ge, B.//Liu, Y.//Liu, B.//Zhang, K. 	Draft Genome Sequence of Streptomyces ahygroscopicus subsp. wuyiensis CK-15, Isolated from Soil in Fujian Province, China.	Genome Announcements	2015	3		e01125-15			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%. 		
@D	Ge, F.//Li, W.//Chen, G.//Liu, Y.//Zhang, G.//Yong, B.//Wang, Q.//Wang, N.//Huang, Z.//Li, W.//Wang, J.//Wu, C.//Xie, Q.//Liu, G. 	Draft genome sequence of Gordonia neofelifaecis NRRL B-59395, a cholesterol-degrading actinomycete.	J. Bacteriol.	2011	193		5045-5046			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. 		
@D	Ge, S.//Ai, W.//Dong, X. 	High-Quality Draft Genome Sequence of Leucobacter sp. Strain G161, a Distinct and Effective Chromium Reducer.	Genome Announcements	2016	4		e01760-15			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. 		
@D	Ge, X.//Zhao, Y.//Hou, W.//Zhang, W.//Chen, W.//Wang, J.//Zhao, N.//Lin, J.//Wang, W.//Chen, M.//Wang, Q.//Jiao, Y.//Yuan, Z.//Xiong, X. 	Complete Genome Sequence of the Industrial Strain Gluconobacter oxydans H24.	Genome Announcements	2013	1		e00003-13			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. 		
@D	Ge, Y.Z.//Pu, M.T.//Gowher, H.//Wu, H.P.//Ding, J.P.//Jeltsch, A.//Xu, G.L. 	Chromatin targeting of de novo DNA methyltransferases by the PWWP domain.	J. Biol. Chem.	2004	279		25447-25454			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. 		
@D	Ge, Z.//Taylor, D.E. 	Contributions of genome sequencing to understanding the biology of Helicobacter pylori.	Annu. Rev. Microbiol.	1999	53		353-387			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. 		
@D	Geahigan, K.B.//Meints, G.A.//Hatcher, M.E.//Orban, J.//Drobny, G.P. 	The dynamic impact of CpG methylation in DNA.	Biochemistry	2000	39		4939-4946			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. 		
@D	Gebreyesus, K.H.//Owens, R.A. 	Selective protection of restriction endonuclease sites.	Biotechniques	2003	34		512-523			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. 		
@D	Geck, P.//Molnar, A.//Nasz, I. 	A mathematical method for the identification of the ATGCAT recognition sequence of a Streptococcus mutans restriction endonuclease.	Acta Microbiol. Hung.	1991	38		43-46			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. 		
@D	Geck, P.//Molnar, A.//Nasz, I. 	Identification of ATGCAT sequence at sites of SmuCI restriction endonuclease by computer and physical mapping of Adenovirus Type I DNA.	Acta Microbiol. Hung.	1991	38		47-53			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. 		
@D	Geck, P.//Molnar, A.//Nasz, J. 	Elimination of non-specific nucleases from restriction endonuclease preparations by different binding on free DNA ligand.	Acta Microbiol. Hung.	1987	34		241-245			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. 		
@D	Gee, J.E.//Marston, C.K.//Sammons, S.A.//Burroughs, M.A.//Hoffmaster, A.R. 	Draft Genome Sequence of Bacillus cereus Strain BcFL2013, a Clinical Isolate Similar to G9241.	Genome Announcements	2014	2		e00469-14			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. 		
@D	Geese, W.J.//Kwon, Y.K.//Wen, X.P.//Waring, R.B. 	In vitro analysis of the relationship between endonuclease and maturase activities in the bi-functional group I intron-encoded protein, I-AniI.	Eur. J. Biochem.	2003	270		1543-1554			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. 		
@D	Geese, W.J.//Waring, R.B. 	A comprehensive characterization of a group IB intron and its encoded maturase reveals that protein-assisted splicing requires an almost intact intron RNA.	J. Mol. Biol.	2001	308		609-622			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. 		
@D	Gefter, M.//Hausmann, R.//Gold, M.//Hurwitz, J. 	The enzymatic methylation of ribonucleic acid and deoxyribonucleic acid.	J. Biol. Chem.	1966	241		1995-2006			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. 		
@D	Gehlot, H.S. et al. 	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.	Standards in Genomic Sciences	2016	11		43			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. 		
@D	Geier, G.E.//Modrich, P. 	Recognition sequence of the dam methylase of Escherichia coli K12 and mode of cleavage of DpnI endonuclease.	J. Biol. Chem.	1979	254		1408-1413			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. 		
@D	Geiger, R.//Ruter, T.//Alves, J.//Fliess, A.//Wolfes, H.//Pingoud, V.//Urbanke, C.//Maass, G.//Pingoud, A.//Dusterhoft, A.//Kroger, M. 	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.	Biochemistry	1989	28		2667-2677			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. 		
@D	Geiman, T.M.//Sankpal, U.T.//Robertson, A.K.//Chen, Y.//Mazumdar, M.//Heale, J.//Schmiesing, J.A.//Kim, W.//Yokomori, K.//Zhao, Y.//Robertson, K.D. 	Isolation and characterization of a novel DNA methyltransferase complex linking DNMT3B with components of the mitotic chromosome condensation machinery.	Nucleic Acids Res.	2004	32		2716-2729			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. 		
@D	Geiman, T.M.//Sankpal, U.T.//Robertson, A.K.//Zhao, Y.X.//Zhao, Y.M.//Robertson, K.D. 	DNMT3B interacts with hSNF2H chromatin remodeling enzyme, HDACs 1 and 2, and components of the histone methylation system.	Biochem. Biophys. Res. Commun.	2004	318		544-555			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. 		
@D	Geis, A.//El Demerdash, H.A.//Heller, K.J. 	Sequence analysis and characterization of plasmids from Streptococcus thermophilus.	Plasmid	2003	50		53-69			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. 		
@D	Geissler, A.J.//Behr, J.//Vogel, R.F. 	Multiple Genome Sequences of the Important Beer-Spoiling Species Lactobacillus backii.	Genome Announcements	2016	4		e00826-16			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. 		
@D	Geissler, A.J.//Behr, J.//Vogel, R.F. 	Multiple Genome Sequences of Important Beer-Spoiling Lactic Acid Bacteria.	Genome Announcements	2016	4		e01077-16			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. 		
@D	Gelfand, M.S.//Koonin, E.V. 	Avoidance of palindromic words in bacterial and archaeal genomes: a close connection with restriction enzymes.	Nucleic Acids Res.	1997	25		2430-2439			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. 		
@D	Gelinas, R.E.//Myers, P.A.//Roberts, R.J. 	Two sequence-specific endonucleases from Moraxella bovis.	J. Mol. Biol.	1977	114		169-179			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. 		
@D	Gelinas, R.E.//Myers, P.A.//Weiss, G.H.//Roberts, R.J.//Murray, K. 	A specific endonuclease from Brevibacterium albidum.	J. Mol. Biol.	1977	114		433-440			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. 		
@D	Gemmen, G.J.//Millin, R.//Smith, D.E. 	Dynamics of single DNA looping and cleavage by Sau3AI and effect of tension applied to the DNA.	Biophys. J.	2006	91		4154-4165			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. 		
@D	Gemmen, G.J.//Millin, R.//Smith, D.E. 	DNA looping by two-site restriction endonucleases: heterogeneous probability distributions for loop size and unbinding force.	Nucleic Acids Res.	2006	34		2864-2877			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. 		
@D	Gemmen, G.J.//Millin, R.//Smith, D.E. 	Tension-dependent DNA cleavage by restriction endonucleases: Two-site enzymes are "switched off" at low force.	Proc. Natl. Acad. Sci. U. S. A.	2006	103		11555-11560			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. 		
@D	Gencay, Y.E.//Sorensen, M.C.H.//Brondsted, L. 	Whole-Genome Sequence of the Bacteriophage-Sensitive Strain Campylobacter jejuni  NCTC12662.	Genome Announcements	2017	5		e00409-17			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. 		
@D	Geng, J.//Chiu, C.H.//Tang, P.//Chen, Y.//Shieh, H.R.//Hu, S.//Chen, Y.Y. 	Complete Genome and Transcriptomes of Streptococcus parasanguinis FW213: Phylogenic Relations and Potential Virulence Mechanisms.	PLoS ONE	2012	7		E34769			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. 		
@D	Geng, J.//Huang, S.C.//Li, S.//Hu, S.//Chen, Y.Y. 	Complete Genome Sequence of the Ureolytic Streptococcus salivarius Strain 57.I.	J. Bacteriol.	2011	193		5596-5597			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. 		
@D	Geng, W.//Cao, M.//Song, C.//Xie, H.//Liu, L.//Yang, C.//Feng, J.//Zhang, W.//Jin, Y.//Du, Y.//Wang, S. 	Complete genome sequence of Bacillus amyloliquefaciens LL3, which exhibits glutamic acid-independent production of poly-{gamma}-glutamic acid.	J. Bacteriol.	2011	193		3393-3394			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. 		
@D	Genger, R.K.//Kovac, K.A.//Dennis, E.S.//Peacock, W.J.//Finnegan, E.J. 	Multiple DNA methyltransferase genes in Arabidopsis thaliana.	Plant Mol. Biol.	1999	41		269-278			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. 		
@D	Gentzbittel, L.//Nicolas, P. 	A basic program to construct evolutionary trees from restriction endonuclease data.	J. Hered.	1989	80		254			None 		
@D	Gentzbittel, L.//Nicolas, P. 	Improvement of "A BASIC program to construct evolutionary trees from restriction endonuclease data" with the use of PASCAL.	J. Hered.	1990	81		491-492			None 		
@D	George, J.//Blakesley, R.W.//Chirikjian, J.G. 	Sequence-specific endonuclease BamHI.	J. Biol. Chem.	1980	255		6521-6524			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. 		
@D	George, J.//Chirikjian, J.G. 	Biospecific fractionation matrices for sequence specific endonucleases.	Nucleic Acids Res.	1978	5		2223-2232			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. 		
@D	George, J.//Chirikjian, J.G. 	Sequence-specific endonuclease BamHI: Relaxation of sequence recognition.	Proc. Natl. Acad. Sci. U. S. A.	1982	79		2432-2436			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. 		
@D	George, J.//Hamada, Y.-Y.T.//Chirikjian, J.G. 	Chemical modifications as structural probes for the recognition of DNA palindromes by BamHI and BglI.	Fed. Proc.	1981	40		1848			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. 		
@D	George, J.//Nardone, G.//Chirikjian, J.G. 	Sequence-specific BamHI endonuclease.	J. Biol. Chem.	1985	260		14387-14392			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. 		
@D	Georgi, E.//Walter, M.C.//Pfalzgraf, M.T.//Northoff, B.H.//Holdt, L.M.//Scholz, H.C.//Zoeller, L.//Zange, S.//Antwerpen, M.H. 	Whole genome sequencing of Brucella melitensis isolated from 57 patients in Germany reveals high diversity in strains from Middle East.	PLoS ONE	2017	12		E0175425			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. 		
@D	Gerasimaite, R.//Klimasauskas, S. 	Novel approaches to engineering sequence-specificity of DNA cytosine-5 methyltransferases.	FEBS J.	2007	274		259			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. 		
@D	Gerasimaite, R.//Merkiene, E.//Klimasauskas, S. 	Direct observation of cytosine flipping and covalent catalysis in a DNA methyltransferase.	Nucleic Acids Res.	2011	39		3771-3780			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. 		
@D	Gerasimaite, R.//Vilkaitis, G.//Klimasauskas, S. 	A directed evolution design of a GCG-specific DNA hemimethylase.	Nucleic Acids Res.	2009	37		7332-7341			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. 		
@D	Gerbore, J.//Brutel, A.//Lemainque, A.//Mairey, B.//Medigue, C.//Vallenet, D.//Lefort, F.//Grizard, D. 	Complete Genome Sequence of Bacillus methylotrophicus Strain B25, a Potential Plant Growth-Promoting Rhizobacterium.	Genome Announcements	2016	4		e00058-16			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. 		
@D	Germann, M.W.//Kalisch, B.W.//Lundberg, P.//Vogel, H.J.//van de Sande, J.H. 	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.	Nucleic Acids Res.	1990	18		1489-1498			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. 		
@D	Germann, M.W.//Kalisch, B.W.//Varnum, J.M.//Vogel, H.J.//van de Sande, J.H. 	NMR spectroscopic and enzymatic studies of DNA hairpins containing mismatches in the EcoRI recognition site.	Biochem. Cell Biol.	1998	76		391-402			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. 		
@D	Gerome, P.//Le Fleche, P.//Blouin, Y.//Scholz, H.C.//Thibault, F.M.//Raynaud, F.//Vergnaud, G.//Pourcel, C. 	Yersinia pseudotuberculosis ST42 (O:1) Strain Misidentified as Yersinia pestis by Mass Spectrometry Analysis.	Genome Announcements	2014	2		e00435-14			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. 		
@D	Gerrish, R.S.//Gill, A.L.//Fowler, V.G.//Gill, S.R. 	Development of pooled suppression subtractive hybridization to analyze the pangenome of Staphylococcus aureus.	J. Microbiol. Methods	2010	81		56-60			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. 		
@D	Gerst, M.M.//Dudley, E.G.//Xiaoli, L.//Yousef, A.E. 	Draft Genome Sequence of Bacillus velezensis GF610, a Producer of Potent Anti-Listeria Agents.	Genome Announcements	2017	5		e01046-17			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%. 		
@D	Gerst, M.M.//Yesil, M.//Yousef, A.E. 	Draft Genome Sequence of Bacillus velezensis OSY-S3, a Producer of Potent Antimicrobial Agents Active against Bacteria and Fungi.	Genome Announcements	2018	6		e01465-17			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%. 		
@D	Getaz, M.//Baeyen, S.//Blom, J.//Maes, M.//Cottyn, B.//Pothier, J.F. 	High-Quality Draft Genome Sequences of Five Xanthomonas arboricola pv. fragariae  Isolates.	Genome Announcements	2018	6		e01585-17			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. 		
@D	Getaz, M.//van der Wolf, J.M.//Blom, J.//Pothier, J.F. 	Complete Genome Sequences of Three Isolates of Xanthomonas fragariae, the Bacterium Responsible for Angular Leaf Spots on Strawberry Plants.	Genome Announcements	2017	5		e00642-17			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. 		
@D	Geue, L.//Menge, C.//Berens, C.//Barth, S.A. 	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.	Genome Announcements	2017	5		e00321-17			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. 		
@D	Gfeller, K.Y.//Roth, M.//Melle, L.//Teuber, M. 	Sequence and genetic organization of the 19.3-kb erythromycin- and dalfopristin-resistance plasmid pLME300 from Lactobacillus fermentum  ROT1.	Plasmid	2003	50		190-201			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. 		
@D	Ghai, R.//Martin-Cuadrado, A.B.//Molto, A.G.//Heredia, I.G.//Cabrera, R.//Martin, J.//Verdu, M.//Deschamps, P.//Moreira, D.//Lopez-Garcia, P.//Mira, A.//Rodriguez-Valera, F. 	Metagenome of the Mediterranean deep chlorophyll maximum studied by direct and fosmid library 454 pyrosequencing.	ISME J.	2010	0		1-13			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. 		
@D	Ghaskadbi, S.//Bharathi, S.//Modak, S.P. 	Inhibition of cleavage by restriction endonucleases due to modifications induced in SV40 DNA by methyl methanesulfonate.	Cell. Mol. Biol. Res.	1995	41		59-66			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. 		
@D	Ghazal, S.//Hurst, S.G.I.V.//Morris, K.//Abebe-Akele, F.//Thomas, W.K.//Badr, U.M.//Hussein, M.A.//Abouzaied, M.A.//Khalil, K.M.//Tisa, L.S. 	Draft Genome Sequence of Photorhabdus luminescens Strain BA1, an Entomopathogenic Bacterium Isolated from Nematodes Found in Egypt.	Genome Announcements	2014	2		e00396-14			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. 		
@D	Ghazal, S.//Oshone, R.//Simpson, S.//Morris, K.//Abebe-Akele, F.//Thomas, W.K.//Khalil, K.M.//Tisa, L.S. 	Draft Genome Sequence of Photorhabdus luminescens subsp. laumondii HP88, an Entomopathogenic Bacterium Isolated from Nematodes.	Genome Announcements	2016	4		e00154-16			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. 		
@D	Ghazal, S.//Swanson, E.//Simpson, S.//Morris, K.//Abebe-Akele, F.//Thomas, W.K.//Khalil, K.M.//Tisa, L.S. 	Permanent Draft Genome Sequence of Photorhabdus temperata Strain Hm, an Entomopathogenic Bacterium Isolated from Nematodes.	Genome Announcements	2017	5		e00974-17			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. 		
@D	Ghequire, M.G.//Rokni-Zadeh, H.//Zarrineh, P.//De Mot, R. 	Draft Genome Sequence of Pseudomonas fluorescens LMG 5329, a White Line-Inducing  Principle-Producing Bioindicator for the Mushroom Pathogen Pseudomonas tolaasii.	Genome Announcements	2013	1		e00383-13			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. 		
@D	Ghequire, M.G.//Swings, T.//Michiels, J.//Gross, H.//De Mot, R. 	Draft Genome Sequence of Pseudomonas putida BW11M1, a Banana Rhizosphere Isolate  with a Diversified Antimicrobial Armamentarium.	Genome Announcements	2016	4		e00251-16			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. 		
@D	Ghio, S.//Martinez, C.A.I.//Talia, P.//Grasso, D.H.//Campos, E. 	Draft Genome Sequence of Cellulolytic and Xylanolytic Paenibacillus sp. A59, Isolated from Decaying Forest Soil from Patagonia, Argentina.	Genome Announcements	2015	3		e01233-15			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. 		
@D	Ghodhbane-Gtari, F. et al. 	Permanent Draft Genome Sequence of Nocardia sp. BMG111209, an Actinobacterium Isolated from Nodules of Casuarina glauca.	Genome Announcements	2016	4		e00770-16			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. 		
@D	Ghodhbane-Gtari, F. et al. 	Permanent Improved High-Quality Draft Genome Sequence of Nocardia casuarinae Strain BMG51109, an Endophyte of Actinorhizal Root Nodules of Casuarina glauca.	Genome Announcements	2016	4		e00799-16			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. 		
@D	Ghodhbane-Gtari, F. et al. 	Draft Genome Sequence of Frankia sp. Strain CN3, an Atypical, Noninfective (Nod-) Ineffective (Fix-) Isolate from Coriaria nepalensis.	Genome Announcements	2013	1		e0008513			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. 		
@D	Ghodhbane-Gtari, F.//Hurst, S.G.I.V.//Oshone, R.//Morris, K.//Abebe-Akele, F.//Thomas, W.K.//Ktari, A.//Salem, K.//Gtari, M.//Tisa, L.S. 	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.	Genome Announcements	2014	2		e00520-14			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. 		
@D	Gholizadeh, A.//Faizi, M.H.//Kohnehrouz, B.B. 	Induced expression of EcoRI endonuclease as an active maltose-binding fusion protein in Escherichia coli.	Microbiology	2010	79		167-172			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. 		
@D	Gholizadeh, A.//Kohnehrouz, B.B. 	Carborundum-dependent entrance of EcoRI restriction enzyme into plant cells and specific cleavage of genomic DNA.	Indian J. Exp. Biol.	2009	47		684-689			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. 		
@D	Ghosh, A.//Chandratre, K.//Chaudhary, A.//Chaudhary, S.//Badani, N.//Chaudhary, P.S.//Dhawan, D.//Vudathala, S.//Chikara, S.K. 	Whole-Genome Sequencing of Brevundimonas diminuta XGC1, Isolated from a Tuberculosis Patient in Gujarat, India.	Genome Announcements	2015	3		e00686-15			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. 		
@D	Ghosh, A.//Chaudhary, S.A.//Apurva, S.R.//Tiwari, T.//Gupta, S.//Singh, A.K.//Katudia, K.H.//Patel, M.P.//Chikara, S.K. 	Whole-Genome Sequencing of Micrococcus luteus Strain Modasa, of Indian Origin.	Genome Announcements	2013	1		e0007613			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. 		
@D	Ghosh, A.//Passaris, I.//Tesfazgi, M.M.//Rocha, S.//Vanoirbeek, K.//Hofkens, J.//Aertsen, A. 	Cellular localization and dynamics of the Mrr type IV restriction endonuclease of Escherichia coli.	Nucleic Acids Res.	2014	42		3908-3918			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. 		
@D	Ghosh, H.//Bunk, B.//Doijad, S.//Schmiedel, J.//Falgenhauer, L.//Sproer, C.//Imirzalioglu, C.//Overmann, J.//Chakraborty, T. 	Complete Genome Sequence of blaCTX-M-27-Encoding Escherichia coli Strain H105 of  Sequence Type 131 Lineage C1/H30R.	Genome Announcements	2017	5		e00736-17			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. 		
@D	Ghosh, I.//Sun, L.//Evans, T.C.//Xu, M.Q. 	An improved method for utilization of peptide substrates for antibody characterization and enzymatic assays.	J. Immunol. Methods	2004	293		85-95			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. 		
@D	Ghosh, S.//LaPara, T.M.//Sadowsky, M.J. 	Draft Genome Sequence of Sphingobacterium sp. Strain PM2-P1-29, a Tetracycline-Degrading TetX-Expressing Aerobic Bacterium Isolated from  Agricultural Soil.	Genome Announcements	2014	2		e00963-14			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. 		
@D	Ghosh, S.S.//Eis, P.S.//Blumeyer, K.//Fearon, K.//Millar, D.P. 	Real time kinetics of restriction endonuclease cleavage monitored by fluorescence resonance energy transfer.	Nucleic Acids Res.	1994	22		3155-3159			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. 		
@D	Ghosh, S.S.//Obermiller, P.S.//Kwoh, T.J.//Gingeras, T.R. 	Analysis of substrate specificity of the PaeR7I endonuclease: effect of base methylation on the kinetics of cleavage.	Nucleic Acids Res.	1990	18		5063-5068			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. 		
@D	Ghosh, W.//George, A.//Agarwal, A.//Raj, P.//Alam, M.//Pyne, P.//Das Gupta, S.K. 	Whole-Genome Shotgun Sequencing of the Sulfur-Oxidizing Chemoautotroph Tetrathiobacter kashmirensis.	J. Bacteriol.	2011	193		5553-5554			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. 		
@D	Giacani, L.//Iverson-Cabral, S.L.//King, J.C.//Molini, B.J.//Lukehart, S.A.//Centurion-Lara, A. 	Complete Genome Sequence of the Treponema pallidum subsp. pallidum Sea81-4 Strain.	Genome Announcements	2014	2		e00333-14			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. 		
@D	Giacani, L.//Jeffrey, B.M.//Molini, B.J.//Le, H.T.//Lukehart, S.A.//Centurion-Lara, A.//Rockey, D.D. 	Complete genome sequence and annotation of the Treponema pallidum subsp. pallidum Chicago strain.	J. Bacteriol.	2010	192		2645-2646			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. 		
@D	Giacomodonato, M.N.//Llana, M.N.//Castaneda, M.R.//Buzzola, F.//Garcia, M.D.//Calderon, M.D.//Sarnacki, S.H.//Cerquetti, M.C. 	Dam methylation regulates the expression of SPI-5-encoded sopB gene in Salmonella enterica serovar Typhimurium.	Microbes Infect.	2014	16		615-622			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. 		
@D	Giammanco, G.M.//Grimont, F.//Grimont, P.A. 	MboII endonuclease heat inactivation before agarose gel electrophoresis to prevent artifactual bands in restriction patterns.	Biotechniques	1999	27		886-887			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. 		
@D	Giampetruzzi, A.//Chiumenti, M.//Saponari, M.//Donvito, G.//Italiano, A.//Loconsole, G.//Boscia, D.//Cariddi, C.//Martelli, G.P.//Saldarelli, P. 	Draft Genome Sequence of the Xylella fastidiosa CoDiRO Strain.	Genome Announcements	2015	3		e01538-14			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. 		
@D	Giampetruzzi, A.//Loconsole, G.//Boscia, D.//Calzolari, A.//Chiumenti, M.//Martelli, G.P.//Saldarelli, P.//Almeida, R.P.//Saponari, M. 	Draft Genome Sequence of CO33, a Coffee-Infecting Isolate of Xylella fastidiosa.	Genome Announcements	2015	3		e01472-15			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%. 		
@D	Giampetruzzi, A.//Saponari, M.//Almeida, R.P.P.//Essakhi, S.//Boscia, D.//Loconsole, G.//Saldarelli, P. 	Complete Genome Sequence of the Olive-Infecting Strain Xylella fastidiosa subsp.  pauca De Donno.	Genome Announcements	2017	5		e00569-17			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. 		
@D	Giannakis, M.//Chen, S.L.//Karam, S.M.//Engstrand, L.//Gordon, J.I. 	Helicobacter pylori evolution during progression from chronic atrophic gastritis to gastric cancer and its impact on gastric stem cells.	Proc. Natl. Acad. Sci. U. S. A.	2008	105		4358-4363			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. 		
@D	Giannino, D.//Mele, G.//Cozza, R.//Bruno, L.//Testone, G.//Ticconi, C.//Frugis, G.//Bitonti, M.B.//Innocenti, A.M.//Mariotti, D. 	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.	J. Exp. Bot.	2003	54		2623-2633			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. 		
@D	Gias, E.//Draper, J.//Brosnahan, C.L.//Orr, D.//McFadden, A.//Jones, B. 	Draft Genome Sequence of a New Zealand Rickettsia-Like Organism Isolated from Farmed Chinook Salmon.	Genome Announcements	2016	4		e00503-16			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. 		
@D	Gibb, E.A.//Edgell, D.R. 	Better late than early: delayed translation of intron-encoded endonuclease I-TevI is required for efficient splicing of its host group I intron.	Mol. Microbiol.	2010	78		35-46			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. 		
@D	Gibson, D.G. et al. 	Complete chemical synthesis, assembly, and cloning of a Mycoplasma genitalium genome.	Science	2008	319		1215-1220			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. 		
@D	Gibson, D.G. et al. 	Creation of a bacterial cell controlled by a chemically synthesized genome.	Science	2010	329		52-56			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. 		
@D	Giebel, H.A.//Klotz, F.//Voget, S.//Poehlein, A.//Grosser, K.//Teske, A.//Brinkhoff, T. 	Draft genome sequence of the marine Rhodobacteraceae strain O3.65, cultivated from oil-polluted seawater of the Deepwater Horizon oil spill.	Standards in Genomic Sciences	2016	11		81			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. 		
@D	Gil, R.//Silva, F.J.//Zientz, E.//Delmotte, F.//Gonzalez-Candelas, F.//Latorre, A.//Rausell, C.//Kamerbeek, J.//Gadau, J.//Holldobler, B.//Van Ham, R.C.//Gross, R.//Moya, A. 	The genome sequence of Blochmannia floridanus: Comparative analysis of reduced genomes.	Proc. Natl. Acad. Sci. U. S. A.	2003	100		9388-9393			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. 		
@D	Gilbert, M.J.//Miller, W.G.//Yee, E.//Blaser, M.J.//Wagenaar, J.A.//Duim, B. 	Complete Genome Sequence of Campylobacter fetus subsp. testudinum Strain 03-427T.	Genome Announcements	2013	1		e01002-13			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. 		
@D	Gilbert, M.J.//Miller, W.G.//Yee, E.//Kik, M.//Wagenaar, J.A.//Duim, B. 	Complete Genome Sequence of Campylobacter iguaniorum Strain 1485ET, Isolated from a Bearded Dragon (Pogona vitticeps).	Genome Announcements	2014	2		e00844-14			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. 		
@D	Gill, J.J.//Berry, J.D.//Russell, W.K.//Lessor, L.//Escobar-Garcia, D.A.//Hernandez, D.//Kane, A.//Keene, J.//Maddox, M.//Martin, R.//Mohan, S.//Thorn, A.M.//Russell, D.H.//Young, R. 	The Caulobacter crescentus phage phiCbK: genomics of a canonical phage.	BMC Genomics	2012	13		542			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. 		
@D	Gill, S.R. et al. 	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.	J. Bacteriol.	2005	187		2426-2438			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. 		
@D	Gillings, M.R.//Labbate, M.//Sajjad, A.//Giguere, N.J.//Holley, M.P.//Stokes, H.W. 	Mobilization of a Tn402-like class 1 integron with a novel cassette array via flanking miniature inverted-repeat transposable element-like structures.	Appl. Environ. Microbiol.	2009	75		6002-6004			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. 		
@D	Gilrane, V.L.//Lobo, S.//Huang, W.//Zhuge, J.//Yin, C.//Chen, D.//Alvarez, K.J.//Budhai, A.//Nadelman, I.//Dimitrova, N.//Fallon, J.T.//Wang, G. 	Complete Genome Sequence of a Colistin-Resistant Escherichia coli Strain Harboring mcr-1 on an IncHI2 Plasmid in the United States.	Genome Announcements	2017	5		e01095-17			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. 		
@D	Gimble, F.S. 	Engineering homing endonucleases to modify complex genomes.	Gene Ther. Regul.	2006	3		33-50			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. 		
@D	Gimble, F.S. 	Engineering homing endonucleases for genomic applications.	Nucleic Acids Mol. Biol.	2005	16		177-192			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. 		
@D	Gimble, F.S. 	Invasion of a multitude of genetic niches by mobile endonuclease genes.	FEMS Microbiol. Lett.	2000	185		99-107			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. 		
@D	Gimble, F.S. 	Degeneration of a homing endonuclease and its target sequence in a wild yeast strain.	Nucleic Acids Res.	2001	29		4215-4223			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. 		
@D	Gimble, F.S. 	Broken symmetry in homing endonucleases.	Structure	2006	14		804-806			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. 		
@D	Gimble, F.S.//Duan, X.//Hu, D.//Quiocho, F.A. 	Identification of lys-403 in the PI-SceI homing endonuclease as part of a symmetric catalytic center.	J. Biol. Chem.	1998	273		30524-30529			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. 		
@D	Gimble, F.S.//Moure, C.M.//Posey, K.L. 	Assessing the plasticity of DNA target site recognition of the PI-SceI homing endonuclease using a bacterial two-hybrid selection system.	J. Mol. Biol.	2003	334		993-1008			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. 		
@D	Gimble, F.S.//Stephens, B.W. 	Substitutions in conserved dodecapeptide motifs that uncouple the DNA binding and DNA cleavage activities of PI-SceI endonuclease.	J. Biol. Chem.	1995	270		5849-5856			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. 		
@D	Gimble, F.S.//Thorner, J. 	Homing of a DNA endonuclease gene by meiotic gene conversion in Saccharomyces cerevisiae.	Nature	1992	357		301-306			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. 		
@D	Gimble, F.S.//Thorner, J. 	Purification and characterization of VDE, a site-specific endonuclease from the yeast Saccharomyces cerevisiae.	J. Biol. Chem.	1993	268		21844-21853			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). 		
@D	Gimble, F.S.//Wang, J. 	Substrate recognition and induced DNA distortion by the PI-SceI endonuclease, an enzyme generated by protein splicing.	J. Mol. Biol.	1996	263		163-180			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. 		
@D	Gingeras, T.R. 	Restriction endonucleases and their recognition sequences.	Biochem. Soc. Trans.	1980	8		397-398			None 		
@A	Gingeras, T.R. 		Restriction-modification systems: Genetic sentries and useful systems in the study of molecular genetics.			Streips, U.N.//Yasbin, R.E. 		Modern Microbial Genetics				New York	Wiley-Liss, Inc.	1991		0		301-321									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. 		
@A	Gingeras, T.R.//Blumenthal, R.M.//Roberts, R.J.//Brooks, J.E. 		The isolation and characterization of the E. coli dam methylase gene.			Zelinka, J.//Balan, J. 		Metabolism and Enzymology of Nucleic Acids				Bratislava	Publishing House of the Slovak Academy of Sciences	1982		4		329-340									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. 		
@D	Gingeras, T.R.//Brooks, J.E. 	Cloned restriction/modification system from Pseudomonas aeruginosa.	Proc. Natl. Acad. Sci. U. S. A.	1983	80		402-406			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. 		
@D	Gingeras, T.R.//Ghosh, S.//Blumeyer, K.//Eis, R.//Millar, D. 	A spectrofluorometric method for measurement of restriction endonuclease activity based on fluorescence polarization.	J. Cell Biochem. Suppl.	1993	17C		173			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. 		
@D	Gingeras, T.R.//Greenough, L.//Schildkraut, I.//Roberts, R.J. 	Two new restriction endonucleases from Proteus vulgaris.	Nucleic Acids Res.	1981	9		4525-4536			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. 		
@D	Gingeras, T.R.//Milazzo, J.P.//Roberts, R.J. 	A computer assisted method for the determination of restriction enzyme recognition sites.	Nucleic Acids Res.	1978	5		4105-4127			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. 		
@D	Gingeras, T.R.//Myers, P.A.//Olson, J.A.//Hanberg, F.A.//Roberts, R.J. 	A new specific endonuclease present in Xanthomonas holcicola, Xanthomonas papavericola and Brevibacterium luteum.	J. Mol. Biol.	1978	118		113-122			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. 		
@A	Gingeras, T.R.//Theriault, G.//Brooks, J.E. 		Organization and expression of a type II restriction-modification system from Pseudomonas aeruginosa.			Zelinka, J.//Balan, J. 		Metabolism and Enzymology of Nucleic Acids				Bratislava	Publishing House of the Slovak Academy of Sciences.	1984		5		267-275									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. 		
@D	Ginn, A.//Ma, Z.//Galvao, K.N.//Jeong, K.C. 	Draft Genome Sequence of an Escherichia coli O8:H19 Sequence Type 708 Strain Isolated from a Holstein Dairy Cow with Metritis.	Genome Announcements	2016	4		e00261-16			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. 		
@D	Gioia, J. et al. 	Paradoxical DNA Repair and Peroxide Resistance Gene Conservation in Bacillus pumilus SAFR-032.	PLoS ONE	2007	2		e928			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. 		
@D	Gioia, J.//Qin, X.//Jiang, H.//Clinkenbeard, K.//Lo, R.//Liu, Y.//Fox, G.E.//Yerrapragada, S.//McLeod, M.P.//McNeill, T.Z.//Hemphill, L.//Sodergren, E.//Wang, Q.//Muzny, D.M.//Homsi, F.J.//Weinstock, G.M.//Highlander, S.K. 	The Genome Sequence of Mannheimia haemolytica A1: Insights into Virulence, Natural Competence, and Pasteurellaceae Phylogeny.	J. Bacteriol.	2006	188		7257-7266			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. 		
@D	Giongo, A.//Tyler, H.L.//Zipperer, U.N.//Triplett, E.W. 	Two genome sequences of the same bacterial strain, Gluconacetobacter diazotrophicus PAl 5, suggest a new standard in genome sequence submission.	Standards in Genomic Sciences	2010	2		309-317			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. 		
@D	Giordani, F.//Fillo, S.//Anselmo, A.//Palozzi, A.M.//Fortunato, A.//Gentile, B.//Pittiglio, V.//Spagnolo, F.//Anniballi, F.//Fiore, A.//Auricchio, B.//De Medici, D.//Lista, F. 	Whole-Genome Sequence of Clostridium botulinum A2B3 87, a Highly Virulent Strain  Involved in a Fatal Case of Foodborne Botulism in Italy.	Genome Announcements	2015	3		e00237-15			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. 		
@D	Giordano, M.//Mattachini, M.E.//Cella, R.//Pedrali-Noy, G. 	Purification and properties of a novel DNA methyltransferase from cultured rice cells.	Biochem. Biophys. Res. Commun.	1991	177		711-719			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. 		
@D	Giorello, F.M.//Romero, V.//Farias, J.//Scavone, P.//Umpierrez, A.//Zunino, P.//Sotelo, S.J.R. 	Draft Genome Sequence and Gene Annotation of the Uropathogenic Bacterium Proteus  mirabilis Pr2921.	Genome Announcements	2016	4		e00564-16			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. 		
@D	Giovannelli, D. et al. 	Complete genome sequence of Thermovibrio ammonificans HB-1(T), a thermophilic, chemolithoautotrophic bacterium isolated from a deep-sea hydrothermal vent.	Standards in Genomic Sciences	2012	7		82-90			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). 		
@D	Giovannelli, D.//Ferriera, S.//Johnson, J.//Kravitz, S.//Perez-Rodriguez, I.//Ricci, J.//O'Brien, C.//Voordeckers, J.W.//Bini, E.//Vetriani, C. 	Draft genome sequence of Caminibacter mediatlanticus strain TB-2, an epsilonproteobacterium isolated from a deep-sea hydrothermal vent.	Standards in Genomic Sciences	2011	5		135-143			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). 		
@D	Giovannoni, S.J.//Tripp, H.J.//Givan, S.//Podar, M.//Vergin, K.L.//Baptista, D.//Bibbs, L.//Eads, J.//Richardson, T.H.//Noordewier, M.//Rappe, M.S.//Short, J.M.//Carrington, J.C.//Mathur, E.J. 	Genome streamlining in a cosmopolitan oceanic bacterium.	Science	2005	309		1242-1245			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. 		
@D	Giraud, C.//Hausmann, S.//Lemeille, S.//Prados, J.//Redder, P.//Linder, P. 	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.	RNA Biol.	2015	12		658-674			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. 		
@D	Girault, G.//Parisot, N.//Peyretaillade, E.//Peyret, P.//Derzelle, S. 	Draft Genomes of Three Strains Representative of the Bacillus anthracis Diversity Found in France.	Genome Announcements	2014	2		e00736-14			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. 		
@D	Girault, G.//Woudstra, C.//Martin, B.//Vorimore, F.//Lucia-de-Assis-Santana, V.//Fach, P.//Madani, N.//Laroucau, K. 	First Draft Genome for a Burkholderia mallei Isolate Originating from a Glanderous Mule from Brazil.	Genome Announcements	2017	5		e00579-17			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. 		
@D	Girlich, D.//Poirel, L.//Nordmann, P. 	A diversity of clavulanic acid-inhibited extended-spectrum {beta}-lactamases in Aeromonas sp. from the Seine River, Paris, France.	Antimicrob. Agents Chemother.	2011	55		1256-1261			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. 		
@D	Girlich, D.//Poirel, L.//Szczepanowski, R.//Schluter, A.//Nordmann, P. 	Carbapenem-Hydrolyzing GES-5-Encoding Gene on Different Plasmid Types Recovered from a Bacterial Community in a Sewage Treatment Plant.	Appl. Environ. Microbiol.	2012	78		1292-1295			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. 		
@D	Gitschier, J. 	A Half-Century of Inspiration: An Interview with Hamilton Smith.	PLoS Genet.	2012	8		e1002466			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. 		
@D	Giufre, M.//Accogli, M.//Graziani, C.//Busani, L.//Cerquetti, M. 	Whole-Genome Sequences of Multidrug-Resistant Escherichia coli Strains Sharing the Same Sequence Type (ST410) and Isolated from Human and Avian Sources in  Italy.	Genome Announcements	2015	3		e00757-15			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. 		
@D	Giufre, M.//Cardines, R.//Cerquetti, M. 	First Whole-Genome Sequence of a Haemophilus influenzae Type e Strain Isolated from a Patient with Invasive Disease in Italy.	Genome Announcements	2017	5		e00059-17			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. 		
@D	Giufre, M.//De Chiara, M.//Censini, S.//Guidotti, S.//Torricelli, G.//De Angelis, G.//Cardines, R.//Pizza, M.//Muzzi, A.//Cerquetti, M.//Soriani, M. 	Whole-Genome Sequences of Nonencapsulated Haemophilus influenzae Strains Isolated in Italy.	Genome Announcements	2015	3		e00110-15			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. 		
@D	Givan, S.A.//Zhou, M.Y.//Bromert, K.//Bivens, N.//Chapman, L.F. 	Genome Sequences of Pseudoalteromonas Strains ATCC BAA-314, ATCC 70018, and ATCC  70019.	Genome Announcements	2015	3		e00390-15			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. 		
@D	Gizard, Y.//Zbinden, A.//Schrenzel, J.//Francois, P. 	Whole-Genome Sequences of Streptococcus tigurinus Type Strain AZ_3a and S. tigurinus 1366, a Strain Causing Prosthetic Joint Infection.	Genome Announcements	2013	1		e00210-12			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. 		
@D	Gkorezis, P.//Bottos, E.M.//Van Hamme, J.D.//Franzetti, A.//Abbamondi, G.R.//Balseiro-Romero, M.//Weyens, N.//Rineau, F.//Vangronsveld, J. 	Draft Genome Sequence of Acinetobacter calcoaceticus Strain GK1, a Hydrocarbon-Degrading Plant Growth-Promoting Rhizospheric Bacterium.	Genome Announcements	2015	3		e00909-15			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. 		
@D	Gkorezis, P.//Bottos, E.M.//Van Hamme, J.D.//Thijs, S.//Rineau, F.//Franzetti, A.//Balseiro-Romero, M.//Weyens, N.//Vangronsveld, J. 	Draft Genome Sequence of Arthrobacter sp. Strain SPG23, a Hydrocarbon-Degrading and Plant Growth-Promoting Soil Bacterium.	Genome Announcements	2015	3		e01517-15			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. 		
@D	Gkorezis, P.//Rineau, F.//Van Hamme, J.//Franzetti, A.//Daghio, M.//Thijs, S.//Weyens, N.//Vangronsveld, J. 	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.	Genome Announcements	2015	3		e01430-14			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. 		
@D	Gkorezis, P.//Van Hamme, J.//Bottos, E.//Thijs, S.//Balseiro-Romero, M.//Monterroso, C.//Kidd, P.S.//Rineau, F.//Weyens, N.//Sillen, W.//Vangronsveld, J. 	Draft Genome Sequence of Bacillus licheniformis Strain GB2, a Hydrocarbon-Degrading and Plant Growth-Promoting Soil Bacterium.	Genome Announcements	2016	4		e00608-16			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. 		
@D	Gkorezis, P.//Van Hamme, J.D.//Bottos, E.M.//Thijs, S.//Balseiro-Romero, M.//Monterroso, C.//Kidd, P.S.//Rineau, F.//Weyens, N.//Vangronsveld, J. 	Draft Genome Sequence of Pantoea ananatis GB1, a Plant-Growth-Promoting Hydrocarbonoclastic Root Endophyte, Isolated at a Diesel Fuel Phytoremediation  Site Planted with Populus.	Genome Announcements	2016	4		e00028-16			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. 		
@D	Gladitz, J.//Shen, K.//Antalis, P.//Hu, F.Z.//Post, J.C.//Ehrlich, G.D. 	Codon usage comparison of novel genes in clinical isolates of Haemophilus influenzae.	Nucleic Acids Res.	2005	33		3644-3658			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 		
@D	Gladney, L.M.//Katz, L.S.//Knipe, K.M.//Rowe, L.A.//Conley, A.B.//Rishishwar, L.//Marino-Ramirez, L.//Jordan, I.K.//Tarr, C.L. 	Genome Sequences of Vibrio navarrensis, a Potential Human Pathogen.	Genome Announcements	2014	2		e01188-14			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. 		
@D	Glady-Croue, J.//Niu, X.-Z.//Ramsay, J.P.//Watkin, E.//Murphy, R.J.T.//Croue, J.-P. 	Survival of antibiotic resistant bacteria following artificial solar radiation of secondary wastewater effluent.	Sci. Total Environ.	2018	626		1005-1011			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. 		
@D	Gladysheva, I.V.//Cherkasov, S.V.//Khlopko, Y.A.//Plotnikov, A.O.//Gogoleva, N.E. 	Draft Genome Sequence of Corynebacterium amycolatum Strain ICIS 53 Isolated from  a Female Urogenital Tract.	Genome Announcements	2016	4		e01267-16			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. 		
@D	Gladysheva, I.V.//Khlopko, Y.A.//Cherkasov, S.V. 	Draft Genome Sequence of the Vaginal Isolate Corynebacterium amycolatum ICIS 9.	Genome Announcements	2017	5		e00975-17			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. 		
@D	Glaser, P. et al. 	Comparative genomics of Listeria species.	Science	2001	294		849-852			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. 		
@D	Glaser, P.//Rusniok, C.//Buchrieser, C.//Chevalier, F.//Frangeul, L.//Msadek, T.//Zouine, M.//Couve, E.//Lalioui, L.//Poyart, C.//Trieu-Cuot, P.//Kunst, F. 	Genome sequence of Streptococcus agalactiae, a pathogen causing invasive neonatal disease.	Mol. Microbiol.	2002	45		1499-1513			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. 		
@D	Glasner, J.D. et al. 	Genome Sequence of the Plant-Pathogenic Bacterium Dickeya dadantii 3937.	J. Bacteriol.	2011	193		2076-2077			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. 		
@D	Glasner, J.D.//Marquez-Villavicencio, M.//Kim, H.S.//Jahn, C.E.//Ma, B.//Biehl, B.S.//Rissman, A.I.//Mole, B.//Yi, X.//Yang, C.H.//Dangl, J.L.//Grant, S.R.//Perna, N.T.//Charkowski, A.O. 	Niche-specificity and the variable fraction of the Pectobacterium pan-genome.	Mol. Plant Microbe Interact.	2008	21		1549-1560			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. 		
@A	Glasner, W.//Hennecke, F.//Fritz, H.J. 		Enzymatic properties and biological functions of VSR DNA mismatch endonuclease.			 		Structural tools for the analysis of protein-nucleic acid complexes advances in life sciences.				Basel	Birkhauser Verlag	1992		0		165-173									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. 		
@D	Glasner, W.//Merkl, R.//Schellenberger, V.//Fritz, H.J. 	Substrate preferences of Vsr DNA mismatch endonuclease and their consequences for the evolution of the Escherichia coli K-12 genome.	J. Mol. Biol.	1995	245		1-7			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. 		
@D	Glass, J.I.//Lefkowitz, E.J.//Glass, J.S.//Heiner, C.R.//Chen, E.Y.//Cassell, G.H. 	The complete sequence of the mucosal pathogen Ureaplasma urealyticum.	Nature	2000	407		757-762			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. 		
@D	Glatman, L.I.//Iablokova, M.B.//Kravets, A.I.//Terekhov, A.A.//Samoilenko, I.I. 	Identification of the plasmid pLG13 coding for the DNA modification-restriction system EcoRV and properties of strains carrying this plasmid.	Mol. Gen. Mikrobiol. Virusol.	1985	10		39-42					
@D	Glatman, L.I.//Kravets, A.N. 	Systems of DNA restriction-modification.	Antibiot. Khimioter	1989	34		932-938			None 		
@D	Glatman, L.I.//Moroz, A.F.//Iablokova, M.B.//Rebentish, B.A.//Kholmina, G.V. 	New DNA modification-restriction plasmid system detected in a clinical strain of Escherichia coli.	Dokl. Akad. Nauk.	1980	252		993-995					
@D	Glatman, L.I.//Moroz, A.F.//Yablokova, M.B.//Rebentish, B.A.//Kcholmina, G.V. 	A novel plasmid-mediated DNA restriction-modification system in E. coli.	Plasmid	1980	4		350-351			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. 		
@D	Glatman, L.I.//Terekhov, A.A.//Kalnin, K.V.//Bolotin, A.P.//Rebentish, B.A. 	New site-specific endodesoxyribonuclease EcoHI.	Mol. Gen. Mikrobiol. Virusol.	1990	3		32			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. 		
@D	Glaub, A.//Bomholt, C.//Gravermann, K.//Brinkrolf, K.//Albersmeier, A.//Ruckert, C.//Tauch, A. 	Complete Genome Sequence of Corynebacterium falsenii DSM 44353 To Study the Evolution of Corynebacterium Cluster 3 Species.	Genome Announcements	2014	2		e00158-14			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. 		
@D	Glavina Del Rio, T. et al. 	Complete genome sequence of Chitinophaga pinensis type strain (UQM 2034).	Standards in Genomic Sciences	2010	2		87-95			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. 		
@D	Glenn, T.C.//Waller, D.R.//Braun, M.J. 	Increasing proportions of uracil in DNA substrates increases inhibition of restriction enzyme digests.	Biotechniques	1994	17		1086-1090			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. 		
@D	Glickman, J.F. 	The murine DNA methyltransferase: Purification, heterologous expression, steady-state kinetics and post-translational processing.	Diss. Abstr.	1997	58		1265B			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. 		
@D	Glickman, J.F.//Flynn, J.//Reich, N.O. 	Purification and characterization of recombinant baculovirus-expressed mouse DNA methyltransferase.	Biochem. Biophys. Res. Commun.	1997	230		280-284			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. 		
@D	Glickman, J.F.//Pavlovich, J.G.//Reich, N.O. 	Peptide mapping of the murine DNA methyltransferase reveals a major phosphorylation site and the start of translation.	J. Biol. Chem.	1997	272		17851-17857			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. 		
@D	Glickman, J.F.//Reich, N.O. 	Baculovirus-mediated high level expression of a mammalian DNA methyltransferase.	Biochem. Biophys. Res. Commun.	1994	204		1003-1008			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. 		
@D	Glickman, J.F.//Reich, N.O. 	The expression of the murine DNA cytosine methyltransferase in cultured cells from Spodoptera frugiperda using a recombinant Baculovirus.	FASEB J.	1993	7		A1291			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. 		
@D	Gliniewicz, K.//Wildung, M.//Orfe, L.H.//Wiens, G.D.//Cain, K.D.//Lahmers, K.K.//Snekvik, K.R.//Call, D.R. 	Potential mechanisms of attenuation for rifampicin-passaged strains of Flavobacterium psychrophilum.	BMC Microbiol.	2015	15		179			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). 		
@D	Glockner, G.//Lehmann, R.//Romualdi, A.//Pradella, S.//Schulte-Spechtel, U.//Schilhabel, M.//Wilske, B.//Suhnel, J.//Platzer, M. 	Comparative analysis of the Borrelia garinii genome.	Nucleic Acids Res.	2004	32		6038-6046			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. 		
@D	Gloeckner, F.O.//Kube, M.//Bauer, M.//Teeling, H.//Lombardot, T.//Ludwig, W.//Gade, D.//Beck, A.//Borzym, K.//Heitmann, K.//Rabus, R.//Schlesner, H.//Amann, R.//Reinhardt, R. 	Complete genome sequence of the marine planctomycete Pirellula sp. strain 1.	Proc. Natl. Acad. Sci. U. S. A.	2003	100		8298-8303			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. 		
@D	Gloeckner, G.//Schulte-Spechtel, U.//Schilhabel, M.//Felder, M.//Suehnel, J.//Wilske, B.//Platzer, M. 	Comparative genome analysis: Selection pressure on the Borrelia vls cassettes is essential for infectivity.	BMC Genomics	2006	7		211			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. 		
@D	Glover, S.W. 	Genetics of the R-M systems in Haemophilus.	Heredity	1978	41		123			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. 		
@D	Glover, S.W. 	Restriction Endonucleases.  Genetics of restriction/modification systems.	Biochem. Soc. Trans.	1980	8		395-400			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. 		
@D	Glover, S.W. 	Functional analysis of host-specificity mutants in Escherichia coli.	Genet. Res.	1970	15		237-250			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. 		
@D	Glover, S.W. 	Host specificity in F' heterogenotes of Escherichia coli.	J. Gen. Microbiol.	1968	53		i-ii			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. 		
@D	Glover, S.W.//Colson, C. 	Genetics of host-controlled restriction and modification in Eschericia coli.	Genet. Res.	1969	13		227-240			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. 		
@D	Glover, S.W.//Colson, C. 	Stable and unstable alterations of the host-induced modification properties of Escherichia coli B, K and C.	Genet. Res.	1966	7		223-234			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. 		
@D	Glover, S.W.//Colson, C. 	The breakdown of the restriction mechanism in zygotes of Escherichia coli.	Genet. Res.	1965	6		153-155			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. 		
@D	Glover, S.W.//Firman, K. 	A novel class of restriction-deficient mutants.	Heredity	1978	41		122-123			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. 		
@A	Glover, S.W.//Firman, K. 		Genetic control of DNA specificity.			Streips, U.N.//Goodgal, S.H.//Guild, W.R.//Wilson, G.A. 		Genetic Exchange				New York	Marcel Dekker	1982		0		331-338									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. 		
@D	Glover, S.W.//Firman, K.//Watson, G.//Price, C.//Donaldson, S. 	The alternate expression of two restriction and modification systems.	Mol. Gen. Genet.	1983	190		65-69			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. 		
@D	Glover, S.W.//Piekarowicz, A. 	Host specificity of DNA in Haemophilus influenzae:  Restriction and modification in strain Rd.	Biochem. Biophys. Res. Commun.	1972	46		1610-1617			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. 		
@D	Glover, S.W.//Schell, J.//Symonds, N.//Stacey, K.A. 	The control of host-induced modification by phage P1.	Genet. Res.	1963	4		480-482			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. 		
@D	Glushka, J.//Barany, F.//Cowburn, D. 	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.	Biochem. Biophys. Res. Commun.	1989	164		88-93			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. 		
@D	Gnaneshan, S.//Hsueh, Y.C.//Liang, L.//Teatero, S.//Fittipaldi, N.//Mallo, G.V. 	Genome Sequence of Listeria monocytogenes Strain F6540 (Sequence Type 360) Collected from Food Samples in Ontario, Canada.	Genome Announcements	2016	4		e01507-15			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. 		
@D	Gochez, A.M.//Huguet-Tapia, J.C.//Minsavage, G.V.//Shantaraj, D.//Jalan, N.//Strauss, A.//Lahaye, T.//Wang, N.//Canteros, B.I.//Jones, J.B.//Potnis, N. 	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.	BMC Genomics	2018	19		16			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. 		
@D	Godany, A.//Bukovska, G.//Farkasovska, J.//Brnakova, Z.//Dmitriev, A.//Tkacikova, L.//Ayele, T.//Mikula, I. 	Characterization of a complex restriction-modification system detected in Staphylococcus aureus and Streptococcus agalactiae strains isolated  from infections of domestic animals.	Folia Microbiol. (Praha)	2004	49		307-314			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. 		
@D	Godany, A.//Farkasovska, J.//Bukovska, G.//Timko, J. 	Connection between foreign DNA replication and induced expression of the restriction-modification system in Streptomyces aureofaciens.	Folia Microbiol. (Praha)	2001	46		193-196			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. 		
@D	Godany, A.//Pristas, P.//Oktavcova, B.//Farkosovska, J.//Ziffova, M.//Sevcikova, B. 	Characterization of an XhoI isoschizomer in Streptomyces aureofaciens after actinophage infection.	FEMS Microbiol. Lett.	1996	138		123-127			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. 		
@D	Goddard, M.R.//Burt, A. 	Recurrent invasion and extinction of a selfish gene.	Proc. Natl. Acad. Sci. U. S. A.	1999	96		13880-13885			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. 		
@D	Godley, L.A.//Mondragon, A. 	Molecular biology. Preference by exclusion.	Science	2011	331		1017-1018			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. 		
@D	Godson, G.N.//Roberts, R.J. 	A catalogue of cleavages of PhiX174, S13, G4, and ST-1 DNA by 26 different restriction endonucleases.	Virology	1976	73		561-567			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. 		
@D	Goedecke, K.//Pignot, M.//Goody, R.S.//Scheidig, A.J.//Weinhold, E. 	Structure of the N6-adenine DNA methyltransferase M.TaqI in complex with DNA and a cofactor analog.	Nat. Struct. Biol.	2001	8		121-125			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. 		
@D	Goen, A.E.//Silverwood, T.//Underriner, A.//Trachtenberg, A.M.//Kelley, C.//MacLea, K.S. 	Draft Genome Sequence of the Psychrotolerant Bacterium Kurthia sibirica ATCC 49154(T).	Microbiol. Resour. Announc.	2018	7		e00841-18			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. 		
@D	Goff, S.P.//Rambach, A. 	SstI: A restriction endonuclease from Streptomyces sp. stanford.	Gene	1978	3		347-352			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. 		
@D	Goffin, J.//Eisenhauer, E. 	DNA methyltransferase inhibitors-state of the art.	Ann. Oncol.	2002	13		1699-1716			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. 		
@D	Goffin, P.//Dehottay, P. 	Complete Genome Sequence of Escherichia coli BLR(DE3), a recA-Deficient Derivative of E. coli BL21(DE3).	Genome Announcements	2017	5		e00441-17			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. 		
@D	Gofton, A.W.//Margos, G.//Fingerle, V.//Hepner, S.//Loh, S.M.//Ryan, U.//Irwin, P.//Oskam, C.L. 	Genome-wide analysis of Borrelia turcica and 'Candidatus Borrelia tachyglossi' shows relapsing fever-like genomes with unique genomic links to Lyme disease Borrelia.	Infect. Genet. Evol.	2018	66		72-81			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. 		
@D	Gogarten, J.P.//Hilario, E. 	Inteins, introns, and homing endonucleases: recent revelations about the life cycle of parasitic genetic elements.	BMC Evol. Biol.	2006	6		94			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. 		
@D	Gogarten, J.P.//Senejani, A.G.//Zhaxybayeva, O.//Olendzenski, L.//Hilario, E. 	Inteins: Structure, function, and evolution.	Annu. Rev. Microbiol.	2002	56		263-287			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. 		
@D	Goguel, V.//Delahodde, A.//Jacq, C. 	Connections between RNA splicing and DNA intron mobility in yeast mitochondria: RNA maturase and DNA endonuclease switching experiments.	Mol. Cell. Biol.	1992	12		696-705			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. 		
@D	Goh, K.M.//Chan, K.G.//Yaakop, A.S.//Chan, C.S.//Ee, R.//Tan, W.S.//Gan, H.M. 	Draft Genome Sequence of Jeotgalibacillus soli DSM 23228, a Bacterium Isolated from Alkaline Sandy Soil.	Genome Announcements	2015	3		e00512-15			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. 		
@D	Goh, S.//Ong, P.F.//Song, K.P.//Riley, T.V.//Chang, B.J. 	The complete genome sequence of Clostridium difficile phage {phi}C2 and comparisons to {phi}CD119 and inducible prophages of CD630.	Microbiology	2007	153		676-685			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. 		
@D	Gohda, K.//Matsuo, N.//Oda, Y.//Ikehara, M.//Uesugi, S. 	Effects of 2'-substituents of the first deoxyguanosine residue in the recognition sequence on EcoRI restriction endonuclease activity.	J. Biochem. (Tokyo)	1997	121		219-224			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. 		
@D	Gokce, A.//Cakar, Z.P.//Yucel, M.//Ozcan, O.//Sencan, S.//Sertdemir, I.//Erguner, B.//Yuceturk, B.//Sarac, A.//Yuksel, B.//Ozturk, Y. 	Draft Genome Sequences of Two Heat-Resistant Mutant Strains (A52 and B41) of the  Photosynthetic Hydrogen-Producing Bacterium Rhodobacter capsulatus.	Genome Announcements	2016	4		e00531-16			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. 		
@D	Goker, M. et al. 	Complete genome sequence of the acetate-degrading sulfate reducer Desulfobacca acetoxidans type strain (ASRB2).	Standards in Genomic Sciences	2011	4		393-401			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. 		
@D	Goker, M. et al. 	Complete genome sequence of the termophilic sulfur-reducer Desulfurobacterium thermolithotrophum type strain (BSA) from a deep-sea hydrothermal vent.	Standards in Genomic Sciences	2011	5		407-415			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. 		
@D	Goker, M. et al. 	Genome sequence of the moderately thermophilic, amino-acid-degrading and sulfur-reducing bacterium Thermovirga lienii type strain (Cas60314(T)).	Standards in Genomic Sciences	2012	6		230-239			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. 		
@D	Goker, M. et al. 	Genome sequence of the Thermotoga thermarum type strain (LA3(T)) from an African  solfataric spring.	Standards in Genomic Sciences	2014	9		1105-1117			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. 		
@D	Goker, M. et al. 	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.	Standards in Genomic Sciences	2014	9		1076-1088			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. 		
@D	Goker, M. et al. 	Complete genome sequence of Ignisphaera aggregans type strain (AQ1.S1).	Standards in Genomic Sciences	2010	3		66-75			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. 		
@D	Goker, M. et al. 	Complete genome sequence of Olsenella uli type strain (VPI D76D-27C).	Standards in Genomic Sciences	2010	3		76-84			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. 		
@D	Goker, M. et al. 	Complete genome sequence of Isosphaera pallida type strain (IS1B).	Standards in Genomic Sciences	2011	4		63-71			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. 		
@D	Goker, M. et al. 	Complete genome sequence of Odoribacter splanchnicus type strain (1651/6).	Standards in Genomic Sciences	2011	4		200-209			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. 		
@D	Golanowska, M.//Galardini, M.//Bazzicalupo, M.//Hugouvieux-Cotte-Pattat, N.//Mengoni, A.//Potrykus, M.//Slawiak, M.//Lojkowska, E. 	Draft Genome Sequence of a Highly Virulent Strain of the Plant Pathogen Dickeya solani, IFB0099.	Genome Announcements	2015	3		e00109-15			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. 		
@D	Gold, M.//Hausmann, R.//Maitra, U.//Hurwitz, J. 	The enzymatic methylation of RNA and DNA, VIII.  Effects of bacteriophage  infection on the activity of the methylating enzymes.	Proc. Natl. Acad. Sci. U. S. A.	1964	52		292-297			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. 		
@D	Gold, M.//Hurwitz, J. 	The enzymatic methylation of ribonucleic acid and deoxyribonucleic acid. V. Purification and properties of the deoxyribonucleic acid-methylating activity of Escherichia coli.	J. Biol. Chem.	1964	239		3858-3865			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. 		
@D	Gold, M.//Hurwitz, J.//Anders, M. 	THE ENZYMATIC METHYLATION OF RNA AND DNA, II. ON THE SPECIES SPECIFICITY OF THE METHYLATION ENZYMES.	Proc. Natl. Acad. Sci. U. S. A.	1963	50		164-169			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. 		
@D	Gold, M.//Hurwitz, J.//Anders, M. 	The enzymatic methylation of RNA and DNA.	Biochem. Biophys. Res. Commun.	1963	11		107-114			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. 		
@D	Gold, S.E.//Blacutt, A.A.//Meinersmann, R.J.//Bacon, C.W. 	Whole-Genome Shotgun Sequence of Bacillus mojavensis Strain RRC101, an Endophytic Bacterium Antagonistic to the Mycotoxigenic Endophytic Fungus Fusarium  verticillioides.	Genome Announcements	2014	2		e01090-14			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. 		
@D	Goldfarb, T.//Sberro, H.//Weinstock, E.//Cohen, O.//Doron, S.//Charpak-Amikam, Y.//Afik, S.//Ofir, G.//Sorek, R. 	BREX is a novel phage resistance system widespread in microbial genomes.	EMBO J.	2015	34		169-183			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. 		
@D	Golding, G.R.//Bryden, L.//Levett, P.N.//McDonald, R.R.//Wong, A.//Graham, M.R.//Tyler, S.//Van Domselaar, G.//Mabon, P.//Kent, H.//Butaye, P.//Smith, T.C.//Kadlec, K.//Schwarz, S.//Weese, S.J.//Mulvey, M.R. 	Whole-Genome Sequence of Livestock-Associated ST398 Methicillin-Resistant Staphylococcus aureus Isolated from Humans in Canada.	J. Bacteriol.	2012	194		6627-6628			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. 		
@D	Golding, M.C.//Westhusin, M.E. 	Analysis of DNA (cytosine 5) methyltransferase mRNA sequence and expression in bovine preimplantation embryos, fetal and adult tissues.	Gene Expr. Patterns	2003	3		551-558			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. 		
@D	Goldstone, R.J.//Amos, M.//Talbot, R.//Schuberth, H.J.//Sandra, O.//Sheldon, I.M.//Smith, D.G. 	Draft Genome Sequence of Trueperella pyogenes, Isolated from the Infected Uterus  of a Postpartum Cow with Metritis.	Genome Announcements	2014	2		e00194-14			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. 		
@D	Goldstone, R.J.//Talbot, R.//Schuberth, H.J.//Sandra, O.//Sheldon, I.M.//Smith, D.G. 	Draft Genome Sequence of Escherichia coli MS499, Isolated from the Infected Uterus of a Postpartum Cow with Metritis.	Genome Announcements	2014	2		e00217-14			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. 		
@D	Golemboski, D.//Eardly, B.D. 	Draft Genome Sequences of Respiratory and Urinary Tract Isolates of Acinetobacter baumannii from the Same Patient.	Genome Announcements	2014	2		e00692-14			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. 		
@D	Golikova, L.N.//Gutorov, V.V.//Evdokimov, A.A.//Shchelkunov, S.N.//Gonchar, D.A.//Okhapkina, S.S.//Degtyarev, S.K.//Netesova, N.A. 	M.BstF5I-4, the fourth DNA-methyltransferase of the BstF5I restriction-modification system from Bacillus stearothermophilus F5.	Bioorg. Khim.	2002	28		84-86			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. 		
@D	Golikova, L.N.//Netosova, N.A.//Gutorov, V.V.//Belavin, P.A.//Abdurashitov, M.A.//Gonchar, D.A.//Degtyarev, S.K. 	Multiplicity of site-specific DNA-methyltransferases of the BstF5I restriction modification system from Bacillus stearothermophilus F5.	Mol. Biol. (Mosk)	2000	34		443-447			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. 		
@D	Goll, M.G.//Bestor, T.H. 	Eukaryotic cytosine methyltransferases.	Annu. Rev. Biochem.	2005	74		481-514			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. 		
@D	Golneshin, A.//Adetutu, E.//Ball, A.S.//May, B.K.//Van, T.T.//Smith, A.T. 	Complete Genome Sequence of Lactobacillus plantarum Strain B21, a Bacteriocin-Producing Strain Isolated from Vietnamese Fermented Sausage Nem Chua.	Genome Announcements	2015	3		e00055-15			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). 		
@D	Golneshin, A.//Gor, M.C.//Van, T.T.H.//May, B.//Moore, R.J.//Smith, A.T. 	Draft Genome Sequence of Lactobacillus plantarum Strain A6, a Strong Acid Producer Isolated from a Vietnamese Fermented Sausage (Nem Chua).	Genome Announcements	2017	5		e00987-17			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). 		
@D	Gololobova, N.S.//Okhapkina, S.S.//Abdurashitov, M.A.//Degtyarev, S.K. 	Determination and analysis of the primary structure of NM.BstSEI operon from Bacillus stearothermophilus SE-589 which produces N.BstSEI site-specific nickase.	Mol. Biol. (Mosk)	2005	39		960-964			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. 		
@D	Golomidova, A.K.//Kulikov, E.E.//Kudryavtseva, A.V.//Letarov, A.V. 	Complete Genome Sequence of Escherichia coli Bacteriophage PGT2.	Genome Announcements	2018	6		e01370-17			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. 		
@D	Golovenko, D.//Manakova, E.//Tamulaitiene, G.//Grazulis, S.//Siksnys, V. 	Structural mechanisms for the 5'-CCWGG sequence recognition by the N- and C-terminal domains of EcoRII.	Nucleic Acids Res.	2009	37		6613-6624			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. 		
@D	Golovenko, D.//Manakova, E.//Zakrys, L.//Zaremba, M.//Sasnauskas, G.//Grazulis, S.//Siksnys, V. 	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.	Nucleic Acids Res.	2014	42		4113-4122			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. 		
@D	Goltsman, D.S.//Denef, V.J.//Singer, S.W.//VerBerkmoes, N.C.//Lefsrud, M.//Mueller, R.S.//Dick, G.J.//Sun, C.L.//Wheeler, K.E.//Zemla, A.//Baker, B.J.//Hauser, L.//Land, M.//Shah, M.B.//Thelen, M.P.//Hettich, R.L.//Banfield, J.F. 	Community genomic and proteomic analyses of chemoautotrophic iron-oxidizing 'Leptospirillum rubarum' (Group II) and 'Leptospirillum ferrodiazotrophum' (Group III) bacteria in acid mine drainage biofilms.	Appl. Environ. Microbiol.	2009	75		4599-4615			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. 		
@D	Golubov, A.//Neubauer, H.//Nolting, C.//Heesemann, J.//Rakin, A. 	Structural organization of the pFra virulence-associated plasmid of rhamnose-positive Yersinia pestis.	Infect. Immun.	2004	72		5613-5621			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. 		
@D	Golyshin, P.N.//Werner, J.//Chernikova, T.N.//Tran, H.//Ferrer, M.//Yakimov, M.M.//Teeling, H.//Golyshina, O.V. 	Genome Sequence of Thalassolituus oleivorans MIL-1 (DSM 14913T).	Genome Announcements	2013	1		e00141-13			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%. 		
@D	Golyshina, O.V.//Toshchakov, S.V.//Makarova, K.S.//Gavrilov, S.N.//Korzhenkov, A.A.//La Cono, V.//Arcadi, E.//Nechitaylo, T.Y.//Ferrer, M.//Kublanov, I.V.//Wolf, Y.I.//Yakimov, M.M.//Golyshin, P.N. 	'ARMAN' archaea depend on association with euryarchaeal host in culture and in situ.	Nat. Commun.	2017	8		60			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. 		
@D	Gomes, L.H.//Otto, T.D.//Vasconcellos, E.A.//Ferrao, P.M.//Maia, R.M.//Moreira, A.S.//Ferreira, M.A.//Castello-Branco, L.R.//Degrave, W.M.//Mendonca-Lima, L. 	Genome Sequence of Mycobacterium bovis BCG Moreau, the Brazilian Vaccine Strain against Tuberculosis.	J. Bacteriol.	2011	193		5600-5601			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. 		
@D	Gomes, L.L.//Marin, M.A.//Lasunskaia, E.//Vasconcellos, S.E.//Araujo, M.E.//de Miranda, A.B.//Suffys, P.N. 	Genome Comparison of an Ancestral Isolate and a Modern Isolate of Mycobacterium tuberculosis of the Beijing Lineage from Sao Paulo, Brazil.	Genome Announcements	2015	3		e01129-15			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. 		
@D	Gomez, O.M.//Alvarez, L.C.//Munoz, J.F.//Misas, E.//Gallo, J.E.//Jimenez, M.D.P.//Arango, M.//McEwen, J.G.//Hernandez, O.//Clay, O.K. 	Draft Genome Sequences of Two Sporothrix schenckii Clinical Isolates Associated with Human Sporotrichosis in Colombia.	Genome Announcements	2018	6		e00495-18			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. 		
@D	Gomez, P.//Ribas-Aparicio, R.M.//Pelaez, A.I.//Gomez, A.//Rodicio, M.R. 	Isolation and nucleotide sequence of the gene encoding the XamI DNA methyltransferase of Xanthomonas campestris pv. amaranthicola.	Biochim. Biophys. Acta	1997	1351		261-266			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. 		
@D	Gomez, P.//Ribas-Aparicio, R.M.//Pelaez, A.I.//Rodicio, M.R. 	Characterization of IS1389, a new member of the IS3 family of insertion sequences isolated from Xanthomonas campestris pv. amaranthicola.	Arch. Microbiol.	1999	172		15-21			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. 		
@D	Gomez-Alvarez, V.//Pfaller, S.//Revetta, R.P. 	Draft Genome Sequence of Two Sphingopyxis sp. Strains, Dominant Members of the Bacterial Community Associated with a Drinking Water Distribution System  Simulator.	Genome Announcements	2016	4		e00183-16			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. 		
@D	Gomez-Alvarez, V.//Revetta, R.P. 	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.	Genome Announcements	2016	4		e01539-15			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. 		
@D	Gomez-Alvarez, V.//Revetta, R.P. 	Draft Genome Sequences of Six Mycobacterium immunogenum Strains Obtained from a Chloraminated Drinking Water Distribution System Simulator.	Genome Announcements	2016	4		e01538-15			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. 		
@D	Gomez-Consarnau, L.//Akram, N.//Lindell, K.//Pedersen, A.//Neutze, R.//Milton, D.L.//Gonzalez, J.M.//Pinhassi, J. 	Proteorhodopsin phototrophy promotes survival of marine bacteria during starvation.	PLoS Biology	2010	8		E1000358			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. 		
@D	Gomez-Consarnau, L.//Gonzalez, J.M.//Coll-Llado, M.//Gourdon, P.//Pascher, T.//Neutze, R.//Pedros-Alio, C.//Pinhassi, J. 	Light stimulates growth of proteorhodopsin-containing marine Flavobacteria.	Nature	2007	445		210-213			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. 		
@D	Gomez-Eichelmann, M.C. 	Deoxyribonucleic Acid Adenine and Cytosine Methylation in Salmonella typhimurium  and Salmonella typhi.	J. Bacteriol.	1979	140		574-579			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: 		
@D	Gomez-Eichelmann, M.C.//Levy-Mustri, A.//Ramirez-Santos, J. 	Presence of 5-methylcytosine in CC(A/T)GG sequences (Dcm methylation) in DNAs from different bacteria.	J. Bacteriol.	1991	173		7692-7694			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. 		
@D	Gomez-Eichelmann, M.C.//Ramirez-Santos, J. 	Methylated cytosine at Dcm (CCA/TGG) sites in Escherichia coli:  Possible function and evolutionary implications.	J. Mol. Evol.	1993	37		11-24			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. 		
@D	Gomez-Gil, B.//Soto-Rodriguez, S.//Lozano, R.//Betancourt-Lozano, M. 	Draft Genome Sequence of Vibrio parahaemolyticus Strain M0605, Which Causes Severe Mortalities of Shrimps in Mexico.	Genome Announcements	2014	2		e00055-14			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. 		
@D	Gomez-Jimenez, S.//Noriega-Orozco, L.//Sotelo-Mundo, R.R.//Cantu-Robles, V.A.//Cobian-Guemes, A.G.//Cota-Verdugo, R.G.//Gamez-Alejo, L.A.//Del Pozo-Yauner, L.//Guevara-Hernandez, E.//Garcia-Orozco, K.D.//Lopez-Zavala, A.A.//Ochoa-Leyva, A. 	High-Quality Draft Genomes of Two Vibrio parahaemolyticus Strains Aid in Understanding Acute Hepatopancreatic Necrosis Disease of Cultured Shrimps in  Mexico.	Genome Announcements	2014	2		e00800-14			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. 		
@D	Gomez-Pereira, P.R.//Schuler, M.//Fuchs, B.M.//Bennke, C.//Teeling, H.//Waldmann, J.//Richter, M.//Barbe, V.//Bataille, E.//Glockner, F.O.//Amann, R. 	Genomic content of uncultured Bacteroidetes from contrasting oceanic provinces in the North Atlantic Ocean.	Environ. Microbiol.	2012	14		52-66			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. 		
@D	Gomez-Rodriguez, J.A.//Huete-Perez, J.A. 	Bioprospeccion de enzimas de restriccion en bacterias de suelos y ambientes volcanicos de Nicaragua.	Encuentro	2008	15		70-87					
@D	Gomila, M.//Busquets, A.//Garcia-Valdes, E.//Michael, E.//Cahan, R.//Nitzan, Y.//Lalucat, J. 	Draft Genome Sequence of the Toluene-Degrading Pseudomonas stutzeri Strain ST-9.	Genome Announcements	2015	3		e00567-15			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. 		
@D	Gomila, M.//Mulet, M.//Lalucat, J.//Garcia-Valdes, E. 	Draft Genome Sequence of the Marine Bacterium Pseudomonas aestusnigri VGXO14T.<jour_book>Genome Announc.		2017	5		e00765-17			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. 		
@D	Gomila, M.//Mulet, M.//Lalucat, J.//Garcia-Valdes, E. 	Draft Genome Sequence of Pseudomonas pachastrellae Strain CCUG 46540T, a Deep-Sea Bacterium.	Genome Announcements	2017	5		e00136-17			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. 		
@D	Goncalves, A.C.//Franco, T.//Califano, G.//Dowd, S.E.//Pohnert, G.//Costa, R. 	Draft Genome Sequence of Vibrio sp. Strain Vb278, an Antagonistic Bacterium Isolated from the Marine Sponge Sarcotragus spinosulus.	Genome Announcements	2015	3		e00521-15			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. 		
@D	Goncalves, L.A.//de Castro, S.S.//Pereira, F.L.//Dorella, F.A.//de Carvalho, A.F.//de Freitas, A.G.M.//Leal, C.A.//Azevedo, V.//Figueiredo, H.C. 	Complete genome sequences of Francisella noatunensis subsp. orientalis strains FNO12, FNO24 and FNO190: a fish pathogen with genomic clonal behavior.	Standards in Genomic Sciences	2016	11		30			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. 		
@D	Gonchar, D.A.//Abdurashitov, M.A.//Belichenko, O.A.//Dedkov, V.S.//Mezentseva, N.V.//Tomilova, J.E.//Degtyarev, S.K. 	PspXI, a novel restriction endonuclease that recognizes the unusual  DNA sequence 5'-VC^TCGAGB-3'.	Ovchinnikov Bull. Biotechnol. Phys. Chem. Biol.	2005	1		18-23			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. 		
@D	Gonchar, D.A.//Abdurashitov, M.A.//Okhapkina, S.S.//Shagin, D.A.//Kileva, E.V.//Degtyarev, S.K. 	Sse9I restriction-modification system: Organization of genes and structural comparison of proteins.	Mol. Biol. (Mosk)	2007	41		491-498			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. 		
@D	Gonchar, D.A.//Akishev, A.G.//Degtyarev, S.K. 	BlsI- and GlaI-PCR assays - a new method of DNA methylation study.	Ovchinnikov Bull. Biotechnol. Phys. Chem. Biol.	2010	6		5-12			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. 		
@D	Gonchar, D.A.//Chernukhin, V.A.//Abdurashitov, M.A.//Kileva, E.V.//Dedkov, V.S.//Mikhnenkova, N.A.//Lomakovskaya, E.N.//Udalyeva, S.G.//Degtyarev, S.K. 	Cloning and characterization of a new site specific methyl-directed DNA endonuclease EcoBLI recognizing 5'-G(5mC)NGC-3'/3'-CGN(5mC)G-5'.	BTAIJ	2016	12		175-181			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'. 		
@D	Gonchar, D.A.//Dedkov, V.S.//Verkhozina, V.A.//Kusner, Y.S.//Shevchenko, A.V.//Degtyarev, S.K. 	Restriction endonuclease Sse9I from Sporosarcina sp. strain 9D recognizes the 5'-AATT-3' DNA sequence.	Prikl. Biokhim. Mikrobiol.	1998	34		139-141			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. 		
@D	Gonchar, D.A.//Dedkov, V.S.//Verkhozina, V.A.//Kusner, Y.S.//Shevchenko, A.V.//Degtyarev, S.K. 	Sse9I, a restriction endonuclease from Sporosarcina sp. 9D which recognizes the sequence 5'AATT-3'.	Mol. Gen. Mikrobiol. Virusol.	1998	2		32-34			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. 		
@D	Gonchar, D.A.//Wolf, Y.I.//Degtyarev, S.K. 	Cloning and characterization of Sse9I DNA-methyltransferase recognizing 5'-AATT-3'.	Nucleic Acids Res.	1996	24		2790-2792			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. 		
@D	Goncharov, A.//Grigorjev, S.//Karaseva, A.//Kolodzhieva, V.//Azarov, D.//Akhremenko, Y.//Tarasova, L.//Tikhonov, A.//Masharskiy, A.//Zueva, L.//Suvorov, A. 	Draft Genome Sequence of Enterococcus faecium Strain 58m, Isolated from Intestinal Tract Content of a Woolly Mammoth, Mammuthus primigenius.	Genome Announcements	2016	4		e01706-15			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. 		
@D	Goncuoglu, M.//Aydin, N.D.//Erol, I. 	Antibiotic resistance of Escherichia coli O157:H7 isolated from cattle and sheep.	Ann. Microbiol. (Paris)	2010	60		489-494			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. 		
@D	Gong, H.Y.//Wu, S.H.//Chen, C.Y.//Huang, C.W.//Lu, J.K.//Chou, H.Y. 	Complete Genome Sequence of Streptococcus iniae 89353, a Virulent Strain Isolated from Diseased Tilapia in Taiwan.	Genome Announcements	2017	5		e01524-16			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. 		
@D	Gong, W.//Kisiela, M.//Schilhabel, M.B.//Xiong, G.//Maser, E. 	Genome Sequence of Comamonas testosteroni ATCC 11996, a Representative Strain Involved in Steroid Degradation.	J. Bacteriol.	2012	194		1633-1634			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%. 		
@D	Gong, W.//O'Gara, M.//Blumenthal, R.M.//Cheng, X. 	Structure of PvuII DNA-(cytosine N4) methyltransferase, an example of domain permutation and protein fold assignment.	Nucleic Acids Res.	1997	25		2702-2715			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. 		
@D	Gong, X.//Skrivergaard, S.//Korsgaard, B.S.//Schreiber, L.//Marshall, I.P.//Finster, K.//Schramm, A. 	High quality draft genome sequence of Janthinobacterium psychrotolerans sp. nov., isolated from a frozen freshwater pond.	Standards in Genomic Sciences	2017	12		8			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. 		
@D	Goni-Urriza, M.//Gassie, C.//Bouchez, O.//Klopp, C.//Guyoneaud, R. 	Draft Genome Sequence of Desulfovibrio BerOc1, a Mercury-Methylating Strain.	Genome Announcements	2017	5		e01483-16			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. 		
@D	Gonzaga, A.//Lopez-Perez, M.//Martin-Cuadrado, A.B.//Ghai, R.//Rodriguez-Valera, F. 	Complete Genome Sequence of the Copiotrophic Marine Bacterium Alteromonas macleodii Strain ATCC 27126T.	J. Bacteriol.	2012	194		6998			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. 		
@D	Gonzaga, A.//Martin-Cuadrado, A.B.//Lopez-Perez, M.//Megumi-Mizuno, C.//Garcia-Heredia, I.//Kimes, N.E.//Lopez-Garcia, P.//Moreira, D.//Ussery, D.//Zaballos, M.//Ghai, R.//Rodriguez-Valera, F. 	Polyclonality of concurrent natural populations of Alteromonas macleodii.	Genome Biol. Evol.	2012	4		1360-1374			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. 		
@D	Gonzalez, D.//Collier, J. 	Genomic Adaptations to the Loss of a Conserved Bacterial DNA Methyltransferase.	MBio	2015	6		e00952-15			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. 		
@D	Gonzalez, D.//Kozdon, J.B.//McAdams, H.H.//Shapiro, L.//Collier, J. 	The functions of DNA methylation by CcrM in Caulobacter crescentus: a global approach.	Nucleic Acids Res.	2014	42		3720-3735			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. 		
@D	Gonzalez, E.//Padilla, C.//Saavedra, C.//Vasquez, C. 	The expression of the bstVIM gene from Bacillus stearothermophilus V is restricted to vegetative cell growth.	Microbiology	1994	140		1337-1340			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. 		
@D	Gonzalez, E.//Vasquez, C. 	Characterization of the bstVIRM genes encoding the Bacillus stearothermophilus V restriction-modification system.	Gene	1993	131		103-106			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. 		
@D	Gonzalez, V.//Santamaria, R.I.//Bustos, P.//Hernandez-Gonzalez, I.//Medrano-Soto, A.//Moreno-Hagelsieb, G.//Janga, S.C.//Ramirez, M.A.//Jimenez-Jacinto, V.//Collado-Vides, J.//Davila, G. 	The partitioned Rhizobium etli genome: Genetic and metabolic redundancy in seven interacting replicons.	Proc. Natl. Acad. Sci. U. S. A.	2006	103		3834-3839			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. 		
@D	Gonzalez-Ceron, G.//Miranda-Olivares, O.J.//Servin-Gonzalez, L. 	Characterization of the methyl-specific restriction system of Streptomyces coelicolor A3(2) and of the role played by laterally acquired nucleases.	FEMS Microbiol. Lett.	2009	301		35-43			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. 		
@D	Gonzalez-Escalona, N.//Haendiges, J.//Miller, J.D.//Sharma, S.K. 	Closed Genome Sequences of Two Clostridium botulinum Strains Obtained by Nanopore Sequencing.	Microbiol. Resour. Announc.	2018	7		e01075-18			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. 		
@D	Gonzalez-Escalona, N.//McFarland, M.A.//Rump, L.V.//Payne, J.//Andrzejewski, D.//Brown, E.W.//Evans, P.S.//Croley, T.R. 	Draft Genome Sequences of Two O104:H21 Escherichia coli Isolates Causing Hemorrhagic Colitis during a 1994 Montana Outbreak Provide Insight into Their  Pathogenicity.	Genome Announcements	2013	1		e00805-13			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. 		
@D	Gonzalez-Escalona, N.//Strain, E.A.//De Jesus, A.J.//Jones, J.L.//Depaola, A. 	Genome sequence of the clinical O4:K12 serotype Vibrio parahaemolyticus strain 10329.	J. Bacteriol.	2011	193		3405-3406			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. 		
@D	Gonzalez-Escalona, N.//Thirunavukkarasu, N.//Singh, A.//Toro, M.//Brown, E.W.//Zink, D.//Rummel, A.//Sharma, S.K. 	Draft Genome Sequence of Bivalent Clostridium botulinum Strain IBCA10-7060, Encoding Botulinum Neurotoxin B and a New FA Mosaic Type.	Genome Announcements	2014	2		e01275-14			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. 		
@D	Gonzalez-Nicieza, R.//Turner, D.P.//Connolly, B.A. 	DNA binding and cleavage selectivity of the Escherichia coli DNA G:T-mismatch endonuclease (vsr protein).	J. Mol. Biol.	2001	310		501-508			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. 		
@D	Gonzalez-Perez, M.//Murcia, M.I.//Landsman, D.//Jordan, I.K.//Marino-Ramirez, L. 	Genome Sequence of the Mycobacterium colombiense Type Strain, CECT 3035.	J. Bacteriol.	2011	193		5866-5867			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. 		
@D	Gonzalez-Perez, M.N.//Murcia, M.I.//Parra-Lopez, C.//Blom, J.//Tauch, A. 	Deciphering the virulence factors of the opportunistic pathogen Mycobacterium colombiense.	New Microbes New Infect.	2016	14		98-105			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. 		
@D	Gonzalez-Torres, P.//Gabaldon, T. 	Genome variation in the model halophilic bacterium Salinibacter ruber.	Front. Microbiol.	2018	9		1499					
@D	Gonzalgo, M.L.//Jones, P.A. 	Mutagenic and epigenetic effects of DNA methylation.	Mutat. Res.	1997	386		107-118			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. 		
@D	Goodgal, S.H.//Gromkova, R. 	Separation of specific segments of transforming DNA after treatment with endodeoxyribonuclease.	Proc. Natl. Acad. Sci. U. S. A.	1973	70		503-506			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. 		
@D	Goodison, S.//Urquidi, V.//Kumar, D.//Reyes, L.//Rosser, C.J. 	Complete Genome Sequence of Mycoplasma hyorhinis Strain SK76.	Genome Announcements	2013	1		e00101-12			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. 		
@A	Goodman, H.M.//Greene, P.J.//Garfin, D.E.//Boyer, H.W. 		DNA site recognition by the EcoRI restriction endonuclease and modification methylase.			Vogel, H.J. 		Nucleic Acid - Protein Recognition				New York	Academic Press	1977		0		239-259									None 		
@D	Goodner, B. et al. 	Genome sequence of the plant pathogen and biotechnology agent Agrobacterium tumefaciens C58.	Science	2001	294		2323-2328			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. 		
@D	Goodrich-Blair, H.//Scarlato, V.//Gott, J.M.//Xu, M.-Q.//Shub, D.A. 	A self-splicing group I intron in the DNA polymerase gene of Bacillus subtilis bacteriophage SPO1.	Cell	1990	63		417-424			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. 		
@D	Goodrich-Blair, H.//Shub, D.A. 	A site- and strand-specific intron-endonuclease is required for marker exclusion.	J. Cell Biochem. Suppl.	1993	17C		177			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. 		
@D	Goodrich-Blair, H.//Shub, D.A. 	Beyond homing: Competition between intron endonucleases confers a selective advantage on flanking genetic markers.	Cell	1996	84		211-221			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. 		
@D	Goodrich-Blair, H.//Shub, D.A. 	The DNA polymerase genes of several HMU-bacteriophages have similar group I introns with highly divergent open reading frames.	Nucleic Acids Res.	1994	22		3715-3721			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. 		
@D	Goodsell, D.S. 	Recognition in action: flipping pyrimidine dimers.	J. Mol. Recognit.	2005	18		193-195			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. 		
@D	Goodsell, D.S. 	The molecular perspective: Restriction endonucleases.	Stem Cells	2002	20		190-191			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. 		
@D	Goodsell, D.S. 	The Molecular Perspective: Restriction Endonucleases.	The Oncologist	2002	7		82-83			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. 		
@D	Goodwin, S.B. et al. 	Finished Genome of the Fungal Wheat Pathogen Mycosphaerella graminicola Reveals Dispensome Structure, Chromosome Plasticity, and Stealth Pathogenesis.	PLoS Genet.	2011	7		E1002070			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. 		
@D	Goordial, J.//Raymond-Bouchard, I.//Ronholm, J.//Shapiro, N.//Woyke, T.//Whyte, L.//Bakermans, C. 	Improved-high-quality draft genome sequence of Rhodococcus sp. JG-3, a eurypsychrophilic Actinobacteria from Antarctic Dry Valley permafrost.	Standards in Genomic Sciences	2015	10		61			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. 		
@D	Goossens, M.D.//Dumez, Y.//Kaplan, L.//Lupker, M.//Chabret, C.//Henrion, R.//Rosa, J. 	Prenatal Diagnosis of Sickle-Cell anemia in the First Trimester of Pregnancy.	N. Engl. J. Med.	1983	309		831-833			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. 		
@D	Gootz, T.D.//Lescoe, M.K.//Dib-Hajj, F.//Dougherty, B.A.//He, W.//Della-Latta, P.//Huard, R.C. 	Genetic organization of transposase regions surrounding blaKPC carbapenemase genes on plasmids from Klebsiella strains isolated in a New York City hospital.	Antimicrob. Agents Chemother.	2009	53		1998-2004			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. 		
@D	Gopal, J. 	Molecular cloning and biochemical characterization of DsaV methyltransferase from Dactylococcopsis salina.	Diss. Abstr.	1995	57		121			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. 		
@D	Gopal, J.//Bhagwat, A.S. 	Determination of methylation specificity of DsaV methyltransferase by a simple biochemical method.	Nucleic Acids Res.	1995	23		29-35			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. 		
@D	Gopal, J.//Yebra, M.J.//Bhagwat, A.S. 	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.	Nucleic Acids Res.	1994	22		4482-4488			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. 		
@D	Gopal, J.//Yebra, M.J.//Bhagwat, A.S. 	Cloning and characterization of the gene encoding the DsaV methyltransferase.	Gene	1995	157		61-63			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. 		
@D	Gopalakrishnan, S. 	Functional characterization of the de novo DNA methyltransferase DNMT3B.	Ph.D. Thesis, Univ. of Florida, Gainesville	2009			1-215			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. 		
@D	Gopinath, G.//Jean-Gilles, B.J.//Grim, C.//Blaylock, M.//Blackwell, R.//Merid, S.//Diallo, A.//Hanes, D. 	Whole-Genome Sequences of Six Salmonella enterica Serovar Bovismorbificans Isolates Associated with a 2011 Multistate Hummus-Borne Outbreak.	Genome Announcements	2014	2		e01239-13			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. 		
@D	Gopinath, G.//Jean-Gilles, B.J.//Grim, C.//Hanes, D. 	Draft Genome Sequences of Nine Salmonella enterica Serovar Bovismorbificans Isolates from Various Sources.	Genome Announcements	2014	2		e01249-13			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. 		
@D	Gopinath, G.R.//Grim, C.J.//Tall, B.D.//Mammel, M.K.//Sathyamoorthy, V.//Trach, L.H.//Chase, H.R.//Fanning, S.//Stephan, R. 	Genome Sequences of Two Enterobacter pulveris Strains, 601/05T (=LMG 24057T =DSM  19144T) and 1160/04 (=LMG 24058 =DSM 19146), Isolated from Fruit Powder.	Genome Announcements	2013	1		e00991-13			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. 		
@D	Goppelt, M.//Langowski, J.//Pingoud, A.//Haupt, W.//Urbanke, C.//Mayer, H. 	The effect of several nucleic acid binding drugs on the cleavage of d(GGAATTCC) and pBR322 by the EcoRI restriction endonuclease.	Nucleic Acids Res.	1981	9		6115-6127			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. 		
@D	Goppelt, M.//Pingoud, A.//Maass, G.//Mayer, H.//Koster, H.//Frank, R. 	The interaction of the EcoRI restriction endonuclease with its substrate:  A physico-chemical study employing natural and synthetic oligonucleotides and polynucleotides.	Eur. J. Biochem.	1980	104		101-107			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. 		
@D	Gorbalenya, A.E. 	Self-splicing group I and group II introns encode homologous (putative) DNA endonucleases of a new family.	Protein Sci.	1994	3		1117-1120			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. 		
@D	Gorbalenya, A.E.//Koonin, E.V. 	Endonuclease (R) subunits of type-I and type-III restriction-modification enzymes contain a helicase-like domain.	FEBS Lett.	1991	291		277-281			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. 		
@D	Gorbunov, Y.A.//Zinovev, V.V.//Rechkunova, N.I.//Ovechkina, L.G.//Popov, S.G.//Malygin, E.G. 	Chemical synthesis and characteristics of oligonucleotide substrates for restriction endonuclease BamHI and methylase Eco dam.	Bioorg. Khim.	1987	13		1629-1637			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. 		
@D	Gordon, S.V.//Brosch, R.//Billault, A.//Garnier, T.//Eiglmeier, K.//Cole, S.T. 	Identification of variable regions in the genomes of tubercle bacilli using bacterial artificial chromosome arrays.	Mol. Microbiol.	1999	32		643-655			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. 		
@D	Gorecki, R.K.//Bardowski, J.K. 	Molecular mechanisms of bacteriophage resistance of lactic acid bacteria.	Postepy Mikrobiologii	2011	50		265-273			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. 		
@D	Gorecki, R.K.//Koryszewska-Baginska, A.//Golebiewski, M.//Zylinska, J.//Grynberg, M.//Bardowski, J.K. 	Adaptative potential of the Lactococcus lactis IL594 strain encoded in its 7 plasmids.	PLoS ONE	2011	6		e22238			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. 		
@D	Goris, T.//Hornung, B.//Kruse, T.//Reinhold, A.//Westermann, M.//Schaap, P.J.//Smidt, H.//Diekert, G. 	Draft genome sequence and characterization of Desulfitobacterium hafniense PCE-S.	Standards in Genomic Sciences	2015	10		15			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. 		
@D	Gorkiewicz, G.//Kienesberger, S.//Schober, C.//Scheicher, S.R.//Gully, C.//Zechner, R.//Zechner, E.L. 	A genomic island defines subspecies-specific virulence features of the host-adapted pathogen Campylobacter fetus subsp. venerealis.	J. Bacteriol.	2010	192		502-517			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. 		
@D	Gorlas, A.//Gimenez, G.//Raoult, D.//Roux, V. 	Draft Genome Sequences of Actinomyces timonensis Strain 7400942T and Its Prophage.	J. Bacteriol.	2012	194		6613-6614			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. 		
@D	Gorlas, A.//Robert, C.//Gimenez, G.//Drancourt, M.//Raoult, D. 	Complete Genome Sequence of Methanomassiliicoccus luminyensis, the Largest Genome of a Human-Associated Archaea Species.	J. Bacteriol.	2012	194		4745			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. 		
@D	Gorlatova, N.V.//Kryuchkova, E.G.//Koltovaya, N.A.//Dolgova, I.N.//Ananyin, V.M.//Velkov, V.V. 	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.	Biotekhnologiya	1991	0		27-30			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. 		
@D	Gorlatova, N.V.//Kryukova, E.G.//Koltovaya, N.A.//Dolgova, I.N.//Velkov, V.V. 	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.	Biotekhnologiya	1991	3		34-38			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. 		
@D	Gormley, N.A.//Bath, A.J.//Halford, S.E. 	Reactions of BglI and other Type II restriction endonucleases with discontinuous recognition sites.	J. Biol. Chem.	2000	275		6928-6936			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. 		
@D	Gormley, N.A.//Hillberg, A.L.//Halford, S.E. 	The type IIs restriction endonuclease BspMI is a tetramer that acts concertedly at two copies of an asymmetric DNA sequence.	J. Biol. Chem.	2002	277		4034-4041			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. 		
@D	Gorovsky, M.A.//Hattman, S.//Pleger, G.L. 	[6N]Methyl adenine in the nuclear DNA of a eucaryote, Tetrahymena pyriformis.	J. Cell Biol.	1973	56		697-701			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). 		
@D	Gorrell, R.//Kwok, T. 	The Helicobacter pylori Methylome: Roles in Gene Regulation and Virulence.	Curr. Top. Microbiol. Immunol.	2017	400		105-127			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. 		
@D	Gorski, L.//Huynh, S.//Cooper, K.K.//Parker, C.T. 	Complete Genomic Sequences of Two Salmonella enterica subsp. enterica Serogroup C2 (O:6,8) Strains from Central California.	Genome Announcements	2017	5		e01234-17			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. 		
@D	Gosse, J.T.//Hill, P.//Dowd, S.E.//Boddy, C.N. 	Draft Genome Sequence of Streptomyces sp. Strain PBH53, Isolated from an Urban Environment.	Genome Announcements	2015	3		e00859-15			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. 		
@D	Goto, T.//Hirakawa, H.//Morita, Y.//Tomida, J.//Sato, J.//Matsumura, Y.//Mitani, A.//Niwano, Y.//Takeuchi, K.//Kubota, H.//Kawamura, Y. 	Complete Genome Sequence of Moraxella osloensis Strain KMC41, a Producer of 4-Methyl-3-Hexenoic Acid, a Major Malodor Compound in Laundry.	Genome Announcements	2016	4		e00705-16			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. 		
@D	Goto, T.//Nagano, K.//Hirakawa, H.//Tanaka, K.//Yoshimura, F. 	Draft Genome Sequence of Porphyromonas gingivalis Strain Ando Expressing a 53-Kilodalton-Type Fimbrilin Variant of Mfa1 Fimbriae.	Genome Announcements	2015	3		e01292-15			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. 		
@D	Goto, T.//Ogura, Y.//Hirakawa, H.//Tomida, J.//Morita, Y.//Akaike, T.//Hayashi, T.//Kawamura, Y. 	Complete Genome Sequence of Helicobacter cinaedi Strain PAGU611, Isolated in a Case of Human Bacteremia.	J. Bacteriol.	2012	194		3744-3745			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. 		
@D	Gott, J.M. 	Genes within genes: independent expression of phage T4 intron open reading frames and the genes in which they reside.	Genes Dev.	1988	2		1791-1799			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. 		
@D	Gottschling, D.E. 	Telomere-proximal DNA in Saccharomyces cerevisiae is refractory to methyltransferase activity in vivo.	Proc. Natl. Acad. Sci. U. S. A.	1992	89		4062-4065			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. 		
@D	Goudenege, D.//Labreuche, Y.//Krin, E.//Ansquer, D.//Mangenot, S.//Calteau, A.//Medigue, C.//Mazel, D.//Polz, M.F.//Le Roux, F. 	Comparative genomics of pathogenic lineages of Vibrio nigripulchritudo identifies virulence-associated traits.	ISME J.	2013	7		1985-1996			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. 		
@D	Gough, J.A.//Murray, N.E. 	Sequence diversity among related genes for recognition of specific targets in DNA molecules.	J. Mol. Biol.	1983	166		1-19			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. 		
@D	Gough, M.//Lederberg, S. 	Methylated bases in the host-modified deoxyribonucleic acid of Escherichia coli and bacteriophage lambda.	J. Bacteriol.	1966	91		1460-1468			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. 		
@D	Gourgues, G.//Barre, A.//Beaudoing, E.//Weber, J.//Magdelenat, G.//Barbe, V.//Schieck, E.//Jores, J.//Vashee, S.//Blanchard, A.//Lartigue, C.//Sirand-Pugnet, P. 	Complete Genome Sequence of Mycoplasma mycoides subsp. mycoides T1/44, a Vaccine  Strain against Contagious Bovine Pleuropneumonia.	Genome Announcements	2016	4		e00263-16			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. 		
@D	Gouvea-Taketani, R.//Domingues, Z.T.//Soares-de-Melo, I.//Mendes, R. 	Whole-Genome Shotgun Sequencing of Rhodococcus erythropolis Strain P27, a Highly  Radiation-Resistant Actinomycete from Antarctica.	Genome Announcements	2013	1		e00763-13			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. 		
@D	Govind, R.//Fralick, J.A.//Rolfe, R.D. 	Genomic Organization and Molecular Characterization of Clostridium difficile Bacteriophage {Phi}CD119.	J. Bacteriol.	2006	188		2568-2577			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. 		
@D	Gowers, D.M.//Bellamy, S.R.W.//Halford, S.E. 	One recognition sequence, seven restriction enzymes, five reaction mechanisms.	Nucleic Acids Res.	2004	32		3469-3479			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. 		
@D	Gowers, D.M.//Halford, S.E. 	Protein motion from non-specific to specific DNA by three-dimensional routes aided by supercoiling.	EMBO J.	2003	22		1410-1418			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. 		
@D	Gowers, D.M.//Wilson, G.G.//Halford, S.E. 	Measurement of the contributions of 1D and 3D pathways to the translocation of a protein along DNA.	Proc. Natl. Acad. Sci. U. S. A.	2005	102		15883-15888			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. 		
@D	Gowher, H.//Ehrlich, K.C.//Jeltsch, A. 	DNA from Aspergillus flavus contains 5-methylcytosine.	FEMS Microbiol. Lett.	2001	205		151-155			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. 		
@D	Gowher, H.//Jeltsch, A. 	Molecular enzymology of the catalytic domains of the Dnmt3a and Dnmt3b DNA methyltransferases.	J. Biol. Chem.	2002	277		20409-20414			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. 		
@D	Gowher, H.//Jeltsch, A. 	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.	J. Mol. Biol.	2000	303		93-110			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. 		
@D	Gowher, H.//Jeltsch, A. 	Enzymatic properties of recombinant Dnmt3a DNA methyltransferase from mouse: the enzyme modifies DNA in a non-processive manner and also methylates non-CpG Sites.	J. Mol. Biol.	2001	309		1201-1208			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. 		
@D	Gowher, H.//Leismann, O.//Jeltsch, A. 	DNA of Drosophila melanogaster contains 5-methylcytosine.	EMBO J.	2000	19		6918-6923			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. 		
@D	Gowher, H.//Liebert, K.//Hermann, A.//Xu, G.L.//Jeltsch, A. 	Mechanism of stimulation of catalytic activity of Dnmt3A and Dnmt3B DNA-(cytosine-C5)-methyltransferases by Dnmt3L.	J. Biol. Chem.	2005	280		13341-13348			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. 		
@D	Gowher, H.//Loutchanwoot, P.//Vorobjeva, G.//Handa, V.//Jurkowska, R.Z.//Jurkowski, T.P.//Jeltsch, A. 	Mutational analysis of the catalytic domain of the murine Dnmt3a DNA-(cytosine C5)-methyltransferase.	J. Mol. Biol.	2006	357		928-941			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. 		
@D	Gowher, H.//Stockdale, C.J.//Goyal, R.//Ferreira, H.//Owen-Hughes, T.//Jeltsch, A. 	De novo methylation of nucleosomal DNA by the mammalian Dnmt1 and Dnmt3A DNA methyltransferases.	Biochemistry	2005	44		9899-9904			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. 		
@D	Goyal, R.//Rathert, P.//Laser, H.//Gowher, H.//Jeltsch, A. 	Phosphorylation of serine-515 activates the mammalian maintenance methyltransferase Dnmt1.	EPIGENETICS	2007	2		155-160			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. 		
@D	Goyal, R.//Reinhardt, R.//Jeltsch, A. 	Accuracy of DNA methylation pattern preservation by the Dnmt1 methyltransferase.	Nucleic Acids Res.	2006	34		1182-1188			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. 		
@D	Goyon, C. 	Isolation and identification by sequence homology of a second putative C5-DNA-methyltransferase gene from Ascobolus immersus.	DNA Seq.	1998	9		109-112			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. 		
@D	Goyon, C.//Nogueira, T.I.V.//Faugeron, G. 	Perpetuation of cytosine methylation in Ascobolus immersus implies a novel type of maintenance methylase.	J. Mol. Biol.	1994	240		42-51			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. 		
@D	Grable, J.//Frederick, C.A.//Samudzi, C.//Jen-Jacobson, L.//Lesser, D.//Greene, P.//Boyer, H.W.//Itakura, K.//Rosenberg, J.M. 	Two-fold symmetry of crystalline DNA-EcoRI endonuclease recognition complexes.	J. Biomol. Struct. Dyn.	1984	1		1149-1160			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. 		
@D	Grabowski, G.//Alves, J. 	Transformation of the EcoRI restriction endonuclease to an enzyme with altered specificity: Development of a positive in vivo selection system.	Biol. Chem. Hoppe Seyler	1995	376		S102			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. 		
@D	Grabowski, G.//Jeltsch, A.//Wolfes, H.//Maass, G.//Alves, J. 	Site-directed mutagenesis in the catalytic center of the restriction endonuclease EcoRI.	Gene	1995	157		113-118			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. 		
@D	Grabowski, G.//Maass, G.//Alves, J. 	Asp-59 is not important for the catalytic activity of the restriction endonuclease EcoRI.	FEBS Lett.	1996	381		106-110			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. 		
@D	Grachev, S.A.//Mamaev, S.V.//Gurevich, A.I.//Igoshin, A.V.//Kolosov, M.N.//Slyusarenko, A.G. 	Restriction endonuclease TaqXI from Thermus aquaticus.	Bioorg. Khim.	1981	7		628-630			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. 		
@D	Grad, Y.H. et al. 	Genomic epidemiology of the Escherichia coli O104:H4 outbreaks in Europe, 2011.	Proc. Natl. Acad. Sci. U. S. A.	2012	109		3065-3070			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. 		
@D	Gradnigo, J.S.//Somerville, G.A.//Huether, M.J.//Kemmy, R.J.//Johnson, C.M.//Oliver, M.G.//Moriyama, E.N. 	Genome Sequence of Streptomyces aureofaciens ATCC Strain 10762.	Genome Announcements	2016	4		e00615-16			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. 		
@D	Graessmann, M.//Graessmann, A.//Wagner, H.//Werner, E.//Simon, D. 	Complete DNA methylation does not prevent polyoma and simian virus 40 virus early gene expression.	Proc. Natl. Acad. Sci. U. S. A.	1983	80		6470-6474			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. 		
@D	Grana-Miraglia, L.//Lozano, L.//Castro-Jaimes, S.//Cevallos, M.A.//Volkow, P.//Castillo-Ramirez, S. 	First Genome Sequence of a Mexican Multidrug-Resistant Acinetobacter baumannii Isolate.	Genome Announcements	2016	4		e00156-16			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. 		
@D	Grande, L.//Michelacci, V.//Tozzoli, R.//Ranieri, P.//Maugliani, A.//Caprioli, A.//Morabito, S. 	Whole genome sequence comparison of vtx2-converting phages from Enteroaggregative Haemorrhagic Escherichia coli strains.	BMC Genomics	2014	15		574			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. 		
@D	Grandori, R.//Sander, C. 	Identification by computer sequence analysis of transcriptional regulator proteins in Dictyostelium discoideum and Serratia marcescens.	Nucleic Acids Res.	1991	19		2359-2362			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. 		
@D	Grant, S.G.//Jessee, J.//Bloom, F.R.//Hanahan, D. 	Differential plasmid rescue from transgenic mouse DNAs into Escherichia coli methylation-restriction mutants.	Proc. Natl. Acad. Sci. U. S. A.	1990	87		4645-4649			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. 		
@D	Grasby, J.A.//Connolly, B.A. 	Stereochemical outcome of the hydrolysis reaction catalyzed by the EcoRV restriction endonuclease.	Biochemistry	1992	31		7855-7861			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. 		
@D	Grass, G.//Bierbaum, G.//Molitor, E.//Gotte, N.//Antwerpen, M. 	Genome Sequence of Bacillus pumilus Strain Bonn, Isolated from an Anthrax-Like Necrotic Skin Infection Site of a Child.	Genome Announcements	2016	4		e01741-15			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. 		
@D	Grass, G.//Hanczaruk, M.//Antwerpen, M. 	Genome Sequence of Bacillus anthracis Larissa, Associated with a Case of Cutaneous Anthrax in Greece.	Genome Announcements	2015	3		e01273-15			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. 		
@D	Grasso, R.J.//Paigen, K. 	Loss of host-controlled restriction of lambda bacteriophage in Escherichia coli following methionine deprivation.	J. Virol.	1968	2		1368-1373			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. 		
@D	Grasso, R.J.//Paigen, K. 	The effect of amino acids on host-controlled restriction of lambda phage.	Virology	1968	36		1-8			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. 		
@D	Grasso, R.J.//Paigen, K. 	Loss of host-controlled restriction and modification of phage lambda in Escherichia coli K12 previously infected with UV-irradiated coli-phage T3.	Virology	1969	38		191-194			Host range properties of bacteriophages are altered not only by genetic mutation, but also by the process of host-controlled modification. 		
@D	Grau, J.//Reschke, M.//Erkes, A.//Streubel, J.//Morgan, R.D.//Wilson, G.G.//Koebnik, R.//Boch, J. 	AnnoTALE: bioinformatic tools for identification, annotation, and nomenclature of TALEs from Xanthomonas genomic sequences.	Sci. Rep.	2016	6		21077			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. 		
@D	Graupner, K.//Lackner, G.//Hertweck, C. 	Genome Sequence of Mushroom Soft-Rot Pathogen Janthinobacterium agaricidamnosum.	Genome Announcements	2015	3		e00277-15			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. 		
@D	Graves, K.L.//Butler, M.M.//Hardy, L.W. 	Site-directed mutagenesis of the gene encoding phage T4 dCMP hydroxymethylase.	FASEB J.	1993	7		A1197			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. 		
@D	Gray, T.A.//Palumbo, M.J.//Derbyshire, K.M. 	Draft Genome Sequence of MKD8, a Conjugal Recipient Mycobacterium smegmatis Strain.	Genome Announcements	2013	1		e00148-13			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. 		
@D	Grazulis, S.//Deibert, M.//Rimseliene, R.//Skirgaila, R.//Sasnauskas, G.//Lagunavicius, A.//Repin, V.//Urbanke, C.//Huber, R.//Siksnys, V. 	Crystal structure of the Bse634I restriction endonuclease: comparison of two enzymes recognizing the same DNA sequence.	Nucleic Acids Res.	2002	30		876-885			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 		
@D	Grazulis, S.//Manakova, E.//Roessle, M.//Bochtler, M.//Tamulaitiene, G.//Huber, R.//Siksnys, V. 	Structure of the metal-independent restriction enzyme BfiI reveals fusion of a specific DNA-binding domain with a nonspecific nuclease.	Proc. Natl. Acad. Sci. U. S. A.	2005	102		15797-15802			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. 		
@D	Green, N.M.//Zhang, S.//Porcella, S.F.//Nagiec, M.J.//Barbian, K.D.//Beres, S.B.//Lefebvre, R.B.//Musser, J.M. 	Genome Sequence of a Serotype M28 Strain of Group A Streptococcus: Potential New Insights into Puerperal Sepsis and Bacterial Disease   Specificity.	J. Infect. Dis.	2005	192		760-770			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. 		
@D	Greenaway, P.J. 	The isolation of a restriction enzyme from Bordetella pertussis.	Biochem. Biophys. Res. Commun.	1980	95		1282-1287			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. 		
@D	Greenberg, D.E.//Porcella, S.F.//Zelazny, A.M.//Virtaneva, K.//Sturdevant, D.E.//Kupko, J.J.//Barbian, K.D.//Babar, A.//Dorward, D.W.//Holland, S.M. 	Genome sequence analysis of the emerging human pathogenic acetic acid bacterium Granulibacter bethesdensis.	J. Bacteriol.	2007	189		8727-8736			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. 		
@D	Greene, P.//Reich, N.O.//McClarin, J.//Boyer, H.W.//Rosenberg, J. 	Site-directed mutagenesis of the EcoRI endonuclease.	J. Cell Biochem. Suppl.	1985	9B		94			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. 		
@D	Greene, P.J.//Ballard, B.T.//Stephenson, F.//Kohr, W.J.//Rodriguez, H.//Rosenberg, J.M.//Boyer, H.W. 	Purification and characterization of the restriction endonuclease RsrI, an isoschizomer of EcoRI.	Gene	1988	68		43-52			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. 		
@D	Greene, P.J.//Betlach, M.C.//Boyer, H.W.//Goodman, H.M. 	The EcoRI restriction endonuclease.	Methods Mol. Biol.	1974	7		87-105			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. 		
@D	Greene, P.J.//Boyer, H.W. 	Genetic and molecular analysis of the EcoRI restriction and modification system.	Fed. Proc.	1981	40		293			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. 		
@D	Greene, P.J.//Gupta, M.//Boyer, H.W.//Brown, W.E.//Rosenberg, J.M. 	Sequence Analysis of the DNA Encoding the EcoRI Endonuclease and Methylase.	J. Biol. Chem.	1981	256		2143-2153			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. 		
@D	Greene, P.J.//Heyneker, H.L.//Bolivar, F.//Rodriguez, R.L.//Betlach, M.C.//Covarrubias, A.A.//Backman, K.//Russel, D.J.//Tait, R.//Boyer, H.W. 	A general method for the purification of restriction enzymes.	Nucleic Acids Res.	1978	5		2373-2380			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. 		
@D	Greene, P.J.//Poonian, M.S.//Nussbaum, A.L.//Tobias, L.//Garfin, D.E.//Boyer, H.W.//Goodman, H.M. 	Restriction and modification of a self-complementary octanucleotide containing the EcoRI substrate.	J. Mol. Biol.	1975	99		237-261			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. 		
@A	Greene, P.J.//Yanofsky, S.//Reich, N.//Day, J.//Hager, P.//Boyer, H.W. 		Structure and function of the EcoRI endonuclease.			Oxender, D.L. 		Protein Structure, Folding and Design 2				NY	Alan R. Liss, Inc.	1987		0		3-7									None 		
@D	Gregoire, S.T. 	The effect of DNA-mediated restriction on conjugation in Neisseria gonorrhoeae.	M.Sc. Thesis. Univ. Maryland.	1986	0		1-138			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. 		
@D	Gregorova, D.//Pravcova, M.//Karpiskova, R.//Rychlik, I. 	Plasmid pC present in Salmonella enterica serovar Enteritidis PT14b strains encodes a restriction modification system.	FEMS Microbiol. Lett.	2002	214		195-198			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. 		
@D	Gregory, R.//Saunders, V.A.//Saunders, J.R. 	Rule-based simulation of temperate bacteriophage infection: Restriction-modification as a limiter to infection in bacterial populations.	Biosystems	2010	100		166-177			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. 		
@D	Greif, G.//Iraola, G.//Berna, L.//Coitinho, C.//Rivas, C.M.//Naya, H.//Robello, C. 	Complete Genome Sequence of Mycobacterium tuberculosis Strain MtURU-001, Isolated from a Rapidly Progressing Outbreak in Uruguay.	Genome Announcements	2014	2		e01220-13			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. 		
@D	Greil, F.//Moorman, C.//van Steensel, B. 	DamID: Mapping of in vivo protein-genome interactions using tethered DNA adenine methyltransferase.	Methods Enzymol.	2006	410		342-359			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. 		
@D	Grenier, F.//Matteau, D.//Baby, V.//Rodrigue, S. 	Complete Genome Sequence of Escherichia coli BW25113.	Genome Announcements	2014	2		e01038-14			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. 		
@D	Greninger, A.L.//Chorny, I.//Knowles, S.//Ng, V.L.//Chaturvedi, V. 	Draft Genome Sequences of Four NDM-1-Producing Klebsiella pneumoniae Strains from a Health Care Facility in Northern California.	Genome Announcements	2015	3		e00421-15			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. 		
@D	Greninger, A.L.//Cunningham, G.//Chiu, C.Y.//Miller, S. 	Draft Genome Sequence of Mycobacterium heckeshornense Strain RLE.	Genome Announcements	2015	3		e00930-15			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. 		
@D	Greninger, A.L.//Cunningham, G.//Chiu, C.Y.//Miller, S. 	Draft Genome Sequence of Mycobacterium heraklionense Strain Davo.	Genome Announcements	2015	3		e00807-15			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. 		
@D	Greninger, A.L.//Cunningham, G.//Hsu, E.D.//Yu, J.M.//Chiu, C.Y.//Miller, S. 	Draft Genome Sequence of Mycobacterium obuense Strain UC1, Isolated from Patient  Sputum.	Genome Announcements	2015	3		e00612-15			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. 		
@D	Greninger, A.L.//Cunningham, G.//Yu, J.M.//Hsu, E.D.//Chiu, C.Y.//Miller, S. 	Draft Genome Sequence of Mycobacterium elephantis Strain Lipa.	Genome Announcements	2015	3		e00691-15			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. 		
@D	Greninger, A.L.//Cunningham, G.//Yu, J.M.//Hsu, E.D.//Chiu, C.Y.//Miller, S. 	Draft Genome Sequence of Mycobacterium arupense Strain GUC1.	Genome Announcements	2015	3		e00630-15			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. 		
@D	Greninger, A.L.//Kozyreva, V.//Truong, C.L.//Graves, M.//Chaturvedi, V. 	Draft Genome Sequence of Turicella otitidis TD1, Isolated from a Patient with Bacteremia.	Genome Announcements	2015	3		e01060-15			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. 		
@D	Greninger, A.L.//Kozyreva, V.//Truong, C.L.//Longoria, R.//Chaturvedi, V. 	Draft Genome Sequence of Kerstersia gyiorum CG1, Isolated from a Leg Ulcer.	Genome Announcements	2015	3		e01036-15			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. 		
@D	Greninger, A.L.//Streithorst, J.//Chiu, C.Y.//Miller, S. 	First Draft Genome Sequences of Neisseria sp. Strain 83E34 and Neisseria sp. Strain 74A18, Previously Identified as CDC Eugonic Fermenter 4b Species.	Genome Announcements	2016	4		e01277-16			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. 		
@D	Greninger, A.L.//Streithorst, J.//Chiu, C.Y.//Miller, S. 	First Complete Genome Sequence of Corynebacterium riegelii.	Genome Announcements	2017	5		e00084-17			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. 		
@D	Grepinet, O.//Boumart, Z.//Virlogeux-Payant, I.//Loux, V.//Chiapello, H.//Gendrault, A.//Gibrat, J.F.//Chemaly, M.//Velge, P. 	Genome Sequence of the Persistent Salmonella enterica subsp. enterica Serotype Senftenberg Strain SS209.	J. Bacteriol.	2012	194		2385-2386			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. 		
@D	Grepinet, O.//Rossignol, A.//Loux, V.//Chiapello, H.//Gendrault, A.//Gibrat, J.F.//Velge, P.//Virlogeux-Payant, I. 	Genome Sequence of the Invasive Salmonella enterica subsp. enterica Serotype Enteritidis Strain LA5.	J. Bacteriol.	2012	194		2387-2388			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. 		
@D	Gressmann, H.//Linz, B.//Ghai, R.//Pleissner, K.P.//Schlapbach, R.//Yamaoka, Y.//Kraft, C.//Suerbaum, S.//Meyer, T.F.//Achtman, M. 	Gain and loss of multiple genes during the evolution of Helicobacter pylori.	PLoS Genet.	2005	1		e43			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. 		
@D	Greub, G.//Kebbi-Beghdadi, C.//Bertelli, C.//Collyn, F.//Riederer, B.M.//Yersin, C.//Croxatto, A.//Raoult, D. 	High throughput sequencing and proteomics to identify immunogenic proteins of a new pathogen: the dirty genome approach.	PLoS ONE	2009	4		E8423			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. 		
@D	Grewal, S.//Vakhlu, J.//Gupta, V.//Sangwan, N.//Kohli, P.//Nayyar, N.//Rani, P.//Sance, S.S.//Lal, R. 	Draft Genome Sequence of Pseudomonas sp. Strain JMM, a Sediment-Hosted Environmental Isolate.	Genome Announcements	2014	2		e00879-14			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%. 		
@D	Griffin, S.//Branch, P.//Xu, Y.-Z.//Karran, P. 	DNA mismatch binding and incision at modified guanine bases by extracts of mammalian cells: implications for tolerance to DNA methylation damage.	Biochemistry	1994	33		4787-4793			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. 		
@D	Grigaite, R.//Maneliene, Z.//Janulaitis, A. 	AarI, a restriction endonuclease from Arthrobacter aurescens SS2-322, which recognizes the novel non-palindromic sequence 5'-CACCTGC(N)4/8-3'.	Nucleic Acids Res.	2002	30		e123			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. 		
@A	Grigorescu, A.//Horvath, M.//Wilkosz, P.A.//Chandrasekhar, K.//Rosenberg, J.M. 		The integration of recognition and cleavage: X-ray structures of pre-transition state complex, post-reactive complex, and the DNA-free endonuclease.			Pingoud, A. 		Nucleic Acids Mol. Biol.				Berlin Heidelberg	Springer-Verlag	2004		14		137-177									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. 		
@D	Grigorescu, A.A.//Rosenberg, J.M. 	A local folding transition coupled to site-specific binding in EcoRI restriction endonuclease.	Biophys. J.	2004	86		591a			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. 		
@D	Grigoryeva, T.V.//Laikov, A.V.//Naumova, R.P.//Manolov, A.I.//Larin, A.K.//Karpova, I.Y.//Semashko, T.A.//Alexeev, D.G.//Kostryukova, E.S.//Muller, R.//Govorun, V.M. 	Draft Genome of the Nitrogen-Fixing Bacterium Pseudomonas stutzeri Strain KOS6 Isolated from Industrial Hydrocarbon Sludge.	Genome Announcements	2013	1		e00072-12			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. 		
@D	Grim, C.J.//Gopinath, G.R.//Jarvis, K.G.//Sathyamoorthy, V.//Trach, L.H.//Chase, H.R.//Tall, B.D. 	Genome Sequence of Cronobacter sakazakii Serogroup O:4, Sequence Type 4 Strain CDC 2009-03746, Isolated from a Fatal Case of Infantile Meningitis.	Genome Announcements	2015	3		e00492-15			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. 		
@D	Grim, C.J.//Gopinath, G.R.//Mammel, M.K.//Sathyamoorthy, V.//Trach, L.H.//Chase, H.R.//Tall, B.D.//Fanning, S.//Stephan, R. 	Genome Sequence of an Enterobacter helveticus Strain, 1159/04 (LMG 23733), Isolated from Fruit Powder.	Genome Announcements	2013	1		e01038-13			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%. 		
@D	Grim, C.J.//Hasan, N.A.//Taviani, E.//Haley, B.//Chun, J.//Brettin, T.S.//Bruce, D.C.//Detter, J.C.//Han, C.S.//Chertkov, O.//Challacombe, J.//Huq, A.//Nair, G.B.//Colwell, R.R. 	Genome Sequence of Hybrid Vibrio cholerae O1 MJ-1236, B-33, and CIRS101 and Comparative Genomics with V. cholerae.	J. Bacteriol.	2010	192		3524-3533			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. 		
@D	Grim, C.J.//Schreier, H.J. 	Draft Genome Sequence of Vibrio (Listonella) anguillarum ATCC 14181.	Genome Announcements	2016	4		e01185-16			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. 		
@D	Grimaud, R.//Ghiglione, J.F.//Cagnon, C.//Lauga, B.//Vaysse, P.J.//Rodriguez-Blanco, A.//Mangenot, S.//Cruveiller, S.//Barbe, V.//Duran, R.//Wu, L.F.//Talla, E.//Bonin, P.//Michotey, V. 	Genome Sequence of the Marine Bacterium Marinobacter hydrocarbonoclasticus SP17,  Which Forms Biofilms on Hydrophobic Organic Compounds.	J. Bacteriol.	2012	194		3539-3540			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. 		
@D	Grime, S.K.//Martin, R.L.//Holaway, B.L. 	Inhibition of restriction enzyme cleavage of DNA modified with 7-deaza-dGTP.	Nucleic Acids Res.	1991	19		2791			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. 		
@D	Grimes, E.//Koob, M.//Szybalski, W. 	Achilles' heel cleavage: creation of rare restriction sites in lambda phage genomes and evaluation of additional operators, repressors and restriction/modification systems .	Gene	1990	90		1-7			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. 		
@D	Grimm, I.//Dumke, J.//Vollmer, T.//Hinse, D.//Ruckert, C.//Kalinowski, J.//Knabbe, C.//Dreier, J. 	Complete Genome Sequence of the Streptococcus gallolyticus subsp. gallolyticus Strain DSM 16831.	Genome Announcements	2017	5		e00108-17			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. 		
@D	Grindl, W.//Wende, W.//Pingoud, V.//Pingoud, A. 	The protein splicing domain of the homing endonuclease PI-SceI is responsible for specific DNA binding.	Nucleic Acids Res.	1998	26		1857-1862			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. 		
@D	Grinkevich, P.//Sinha, D.//Iermak, I.//Guzanova, A.//Weiserova, M.//Ludwig, J.//Mesters, J.R.//Ettrich, R.H. 	Crystal structure of a novel domain of the motor subunit of the Type I restriction enzyme EcoR124 involved in complex assembly and DNA binding.	J. Biol. Chem.	2018	293		15043-15054			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. 		
@D	Grishin, A.//Fonfara, I.//Alexeevski, A.//Spirin, S.//Zanegina, O.//Karyagina, A.//Alexeyevsky, D.//Wende, W. 	IDENTIFICATION OF CONSERVED FEATURES OF LAGLIDADG HOMING ENDONUCLEASES.	J. Bioinform. Comput. Biol.	2010	8		453-469			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. 		
@D	Gritsenko, O.M.//Koudan, E.V.//Mikhailov, S.N.//Ermolinsky, B.S.//VanAerschot, A.//Herdewijn, P.//Gromova, E.S. 	Affinity modification of EcoRII DNA methyltransferase by the dialdehyde-substituted DNA duplexes: mapping the enzyme region that interacts with DNA.	Nucleosides Nucleotides Nucleic Acids	2002	21		753-764			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. 		
@D	Gritsenko, O.M.//Mikhailov, S.N.//Efimtseva, E.V.//Van Aerschot, A.//Herdewijn, P.//Gromova, E.S. 	Probing the MvaI methyltransferase region that interacts with DNA: Affinity labeling with the dialdehyde-containing DNA duplexes.	Nucleosides Nucleotides Nucleic Acids	2000	19		1805-1820			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. 		
@D	Grivell, L.A. 	Homing in on an endosymbiotic endonuclease.	Curr. Biol.	1992	2		450-452			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. 		
@D	Grivell, L.A. 	Transposition: Mobile introns get into line.	Curr. Biol.	1996	6		48-51			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. 		
@D	Grizot, S.//Duclert, A.//Thomas, S.//Duchateau, P.//Paques, F. 	Context dependence between subdomains in the DNA binding interface of the I-CreI homing endonuclease.	Nucleic Acids Res.	2011	39		6124-6136			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. 		
@D	Grizot, S.//Epinat, J.C.//Thomas, S.//Duclert, A.//Rolland, S.//Paques, F.//Duchateau, P. 	Generation of redesigned homing endonucleases comprising DNA-binding domains derived from two different scaffolds.	Nucleic Acids Res.	2010	38		2006-2018			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. 		
@D	Grizot, S.//Smith, J.//Daboussi, F.//Prieto, J.//Redondo, P.//Merino, N.//Villate, M.//Thomas, S.//Lemaire, L.//Montoya, G.//Blanco, F.J.//Paques, F.//Duchateau, P. 	Efficient targeting of a SCID gene by an engineered single-chain homing endonuclease.	Nucleic Acids Res.	2009	37		5405-5419			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. 		
@D	Grogan, D.W. 	Cytosine methylation by the SuaI restriction-modification system: implications for genetic fidelity in a hyperthermophilic archaeon.	J. Bacteriol.	2003	185		4657-4661			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. 		
@D	Groll, D.H.//Jeltsch, A.//Selent, U.//Pingoud, A. 	Does the restriction endonuclease EcoRV employ a two-metal-ion mechanism for DNA cleavage?	Biochemistry	1997	36		11389-11401			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. 		
@D	Gromek, S.M.//Sung, A.A.//Klassen, J.L.//Balunas, M.J. 	Draft Genome Sequence of Streptomyces sp. Strain PTY087I2, Isolated from Styela canopus, a Panamanian Tunicate.	Genome Announcements	2016	4		e00856-16			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. 		
@D	Gromkova, R.//Bendler, J.//Goodgal, S. 	Restriction and modification of bacteriophage S2 in Haemophilus influenzae.	J. Bacteriol.	1973	114		1151-1157			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. 		
@D	Gromkova, R.//Goodgal, S. 	On the restriction-modification systems of Haemophilus aegyptius.	Abstr. Gen. Meet. Am. Soc. Microbiol.	1975	75		103			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. 		
@D	Gromkova, R.//Goodgal, S.H. 	Biological Properties of a Haemophilus influenzae Restriction Enzyme, HindI.	J. Bacteriol.	1976	127		848-854			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. 		
@D	Gromkova, R.//Goodgal, S.H. 	On the effect of a restriction modification system on transformation in Haemophilus influenzae.	Fed. Proc.	1975	34		588			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. 		
@D	Gromkova, R.//Goodgal, S.H. 	Action of Haemophilus endodeoxyribonuclease on biologically active deoxyribonucleic acid.	J. Bacteriol.	1972	109		987-992			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. 		
@A	Gromkova, R.//Goodgal, S.H. 		On the role of restriction enzymes in transformation and transfection.			Grell, R.F. 		Mechanisms of recombination				New York	Plenum	1974		0		209-215									None 		
@D	Gromkova, R.//LaPorte, J.//Goodgal, S.H. 	A restriction enzyme from Haemophilus influenzae requiring adenosine triphosphate and S-adenosyl methionine.	Abstr. Gen. Meet. Am. Soc. Microbiol.	1973	73		72			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. 		
@D	Gromova, E.S.//Elob, A.A.//Kubareva, E.A.//Metelev, V.G.//Shabarova, Z.A. 	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.	Mol. Biol. (Mosk)	1986	20		29-40			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. 		
@D	Gromova, E.S.//Elob, A.A.//Kubareva, E.A.//Metelev, V.G.//Shabarova, Z.A. 	Interaction of EcoRII restriction and modification enzymes with synthetic fragments of DNA.	Mol. Biol. (Mosk)	1986	20		22-32			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. 		
@D	Gromova, E.S.//Khoroshaev, A.V. 	Prokaryotic DNA methyltransferases: The structure and the mechanism of interaction with DNA.	Mol. Biol. (Mosk)	2003	37		300-314			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. 		
@D	Gromova, E.S.//Kubareva, E.A.//Vinogradova, M.N.//Oretskaya, T.S.//Shabarova, Z.A. 	Peculiarities of recognition of CCA/TGG sequences in DNA by restriction endonucleases MvaI and EcoRII.	J. Mol. Recognit.	1991	4		133-141			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. 		
@D	Gromova, E.S.//Kubareva, E.A.//Yolov, A.A.//Akatova, E.A.//Nikolskaya, I.I.//Shabarova, Z.A. 	Cleavage of concatemeric substrates by restriction endonucleases MvaI and SsoII.	Biokhimiia	1991	56		552-559			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. 		
@D	Gromova, E.S.//Kuchava, E.A.//Pein, C.-D.//Oreshkaya, T.S.//Shabarova, Z.A.//Check, D. 	Study of the DNA cleavage mechanism of the restriction endonuclease MvaI.	Dokl. Akad. Nauk.	1987	295		1493-1497			None 		
@D	Gromova, E.S.//Oretskaya, T.S.//Eritja, R.//Guschlbauer, W. 	Kinetic studies of MvaI DNA methyltransferase interaction with modified oligonucleotide duplexes.	Biochem. Mol. Biol. Int.	1995	36		247-255			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. 		
@D	Gromova, E.S.//Petrauskene, O.V.//Kubareva, E.A. 	Study of the mechanism of EcoRII endonuclease activation with synthetic substrates.	Nucleic Acids Symp. Ser.	1991	24		217-218			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. 		
@D	Gromova, E.S.//Shabarova, A.Z. 	DNA-Protein interactions:  The use of synthetic oligo- and polynucleotides for studying single-stranded-DNA-binding proteins and restriction endonucleases.	Prog. Nucleic Acid Res. Mol. Biol.	1990	39		1-47			None 		
@D	Gromova, E.S.//Vinogradova, M.N.//Uporova, T.M.//Gryaznova, O.I.//Isagulyants, M.G.//Kosykh, V.G.//Nikolskaya, I.I.//Shabarova, Z.A. 	DNA duplexes with phosphoamide bonds:  the interaction with EcoRII and SsoII restriction endonucleases.	Bioorg. Khim.	1987	13		269-272			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. 		
@D	Gronenborn, B.//Messing, J. 	Methylation of single-stranded DNA in vitro introduces new restriction endonuclease cleavage sites.	Nature	1978	272		375-377			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. 		
@D	Grones, J.//Turna, J. 	Some properties of restriction endonucleases from Acetobacter pasteurianus.	Biologia (Bratisl)	1991	46		1103-1108			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. 		
@D	Grones, J.//Turna, J. 	Some properties of restriction endonuclease ApaBI from Acetobacter pasteurianus.	Biochim. Biophys. Acta	1993	1162		323-325			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. 		
@D	Grones, J.//Turna, J. 	Isolation of a new restriction enzyme, ApaCI, an isoschizomer of BamHI produced by Acetobacter pasteurianus.	Folia Microbiol. (Praha)	1992	37		353-356			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. 		
@D	Grones, J.//Turna, J. 	ApaCI, an isoschizomer of BamHI isolated from Acetobacter pasteurianus.	Nucleic Acids Res.	1992	20		3513					
@D	Gronow, S. et al. 	Complete genome sequence of Veillonella parvula type strain (Te3).	Standards in Genomic Sciences	2010	2		57-65			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. 		
@D	Gronow, S. et al. 	Complete genome sequence of Paludibacter propionicigenes type strain (WB4).	Standards in Genomic Sciences	2011	4		36-44			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. 		
@D	Gronow, S. et al. 	Complete genome sequence of Bacteroides salanitronis type strain (BL78).	Standards in Genomic Sciences	2011	4		191-199			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. 		
@D	Groot, M.N.//Nieboer, F.//Abee, T. 	Enhanced Transformation Efficiency of Recalcitrant Bacillus cereus and Bacillus weihenstephanensis Isolates upon In Vitro Methylation of Plasmid DNA.	Appl. Environ. Microbiol.	2008	74		7817-7820			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. 		
@D	Gros, C.//Chauvigne, L.//Poulet, A.//Menon, Y.//Ausseil, F.//Dufau, I.//Arimondo, P.B. 	Development of a universal radioactive DNA methyltransferase inhibition test for high-throughput screening and mechanistic studies.	Nucleic Acids Res.	2013	41		12			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. 		
@D	Gross, U.//Brzuszkiewicz, E.//Gunka, K.//Starke, J.//Riedel, T.//Bunk, B.//Sproer, C.//Wetzel, D.//Poehlein, A.//Chibani, C.//Bohne, W.//Overmann, J.//Zimmermann, O.//Daniel, R.//Liesegang, H. 	Comparative genome and phenotypic analysis of three Clostridioides difficile strains isolated from a single patient provide insight into multiple infection of C. difficile.	BMC Genomics	2018	19		1			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. 		
@D	Grosskopf, R.//Wolf, W.//Kessler, C. 	Two new restriction endonucleases DraII and DraIII from Deinococcus radiophilus.	Nucleic Acids Res.	1985	13		1517-1528			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. 		
@D	Grote, J. et al. 	Draft genome sequence of strain HIMB100, a cultured representative of the SAR116 clade of marine Alphaproteobacteria.	Standards in Genomic Sciences	2011	5		269-278			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. 		
@D	Grote, J.//Schott, T.//Bruckner, C.G.//Glockner, F.O.//Jost, G.//Teeling, H.//Labrenz, M.//Jurgens, K. 	Genome and physiology of a model Epsilonproteobacterium responsible for sulfide detoxification in marine oxygen depletion zones.	Proc. Natl. Acad. Sci. U. S. A.	2012	109		506-510			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. 		
@D	Grothusen, H.//Castillo, A.//Henriquez, P.//Navas, E.//Bohle, H.//Araya, C.//Bustamante, F.//Bustos, P.//Mancilla, M. 	First Complete Genome Sequence of Tenacibaculum dicentrarchi, an Emerging Bacterial Pathogen of Salmonids.	Genome Announcements	2016	4		e01756-15			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. 		
@D	Grouzdev, D.S.//Babich, T.L.//Tourova, T.P.//Sokolova, D.S.//Abdullin, R.R.//Poltaraus, A.B.//Schevchenko, M.A.//Toshchakov, S.V.//Nazina, T.N. 	Draft Genome Sequence of Roseomonas aestuarii Strain JR1/69-1-13 Isolated from Nitrate- and Radionuclide-Contaminated Groundwater in Russia.	Genome Announcements	2018	6		e00583-18			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. 		
@D	Grouzdev, D.S.//Dziuba, M.V.//Sukhacheva, M.S.//Mardanov, A.V.//Beletskiy, A.V.//Kuznetsov, B.B.//Skryabin, K.G. 	Draft Genome Sequence of Magnetospirillum sp. Strain SO-1, a Freshwater Magnetotactic Bacterium Isolated from the Ol'khovka River, Russia.	Genome Announcements	2014	2		e00235-14			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. 		
@D	Grouzdev, D.S.//Rysina, M.S.//Bryantseva, I.A.//Gorlenko, V.M.//Gaisin, V.A. 	Draft genome sequences of 'Candidatus Chloroploca asiatica' and 'Candidatus Viridilinea mediisalina', candidate representatives of the Chloroflexales order:  phylogenetic and taxonomic implications.	Standards in Genomic Sciences	2018	13		24			'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. 		
@D	Grouzdev, D.S.//Safonov, A.V.//Babich, T.L.//Tourova, T.P.//Krutkina, M.S.//Nazina, T.N. 	Draft Genome Sequence of a Dissimilatory U(VI)-Reducing Bacterium, Shewanella xiamenensis Strain DCB2-1, Isolated from Nitrate- and Radionuclide-Contaminated Groundwater in Russia.	Genome Announcements	2018	6		e00555-18			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. 		
@D	Grouzdev, D.S.//Tikhonova, E.N.//Krutkina, M.S.//Kravchenko, I.K. 	Genome Sequence of Methylotrophic Azospirillum sp. Strain B2, Isolated from a Raised Sphagnum Bog.	Genome Announcements	2018	6		e00492-18			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. 		
@D	Grover, S.//Sharma, V.K.//Mallapa, R.H.//Batish, V.K. 	Draft Genome Sequence of Lactobacillus fermentum Lf1, an Indian Isolate of Human  Gut Origin.	Genome Announcements	2013	1		e00883-13			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. 		
@D	Grover, S.//Sharma, V.K.//Mallapa, R.H.//Batish, V.K. 	Draft Genome Sequence of Lactobacillus plantarum Strain Lp91, a Promising Indian  Probiotic Isolate of Human Gut Origin.	Genome Announcements	2013	1		e00976-13			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. 		
@D	Gruber, I.M.//Nikolskaya, I.I.//Uporova, T.M.//Nisilevich, V.F. 	Growth and bioenergetic characteristics of Escherichia coli CK, capable of producing restriction endonuclease, under the conditions of batch cultivation.	Zh. Mikrobiol. Epidemiol. Immunobiol.	1984	6		50-55			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. 		
@D	Gruen, M.//Chang, K.//Serbanescu, I.//Liu, D.R. 	An in vivo selection system for homing endonuclease activity.	Nucleic Acids Res.	2002	30		e29			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. 		
@D	Gruenbaum, Y.//Cedar, H.//Razin, A. 	Restriction enzyme digestion of hemimethylated DNA.	Nucleic Acids Res.	1981	9		2509-2515			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. 		
@D	Grumaz, C.//Rais, D.//Kirstahler, P.//Vainshtein, Y.//Rupp, S.//Zibek, S.//Sohn, K. 	Draft Genome Sequence of Pseudonocardia autotrophica Strain DSM 43083, an Efficient Producer of Peroxidases for Lignin Modification.	Genome Announcements	2017	5		e01562-16			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. 		
@D	Grumaz, C.//Vainshtein, Y.//Kirstahler, P.//Luetz, S.//Kittelmann, M.//Schroer, K.//Eggimann, F.K.//Czaja, R.//Vogel, A.//Hilberath, T.//Worsch, A.//Girhard, M.//Urlacher, V.B.//Sandberg, M.//Sohn, K. 	Draft Genome Sequences of Three Actinobacteria Strains Presenting New Candidate Organisms with High Potentials for Specific P450 Cytochromes.	Genome Announcements	2017	5		e00532-17			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. 		
@D	Grunau, C.//Schattevoy, R.//Mache, N.//Rosenthal, A. 	MethTools-a toolbox to visualize and analyze DNA methylation data.	Nucleic Acids Res.	2000	28		1053-1058			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/ 		
@D	Gruning, B.A.//Erxleben, A.//Hahnlein, A.//Gunther, S. 	Draft Genome Sequence of Streptomyces viridochromogenes Strain Tu57, Producer of  Avilamycin.	Genome Announcements	2013	1		e00384-13			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. 		
@D	Grunwald, S.//Driever, P.H.//Hoelzer, D.//Drahovsky, D. 	Reduced methyl group acceptance of 1-beta-D-arabinofuranosylcytosine-containing DNA polymers.	Biochim. Biophys. Acta	1988	950		366-373			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. 		
@D	Gu, H.H.//Xu, J.//Gallagher, M.//Dean, G.E. 	Peptide splicing in the vacuolar ATPase subunit A from Candida tropicalis.	J. Biol. Chem.	1993	268		7372-7381			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. 		
@D	Gu, J.J.//Zhou, Y.//Lu, J.J.//Ye, B.C. 	Draft Genome Sequence of a Polydroxyalkanoate-Synthesizing Bacterium, Bacillus sp. Strain PJC48, Isolated from Activated Sludge.	Genome Announcements	2017	5		e01751-16			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. 		
@D	Gu, Y.//Yang, C.//Wang, X.//Geng, W.//Sun, Y.//Feng, J.//Wang, Y.//Quan, Y.//Che, Y.//Zhang, C.//Gong, T.//Zhang, W.//Gao, W.//Zuo, Z.//Song, C.//Wang, S. 	Genome Sequence of the epsilon-Poly-l-Lysine-Producing Strain Streptomyces albulus NK660, Isolated from Soil in Gutian, Fujian Province, China.	Genome Announcements	2014	2		e00532-14			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. 		
@D	Gualtieri, M.//Ogier, J.C.//Pages, S.//Givaudan, A.//Gaudriault, S. 	Draft Genome Sequence and Annotation of the Entomopathogenic Bacterium Xenorhabdus szentirmaii Strain DSM16338.	Genome Announcements	2014	2		e00190-14			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. 		
@D	Guan, P.//Ai, P.//Dai, X.//Zhang, J.//Xu, L.//Zhu, J.//Li, Q.//Deng, Q.//Li, S.//Wang, S.//Liu, H.//Wang, L.//Li, P.//Zheng, A. 	Complete Genome Sequence of Bacillus thuringiensis Serovar Sichuansis Strain MC28.	J. Bacteriol.	2012	194		6975			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. 		
@D	Guan, S.X.//Blanchard, A.//Zhang, P.H.//Zhu, Z.Y. 	Alteration of Sequence Specificity of the Type IIS Restriction Endonuclease BtsI.	PLoS ONE	2010	5		e11787			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. 		
@D	Guan, W.//Shao, J.//Davis, R.E.//Zhao, T.//Huang, Q. 	Genome Sequence of a Xylella fastidiosa Strain Causing Sycamore Leaf Scorch Disease in Virginia.	Genome Announcements	2014	2		e00773-14			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%. 		
@D	Guan, W.//Shao, J.//Zhao, T.//Huang, Q. 	Genome Sequence of a Xylella fastidiosa Strain Causing Mulberry Leaf Scorch Disease in Maryland.	Genome Announcements	2014	2		e00916-13			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. 		
@D	Guan, Y.//Ngugi, D.K.//Blom, J.//Ali, S.//Ferry, J.G.//Stingl, U. 	Draft Genome Sequence of an Obligately Methylotrophic Methanogen, Methanococcoides methylutens, Isolated from Marine Sediment.	Genome Announcements	2014	2		e01184-14			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%. 		
@D	Guard, J.//Cao, G.//Kastanis, G.J.//Davison, S.//McClelland, M.//Sanchez, L.M.//Zheng, J.//Brown, E.//Allard, M.W. 	Draft Genome Sequences of 64 Salmonella enterica Serotype Enteritidis Isolates Obtained from Wild Mice.	Genome Announcements	2017	5		e00953-17			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. 		
@D	Guardiola-Avila, I.//Acedo-Felix, E.//Noriega-Orozco, L.//Yepiz-Plascencia, G.//Sifuentes-Romero, I.//Gomez-Gil, B. 	Draft Genome Sequence of Vibrio mimicus Strain CAIM 602T.	Genome Announcements	2013	1		e0008413			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)). 		
@D	Guarischi-Sousa, R.//Puigvert, M.//Coll, N.S.//Siri, M.I.//Pianzzola, M.J.//Valls, M.//Setubal, J.C. 	Complete genome sequence of the potato pathogen Ralstonia solanacearum UY031.	Standards in Genomic Sciences	2016	11		7			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. 		
@D	Gubler, M.//Bickle, T.A. 	Increased protein flexibility leads to promiscuous protein-DNA interactions in type IC restriction-modification systems.	EMBO J.	1991	10		951-957			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. 		
@D	Gubler, M.//Braguglia, D.//Meyer, J.//Piekarowicz, A.//Bickle, T.A. 	Recombination of constant and variable modules alters DNA sequence recognition by type IC restriction-modification enzymes.	EMBO J.	1992	11		233-240			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. 		
@D	Gueddou, A.//Swanson, E.//Ktari, A.//Nouioui, I.//Hezbri, K.//Ghodhbane-Gtari, F.//Simpson, S.//Morris, K.//Thomas, W.K.//Sen, A.//Gtari, M.//Tisa, L.S. 	Permanent Draft Genome Sequences of Three Frankia sp. Strains That Are Atypical,  Noninfective, Ineffective Isolates.	Genome Announcements	2017	5		e00174-17			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. 		
@D	Guedon, E.//Delorme, C.//Pons, N.//Cruaud, C.//Loux, V.//Couloux, A.//Gautier, C.//Sanchez, N.//Layec, S.//Galleron, N.//Almeida, M.//van de Guchte, M.//Kennedy, S.P.//Ehrlich, S.D.//Gibrat, J.F.//Wincker, P.//Renault, P. 	Complete Genome Sequence of the commensal Streptococcus salivarius strain JIM8777.	J. Bacteriol.	2011	193		5024-5025			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. 		
@D	Gueimonde, M.//Bottacini, F.//van Sinderen, D.//Ventura, M.//Margolles, A.//Sanchez, B. 	Genome Sequence of Parascardovia denticolens IPLA 20019, Isolated from Human Breast Milk.	J. Bacteriol.	2012	194		4776-4777			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. 		
@D	Gueimonde, M.//Ventura, M.//Margolles, A.//Sanchez, B. 	Genome Sequence of the Immunomodulatory Strain Bifidobacterium bifidum LMG 13195.	J. Bacteriol.	2012	194		6997			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. 		
@D	Guellerin, M.//Passerini, D.//Fontagne-Faucher, C.//Robert, H.//Gabriel, V.//Loux, V.//Klopp, C.//Le Loir, Y.//Coddeville, M.//Daveran-Mingot, M.L.//Ritzenthaler, P.//Le Bourgeois, P. 	Complete Genome Sequence of Lactococcus lactis subsp. lactis A12, a Strain Isolated from Wheat Sourdough.	Genome Announcements	2016	4		e00692-16			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. 		
@D	Guenthner, C.//Kim, S.//Bednarik, D.P. 	Cloning, isolation, and characterization of the human T-cell DNA-cytosine 5-methyltransferase gene.	J. Cell Biochem. Suppl.	1992	16E		179			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. 		
@D	Guerrero, L.D.//Makhalanyane, T.P.//Aislabie, J.M.//Cowan, D.A. 	Draft Genome Sequence of Williamsia sp. Strain D3, Isolated From the Darwin Mountains, Antarctica.	Genome Announcements	2014	2		e01230-13			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. 		
@D	Guerrero-Araya, E.//Plaza-Garrido, A.//Diaz-Yanez, F.//Pizaro-Guajardo, M.//Valenzuela, S.L.//Meneses, C.//Gil, F.//Castro-Nallar, E.//Paredes-Sabja, D. 	Genome Sequence of Clostridium paraputrificum 373-A1 Isolated in Chile from a Patient Infected with Clostridium difficile.	Genome Announcements	2016	4		e01178-16			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. 		
@D	Guha, S. 	Determination of DNA Sequences Containing Methylcytosine in Bacillus subtilis Marburg.	J. Bacteriol.	1985	163		573-579			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. 		
@D	Guha, S. 	DNA methyltransferase of Bacillus subtilis Marburg:  purification, properties and further evidence of specificity.	Gene	1988	74		77-81			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. 		
@D	Guha, S.//Guschlbauer, W. 	Expression of Escherichia coli dam gene in Bacillus subtilis provokes DNA damage response: N6-methyladenine is removed by two repair pathways.	Nucleic Acids Res.	1992	20		3607-3615			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. 		
@D	Guha, S.//Guschlbauer, W. 	Improved plasmids containing the Escherichia coli dam gene under the control of the tac promoter.	Biochim. Biophys. Acta	1992	1132		309-310			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. 		
@D	Guhan, N.//Muniyappa, K. 	The RecA intein of Mycobacterium tuberculosis promotes cleavage of ectopic DNA sites: Implications for the dispersal of inteins in natural populations.	J. Biol. Chem.	2002	277		40352-40361			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. 		
@D	Guhan, N.//Muniyappa, K. 	Mycobacterium tuberculosis RecA intein, a LAGLIDADG homing endonuclease, displays Mn2+ and DNA-dependent ATPase activity.	Nucleic Acids Res.	2003	31		4184-4191			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. 		
@D	Guhan, N.//Muniyappa, K. 	Mycobacterium tuberculosis RecA intein possesses a novel ATP-dependent site-specific double-stranded DNA endonuclease activity.	J. Biol. Chem.	2002	277		16257-16264			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. 		
@D	Guhan, N.//Muniyappa, K. 	Structural and functional characteristics of homing endonucleases.	Crit. Rev. Biochem. Mol. Biol.	2003	38		199-248			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. 		
@D	Guida, B.S.//Garcia-Pichel, F. 	Draft Genome Assembly of a Filamentous Euendolithic (True Boring) Cyanobacterium, Mastigocoleus testarum Strain BC008.	Genome Announcements	2016	4		e01574-15			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. 		
@A	Guild, W.R.//Smith, M.D.//Shoemaker, N.B. 		Conjugative transfer of chromosomal R determinants in Streptococcus pneumoniae.			Schlessinger, D. 		Microbiology-1982				Washington, DC	American Society for Microbiology	1982		0		88-92											
@D	Guilhen, C.//Iltis, A.//Forestier, C.//Balestrino, D. 	Genome Sequence of a Clinical Klebsiella pneumoniae Sequence Type 6 Strain.	Genome Announcements	2015	3		e01311-15			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. 		
@D	Guillen, Y.//Casadella, M.//Garcia-de-la-Guarda, R.//Espinoza-Culupu, A.//Paredes, R.//Ruiz, J.//Noguera-Julian, M. 	Whole-Genome Sequencing of Two Bartonella bacilliformis Strains.	Genome Announcements	2016	4		e00659-16			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. 		
@D	Guillen-Nepita, A.L.//Negrete-Paz, A.M.//Vazquez-Marrufo, G.//Cruz-Hernandez, A.//Fresia, P.//Naya, H.//Vazquez-Garciduenas, M.S. 	Sequencing and Annotation of the Genome of Mycobacterium tuberculosis MYC004, a Strain Causing Meningitis in Mexico.	Genome Announcements	2018	6		e00523-18			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. 		
@D	Guimaraes, A.M.//Toth, B.//Santos, A.P.//do Nascimento, N.C.//Kritchevsky, J.E.//Messick, J.B. 	Genome Sequence of 'Candidatus Mycoplasma haemolamae' Strain Purdue, a Red Blood  Cell Pathogen of Alpacas (Vicugna pacos) and Llamas (Lama glama).	J. Bacteriol.	2012	194		6312-6313			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. 		
@D	Guimaraes, A.M.//Zimpel, C.K.//Ikuta, C.Y.//do Nascimento, N.C.//Dos Santos, A.P.//Messick, J.B.//Heinemann, M.B.//Ferreira, N.J.S.//Brandao, P.E. 	Draft Genome Sequence of Mycobacterium bovis Strain SP38, a Pathogenic Bacterium  Isolated from a Bovine in Brazil.	Genome Announcements	2015	3		e00511-15			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. 		
@D	Guimaraes, L.C.//Soares, S.C.//Albersmeier, A.//Blom, J.//Jaenicke, S.//Azevedo, V.//Soriano, F.//Tauch, A.//Trost, E. 	Complete Genome Sequence of Corynebacterium urealyticum Strain DSM 7111, Isolated from a 9-Year-Old Patient with Alkaline-Encrusted Cystitis.	Genome Announcements	2013	1		e00264-13			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. 		
@D	Guimaraes, L.C.//Viana, M.V.//Benevides, L.J.//Mariano, D.C.//Veras, A.A.//Sa, P.H.//Rocha, F.S.//Vilas, B.P.C.//Soares, S.C.//Barbosa, M.S.//Guiso, N.//Badell, E.//Azevedo, V.//Ramos, R.T.//Silva, A. 	Draft Genome Sequence of Toxigenic Corynebacterium ulcerans Strain 03-8664 Isolated from a Human Throat.	Genome Announcements	2016	4		e00719-16			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. 		
@D	Guimaraes, L.C.//Viana, M.V.//Benevides, L.J.//Mariano, D.C.//Veras, A.A.//Sa, P.H.//Rocha, F.S.//Vilas, B.P.C.//Soares, S.C.//Barbosa, M.S.//Guiso, N.//Badell, E.//Carneiro, A.R.//Azevedo, V.//Ramos, R.T.//Silva, A. 	Draft Genome Sequence of Corynebacterium ulcerans Strain 04-3911, Isolated from Humans.	Genome Announcements	2016	4		e00171-16			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. 		
@D	Guimaraes, L.C.//Viana, M.V.//Benevides, L.J.//Mariano, D.C.//Veras, A.A.//Sa, P.H.//Rocha, F.S.//Vilas, B.P.C.//Soares, S.C.//Barbosa, M.S.//Guiso, N.//Badell, E.//Carneiro, A.R.//Azevedo, V.//Ramos, R.T.//Silva, A. 	Draft Genome Sequence of Toxigenic Corynebacterium ulcerans Strain 04-7514, Isolated from a Dog in France.	Genome Announcements	2016	4		e00172-16			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%. 		
@D	Guimaraes, P.I.//Leao, T.F.//de Melo, A.G.//Ramos, R.T.//Silva, A.//Fiore, M.F.//Schneider, M.P. 	Draft Genome Sequence of the Picocyanobacterium Synechococcus sp. Strain GFB01, Isolated from a Freshwater Lagoon in the Brazilian Amazon.	Genome Announcements	2015	3		e00876-15			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. 		
@D	Guimont, C.//Henry, P.//Linden, G. 	Restriction/modification in Streptococcus thermophilus: isolation and characterization of a type II restriction endonuclease Sth455I.	Appl. Microbiol. Biotechnol.	1993	39		216-220			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. 		
@D	Guinane, C.M.//Barrett, E.//Fitzgerald, G.F.//van Sinderen, D.//Ross, R.P.//Stanton, C. 	Genome Sequence of Bifidobacterium breve DPC 6330, a Strain Isolated from the Human Intestine.	J. Bacteriol.	2011	193		6799-6800			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. 		
@D	Guinane, C.M.//Kent, R.M.//Norberg, S.//Hill, C.//Fitzgerald, G.F.//Stanton, C.//Ross, R.P. 	Host Specific Diversity in Lactobacillus johnsonii as Evidenced by a Major Chromosomal Inversion and Phage Resistance Mechanisms.	PLoS ONE	2011	6		e18740			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. 		
@D	Guinard, J.//Vinatzer, B.A.//Poussier, S.//Lefeuvre, P.//Wicker, E. 	Draft Genome Sequences of Nine Strains of Ralstonia solanacearum Differing in Virulence to Eggplant (Solanum melongena).	Genome Announcements	2016	4		e01415-15			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. 		
@D	Guinebretiere, M.H.//Loux, V.//Martin, V.//Nicolas, P.//Sanchis, V.//Broussolle, V. 	Draft Genome Sequences of 18 Psychrotolerant and 2 Thermotolerant Strains Representative of Particular Ecotypes in the Bacillus cereus Group.	Genome Announcements	2017	5		e01568-16			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. 		
@D	Guio, H.//Tarazona, D.//Galarza, M.//Borda, V.//Curitomay, R. 	Genome analysis of 17 extensively drug-resistant strains reveals new potential mutations for resistance.	Genome Announcements	2014	2		e00759-14			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. 		
@D	Guizelini, D.//Saizaki, P.M.//Coimbra, N.A.//Weiss, V.A.//Faoro, H.//Sfeir, M.Z.//Baura, V.A.//Monteiro, R.A.//Chubatsu, L.S.//Souza, E.M.//Cruz, L.M.//Pedrosa, F.O.//Raittz, R.T.//Marchaukoski, J.N.//Steffens, M.B. 	Complete Genome Sequence of Herbaspirillum hiltneri N3 (DSM 17495), Isolated from Surface-Sterilized Wheat Roots.	Genome Announcements	2015	3		e01288-15			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. 		
@D	Gul, D.//Potter, R.F.//Riaz, H.//Ashraf, S.T.//Wallace, M.A.//Munir, T.//Ali, A.//Burnham, C.A.//Dantas, G.//Andleeb, S. 	Draft Genome Sequence of a Salmonella enterica Serovar Typhi Strain Resistant to  Fourth-Generation Cephalosporin and Fluoroquinolone Antibiotics.	Genome Announcements	2017	5		e00850-17			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. 		
@D	Gulati, A.//Swarnkar, M.K.//Vyas, P.//Rahi, P.//Thakur, R.//Thakur, N.//Singh, A.K. 	Complete Genome Sequence of the Rhizobacterium Pseudomonas trivialis Strain IHBB745 with Multiple Plant Growth-Promoting Activities and Tolerance to Desiccation and Alkalinity.	Genome Announcements	2015	3		e00943-15			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. 		
@D	Gully, D.//Teulet, A.//Busset, N.//Nouwen, N.//Fardoux, J.//Rouy, Z.//Vallenet, D.//Cruveiller, S.//Giraud, E. 	Complete Genome Sequence of Bradyrhizobium sp. ORS285, a Photosynthetic Strain Able To Establish Nod Factor-Dependent or Nod Factor-Independent Symbiosis with  Aeschynomene Legumes.	Genome Announcements	2017	5		e00421-17			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. 		
@D	Gumerov, V.M.//Mardanov, A.V.//Beletsky, A.V.//Prokofeva, M.I.//Bonch-Osmolovskaya, E.A.//Ravin, N.V.//Skryabin, K.G. 	Complete genome sequence of 'Vulcanisaeta moutnovskia' strain 768-28, a novel member of the hyperthermophilic crenarchaeal genus Vulcanisaeta.	J. Bacteriol.	2011	193		2355-2356			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. 		
@D	Gummadidala, P.M.//Holder, M.E.//O'Brien, J.L.//Ajami, N.J.//Petrosino, J.F.//Mitra, C.//Chen, Y.P.//Decho, A.W.//Chanda, A. 	Complete Genome Sequence of Vibrio gazogenes ATCC 43942.	Genome Announcements	2017	5		e00733-17			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. 		
@D	Gumulak-Smith, J.//Teachman, A.//Tu, A.H.//Simecka, J.W.//Lindsey, J.R.//Dybvig, K. 	Variations in the surface proteins and restriction enzyme systems of Mycoplasma pulmonis in the respiratory tract of infected rats.	Mol. Microbiol.	2001	40		1037-1044			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. 		
@D	Gunaletchumy, S.P.//Teh, X.//Khosravi, Y.//Ramli, N.S.//Chua, E.G.//Kavitha, T.//Mason, J.N.//Lee, H.T.//Alias, H.//Zaidan, N.Z.//Yassin, N.B.//Tay, L.C.//Rudd, S.//Mitchell, H.M.//Kaakoush, N.O.//Loke, M.F.//Goh, K.L.//Vadivelu, J. 	Draft Genome Sequences of Helicobacter pylori Isolates from Malaysia, Cultured from Patients with Functional Dyspepsia and Gastric Cancer.	J. Bacteriol.	2012	194		5695-5696			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. 		
@D	Gunn, J.S.//Piekarowicz, A.//Chien, R.//Stein, D.C. 	Cloning and linkage analysis of Neisseria gonorrhoeae DNA methyltransferases.	J. Bacteriol.	1992	174		5654-5660			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. 		
@D	Gunn, J.S.//Stein, D.C. 	The Neisseria gonorrhoeae S.NgoVIII restriction/modification system: a type IIs system homologous to the Haemophilus parahaemolyticus HphI restriction/modification system.	Nucleic Acids Res.	1997	25		4147-4152			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. 		
@D	Gunn, J.S.//Stein, D.C. 	Natural variation of the NgoII restriction-modification of Neisseria gonorrhoeae.	Gene	1993	132		15-20			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. ] 		
@D	Gunn, J.S.//Stein, D.C. 	Use of a non-selective transformation technique to construct a multiply restriction/modification-deficient mutant of Neisseria gonorrhoeae.	Mol. Gen. Genet.	1996	251		509-517			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. 		
@D	Gunsalus, R.P.//Cook, L.E.//Crable, B.//Rohlin, L.//McDonald, E.//Mouttaki, H.//Sieber, J.R.//Poweleit, N.//Zhou, H.//Lapidus, A.L.//Daligault, H.E.//Land, M.//Gilna, P.//Ivanova, N.//Kyrpides, N.//Culley, D.E.//McInerney, M.J. 	Complete genome sequence of Methanospirillum hungatei type strain JF1.	Standards in Genomic Sciences	2016	11		2			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. 		
@D	Gunther, N.W. IV//Bono, J.L.//Needleman, D.S. 	Complete Genome Sequence of Campylobacter jejuni RM1285, a Rod-Shaped Morphological Variant.	Genome Announcements	2015	3		e01361-15			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%. 		
@D	Gunther, N.W. IV//Reichenberger, E.R. 	Complete Genome Sequence of Campylobacter jejuni RM1246-ERRC, Which Exhibits Resistance to Quaternary Ammonium Compounds.	Genome Announcements	2017	5		e00978-17			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. 		
@D	Gunther, N.W. IV//Reichenberger, E.R.//Bono, J.L. 	Complete Genome Sequence of UV-Resistant Campylobacter jejuni RM3194, Including an 81.08-Kilobase Plasmid.	Genome Announcements	2016	4		e00305-16			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%. 		
@D	Gunthert, U.//Freund, M.//Trautner, T.A. 	Restriction and modification in Bacillus subtilis:  Two DNA methyltransferases with BsuRI specificity.  I.  Purification and Physical Properties.	J. Biol. Chem.	1981	256		9340-9345			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. 		
@D	Gunthert, U.//Jentsch, S.//Freund, M. 	Restriction and modification in Bacillus subtilis:  Two DNA Methyltransferases with BsuRI specificity.  II.  Catalytic properties, substrate specificity, and mode of action.	J. Biol. Chem.	1981	256		9346-9351			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. 		
@D	Gunthert, U.//Lauster, R.//Reiners, L. 	Multispecific DNA methyltransferases from Bacillus subtilis phages Properties of wild-type and various mutant enzymes with altered DNA affinity.	Eur. J. Biochem.	1986	159		485-492			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. 		
@D	Gunthert, U.//Pawlek, B.//Stutz, J.//Trautner, T.A. 	Restriction and Modification in Bacillus subtilis: Inducibility of a DNA Methylating Activity in Nonmodifying Cells.	J. Virol.	1976	20		188-195			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. 		
@D	Gunthert, U.//Reiners, L. 	Bacillus subtilis phage SPR codes for a DNA methyltransferase with triple sequence specificity.	Nucleic Acids Res.	1987	15		3689-3701			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. 		
@D	Gunthert, U.//Reiners, L.//Lauster, R. 	Cloning and expression of Bacillus subtilis phage DNA methyltransferase genes in Escherichia coli and B. subtilis.	Gene	1986	41		261-270			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. 		
@D	Gunthert, U.//Storm, K.//Bald, R. 	Restriction and modification in Bacillus subtilis. Localization of the methylated nucleotide in the BsuRI recognition sequence.	Eur. J. Biochem.	1978	90		581-583			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'. 		
@D	Gunthert, U.//Stutz, J.//Klotz, G. 	Restriction and modification in B. subtilis.	Mol. Gen. Genet.	1975	142		185-191			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. 		
@D	Gunthert, U.//Trautner, T.A. 	DNA methyltransferases of Bacillus subtilis and its bacteriophages.	Curr. Top. Microbiol. Immunol.	1984	108		11-22			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). 		
@D	Guo, H.//Karberg, M.//Long, M.//Jones, J.P. III//Sullenger, B.//Lambowitz, A.M. 	Group II introns designed to insert into therapeutically relevant DNA target sites in human cells.	Science	2000	289		452-457			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. 		
@D	Guo, H.//Zimmerly, S.//Perlman, P.S.//Lambowitz, A.M. 	Group II intron endonucleases use both RNA and protein subunits for recognition of specific sequences in double-stranded DNA.	EMBO J.	1997	16		6835-6848			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. 		
@D	Guo, H.-C. 	Type II restriction endonucleases: Structures and applications.	Recent Res. Devel. Macromol.	2003	7		225-245			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. 		
@D	Guo, H.T.//Xu, X.D. 	Broad host range plasmid-based gene transfer system in the cyanobacterium Gloeobacter violaceus which lacks thylakoids.	Prog. Nat. Sci.	2004	14		31-35			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. 		
@D	Guo, J.//Gaj, T.//Barbas, C.F.I.I.I. 	Directed Evolution of an Enhanced and Highly Efficient FokI Cleavage Domain for Zinc Finger Nucleases.	J. Mol. Biol.	2010	400		96-107			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. 		
@D	Guo, M.//Han, X.//Jin, T.//Zhou, L.//Yang, J.//Li, Z.//Chen, J.//Geng, B.//Zou, Y.//Wan, D.//Li, D.//Dai, W.//Wang, H.//Chen, Y.//Ni, P.//Fang, C.//Yang, R. 	Genome sequences of three species in the family planctomycetaceae.	J. Bacteriol.	2012	194		3740-3741			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). 		
@D	Guo, P.//Cao, B.//Qiu, X.//Lin, J. 	Draft Genome Sequence of the Crude Oil-Degrading and Biosurfactant-Producing Strain Cobetia sp. QF-1.	Genome Announcements	2018	6		e01456-17			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. 		
@D	Guo, Q.//Li, S.//Lu, X.//Zhang, X.//Wang, P.//Ma, P. 	Complete Genome Sequence of Bacillus subtilis BAB-1, a Biocontrol Agent for Suppression of Tomato Gray Mold.	Genome Announcements	2014	2		e00744-14			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. 		
@D	Guo, S.//Mao, Z.//Wu, Y.//Hao, K.//He, P.//He, Y. 	Genome Sequencing of Bacillus subtilis Strain XF-1 with High Efficiency in the Suppression of Plasmodiophora brassicae.	Genome Announcements	2013	1		e0006613			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. 		
@D	Guo, W.//Wang, Y.//Song, C.//Yang, C.//Li, Q.//Li, B.//Su, W.//Sun, X.//Song, D.//Yang, X.//Wang, S. 	Complete genome of Pseudomonas mendocina NK-01, which synthesizes medium-chain-length polyhydroxyalkanoates and alginate oligosaccharides.	J. Bacteriol.	2011	193		3413-3414			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. 		
@D	Guo, X.//Liao, Z.//Holtzapple, M.//Hu, Q.//Zhao, B. 	Draft Genome Sequence of Natranaerobius trueperi DSM 18760T, an Anaerobic, Halophilic, Alkaliphilic, Thermotolerant Bacterium Isolated from a Soda Lake.	Genome Announcements	2017	5		e00785-17			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. 		
@D	Guo, X.//Liao, Z.//Yan, Y.//Holtzapple, M.//Hu, Q.//Zhao, B. 	Draft Genome Sequence of Natronolimnobius baerhuensis CGMCC 1.3597T, an Aerobic Haloalkaliphilic Archaeon Isolated from a Soda Lake.	Genome Announcements	2017	5		e00710-17			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. 		
@D	Guo, X.//Wang, L.//Li, J.//Ding, Z.//Xiao, J.//Yin, X.//He, S.//Shi, P.//Dong, L.//Li, G.//Tian, C.//Wang, J.//Cong, Y.//Xu, Y. 	Structural insight into autoinhibition and histone H3-induced activation of DNMT3A.	Nature	2015	517		640-644			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. 		
@D	Guo, X.P.//Ding, D.W.//Bao, W.Y.//Yang, J.L. 	Draft Genome Sequence of Pseudoalteromonas sp. Strain ECSMB14103, Isolated from the East China Sea.	Genome Announcements	2015	3		e00330-15			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. 		
@D	Guo, Y.//Cen, Z.//Zou, Y.//Fang, X.//Li, T.//Wang, J.//Chang, D.//Su, L.//Liu, Y.//Chen, Y.//Yang, R.//Liu, C. 	Whole-Genome Sequence of Klebsiella pneumonia Strain LCT-KP214.	J. Bacteriol.	2012	194		3281			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. 		
@D	Guo, Y.//Jiao, Z.//Li, L.//Wu, D.//Crowley, D.E.//Wang, Y.//Wu, W. 	Draft Genome Sequence of Rahnella aquatilis Strain HX2, a Plant Growth-Promoting  Rhizobacterium Isolated from Vineyard Soil in Beijing, China.	J. Bacteriol.	2012	194		6646-6647			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. 		
@D	Guo, Y.//Wang, H.//Li, Y.//Song, Y.//Chen, C.//Liao, Y.//Ren, L.//Guo, C.//Tong, W.//Shen, W.//Chen, M.//Mao, X.//Guo, G.//Zou, Q. 	Genome of Helicobacter pylori Strain XZ274, an Isolate from a Tibetan Patient with Gastric Cancer in China.	J. Bacteriol.	2012	194		4146-4147			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. 		
@D	Guo, Z.//Chen, P.//Ren, P.//Kuang, S.//Zhou, Z.//Li, Z.//Liu, M.//Shi, D.//Xiao, Y.//Wang, X.//Zhou, R.//Jin, H.//Bi, D. 	Genome Sequence of Duck Pathogen Mycoplasma anatis Strain 1340.	J. Bacteriol.	2011	193		5883-5884			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. 		
@D	Guo, Z.//Xu, X.//Zheng, Q.//Li, T.//Kuang, S.//Zhang, Z.//Chen, Y.//Lu, X.//Zhou, R.//Bi, D.//Jin, H. 	Genome Sequence of Mycoplasma columbinum Strain SF7.	Genome Announcements	2013	1		e00157-13			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. 		
@D	Guolin, A.//Shiwen, L.//Yong, Z.//Mingyi, Q.//Tong, Z. 	Effects of organic solvents on the specificity and activity of restriction endonuclease Bsp63I and Bsp78I.	J. Wuhan Univ.	1991	3		135-138					
@D	Gupta, H.K.//Gupta, R.D.//Singh, A.//Chauhan, N.S.//Sharma, R. 	Genome Sequence of Rheinheimera sp. Strain A13L, Isolated from Pangong Lake, India.	J. Bacteriol.	2011	193		5873-5874			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. 		
@D	Gupta, R.//Capalash, N.//Sharma, P. 	Restriction endonucleases: natural and directed evolution.	Appl. Microbiol. Biotechnol.	2012	94		583-599			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. 		
@D	Gupta, R.//Vakhlu, J.//Agarwal, A.//Nilawe, P.D. 	Draft Genome Sequence of Plant Growth-Promoting Bacillus amyloliquefaciens Strain W2 Associated with Crocus sativus (Saffron).	Genome Announcements	2014	2		e00862-14			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. 		
@D	Gupta, R.//Xu, S.-Y.//Sharma, P.//Capalsh, N. 	Characterization of MspNI (G/GWCC) and MspNII (R/GATCY), novel thermostable Type II restriction endonucleases from Meiothermus sp., isoschizomers of AvaII and BstYI.	Mol. Biol. Rep.	2012	39		5607-5614			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. 		
@D	Gupta, S.K.//McMillan, E.A.//Jackson, C.R.//Desai, P.T.//Porwollik, S.//McCleland, M.//Hiott, L.M.//Humayoun, S.B.//Frye, J.G. 	Draft Genome Sequence of Salmonella enterica subsp. enterica Serovar Putten Strain CRJJGF_00159 (Phylum Gammaproteobacteria).	Genome Announcements	2016	4		e00895-16			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. 		
@D	Gupta, S.K.//McMillan, E.A.//Jackson, C.R.//Desai, P.T.//Porwollik, S.//McClelland, M.//Hiott, L.M.//Humayoun, S.B.//Barrett, J.B.//Frye, J.G. 	Draft Genome Sequence of Salmonella enterica subsp. diarizonae Serovar 61:k:1,5,(7) Strain CRJJGF_00165 (Phylum Gammaproteobacteria).	Genome Announcements	2016	4		e01322-16			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. 		
@D	Gupta, S.K.//McMillan, E.A.//Jackson, C.R.//Desai, P.T.//Porwollik, S.//McClelland, M.//Hiott, L.M.//Humayoun, S.B.//Frye, J.G. 	Draft Genome Sequence of Salmonella enterica subsp. enterica Serovar Bardo Strain CRJJGF_00099 (Phylum Gammaproteobacteria).	Genome Announcements	2016	4		e00964-16			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. 		
@D	Gupta, S.K.//McMillan, E.A.//Jackson, C.R.//Desai, P.T.//Porwollik, S.//McClelland, M.//Hiott, L.M.//Humayoun, S.B.//Frye, J.G. 	Draft Genome Sequence of Salmonella enterica subsp. enterica Serovar Widemarsh Strain CRJJGF_00058 (Phylum Gammaproteobacteria).	Genome Announcements	2016	4		e00604-16			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. 		
@D	Gupta, S.K.//McMillan, E.A.//Jackson, C.R.//Desai, P.T.//Porwollik, S.//McClelland, M.//Hiott, L.M.//Humayoun, S.B.//Frye, J.G. 	Draft Genome Sequence of Salmonella enterica subsp. enterica Serovar Lille Strain CRJJGF_000101 (Phylum Gammaproteobacteria).	Genome Announcements	2016	4		e00603-16			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. 		
@D	Gupta, S.K.//McMillan, E.A.//Jackson, C.R.//Desai, P.T.//Porwollik, S.//McClelland, M.//Hiott, L.M.//Humayoun, S.B.//Frye, J.G. 	Draft Genome Sequence of Salmonella enterica subsp. enterica Serovar Orion Strain CRJJGF_00093 (Phylum Gammaproteobacteria).	Genome Announcements	2016	4		e01063-16			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. 		
@D	Gupta, S.K.//McMillan, E.A.//Jackson, C.R.//Desai, P.T.//Porwollik, S.//McClelland, M.//Hiott, L.M.//Humayoun, S.B.//Frye, J.G. 	Draft Genome Sequence of Salmonella enterica subsp. enterica Serovar Kiambu Strain CRJJGF_00061 (Phylum Gammaproteobacteria).	Genome Announcements	2016	4		e00588-16			We report a 4.58 Mbp draft genome sequence of Salmonella enterica subsp. enterica serovar Kiambu strain CRJJGF_00061 isolated from cattle in 2004. 		
@D	Gupta, S.K.//McMillan, E.A.//Jackson, C.R.//Desai, P.T.//Porwollik, S.//McClelland, M.//Hiott, L.M.//Humayoun, S.B.//Frye, J.G. 	Draft Genome Sequence of Salmonella enterica subsp. enterica Serovar Blockley Strain CRJJGF_00147 (Phylum Gammaproteobacteria).	Genome Announcements	2016	4		e00954-16			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. 		
@D	Gupta, Y.K.//Chan, S.H.//Xu, S.Y.//Aggarwal, A.K. 	Structural basis of asymmetric DNA methylation and ATP-triggered long-range diffusion by EcoP15I.	Nat. Commun.	2015	6		7363			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. 		
@D	Gupta, Y.K.//Yang, L.//Chan, S.H.//Samuelson, J.C.//Xu, S.Y.//Aggarwal, A.K. 	Structural Insights into the Assembly and Shape of Type III Restriction-Modification (R-M) EcoP15I Complex by Small-Angle X-ray Scattering.	J. Mol. Biol.	2012	420		261-268			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. 		
@D	Guray, A.//Erarslan, A.//Ozbilen, O. 	A buffer system suitable for most restriction enzymes.	DOGA TU J. Biol.	1989	13		14-17			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. 		
@D	Guschlbauer, W. 	The DNA and S-adenosylmethionine-binding regions of EcoDam and related methyltransferases.	Gene	1988	74		211-214			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. 		
@D	Guseinov, O.A.//Bogdarina, I.G.//Kossykh, V.G.//Buryanov, Y.I.//Baev, A.A. 	Sensitivity of chromosomal and plasmid E. coli DNA to restriction endonuclease EcoRII.	Biokhimiia	1978	43		1718-1720			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. 		
@D	Guss, A.M.//Olson, D.G.//Caiazza, N.C.//Lynd, L.R. 	Dcm methylation is detrimental to plasmid transformation in Clostridium thermocellum.	Biotechnol. Biofuels.	2012	5		30			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. 		
@D	Guthrie, E.P.//Quinton-Jager, T.//Moran, L.S.//Slatko, B.E.//Kucera, R.B.//Benner, J.S.//Wilson, G.G.//Brooks, J.E. 	Cloning, expression and sequence analysis of the SphI restriction-modification system.	Gene	1996	180		107-112			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. 		
@D	Gutierrez, G. 	Draft Genome Sequence of Methanobacterium formicicum DSM 3637, an Archaebacterium Isolated from the Methane Producer Amoeba Pelomyxa palustris.	J. Bacteriol.	2012	194		6967-6968			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. 		
@D	Gutierrez, T. et al. 	Genome Sequence of Porticoccus hydrocarbonoclasticus Strain MCTG13d, an Obligate  Polycyclic Aromatic Hydrocarbon-Degrading Bacterium Associated with Marine Eukaryotic Phytoplankton.	Genome Announcements	2015	3		e00672-15			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%. 		
@D	Gutierrez, T. et al. 	Genome Sequence of Polycyclovorans algicola Strain TG408, an Obligate Polycyclic  Aromatic Hydrocarbon-Degrading Bacterium Associated with Marine Eukaryotic  Phytoplankton.	Genome Announcements	2015	3		e00207-15			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%. 		
@D	Gutierrez, T. et al. 	Genome Sequence of Arenibacter algicola Strain TG409, a Hydrocarbon-Degrading Bacterium Associated with Marine Eukaryotic Phytoplankton.	Genome Announcements	2016	4		e00765-16			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%. 		
@D	Gutierrez, T. et al. 	Genome Sequence of Halomonas sp. Strain MCTG39a, a Hydrocarbon-Degrading and Exopolymeric Substance-Producing Bacterium.	Genome Announcements	2015	3		e00793-15			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%. 		
@D	Gutierrez, T. et al. 	Genome Sequence of Marinobacter sp. Strain MCTG268 Isolated from the Cosmopolitan Marine Diatom Skeletonema costatum.	Genome Announcements	2016	4		e00937-16			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%. 		
@D	Gutierrez, T.//Whitman, W.B.//Huntemann, M.//Copeland, A.//Chen, A.//Vargese, N.//Kyrpides, N.C.//Pillay, M.//Ivanova, N.//Mikhailova, N.//Mukherjee, S.//Stamatis, D.//Reddy, T.B.K.//Ngan, C.Y.//Chovatia, M.//Daum, C.//Shapiro, N.//Woyke, T. 	Genome Sequence of Roseovarius sp. Strain MCTG156(2b) Isolated from a Phytoplankton Net Trawl on the Scottish West Coast.	Genome Announcements	2017	5		e00837-17			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%. 		
@D	Gutierrez, T.//Whitman, W.B.//Huntemann, M.//Copeland, A.//Chen, A.//Vargese, N.//Kyrpides, N.C.//Pillay, M.//Ivanova, N.//Mikhailova, N.//Mukherjee, S.//Stamatis, D.//Reddy, T.B.K.//Ngan, C.Y.//Chovatia, M.//Daum, C.//Shapiro, N.//Woyke, T. 	Genome Sequence of Oceanicola sp. Strain MCTG156(1a), Isolated from a Scottish Coastal Phytoplankton Net Sample.	Genome Announcements	2017	5		e00796-17			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%. 		
@D	Gutierrez-Escobar, A.J.//Bayona, R.M.//Barragan, V.C.//Trujillo, C.E.//Bravo, M.M. 	Draft Genome Sequence of a Helicobacter pylori Strain Isolated from a Patient with Diffuse Gastritis from a Region of High Cancer Risk in Colombia.	Genome Announcements	2015	3		e00244-15			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. 		
@D	Gutjahr, A.//Xu, S.Y. 	Engineering nicking enzymes that preferentially nick 5-methylcytosine-modified DNA.	Nucleic Acids Res.	2014	42		e77			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. 		
@D	Guyot, J.-B.//Caudron, B. 	Statistical significance of amino acid sequence similarity in type II DNA methyltransferases.	C.R. Acad. Sci. III	1994	317		20-24			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. 		
@D	Guyot, J.B.//Grassi, J.//Hahn, U.//Guschlbauer, W. 	The role of the preserved sequences of Dam methylase.	Nucleic Acids Res.	1993	21		3183-3190			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. 		
@D	Guzman, M.S.//McGinley, B.//Santiago-Merced, N.//Gupta, D.//Bose, A. 	Draft Genome Sequences of Three Closely Related Isolates of the Purple Nonsulfur  Bacterium Rhodovulum sulfidophilum.	Genome Announcements	2017	5		e00029-17			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. 		
@D	Gwinn, D.D.//Lawton, W.D. 	Alteration of host specificity in Bacillus subtilis.	Bacteriol. Rev.	1968	32		297-301			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. 		
@D	Gyllborg, M.C.//Sahl, J.W.//Cronin, D.C.I.I.I.//Rasko, D.A.//Mandel, M.J. 	Draft Genome Sequence of Vibrio fischeri SR5, a Strain Isolated from the Light Organ of the Mediterranean Squid Sepiola robusta.	J. Bacteriol.	2012	194		1639			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. 		
@D	Ha, J.-H.//Spolar, R.S.//Record, M.T. 	Role of the hydrophobic effect in stability of site-specific protein-DNA complexes.	J. Mol. Biol.	1989	209		801-816			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. 		
@D	Haake, S.K.//Yoder, S.C.//Attarian, G.//Podkaminer, K. 	Native plasmids of Fusobacterium nucleatum: Characterization and use in development of genetic systems.	J. Bacteriol.	2000	182		1176-1180			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. 		
@D	Haas, D.//Gerbaud, C.//Sahin, N.//Pernodet, J.L.//Lautru, S. 	Draft Genome Sequence of Streptomyces sp. M1013, a Close Relative of Streptomyces ambofaciens and Streptomyces coelicolor.	Genome Announcements	2017	5		e00643-17			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. 		
@D	Habe, H.//Kobuna, A.//Hosoda, A.//Kouzuma, A.//Yamane, H.//Nojiri, H.//Omori, T.//Watanabe, K. 	Subtractive hybridization and random arbitrarily primed PCR analyses of a benzoate-assimilating bacterium, Desulfotignum balticum.	Appl. Microbiol. Biotechnol.	2008	79		87-95			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. 		
@A	Haber, J.E.//Wolfe, K.H. 		Function and evolution of HO and VDE endonucleases in fungi.			Belfort, M. 		Nucleic Acids Mol. Biol.				Berlin Heidelberg	Springer-Verlag	2005		16		161-175									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. 		
@D	Haber, K.//Neumark, T.//Foldes, I. 	Restriction-modification like phenomenon observed in Mycobacterium smegmatis strains are consequences of natural polylysogeny.	Acta Microbiol. Hung.	1988	35		180-181			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. 		
@D	Haberman, A. 	The bacteriophage P1 restriction endonuclease.	J. Mol. Biol.	1974	89		545-563			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. 		
@D	Haberman, A.//Heywood, J.//Meselson, M. 	DNA modification methylase activity of Escherichia coli restriction endonucleases K and P.	Proc. Natl. Acad. Sci. U. S. A.	1972	69		3138-3141			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. 		
@D	Habibi, R.//Tarighi, S.//Behravan, J.//Taheri, P.//Kjoller, A.H.//Brejnrod, A.//Madsen, J.S.//Sorensen, S.J. 	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.	Genome Announcements	2017	5		e00026-17			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. 		
@D	Hadi, S.M. 	A site-specific DNA methylase from Escherichia coli K.	Indian J. Biochem. Biophys.	1981	18		295-297			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. 		
@D	Hadi, S.M.//Bachi, B.//Iida, S.//Bickle, T.A. 	DNA restriction-modification enzymes of phage P1 and plasmid p15B.	J. Mol. Biol.	1983	165		19-34			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. 		
@D	Hadi, S.M.//Bachi, B.//Shepherd, J.C.W.//Yuan, R.//Ineichen, K.//Bickle, T.A. 	DNA Recognition and Cleavage by the EcoP15 Restriction Endonuclease.	J. Mol. Biol.	1979	134		655-666			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. 		
@D	Hadi, S.M.//Bickle, T.A.//Yuan, R. 	The role of S-adenosylmethionine in the cleavage of deoxyribonucleic acid by the restriction endonuclease from Escherichia coli K.	J. Biol. Chem.	1975	250		4159-4164			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. 		
@D	Hadi, S.M.//Yuan, R. 	Complementation in vitro by restriction enzymes from mutant strains E. coli K12.	Experientia	1973	29		752			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. 		
@D	Hadi, S.M.//Yuan, R. 	Complementation in vitro by mutant restriction enzymes from Escherichia coli K.	J. Biol. Chem.	1974	249		4580-4586			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. 		
@D	Hadjadj, L.//Jiyipong, T.//Bittar, F.//Morand, S.//Rolain, J.M. 	First Draft Genome Sequences of Two Bartonella tribocorum Strains from Laos and Cambodia.	Genome Announcements	2018	6		e01435-17			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. 		
@D	Hadjadj, L.//Rathored, J.//Keita, M.B.//Michelle, C.//Levasseur, A.//Raoult, D.//Fournier, P.E.//Rolain, J.M.//Bittar, F. 	Non contiguous-finished genome sequence and description of Microbacterium gorillae sp. nov.	Standards in Genomic Sciences	2016	11		32			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). 		
@D	Hadziabdic, S.//Borowiak, M.//Bloch, A.//Malorny, B.//Szabo, I.//Guerra, B.//Kaesbohrer, A.//Fischer, J. 	Complete Genome Sequence of an Avian Native NDM-1-Producing Salmonella enterica subsp. enterica Serovar Corvallis Strain.	Genome Announcements	2018	6		e00593-18			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. 		
@D	Haendiges, J.//Blessington, T.//Zheng, J.//Davidson, G.//Miller, J.D.//Hoffmann, M. 	Complete Genome Sequences of Four Salmonella enterica subsp. enterica Serovar Senftenberg and Montevideo Isolates Associated with a 2016 Multistate Outbreak in the United States.	Genome Announcements	2018	6		e00630-18			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. 		
@D	Haendiges, J.//Timme, R.//Allard, M.//Myers, R.A.//Payne, J.//Brown, E.W.//Evans, P.//Gonzalez-Escalona, N. 	Draft Genome Sequences of Clinical Vibrio parahaemolyticus Strains Isolated in Maryland (2010 to 2013).	Genome Announcements	2014	2		e00776-14			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. 		
@D	Haesendonck, R.//Van Nieuwerburgh, F.//Haesebrouck, F.//Deforce, D.//Pasmans, F.//Martel, A. 	Genome Sequence of Devriesea agamarum, Isolated from Agamid Lizards with Dermatitis.	Genome Announcements	2015	3		e00949-15			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. 		
@D	Hafez, M.//Guha, T.K.//Hausner, G. 	I-OmiI and I-OmiII: Two intron-encoded homing endonucleases within the Ophiostoma minus rns gene.	Fungal Biol.	2014	118		721-731			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. 		
@D	Hafstrom, T.//Jansson, D.S.//Segerman, B. 	Complete Genome Sequence of Brachyspira intermedia Reveals Unique Genomic Features in Brachyspira Species and Phage-mediated Horizontal Gene Transfer.	BMC Genomics	2011	12		395			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. 		
@D	Hagemann, M.//Gartner, K.//Scharnagl, M.//Bolay, P.//Lott, S.C.//Fuss, J.//Huettel, B.//Reinhardt, R.//Klahn, S.//Hess, W.R. 	Identification of the DNA methyltransferases establishing the methylome of the cyanobacterium Synechocystis sp. PCC 6803.	DNA Res.	2018	25		343-352			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. 		
@D	Hager, P.W.//Boyer, H.W.//Day, J.O.//Reich, N.O.//Greene, P. 	Analysis of noncanonical DNA cleavage by EcoRI endonuclease mutants.	J. Cell Biochem. Suppl.	1987	11C		206			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. 		
@D	Hager, P.W.//Reich, N.O.//Day, J.P.//Coche, T.G.//Boyer, H.W.//Rosenberg, J.M.//Greene, P.J. 	Probing the role of glutamic acid 144 in the EcoRI endonuclease using aspartic acid and glutamine replacements.	J. Biol. Chem.	1990	265		21520-21526			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. 		
@D	Hahn, C.//Harrison, E.M.//Parkhill, J.//Holmes, M.A.//Paterson, G.K. 	Draft Genome Sequence of the Streptococcus pneumoniae Avery Strain A66.	Genome Announcements	2015	3		e00697-15			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. 		
@D	Hahn, D.R.//McHenney, M.A.//Baltz, R.H. 	Characterization of FP22, a large streptomycete bacteriophage with DNA insensitive to cleavage by many restriction enzymes.	J. Gen. Microbiol.	1990	136		2395-2404			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). 		
@D	Hahnke, R.L. et al. 	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.	Standards in Genomic Sciences	2015	10		46			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. 		
@D	Hahnke, S.//Abendroth, C.//Langer, T.//Codoner, F.M.//Ramm, P.//Porcar, M.//Luschnig, O.//Klocke, M. 	Complete Genome Sequence of a New Ruminococcaceae Bacterium Isolated from Anaerobic Biomass Hydrolysis.	Genome Announcements	2018	6		e00030-18			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. 		
@D	Haigh, R.D.//Crawford, L.A.//Ralph, J.D.//Wanford, J.J.//Vartoukian, S.R.//Hijazi, K.//Wade, W.//Oggioni, M.R. 	Draft Whole-Genome Sequences of Periodontal Pathobionts Porphyromonas gingivalis, Prevotella intermedia, and Tannerella forsythia Contain Phase-Variable  Restriction-Modification Systems.	Genome Announcements	2017	5		e01229-17			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. 		
@D	Haim, M.S.//Mollerach, M.//Van Domselaar, G.//Teves, S.A.//Degrossi, J.//Cardona, S.T. 	Draft Genome Sequences of Burkholderia contaminans FFI-28, a Strain Isolated from a Contaminated Pharmaceutical Solution.	Genome Announcements	2016	4		e01177-16			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. 		
@D	Haima, P.//Bron, S.//Venema, G. 	The effect of restriction on shotgun cloning and plasmid stability in Bacillus subtilis Marburg.	Mol. Gen. Genet.	1987	209		335-342			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. 		
@D	Hain, T. et al. 	Whole-Genome Sequence of Listeria welshimeri Reveals Common Steps in Genome Reduction with Listeria innocua as Compared to Listeria  monocytogenes.	J. Bacteriol.	2006	188		7405-7415			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. 		
@D	Haines, A.//Nebergall, E.//Besong, E.//Council, K.//Lambert, O.//Gauthier, D. 	Draft Genome Sequences for Seven Streptococcus parauberis Isolates from Wild Fish in the Chesapeake Bay.	Genome Announcements	2016	4		e00741-16			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. 		
@D	Halazonetis, T.D.//Kandil, A.N. 	Predicted structural similarities of the DNA binding domains of c-Myc and endonuclease EcoRI.	Science	1992	255		464-466			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. 		
@D	Halden, N.F.//Wolf, J.B.//Cross, S.L.//Leonard, W.J. 	Identification and characterization of a novel restriction enzyme derived from Mycoplasma fermentans.	Clin. Res.	1988	36		404a			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. 		
@D	Halden, N.F.//Wolf, J.B.//Leonard, W.J. 	Identification of a novel site specific endonuclease produced by Mycoplasma fermentans:  discovery while characterizing DNA binding proteins in T lymphocyte cell lines.	Nucleic Acids Res.	1989	17		3491-3499			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. 		
@D	Halder, U.//Banerjee, A.//Chaudhry, V.//Varshney, R.K.//Mantri, S.//Bandopadhyay, R. 	Draft Genome Report of Bacillus altitudinis SORB11, Isolated from the Indian Sector of the Southern Ocean.	Genome Announcements	2017	5		e00339-17			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. 		
@D	Hale, W.B.//van der Woude, M.W.//Low, D.A. 	Analysis of nonmethylated GATC sites in the Escherichia coli chromosome and identification of sites that are differentially methylated in response to environmental stimuli.	J. Bacteriol.	1994	176		3438-3441			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. 		
@D	Haley, B.J.//Choi, S.Y.//Hasan, N.A.//Abdullah, A.S.//Cebula, T.A.//Huq, A.//Colwell, R.R. 	Genome Sequences of Clinical Vibrio cholerae Isolates from an Oyster-Borne Cholera Outbreak in Florida.	Genome Announcements	2013	1		e00966-13			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. 		
@D	Haley, B.J.//Kim, S.W.//Liljebjelke, K.//Guard, J.//Van Kessel, J.A. 	Genome Sequences of Two Salmonella enterica Serovar Kentucky Isolates Recovered from Poultry Carcasses in the United States.	Genome Announcements	2016	4		e01289-16			We report here the draft genome sequences of two Salmonella enterica serovar Kentucky eBurstGroup 15 isolates collected from poultry carcasses in Georgia (USA). 		
@D	Haley, B.J.//Kim, S.W.//Whitehead, T.R. 	Genome Sequence of a Novel Multiple-Antibiotic-Resistant Member of the Erysipelotrichaceae Family Isolated from a Swine Manure Storage Pit.	Genome Announcements	2016	4		e00978-16			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. 		
@D	Haley, B.J.//Luo, Y.//Wang, C.//Brown, E.//Allard, M.//Karns, J.S.//Van Kessel, J.A.S. 	Genome Sequences of Salmonella enterica subsp. enterica Serovar Kentucky Sequence Type 152 Isolated from Dairy Cows in the United States.	Genome Announcements	2017	5		e01119-17			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. 		
@D	Haley, B.J.//Luo, Y.//Wang, C.//Pettengill, J.//Allard, M.//Brown, E.//Karns, J.S.//Van Kessel, J.A. 	Genome Sequences of Eight Salmonella enterica subsp. enterica Serovars Isolated from a Single Dairy Farm.	Genome Announcements	2014	2		e00082-14			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. 		
@D	Haley, B.J.//Pirone, C.//Muruvanda, T.//Brown, E.//Allard, M.//Karns, J.S.//Van Kessel, J.A. 	Complete Genome Sequence and Methylome of Salmonella enterica subsp. enterica Cerro, a Frequent Dairy Cow Serovar.	Genome Announcements	2016	4		e01350-15			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. 		
@D	Halford, S. 	Restriction enzymes in DNA-protein interactions.	SERC Bulletin	1986	3		12-13			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. 		
@D	Halford, S.E. 	The specificity of the EcoRI restriction endonuclease.	Biochem. Soc. Trans.	1980	8		399-400			None 		
@D	Halford, S.E. 	How does EcoRI cleave its recognition site on DNA?	Trends Biochem. Sci.	1983	8		455-460			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. 		
@D	Halford, S.E. 	Restriction enzymes that act simultaneously at two DNA sites.	Biochem. Soc. Trans.	1999	27		A88			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. 		
@D	Halford, S.E. 	The (billion dollar) consequences of studying why certain isolates of phage lambda infect only certain strains of E. coli: restriction enzymes.	Biochemist	2009	31		10-13			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. 		
@D	Halford, S.E. 	Hopping, jumping and looping by restriction enzymes.	Biochem. Soc. Trans.	2001	29		363-373			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. 		
@A	Halford, S.E. 		Restriction enzymes.			Kendrew, J. 		Encyclopaedia of Molecular Biology				Oxford	Blackwell	1994				954-956									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. 		
@D	Halford, S.E.//Baldwin, G.S.//Vipond, I.B. 	DNA recognition by EcoRV.	J. Cell Biochem. Suppl.	1993	17C		152			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. 		
@D	Halford, S.E.//Bilcock, D.T.//Stanford, N.P.//Williams, S.A.//Milsom, S.E.//Gormley, N.A.//Watson, M.A.//Bath, A.J.//Embleton, M.L.//Gowers, D.M.//Daniels, L.E.//Parry, S.H.//Szczelkun, M.D. 	Restriction endonuclease reactions requiring two recognition sites.	Biochem. Soc. Trans.	1999	27		696-699			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. 		
@D	Halford, S.E.//Catto, L.E.//Pernstich, C.//Rusling, D.A.//Sanders, K.L. 	The reaction mechanism of FokI excludes the possibility of targeting zinc finger nucleases to unique DNA sites.	Biochem. Soc. Trans.	2011	39		584-588			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. 		
@D	Halford, S.E.//Goodall, A.J. 	Modes of DNA cleavage by the EcoRV restriction endonuclease.	Biochemistry	1988	27		1771-1777			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. 		
@D	Halford, S.E.//Gowers, D.M.//Sessions, R.B. 	Two are better than one.	Nat. Struct. Biol.	2000	7		705-707			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. 		
@D	Halford, S.E.//Johnson, N.P. 	Single turnovers of the EcoRI restriction endonuclease.	Biochem. J.	1983	211		405-415			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. 		
@D	Halford, S.E.//Johnson, N.P. 	The EcoRI restriction endonuclease, covalently closed DNA and ethidium bromide.	Biochem. J.	1981	199		767-777			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. 		
@D	Halford, S.E.//Johnson, N.P. 	The EcoRI restriction endonuclease with bacteriophage lambda DNA.  Equilibrium binding sites.	Biochem. J.	1980	191		593-604			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. 		
@D	Halford, S.E.//Johnson, N.P.//Grinsted, J. 	The EcoRI restriction endonuclease with bacteriophage lambda DNA.  Kinetic studies.	Biochem. J.	1980	191		581-592			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. 		
@D	Halford, S.E.//Johnson, N.P.//Grinsted, J. 	The reactions of the EcoRI and other restriction endonucleases.	Biochem. J.	1979	179		353-365			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. 		
@D	Halford, S.E.//Lovelady, B.M.//McCallum, S. 	Altered specificity of the EcoRV restriction endonuclease.	Biochem. Soc. Trans.	1986	14		260-261			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. 		
@D	Halford, S.E.//Lovelady, B.M.//McCallum, S.A. 	Relaxed specificity of the EcoRV restriction endonuclease.	Gene	1986	41		173-181			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. 		
@D	Halford, S.E.//Marko, J.F. 	How do site-specific DNA-binding proteins find their targets?	Nucleic Acids Res.	2004	32		3040-3052			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. 		
@D	Halford, S.E.//Taylor, J.D.//Vermote, C.L.M.//Vipond, I.B. 	Assays for restriction endonucleases using plasmid substrates.	Methods Mol. Biol.	1994	30		385-396			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. 		
@A	Halford, S.E.//Taylor, J.D.//Vermote, C.L.M.//Vipond, I.B. 		Mechanism of action of restriction endonuclease EcoRV.			Eckstein, F.//Lilley, D.M.J. 		Nucl. Acids and Mol. Biol.				Berlin	Springer-Verlag	1993		7		47-69									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). 		
@D	Halford, S.E.//Welsh, A.J.//Szczelkun, M.D. 	Enzyme-mediated DNA looping.	Annu. Rev. Biophys. Biomol. Struct.	2004	33		1-24			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. 		
@D	Halim, M.A.//Rahman, A.Y.//Sim, K.S.//Yam, H.C.//Rahim, A.A.//Ghazali, A.H.//Najimudin, N. 	Genome Sequence of a Gram-Positive Diazotroph, Paenibacillus durus Type Strain ATCC 35681.	Genome Announcements	2016	4		e00005-16			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. 		
@D	Halim, M.Z.A.//Jaafar, M.M.//Teh, L.K.//Ismail, M.I.//Lee, L.S.//Ngeow, Y.F.//Nor, N.M.//Zainuddin, Z.F.//Tang, T.H.//Najimudin, M.N.//Salleh, M.Z. 	Genome sequencing and annotation of multidrug resistant Mycobacterium tuberculosis (MDR-TB) PR10 strain.	Genomics Data	2016	7		245-246			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. 		
@D	Hall, M.F.//Noren, C.J.//Perler, F.B.//Schildkraut, I. 	Creation of an artificial bifunctional intein by grafting a homing endonuclease into a mini-intein.	J. Mol. Biol.	2002	323		173-179			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. 		
@D	Hall, R.K.//Larcom, L.L. 	Blockage of restriction endonuclease cleavage by thymine dimers.	Photochem. Photobiol.	1982	36		429-432			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. 		
@D	Hall, R.M. 	The DNA adenine methyltransferase (dam+) gene of bacteriophage T4 reverses the mutator phenotype of an Escherichia coli dam mutant.	J. Bacteriol.	1990	172		2812-2813			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. 		
@D	Hallam, S.J.//Konstantinidis, K.T.//Putnam, N.//Schleper, C.//Watanabe, Y.//Sugahara, J.//Preston, C.//de la Torre, J.//Richardson, P.M.//DeLong, E.F. 	Genomic analysis of the uncultivated marine crenarchaeote Cenarchaeum symbiosum.	Proc. Natl. Acad. Sci. U. S. A.	2006	103		18296-18301			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. 		
@D	Hallam, S.J.//Mincer, T.J.//Schleper, C.//Preston, C.M.//Roberts, K.//Richardson, P.M.//DeLong, E.F. 	Pathways of carbon assimilation and ammonia oxidation suggested by environmental genomic analyses of marine Crenarchaeota.	PLoS Biology	2006	4		e95			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. 		
@D	Hallam, S.J.//Putnam, N.//Preston, C.M.//Detter, J.C.//Rokhsar, D.//Richardson, P.M.//DeLong, E.F. 	Reverse methanogenesis: Testing the hypothesis with environmental genomics.	Science	2004	305		1457-1462			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. 		
@D	Hallenbeck, P.C.//Grogger, M.//Mraz, M.//Veverka, D. 	Draft Genome Sequence of a Thermophilic Cyanobacterium from the Family Oscillatoriales (Strain MTP1) from the Chalk River, Colorado.	Genome Announcements	2016	4		e01571-15			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. 		
@D	Hallenbeck, P.C.//Grogger, M.//Mraz, M.//Veverka, D. 	Draft Genome Sequence of the Photoheterotrophic Chloracidobacterium thermophilum  Strain OC1 Found in a Mat at Ojo Caliente.	Genome Announcements	2016	4		e01570-15			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. 		
@D	Hallet, B. 	Playing Dr Jekyll and Mr Hyde: combined mechanisms of phase variation in bacteria.	Curr. Opin. Microbiol.	2001	4		570-581			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. 		
@D	Halling, S.M.//Peterson-Burch, B.D.//Bricker, B.J.//Zuerner, R.L.//Qing, Z.//Li, L.L.//Kapur, V.//Alt, D.P.//Olsen, S.C. 	Completion of the genome sequence of Brucella abortus and comparison to the highly similar genomes of Brucella melitensis and Brucella suis.	J. Bacteriol.	2005	187		2715-2726			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. 		
@D	Halpin, J.L.//Hill, K.//Johnson, S.L.//Bruce, D.C.//Shirey, T.B.//Dykes, J.K.//Luquez, C. 	Finished Whole-Genome Sequences of Clostridium butyricum Toxin Subtype E4 and Clostridium baratii Toxin Subtype F7 Strains.	Genome Announcements	2017	5		e00375-17			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. 		
@D	Halpin, J.L.//Hill, K.//Johnson, S.L.//Bruce, D.C.//Shirey, T.B.//Dykes, J.K.//Luquez, C. 	Finished Whole-Genome Sequence of Clostridium argentinense Producing Botulinum Neurotoxin Type G.	Genome Announcements	2017	5		e00380-17			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. 		
@D	Halpin, J.L.//Hill, K.//Johnson, S.L.//Bruce, D.C.//Shirey, T.B.//Dykes, J.K.//Luquez, C. 	Finished Whole-Genome Sequences of Two Clostridium botulinum Type A(B) Isolates.	Genome Announcements	2017	5		e00381-17			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. 		
@D	Ham, J.S.//Kim, H.W.//Seol, K.H.//Jang, A.//Jeong, S.G.//Oh, M.H.//Kim, D.H.//Kang, D.K.//Kim, G.B.//Cha, C.J. 	Genome Sequence of Lactobacillus salivarius NIAS840, Isolated from Chicken Intestine.	J. Bacteriol.	2011	193		5551-5552			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. 		
@D	Ham, J.S.//Lee, T.//Byun, M.J.//Lee, K.T.//Kim, M.K.//Han, G.S.//Jeong, S.G.//Oh, M.H.//Kim, D.H.//Kim, H. 	Complete Genome Sequence of Bifidobacterium longum subsp. longum KACC 91563.	J. Bacteriol.	2011	193		5044			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. 		
@D	Hamablet, L.//Chen, G.C.//Brown, A.//Roberts, R.J. 	LpnI, from Legionella pneumophila, is a neoschiozmer of HaeII.	Nucleic Acids Res.	1989	17		6417			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). 		
@D	Hamada, M.//Ichikawa, N.//Oguchi, A.//Fujita, N. 	Draft Genome Sequence of Lysinimicrobium mangrovi NBRC 105856T, Isolated from the Rhizosphere of a Mangrove.	Genome Announcements	2014	2		e01131-14			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. 		
@D	Hamada, M.//Ichikawa, N.//Oguchi, A.//Komaki, H.//Tamura, T.//Fujita, N. 	Draft genome sequences of eight type strains of the genus demequina.	Genome Announcements	2015	3		e00281-15			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. 		
@D	Hamblin, M.//Spinard, E.//Gomez-Chiarri, M.//Nelson, D.R.//Rowley, D.C. 	Draft Genome Sequence of the Shellfish Larval Probiotic Bacillus pumilus RI06-95.	Genome Announcements	2015	3		e00858-15			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. 		
@D	Hamidian, M.//Hawkey, J.//Holt, K.E.//Hall, R.M. 	Genome Sequence of Acinetobacter baumannii Strain D36, an Antibiotic-Resistant Isolate from Lineage 2 of Global Clone 1.	Genome Announcements	2015	3		e01478-15			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). 		
@D	Hamidian, M.//Venepally, P.//Hall, R.M.//Adams, M.D. 	Corrected Genome Sequence of Acinetobacter baumannii Strain AB0057, an Antibiotic-Resistant Isolate from Lineage 1 of Global Clone 1.	Genome Announcements	2017	5		e00836-17			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. 		
@D	Hamilton, R. et al. 	Draft genomes of gammaproteobacterial methanotrophs isolated from terrestrial ecosystems.	Genome Announcements	2015	3		e00515-15			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. 		
@D	Hammer, A.J.//Walters, A.//Carroll, C.//Newell, P.D.//Chaston, J.M. 	Draft Genome Sequence of Lactobacillus paracasei DmW181, a Bacterium Isolated from Wild Drosophila.	Genome Announcements	2017	5		e00545-17			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. 		
@D	Hammerl, J.A.//Irrgang, A.//Grobbel, M.//Tenhagen, B.A.//Kasbohrer, A. 	Complete Genome Sequence of a blaCTX-M-1-Harboring Escherichia coli Isolate Recovered from Cattle in Germany.	Genome Announcements	2018	6		e01476-17			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. 		
@D	Hammerl, J.A.//Jackel, C.//Reetz, J.//Beck, S.//Alter, T.//Lurz, R.//Barretto, C.//Brussow, H.//Hertwig, S. 	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.	J. Virol.	2011	85		8597-8605			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. 		
@D	Hammerl, J.A.//Jackel, C.//Reetz, J.//Hertwig, S. 	The Complete Genome Sequence of Bacteriophage CP21 Reveals Modular Shuffling in Campylobacter Group II Phages.	J. Virol.	2012	86		8896			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. 		
@D	Hammerl, J.A.//Klein, I.//Lanka, E.//Appel, B.//Hertwig, S. 	Genetic and functional properties of the self-transmissible Yersinia enterocolitica plasmid pYE854, which mobilizes the virulence plasmid pYV.	J. Bacteriol.	2008	190		991-1010			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. 		
@D	Hammerl, J.A.//Lasch, P.//Nitsche, A.//Dabrowski, P.W.//Hahmann, H.//Wicke, A.//Kleta, S.//Dahouk, S.A.//Dieckmann, R. 	Draft Genome Sequences of Klebsiella oxytoca Isolates Originating from a Highly Contaminated Liquid Hand Soap Product.	Genome Announcements	2015	3		e00820-15			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. 		
@D	Hammond, A.W.//Gerard, G.F.//Campbell, J.H.//Chatterjee, D.K. 	Characterization of a restriction enzyme from a strain of Neisseria gonorrhoea which recognizes 5'G^CCGGC3', an isoschizomer of NaeI.	Nucleic Acids Res.	1989	17		3320			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. 		
@D	Hammond, A.W.//Gerard, G.F.//Chatterjee, D.K. 	Characterization of NgoAIII, an isoschizomer of SstII from a strain of Neisseria gonorrhoea.	Nucleic Acids Res.	1989	17		6750			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. 		
@D	Hammond, A.W.//Gerard, G.F.//Chatterjee, D.K. 	Cloning the KpnI restriction-modification system in Escherichia coli.	Gene	1991	97		97-102			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. 		
@D	Han, C. et al. 	Complete genome sequence of Pedobacter heparinus type strain (HIM 762-3).	Standards in Genomic Sciences	2009	1		54-62			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. 		
@D	Han, C. et al. 	Complete genome sequence of Kangiella koreensis type strain (SW-125).	Standards in Genomic Sciences	2009	1		226-233			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. 		
@D	Han, C. et al. 	Complete genome sequence of the sulfur compounds oxidizing chemolithoautotroph Sulfuricurvum kujiense type strain (YK-1(T)).	Standards in Genomic Sciences	2012	6		94-103			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. 		
@D	Han, C. et al. 	Complete genome sequence of Thermaerobacter marianensis type strain (7p75a).	Standards in Genomic Sciences	2010	3		337-345			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. 		
@D	Han, C. et al. 	Complete genome sequence of Treponema succinifaciens type strain (6091).	Standards in Genomic Sciences	2011	4		361-370			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. 		
@D	Han, C. et al. 	Complete genome sequence of Syntrophobotulus glycolicus type strain (FlGlyR).	Standards in Genomic Sciences	2011	4		371-380			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. 		
@D	Han, C.S. et al. 	Pathogenomic Sequence Analysis of Bacillus cereus and Bacillus thuringiensis Isolates Closely Related to Bacillus anthracis.	J. Bacteriol.	2006	188		3382-3390			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. 		
@D	Han, G.H.//Kim, W.//Chun, J.//Kim, S.W. 	Draft Genome Sequence of Methylophaga aminisulfidivorans MPT.	J. Bacteriol.	2011	193		4265			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). 		
@D	Han, J.//Park, B.S.//Shin, D.J.//Song, S.Y.//Jeong, Y.J.//Lee, N. 	Complete Genome Sequence of Mycoplasma hyopneumoniae Strain KM014, a Clinical Isolate from South Korea.	Genome Announcements	2017	5		e01012-17			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. 		
@D	Han, J.//Zhang, F.//Hou, J.//Liu, X.//Li, M.//Liu, H.//Cai, L.//Zhang, B.//Chen, Y.//Zhou, J.//Hu, S.//Xiang, H. 	Complete Genome Sequence of the Metabolically Versatile Halophilic Archaeon Haloferax mediterranei, a Poly(3-Hydroxybutyrate-co-3-Hydroxyvalerate) Producer.	J. Bacteriol.	2012	194		4463-4464			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. 		
@D	Han, J.E.//Hwang, S.Y.//Kim, J.H.//Shin, S.P.//Jun, J.W.//Chai, J.Y.//Park, Y.H.//Park, S.C. 	CPRMethicillin resistant coagulase-negative staphylococci isolated from South Korean ducks exhibiting tremor.	Acta Vet. Scand.	2013	55		88			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. 		
@D	Han, J.E.//Kim, J.H.//Choresca, C.//Shin, S.P.//Jun, J.W.//Park, S.C. 	Draft Genome Sequence of a Clinical Isolate, Aeromonas hydrophila SNUFPC-A8, from a Moribund Cherry Salmon (Oncorhynchus masou masou).	Genome Announcements	2013	1		e00133-12			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). 		
@D	Han, J.E.//Kim, J.H.//Shin, S.P.//Jun, J.W.//Chai, J.Y.//Park, S.C. 	Draft Genome Sequence of Aeromonas salmonicida subsp. achromogenes AS03, an Atypical Strain Isolated from Crucian Carp (Carassius carassius) in the Republic   of Korea.	Genome Announcements	2013	1		e00791-13			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. 		
@D	Han, J.I.//Choi, H.K.//Lee, S.W.//Orwin, P.M.//Kim, J.//Laroe, S.L.//Kim, T.G.//O'Neil, J.//Leadbetter, J.R.//Lee, S.Y.//Hur, C.G.//Spain, J.C.//Ovchinnikova, G.//Goodwin, L.//Han, C. 	Complete genome sequence of the metabolically versatile plant growth-promoting endophyte, Variovorax paradoxus S110.	J. Bacteriol.	2010	193		1183-1190			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. 		
@D	Han, J.I.//Spain, J.C.//Leadbetter, J.R.//Ovchinnikova, G.//Goodwin, L.A.//Han, C.S.//Woyke, T.//Davenport, K.W.//Orwin, P.M. 	Genome of the Root-Associated Plant Growth-Promoting Bacterium Variovorax paradoxus Strain EPS.	Genome Announcements	2013	1		e00843-13			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. 		
@D	Han, J.W.//Oh, M.//Choi, G.J.//Kim, H. 	Genome Sequence of Delftia acidovorans HK171, a Nematicidal Bacterium Isolated from Tomato Roots.	Genome Announcements	2017	5		e01746-16			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. 		
@D	Han, K.//Li, Z.F.//Peng, R.//Zhu, L.P.//Zhou, T.//Wang, L.G.//Li, S.G.//Zhang, X.B.//Hu, W.//Wu, Z.H.//Qin, N.//Li, Y.Z. 	Extraordinary expansion of a Sorangium cellulosum genome from an alkaline milieu.	Sci. Rep.	2013	3		2101			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. 		
@D	Han, S.J.//Song, T.//Cho, Y.J.//Kim, J.S.//Choi, S.Y.//Bang, H.E.//Chun, J.//Bai, G.H.//Cho, S.N.//Shin, S.J. 	Complete genome sequence of Mycobacterium tuberculosis K from a Korean high school outbreak, belonging to the Beijing family.	Standards in Genomic Sciences	2015	10		78			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. 		
@D	Han, T.//Yamada-Mabuchi, M.//Zhao, G.//Li, L.//Liu, G.//Ou, H.Y.//Deng, Z.//Zheng, Y.//He, X. 	Recognition and cleavage of 5-methylcytosine DNA by bacterial SRA-HNH proteins.	Nucleic Acids Res.	2015	43		1147-1159			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. 		
@D	Han, X.//Li, M.//Ding, Z.//Zhao, J.//Ji, K.//Wen, M.//Lu, T. 	Genome Sequence of Streptomyces auratus Strain AGR0001, a Phoslactomycin-Producing Actinomycete.	J. Bacteriol.	2012	194		5472-5473			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. 		
@D	Han, X.Y.//Mistry, N.A.//Thompson, E.J.//Tang, H.L.//Khanna, K.//Zhang, L. 	Draft Genome Sequence of New Leprosy Agent Mycobacterium lepromatosis.	Genome Announcements	2015	3		e00513-15			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. 		
@D	Han, Y.//Dai, B.//Zhou, Y.//Wu, Z.//Ye, B.C. 	Draft Genome Sequence of the Plant Growth-Promoting Bacterium Pseudomonas sp. SCPG-7, Isolated from Saline Soil.	Genome Announcements	2017	5		e00702-17			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. 		
@A	Hanahan, D. 		Mechanisms of DNA Transformation:  Restrictionlike effects in Transformation in Escherichia coli and Salmonella typhimurium.			Neidhardt, F.C. 		Escherichia coli and Salmonella typhimurium: Cellular and molecular biology.				Washington D.C.	American Society for Microbiology	1986		0		1-7									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. 		
@D	Hanak, A.M.//Nagler, M.//Weinmaier, T.//Sun, X.//Fragner, L.//Schwab, C.//Rattei, T.//Ulrich, K.//Ewald, D.//Engel, M.//Schloter, M.//Bittner, R.//Schleper, C.//Weckwerth, W. 	Draft Genome Sequence of the Growth-Promoting Endophyte Paenibacillus sp. P22, Isolated from Populus.	Genome Announcements	2014	2		e00276-14			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. 		
@D	Hanawa, F.//Okamoto, M.//Towers, G.H.N. 	Inhibition of restriction enzyme's DNA sequence recognition by PUVA treatment.	Photochem. Photobiol.	2001	74		269-273			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. 		
@D	Hanck, T.//Gerwin, N.//Fritz, H.-J. 	Nucleotide sequence of the dcm locus of Escherichia coli K12.	Nucleic Acids Res.	1989	17		5844			None 		
@D	Hanck, T.//Schmidt, S.//Fritz, H.J. 	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.	Nucleic Acids Res.	1993	21		303-309			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. 		
@D	Hancox, E.L.//Connolly, B.A.//Walker, R.T. 	Synthesis and properties of oligodeoxynucleotides containing the analogue 2'-deoxy-4'-thiothymidine.	Nucleic Acids Res.	1993	21		3485-3491			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. 		
@D	Hancox, E.L.//Halford, S.E. 	Kinetic analysis of a mutational hot spot in the EcoRV restriction endonuclease.	Biochemistry	1997	36		7577-7585			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. 		
@D	Handa, N.//Ichige, A.//Kobayashi, I. 	Contribution of RecFOR machinery of homologous recombination to cell survival after loss of a restriction-modification gene complex.	Microbiology	2009	155		2320-2332			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. 		
@D	Handa, N.//Ichige, A.//Kusano, K.//Kobayashi, I. 	Cellular responses to postsegregational killing by restriction-modification genes.	J. Bacteriol.	2000	182		2218-2229			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. 		
@D	Handa, N.//Kobayashi, I. 	Post-segregational killing by restriction modification gene complexes: Observations of individual cell deaths.	Biochimie	1999	81		931-938			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. 		
@D	Handa, N.//Kobayashi, I. 	Type III restriction is alleviated by bacteriophage (RecE) homologous recombination function but enhanced by bacterial (RecBCD) function.	J. Bacteriol.	2005	187		7362-7373			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. 		
@D	Handa, N.//Naito, Y.//Kobayashi, I. 	Experimental genome evolution: Large-scale genome rearrangements associated with resistance of a chromosomal restriction-modification gene complex to replacement.	Genes Genet. Syst.	2000	75		381			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. 		
@D	Handa, N.//Nakayama, Y.//Sadykov, M.//Kobayashi, I. 	Experimental genome evolution: large-scale genome rearrangements associated with resistance to replacement of a chromosomal restriction-modification gene complex.	Mol. Microbiol.	2001	40		932-940			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. 		
@D	Handa, V.//Jeltsch, A. 	Profound flanking sequence preference of Dnmt3a and Dnmt3b mammalian DNA methyltransferases shape the human epigenome.	J. Mol. Biol.	2005	348		1103-1112			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. 		
@D	Handayani, I.//Ratnakomala, S.//Lisdiyanti, P.//Fahrurrozi, A.M.//Wohlleben, W.//Mast, Y. 	Complete Genome Sequence of Streptomyces sp. Strain BSE7F, a Bali Mangrove Sediment Actinobacterium with Antimicrobial Activities.	Genome Announcements	2018	6		e00618-18			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. 		
@D	Handique, A.K. 	New technique for thermostability of restriction and modifying enzymes.	Curr. Sci.	1994	66		103-104			Commentary on the use of trehalose to stabilize restriction enzymes 		
@D	Handley, K.M.//Upton, M.//Beatson, S.A.//Hery, M.//Lloyd, J.R. 	Genome Sequence of Hydrothermal Arsenic-Respiring Bacterium Marinobacter santoriniensis NKSG1T.	Genome Announcements	2013	1		E00231-13			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. 		
@D	Handtke, S.//Volland, S.//Methling, K.//Albrecht, D.//Becher, D.//Nehls, J.//Bongaerts, J.//Maurer, K.-H.//Lalk, M.//Liesegang, H.//Voigt, B.//Daniel, R.//Hecker, M. 	Cell physiology of the biotechnological relevant bacterium Bacillus pumilus-An omics-based approach.	J. Biotechnol.	2014	192		204-214			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. 		
@D	Hang, J.//Mullins, K.E.//Clifford, R.J.//Onmus-Leone, F.//Yang, Y.//Jiang, J.//Leguia, M.//Kasper, M.R.//Maguina, C.//Lesho, E.P.//Jarman, R.G.//Richards, A.L.//Blazes, D. 	Complete Genome Sequence of Bartonella ancashensis Strain 20.00, Isolated from the Blood of a Patient with Verruga Peruana.	Genome Announcements	2015	3		e01217-15			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. 		
@D	Hanish, J.//McClelland, M. 	Controlled partial restriction digestions of DNA by competition with modification methyltransferases.	Anal. Biochem.	1989	179		357-360			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. 		
@D	Hanish, J.//McClelland, M. 	Methylase-limited partial NotI cleavage for physical mapping of genomic DNA.	Nucleic Acids Res.	1990	18		3287-3291			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. 		
@D	Hanish, J.//McClelland, M. 	Activity of DNA modification and restriction enzymes in KGB, a potassium glutamate buffer.	Gene Anal. Tech.	1988	5		105-107			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.). 		
@D	Hanish, J.//McClelland, M. 	Enzymatic cleavage of a bacterial chromosome at a transposon-inserted rare site.	Nucleic Acids Res.	1991	19		829-832			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. 		
@D	Hanish, J.//Rebelsky, M.//McClelland, M.//Westbrook, C. 	Application of methylase-limited partial NotI cleavage for a long-range restriction map of the human ABL locus.	Genomics	1991	10		681-685			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. 		
@D	Hanley, A.B.//Furniss, C.S.M.//Kwiatkowska, C.A.//Mackie, A.R. 	The manipulation of DNA with restriction enzymes in low water systems.	Biochim. Biophys. Acta	1991	1074		40-44			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. 		
@D	Hanley, A.B.//Grinfeld, E.//Baxter, R.L. 	The cleavage of nucleic acids in reversed micelles using site specific endonucleases.	Biocatalysis	1990	3		253-258			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. 		
@D	Hansen, C.M.//Choi, S.C.//Parker, J.//Hueffer, K.//Chen, J. 	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.	Genome Announcements	2015	3		e00772-15			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%. 		
@D	Hansen, R.S.//Wijmenga, C.//D'Esposito, M.//Weemaes, C.M.R.//Gartier, S.M. 	Mutations in the DNMT3B DNA methyltransferase gene cause the ICF syndrome.	Am. J. Hum. Genet.	2000	66		1724			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. 		
@D	Hansen, R.S.//Wijmenga, C.//Luo, P.//Stanek, A.M.//Canfield, T.K.//Weemaes, C.M.//Gartler, S.M. 	The DNMT3B DNA methyltransferase gene is mutated in the ICF immunodeficiency syndrome.	Proc. Natl. Acad. Sci. U. S. A.	1999	96		14412-14417			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. 		
@D	Hanson, D.K.//Lamb, M.R.//Mahler, H.R.//Perlman, P.S. 	Evidence for translated intervening sequences in the mitochondrial genome of Saccharomyces cerevisiae.	J. Biol. Chem.	1982	257		3218-3224			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. 		
@D	Hanson-Drury, S.//To, T.T.//Liu, Q.//Vo, A.T.//Kim, M.//Watling, M.//Bumgarner, R.S.//McLean, J.S. 	Draft Genome Sequence of Tannerella forsythia Clinical Isolate 9610.	Genome Announcements	2017	5		e00024-17			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%. 		
@D	Hanvey, J.C.//Shimizu, M.//Wells, R.D. 	Site-specific inhibition of EcoRI restriction/modification enzymes by a DNA triple helix.	Nucleic Acids Res.	1990	18		157-161			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. 		
@D	Hao, H.//Chen, S.//Li, Y.//Sun, H.//Zhao, P.//Jian, Y.//Gao, Y.//Wu, C.//Liu, Y.//Chu, Y. 	Complete Genome Sequence of Mycoplasma capricolum subsp. capripneumoniae Strain zly1309F, Isolated from Endangered Tibetan Antelope.	Genome Announcements	2017	5		e00496-17			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. 		
@D	Hao, K.//He, P.//Blom, J.//Rueckert, C.//Mao, Z.//Wu, Y.//He, Y.//Borriss, R. 	The Genome of Plant Growth-Promoting Bacillus amyloliquefaciens subsp. plantarum  Strain YAU B9601-Y2 Contains a Gene Cluster for Mersacidin Synthesis.	J. Bacteriol.	2012	194		3264-3265			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. 		
@D	Hao, K.//Li, H.//Li, F.//Guo, P. 	Complete Genome Sequence of Bacillus pumilus PDSLzg-1, a Hydrocarbon-Degrading Bacterium Isolated from Oil-Contaminated Soil in China.	Genome Announcements	2016	4		e01079-16			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. 		
@D	Hao, P.//Zheng, H.//Yu, Y.//Ding, G.//Gu, W.//Chen, S.//Yu, Z.//Ren, S.//Oda, M.//Konno, T.//Wang, S.//Li, X.//Ji, Z.-S.//Zhao, G. 	Complete Sequencing and Pan-Genomic Analysis of Lactobacillus delbrueckii subsp bulgaricus Reveal Its Genetic Basis for Industrial Yogurt Production.	PLoS ONE	2011	6		e15964			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. 		
@D	Hao, X.//Lin, Y.//Johnstone, L.//Baltrus, D.A.//Miller, S.J.//Wei, G.//Rensing, C. 	Draft Genome Sequence of Plant Growth-Promoting Rhizobium Mesorhizobium amorphae, Isolated from Zinc-Lead Mine Tailings.	J. Bacteriol.	2012	194		736-737			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. 		
@D	Hao, X.//Lin, Y.//Johnstone, L.//Liu, G.//Wang, G.//Wei, G.//McDermott, T.//Rensing, C. 	Genome Sequence of the Arsenite-Oxidizing Strain Agrobacterium tumefaciens 5A.	J. Bacteriol.	2012	194		903			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. 		
@D	Hao, Y.//Huang, D.//Guo, H.//Xiao, M.//An, H.//Zhao, L.//Zuo, F.//Zhang, B.//Hu, S.//Song, S.//Chen, S.//Ren, F. 	Complete Genome Sequence of Bifidobacterium longum subsp. longum BBMN68, a New Strain from Healthy Chinese Centenarian.	J. Bacteriol.	2010	193		787-788			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. 		
@D	Hao, Z.//Li, L.//Liu, J.//Ren, Y.//Wang, L.//Bartlam, M.//Egli, T.//Wang, Y. 	Genome Sequence of a Freshwater Low-Nucleic-Acid-Content Bacterium, Betaproteobacterium Strain CB.	Genome Announcements	2013	1		e00135-13			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. 		
@D	Haq, I.//O'Brien, R.//Lagunavicius, A.//Siksnys, V.//Ladbury, J.E. 	Specific DNA Recognition by the Type II Restriction Endonuclease MunI: The Effect of pH.	Biochemistry	2001	40		14960-14967			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. 		
@D	Haqqi, T.M.//Ahmad, S.//Ahmad, N.S.//Ahmad, M.//Hasnain, A.//Siddiqi, M.//Hadi, S.M. 	Cloning and expression of EcoRI specific restriction modification system.	Indian J. Biochem. Biophys.	1985	22		252-254			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. 		
@D	Harada, J.//Yamada, T.//Giri, S.//Hamada, M.//Nobu, M.K.//Narihiro, T.//Tsuji, H.//Daimon, H. 	Draft Genome Sequence of Moorella sp. Strain Hama-1, a Novel Acetogenic Bacterium Isolated from a Thermophilic Digestion Reactor.	Genome Announcements	2018	6		e00517-18			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%. 		
@D	Harden, L.K.//Morales, K.M.//Hughey, J.R. 	Complete Genome Sequence of Nonhemolytic Streptococcus agalactiae Serotype V Strain 1, Isolated from the Buccal Cavity of a Canine.	Genome Announcements	2016	4		e01612-15			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. 		
@D	Hardwick, J.M.//von Sprecken, R.S.//Yielding, K.L.//Yielding, L.W. 	Ethidium binding sites on plasmid DNA determined by photoaffinity labeling.	J. Biol. Chem.	1984	259		11090-11097			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. 		
@D	Hargrove, E.C.//Lopez, M.S.//Hernandez, A.C.//Kuty, E.G.F. 	Complete Genome Sequence of Bacillus megaterium Podophage Palmer.	Genome Announcements	2015	3		e00358-15			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. 		
@D	Harhay, D.M.//Bono, J.L.//Smith, T.P.//Fields, P.I.//Dinsmore, B.A.//Santovenia, M.//Kelley, C.M.//Wang, R.//Harhay, G.P. 	Complete Closed Genome Sequences of Salmonella enterica subsp. enterica Serotypes Anatum, Montevideo, Typhimurium, and Newport, Isolated from Beef, Cattle, and  Humans.	Genome Announcements	2016	4		e01683-15			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. 		
@D	Harhay, G.P.//Harhay, D.M.//Bono, J.L.//Smith, T.P.L.//Capik, S.F.//DeDonder, K.D.//Apley, M.D.//Lubbers, B.V.//White, B.J.//Larson, R.L. 	Closed Genome Sequences of Seven Histophilus somni Isolates from Beef Calves with Bovine Respiratory Disease Complex.	Genome Announcements	2017	5		e01099-17			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. 		
@D	Harhay, G.P.//Koren, S.//Phillippy, A.M.//McVey, D.S.//Kuszak, J.//Clawson, M.L.//Harhay, D.M.//Heaton, M.P.//Chitko-McKown, C.G.//Smith, T.P. 	Complete Closed Genome Sequences of Mannheimia haemolytica Serotypes A1 and A6, Isolated from Cattle.	Genome Announcements	2013	1		e00188-13			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. 		
@D	Harhay, G.P.//McVey, D.S.//Koren, S.//Phillippy, A.M.//Bono, J.//Harhay, D.M.//Clawson, M.L.//Heaton, M.P.//Chitko-McKown, C.G.//Korlach, J.//Smith, T.P. 	Complete Closed Genome Sequences of Three Bibersteinia trehalosi Nasopharyngeal Isolates from Cattle with Shipping Fever.	Genome Announcements	2014	2		e00084-14			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. 		
@D	Harhay, G.P.//Murray, R.W.//Lubbers, B.//Griffin, D.//Koren, S.//Phillippy, A.M.//Harhay, D.M.//Bono, J.//Clawson, M.L.//Heaton, M.P.//Chitko-McKown, C.G.//Smith, T.P. 	Complete Closed Genome Sequences of Four Mannheimia varigena Isolates from Cattle with Shipping Fever.	Genome Announcements	2014	2		e00088-14			Mannheimia varigena is an occasional respiratory pathogen of cattle and pigs. We  present the first four complete closed genome sequences of this species. 		
@D	Harish, S.M.//Sim, K.S.//Najimudin, N.//Aziah, I. 	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.	Genome Announcements	2015	3		e01261-15			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. 		
@D	Harish, S.M.//Sim, K.S.//Nor, F.M.//Hussin, H.M.//Hamzah, W.M.//Najimudin, N.//Aziah, I. 	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.	Genome Announcements	2015	3		e01285-15			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. 		
@D	Harjes, J.//Ryu, T.//Abdelmohsen, U.R.//Moitinho-Silva, L.//Horn, H.//Ravasi, T.//Hentschel, U. 	Draft Genome Sequence of the Antitrypanosomally Active Sponge-Associated Bacterium Actinokineospora sp. Strain EG49.	Genome Announcements	2014	2		e00160-14			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. 		
@D	Harmon-Smith, M. et al. 	Complete genome sequence of Sebaldella termitidis type strain (NCTC 11300).	Standards in Genomic Sciences	2010	2		220-227			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. 		
@D	Harms, A.//Segers, F.H.//Quebatte, M.//Mistl, C.//Manfredi, P.//Korner, J.//Chomel, B.B.//Kosoy, M.//Maruyama, S.//Engel, P.//Dehio, C. 	Evolutionary Dynamics of Pathoadaptation Revealed by Three Independent Acquisitions of the VirB/D4 Type IV Secretion System in Bartonella.	Genome Biol. Evol.	2017	9		761-776			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. 		
@D	Harms, H.//Poehlein, A.//Thurmer, A.//Konig, G.M.//Schaberle, T.F. 	Draft Genome Sequence of Zobellia sp. Strain OII3, Isolated from the Coastal Zone of the Baltic Sea.	Genome Announcements	2017	5		e00737-17			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. 		
@D	Haroon, M.F.//Thompson, L.R.//Stingl, U. 	Draft Genome Sequence of Uncultured SAR324 Bacterium lautmerah10, Binned from a Red Sea Metagenome.	Genome Announcements	2016	4		e01711-15			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. 		
@A	Harper, S.H.//Firman, K.//Glover, S.W. 		The interactions of mini-F with the plasmids R124 and R124/3.			Helsinki, D.R.//Cohen, S.N.//Clewell, D.B.//Jackson, D.A.//Hollaender, A. 		Plasmids in Bacteria				New York	Plenum Press	1984		0		920									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. 		
@D	Harrell, E.A.//Miller, E.S. 	Genome Sequence of Aeromicrobium erythreum NRRL B-3381, an Erythromycin-Producing Bacterium of the Nocardioidaceae.	Genome Announcements	2016	4		e00300-16			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. 		
@D	Harrington, A.//Hill, C. 	Plasmid involvement in the formation of a spontaneous bacteriophage insensitive mutant of Lactococcus lactis.	FEMS Microbiol. Lett.	1992	96		135-141			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. 		
@D	Harrington, R.//Ondov, B.D.//Radune, D.//Friss, M.B.//Klubnik, J.//Diviak, L.//Hnath, J.//Cendrowski, S.R.//Blank, T.E.//Karaolis, D.//Friedlander, A.M.//Burans, J.P.//Rosovitz, M.J.//Treangen, T.//Phillippy, A.M.//Bergman, N.H. 	Genome Sequence of the Attenuated Carbosap Vaccine Strain of Bacillus anthracis.	Genome Announcements	2013	1		e00067-12			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. 		
@D	Harris, A.P.//Techtmann, S.M.//Stelling, S.C.//Utturkar, S.M.//Alshibli, N.K.//Brown, S.D.//Hazen, T.C. 	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.	Genome Announcements	2014	2		e01212-14			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. 		
@D	Harris, V.H.//Hamilton, A.//Williams, D.M.//Hornby, D.P. 	Studying the function of methyltransferases using nucleotide analogue based random mutagenesis.	Collection Symposium Series	1999	2		209-212			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. 		
@D	Harris-Warrick, R.M.//Elkana, Y.//Ehrlich, S.D.//Lederberg, J. 	Electrophoretic separation of Bacillus subtilis genes.	Proc. Natl. Acad. Sci. U. S. A.	1975	72		2207-2211			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. 		
@D	Harrison, A.//Dyer, D.W.//Gillaspy, A.//Ray, W.C.//Mungur, R.//Carson, M.B.//Zhong, H.//Gipson, J.//Gipson, M.//Johnson, L.S.//Lewis, L.//Bakaletz, L.O.//Munson, R.S. Jr. 	Genomic sequence of an otitis media isolate of nontypeable Haemophilus influenzae: Comparative study with H. influenzae serotype d, strain KW20.	J. Bacteriol.	2005	187		4627-4636			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. 		
@D	Harrison, J.//Dornbusch, M.R.//Samac, D.//Studholme, D.J. 	Draft Genome Sequence of Pseudomonas syringae pv. syringae ALF3 Isolated from Alfalfa.	Genome Announcements	2016	4		e01722-15			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. 		
@D	Harrison, J.//Grant, M.R.//Studholme, D.J. 	Draft Genome Sequences of Two Strains of Xanthomonas arboricola pv. celebensis Isolated from Banana Plants.	Genome Announcements	2016	4		e01705-15			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. 		
@D	Harrison, L.B.//Hanson, N.D. 	Draft Genome Sequence of the Mucoid Pseudomonas aeruginosa Clinical Isolate PA34.	Genome Announcements	2017	5		e01307-17			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. 		
@D	Harro, J.M.//Daugherty, S.//Bruno, V.M.//Jabra-Rizk, M.A.//Rasko, D.A.//Shirtliff, M.E. 	Draft Genome Sequence of the Methicillin-Resistant Staphylococcus aureus Isolate  MRSA-M2.	Genome Announcements	2013	1		e00037-12			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. 		
@D	Hartke, A.//Benachour, A.//Boutibonnes, P.//Auffray, Y. 	Characterization of a complex restriction/modification system detected in a Bifidobacterium longum strain.	Appl. Microbiol. Biotechnol.	1996	45		132-136			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. 		
@D	Hartman, A.L.//Norais, C.//Badger, J.H.//Delmas, S.//Haldenby, S.//Madupu, R.//Robinson, J.//Khouri, H.//Ren, Q.//Lowe, T.M.//Maupin-Furlow, J.//Pohlschroder, M.//Daniels, C.//Pfeiffer, F.//Allers, T.//Eisen, J.A. 	The Complete Genome Sequence of Haloferax volcanii DS2, a Model Archaeon.	PLoS ONE	2010	5		E9605			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. 		
@D	Hartman, N.//Zinder, N.D. 	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.	J. Mol. Biol.	1974	85		357-369			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. 		
@D	Hartman, N.//Zinder, N.D. 	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.	J. Mol. Biol.	1974	85		345-356			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. 		
@D	Hartmann, H.//Goebel, W. 	A new restriction enzyme from Enterobacter cloacae (EclI).	FEBS Lett.	1977	80		285-287			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. 		
@D	Harunari, E.//Komaki, H.//Ichikawa, N.//Hosoyama, A.//Kimura, A.//Hamada, M.//Igarashi, Y. 	Draft genome sequence of Streptomyces hyaluromycini MB-PO13(T), a hyaluromycin producer.	Standards in Genomic Sciences	2018	13		2			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. 		
@D	Harvey, Z.H.//Snider, M.J. 	Draft Genome Sequence of the Nicotinate-Metabolizing Soil Bacterium Bacillus niacini DSM 2923.	Genome Announcements	2014	2		e01251-14			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. 		
@D	Harvill, E.T.//Goodfield, L.L.//Ivanov, Y.//Meyer, J.A.//Newth, C.//Cassiday, P.//Tondella, M.L.//Liao, P.//Zimmerman, J.//Meert, K.//Wessel, D.//Berger, J.//Dean, J.M.//Holubkov, R.//Burr, J.//Liu, T.//Brinkac, L.//Kim, M.//Losada, L. 	Genome Sequences of 28 Bordetella pertussis U.S. Outbreak Strains Dating from 2010 to 2012.	Genome Announcements	2013	1		e01075-13			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. 		
@D	Harvill, E.T.//Goodfield, L.L.//Ivanov, Y.//Smallridge, W.E.//Meyer, J.A.//Cassiday, P.K.//Tondella, M.L.//Brinkac, L.//Sanka, R.//Kim, M.//Losada, L. 	Genome Sequences of Nine Bordetella holmesii Strains Isolated in the United States.	Genome Announcements	2014	2		e00438-14			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. 		
@D	Harwich, M.D. Jr.//Alves, J.M.//Buck, G.A.//Strauss, J.F. III//Patterson, J.L.//Oki, A.T.//Girerd, P.H.//Jefferson, K.K. 	Drawing the line between commensal and pathogenic Gardnerella vaginalis through genome analysis and virulence studies.	BMC Genomics	2010	11		375			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. 		
@D	Harwich, M.D. Jr.//Serrano, M.G.//Fettweis, J.M.//Alves, J.M.//Reimers, M.A.//Buck, G.A.//Jefferson, K.K. 	Genomic sequence analysis and characterization of Sneathia amnii sp. nov.	BMC Genomics	2012	13		S4			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. 		
@D	Haryono, M.//Lo, W.S.//Gasparich, G.E.//Kuo, C.H. 	Complete Genome Sequence of Spiroplasma sp. NBRC 100390.	Genome Announcements	2017	5		e00008-17			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. 		
@D	Hasan, N.//Kim, S.C.//Podhajska, A.J.//Szybalski, W. 	A novel multistep method for generating precise unidirectional deletions using BspMI, a class-IIS restriction enzyme.	Gene	1986	50		55-62			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. 		
@D	Hasan, N.A.//Davidson, R.M.//de Moura, V.C.//Garcia, B.J.//Reynolds, P.R.//Epperson, L.E.//Farias-Hesson, E.//DeGroote, M.A.//Jackson, M.//Strong, M. 	Draft Genome Sequence of Mycobacterium chelonae Type Strain ATCC 35752.	Genome Announcements	2015	3		e00536-15			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. 		
@D	Hasan, N.A.//Grim, C.J.//Haley, B.J.//Chun, J.//Alam, M.//Taviani, E.//Hoq, M.//Munk, A.C.//Saunders, E.//Brettin, T.S.//Bruce, D.C.//Challacombe, J.F.//Detter, J.C.//Han, C.S.//Xie, G.//Nair, G.B.//Huq, A.//Colwell, R.R. 	Comparative genomics of clinical and environmental Vibrio mimicus.	Proc. Natl. Acad. Sci. U. S. A.	2010	107		21134-21139			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. 		
@D	Hasan, N.A.//Honda, J.R.//Davidson, R.M.//Epperson, L.E.//Bankowski, M.J.//Chan, E.D.//Strong, M. 	Complete Genome Sequence of Mycobacterium chimaera Strain AH16.	Genome Announcements	2016	4		e01276-16			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. 		
@D	Hasan, N.A.//Lawsin, A.//Perry, K.A.//Alyanak, E.//Toney, N.C.//Malecha, A.//Rowe, L.A.//Batra, D.//Moulton-Meissner, H.//Miller, J.R.//Strong, M.//Laufer, H.A. 	Complete Genome Sequence of Mycobacteriumchimaera Strain CDC2015-22-71.	Genome Announcements	2017	5		e00693-17			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. 		
@D	Hasan, N.A.//Warren, R.L.//Epperson, L.E.//Malecha, A.//Alexander, D.C.//Turenne, C.Y.//MacMillan, D.//Birol, I.//Pleasance, S.//Coope, R.//Jones, S.J.M.//Romney, M.G.//Ng, M.//Chan, T.//Rodrigues, M.//Tang, P.//Gardy, J.L.//Strong, M. 	Complete Genome Sequence of Mycobacterium chimaera SJ42, a Nonoutbreak Strain from an Immunocompromised Patient with Pulmonary Disease.	Genome Announcements	2017	5		e00963-17			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. 		
@D	Hasegawa, M.//Nakajima, Y.//Wong, S.K.//Nakamura, K.//Ogura, Y.//Hayashi, T.//Kogure, K.//Yoshizawa, S. 	Draft Genome Sequence of Saccharospirillum sp. Strain MSK14-1, Isolated from Surface Seawater Collected at Aburatsubo Inlet in Japan.	Genome Announcements	2018	6		e00469-18			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. 		
@D	Hasegawa, N.//Sekizuka, T.//Sugi, Y.//Kawakami, N.//Ogasawara, Y.//Kato, K.//Yamashita, A.//Takeuchi, F.//Kuroda, M. 	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.	Infect. Immun.	2017	85		e00886-16			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. 		
@D	Hashimoto, H.//Shimizu, T.//Imasaki, T.//Kato, M.//Shichijo, N.//Kita, K.//Sato, M. 	Crystal structures of type II restriction endonuclease Eco0109I and its complex with cognate DNA.	J. Biol. Chem.	2005	280		5605-5610			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. 		
@D	Hashimoto, H.//Takahashi, H.//Nishioka, M.//Fujiwara, S.//Takagi, M.//Imanaka, T.//Inoue, T.//Kai, Y. 	Crystallographic study of intein homing endonuclease II encoded in the archaeal DNA polymerase gene.	Acta Crystallogr. D Biol. Crystallogr.	2000	56		1185-1186			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%. 		
@D	Hashimoto-Gotoh, T. 	Quantitative determination of effective nibbling activities contaminating restriction endonuclease preparations.	Anal. Biochem.	1995	231		230-236			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. 		
@D	Hashimoto-Gotoh, T.//Tsujimura, A.//Ogasahara, Y. 	Detection of exonuclease activities in restriction endonuclease preparations using an enforcement plasmid for kanamycin-resistance selection.	Gene	1995	164		41-44			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. 		
@D	Haskett, T.//Wang, P.//Ramsay, J.//O'Hara, G.//Reeve, W.//Howieson, J.//Terpolilli, J. 	Complete Genome Sequence of Mesorhizobium ciceri Strain CC1192, an Efficient Nitrogen-Fixing Microsymbiont of Cicer arietinum.	Genome Announcements	2016	4		e00516-16			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). 		
@D	Haskett, T.//Wang, P.//Ramsay, J.//O'Hara, G.//Reeve, W.//Howieson, J.//Terpolilli, J. 	Complete Genome Sequence of Mesorhizobium ciceri bv. biserrulae Strain WSM1284, an Efficient Nitrogen-Fixing Microsymbiont of the Pasture Legume Biserrula  pelecinus.	Genome Announcements	2016	4		e00514-16			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). 		
@D	Hasman, H.//Mevius, D.//Veldman, K.//Olesen, I.//Aarestrup, F.M. 	beta-Lactamases among extended-spectrum beta-lactamase (ESBL)-resistant Salmonella from poultry, poultry products and human patients in The Netherlands.	J. Antimicrob. Chemother.	2005	56		115-121			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. 		
@D	Hassan, I.//Eastman, A.W.//Weselowski, B.//Mohamedelhassan, E.//Yanful, E.K.//Yuan, Z.C. 	Complete Genome Sequence of Arthrobacter sp. Strain LS16, Isolated from Agricultural Soils with Potential for Applications in Bioremediation and  Bioproducts.	Genome Announcements	2016	4		e01586-15			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. 		
@D	Hassan, K.A.//Elbourne, L.D.//Tetu, S.G.//Johnson, E.A.//Paulsen, I.T. 	Genome Sequence of the Neurotoxigenic Clostridium butyricum Strain 5521.	Genome Announcements	2014	2		e00632-14			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. 		
@D	Hassan, K.A.//Tetu, S.G.//Elbourne, L.D.//Johnson, E.A.//Paulsen, I.T. 	Genome Sequence of the Group III Clostridium botulinum Strain Eklund-C.	Genome Announcements	2013	1		e0004413			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. 		
@D	Hassan, S.S. et al. 	Complete genome sequence of Corynebacterium pseudotuberculosis biovar ovis strain P54B96 isolated from antelope in South Africa obtained by rapid next generation  sequencing technology.	Standards in Genomic Sciences	2012	7		189-199			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. 		
@D	Hassan, S.S. et al. 	Whole-genome sequence of Corynebacterium pseudotuberculosis strain Cp162, isolated from camel.	J. Bacteriol.	2012	194		5718-5719			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. 		
@D	Hassan, Y.I.//Lepp, D.//He, J.//Zhou, T. 	Draft Genome Sequences of Devosia sp. Strain 17-2-E-8 and Devosia riboflavina Strain IFO13584.	Genome Announcements	2014	2		e00994-14			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. 		
@D	Hassan, Y.I.//Lepp, D.//Li, X.Z.//Zhou, T. 	Insights into the Hydrocarbon Tolerance of Two Devosia Isolates, D. chinhatensis  Strain IPL18T and D. geojensis Strain BD-c194T, via Whole-Genome Sequence  Analysis.	Genome Announcements	2015	3		e00890-15			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. 		
@D	Hassan, Y.I.//Lepp, D.//Zhou, T. 	Genome Assemblies of Three Soil-Associated Devosia species: D. insulae, D. limi,  and D. soli.	Genome Announcements	2015	3		e00514-15			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. 		
@D	Hassani, I.I.//Robert, C.//Michelle, C.//Raoult, D.//Hacene, H.//Desnues, C. 	Non-contiguous finished genome sequence and description of Halopiger djelfamassiliensis sp. nov.	Standards in Genomic Sciences	2013	9		160-174			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. 		
@D	Hassaninasab, A.//Hashimoto, Y.//Tomita-Yokotani, K.//Kobayashi, M. 	Discovery of the curcumin metabolic pathway involving a unique enzyme in an intestinal microorganism.	Proc. Natl. Acad. Sci. U. S. A.	2011	108		6615-6620			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. 		
@D	Hassen, W.//Neifar, M.//Cherif, H.//Najjari, A.//Chouchane, H.//Driouich, R.C.//Salah, A.//Naili, F.//Mosbah, A.//Souissi, Y.//Raddadi, N.//Ouzari, H.I.//Fava, F.//Cherif, A. 	Pseudomonas rhizophila S211, a New Plant Growth-Promoting Rhizobacterium with Potential in Pesticide-Bioremediation.	Front. Microbiol.	2018	9		34			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. 		
@D	Hata, E. 	Complete Genome Sequence of Mycoplasma canadense Strain HAZ 360_1 from Bovine Mastitic Milk in Japan.	Genome Announcements	2014	2		e00984-14			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. 		
@D	Hata, E. 	Complete Genome Sequence of Mycoplasma arginini Strain HAZ 145_1 from Bovine Mastitic Milk in Japan.	Genome Announcements	2015	3		e00265-15			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. 		
@D	Hata, E.//Murakami, K. 	Complete Genome Sequence of Mycoplasma californicum Strain HAZ160_1 from Bovine Mastitic Milk in Japan.	Genome Announcements	2014	2		e00684-14			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. 		
@D	Hata, E.//Nagai, K.//Murakami, K. 	Complete Genome Sequence of Mycoplasma bovirhinis Strain HAZ141_2 from Bovine Nasal Discharge in Japan.	Genome Announcements	2017	5		e01000-17			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. 		
@D	Hata, E.//Nagai, K.//Murakami, K. 	Complete Genome Sequence of Mycoplasma bovigenitalium Strain HAZ 596 from a Bovine Vagina in Japan.	Genome Announcements	2017	5		e01554-16			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. 		
@D	Hata, K.//Okano, M.//Lei, H.//Li, E. 	Dnmt3L cooperates with the Dnmt3 family of de novo DNA methyltransferases to establish maternal imprints in mice.	Development	2002	129		1983-1993			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. 		
@D	Hatch, M.//Allison, M.J.//Yu, F.//Farmerie, W. 	Genome Sequence of Oxalobacter formigenes Strain HC-1.	Genome Announcements	2017	5		e00533-17			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. 		
@D	Hatch, M.//Allison, M.J.//Yu, F.//Farmerie, W. 	Genome Sequence of Oxalobacter formigenes Strain OXCC13.	Genome Announcements	2017	5		e00534-17			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. 		
@D	Hatfull, G.F. 	Complete Genome Sequences of 138 Mycobacteriophages.	J. Virol.	2012	86		2382-2384			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. 		
@D	Hatfull, G.F. et al. 	Exploring the mycobacteriophage metaproteome: phage genomics as an educational platform.	PLoS Genet.	2006	2		e92			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. 		
@D	Hatmaker, E.A.//Riley, L.A.//O'Dell, K.B.//Papanek, B.//Graveley, B.R.//Garrett, S.C.//Wei, Y.//Terns, M.P.//Guss, A.M. 	Complete Genome Sequence of Industrial Dairy Strain Streptococcus thermophilus DGCC 7710.	Genome Announcements	2018	6		e01587-17			We report here the complete genome sequence of Streptococcus thermophilus DGCC 7710. S. thermophilus is widely used in industrial dairy production. 		
@D	Hatolkar, S.M.//Misra, R.N.//Mahato, R.//Jadhav, S. 	Whole-Genome Sequencing and Annotation of a Drug-Resistant Extrapulmonary Clinical Isolate of Beijing Genotype Mycobacterium tuberculosis from Pune, India.	Genome Announcements	2018	6		e00504-18			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. 		
@D	Hattman, S. 	The functioning of T-even phages with unglucosylated DNA in restricting Escherichia coli host cells.	Virology	1964	24		333-348			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. 		
@D	Hattman, S. 	Methylation of adenine residues in bacteriophage T2 DNA.	Virology	1972	49		404-412			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. 		
@D	Hattman, S. 	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.	J. Bacteriol.	1977	129		1330-1334			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. 		
@D	Hattman, S. 	Specificity of the bacteriophage Mu mom+-controlled DNA modification.	J. Virol.	1980	34		277-279			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'. 		
@D	Hattman, S. 	Plasmid-controlled variation in the content of methylated bases in bacteriophage lambda deoxyribonucleic acid.	J. Virol.	1972	10		356-361			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. 		
@D	Hattman, S. 	Unusual Modification of Bacteriophage Mu DNA.	J. Virol.	1979	32		468-475			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. 		
@D	Hattman, S. 	Plasmid-controlled variation in the content of methylated bases in single-stranded DNA phages M13 and fd.	J. Mol. Biol.	1973	74		749-752			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. 		
@D	Hattman, S. 	DNA methylation of T-even bacteriophages and of their nonglucosylated mutants:  its role in P1-directed restriction.	Virology	1970	42		359-367			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+. 		
@D	Hattman, S. 	Variation of 6-methylaminopurine content in bacteriophage P22 deoxyribonucleic acid as a function of host specificity.	J. Virol.	1971	7		690-691			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. 		
@D	Hattman, S. 	DNA methyltransferase-dependent transcription of the phage Mu mom gene.	Proc. Natl. Acad. Sci. U. S. A.	1982	79		5518-5521			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. 		
@A	Hattman, S. 		DNA Modification:  Methylation.			Mathews, C.K.//Berget, P.//Mosig, G.//Kutter, B. 		Bacteriophage T4					ASM Publications	1983		0		152-155									None 		
@A	Hattman, S. 		DNA methylation.			Boyer, P. 		The Enzymes					Academic Press	1981		14		517-548									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. 		
@D	Hattman, S.//Brooks, J.E.//Masurekar, M. 	Sequence specificity of the P1 modification methylase (M.EcoP1) and the DNA methylase (M.Ecodam) controlled by the Escherichia coli dam gene.	J. Mol. Biol.	1978	126		367-380			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). 		
@D	Hattman, S.//Cousens, L. 	Location of the region controlling host specificity (hsII) with respect to drug resistance markers on the fi- R factor, N-3.	J. Bacteriol.	1972	112		1428-1430			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. 		
@D	Hattman, S.//Fukasawa, T. 	Host-induced modification of T-even phages due to defective glucosylation of their DNA.	Proc. Natl. Acad. Sci. U. S. A.	1963	50		297-300			None 		
@D	Hattman, S.//Gold, E.//Plotnik, A. 	Methylation of cytosine residues in DNA controlled by a drug resistance factor.	Proc. Natl. Acad. Sci. U. S. A.	1972	69		187-190			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. 		
@D	Hattman, S.//Goradia, M.//Monaghan, C.//Bukhari, A.I. 	Regulation of the DNA-modification function of bacteriophage Mu.	Cold Spring Harb. Symp. Quant. Biol.	1983	47		647-653			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. 		
@D	Hattman, S.//Gribbin, C.//Hutchison, C.A. 	In vivo methylation of bacteriophage PhiX174 DNA.	J. Virol.	1979	32		845-851			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. 		
@D	Hattman, S.//Keister, T.//Gottehrer, A. 	Sequence specificity of DNA methylases from Bacillus amyloliquefaciens and Bacillus brevis.	J. Mol. Biol.	1978	124		701-711			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. 		
@D	Hattman, S.//Malygin, E.G. 	Bacteriophage T2Dam and T4Dam DNA-[N6-adenine]-methyltransferases.	Prog. Nucleic Acid Res. Mol. Biol.	2004	77		67-126			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. 		
@D	Hattman, S.//Revel, H.R.//Luria, S.E. 	Enzyme synthesis directed by nonglucosylated T-even bacteriophages in restriction hosts.	Virology	1966	30		427-438			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. 		
@D	Hattman, S.//Schlagman, S.//Cousens, L. 	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.	J. Bacteriol.	1973	115		1103-1107			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. 		
@D	Hattman, S.//Schlagman, S.//Goldstein, L.//Frohlich, M. 	Salmonella typhimurium SA Host Specificity System is based on Deoxyribonucleic Acid-Adenine Methylation.	J. Bacteriol.	1976	127		211-217			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. 		
@D	Hattman, S.//van Ormondt, H.//de Waard, A. 	Sequence specificity of the wild-type (dam+) and mutant (damh) forms of bacteriophage T2 DNA adenine methylase.	J. Mol. Biol.	1978	119		361-376			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'. 		
@D	Hattman, S.//Wilkinson, J.//Swinton, D.//Schlagman, S.//MacDonald, P.M.//Mosig, G. 	Common evolutionary origin of the Phage T4 dam and host Escherichia coli dam DNA-adenine methyltransferase genes.	J. Bacteriol.	1985	164		932-937			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. 		
@D	Hattori, M. et al. 	The DNA sequence of human chromosome 21.	Nature	2000	405		311-319			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. 		
@D	Hau, S.J.//Bayles, D.O.//Alt, D.P.//Brockmeier, S.L.//Frana, T.S.//Nicholson, T.L. 	Draft Genome Sequences of Nine Streptococcus suis Strains Isolated in the United  States.	Genome Announcements	2015	3		e01301-15			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. 		
@D	Hau, S.J.//Bayles, D.O.//Alt, D.P.//Davies, P.R.//Haan, J.S.//Nicholson, T.L. 	Draft Genome Sequences of Nine Livestock-Associated Methicillin-Resistant Staphylococcus aureus Sequence Type 5 Isolates from Humans with Long-Term Swine  Contact.	Genome Announcements	2017	5		e01079-17			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. 		
@D	Hau, S.J.//Bayles, D.O.//Alt, D.P.//Frana, T.S.//Nicholson, T.L. 	Complete Genome Sequence of a Livestock-Associated Methicillin-Resistant Staphylococcus aureus Sequence Type 5 Isolate from the United States.	Genome Announcements	2017	5		e00791-17			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. 		
@D	Hau, S.J.//Bayles, D.O.//Alt, D.P.//Frana, T.S.//Nicholson, T.L. 	Complete Genome Sequence of Livestock-Associated Methicillin-Resistant Staphylococcus aureus Sequence Type 398 Isolated from Swine in the United States.	Genome Announcements	2017	5		e00790-17			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. 		
@D	Hau, S.J.//Bayles, D.O.//Alt, D.P.//Frana, T.S.//Nicholson, T.L. 	Draft Genome Sequences of Nine Livestock-Associated Methicillin-Resistant Staphylococcus aureus Sequence Type 5 Isolates Obtained from Humans after  Short-Term Swine Contact.	Genome Announcements	2017	5		e01080-17			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. 		
@D	Hau, S.J.//Bayles, D.O.//Alt, D.P.//Frana, T.S.//Nicholson, T.L. 	Draft Genome Sequences of 14 Livestock-Associated Methicillin-Resistant Staphylococcus aureus Sequence Type 398 Isolates from Swine Farms in the United  States.	Genome Announcements	2017	5		e01082-17			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. 		
@D	Hau, S.J.//Bayles, D.O.//Alt, D.P.//Frana, T.S.//Nicholson, T.L. 	Draft Genome Sequences of 63 Swine-Associated Methicillin-Resistant Staphylococcus aureus Sequence Type 5 Isolates from the United States.	Genome Announcements	2017	5		e01081-17			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. 		
@D	Hau, S.J.//Bayles, D.O.//Alt, D.P.//Nicholson, T.L. 	Complete Genome Sequences of Two Staphylococcus aureus Sequence Type 5 Isolates from California, USA.	Genome Announcements	2017	5		e00099-17			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. 		
@D	Hau, S.J.//Bayles, D.O.//Alt, D.P.//Nicholson, T.L. 	Draft Genome Sequences of 14 Staphylococcus aureus Sequence Type 5 Isolates from  California, USA.	Genome Announcements	2017	5		e00098-17			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. 		
@D	Hau, S.J.//Bayles, D.O.//Alt, D.P.//Nicholson, T.L. 	Draft Genome Sequences of One Methicillin-Sensitive and Seven Methicillin-Resistant Staphylococcus aureus Sequence Type 5 Isolates Obtained in   California.	Genome Announcements	2017	5		e01084-17			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. 		
@D	Hau, S.J.//Bayles, D.O.//Alt, D.P.//Nicholson, T.L. 	Draft Genome Sequences of 50 Methicillin-Resistant Staphylococcus aureus Sequence Type 5 Isolates Obtained from a U.S. Hospital.	Genome Announcements	2017	5		e01083-17			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. 		
@D	Haugen, P.//Bhattacharya, D. 	The spread of LAGLIDADG homing endonuclease genes in rDNA.	Nucleic Acids Res.	2004	32		2049-2057			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. 		
@D	Haugen, P.//De Jonckheere, J.F.//Johansen, S. 	Characterization of the self-splicing products of two complex Naegleria LSU rDNA group I introns containing homing endonuclease genes.	Eur. J. Biochem.	2002	269		1641-1649			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. 		
@D	Haugen, P.//Huss, V.A.R.//Nielsen, H.//Johansen, S. 	Complex group-I introns in nuclear SSU rDNA of red and green algae: Evidence of homing-endonuclease pseudogenes in the Bangiophyceae.	Curr. Genet.	1999	36		345-353			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. 		
@D	Haugen, P.//Simon, D.M.//Bhattacharya, D. 	The natural history of group I introns.	Trends Genet.	2005	21		111-119			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. 		
@D	Haugen, P.//Wikmark, O.-G.//Vader, A.//Coucheron, D.H.//Sjottem, E.//Johansen, S.D. 	The recent transfer of a homing endonuclease gene.	Nucleic Acids Res.	2005	33		2734-2741			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. 		
@D	Hauglund, M.J.//Tatum, F.M.//Bayles, D.O.//Maheswaran, S.K.//Briggs, R.E. 	Genome Sequences of Mannheimia haemolytica Serotype A2 Isolates D171 and D35, Recovered from Bovine Pneumonia.	Genome Announcements	2015	3		e00093-15			Here, we report two genomes, one complete and one draft, from isolates of serotype A2 Mannheimia haemolytica recovered from pneumonic bovine lung. 		
@D	Hauglund, M.J.//Tatum, F.M.//Bayles, D.O.//Maheswaran, S.K.//Briggs, R.E. 	Genome Sequences of Serotype A6 Mannheimia haemolytica Isolates D174 and D38 Recovered from Bovine Pneumonia.	Genome Announcements	2015	3		e00086-15			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. 		
@D	Hauglund, M.J.//Tatum, F.M.//Bayles, D.O.//Maheswaran, S.K.//Briggs, R.E. 	Genome Sequences of Mannheimia haemolytica Serotype A1 Strains D153 and D193 from Bovine Pneumonia.	Genome Announcements	2013	1		e00848-13			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. 		
@D	Hauptmann, A.L.//Glaring, M.A.//Hallin, P.F.//Prieme, A.//Stougaard, P. 	Draft Genome Sequence of the Psychrophilic and Alkaliphilic Rhodonellum psychrophilum Strain GCM71T.	Genome Announcements	2013	1		e01014-13			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. 		
@D	Hauser, H.//Richter, D.C.//van Tonder, A.//Clark, L.//Preston, A. 	Comparative genomic analyses of the Taylorellae.	Vet. Microbiol.	2012	159		195-203			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. 		
@D	Hausmann, B.//Pjevac, P.//Schreck, K.//Herbold, C.W.//Daims, H.//Wagner, M.//Loy, A. 	Draft Genome Sequence of Telmatospirillum siberiense 26-4b1, an Acidotolerant Peatland Alphaproteobacterium Potentially Involved in Sulfur Cycling.	Genome Announcements	2018	6		e01524-17			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. 		
@D	Hausmann, R.//Gold, M. 	The enzymatic methylation of ribonucleic acid and deoxyribonucleic acid.	J. Biol. Chem.	1966	241		1985-1994			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. 		
@D	Hausner, G.//Iranpour, M.//Kim, J.-J.//Breuil, C.//Davis, C.N.//Gibb, E.A.//Reid, J.//Loewen, P.C.//Hopkin, A.A. 	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.	Can. J. Bot.	2005	83		1222-1237			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. 		
@D	Havelaar, K.J.//Korsuize, J. 	Differences in susceptibility to restriction by E. coli B between various heteroduplex molecules of bacteriophage FD DNA.	Mol. Biol. Rep.	1974	1		453-455			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. 		
@D	Havelsrud, O.E.//Sorum, H.//Gaustad, P. 	Genome Sequences of Corynebacterium pseudotuberculosis Strains 48252 (Human, Pneumonia), CS_10 (Lab Strain), Ft_2193/67 (Goat, Pus), and CCUG 27541.	Genome Announcements	2014	2		e00869-14			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. 		
@D	Hawkey, J.//Edwards, D.J.//Dimovski, K.//Hiley, L.//Billman-Jacobe, H.//Hogg, G.//Holt, K.E. 	Evidence of microevolution of Salmonella Typhimurium during a series of egg-associated outbreaks linked to a single chicken farm.	BMC Genomics	2013	14		800			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. 		
@D	Hawtrey, A.O.//Ariatti, M. 	A possible model for the methylation of deoxycytidine in DNA.	Med. Hypotheses	1984	15		125-134			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. 		
@D	Hayakawa, T.//Ono, A.//Ueda, T. 	Synthesis of decadeoxyribonucleotides containing 5-modified uracils and their interactions with restriction endonucleases BglII, Sau3AI and MboI (Nucleosides and Nucleotides 82).	Nucleic Acids Res.	1988	16		4761-4776			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. 		
@D	Hayano-Kanashiro, C.//Lopez-Arredondo, D.L.//Cruz-Morales, P.//Alcaraz, L.D.//Olmedo, G.//Barona-Gomez, F.//Herrera-Estrella, L. 	First draft genome sequence of a strain from the genus citricoccus.	J. Bacteriol.	2011	193		6092-6093			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. 		
@D	Hayashi, K.//Morooka, N.//Yamamoto, Y.//Fujita, K.//Isono, K.//Choi, S.//Ohtsubo, E.//Baba, T.//Wanner, B.L.//Mori, H.//Horiuchi, T. 	Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110.	Mol. Syst. Biol.	2006	2		2006.0007			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. 		
@D	Hayashi, T. et al. 	Complete genome sequence of Enterohemorrhagic Escherichia coli O157:H7 and genomic comparison with a laboratory strain K-12.	DNA Res.	2001	8		11-22			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. 		
@D	Hayashi, T.//Kamio, Y.//Hishinuma, F.//Usami, Y.//Titani, K.//Terawaki, Y. 	Pseudomonas aeruginosa cytotoxin: the nucleotide sequence of the gene and the mechanism of activation of the protoxin.	Mol. Microbiol.	1989	3		861-868			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. 		
@D	Hayashimoto, N.//Morita, H.//Inoue, T.//Yasuda, M.//Yamamoto, M.//Itoh, T. 	Draft Genome Sequence of Enteropathogenic Escherichia coli, Isolated from the Bloody Stool Sample of a Common Marmoset (Callithrix jacchus).	Genome Announcements	2015	3		e01161-15			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. 		
@D	Hayatsu, M.//Tago, K.//Uchiyama, I.//Toyoda, A.//Wang, Y.//Shimomura, Y.//Okubo, T.//Kurisu, F.//Hirono, Y.//Nonaka, K.//Akiyama, H.//Itoh, T.//Takami, H. 	An acid-tolerant ammonia-oxidizing gamma-proteobacterium from soil.	ISME J.	2017	11		1130-1141			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. 		
@D	Hayden, H.S.//Gillett, W.//Saenphimmachak, C.//Lim, R.//Zhou, Y.//Jacobs, M.A.//Chang, J.//Rohmer, L.//D'Argenio, D.A.//Palmieri, A.//Levy, R.//Haugen, E.//Wong, G.K.//Brittnacher, M.J.//Burns, J.L.//Miller, S.I.//Olson, M.V.//Kaul, R. 	Large-insert genome analysis technology detects structural variation in Pseudomonas aeruginosa clinical strains from cystic fibrosis patients.	Genomics	2008	91		530-537			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. 		
@D	Hayes, M.M.//MacIntyre, A.M.//Allen, C. 	Complete Genome Sequences of the Plant Pathogens Ralstonia solanacearum Type Strain K60 and R. solanacearum Race 3 Biovar 2 Strain UW551.	Genome Announcements	2017	5		e01088-17			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. 		
@D	Hayrapetyan, H.//Boekhorst, J.//de Jong, A.//Kuipers, O.P.//Nierop, G.M.N.//Abee, T. 	Draft Whole-Genome Sequences of 11 Bacillus cereus Food Isolates.	Genome Announcements	2016	4		e00485-16			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. 		
@D	Hayward, G.S.//Frenkel, N.//Roizman, B. 	Anatomy of herpes simplex virus DNA: Strain differences and heterogeneity in the locations of restriction endonuclease cleavage sites.	Proc. Natl. Acad. Sci. U. S. A.	1975	72		1768-1772			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. 		
@D	Hazen, T.H.//Humphrys, M.S.//Ochieng, J.B.//Parsons, M.//Bopp, C.A.//O'Reilly, C.E.//Mintz, E.//Rasko, D.A. 	Draft Genome Sequences of Nine Enteropathogenic Escherichia coli Strains from Kenya.	Genome Announcements	2014	2		e00582-14			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. 		
@D	Hazen, T.H.//Mettus, R.T.//McElheny, C.L.//Bowler, S.L.//Doi, Y.//Rasko, D.A. 	Draft Genome Sequences of blaKPC-Containing Enterobacter aerogenes, Citrobacter freundii, and Citrobacter koseri Strains.	Genome Announcements	2018	6		e00035-18			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. 		
@D	Hazen, T.H.//Robinson, G.L.//Harris, A.D.//Rasko, D.A.//Johnson, J.K. 	Genome Sequence of Klebsiella oxytoca 11492-1, a Nosocomial Isolate Possessing a  FOX-5 AmpC beta-Lactamase.	J. Bacteriol.	2012	194		3028-3029			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. 		
@D	Hazen, T.H.//Sahl, J.W.//Fraser, C.M.//Donnenberg, M.S.//Scheutz, F.//Rasko, D.A. 	Draft Genome Sequences of Three O157 Enteropathogenic Escherichia coli Isolates.	Genome Announcements	2013	1		e00516-13			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. 		
@D	Hazen, T.H.//Sahl, J.W.//Redman, J.C.//Morris, C.R.//Daugherty, S.C.//Chibucos, M.C.//Sengamalay, N.A.//Fraser-Liggett, C.M.//Steinsland, H.//Whittam, T.S.//Whittam, B.//Manning, S.D.//Rasko, D.A. 	Draft Genome Sequences of the Diarrheagenic Escherichia coli Collection.	J. Bacteriol.	2012	194		3026-3027			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. 		
@D	Hazen, T.H.//Wu, D.//Eisen, J.A.//Sobecky, P.A. 	Sequence Characterization and Comparative Analysis of Three Plasmids Isolated from Environmental Vibrio spp.	Appl. Environ. Microbiol.	2007	73		7703-7710			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. 		
@D	He, H.//Deng, M.//He, J.//Weng, S. 	Structure and sequence analysis of cytosine DNA methyltransferase gene form infectious spleen and kidney necrosis virus.	Bingdu Xuebao	2001	17		349-355			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. 		
@D	He, J.//Shao, X.//Zheng, H.//Li, M.//Wang, S.//Zhang, Q.//Li, L.//Liu, Z.//Sun, M.//Wang, S.//Yu, Z. 	The Complete Genome Sequence of Bacillus thuringiensis Mutant Strain BMB171.	J. Bacteriol.	2010	192		4074-4075			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. 		
@D	He, J.//Sundararajan, A.//Devitt, N.P.//Schilkey, F.D.//Ramaraj, T.//Melancon, C.E.I.I.I. 	Complete Genome Sequence of Streptomyces venezuelae ATCC 15439, Producer of the Methymycin/Pikromycin Family of Macrolide Antibiotics, Using PacBio Technology.	Genome Announcements	2016	4		e00337-16			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. 		
@D	He, J.//Wang, J.//Yin, W.//Shao, X.//Zheng, H.//Li, M.//Zhao, Y.//Sun, M.//Wang, S.//Yu, Z. 	Complete Genome Sequence of Bacillus thuringiensis subsp. chinensis strain CT-43.	J. Bacteriol.	2011	193		3407-3408			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. 		
@D	He, J.G.//Deng, M.//Weng, S.P.//Li, Z.//Zhou, S.Y.//Long, Q.X.//Wang, X.Z.//Chan, S.M. 	Complete genome analysis of the mandarin fish infectious spleen and kidney necrosis iridovirus.	Virology	2001	291		126-139			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. 		
@D	He, M. et al. 	Evolutionary dynamics of Clostridium difficile over short and long time scales.	Proc. Natl. Acad. Sci. U. S. A.	2010	107		7527-7532			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. 		
@D	He, P.//Hao, K.//Blom, J.//Rueckert, C.//Vater, J.//Mao, Z.//Wu, Y.//Hou, M.//He, P.//He, Y.//Borriss, R. 	Genome sequence of the plant growth promoting strain Bacillus amyloliquefaciens subsp plantarum B9601-Y2 and expression of mersacidin and other secondary metabolites.	J. Biotechnol.	2012	164		281-291			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. 		
@D	He, X.//Hull, V.//Thomas, J.A.//Fu, X.//Gidwani, S.//Gupta, Y.K.//Black, L.W.//Xu, S.Y. 	Expression and purification of a single-chain Type IV restriction enzyme Eco94GmrSD and determination of its substrate preference.	Sci. Rep.	2015	5		9747			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. 		
@D	He, X.//Ou, H.Y.//Yu, Q.//Zhou, X.//Wu, J.//Liang, J.//Zhang, W.//Rajakumar, K.//Deng, Z. 	Analysis of a genomic island housing genes for DNA S-modification system in Streptomyces lividans 66 and its counterparts in other distantly related  bacteria.	Mol. Microbiol.	2007	65		1034-1048			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. 		
@D	He, Y.//Wei, K.//Si, K.//Mathieu, J.//Li, M.//Alvarez, P.J.J. 	Whole-Genome Sequence of the 1,4-Dioxane-Degrading Bacterium Mycobacterium dioxanotrophicus PH-06.	Genome Announcements	2017	5		e00625-17			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. 		
@D	He, Y.//Yan, X.//Reed, S.//Xie, Y.//Chen, C.Y.//Irwin, P. 	Complete Genome Sequence of Campylobacter jejuni YH001 from Beef Liver, Which Contains a Novel Plasmid.	Genome Announcements	2015	3		e01492-14			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. 		
@D	He, Z.//Crist, M.//Yen, H.-C.//Duan, X.//Quiocho, F.A.//Gimble, F.S. 	Amino acid residues in both the protein splicing and endonuclease domains of the PI-SceI intein mediate DNA binding.	J. Biol. Chem.	1998	273		4607-4615			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. 		
@D	He, Z.//Jiang, X.//Xue, J.//Zheng, W. 	Purification of BamHI DNA methylase and protection function of DNA methylation against restriction endonuclease BamHI.	Weishengwuxue Tongbao	1989	16		217-220			None 		
@D	Heard, E.//Fried, M. 	The use of 5-azacytidine to increase cleavage of methylation sensitive rare cutting restriction enzymes sites in amplified DNA.	Nucleic Acids Res.	1990	18		6147-6148			None 		
@D	Heath, P.J.//Stephens, K.M.//Monnat, R.J. Jr.//Stoddard, B.L. 	The structure of I-Crel, a group I intron-encoded homing endonuclease.	Nat. Struct. Biol.	1997	4		468-476			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. 		
@D	Heather, Z.//Holden, M.T.//Steward, K.F.//Parkhill, J.//Song, L.//Challis, G.L.//Robinson, C.//Davis-Poynter, N.//Waller, A.S. 	A novel streptococcal integrative conjugative element involved in iron acquisition.	Mol. Microbiol.	2008	70		1274-1292			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. 		
@D	Heaton, M.P.//Harhay, G.P.//Smith, T.P.//Bono, J.L.//Chitko-McKown, C.G. 	Complete Closed Genome Sequences of a Mannheimia haemolytica Serotype A1 Leukotoxin Deletion Mutant and Its Wild-Type Parent Strain.	Genome Announcements	2015	3		e00417-15			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. 		
@D	Heavens, D.//Tailford, L.E.//Crossman, L.//Jeffers, F.//Mackenzie, D.A.//Caccamo, M.//Juge, N. 	Genome sequence of the vertebrate gut symbiont Lactobacillus reuteri ATCC 53608.	J. Bacteriol.	2011	193		4015-4016			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. 		
@D	Hebert, E.M.//Raya, R.R.//Brown, L.//Font-de-Valdez, G.//Savoy-de-Giori, G.//Taranto, M.P. 	Genome Sequence of the Cheese-Starter Strain Lactobacillus delbrueckii subsp. lactis CRL 581.	Genome Announcements	2013	1		e00602-13			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. 		
@D	Hebert, E.M.//Saavedra, L.//Taranto, M.P.//Mozzi, F.//Magni, C.//Nader, M.E.//Font-de-Valdez, G.//Sesma, F.//Vignolo, G.//Raya, R.R. 	Genome Sequence of the Bacteriocin-Producing Lactobacillus curvatus Strain CRL705.	J. Bacteriol.	2012	194		538-539			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%). 		
@D	Hebert, L.//Moumen, B.//Duquesne, F.//Breuil, M.F.//Laugier, C.//Batto, J.M.//Renault, P.//Petry, S. 	Genome sequence of Taylorella equigenitalis MCE9, the causative agent of contagious equine metritis.	J. Bacteriol.	2011	193		1785			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. 		
@D	Hebert, L.//Touzain, F.//de Boisseson, C.//Breuil, M.F.//Duquesne, F.//Laugier, C.//Blanchard, Y.//Petry, S. 	Draft Genome Sequence of Taylorella equigenitalis Strain MCE529, Isolated from a  Belgian Warmblood Horse.	Genome Announcements	2014	2		e01214-14			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. 		
@D	Hedges, R.W. 	Phenotypic characterization of fi- R factors determining the restriction and modification hspII specificity.	Mol. Gen. Genet.	1972	115		225-233			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. 		
@D	Hedges, R.W.//Datta, N. 	R124, an fi+ R factor of a new compatibility class.	J. Gen. Microbiol.	1972	71		403-405			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. 		
@D	Hedgpeth, J.//Boyer, H.W. 	Hydrolysis of adenosine triphosphate accompanying interaction between Escherichia coli B restriction endonuclease and unmodified deoxyribonucleic acid.	Biochim. Biophys. Acta	1973	331		310-317			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. 		
@D	Hedgpeth, J.//Goodman, H.M.//Boyer, H.W. 	DNA nucleotide sequence restricted by the RI Endonuclease.	Proc. Natl. Acad. Sci. U. S. A.	1972	69		3448-3452			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. 		
@D	Hedlund, B.P. et al. 	High-Quality Draft Genome Sequence of Kallotenue papyrolyticum JKG1T Reveals Broad Heterotrophic Capacity Focused on Carbohydrate and Amino Acid Metabolism.	Genome Announcements	2015	3		e01410-15			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. 		
@D	Hegna, I.K.//Bratland, H.//Kolsto, A. 	BceS1, a new addition to the type III restriction and modification family.	FEMS Microbiol. Lett.	2001	202		189-193			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. 		
@D	Hegna, I.K.//Karlstrom, E.S.//Lopez, R.//Kristensen, T.//Kolsto, A.-B. 	A type-II DNA restriction and modification system in Bacillus cereus?	Gene	1992	114		149-150			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. 		
@D	Hehlmann, R.//Hattman, S. 	Mutants of bacteriophage T2 gt with altered DNA methylase activity.	J. Mol. Biol.	1972	67		351-360			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. 		
@D	Heidelberg, J.F. et al. 	DNA sequence of both chromosomes of the cholera pathogen Vibrio cholerae.	Nature	2000	406		477-483			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. 		
@D	Heidelberg, J.F. et al. 	Genome sequence of the dissimilatory metal ion-reducing bacterium Shewanella oneidensis.	Nat. Biotechnol.	2002	20		1118-1123			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. 		
@D	Heidmann, S.//Seifert, W.//Kessler, C.//Domdey, H. 	Cloning, characterization and heterologous expression of the SmaI restriction-modification system.	Nucleic Acids Res.	1989	17		9783-9796			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. 		
@D	Heikal, A.//Samuelsen, O.//Kristensen, T.//Okstad, O.A. 	Complete Genome Sequence of a Multidrug-Resistant, blaNDM-1-Expressing Klebsiella pneumoniae K66-45 Clinical Isolate from Norway.	Genome Announcements	2017	5		e00601-17			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. 		
@D	Heil, J.R.//Lynch, M.D.J.//Cheng, J.//Matysiakiewicz, O.//D'Alessio, M.//Charles, T.C. 	The Completed PacBio Single-Molecule Real-Time Sequence of Methylosinus trichosporium Strain OB3b Reveals the Presence of a Third Large Plasmid.	Genome Announcements	2017	5		e01349-17			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. 		
@D	Heininger, K.//Horz, W.//Zachau, H.G. 	Specificity of cleavage by a restriction nuclease from Bacillus subtilis.	Gene	1977	1		291-303			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. 		
@D	Heinl, S.//Wibberg, D.//Eikmeyer, F.//Szczepanowski, R.//Blom, J.//Linke, B.//Goesmann, A.//Grabherr, R.//Schwab, H.//Puhler, A.//Schluter, A. 	Insights into the completely annotated genome of Lactobacillus buchneri CD034, a strain isolated from stable grass silage.	J. Biotechnol.	2012	161		153-166			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. 		
@D	Heinle, C.E. et al. 	Complete Genome Sequence of Lelliottia nimipressuralis Type Strain SGAir0187, Isolated from Tropical Air Collected in Singapore.	Genome Announcements	2018	6		e00231-18			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. 		
@D	Heinsch, S.C.//Otto-Hanson, L.//Hsu, S.Y.//Kinkel, L.//Smanski, M.J. 	Genome Sequences for Streptomyces spp. Isolated from Disease-Suppressive Soils and Long-Term Ecological Research Sites.	Genome Announcements	2017	5		e00493-17			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). 		
@D	Heintschel von Heinegg, E.//Nalik, H.P.//Schmid, E.N. 	Characterisation of a Helicobacter pylori phage (HP1).	J. Med. Microbiol.	1993	38		245-249			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. 		
@D	Heinze, R.J.//Giron-Monzon, L.//Solovyova, A.//Elliot, S.L.//Geisler, S.//Cupples, C.G.//Connolly, B.A.//Friedhoff, P. 	Physical and functional interactions between Escherichia coli MutL and the Vsr repair endonuclease.	Nucleic Acids Res.	2009	37		4453-4463			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. 		
@D	Heip, J.//Rolfe, B.//Schell, J. 	Abolition of host cell restriction by high multiplicity of phage infection.	Virology	1974	59		356-370			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. 		
@D	Heiter, D.F.//Lunnen, K.D.//Wilson, G.G. 	Site-specific DNA-nicking mutants of the heterodimeric restriction endonuclease R.BbvCI.	J. Mol. Biol.	2005	348		631-640			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. 		
@D	Heithoff, D.M.//Enioutina, E.Y.//Daynes, R.A.//Sinsheimer, R.L.//Low, D.A.//Mahan, M.J. 	Salmonella DNA adenine methylase mutants confer cross-protective immunity.	Infect. Immun.	2001	69		6725-6730			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. 		
@D	Heithoff, D.M.//House, J.K.//Thomson, P.C.//Mahan, M.J. 	Development of a Salmonella cross-protective vaccine for food animal production systems.	Vaccine	2015	33		100-107			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. 		
@D	Heithoff, D.M.//Julio, S.M.//Mahan, M.J. 	Regulation of bacterial virulence by DNA methylation.	Abstr. Gen. Meet. Am. Soc. Microbiol.	2002	102		73			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. 		
@D	Heithoff, D.M.//Julio, S.M.//Mahan, M.J. 	The role of DNA adenine methylation in controlling bacterial virulence.	Abstr. Gen. Meet. Am. Soc. Microbiol.	2001	101		59			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. 		
@D	Heithoff, D.M.//Sinsheimer, R.L.//Low, D.A.//Mahan, M.J. 	In vivo gene expression and the adaptive response: From pathogenesis to vaccines and antimicrobials.	Philos. Trans. R. Soc. Lond. B. Biol. Sci.	2000	355		633-642			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. 		
@D	Heithoff, D.M.//Sinsheimer, R.L.//Low, D.A.//Mahan, M.J. 	An essential role for DNA adenine methylation in bacterial virulence.	Science	1999	284		967-970			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. 		
@D	Heitman, J. 	How the EcoRI endonuclese recognizes and cleaves DNA.	Bioessays	1992	14		445-454			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. 		
@D	Heitman, J. 	On the repair of DNA breaks and the specificity of the EcoRI restriction enzyme.	Ph.D. Thesis, Rockefeller University, NY, USA	1989			1-209			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. 		
@A	Heitman, J. 		On the origins, structures and functions of restriction-modification enzymes.			Setlow, J.K. 		Genet. Eng. (N Y)				New York	Plenum Press	1993		15		57-108									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. 		
@D	Heitman, J.//Fulford, W.//Model, P. 	Phage Trojan horses: a conditional expression system for lethal genes.	Gene	1989	85		193-197			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. 		
@D	Heitman, J.//Ivanenko, T.//Kiss, A. 	DNA nicks inflicted by restriction endonucleases are repaired by a RecA- and RecB-dependent pathway in Escherichia coli.	Mol. Microbiol.	1999	33		1141-1151			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. 		
@D	Heitman, J.//Model, P. 	Site-specific methylases induce the SOS DNA repair response in Escherichia coli.	J. Bacteriol.	1987	169		3243-3250			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). 		
@D	Heitman, J.//Model, P. 	Substrate recognition by the EcoRI endonuclease.	Proteins	1990	7		185-197			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. 		
@D	Heitman, J.//Model, P. 	Mutants of the EcoRI endonuclease with promiscuous substrate specificity implicate residues involved in substrate recognition.	EMBO J.	1990	9		3369-3378			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. 		
@D	Heitman, J.//Model, P. 	SOS induction as an in vivo assay of enzyme-DNA interactions.	Gene	1991	103		1-9			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. 		
@D	Heitman, J.//Zinder, N.D.//Model, P. 	Repair of the Escherichia coli chromosome after in vivo scission by the EcoRI endonuclease.	Proc. Natl. Acad. Sci. U. S. A.	1989	86		2281-2285			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. 		
@D	Heitman, J.B. 	On the repair of DNA breaks and the specificity of the EcoRI restriction enzyme.	Diss. Abstr.	1990	51		562B			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. 		
@D	Hejnova, J.//Dobrindt, U.//Nemcova, R.//Rusniok, C.//Bomba, A.//Frangeul, L.//Hacker, J.//Glaser, P.//Sebo, P.//Buchrieser, C. 	Characterization of the flexible genome complement of the commensal Escherichia coli strain A0 34/86 (O83 : K24 : H31).	Microbiology	2005	151		385-398			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. 		
@D	Helene, C. 	Sequence-selective recognition and cleavage of double-helical DNA.	Curr. Opin. Biotechnol.	1993	4		29-36			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. 		
@D	Helene, L.C.//Gomes, D.F.//Delamuta, J.R.//Ribeiro, R.A.//Souza, R.C.//Almeida, L.G.//Vasconcelos, A.T.//Hungria, M. 	Genome Sequence of Bradyrhizobium viridifuturi Strain SEMIA 690T, a Nitrogen-Fixing Symbiont of Centrosema pubescens.	Genome Announcements	2015	3		e01481-15			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. 		
@D	Helene, L.C.F.//Ribeiro, R.A.//Hungria, M. 	Genome Sequence of Rhizobium esperanzae Type Strain CNPSo 668, Isolated from Phaseolus vulgaris Nodules in Mexico.	Genome Announcements	2017	5		e00935-17			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. 		
@D	Helling, R.B.//Goodman, H.M.//Boyer, H.W. 	Analysis of endonuclease R EcoRI fragments of DNA from lambdoid bacteriophages and other viruses by agarose-gel electrophoresis.	J. Virol.	1974	14		1235-1243			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. 		
@D	Hemavathy, K.C.//Nagaraja, V. 	DNA methylation in mycobacteria: absence of methylation at GATC (Dam) and CCA/TGG (Dcm) sequences.	FEMS Immunol Med Microbiol	1995	11		291-296			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. 		
@D	Hemeon, I.//Gutierrez, J.A.//Ho, M.-C.//Schramm, V.L. 	Characterizing DNA methyltransferases with an ultrasensitive luciferase-linked continuous assay.	Anal. Chem.	2011	83		4996-5004			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. 		
@D	Hemme, C.L. et al. 	Sequencing of multiple clostridial genomes related to biomass conversion and biofuel production.	J. Bacteriol.	2010	192		6494-6496			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. 		
@D	Hemp, J.//Ward, L.M.//Pace, L.A.//Fischer, W.W. 	Draft Genome Sequence of Levilinea saccharolytica KIBI-1, a Member of the Chloroflexi Class Anaerolineae.	Genome Announcements	2015	3		e01357-15			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. 		
@D	Hemp, J.//Ward, L.M.//Pace, L.A.//Fischer, W.W. 	Draft Genome Sequence of Ornatilinea apprima P3M-1, an Anaerobic Member of the Chloroflexi Class Anaerolineae.	Genome Announcements	2015	3		e01353-15			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. 		
@D	Hemp, J.//Ward, L.M.//Pace, L.A.//Fischer, W.W. 	Draft Genome Sequence of Ardenticatena maritima 110S, a Thermophilic Nitrate- and Iron-Reducing Member of the Chloroflexi Class Ardenticatenia.	Genome Announcements	2015	3		e01347-15			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. 		
@D	Henaut, A.//Rouxel, T.//Gleizes, A.//Moszer, I.//Danchin, A. 	Uneven distribution of GATC motifs in the Escherichia coli chromosome, its plasmids and its phages.	J. Mol. Biol.	1996	257		574-585			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. 		
@D	Henderson, I.R.//Deleris, A.//Wong, W.//Zhong, X.H.//Chin, H.G.//Horwitz, G.A.//Kelly, K.A.//Pradhan, S.//Jacobsen, S.E. 	The De Novo Cytosine Methyltransferase DRM2 Requires Intact UBA Domains and a Catalytically Mutated Paralog DRM3 during RNA-Directed DNA Methylation in Arabidopsis thaliana.	PLoS Genet.	2010	6		e1001182			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. 		
@D	Hendrich, B.//Bird, A. 	Mammalian methyltransferases and methyl-CpG-binding domains: proteins involved in DNA methylation.	Curr. Top. Microbiol. Immunol.	2000	249		55-74			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. 		
@D	Hendrich, B.//Bird, A. 	Identification and characterization of a family of mammalian methyl-CpG binding proteins.	Mol. Cell. Biol.	1998	18		6538-6547			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. 		
@D	Hendrickson, E.L. et al. 	Complete genome sequence of the genetically tractable hydrogenotrophic methanogen Methanococcus maripaludis.	J. Bacteriol.	2004	186		6956			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. 		
@D	Hendrix, J.//Read, T.//Lalonde, J.-F.//Jensen, P.K.//Heymann, W.//Lovelace, E.//Zimmermann, S.A.//Brasino, M.//Rokicki, J.//Dowell, R.D. 	Engineered Calcium-Precipitable Restriction Enzyme.	ACS Synth. Biol.	2014	3		969-971			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. 		
@D	Hendrix, J.D.//Welker, N.E. 	Isolation of a Bacillus stearothermophilus mutant exhibiting increased thermostability in its restriction endonuclease.	J. Bacteriol.	1985	162		682-692			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. 		
@D	Hendrix, R.W.//Ko, C.C.//Jacobs-Sera, D.//Hatfull, G.F.//Erhardt, M.//Hughes, K.T.//Casjens, S.R. 	Genome Sequence of Salmonella Phage chi.	Genome Announcements	2015	3		e01229-14			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. 		
@D	Hendrix, R.W.//Smith, M.C.M.//Burns, R.N.//Ford, M.E.//Hatfull, G.F. 	Evolutionary relationships among diverse bacteriophages and prophages: All the world's a phage.	Proc. Natl. Acad. Sci. U. S. A.	1999	96		2192-2197			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. 		
@D	Heng, N.C.//Haji-Ishak, N.S.//Kalyan, A.//Wong, A.Y.//Lovric, M.//Bridson, J.M.//Artamonova, J.//Stanton, J.A.//Wescombe, P.A.//Burton, J.P.//Cullinan, M.P.//Tagg, J.R. 	Genome Sequence of the Bacteriocin-Producing Oral Probiotic Streptococcus salivarius Strain M18.	J. Bacteriol.	2011	193		6402-6403			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. 		
@D	Heng, N.C.//Yeh, C.W.//Malik, A. 	Draft Genome Sequence of Weissella confusa MBF8-1, a Glucansucrase- and Bacteriocin-Producing Strain Isolated from a Homemade Soy Product.	Genome Announcements	2017	5		e01497-16			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. 		
@D	Henikoff, S.//Comai, L. 	A DNA methyltransferase homolog with a chromodomain exists in multiple polymorphic forms in Arabidopsis.	Genetics	1998	149		307-318			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. 		
@D	Henke, R.M. 	Molecular and biochemical studies on a bifunctional group I intron encoded protein of yeast mitochondria.	Diss. Abstr.	2000	61		2899			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. 		
@D	Henke, R.M.//Butow, R.A.//Perlman, P.S. 	Maturase and endonuclease functions depend on separate conserved domains of the bifunctional protein encoded by the group I intron aI4a of yeast mitochondrial DNA.	EMBO J.	1995	14		5094-5099			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. 		
@D	Henkel, C.V.//den Dulk-Ras, A.//Zhang, X.//Hooykaas, P.J. 	Genome Sequence of the Octopine-Type Agrobacterium tumefaciens Strain Ach5.	Genome Announcements	2014	2		e00225-14			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. 		
@D	Henkin, T.M. 	Classic spotlight: Bacteria versus phage--the Battle Rages!	J. Bacteriol.	2016	198		1007			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). 		
@D	Hennecke, F.//Kolmar, H.//Brundl, K.//Fritz, H.-J. 	The vsr gene product of E. coli K-12 is a strand- and sequence-specific DNA mismatch endonuclease.	Nature	1991	253		776-778			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. 		
@D	Hennessy, R.C.//Glaring, M.A.//Michelsen, C.F.//Olsson, S.//Stougaard, P. 	Draft Genome Sequence of Pseudomonas sp. Strain In5 Isolated from a Greenlandic Disease Suppressive Soil with Potent Antimicrobial Activity.	Genome Announcements	2015	3		e01251-15			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. 		
@D	Henriques, A.C.//De Marco, P. 	Genome Sequence of Rhodococcus sp. Strain RD6.2 DSM 46800, a Methanesulfonate-Degrading Strain.	Genome Announcements	2015	3		e00730-15			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). 		
@D	Henriques, A.C.//De Marco, P. 	Complete Genome Sequences of Two Strains of 'Candidatus Filomicrobium marinum,' a Methanesulfonate-Degrading Species.	Genome Announcements	2015	3		e00160-15			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. 		
@D	Henriques, A.O.//Beall, B.W.//Roland, K.//Moran, C.P. Jr. 	Characterization of cotJ, a sigma E-controlled operon affecting the polypeptide composition of the coat of Bacillus subtilis spores.	J. Bacteriol.	1995	177		3394-3406			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. 		
@D	Henriques, I.//Juca, R.R.T.//Barauna, R.A.//de Sa, P.H.//Marinho, A.D.//Carneiro, A.R.//Barbosa, S.//Pereira, A.//Alves, A.//Saavedra, M.J.//Egas, C.//Silva, A.//Correia, A. 	Draft Genome Sequence of Serratia fonticola UTAD54, a Carbapenem-Resistant Strain Isolated from Drinking Water.	Genome Announcements	2013	1		e00970-13			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. 		
@D	Henry, P.M.//Leveau, J.H. 	Finished Genome Sequences of Xanthomonas fragariae, the Cause of Bacterial Angular Leaf Spot of Strawberry.	Genome Announcements	2016	4		e01271-16			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. 		
@D	Hensgens, L.A.M.//Bonen, L.//de Haan, M.//van der Horst, G.//Grivell, L.A. 	Two intron sequences in yeast mitochondrial COX1 gene:  homology among URF-containing introns and strain-dependent variation in flanking exons.	Cell	1983	32		379-389			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. 		
@D	Hensley, P.//Nardone, G.//Chirikjian, J.G.//Wastney, M.E. 	The time-resolved kinetics of superhelical DNA cleavage by BamHI restriction endonuclease.	J. Biol. Chem.	1990	265		15300-15307			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. 		
@D	Hentosh, P.//McCastlain, J.C. 	Effects of 2-chloroadenine substitution in DNA on restriction endonuclease cleavage reactions.	Nucleic Acids Res.	1991	19		3143-3148			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. 		
@D	Hepburn, P.A.//Margison, G.P.//Tisdale, M.J. 	Enzymatic methylation of cytosine in DNA is prevented by adjacent 06-methylguanine residues.	J. Biol. Chem.	1991	266		7985-7987			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. 		
@D	Hepburn, P.A.//Tisdale, M.J. 	Importance of the O6 position of guanine residues in the binding of DNA methylase to DNA.	Biochim. Biophys. Acta	1991	1088		341-344			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. 		
@D	Hepworth, P.J.//Ashelford, K.E.//Hinds, J.//Gould, K.A.//Witney, A.A.//Williams, N.J.//Leatherbarrow, H.//French, N.P.//Birtles, R.J.//Mendonca, C.//Dorrell, N.//Wren, B.W.//Wigley, P.//Hall, N.//Winstanley, C. 	Genomic variations define divergence of water/wildlife-associated Campylobacter jejuni niche specialists from common clonal complexes.	Environ. Microbiol.	2011	13		1549-1560			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. 		
@D	Herbert, J.A.//Mitchell, A.M.//Ritchie, R.//Ma, J.//Ross-Hutchinson, K.//Mitchell, T.J. 	Expression of the lux genes in Streptococcus pneumoniae modulates pilus expression and virulence.	PLoS ONE	2018	13		e0189426			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. 		
@D	Herbert, M.//O'Keeffe, T.A.//Purdy, D.//Elmore, M.//Minton, N.P. 	Gene transfer into Clostridium difficile CD630 and characterisation of its methylase genes.	FEMS Microbiol. Lett.	2003	229		103-110			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. 		
@D	Herd, M.//Kocks, C. 	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.	Infect. Immun.	2001	69		3972-3979			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. 		
@D	Herman, G.E.//Modrich, P. 	Escherichia coli K-12 clones that overproduce dam methylase are hypermutable.	J. Bacteriol.	1981	145		644-646			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. 		
@D	Herman, G.E.//Modrich, P. 	Escherichia coli dam methylase physical and catalytic properties of the homogeneous enzyme.	J. Biol. Chem.	1982	257		2605-2612			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. 		
@D	Herman, J.//Nelkin, B.//Mabry, M.//Wilson, G.//Baylin, S. 	Introduction and expression of HhaI DNA methyltransferase in eukaryotic cells.	J. Cell Biochem. Suppl.	1989	13D		223			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. 		
@D	Herman, J.//Nelkin, B.//Mabry, M.//Wilson, G.//Baylin, S. 	Introduction of prokaryotic HhaI DNA methyltransferase alters the phenotype of 3T3 cells.	Proc. Amer. Assoc. Cancer Res.	1989	30		428			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. 		
@D	Hermann, A.//Fatemi, M.//Jeltsch, A. 	Molecular enzymology of the Dnmt1 DNA methyltransferase explains the mechanism of cis-spreading of DNA methylation.	Biochem. Soc. Trans.	2000	28		A248			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. 		
@D	Hermann, A.//Gowher, H.//Jeltsch, A. 	Biochemistry and biology of mammalian DNA methyltransferases.	Cell. Mol. Life Sci.	2004	61		2571-2587			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. 		
@D	Hermann, A.//Goyal, R.//Jeltsch, A. 	The Dnmt1 DNA-(cytosine-C5)-methyltransferase methylates DNA processively with high preference for hemimethylated target sites.	J. Biol. Chem.	2004	279		48350-48359			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. 		
@D	Hermann, A.//Jeltsch, A. 	Methylation sensitivity of restriction enzymes interacting with GATC sites.	Biotechniques	2003	34		924-930			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. 		
@D	Hermann, A.//Schmitt, S.//Jeltsch, A. 	The human Dnmt2 has residual DNA-(cytosine-C5)-methyltransferase activity.	J. Biol. Chem.	2003	278		31717-31721			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. 		
@D	Hernandez, D.//Seidl, K.//Corvaglia, A.R.//Bayer, A.S.//Xiong, Y.Q.//Francois, P. 	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.	Genome Announcements	2014	2		e00174-14			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. 		
@D	Hernandez, D.//van der Mee-Marquet, N.//Kluytmans, J.//Donnio, P.Y.//Quentin, R.//Corvaglia, A.R.//Francois, P. 	Whole-Genome Sequences of Staphylococcus aureus ST398 Strains of Animal Origin.	Genome Announcements	2013	1		e00689-13			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. 		
@D	Hernandez, I.//Fernandez, C. 	Draft Genome Sequence and Assembly of a Lysobacter enzymogenes Strain with Biological Control Activity against Root Knot Nematodes.	Genome Announcements	2017	5		e00271-17			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. 		
@D	Hernandez-Gonzalez, I.L.//Olmedo-Alvarez, G. 	Draft Whole-Genome Sequence of the Type Strain Bacillus aquimaris TF12T.	Genome Announcements	2016	4		e00640-16			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. 		
@D	Hernandez-Gonzalez, I.L.//Olmedo-Alvarez, G. 	Draft Whole-Genome Sequence of the Type Strain Bacillus horikoshii DSM 8719.	Genome Announcements	2016	4		e00641-16			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. 		
@D	Hernandez-Maldonado, J.//Stoneburner, B.//Boren, A.//Miller, L.//Rosen, M.//Oremland, R.S.//Saltikov, C.W. 	Genome Sequence of the Photoarsenotrophic Bacterium Ectothiorhodospira sp. Strain BSL-9, Isolated from a Hypersaline Alkaline Arsenic-Rich Extreme Environment.	Genome Announcements	2016	4		e01139-16			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. 		
@D	Hernandez-Mendoza, A.//Lozano-Aguirre, B.L.F.//Martinez-Ocampo, F.//Quiroz-Castaneda, R.E.//Dantan-Gonzalez, E. 	A Newly Sequenced Alcaligenes faecalis Strain: Implications for Novel Temporal Symbiotic Relationships.	Genome Announcements	2014	2		e01246-14			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. 		
@D	Hernandez-Mendoza, A.//Martinez-Ocampo, F.//Lozano-Aguirre, B.L.F.//Popoca-Ursino, E.C.//Ortiz-Hernandez, L.//Sanchez-Salinas, E.//Dantan-Gonzalez, E. 	Draft Genome Sequence of the Organophosphorus Compound-Degrading Burkholderia zhejiangensis Strain CEIB S4-3.	Genome Announcements	2014	2		e01323-14			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. 		
@D	Hernandez-Salmeron, J.E.//Hernandez-Leon, R.//Orozco-Mosqueda, M.C.//Valencia-Cantero, E.//Moreno-Hagelsieb, G.//Santoyo, G. 	Draft Genome Sequence of the Biocontrol and Plant Growth-Promoting Rhizobacterium Pseudomonas fluorescens strain UM270.	Standards in Genomic Sciences	2016	11		5			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. 		
@D	Hernandez-Santana, A.//Gomez-Garzon, C.//Dussan, J. 	Complete Genome Sequence of Lysinibacillus sphaericus WHO Reference Strain 2362.	Genome Announcements	2016	4		e00545-16			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. 		
@D	Herren, C.D. et al. 	Genome Sequences of Four Subcluster L2 Mycobacterium Phages, Finemlucis, Miley16, Wilder, and Zakai.	Genome Announcements	2017	5		e01233-17			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. 		
@D	Herrin, D.L.//Chen, Y.-F.//Schmidt, G.W. 	RNA splicing in Chlamydomonas chloroplasts.	J. Biol. Chem.	1990	265		21134-21140			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. 		
@D	Herschend, J.//Raghupathi, P.K.//Roder, H.L.//Sorensen, S.J.//Burmolle, M. 	Draft Genome Sequences of Two Kocuria Isolates, K. salsicia G1 and K. rhizophila  G2, Isolated from a Slaughterhouse in Denmark.	Genome Announcements	2016	4		e00075-16			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. 		
@D	Herschend, J.//Raghupathi, P.K.//Roder, H.L.//Sorensen, S.J.//Burmolle, M. 	Genome Sequence of Kocuria palustris Strain W4.	Genome Announcements	2016	4		e00074-16			We report the 3.09 Mb draft genome sequence ofKocuria palustrisW4, isolated from  a slaughterhouse in Denmark. 		
@D	Herschend, J.//Raghupathi, P.K.//Roder, H.L.//Sorensen, S.J.//Burmolle, M. 	Genome Sequence of Arthrobacter antarcticus Strain W2, Isolated from a Slaughterhouse.	Genome Announcements	2016	4		e00073-16			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. 		
@D	Hersemann, L.//Wibberg, D.//Blom, J.//Widmer, F.//Kolliker, R. 	Draft Genome Sequence of the Xanthomonas bromi Type Strain LMG 947.	Genome Announcements	2016	4		e00961-16			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. 		
@D	Hersemann, L.//Wibberg, D.//Widmer, F.//Vorholter, F.J.//Kolliker, R. 	Draft genome sequences of three Xanthomonas translucens pathovar reference strains (pv. arrhenatheri, pv. poae and pv. phlei) with different specificities  for forage grasses.	Standards in Genomic Sciences	2016	11		50			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. 		
@D	Hertwig, S.//Klein, I.//Schmidt, V.//Beck, S.//Hammerl, J.A.//Appel, B. 	Sequence analysis of the genome of the temperate Yersinia enterocolitica phage PY54.	J. Mol. Biol.	2003	331		605-622			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. 		
@D	Hess, J.F.//FitzGerald, P.G. 	Protection of a restriction enzyme from heat inactivation by alpha-crystallin.	Mol. Vis.	1998	4		29-32			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. 		
@D	Heuer, H.//Kopmann, C.//Binh, C.T.//Top, E.M.//Smalla, K. 	Spreading antibiotic resistance through spread manure: characteristics of a novel plasmid type with low %G+C content.	Environ. Microbiol.	2009	11		937-949			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. 		
@D	Heuer, H.//Szczepanowski, R.//Schneiker, S.//Puhler, A.//Top, E.M.//Schluter, A. 	The complete sequences of plasmids pB2 and pB3 provide evidence for a recent ancestor of the IncP-1{beta} group without any accessory genes.	Microbiology	2004	150		3591-3599			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. 		
@D	Heuermann, D.//Haas, R. 	A stable shuttle vector system for efficient genetic complementation of Helicobacter pylori strains by transformation and conjugation.	Mol. Gen. Genet.	1998	257		519-528			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. 		
@D	Heumann, W. 	Rhizobium lupini genetics.	Curr. Top. Microbiol. Immunol.	1979	88		1-24			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. 		
@D	Heurgue-Hamard, V.//Champ, S.//Engstrom, A.//Ehrenberg, M.//Buckingham, R.H. 	The hemK gene in Escherichia coli encodes the N5-glutamine methyltransferase that modifies peptide release factors.	EMBO J.	2002	21		769-778			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. 		
@D	Heusipp, G.//Falker, S.//Schmidt, M.A. 	DNA adenine methylation and bacterial pathogenesis.	Int. J. Med. Microbiol.	2007	297		1-7			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. 		
@D	Heylen, K.//De Vos, P.//Vekeman, B. 	Draft Genome Sequences of Eight Obligate Methane Oxidizers Occupying Distinct Niches Based on Their Nitrogen Metabolism.	Genome Announcements	2016	4		e00421-16			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. 		
@D	Heyrman, J.//Logan, N.A.//Busse, H.J.//Balcaen, A.//Lebbe, L.//Rodriguez-Diaz, M.//Swings, J.//De Vos, P. 	Virgibacillus carmonensis sp. nov., Virgibacillus necropolis sp. nov. and Virgibacillus picturae sp. nov.	Int. J. Syst. Evol. Microbiol.	2003	53		501-511			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. 		
@D	Hickman, A.B.//Li, Y.//Mathew, S.V.//May, E.W.//Craig, N.L.//Dyda, F. 	Unexpected structural diversity in DNA recombination: the restriction endonuclease connection.	Mol. Cell	2000	5		1025-1034			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. 		
@D	Hicks, M.R.//Rodger, A.//Thomas, C.M.//Batt, S.M.//Dafforn, T.R. 	Restriction enzyme kinetics monitored by UV linear dichroism.	Biochemistry	2006	45		8912-8917			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. 		
@D	Hien, L.-T.//Zatsepin, T.S.//Schierling, B.//Volkov, E.M.//Wende, W.//Pingoud, A.//Kubareva, E.A.//Oretskaya, T.S. 	Restriction Endonuclease SsoII with Photoregulated Activity: A 'Molecular Gate' Approach.	Bioconjugate Chem.	2011	22		1366-1373			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. 		
@D	Hiessl, S.//Schuldes, J.//Thurmer, A.//Halbsguth, T.//Broker, D.//Angelov, A.//Liebl, W.//Daniel, R.//Steinbuchel, A. 	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.	Appl. Environ. Microbiol.	2012	78		2874-2887			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. 		
@D	Hiett, K.//Meinersmann, R. 	Isolation of a putative retriction/modification system from Campylobacter jejuni.	Abstr. Gen. Meet. Am. Soc. Microbiol.	1994	94		224			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.
 
 		
@D	Higashide, M.//Kuroda, M.//Omura, C.T.//Kumano, M.//Ohkawa, S.//Ichimura, S.//Ohta, T. 	Methicillin-resistant Staphylococcus saprophyticus Carrying Staphylococcal Cassette Chromosome mec (SCCmec) Have Emerged in Urogenital Tract  Infections.	Antimicrob. Agents Chemother.	2008	52		2061-2068			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. 		
@D	Higashioka, Y.//Kojima, H.//Watanabe, T.//Fukui, M. 	Draft Genome Sequence of Desulfatitalea tepidiphila S28bFT.	Genome Announcements	2015	3		e01326-15			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. 		
@D	Higgins, D.L.//Sanozky-Dawes, R.//Klaenhammer, T.R. 	Characterization of a cointegrate conjugal plasmid encoding phage restriction and modification activities in lactic streptococci.	Abstr. Gen. Meet. Am. Soc. Microbiol.	1987	87		154			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. 		
@D	Higgins, D.L.//Sanozky-Dawes, R.B.//Klaenhammer, T.R. 	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.	J. Bacteriol.	1988	170		3435-3442			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. 		
@D	Higgins, L.S.//Besnier, C.//Kong, H. 	The nicking endonuclease N.BstNBI is closely related to Type IIs restriction endonucleases MlyI and PleI.	Nucleic Acids Res.	2001	29		2492-2501			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. 		
@D	Higgins, P.G.//Chan, J.Z.//Seifert, H.//Pallen, M.J.//Millard, A.D. 	Draft Genome Sequences of 11 Clinical Isolates of Acinetobacter baumannii.	Genome Announcements	2016	4		e00269-16			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. 		
@D	Higgins, P.G.//Koehler, D.//Chan, J.Z.//Cornely, O.A.//Fatkenheuer, G.//Gillis, M.//Pallen, M.J.//Tien, J.//Seifert, H.//Vehreschild, M.J.//Millard, A.D. 	Draft Genome Sequences of Nine Clinical Isolates of Vancomycin-Resistant Enterococci.	Genome Announcements	2016	4		e00803-16			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. 		
@D	Highlander, S.K. et al. 	Subtle genetic changes enhance virulence of methicillin resistant and sensitive Staphylococcus aureus.	BMC Microbiol.	2007	7		99			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. 		
@D	Highlander, S.K.//Garza, O. 	The restriction-modification system of Pasteurella haemolytica is a member of a new family of type I enzymes.	Gene	1996	178		89-96			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. 		
@D	Highlander, S.K.//Hang, V.T. 	A putative leucine zipper activator of Pasteurella haemolytica leukotoxin transcription and the potential for modulation of its synthesis by slipped-strand  mispairing.	Infect. Immun.	1997	65		3970-3975			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. 		
@D	Higuchi, Y.//Mori, K.//Suyama, A.//Huang, Y.//Tashiro, K.//Kuhara, S.//Takegawa, K. 	Draft Genome Sequence of Bacillus clausii AKU0647, a Strain That Produces Endo-beta-N-Acetylglucosaminidase A.	Genome Announcements	2016	4		e00310-16			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. 		
@D	Higuera, G.//Gonzalez-Escalona, N.//Veliz, C.//Vera, F.//Romero, J. 	Draft Genome Sequences of Four Xanthomonas arboricola pv. juglandis Strains Associated with Walnut Blight in Chile.	Genome Announcements	2015	3		e01160-15			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. 		
@D	Hikida, Y.//Kimoto, M.//Hirao, I.//Yokoyama, S. 	Crystal structure of Deep Vent DNA polymerase.	Biochem. Biophys. Res. Commun.	2017	483		52-57			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. 		
@D	Hikima, J.//Sakai, M.//Aoki, T.//Takeyama, H.//Hawke, J.//Mori, K.//Tashiro, K.//Kuhara, S. 	Draft Genome Sequence of the Fish Pathogen Mycobacterium pseudoshottsii Strain JCM15466, a Species Closely Related to M. marinum.	Genome Announcements	2016	4		e01630-15			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. 		
@D	Hilbert, H.//Himmelreich, R.//Plagens, H.//Herrmann, R. 	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.	Nucleic Acids Res.	1996	24		628-639			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. 		
@D	Hill, A.E.//Lainson, F.A. 	Survey of restriction-modification systems and transformation in Mannheimia haemolytica and Pasteurella trehalosi.	Vet. Microbiol.	2003	92		103-109			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. 		
@D	Hill, C. 	Bacteriophage and bacteriophage resistance in lactic acid bacteria.	FEMS Microbiol. Rev.	1993	12		87-108			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. 		
@D	Hill, C.//Garvey, P.//Fitzgerald, G.F. 	Bacteriophage-host interactions and resistance mechanisms, analysis of the conjugative bacteriophage resistance plasmid pNP40.	Lait	1996	76		67-79			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. 		
@D	Hill, C.//Miller, L.//Klaenhammer, T. 	Molecular characterization of a Type II methylase gene exchanged between pTR2030 and a virulent phage in Lactococci.	Plasmid	1990	23		167-168			None 		
@D	Hill, C.//Miller, L.A.//Klaenhammer, T.R. 	Nucleotide sequence and distribution of the pTR2030 resistance determinant (hsp) which aborts bacteriophage infection in Lactococci.	Appl. Environ. Microbiol.	1990	56		2255-2258			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. 		
@D	Hill, C.//Miller, L.A.//Klaenhammer, T.R. 	Cloning, expression, and sequence determination of a bacteriophage fragment encoding bacteriophage resistance in Lactococcus lactis.	J. Bacteriol.	1990	172		6419-6426			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. 		
@D	Hill, C.//Miller, L.A.//Klaenhammer, T.R. 	In vivo genetic exchange of a functional domain from a Type II A methylase between lactococcal plasmid pTR2030 and a virulent bacteriophage.	J. Bacteriol.	1991	173		4363-4370			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. 		
@D	Hill, C.//Miller, L.A.//Klaenhammer, T.R. 	The bacteriophage resistance plasmid pTR2030 forms high-molecular-weight multimers in Lactococci.	Plasmid	1991	25		105-112			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. 		
@D	Hill, C.//Pierce, K.//Klaenhammer, T.R. 	The conjugative plasmid pTR2030 encodes two bacteriophage defense mechanisms in Lactococci, restriction modification (R+/M+) and abortive infection (Hsp+).	Appl. Environ. Microbiol.	1989	55		2416-2419			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. 		
@D	Hill, C.//Romero, D.A.//McKenney, D.S.//Finer, K.R.//Klaenhammer, T.R. 	Localization, cloning, and expression of genetic determinants for bacteriophage resistance (Hsp) from the conjugative plasmid pTR2030.	Appl. Environ. Microbiol.	1989	55		1684-1689			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. 		
@D	Hill, S.A. 	Cell to cell transmission of donor DNA overcomes differential incorporation of non-homologous and homologous markers in Neisseria gonorrhoeae.	Gene	1999	240		175-182			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. 		
@D	Hiller, D.A. 	Mechanism of DNA bending and its role in the specificity of EcoRV restriction endonuclease.	Ph.D. Thesis, Univ. of California, Santa Barbara	2005			1-160			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. 		
@D	Hiller, D.A.//Fogg, J.M.//Martin, A.M.//Beechem, J.M.//Reich, N.O.//Perona, J.J. 	Simultaneous DNA binding and bending by EcoRV endonuclease observed by real-time fluorescence.	Biochemistry	2003	42		14375-14385			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. 		
@D	Hiller, D.A.//Perona, J.J. 	Positively charged C-terminal subdomains of EcoRV endonuclease: contributions to DNA binding, bending, and cleavage.	Biochemistry	2006	45		11453-11463			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. 		
@D	Hiller, D.A.//Rodriguez, A.M.//Perona, J.J. 	Non-cognate enzyme-DNA complex: structural and kinetic analysis of EcoRV endonuclease bound to the EcoRI recognition site GAATTC.	J. Mol. Biol.	2005	354		121-136			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. 		
@D	Hiller, N.L.//Janto, B.//Hogg, J.S.//Boissy, R.//Yu, S.//Powell, E.//Keefe, R.//Ehrlich, N.E.//Shen, K.//Hayes, J.//Barbadora, K.//Klimke, W.//Dernovoy, D.//Tatusova, T.//Parkhill, J.//Bentley, S.D.//Post, J.C.//Ehrlich, G.D.//Hu, F.Z. 	Comparative genomic analyses of seventeen Streptococcus pneumoniae strains: insights into the pneumococcal supragenome.	J. Bacteriol.	2007	189		8186-8195			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. 		
@D	Hilt, E.E.//Price, T.K.//Diebel, K.//Putonti, C.//Wolfe, A.J. 	Draft Genome Sequence for a Urinary Isolate of Nosocomiicoccus ampullae.	Genome Announcements	2016	4		e01248-16			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. 		
@D	Hilty, M. et al. 	Global phylogenomic analysis of nonencapsulated Streptococcus pneumoniae reveals  a deep-branching classic lineage that is distinct from multiple sporadic lineages.	Genome Biol. Evol.	2014	6		3281-3294			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. 		
@D	Himmelreich, R.//Hilbert, H.//Plagens, H.//Pirkl, E.//Li, B.-C.//Herrmann, R. 	Complete sequence analysis of the genome of the bacterium Mycoplasma pneumoniae.	Nucleic Acids Res.	1996	24		4420-4449			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. 		
@D	Himmelreich, R.//Plagens, H.//Hilbert, H.//Reiner, B.//Herrmann, R. 	Comparative anlaysis of the genomes of the bacteria Mycoplasma pneumoniae and Mycoplasma genitalium.	Nucleic Acids Res.	1997	25		701-712			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. 		
@D	Hines, J.L.//Agarwal, K.L. 	Purification and characterization of HpaI and HpaII.	Fed. Proc.	1979	38		294			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. 		
@D	Hines, J.L.//Chauncey, T.R.//Agarwal, K.L. 	Preparation and properties of HpaI and HpaII endonucleases.	Methods Enzymol.	1980	65		153-163			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. 		
@D	Hingorani-Varma, K.//Bitinaite, J. 	Kinetic analysis of the coordinated interaction of SgrAI restriction endonuclease with different DNA targets.	J. Biol. Chem.	2003	278		40392-40399			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. 		
@D	Hinkle, N.F.//Miller, R.V. 	pMG7-mediated restriction of Pseudomonas aeruginosa phage DNAs is determined by a class II restriction endonuclease.	Plasmid	1979	2		387-393			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. 		
@D	Hinsch, B.//Kula, M.-R. 	Physical and kinetic properties of the site specific endonuclease BamHI from Bacillus amyloliquefaciens.	Nucleic Acids Res.	1980	8		623-633			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. 		
@D	Hinsch, B.//Kula, M.-R. 	Reaction kinetics of some important site-specific endonucleases.	Nucleic Acids Res.	1981	9		3159-3174			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. 		
@D	Hinsch, B.//Mayer, H.//Kula, M.-R. 	Binding of non-substrate nucleotides to a restriction endonuclease: a model for the interaction of Bam HI with its recognition sequence.	Nucleic Acids Res.	1980	8		2547-2559			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. 		
@D	Hiom, K.//Sedgwick, S.G. 	Simple methods for making EcoK and McrA restrictionless mutants.	Nucleic Acids Res.	1991	19		2502			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. 		
@D	Hiom, K.//Sedgwick, S.G. 	Cloning and structural characterization of the mcrA locus of Escherichia coli.	J. Bacteriol.	1991	173		7368-7373			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. 		
@D	Hiom, K.//Thomas, S.M.//Sedgwick, S.G. 	Different mechanisms for SOS induced alleviation of DNA restriction in Escherichia coli.	Biochimie	1991	73		399-405			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. 		
@D	Hiom, K.J.//Sedgwick, S.G. 	Alleviation of EcoK DNA restriction in Escherichia coli and involvement of umuDC activity.	Mol. Gen. Genet.	1992	231		265-275			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. 		
@D	Hiraide, Y.//Oshima, K.//Fujisawa, T.//Uesaka, K.//Hirose, Y.//Tsujimoto, R.//Yamamoto, H.//Okamoto, S.//Nakamura, Y.//Terauchi, K.//Omata, T.//Ihara, K.//Hattori, M.//Fujita, Y. 	Loss of Cytochrome cM Stimulates Cyanobacterial Heterotrophic Growth in the Dark.	Plant Cell Physiol.	2015	56		334-345			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. 		
@D	Hiramatsu, K.//Aritaka, N.//Hanaki, H.//Kawasaki, S.//Hosoda, Y.//Hori, S.//Fukuchi, Y.//Kobayashi, I. 	Dissemination in Japanese hospitals of strains of Staphylococcus aureus heterogeneously resistant to vancomycin.	Lancet	1997	350		1670-1673			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. 		
@D	Hiraoka, N.//Kita, K.//Nakajima, H.//Kimizuka, F.//Obayashi, A. 	Site-Specific Restriction Endonucleases of Several Non-Pathogenic Bacteria.	J. Ferment. Technol.	1985	63		151-157			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. 		
@D	Hiraoka, N.//Kita, K.//Nakajima, H.//Obayashi, A. 	Purification and characterization of sequence-specific restriction endonuclease MflI.	J. Ferment. Technol.	1984	62		583-588			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. 		
@D	Hirata, R.//Anraku, Y. 	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.	Biochem. Biophys. Res. Commun.	1992	188		40-47			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. 		
@D	Hirata, R.//Ohsumi, Y.//Nakano, A.//Kawasaki, H.//Suzuki, K.//Anraku, Y. 	Molecular structure of a gene, VMA1, encoding the catalytic subunit of H+-translocating adenosine triphosphatase from vacuolar membranes of Saccharomyces cerevisiae.	J. Biol. Chem.	1990	265		6726-6733			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. 		
@D	Hirayama, N. 	Molecules controlling genetic information, Part 4, Restriction endonucleases.	Gendai Kagaku	2001	368		52-54					
@D	Hirk, S.//Lepuschitz, S.//Cabal, R.A.//Huhulescu, S.//Blaschitz, M.//Stoger, A.//Stadlbauer, S.//Hasenberger, P.//Indra, A.//Schmid, D.//Ruppitsch, W.//Allerberger, F. 	Draft Genome Sequences of Interpatient and Intrapatient Epidemiologically Linked  Neisseria gonorrhoeae Isolates.	Genome Announcements	2018	6		e00319-18			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. 		
@D	Hirose, J.//Tsuda, N.//Miyatake, M.//Yokoi, H.//Shimodaira, J. 	Draft Genome Sequence of Pseudomonas sp. Strain LLC-1 (NBRC 111237), Capable of Metabolizing Lignin-Derived Low-Molecular-Weight Compounds.	Genome Announcements	2018	6		e00308-18			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. 		
@D	Hirose, J.//Yamazoe, A.//Hosoyama, A.//Kimura, N.//Suenaga, H.//Watanabe, T.//Fujihara, H.//Futagami, T.//Goto, M.//Furukawa, K. 	Draft Genome Sequence of the Polychlorinated Biphenyl-Degrading Bacterium Pseudomonas stutzeri KF716 (NBRC 110668).	Genome Announcements	2015	3		e01215-15			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. 		
@D	Hirose, J.//Yamazoe, A.//Hosoyama, A.//Kimura, N.//Suenaga, H.//Watanabe, T.//Fujihara, H.//Futagami, T.//Goto, M.//Furukawa, K. 	Draft Genome Sequence of the Polychlorinated Biphenyl-Degrading Bacterium Comamonas testosteroni KF712 (NBRC 110673).	Genome Announcements	2015	3		e01214-15			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. 		
@D	Hirose, Y.//Fujisawa, T.//Ohtsubo, Y.//Katayama, M.//Misawa, N.//Wakazuki, S.//Shimura, Y.//Nakamura, Y.//Kawachi, M.//Yoshikawa, H.//Eki, T.//Kanesaki, Y. 	Complete Genome Sequence of Cyanobacterium Leptolyngbya sp. NIES-3755.	Genome Announcements	2016	4		e00090-16			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. 		
@D	Hirose, Y.//Katayama, M.//Ohtsubo, Y.//Misawa, N.//Iioka, E.//Suda, W.//Oshima, K.//Hanaoka, M.//Tanaka, K.//Eki, T.//Ikeuchi, M.//Kikuchi, Y.//Ishida, M.//Hattori, M. 	Complete Genome Sequence of Cyanobacterium Geminocystis sp. Strain NIES-3709, Which Harbors a Phycoerythrin-Rich Phycobilisome.	Genome Announcements	2015	3		e00385-15			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. 		
@D	Hirose, Y.//Katayama, M.//Ohtsubo, Y.//Misawa, N.//Iioka, E.//Suda, W.//Oshima, K.//Hanaoka, M.//Tanaka, K.//Eki, T.//Ikeuchi, M.//Kikuchi, Y.//Ishida, M.//Hattori, M. 	Complete Genome Sequence of Cyanobacterium Geminocystis sp. Strain NIES-3708, Which Performs Type II Complementary Chromatic Acclimation.	Genome Announcements	2015	3		e00357-15			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). 		
@D	Hirsch, A.M. et al. 	Complete Genome Sequence of Micromonospora Strain L5, a Potential Plant-Growth-Regulating Actinomycete, Originally Isolated from Casuarina  equisetifolia Root Nodules.	Genome Announcements	2013	1		e00759-13			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. 		
@D	Hirsch, J.A.//Wah, D.A.//Dorner, L.F.//Shildkraut, I.//Aggarwal, A.K. 	Crystallization and preliminary X-ray analysis of restriction endonuclease FokI bound to DNA.	FEBS Lett.	1997	403		136-138			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. 		
@D	Hirsch-Kauffmann, M.//Sauerbier, W. 	Inhibition of modification and restriction for phages lambda and Tl by co-infecting T3.	Mol. Gen. Genet.	1968	102		89-94			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. 		
@D	Hisata, K.//Ito, T.//Matsunaga, N.//Komatsu, M.//Jin, J.//Li, S.//Watanabe, S.//Shimizu, T.//Hiramatsu, K. 	Dissemination of multiple MRSA clones among community-associated methicillin-resistant Staphylococcus aureus infections from Japanese children with impetigo.	J. Infect. Chemother.	2011	17		609-621			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 		
@D	Hisatsune, J.//Hagiya, H.//Shiota, S.//Sugai, M. 	Complete Genome Sequence of Systemically Disseminated Sequence Type 8 Staphylococcal Cassette Chromosome mec Type IVl Community-Acquired  Methicillin-Resistant Staphylococcus aureus.	Genome Announcements	2017	5		e00852-17			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. 		
@D	Hishinuma, T.//Katayama, Y.//Matsuo, M.//Sasaki, T.//Hiramatsu, K. 	Complete Genome Sequence of Vancomycin-Intermediate Staphylococcus aureus Strain  MI (HIP5827).	Genome Announcements	2016	4		e00123-16			We report the complete genome sequence of vancomycin-intermediate Staphylococcus  aureus (VISA) strain MI (HIP5827). 		
@D	Hjerde, E.//Pierechod, M.M.//Williamson, A.K.//Bjerga, G.E.//Willassen, N.P.//Smalas, A.O.//Altermark, B. 	Draft Genome Sequence of the Actinomycete Rhodococcus sp. Strain AW25M09, Isolated from the Hadsel Fjord, Northern Norway.	Genome Announcements	2013	1		e0005513			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. 		
@D	Hjorleifsdottir, S.//Pelursdottir, S.//Kristjansson, J.K.//Korpela, J.//Torsti, A.-M.//Mattila, P. 	Screening of Rhodothermus marinus for restriction endonucleases.	Thermophiles Sci. Technol.	1992	20		17			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. 		
@D	Hjorleifsdottir, S.//Petursdottir, S.K.//Korpela, J.//Torsti, A.-M.//Mattila, P.//Kristjansson, J.K. 	Screening for restriction endonucleases in aerobic, thermophilic eubacteria.	Biotechnol. Tech.	1996	10		13-18			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. 		
@D	Hlavaty, J.J.//Benner, J.S.//Hornstra, L.J.//Schildkraut, I. 	Identification of the metal-binding sites of restriction endonucleases by Fe(2+)-mediated oxidative cleavage.	Biochemistry	2000	39		3097-3105			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. 		
@D	Ho, A.Y.//Chow, K.H.//Law, P.Y.//Tse, H.//Ho, P.L. 	Draft Genome Sequences of Two Multidrug-Resistant Acinetobacter baumannii Strains of Sequence Type ST92 and ST96.	Genome Announcements	2013	1		e00296-13			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. 		
@D	Ho, D.K.//Wu, J.C.//Santi, D.V.//Floss, H.G. 	Stereochemical studies of the C-methylation of deoxycytidine catalyzed by HhaI methylase and the N-methylation of deoxyadenosine catalyzed by EcoRI methylase.	Arch. Biochem. Biophys.	1991	284		264-269			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. 		
@D	Ho, M.T.//Weselowski, B.//Yuan, Z.C. 	Complete Genome Sequence of Acinetobacter calcoaceticus CA16, a Bacterium Capable of Degrading Diesel and Lignin.	Genome Announcements	2017	5		e00494-17			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. 		
@D	Ho, N.//Lingohr, E.J.//Villegas, A.//Cole, L.//Kropinski, A.M. 	Genomic characterization of two new Salmonella bacteriophages: vB_SosS_Oslo and vB_SemP_Emek.	Ann. Agrar. Sci.	2012	10		18-23			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. 		
@D	Ho, P.L.//Liu, M.C.//Chow, K.H.//Tse, C.W.//Lo, W.U.//Mak, S.K.//Lo, W.K. 	Emergence of ileS2-Carrying, Multidrug-Resistant Plasmids in Staphylococcus lugdunensis.	Antimicrob. Agents Chemother.	2016	60		6411-6414			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. 		
@D	Ho, P.L.//Lo, W.U.//Chan, J.//Cheung, Y.Y.//Chow, K.H.//Yam, W.C.//Lin, C.H.//Que, T.L. 	pIMP-PH114 Carrying bla IMP-4 in a Klebsiella pneumoniae Strain is Closely Related to Other Multidrug-Resistant IncA/C2 Plasmids.	Curr. Microbiol.	2014	68		227-232			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. 		
@D	Ho, P.L.//Poon, W.W.//Loke, S.L.//Leung, M.S.//Chow, K.H.//Wong, R.C.//Yip, K.S.//Lai, E.L.//Tsang, K.W. 	Community emergence of CTX-M type extended-spectrum beta-lactamases among urinary Escherichia coli from women.	J. Antimicrob. Chemother.	2007	60		140-144			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. 		
@D	Ho, W.S.//Gan, H.M.//Yap, K.P.//Balan, G.//Yeo, C.C.//Thong, K.L. 	Genome Sequence of Multidrug-Resistant Escherichia coli EC302/04, Isolated from a Human Tracheal Aspirate.	J. Bacteriol.	2012	194		6691-6692			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. 		
@D	Ho, W.S.//Ou, H.Y.//Yeo, C.C.//Thong, K.L. 	The dnd operon for DNA phosphorothioation modification system in Escherichia coli is located in diverse genomic islands.	BMC Genomics	2015	16		199			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. 		
@D	Ho, W.S.//Yap, K.P.//Yeo, C.C.//Rajasekaram, G.//Thong, K.L. 	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.	Front. Microbiol.	2016	6		1547			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. 		
@D	Ho, Y.//Kim, S.-J.//Waring, R.B. 	A protein encoded by a group I intron in Aspergillus nidulans directly assists RNA splicing and is a DNA endonuclease.	Proc. Natl. Acad. Sci. U. S. A.	1997	94		8994-8999			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. 		
@D	Ho, Y.//Waring, R.B. 	The maturase encoded by a group I intron from Aspergillus nidulans stabilizes RNA tertiary structure and promotes rapid splicing.	J. Mol. Biol.	1999	292		987-1001			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. 		
@D	Ho, Y.N.//Huang, C.C. 	Draft Genome Sequence of Burkholderia cenocepacia Strain 869T2, a Plant-Beneficial Endophytic Bacterium.	Genome Announcements	2015	3		e01327-15			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. 		
@D	Ho, Y.S.//Adroub, S.A.//Abadi, M.//Al, A.B.//Alkhateeb, R.//Gao, G.//Ragab, A.//Ali, S.//van Soolingen, D.//Bitter, W.//Pain, A.//Abdallah, A.M. 	Complete Genome Sequence of Mycobacterium vaccae Type Strain ATCC 25954.	J. Bacteriol.	2012	194		6339-6340			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. 		
@D	Ho, Y.S.//Adroub, S.A.//Aleisa, F.//Mahmood, H.//Othoum, G.//Rashid, F.//Zaher, M.//Ali, S.//Bitter, W.//Pain, A.//Abdallah, A.M. 	Complete Genome Sequence of Mycobacterium fortuitum subsp. fortuitum Type Strain  DSM46621.	J. Bacteriol.	2012	194		6337-6338			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. 		
@D	Hoang, V.A.//Kim, Y.J.//Nguyen, N.L.//Yang, D.C. 	Brachybacterium ginsengisoli sp. nov., isolated from soil of a ginseng field.	Int. J. Syst. Evol. Microbiol.	2014	64		3063-3068			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)). 		
@D	Hobley, G.//McKelvie, J.C.//Harmer, J.E.//Howe, J.//Oyston, P.C.F.//Roach, P.L. 	Development of rationally designed DNA N6 adenine methyltransferase inhibitors.	Bioorg. Med. Chem. Lett.	2012	22		3079-3082			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. 		
@D	Hobom, G.//Schwarz, E.//Melzer, M.//Mayer, H. 	Restriction endonuclease EcaI from Enterobacter cloacae.	Nucleic Acids Res.	1981	9		4823-4832			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. 		
@D	Hobson, N.//Price, N.L.//Ward, J.D.//Raivio, T.L. 	Generation of a restriction minus enteropathogenic Escherichia coli E2348/69 strain that is efficiently transformed with large, low copy plasmids.	BMC Microbiol.	2008	8		13			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. 		
@D	Hobson, S.D.//Falick, A.M.//Reich, N.O. 	Identification of a critical histidine in EcoRI DNA methyltransferase using protein modification and tandem mass spectrometry.	FASEB J.	1993	7		A1275			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. 		
@D	Hochhut, B.//Wilde, C.//Balling, G.//Middendorf, B.//Dobrindt, U.//Brzuszkiewicz, E.//Gottschalk, G.//Carniel, E.//Hacker, J. 	Role of pathogenicity island-associated integrases in the genome plasticity of uropathogenic Escherichia coli strain 536.	Mol. Microbiol.	2006	61		584-595			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. 		
@D	Hochwind, K.//Weinmaier, T.//Schmid, M.//van Hemert, S.//Hartmann, A.//Rattei, T.//Rothballer, M. 	Draft Genome Sequence of Lactobacillus casei W56.	J. Bacteriol.	2012	194		6638			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. 		
@D	Hodges, R.A.//Perler, F.B.//Noren, C.J.//Jack, W.E. 	Protein splicing removes intervening sequences in an archaea DNA polymerase.	Nucleic Acids Res.	1992	20		6153-6157			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. 		
@D	Hodges-Garcia, Y.//Hagerman, P.J. 	Cytosine methylation can induce local distortion in the structure of duplex DNA.	Biochemistry	1992	31		7595-7599			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. 		
@D	Hodgson, C.P. 	A rapid visual method for the identification of 4- or 6-base restriction endonuclease sites.	Biotechniques	1989	7		148-149			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. 		
@D	Hoefler, B.C.//Konganti, K.//Straight, P.D. 	De Novo Assembly of the Streptomyces sp. Strain Mg1 Genome Using PacBio Single-Molecule Sequencing.	Genome Announcements	2013	1		e00535-13			We report a draft genome assembly of Streptomyces sp. strain Mg1, a competitive soil isolate with multiple secondary metabolite gene clusters. 		
@D	Hoekstra, M.F.//Malone, R.E. 	Expression of the Escherichia coli dam methylase in Saccharomyces cerevisiae:  Effect of in vivo adenine methylation on genetic recombination and mutation.	Mol. Cell. Biol.	1985	5		610-618			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. 		
@D	Hoekstra, W.P.M.//DeHaan, P.G. 	The location of the restriction locus for lambda.K in Escherichia coli.	Mutat. Res.	1965	2		204-212			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. 		
@D	Hoelzer, K.//Shackelton, L.A.//Parrish, C.R. 	Presence and role of cytosine methylation in DNA viruses of animals.	Nucleic Acids Res.	2008	36		2825-2837			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. 		
@D	Hoet, P.P.//Coene, M.M.//Cocito, C.G. 	Replication cycle of Bacillus subtilis hydroxymethyluracil-containing phages.	Annu. Rev. Microbiol.	1992	46		95-116			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. 		
@D	Hoetzinger, M.//Schmidt, J.//Jezberova, J.//Koll, U.//Hahn, M.W. 	Microdiversification of a Pelagic Polynucleobacter Species Is Mainly Driven by Acquisition of Genomic Islands from a Partially Interspecific Gene Pool.	Appl. Environ. Microbiol.	2017	83		e02266-16			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. 		
@D	Hofer, B. 	The sensitivity of DNA cleavage by SpeI and ApaLI to methylation by M.EcoK.	Nucleic Acids Res.	1988	16		5206			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. 		
@D	Hofer, B.//Koster, H. 	On the influence of thymidine analogues on the activity of phage fd promoters in vitro.	Nucleic Acids Res.	1980	8		6143-6162			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. 		
@D	Hofer, B.//Kuhlein, B. 	The sensitivity of DNA cleavage by SnoI to methylation by M.EcoK.	Nucleic Acids Res.	1989	17		8009			None 		
@D	Hofer, B.//Ruhe, G.//Koch, A.//Koster, H. 	Primary and secondary structure specificity of the cleavage of single-stranded DNA by endonuclease HinfI.	Nucleic Acids Res.	1982	10		2763-2773			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. 		
@D	Hoffmann, L.//Ramos, R.J.T.//Guedes, I.A.//Costa, P.F.//Miguel, C.R.D.//Azevedo, S.M.F.O.E.//Silva, R. 	Draft Genome Sequences of Two Brazilian Cyanobacterial Strains of Cylindrospermopsis raciborskii: Differences in Membrane Transporters, Saxitoxin  Production, and Antioxidant Activities.	Genome Announcements	2017	5		e00879-17			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. 		
@D	Hoffmann, M.//Luo, Y.//Lafon, P.C.//Timme, R.//Allard, M.W.//McDermott, P.F.//Brown, E.W.//Zhao, S. 	Genome Sequences of Salmonella enterica Serovar Heidelberg Isolates Isolated in the United States from a Multistate Outbreak of Human Salmonella Infections.	Genome Announcements	2013	1		e00004-12			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. 		
@D	Hoffmann, M.//Muruvanda, T.//Allard, M.W.//Korlach, J.//Roberts, R.J.//Timme, R.//Payne, J.//McDermott, P.F.//Evans, P.//Meng, J.//Brown, E.W.//Zhao, S. 	Complete Genome Sequence of a Multidrug-Resistant Salmonella enterica Serovar Typhimurium var. 5- Strain Isolated from Chicken Breast.	Genome Announcements	2014	2		e00294-14			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." 		
@D	Hoffmann, M.//Muruvanda, T.//Allard, M.W.//Korlach, J.//Roberts, R.J.//Timme, R.//Payne, J.//McDermott, P.F.//Evans, P.//Meng, J.//Brown, E.W.//Zhao, S. 	Complete Genome Sequence of a Multidrug-Resistant Salmonella enterica Serovar Typhimurium var. 5- Strain Isolated from Chicken Breast.	Genome Announcements	2013	1		e01068-13			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. 		
@D	Hoffmann, M.//Muruvanda, T.//Pirone, C.//Korlach, J.//Timme, R.//Payne, J.//Evans, P.//Meng, J.//Brown, E.W.//Allard, M.W. 	First Fully Closed Genome Sequence of Salmonella enterica subsp. enterica Serovar Cubana Associated with a Food-Borne Outbreak.	Genome Announcements	2014	2		e01112-14			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. 		
@D	Hoffmann, M.//Payne, J.//Roberts, R.J.//Allard, M.W.//Brown, E.W.//Pettengill, J.B. 	Complete Genome Sequence of Salmonella enterica subsp. enterica Serovar Agona 460004 2-1, Associated with a Multistate Outbreak in the United States.	Genome Announcements	2015	3		e00690-15			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. 		
@D	Hoffmann, M.//Zhao, S.//Luo, Y.//Li, C.//Folster, J.P.//Whichard, J.//Allard, M.W.//Brown, E.W.//McDermott, P.F. 	Genome Sequences of Five Salmonella enterica Serovar Heidelberg Isolates Associated with a 2011 Multistate Outbreak in the United States.	J. Bacteriol.	2012	194		3274-3275			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. 		
@D	Hofreuter, D.//Tsai, J.//Watson, R.O.//Novik, V.//Altman, B.//Benitez, M.//Clark, C.//Perbost, C.//Jarvie, T.//Du, L.//Galan, J.E. 	Unique features of a highly pathogenic Campylobacter jejuni strain.	Infect. Immun.	2006	74		4694-4707			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. 		
@D	Hogg, G.//Dimovski, K.//Hiley, L.//Holt, K.E. 	Draft Genome Sequences for Ten Salmonella enterica Serovar Typhimurium Phage Type 135 Variants.	Genome Announcements	2013	1		e00293-13			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. 		
@D	Hogg, J.S.//Hu, F.Z.//Janto, B.//Boissy, R.//Hayes, J.//Keefe, R.//Post, J.C.//Ehrlich, G.D. 	Characterization and modeling of the Haemophilus influenzae core and supragenomes based on the complete genomic sequences of Rd and 12 clinical nontypeable strains.	Genome Biology	2007	8		R103			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. 		
@D	Hoheisel, J.D.//Nizetic, D.//Lehrach, H. 	Control of partial digestion combining the enzymes dam methylase and MboI.	Nucleic Acids Res.	1989	17		9571-9582			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. 		
@D	Holden, M.T. et al. 	The genome of Burkholderia cenocepacia J2315, an epidemic pathogen of cystic fibrosis patients.	J. Bacteriol.	2009	191		261-277			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. 		
@D	Holden, M.T. et al. 	Complete genome of acute rheumatic fever-associated serotype M5 Streptococcus pyogenes strain manfredo.	J. Bacteriol.	2007	189		1473-1477			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. 		
@D	Holden, M.T.//Lindsay, J.A.//Corton, C.//Quail, M.A.//Cockfield, J.D.//Pathak, S.//Batra, R.//Parkhill, J.//Bentley, S.D.//Edgeworth, J.D. 	Genome Sequence of a Recently Emerged, Highly Transmissible, Multi-Antibiotic- and Antiseptic-Resistant Variant of  Methicillin-Resistant Staphylococcus aureus, Sequence Type 239 (TW).	J. Bacteriol.	2010	192		888-892			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. 		
@D	Holden, M.T.G. et al. 	Genomic plasticity of the causative agent of melioidosis, Berkholderia pseudomallei.	Proc. Natl. Acad. Sci. U. S. A.	2004	101		14240-14245			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. 		
@D	Holden, M.T.G. et al. 	Complete genomes of two clinical Staphylococcus aureus strains: Evidence for the rapid evolution of virulence and drug resistance.	Proc. Natl. Acad. Sci. U. S. A.	2004	101		9786-9791			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. 		
@D	Holden, M.T.G. et al. 	Rapid Evolution of Virulence and Drug Resistance in the Emerging Zoonotic Pathogen Streptococcus suis.	PLoS ONE	2009	4		e6072-e6072			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. 		
@D	Holert, J.//Alam, I.//Larsen, M.//Antunes, A.//Bajic, V.B.//Stingl, U.//Philipp, B. 	Genome Sequence of Pseudomonas sp. Strain Chol1, a Model Organism for the Degradation of Bile Salts and Other Steroid Compounds.	Genome Announcements	2013	1		e00014-12			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. 		
@D	Holland-Moritz, H.E.//Bevans, D.R.//Lang, J.M.//Darling, A.E.//Eisen, J.A.//Coil, D.A. 	Draft Genome Sequence of Leucobacter sp. Strain UCD-THU (Phylum Actinobacteria).	Genome Announcements	2013	1		e00325-13			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. 		
@D	Holland-Moritz, H.E.//Coil, D.A.//Badger, J.H.//Dmitrov, G.I.//Khouri, H.//Ward, N.L.//Robb, F.T.//Eisen, J.A. 	Draft Genome Sequence of the Pyridinediol-Fermenting Bacterium Synergistes jonesii 78-1.	Genome Announcements	2014	2		e00833-14			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. 		
@D	Hollander, A.//Kalily, E.//Shachar, D.//Yaron, S.//Danin-Poleg, Y. 	Draft Genome Sequence of Salmonella enterica Serovar Senftenberg 070885 and Its Linalool-Adapted Mutant.	Genome Announcements	2017	5		e01036-17			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. 		
@D	Hollensteiner, J.//Poehlein, A.//Daniel, R.//Liesegang, H.//Vidal, S.//Wemheuer, F. 	Draft Genome Sequence of Bacillus pumilus Strain GM3FR, an Endophyte Isolated from Aerial Plant Tissues of Festuca rubra L.	Genome Announcements	2017	5		e00085-17			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. 		
@D	Hollensteiner, J.//Poehlein, A.//Granzow, S.//Liesegang, H.//Daniel, R.//Vidal, S.//Wemheuer, F. 	Draft Genome Sequence of the Endophyte Bacillus mycoides Strain GM5LP Isolated from Lolium perenne.	Genome Announcements	2018	6		e01517-17			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. 		
@D	Hollensteiner, J.//Poehlein, A.//Sproer, C.//Bunk, B.//Sheppard, A.E.//Rosenstiel, P.//Schulenburg, H.//Liesegang, H. 	Complete genome sequence of the nematicidal Bacillus thuringiensis MYBT18247.	J. Biotechnol.	2017	260		48-52			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. 		
@D	Hollensteiner, J.//Poehlein, A.//Sproer, C.//Bunk, B.//Sheppard, A.E.//Rosentstiel, P.//Schulenburg, H.//Liesegang, H. 	Complete Genome sequence of the nematicidal Bacillus thuringiensis MYBT18246.	Standards in Genomic Sciences	2017	12		48			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. 		
@D	Holloway, S.P.//Deshpande, N.N.//Herrin, D.L. 	The catalytic group-I introns of the psbA gene of Chlamydomonas reinhardtii: core structures, ORFs and evolutionary implications.	Curr. Genet.	1999	36		69-78			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. 		
@D	Holm, K.O.//Nilsson, K.//Hjerde, E.//Willassen, N.P.//Milton, D.L. 	Complete genome sequence of Vibrio anguillarum strain NB10, a virulent isolate from the Gulf of Bothnia.	Standards in Genomic Sciences	2015	10		60			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. 		
@D	Holm-Hansen, A.C.//Paulino-Lima, I.G.//Fujishima, K.//Rothschild, L.J.//Jensen, P.R. 	Draft Genome Sequence of Hymenobacter sp. Strain AT01-02, Isolated from a Surface Soil Sample in the Atacama Desert, Chile.	Genome Announcements	2016	4		e01701-15			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. 		
@D	Holmes, M.L.//Nuttall, S.D.//Dyall-Smith, M.L. 	Construction and use of Halobacterial shuttle vectors and further studies on Haloferax DNA gyrase.	J. Bacteriol.	1991	173		3807-3813			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. 		
@D	Holmfeldt, K.//Howard-Varona, C.//Solonenko, N.//Sullivan, M.B. 	Contrasting genomic patterns and infection strategies of two co-existing Bacteroidetes podovirus genera.	Environ. Microbiol.	2014	16		2501-2513			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. 		
@D	Hols, P.//Hancy, F.//Fontaine, L.//Grossiord, B.//Prozzi, D.//Leblond-Bourget, N.//Decaris, B.//Bolotin, A.//Delorme, C.//Ehrlich, S.D.//Guedon, E.//Monnet, W.//Renault, P.//Kleerebezem, M. 	New insights in the molecular biology and physiology of Streptococcus thermophilus revealed by comparative genomics.	FEMS Microbiol. Rev.	2005	29		435-463			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. 		
@D	Holt, D.C.//Holden, M.T.//Tong, S.Y.//Castillo-Ramirez, S.//Clarke, L.//Quail, M.A.//Currie, B.J.//Parkhill, J.//Bentley, S.D.//Feil, E.J.//Giffard, P.M. 	A very early-branching Staphylococcus aureus lineage lacking the carotenoid pigment staphyloxanthin.	Genome Biol. Evol.	2011	3		881-895			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. 		
@D	Holt, J.P.//Grant, A.J.//Coward, C.//Maskell, D.J.//Quinlan, J.J. 	Identification of Cj1051c as a Major Determinant for the Restriction Barrier of Campylobacter jejuni Strain NCTC11168.	Appl. Environ. Microbiol.	2012	78		7841-7848			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. 		
@D	Holt, K.E.//Baker, S.//Weill, F.X.//Holmes, E.C.//Kitchen, A.//Yu, J.//Sangal, V.//Brown, D.J.//Coia, J.E.//Kim, D.W.//Choi, S.Y.//Kim, S.H.//da Silveira, W.D.//Pickard, D.J.//Farrar, J.J.//Parkhill, J.//Dougan, G.//Thomson, N.R. 	Shigella sonnei genome sequencing and phylogenetic analysis indicate recent global dissemination from Europe.	Nat. Genet.	2012	44		1056-1059			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. 		
@D	Holt, K.E.//Hamidian, M.//Kenyon, J.J.//Wynn, M.T.//Hawkey, J.//Pickard, D.//Hall, R.M. 	Genome Sequence of Acinetobacter baumannii Strain A1, an Early Example of Antibiotic-Resistant Global Clone 1.	Genome Announcements	2015	3		e00032-15			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. 		
@D	Holt, K.E.//Thomson, N.R.//Wain, J.//Phan, M.D.//Nair, S.//Hasan, R.//Bhutta, Z.A.//Quail, M.A.//Norbertczak, H.//Walker, D.//Dougan, G.//Parkhill, J. 	Multidrug-Resistant Salmonella enterica Serovar Paratyphi A Harbors IncHI1 Plasmids Similar to Those Found in Serovar Typhi.	J. Bacteriol.	2007	189		4257-4264			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. 		
@D	Holtz, J.K.//Topal, M.D. 	Location of putative binding and catalytic sites of NaeI by random mutagenesis.	J. Biol. Chem.	1994	269		27286-27290			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. 		
@D	Holubova, I.//Vejsadova, I.//Firman, K.//Weiserovda, M. 	Cellular localization of type I restriction-modification enzymes is family dependent.	Biochem. Biophys. Res. Commun.	2004	319		375-380			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. 		
@D	Holubova, I.//Vejsadova, S.//Weiserova, M.//Firman, K. 	Localization of the Type I Restriction-Modification Enzyme EcoKI in the Bacterial Cell.	Biochem. Biophys. Res. Commun.	2000	270		46-51			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. 		
@D	Holubova, J.//Josephsen, J. 	Potential of AbiS as defence mechanism determined by conductivity measurement.	J. Appl. Microbiol.	2007	103		2382-2391			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. 		
@D	Holz, B.//Dank, N.//Eickhoff, J.E.//Lipps, G.//Krauss, G.//Weinhold, E. 	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.	J. Biol. Chem.	1999	274		15066-15072			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. 		
@D	Holz, B.//Klimasauskas, S.//Serva, S.//Weinhold, E. 	2-Aminopurine as a fluorescent probe for DNA base flipping by methyltransferases.	Nucleic Acids Res.	1998	26		1076-1083			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. 		
@D	Holz, B.//Pues, H.//Wolcke, J.//Weinhold, E. 	Fluorescence studies on the base flipping mechanism of the DNA methyltransferase M.TaqI.	FASEB J.	1997	11		A1151			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. 		
@A	Holz, B.//Weinhold, E. 		Probes for DNA base flipping by DNA methyltransferases.			Diederichsen, U.//Lindhorst, T.K.//Westermann, B.//Wessjohann, L.A. 		Bioorganic Chemistry: Highlights and New Aspects				Weinheim	Wiley-VCH	1999				337-345									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. 		
@D	Holz-Schietinger, C.//Reich, N.O. 	The Inherent Processivity of the Human de Novo Methyltransferase 3A (DNMT3A) Is Enhanced by DNMT3L.	J. Biol. Chem.	2010	285		29091-29100			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. 		
@D	Holz-Schietinger, C.//Reich, N.O. 	RNA modulation of the human DNA methyltransferase 3A.	Nucleic Acids Res.	2012	40		8550-8557			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. 		
@D	Honda, S.//Selker, E.U. 	Direct interaction between DNA methyltransferase DIM-2 and HP1 is required for DNA methylation in Neurospora crassa.	Mol. Cell. Biol.	2008	28		6044-6055			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. 		
@D	Honda, T.//Liang, Y.//Arai, D.//Ito, Y.//Yoshino, T.//Tanaka, T. 	Draft Genome Sequence of Marine Cyanobacterium Synechococcus sp. Strain NKBG042902, Which Harbors a Homogeneous Plasmid Available for Metabolic  Engineering.	Genome Announcements	2014	2		e00704-14			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%. 		
@D	Honein, K.//Jagoda, S.S.//Arulkanthan, A.//Ushio, H.//Asakawa, S. 	Draft Genome Sequences of Citrobacter freundii Strains CF04 and A41 Isolated from Moribund, Septicemic Giant Gourami (Osphronemus goramy) in Sri Lanka.	Genome Announcements	2016	4		e00820-16			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. 		
@D	Honein, K.//Jagoda, S.S.S.S.//Arulkanthan, A.//Ushio, H.//Asakawa, S. 	Draft Genome Sequence of Aeromonas hydrophila Strain Ae25, Isolated from a Septicemic Moribund Koi Carp (Cyprinus carpio) in Sri Lanka.	Genome Announcements	2018	6		e01523-17			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. 		
@D	Hong, C.E.//Jo, S.H.//Jeong, H.//Park, J.M. 	Draft Genome Sequence of the Endophytic Strain Rhodococcus kyotonensis KB10, a Potential Biodegrading and Antibacterial Bacterium Isolated from Arabidopsis  thaliana.	Genome Announcements	2016	4		e00636-16			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. 		
@D	Hong, C.E.//Jo, S.H.//Jo, I.H.//Jeong, H.//Park, J.M. 	Draft Genome Sequence of the Endophytic Bacterium Variovorax paradoxus KB5, Which Has Antagonistic Activity against a Phytopathogen, Pseudomonas syringae pv.  tomato DC3000.	Genome Announcements	2017	5		e00950-17			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. 		
@D	Hong, H.H.//Choi, H.//Cheon, S.//Lee, H.G.//Park, C. 	Genome Sequences of Two Shewanella spp. Isolated from the Gut of the Sea Cucumber Apostichopus japonicus (Selenka, 1867).	Genome Announcements	2017	5		e00674-17			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. 		
@D	Hong, J.//Kim, J.//Kim, B.Y.//Park, J.W.//Ryu, J.G.//Roh, E. 	Complete Genome Sequence of Biofilm-Forming Strain Staphylococcus haemolyticus S167.	Genome Announcements	2016	4		e00567-16			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. 		
@D	Hong, K.W.//Gan, H.M.//Low, S.M.//Lee, P.K.//Chong, Y.M.//Yin, W.F.//Chan, K.G. 	Draft Genome Sequence of Pantoea sp. Strain A4, a Rafflesia-Associated Bacterium  That Produces N-Acylhomoserine Lactones as Quorum-Sensing Molecules.	J. Bacteriol.	2012	194		6610			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. 		
@D	Hong, K.W.//Koh, C.L.//Sam, C.K.//Yin, W.F.//Chan, K.G. 	Complete Genome Sequence of Burkholderia sp. Strain GG4, a Betaproteobacterium That Reduces 3-Oxo-N-Acylhomoserine Lactones and Produces Different  N-Acylhomoserine Lactones.	J. Bacteriol.	2012	194		6317			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. 		
@D	Hong, K.W.//Koh, C.L.//Sam, C.K.//Yin, W.F.//Chan, K.G. 	Whole-Genome Sequence of N-Acylhomoserine Lactone-Synthesizing and -Degrading Acinetobacter sp. Strain GG2.	J. Bacteriol.	2012	194		6318			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. 		
@D	Hong, K.W.//Thinagaran, D.A.//Gan, H.M.//Yin, W.F.//Chan, K.G. 	Whole-Genome Sequence of Cupriavidus sp. Strain BIS7, a Heavy-Metal-Resistant Bacterium.	J. Bacteriol.	2012	194		6324			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. 		
@D	Hong, S.H.//Kim, J.S.//Lee, S.Y.//In, Y.H.//Choi, S.S.//Rih, J.K.//Kim, C.H.//Jeong, H.//Hur, C.G.//Kim, J.J. 	The genome sequence of the capnophilic rumen bacterium Mannheimia succiniciproducens.	Nat. Biotechnol.	2004	22		1275-1281			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. 		
@D	Hong, S.J.//Park, G.S.//Khan, A.R.//Jung, B.K.//Park, Y.J.//Yoo, N.K.//Lee, C.//Park, C.K.//Shin, J.H. 	Draft Genome Sequence of Caprolactam-Degrading Pseudomonas putida Strain SJ3.	Genome Announcements	2015	3		e00810-15			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. 		
@D	Hong, S.J.//Ullah, I.//Park, G.S.//Jung, B.K.//Choi, J.//Khan, A.R.//Kim, M.C.//Shin, J.H. 	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.	Genome Announcements	2015	3		e01521-14			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. 		
@D	Honger, J.//Monson, R.E.//Rawlinson, A.//Salmond, G.P.C. 	Draft Genome Sequences of Serratia marcescens Strains CAPREx SY13 and CAPREx SY21 Isolated from Yams.	Genome Announcements	2017	5		e00191-17			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. 		
@D	Hongoh, Y.//Sharma, V.K.//Prakash, T.//Noda, S.//Taylor, T.D.//Kudo, T.//Sakaki, Y.//Toyoda, A.//Hattori, M.//Ohkuma, M. 	Complete genome of the uncultured Termite Group 1 bacteria in a single host protist cell.	Proc. Natl. Acad. Sci. U. S. A.	2008	105		5555-5560			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. 		
@D	Hongoh, Y.//Sharma, V.K.//Prakash, T.//Noda, S.//Toh, H.//Taylor, T.D.//Kudo, T.//Sakaki, Y.//Toyoda, A.//Hattori, M.//Ohkuma, M. 	Genome of an Endosymbiont Coupling N2 Fixation to Cellulolysis within Protist Cells in Termite Gut.	Science	2008	322		1108-1109			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. 		
@D	Honma, Y.//Fernandez, R.E.//Maurelli, A.T. 	A DNA adenine methylase mutant of Shigella flexneri shows no significant attenuation of virulence.	Microbiology	2004	150		1073-1078			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. 		
@D	Hood, D.W.//Deadman, M.E.//Jennings, M.P.//Bisercic, M.//Fleischmann, R.D.//Venter, J.C.//Moxon, E.R. 	DNA repeats identify novel virulence genes in Hemophilus influenzae.	Proc. Natl. Acad. Sci. U. S. A.	1996	93		11121-11125			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. 		
@D	Hooper, C. 	Molecular Evolution: Sampling the New Synthesis.	J. NIH Res.	1993	5		66-70			Contains a discussion of the evolution of restriction enzymes. 		
@D	Hoose, S.A.//Kladde, M.P. 	DNA methyltransferase probing of DNA-protein interactions.	Methods Mol. Biol.	2006	338		225-244			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. 		
@D	Hooton, S.P.//Timms, A.R.//Moreton, J.//Wilson, R.//Connerton, I.F. 	Complete Genome Sequence of Salmonella enterica Serovar Typhimurium U288.	Genome Announcements	2013	1		e00467-13			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. 		
@D	Hooven, T.A.//Randis, T.M.//Daugherty, S.C.//Narechania, A.//Planet, P.J.//Tettelin, H.//Ratner, A.J. 	Complete Genome Sequence of Streptococcus agalactiae CNCTC 10/84, a Hypervirulent Sequence Type 26 Strain.	Genome Announcements	2014	2		e01338-14			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. 		
@D	Hopkins, B.B.//Reich, N.O. 	Simultaneous DNA binding, bending, and base flipping - Evidence for a novel M. EcoRI methyltransferase-DNA complex.	J. Biol. Chem.	2004	279		37049-37060			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. 		
@D	Horiuchi, K. 	Studies on restriction endonucleases.	Tanpakushitsu Kakusan Koso	1977	22		981-991					
@D	Horiuchi, K.//Vovis, G.F.//Enea, V.//Zinder, N.D. 	Cleavage map of bacteriophage f1: Location of the Escherichia coli B-specific modification sites.	J. Mol. Biol.	1975	95		147-165			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. 		
@D	Horiuchi, K.//Vovis, G.F.//Enea, V.//Zinder, N.D. 	Cleavage mapping of the Escherichia coli B-specific modification sites of bacteriophage fl.	Abstr. Gen. Meet. Am. Soc. Microbiol.	1975	75		225			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. 		
@D	Horiuchi, K.//Vovis, G.F.//Zinder, N.D. 	Effect of deoxyribonucleic acid length on the adenosine triphosphatase activity of Escherichia coli restriction endonuclease B.	J. Biol. Chem.	1974	249		543-552			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. 		
@D	Horiuchi, K.//Zinder, N. 	Cleavage of bacteriophage f1 DNA by the restriction enzyme of Escherichia coli.	Proc. Natl. Acad. Sci. U. S. A.	1972	69		3220-3224			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. 		
@D	Horiuchi, K.//Zinder, N.D. 	Site-specific cleavage of single-stranded DNA by a Hemophilus restriction endonuclease.	Proc. Natl. Acad. Sci. U. S. A.	1975	72		2555-2558			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. 		
@D	Horn, F.//Schroeckh, V.//Netzker, T.//Guthke, R.//Brakhage, A.A.//Linde, J. 	Draft Genome Sequence of Streptomyces iranensis.	Genome Announcements	2014	2		e00616-14			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. 		
@D	Horn, G.//Taubeneck, U. 	Comparative experiments with DNA restriction factors Escherichia coli and Shigella sonnei.	Z. Allg. Mikrobiol.	1970	10		103-119			None 		
@D	Horn, H.//Hentschel, U.//Abdelmohsen, U.R. 	Mining Genomes of Three Marine Sponge-Associated Actinobacterial Isolates for Secondary Metabolism.	Genome Announcements	2015	3		e01106-15			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. 		
@D	Horn, H.//Keller, A.//Hildebrandt, U.//Kampfer, P.//Riederer, M.//Hentschel, U. 	Draft genome of the Arabidopsis thaliana phyllosphere bacterium, Williamsia sp. ARP1.	Standards in Genomic Sciences	2016	11		8			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. 		
@D	Hornby, D.P. 	DNA Methyltransferases (EC 2.1.1.72 and EC 2.1.1.73).	Methods Mol. Biol.	1993	16		201-211			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. 		
@D	Hornby, D.P.//Bickle, T.A. 	Characterization of EcoPI DNA adenine methylase.	Biochem. Soc. Trans.	1987	15		1039			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. 		
@D	Hornby, D.P.//Ford, G.C. 	Protein-mediated base flipping.	Curr. Opin. Biotechnol.	1998	9		354-358			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. 		
@D	Hornby, D.P.//Muller, M.//Bickle, T.A. 	High level expression of the EcoPI modification methylase gene and characterization of the gene product.	Gene	1987	54		239-245			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. 		
@D	Hornby, D.P.//Whitmarsh, A.//Pinarbasi, H.//Kelly, S.M.//Price, N.C.//Shore, P.//Baldwin, G.S.//Waltho, J. 	The DNA recognition subunit of a DNA methyltransferase is predominantly a molten globule in the absence of DNA.	FEBS Lett.	1994	355		57-60			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. 		
@D	Horst, J.-P.//Fritz, H.-J. 	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.	EMBO J.	1996	15		5459-5469			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. 		
@D	Horta-Valerdi, G.//Sanchez-Alonso, M.P.//Perez-Marquez, V.M.//Negrete-Abascal, E.//Vaca-Pacheco, S.//Hernandez-Gonzalez, I.//Gomez-Lunar, Z.//Olmedo-Alvarez, G.//Vazquez-Cruz, C. 	The Genome Sequence of Avibacterium paragallinarum Strain CL Has a Large Repertoire of Insertion Sequence Elements.	Genome Announcements	2017	5		e00152-17			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. 		
@A	Horton, J.R.//Blumenthal, R.M.//Cheng, X. 		Restriction endonucleases: Structure of the conserved catalytic core and the role of metal ions in DNA cleavage.			Pingoud, A. 		Nucleic Acids Mol. Biol.				Berlin, Heidelberg	Springer-Verlag	2004		14		361-392									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. 		
@D	Horton, J.R.//Bonventre, J.//Cheng, X. 	How is modification of the DNA substrate recognized by the PvuII restriction endonuclease?	Biol. Chem.	1998	379		451-458			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. 		
@D	Horton, J.R.//Borgaro, J.G.//Griggs, R.M.//Quimby, A.//Guan, S.//Zhang, X.//Wilson, G.G.//Zheng, Y.//Zhu, Z.//Cheng, X. 	Structure of 5-hydroxymethylcytosine-specific restriction enzyme, AbaSI, in complex with DNA.	Nucleic Acids Res.	2014	42		7947-7959			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. 		
@D	Horton, J.R.//Cheng, X. 	PvuII endonuclease contains two calcium ions in active sites.	J. Mol. Biol.	2000	300		1049-1056			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. 		
@D	Horton, J.R.//Liebert, K.//Bekes, M.//Jeltsch, A.//Cheng, X.D. 	Structure and Substrate Recognition of the Escherichia coli DNA Adenine Methyltransferase.	J. Mol. Biol.	2006	358		559-570			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. 		
@D	Horton, J.R.//Liebert, K.//Hattman, S.//Jeltsch, A.//Cheng, X. 	Transition from nonspecific to specific DNA interactions along the substrate-recognition pathway of Dam methyltransferase.	Cell	2005	121		349-361			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. 		
@D	Horton, J.R.//Mabuchi, M.Y.//Cohen-Karni, D.//Zhang, X.//Griggs, R.M.//Samaranayake, M.//Roberts, R.J.//Zheng, Y.//Cheng, X. 	Structure and cleavage activity of the tetrameric MspJI DNA modification-dependent restriction endonuclease.	Nucleic Acids Res.	2012	40		9763-9773			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. 		
@D	Horton, J.R.//Nastri, H.G.//Riggs, P.D.//Cheng, X. 	Asp34 of PvuII endonuclease is directly involved in DNA minor groove recognition and indirectly involved in catalysis.	J. Mol. Biol.	1998	284		1491-1504			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. 		
@D	Horton, J.R.//Nugent, R.L.//Li, A.//Mabuchi, M.Y.//Fomenkov, A.//Cohen-Karni, D.//Griggs, R.M.//Zhang, X.//Wilson, G.G.//Zheng, Y.//Xu, S.-Y.//Cheng, X. 	Structure and mutagenesis of the DNA modification-dependent restriction endonuclease AspBHI.	Sci. Rep.	2014	4		9			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. 		
@D	Horton, J.R.//Ratner, G.//Banavali, N.K.//Huang, N.//Choi, Y.//Maier, M.A.//Marquez, V.E.//MacKerell, A.D. Jr.//Cheng, X. 	Caught in the act: visualization of an intermediate in the DNA base-flipping pathway induced by HhaI methyltransferase.	Nucleic Acids Res.	2004	32		3877-3886			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. 		
@D	Horton, J.R.//Wang, H.//Mabuchi, M.Y.//Zhang, X.//Roberts, R.J.//Zheng, Y.//Wilson, G.G.//Cheng, X. 	Modification-dependent restriction endonuclease, MspJI, flips 5-methylcytosine out of the DNA helix.	Nucleic Acids Res.	2014	42		12092-12101			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. 		
@D	Horton, J.R.//Zhang, X.//Blumenthal, R.M.//Cheng, X. 	Structures of Escherichia coli DNA adenine methyltransferase (Dam) in complex with a non-GATC sequence: potential implications for methylation-independent  transcriptional repression.	Nucleic Acids Res.	2015	43		4296-4308			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. 		
@D	Horton, J.R.//Zhang, X.//Maunus, R.//Yang, Z.//Wilson, G.G.//Roberts, R.J.//Cheng, X. 	DNA nicking by HinP1I endonuclease: bending, base flipping and minor groove expansion.	Nucleic Acids Res.	2006	34		939-948			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. 		
@D	Horton, N.C.//Connolly, B.A.//Perona, J.J. 	Inhibition of EcoRV endonuclease by deoxyribo-3'-S-phosphorothiolates: A high-resolution X-ray crystallographic study.	J. Am. Chem. Soc.	2000	122		3314-3324			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. 		
@D	Horton, N.C.//Dorner, L.F.//Perona, J.J. 	Sequence selectivity and degeneracy of a restriction endonuclease mediated by DNA intercalation.	Nat. Struct. Biol.	2002	9		42-47			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. 		
@D	Horton, N.C.//Dorner, L.F.//Schildkraut, I.//Perona, J.J. 	Crystallization and preliminary diffraction analysis of the HincII restriction endonuclease-DNA complex.	Acta Crystallogr. D Biol. Crystallogr.	1999	55		1943-1945			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%. 		
@D	Horton, N.C.//Newberry, K.J.//Perona, J.J. 	Metal ion-mediated substrate-assisted catalysis in type II restriction endonucleases.	Proc. Natl. Acad. Sci. U. S. A.	1998	95		13489-13494			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. 		
@D	Horton, N.C.//Otey, C.//Lusetti, S.//Sam, M.D.//Kohn, J.//Martin, A.M.//Ananthnarayan, V.//Perona, J.J. 	Electrostatic contributions to site specific DNA cleavage by EcoRV endonuclease.	Biochemistry	2002	41		10754-10763			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. 		
@D	Horton, N.C.//Perona, J.J. 	Role of protein-induced bending in the specificity of DNA recognition: crystal structure of EcoRV endonuclease complexes with d(AAAGAT) + d(ATCTT).	J. Mol. Biol.	1998	277		779-787			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. 		
@D	Horton, N.C.//Perona, J.J. 	Making the most of metal ions.	Nat. Struct. Biol.	2001	8		290-293			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. 		
@D	Horton, N.C.//Perona, J.J. 	DNA cleavage by EcoRV endonuclease: Two metal ions in three metal ion binding sites.	Biochemistry	2004	43		6841-6857			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. 		
@D	Horton, N.C.//Perona, J.J. 	Recognition of flanking DNA sequences by EcoRV endonuclease involves alternative patterns of water-mediated contacts.	J. Biol. Chem.	1998	273		21721-21729			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. 		
@D	Horton, N.C.//Perona, J.J. 	Crystallographic snapshots along a protein-induced DNA-bending pathway.	Proc. Natl. Acad. Sci. U. S. A.	2000	97		5729-5734			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. 		
@D	Horton, N.C.//Sam, M.D.//Connolly, B.A.//Perona, J.J. 	Structural mechanism of phosphoryl transfer in EcoRV restriction endonuclease.	Biophys. J.	2000	78		417A			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. 		
@D	Horvath, B.//Hunyadkurti, J.//Voros, A.//Fekete, C.//Urban, E.//Kemeny, L.//Nagy, I. 	Genome sequence of Propionibacterium acnes Type II strain ATCC 11828.	J. Bacteriol.	2011	194		202-203			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. 		
@A	Horvath, P.//Barrangou, R. 		Protection against Foreign DNA.			Storz, G.//Hengge, R. 		Bacterial Stress Responses, 2nd Edition				Washington, D.C.	Amer. Soc. Microbiology	2011		0		333-348									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. 		
@D	Hosford, C.J.//Chappie, J.S. 	The crystal structure of the Helicobacter pylori LlaJI.R1 N-terminal domain provides a model for site-specific DNA binding.	J. Biol. Chem.	2018	293		11758-11771			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. 		
@D	Hoshino, T.//Uozumi, T.//Horinouchi, S.//Ozaki, A.//Beppu, T.//Arima, K. 	Purification of cohesive-end-producing restriction endonuclease from Bacillus subtilis G.	Biochim. Biophys. Acta	1977	479		367-369			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. 		
@D	Hoskins, I.C.//Lax, A.J. 	Identification of restriction barriers in Pasteurella multocida.	FEMS Microbiol. Lett.	1997	156		223-226			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. 		
@D	Hoskins, J. et al. 	Genome of the bacterium Streptococcus pneumoniae strain R6.	J. Bacteriol.	2001	183		5709-5717			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. 		
@D	Hoskisson, P.A.//Smith, M.C.M. 	Hypervariation and phase variation in the bacteriophage resistome.	Curr. Opin. Microbiol.	2007	10		396-400			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. 		
@D	Hoskisson, P.A.//Sumby, P.//Smith, M.C. 	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.	Virology	2015	477		100-109			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. 		
@D	Hossain, M.//Alam, M.//Khaleque, A.//Islam, S.//Sadique, A.//Khan, N.//Halim, Z.//Sarker, M.//El-Sayed, N.M.//Huq, A.//Ahsan, G.U.//Colwell, R.R. 	Virulence-Related Genes Identified from the Genome Sequence of the Non-O1/Non-O139 Vibrio cholerae Strain VcN1, Isolated from Dhaka, Bangladesh.	Genome Announcements	2018	6		e01513-17			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. 		
@D	Hossain, M.J.//Beaz-Hidalgo, R.//Figueras, M.J.//Liles, M.R. 	Draft Genome Sequences of Two Novel Aeromonas Species Recovered in Association with Cyanobacterial Blooms.	Genome Announcements	2014	2		e01181-14			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. 		
@D	Hossain, M.S.//Akhter, M.Z.//Hossain, M.M.//Shishir, M.A.//Khan, S.N.//Hoq, M.M. 	Complete Genome Sequence of Bacillus subtilis Strain MH1, Which Has a High Level  of Bacteriocin-Like Activity, Isolated from Soil in Bangladesh.	Genome Announcements	2018	6		e00516-18			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). 		
@D	Hosseinkhani, F.//Emaneini, M.//van Leeuwen, W. 	High-Quality Genome Sequence of the Highly Resistant Bacterium Staphylococcus haemolyticus, Isolated from a Neonatal Bloodstream Infection.	Genome Announcements	2017	5		e00683-17			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. 		
@D	Hotchkiss, R.D. 	The quantitative separation of purines, pyrimidines, and nucleosides by paper chromatography.	J. Biol. Chem.	1948	175		315-332			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. 		
@D	Hotz, H.R.//Peters, A.H. 	Protein demethylation required for DNA methylation.	Nat. Genet.	2009	41		10-11			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. 		
@D	Hou, L.//Jiang, J.//Xu, Z.//Zhou, Y.//Leung, F.C. 	Complete Genome Sequence of Pseudoxanthomonas suwonensis Strain J1, a Cellulose-Degrading Bacterium Isolated from Leaf- and Wood-Enriched Soil.	Genome Announcements	2015	3		e00614-15			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. 		
@D	Hou, L.//Sun, J.//Xie, X.//Jiao, N.//Zhang, Y. 	Genome sequence of Acuticoccus yangtzensis JL1095T (DSM 28604T) isolated from the Yangtze Estuary.	Standards in Genomic Sciences	2017	12		91			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. 		
@D	Hou, P.//Ji, M.//He, N.//Lu, Z. 	A microarray method to evaluate the effect of CA mispairs on the accuracy of BstUI restriction endonuclease.	Anal. Biochem.	2003	317		276-279			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. 		
@D	Hou, P.//Ji, M.J.//He, N.Y.//Lu, Z.H. 	Microarray-based method to evaluate the accuracy of restriction endonucleases HpaII and MspI.	Biochem. Biophys. Res. Commun.	2004	314		110-117			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. 		
@D	Hou, Q.//Wang, C.//Guo, H.//Xia, Z.//Ye, J.//Liu, K.//Yang, Y.//Hou, X.//Liu, H.//Wang, J.//Du, B.//Ding, Y. 	Draft Genome Sequence of Delftia tsuruhatensis MTQ3, a Strain of Plant Growth-Promoting Rhizobacterium with Antimicrobial Activity.	Genome Announcements	2015	3		e00822-15			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. 		
@D	Hou, Q.//Wang, C.//Hou, X.//Xia, Z.//Ye, J.//Liu, K.//Liu, H.//Wang, J.//Guo, H.//Yu, X.//Yang, Y.//Du, B.//Ding, Y. 	Draft Genome Sequence of Brevibacillus brevis DZQ7, a Plant Growth-Promoting Rhizobacterium with Broad-Spectrum Antimicrobial Activity.	Genome Announcements	2015	3		e00831-15			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. 		
@D	Hou, S. et al. 	Genome sequence of the deep-sea {gamma}-proteobacterium Idiomarina loihiensis reveals amino acid fermentation as a source of carbon and   energy.	Proc. Natl. Acad. Sci. U. S. A.	2004	101		18036-18041			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. 		
@D	Hou, S.P.//He, P.//Zhou, Y.//Wu, X.W. 	Complete Genome Sequence of Campylobacter fetus subsp. testudinum Strain 772, Isolated from Ascites of a Patient with Chronic Kidney Disease.	Genome Announcements	2018	6		e00432-18			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. 		
@D	Houlston, C.E.//Lindsay, H.//Pradhan, S.//Adams, R.L.P. 	DNA substrate specificity of pea DNA methylase.	Biochem. J.	1993	293		617-624			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. 		
@D	Howard, K.A.//Card, C.//Benner, J.S.//Callahan, H.L.//Maunus, R.//Silber, K.//Wilson, G.//Brooks, J.E. 	Cloning the DdeI restriction-modification system using a two-step method.	Nucleic Acids Res.	1986	14		7939-7951			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. 		
@D	Howden, B.P.//Seemann, T.//Harrison, P.F.//McEvoy, C.R.//Stanton, J.A.//Rand, C.J.//Mason, C.W.//Jensen, S.O.//Firth, N.//Davies, J.K.//Johnson, P.D.//Stinear, T.P. 	Complete Genome Sequence of Staphylococcus aureus Strain JKD6008, an ST239 Clone of Methicillin-Resistant Staphylococcus aureus with  Intermediate-Level Vancomycin Resistance.	J. Bacteriol.	2010	192		5848-5849			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. 		
@D	Hoyos-Mallecot, Y.//Rojo-Martin, M.D.//Bonnin, R.A.//Creton, E.//Navarro, M.J.M.//Naas, T. 	Draft Genome Sequence of NDM-1-Producing Leclercia adecarboxylata.	Genome Announcements	2017	5		e00135-17			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%. 		
@D	Hsieh, C.-L. 	In vivo activity of murine de novo methyltransferases, Dnmt3a and Dnmt3b.	Mol. Cell. Biol.	1999	19		8211-8218			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. 		
@D	Hsieh, P.-C.//Xiao, J.-P.//O'Loane, D.//Xu, S.-Y. 	Cloning, expression, and purification of a thermostable nonhomodimeric restriction enzyme, BslI.	J. Bacteriol.	2000	182		949-955			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. 		
@D	Hsu, D.W.//Lin, M.J.//Lee, T.L.//Wen, S.C.//Chen, X.//Shen, C.J. 	Two major forms of DNA (cytosine-5) methyltransferase in human somatic tissues.	Proc. Natl. Acad. Sci. U. S. A.	1999	96		9751-9756			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. 		
@D	Hsu, M.//Berg, P. 	Altering the specificity of restriction endonuclease:  effect of replacing Mg2+ with Mn2+.	Biochemistry	1978	17		131-138			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. 		
@D	Hsu, M.-Y.//Inouye, M.//Inouye, S. 	Retron for the 67-base multicopy single-stranded DNA from Escherichia coli: A potential transposable element encoding both reverse transcriptase and Dam methylase functions.	Proc. Natl. Acad. Sci. U. S. A.	1990	87		9454-9458			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. 		
@D	Hsueh, P.T.//Chen, Y.S.//Lin, H.H.//Liu, P.J.//Ni, W.F.//Liu, M.C.//Chen, Y.L. 	Comparison of Whole-Genome Sequences from Two Colony Morphovars of Burkholderia pseudomallei.	Genome Announcements	2015	3		e01194-15			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. 		
@D	Hsueh, P.T.//Liu, J.K.//Chen, Y.L.//Liu, P.J.//Ni, W.F.//Chen, Y.S.//Wu, K.M.//Lin, H.H. 	Genomic Sequence of Burkholderia multivorans NKI379, a Soil Bacterium That Inhibits the Growth of Burkholderia pseudomallei.	Genome Announcements	2015	3		e01294-15			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. 		
@D	Hu, A.//He, J.//Chu, K.H.//Yu, C.P. 	Genome Sequence of the 17{beta}-Estradiol-Utilizing Bacterium Sphingomonas Strain KC8.	J. Bacteriol.	2011	193		4266-4267			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. 		
@D	Hu, A.//Lv, M.//Yu, C.P. 	Draft Genome Sequence of the Bisphenol A-Degrading Bacterium Sphingobium sp. Strain YL23.	Genome Announcements	2013	1		e00549-13			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. 		
@D	Hu, A.-L.W. 	NgoAIV--a new restriction endonuclease compared to its commercially available isoschizomers.	BRL Focus	1994	15		42-43			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. 		
@D	Hu, A.W.//Marschel, A.H. 	Endonuclease NciI generates atypical termini.	Fed. Proc.	1982	41		1119			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. 		
@D	Hu, D.//Crist, M.//Duan, X.//Gimble, F.S. 	Mapping of a DNA binding region of the PI-SceI homing endonuclease by affinity cleavage and alanine-scanning mutagenesis.	Biochemistry	1999	38		12621-12628			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. 		
@D	Hu, D.//Crist, M.//Duan, X.//Quiocho, F.A.//Gimble, F.S. 	Probing the Structure of the PI-SceI-DNA Complex by Affinity Cleavage and Affinity Photocross-linking.	J. Biol. Chem.	2000	275		2705-2712			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. 		
@D	Hu, D.//Li, X.//Chang, Y.//He, H.//Zhang, C.//Jia, N.//Li, H.//Wang, Z. 	Genome Sequence of Streptomyces sp. Strain TOR3209, a Rhizosphere Microecology Regulator Isolated from Tomato Rhizosphere.	J. Bacteriol.	2012	194		1627			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. 		
@D	Hu, D.//Liu, B.//Feng, L.//Ding, P.//Guo, X.//Wang, M.//Cao, B.//Reeves, P.R.//Wang, L. 	Origins of the current seventh cholera pandemic.	Proc. Natl. Acad. Sci. U. S. A.	2016	113		E7730-E7739			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. 		
@D	Hu, K.-Y.//Wuu, J.-A.//Kao, M.-C.//Liu, Y.-T.//Pai, S.-H. 	Isolation and characterization of a newly identified type II restriction endonuclease from a local Streptomyces sp. in Taiwan.	Appl. Biochem. Biotechnol.	1998	73		231-241			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. 		
@D	Hu, L.//Li, N.//Xu, C.//Zhong, S.//Lin, X.//Yang, J.//Zhou, T.//Yuliang, A.//Wu, Y.//Chen, Y.R.//Cao, X.//Zemach, A.//Rustgi, S.//von Wettstein, D.//Liu, B. 	Mutation of a major CG methylase in rice causes genome-wide hypomethylation, dysregulated genome expression, and seedling lethality.	Proc. Natl. Acad. Sci. U. S. A.	2014	111		10642-10647			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. 		
@D	Hu, L.//Zhang, G.//Allard, M.W.//Yao, K.//Stones, R.//Hoffmann, M.//Brown, E.W. 	Complete Genome Sequences of Two Salmonella enterica subsp. enterica Serovar Enteritidis Strains Isolated from Egg Products in the United States.	Genome Announcements	2017	5		e00614-17			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. 		
@D	Hu, P.//Elliott, J.//McCready, P.//Skowronski, E.//Garnes, J.//Kobayashi, A.//Brubaker, R.R.//Garcia, E. 	Structural organization of virulence-associated plasmids of Yersinia pestis.	J. Bacteriol.	1998	180		5192-5202			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. 		
@D	Hu, P.//Lang, J.//Wawrousek, K.//Yu, J.//Maness, P.C.//Chen, J. 	Draft Genome Sequence of Rubrivivax gelatinosus CBS.	J. Bacteriol.	2012	194		3262			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. 		
@D	Hu, P.//Yang, M.//Zhang, A.//Wu, J.//Chen, B.//Hua, Y.//Yu, J.//Chen, H.//Xiao, J.//Jin, M. 	Complete Genome Sequence of Streptococcus suis Serotype 3 Strain ST3.	J. Bacteriol.	2011	193		3428-3429			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. 		
@D	Hu, P.//Yang, M.//Zhang, A.//Wu, J.//Chen, B.//Hua, Y.//Yu, J.//Xiao, J.//Jin, M. 	Complete Genome Sequence of Streptococcus suis Serotype 14 Strain JS14.	J. Bacteriol.	2011	193		2375-2376			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. 		
@D	Hu, Q.//Qi, J.//Bo, H.//Liu, G.//Tao, M.//Ding, Y.//Xue, Y. 	Complete Genome Sequence of Riemerella anatipestifer Serotype 10 Strain HXb2.	Genome Announcements	2017	5		e00278-17			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. 		
@D	Hu, S.//Yuan, S.//Qu, H.//Jiang, T.//Zhou, Y.//Wang, M.//Ming, D. 	Antibiotic resistance mechanisms of Myroides sp.	J. Zhejiang Univ. Sci. B	2016	17		188-199			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. 		
@D	Hu, S.//Zheng, H.//Gu, Y.//Zhao, J.//Zhang, W.//Yang, Y.//Wang, S.//Zhao, G.//Yang, S.//Jiang, W. 	Comparative genomic and transcriptomic analysis revealed genetic characteristics related to solvent formation and xylose utilization in Clostridium acetobutylicum EA 2018.	BMC Genomics	2011	12		93			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. 		
@D	Hu, W.//Wang, C.//Liang, J.//Zhang, T.//Hu, Z.//Wang, Z.//Lan, W.//Li, F.//Wu, H.//Ding, J.//Wu, G.//Deng, Z.//Cao, C. 	Structural insights into DndE from Escherichia coli B7A involved in DNA phosphorothioation modification.	Cell Res.	2012	22		1203-1206			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. 		
@D	Hu, W.P.//Yu, H.S.//Hsieh, M.C.//Chen, Y.C.//Wang, J.J. 	Evaluation of DNA-binding ability of antibiotic DC-81 - indole conjugates by restriction endonuclease BamHI and molecular modeling studies.	Chin. Pharm. J.	2002	54		465-470			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. 		
@D	Hu, X.//Fan, W.//Han, B.//Liu, H.//Zheng, D.//Li, Q.//Dong, W.//Yan, J.//Gao, M.//Berry, C.//Yuan, Z. 	Complete genome sequence of the mosquitocidal bacterium Bacillus sphaericus C3-41 and comparison with those of closely related Bacillus  species.	J. Bacteriol.	2008	190		2892-2902			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. 		
@D	Hu, X.//Li, A.//Lv, L.//Yuan, C.//Guo, L.//Jiang, X.//Jiang, H.//Qian, G.//Zheng, B.//Guo, J.//Li, L. 	High quality draft genome sequence of Staphylococcus cohnii subsp. cohnii strain  hu-01.	Standards in Genomic Sciences	2014	9		755-762			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. 		
@D	Hu, X.//Shang, Y.//Guo, J.//Zhang, H.//Liang, Y.//Sun, J.//Yue, F. 	Draft Genome Sequence of Staphylococcus microti DSM 22147, Isolated from the Common Vole.	Genome Announcements	2018	6		e00420-18			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. 		
@D	Hu, X.//Wang, J.//Wang, F.//Chen, Q.//Huang, Y.//Cui, Z. 	Complete Genome Sequence of the p-Nitrophenol-Degrading Bacterium Pseudomonas putida DLL-E4.	Genome Announcements	2014	2		e00596-14			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%. 		
@D	Hu, X.//Zheng, B.//Jiang, H.//Kang, Y.//Cao, Q.//Ning, H.//Shang, J. 	Draft Genome Sequence of Staphylococcus sciuri subsp. sciuri Strain Z8, Isolated  from Human Skin.	Genome Announcements	2015	3		e00714-15			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. 		
@D	Hu, Y.//Feng, Y.//Qin, J.//Radolfova-Krizova, L.//Maixnerova, M.//Zhang, X.//Nemec, A.//Zong, Z. 	Acinetobacter wuhouensis sp. nov., isolated from hospital sewage.	Int. J. Syst. Evol. Microbiol.	2018	68		3212-3216			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)). 		
@D	Hu, Y.//Li, T.//Yang, Z.//Zhang, B.//Li, Y. 	Phage resistance of Corynebacterium crenatum conferred by the restriction and modification system cglI.	Sheng Wu Gong Cheng Xue Bao	2008	24		760-765					
@D	Hu, Y.//Wu, W.//Feng, Y.//Zhang, X.//Zong, Z. 	Draft Genome Sequence of a Pseudomonas sp. Strain Carrying blaIMP-25 and blaVIM-2 Carbapenemase Genes from Hospital Sewage.	Genome Announcements	2016	4		e01027-16			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. 		
@D	Hu, Y.//Xu, X.//Song, P.//Jiang, L.//Zhang, Z.//Huang, H. 	Draft Genome Sequence of Deinococcus xibeiensis R13, a New Carotenoid-Producing Strain.	Genome Announcements	2013	1		e00987-13			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. 		
@D	Hu, Y.//Zhang, W.//Liang, H.//Liu, L.//Peng, G.//Pan, Y.//Yang, X.//Zheng, B.//Gao, G.F.//Zhu, B.//Hu, H. 	Whole-Genome Sequence of a Multidrug-Resistant Clinical Isolate of Acinetobacter lwoffii.	J. Bacteriol.	2011	193		5549-5550			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. 		
@D	Hu, Z.Y.//Wang, Y.Z.//Im, W.T.//Wang, S.Y.//Zhao, G.P.//Zheng, H.J.//Quan, Z.X. 	The first complete genome sequence of the class fimbriimonadia in the phylum armatimonadetes.	PLoS ONE	2014	9		E100794			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. 		
@D	Hua, N.M.//Karska-Wysocki, B.//Szatmari, G.//Mamet-Bratley, M.D. 	Purification and characterization of the LlaGI restriction  enodnuclease from Lactococcus lactis subsp. cremoris G2.	Life Sc. Confer. Ottawa	1998	0		P001			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. 		
@D	Hua, X.//Chen, Q.//Li, X.//Feng, Y.//Ruan, Z.//Yu, Y. 	Complete Genome Sequence of Klebsiella pneumoniae Sequence Type 17, a Multidrug-Resistant Strain Isolated during Tigecycline Treatment.	Genome Announcements	2014	2		e01337-14			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. 		
@D	Hua, X.//Hua, Y. 	Improved Complete Genome Sequence of the Extremely Radioresistant Bacterium Deinococcus radiodurans R1 Obtained Using PacBio Single-Molecule Sequencing.	Genome Announcements	2016	4		e00886-16			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. 		
@D	Hua, X.//Zhou, H.//Jiang, Y.//Feng, Y.//Chen, Q.//Ruan, Z.//Yu, Y. 	Genome Sequences of Two Multidrug-Resistant Acinetobacter baumannii Strains Isolated from a Patient before and after Treatment with Tigecycline.	J. Bacteriol.	2012	194		6979-6980			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. 		
@D	Huai, Q.//Colandene, J.D.//Chen, Y.//Luo, F.//Zhao, Y.//Topal, M.D.//Ke, H. 	Crystal structure of NaeI - an evolutionary bridge between DNA endonuclease and topoisomerase.	EMBO J.	2000	19		3110-3118			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. 		
@D	Huai, Q.//Colandene, J.D.//Topal, M.D.//Ke, H. 	Structure of NaeI-DNA complex reveals dual-mode DNA recognition and complete dimer rearrangement.	Nat. Struct. Biol.	2001	8		665-669			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. 		
@D	Huang, B.//Schaeffer, C.J.//Li, Q.//Tsai, M.-D. 	Splase: A new class IIS zinc-finger restriction endonuclease with specificity for Sp1 binding sites.	J. Protein Chem.	1996	15		481-489			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. 		
@D	Huang, B.F.//Kropinski, A.M.//Bujold, A.R.//MacInnes, J.I. 	Complete genome sequence of Actinobacillus equuli subspecies equuli ATCC 19392(T).	Standards in Genomic Sciences	2015	10		32			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. 		
@D	Huang, C.H.//Liou, J.S.//Wang, C.L.//Huang, L. 	Draft Genome Sequence of Clostridium sp. Strain chh4-2 Isolated from Human Feces.	Genome Announcements	2018	6		e00070-18			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. 		
@D	Huang, C.J.//Zheng, P.X.//Ou, J.Y.//Lin, Y.C.//Chen, C.Y. 	Complete Genome Sequence of Bacillus cereus C1L, a Plant Growth-Promoting Rhizobacterium from the Rhizosphere of Formosa Lily in Taiwan.	Genome Announcements	2017	5		e01290-17			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. 		
@D	Huang, E.//Guo, Y.//Yousef, A.E. 	Draft Genome Sequence of Paenibacillus sp. Strain OSY-SE, a Bacterium Producing the Novel Broad-Spectrum Lipopeptide Antibiotic Paenibacterin.	J. Bacteriol.	2012	194		6306			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. 		
@D	Huang, E.//Yousef, A.E. 	Draft Genome Sequence of Paenibacillus polymyxa OSY-DF, Which Coproduces a Lantibiotic, Paenibacillin, and Polymyxin E1.	J. Bacteriol.	2012	194		4739-4740			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. 		
@D	Huang, E.-S.//Newbold, J.E.//Pagano, J.S. 	Analysis of simian virus 40 DNA with the restriction enzyme of Haemophilus aegyptius, endonuclease Z.	J. Virol.	1973	11		508-514			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. 		
@D	Huang, H.//Duceppe, M.O.//Phipps-Todd, B. 	Draft Genome Sequence of Raoultella ornithinolytica Strain HH3.	Genome Announcements	2018	6		e00270-18			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. 		
@D	Huang, H.R.//Chao, M.Y.//Armstrong, B.//Wang, Y.//Lambowitz, A.M.//Perlman, P.S. 	The DIVa maturase binding site in the yeast group II intron aI2 is essential for intron homing but not for in vivo splicing.	Mol. Cell. Biol.	2003	23		8809-8819			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. 		
@D	Huang, J.//Qiao, Z.X.//Tang, J.W.//Wang, G. 	High quality draft genome sequence of the moderately halophilic bacterium Pontibacillus yanchengensis Y32(T) and comparison among Pontibacillus genomes.	Standards in Genomic Sciences	2015	10		93			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. 		
@D	Huang, J.//Wang, H.//Liang, W.//Xie, X.//Guo, G. 	Developmental expression of Arabidopsis methyltransferase genes MET1, DRM2, and CMT3.	Mol. Biol. (Mosk)	2014	48		681-687			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. 		
@D	Huang, J.J.//Wang, H.H.//Xie, X.J.//Zhang, D.//Liu, Y.//Guo, G.Q. 	Roles of DNA methyltransferases in Arabidopsis development.	Afr. J. Biotechnol.	2010	9		8506-8514			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. 		
@D	Huang, K.//Ni, J.//Xu, K.//Tang, H.//Tao, F.//Xu, P. 	Genome Sequence of Sporolactobacillus terrae DSM 11697, the Type Strain of the Species.	Genome Announcements	2014	2		e00465-14			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. 		
@D	Huang, L.//Zhao, L.//Su, Y.//Yan, Q. 	Genome Sequence of Pseudomonas plecoglossicida Strain NZBD9.	Genome Announcements	2018	6		e01412-17			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%. 		
@D	Huang, L.-H.//Farnet, C.M.//Ehrlich, K.C.//Ehrlich, M. 	Digestion of highly modified bacteriophage DNA by restriction endonucleases.	Nucleic Acids Res.	1982	10		1579-1591			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. 		
@D	Huang, L.H.//Farnet, C.//Ehrlich, K.C.//Ehrlich, M. 	Digestion of highly modified phage DNA by restriction endonucleases.	Fed. Proc.	1982	41		1199			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. 		
@D	Huang, N.//Banavali, N.K.//MacKerell, A.D. Jr. 	Protein-facilitated base flipping in DNA by cytosine-5-methyltransferase.	Proc. Natl. Acad. Sci. U. S. A.	2003	100		68-73			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. 		
@D	Huang, N.//MacKerell, A.D. 	Specificity in protein-DNA interactions: Energetic recognition by the (cytosine-C5)-methyltransferase from HhaI.	J. Mol. Biol.	2005	345		265-274			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. 		
@D	Huang, N.//Zou, G.//Cao, X.//Zhu, R. 	Studies on chemical modification and kinetics of restriction endonuclease Bsp78I.	Wuhan Daxue Xuebao	1996	42		233-236			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. 		
@D	Huang, S.//Qian, Y.//Wei, T.//Jia, C.//Yang, P.//Mao, D. 	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.	Genome Announcements	2018	6		e00136-18			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. 		
@D	Huang, S.//Vieira, S.//Bunk, B.//Riedel, T.//Sproer, C.//Overmann, J. 	First Complete Genome Sequence of a Subdivision 6 Acidobacterium Strain.	Genome Announcements	2016	4		e00469-16			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. 		
@D	Huang, S.L.//Chen, H.//Hu, A.//Tuan, N.N.//Yu, C.P. 	Draft Genome Sequence of Pseudomonas nitroreducens Strain TX1, Which Degrades Nonionic Surfactants and Estrogen-Like Alkylphenols.	Genome Announcements	2014	2		e01262-13			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. 		
@D	Huang, T.W.//Chen, F.J.//Miu, W.C.//Liao, T.L.//Lin, A.C.//Huang, I.W.//Wu, K.M.//Tsai, S.F.//Chen, Y.T.//Lauderdale, T.L. 	Complete Genome Sequence of Staphylococcus aureus M013, a pvl-Positive, ST59-SCCmec Type V Strain Isolated in Taiwan.	J. Bacteriol.	2012	194		1256-1257			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. 		
@D	Huang, T.W.//Chen, T.L.//Chen, Y.T.//Lauderdale, T.L.//Liao, T.L.//Lee, Y.T.//Chen, C.P.//Liu, Y.M.//Lin, A.C.//Chang, Y.H.//Wu, K.M.//Kirby, R.//Lai, J.F.//Tan, M.C.//Siu, L.K.//Chang, C.M.//Fung, C.P.//Tsai, S.F. 	Copy Number Change of the NDM-1 Sequence in a Multidrug-Resistant Klebsiella pneumoniae Clinical Isolate.	PLoS ONE	2013	8		e62774			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. 		
@D	Huang, W.//Ojaimi, C.//Fallon, J.T.//Travisany, D.//Maass, A.//Ivanova, L.//Tomova, A.//Gonzalez-Acuna, D.//Godfrey, H.P.//Cabello, F.C. 	Genome Sequence of Borrelia chilensis VA1, a South American Member of the Lyme Borreliosis Group.	Genome Announcements	2015	3		e01535-14			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. 		
@D	Huang, X.//Jiang, W.//Zhang, F.//Liang, Z. 	A simplified method for preparation of restriction endonuclease BamHI.	Zhongguo Yi Xue Ke Xue Yuan Xue Bao	1982	4		60-62			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. 		
@D	Huang, X.//Palmer, S.//Ahn, S.J.//Richards, V.P.//Williams, M.L.//Nascimento, M.M.//Burne, R.A. 	Characterization of a highly arginolytic Streptococcus species that potently antagonizes Streptococcus mutans.	Appl. Environ. Microbiol.	2016	82		2187			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. 		
@D	Huang, X.//Wang, Z.//Liu, Y.//Zhang, X. 	Complete Genome Sequence of Pseudomonas protegens H78, a Plant Growth-Promoting Rhizobacterium.	Genome Announcements	2017	5		e00233-17			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. 		
@D	Huang, X.J.//Lu, H.L.//Wang, J.W.//Xu, L.Q.//Liu, S.Y.//Sun, J.H.//Gao, F. 	High-throughput sequencing of methylated cytosine enriched by modification-dependent restriction endonuclease MspJI.	BMC Genet.	2013	14		56			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. 		
@D	Huang, Y.//Fang, T.//Wang, H.//Zhou, H. 	Draft Genome Sequence of Oleiagrimonas soli 3.5XT, a Type Species in a Newly Identified Genus, Isolated from an Oil Field in China.	Genome Announcements	2015	3		e00469-15			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. 		
@D	Huang, Y.//Friedman, S. 	The inhibition of RecA-mediated strand exchange by adducts of azacytosine-containing DNA and EcoRII methylase.	FASEB J.	1990	4		A2294			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. 		
@D	Huang, Y.//Friedman, S. 	Inhibition of recA-mediated strand exchange by adducts of Azacytosine-containing DNA and the EcoRII methylase.	J. Biol. Chem.	1991	266		17424-17429			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. 		
@D	Huang, Y.//Higuchi, Y.//Mori, K.//Yamashita, R.//Okino, N.//Tashiro, K.//Takegawa, K. 	Draft Genome Sequence of Sphingobacterium sp. Strain HMA12, Which Encodes Endo-beta-N-Acetylglucosaminidases and Can Specifically Hydrolyze  Fucose-Containing Oligosaccharides.	Genome Announcements	2018	6		e01525-17			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. 		
@D	Huang, Y.//Jian, J.//Lu, Y.//Cai, S.//Wang, B.//Tang, J.//Pang, H.//Ding, Y.//Wu, Z. 	Draft Genome Sequence of the Fish Pathogen Vibrio harveyi Strain ZJ0603.	J. Bacteriol.	2012	194		6644-6645			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. 		
@D	Huang, Y.//Li, H.//Rensing, C.//Zhao, K.//Johnstone, L.//Wang, G. 	Genome Sequence of the Facultative Anaerobic Arsenite-Oxidizing and Nitrate-Reducing Bacterium Acidovorax sp. Strain NO1.	J. Bacteriol.	2012	194		1635-1636			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. 		
@D	Huang, Y.H.//Chou, S.H.//Liang, S.W.//Ni, C.E.//Lin, Y.T.//Huang, Y.W.//Yang, T.C. 	Emergence of an XDR and carbapenemase-producing hypervirulent Klebsiella pneumoniae strain in Taiwan.	J. Antimicrob. Chemother.	2018	73		20392046			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. 		
@D	Huang, Y.J.//Parker, M.M.//Belfort, M. 	Role of exonucleolytic degradation in group I intron homing in phage T4.	Genetics	1999	153		1501-1512			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. 		
@D	Huang, Y.Y.//Cho, S.T.//Lo, W.S.//Wang, Y.C.//Lai, E.M.//Kuo, C.H. 	Complete Genome Sequence of Agrobacterium tumefaciens Ach5.	Genome Announcements	2015	3		e00570-15			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. 		
@D	Hubacek, J. 	Biological function of DNA methylation.	Folia Microbiol. (Praha)	1992	37		323-329			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. 		
@D	Hubacek, J. 	Functional analysis of second-step host specificity mutations in unstable escherichia coli heterozygotes.	J. Gen. Microbiol.	1973	79		257-264			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. 		
@D	Hubacek, J.//Glover, S.W. 	Complementation analysis of temperature-sensitive host specificity mutations in Escherichia coli.	J. Mol. Biol.	1970	50		111-127			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. 		
@D	Hubacek, J.//Holubova, I.//Weiserova, M. 	The effect of recA mutation on the expression of EcoKI and EcoR124I hsd genes cloned in a multicopy plasmid.	Folia Microbiol. (Praha)	1998	43		353-359			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. 		
@D	Hubacek, J.//Weiserova, M. 	DNA restriction and modification in Escherichia coli: Functional analysis of the role of the dnaC(D) gene product.	J. Gen. Microbiol.	1980	119		231-238			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. 		
@A	Hubacek, J.//Weiserova, M. 		Biological function of type I restriction enzymes.			Glass, R.E.//Spizek, J. 		Gene Manipulation and Expression				London	Croom-Helm	1985		0		95-109									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. 		
@D	Hubacek, J.//Weiserova, M.//Janscak, P.//Firman, K. 	Restriction endonucleases R.EcoKI and R.EcoR124I are probably located in different environments within the bacterial cell.	Folia Microbiol. (Praha)	1994	39		162-165			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. 		
@D	Hubacek, J.//Zinkevich, V.E.//Weiserova, M. 	The location of a temperature-sensitive trans-dominant mutation and its effect on restriction and modification in Escherichia coli K12.	J. Gen. Microbiol.	1989	135		3057-3065			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. 		
@D	Hubbard, A.T.//Davies, S.E.//Baxter, L.//Thompson, S.//Collery, M.M.//Hand, D.C.//Fink, C.G.//Thomas, D.J. 	Draft Whole-Genome Sequence of a Haemophilus quentini Strain Isolated from an Infant in the United Kingdom.	Genome Announcements	2016	4		e01075-16			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. 		
@D	Hubscher, U.//Pedrali-Noy, G.//Knust-Kron, B.//Doerfler, W.//Spadari, S. 	DNA methyltransferases: Activity minigel analysis and determination with DNA covalently bound to a solid matrix.	Anal. Biochem.	1985	150		442-448			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. 		
@D	Hudson, C.M.//Bent, Z.W.//Meagher, R.J.//Williams, K.P. 	Resistance determinants and mobile genetic elements of an NDM-1-encoding Klebsiella pneumoniae strain.	PLoS ONE	2014	9		E99209			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. 		
@D	Hue, F.//Ghalyanchi, L.A.//Barbour, A.G. 	Chromosome Sequence of Borrelia miyamotoi, an Uncultivable Tick-Borne Agent of Human Infection.	Genome Announcements	2013	1		e00713-13			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. 		
@D	Huedo, P.//Conchillo-Sole, O.//Yero, D.//Martinez-Servat, S.//Daura, X.//Gibert, I. 	Draft Genome Sequence of Stenotrophomonas maltophilia Strain M30, Isolated from a Chronic Pressure Ulcer in an Elderly Patient.	Genome Announcements	2014	2		e00576-14			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. 		
@D	Huedo, P.//Gori, M.//Scaltriti, E.//Morganti, M.//Casadei, G.//Amato, E.//Pontello, M. 	Draft Genome Sequence of Salmonella enterica subsp. enterica Serovar Napoli Strain SN310, Cause of a Multischool Outbreak in Milan, Italy, in 2014.	Genome Announcements	2015	3		e01044-15			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. 		
@D	Huggett, M.J.//Hayakawa, D.H.//Rappe, M.S. 	Genome sequence of strain HIMB624, a cultured representative from the OM43 clade  of marine Betaproteobacteria.	Standards in Genomic Sciences	2012	6		11-20			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. 		
@D	Hughes, C.A.N.//Johnson, R.C. 	Methylated DNA in Borrelia species.	J. Bacteriol.	1990	172		6602-6604			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. 		
@D	Hughes, G.L.//Raygoza, G.J.A.//Koundal, V.//Rasgon, J.L.//Mwangi, M.M. 	Genome Sequence of Stenotrophomonas maltophilia Strain SmAs1, Isolated From the Asian Malaria Mosquito Anopheles stephensi.	Genome Announcements	2016	4		e00086-16			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. 		
@D	Hughes, G.L.//Raygoza, G.J.A.//Koundal, V.//Rasgon, J.L.//Mwangi, M.M. 	Genome Sequences of Staphylococcus hominis Strains ShAs1, ShAs2, and ShAs3, Isolated from the Asian Malaria Mosquito Anopheles stephensi.	Genome Announcements	2016	4		e00085-16			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. 		
@D	Hughes, H.Y.//Conlan, S.P.//Lau, A.F.//Dekker, J.P.//Michelin, A.V.//Youn, J.H.//Henderson, D.K.//Frank, K.M.//Segre, J.A.//Palmore, T.N. 	Detection and Whole-Genome Sequencing of Carbapenemase-Producing Aeromonas hydrophila Isolates from Routine Perirectal Surveillance Culture.	J. Clin. Microbiol.	2016	54		1167-1170			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. 		
@D	Hughes, S.G. 	A map of the cleavage sites for endonuclease AvaI in the chromosome of bacteriophage lambda.	Biochem. J.	1977	163		503-509			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. 		
@A	Hughes, S.G. 		Studies of plasmid encoded restriction and modification systems.			 		Ph.D. Thesis, University of Edinburgh, Edinburgh, Scotland				Edinburgh		1977				1-70									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. 		
@D	Hughes, S.G.//Bruce, T.//Murray, K. 	The Isolation and Characterization of a Sequence-Specific Endonuclease from Anabaena subcylindrica.	Biochem. J.	1980	185		59-63			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. 		
@D	Hughes, S.G.//Hattman, S. 	The sensitivity of bacteriophage lambda DNA to restriction endonuclease RII.	J. Mol. Biol.	1975	98		645-647			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. 		
@D	Hughes, S.G.//Murray, K. 	The Nucleotide Sequences Recognized by Endonucleases AvaI and AvaII from Anabaena variabilis.	Biochem. J.	1980	185		65-75			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. 		
@D	Hugon, P.//Mishra, A.K.//Lagier, J.C.//Nguyen, T.T.//Couderc, C.//Raoult, D.//Fournier, P.E. 	Non-contiguous finished genome sequence and description of Brevibacillus massiliensis sp. nov.	Standards in Genomic Sciences	2013	8		1-14			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%. 		
@D	Hugon, P.//Mishra, A.K.//Robert, C.//Raoult, D.//Fournier, P.E. 	Non-contiguous finished genome sequence and description of Anaerococcus vaginalis.	Standards in Genomic Sciences	2012	6		356-365			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. 		
@D	Hugon, P.//Ramasamy, D.//Lagier, J.C.//Rivet, R.//Couderc, C.//Raoult, D.//Fournier, P.E. 	Non contiguous-finished genome sequence and description of Alistipes obesi sp. nov.	Standards in Genomic Sciences	2013	7		427-439			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. 		
@D	Hugon, P.//Ramasamy, D.//Robert, C.//Couderc, C.//Raoult, D.//Fournier, P.E. 	Non-contiguous finished genome sequence and description of Kallipyga massiliensis gen. nov., sp. nov., a new member of the family Clostridiales Incertae Sedis XI.	Standards in Genomic Sciences	2013	8		500-515			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. 		
@D	Huguet-Tapia, J.C.//Loria, R. 	Draft Genome Sequence of Streptomyces acidiscabies 84-104, an Emergent Plant Pathogen.	J. Bacteriol.	2012	194		1847			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. 		
@D	Huguet-Tapia, J.C.//Peng, Z.//Yang, B.//Yin, Z.//Liu, S.//White, F.F. 	Complete Genome Sequence of the African Strain AXO1947 of Xanthomonas oryzae pv.  oryzae.	Genome Announcements	2016	4		e01730-15			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. 		
@D	Hui, R.K.//Chen, J.W.//Chan, K.G.//Leung, F.C. 	Complete Genome Sequence of Dyella japonica Strain A8 Isolated from Malaysian Tropical Soil.	Genome Announcements	2014	2		e01164-14			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. 		
@D	Huja, S.//Oren, Y.//Trost, E.//Brzuszkiewicz, E.//Biran, D.//Blom, J.//Goesmann, A.//Gottschalk, G.//Hacker, J.//Ron, E.Z.//Dobrindt, U. 	Genomic Avenue to Avian Colisepticemia.	MBio	2015	6		e01681-14			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. 		
@D	Hulsmann, K.-H.//Quaas, R.//Georgalis, Y.//Saenger, W.//Hahn, U. 	High-level expression of a semisynthetic dam gene in Escherichia coli.	Gene	1991	98		83-88			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. 		
@D	Humann, J.L.//Wildung, M.//Cheng, C.-H.//Lee, T.//Drew, J.C.//Triplett, E.W.//Main, D.//Schroeder, B.K. 	Complete genome of the onion pathogen Enterobacter cloacae EcWSU1.	Standards in Genomic Sciences	2011	5		279-286					
@D	Humann, J.L.//Wildung, M.//Pouchnik, D.//Bates, A.A.//Drew, J.C.//Zipperer, U.N.//Triplett, E.W.//Main, D.//Schroeder, B.K. 	Complete genome of the switchgrass endophyte Enterobacter clocace P101.	Standards in Genomic Sciences	2014	9		726-734			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. 		
@D	Humbelin, M.//Suri, B.//Rao, D.N.//Hornby, D.P.//Eberle, H.//Pripfl, T.//Kenel, S.//Bickle, T.A. 	Type III DNA restriction and modification systems EcoP1 and EcoP15.	J. Mol. Biol.	1988	200		23-29			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. 		
@D	Humbert, O.//Dorer, M.S.//Salama, N.R. 	Characterization of Helicobacter pylori factors that control transformation frequency and integration length during inter-strain DNA  recombination.	Mol. Microbiol.	2011	79		387-401			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. 		
@D	Humbert, O.//Salama, N.R. 	Functional characterization of HP0503: An adenine methyltransferase required for the virulence of Helicobacter pylori.	Abstr. Gen. Meet. Am. Soc. Microbiol.	2007	107		39			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. 		
@D	Humbert, O.//Salama, N.R. 	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.	Nucleic Acids Res.	2008	36		6893-6906			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. 		
@D	Humbert, O.M. 	Restriction-modification systems and the regulation of genetic exchange in Helicobacter pylori.	Ph.D. Thesis, University of Washington, Seattle, USA	2010			1-127			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. 		
@D	Humeny, A.//Beck, C.//Becker, C.M.//Jeltsch, A. 	Detection and analysis of enzymatic DNA methylation of oligonucleotide substrates by matrix-assisted laser desorption ionization time-of-flight mass spectrometry.	Anal. Biochem.	2003	313		160-166			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. 		
@D	Humphreys, C.M. et al. 	Whole genome sequence and manual annotation of Clostridium autoethanogenum, an industrially relevant bacterium.	BMC Genomics	2015	16		1085			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. 		
@D	Humphreys, J.R.//Daniel, R.//Poehlein, A. 	Insights into the Genome of the Anaerobic Acetogen Sporomusa silvacetica DSM 10669.	Genome Announcements	2017	5		e00983-17			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. 		
@D	Humphreys, J.R.//Daniel, R.//Poehlein, A. 	Genome Sequence of the Homoacetogenic, Gram-Negative, Endospore-Forming Bacterium Sporomusa acidovorans DSM 3132.	Genome Announcements	2017	5		e00981-17			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. 		
@D	Humphries, P.//Gordon, R.L.//McConnell, D.J.//Connolly, P. 	Endonuclease R. Hind fragments of T7 DNA.	Virology	1974	58		25-31			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. 		
@D	Hung, J.E.//Mill, C.P.//Clifton, S.W.//Magrini, V.//Bhide, K.//Francois, J.A.//Ransome, A.E.//Fulton, L.//Thimmapuram, J.//Wilson, R.K.//Kappock, T.J. 	Draft Genome Sequence of Acetobacter aceti Strain 1023, a Vinegar Factory Isolate.	Genome Announcements	2014	2		e00550-14			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. 		
@D	Hung, M.S.//Karthikeyan, N.//Huang, B.//Koo, H.C.//Kiger, J.//Shen, C.J. 	Drosophila proteins related to vertebrate DNA (5-cytosine) methyltransferases.	Proc. Natl. Acad. Sci. U. S. A.	1999	96		11940-11945			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. 		
@D	Hungria, M.//Ribeiro, R.A.//Nogueira, M.A. 	Draft Genome Sequences of Azospirillum brasilense Strains Ab-V5 and Ab-V6, Commercially Used in Inoculants for Grasses and Legumes in Brazil.	Genome Announcements	2018	6		e00393-18			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. 		
@D	Huntemann, M. et al. 	Complete genome sequence of the facultatively anaerobic, appendaged bacterium Muricauda ruestringensis type strain (B1(T)).	Standards in Genomic Sciences	2012	6		185-193			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. 		
@D	Huntemann, M. et al. 	Genome sequence of the phylogenetically isolated spirochete Leptonema illini type strain (3055(T)).	Standards in Genomic Sciences	2013	8		177-187			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. 		
@D	Huntemann, M. et al. 	Complete genome sequence of the thermophilic sulfur-reducer Hippea maritima type  strain (MH(2)).	Standards in Genomic Sciences	2011	4		303-311			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. 		
@D	Hunter, S.S.//Yano, H.//Loftie-Eaton, W.//Hughes, J.//De Gelder, L.//Stragier, P.//De Vos, P.//Settles, M.L.//Top, E.M. 	Draft Genome Sequence of Pseudomonas moraviensis R28-S.	Genome Announcements	2014	2		e00035-14			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. 		
@D	Huntley, S.//Kneip, S.//Treuner-Lange, A.//Sogaard-Andersen, L. 	Complete Genome Sequence of Myxococcus stipitatus Strain DSM 14675, a Fruiting Myxobacterium.	Genome Announcements	2013	1		e0010013			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. 		
@D	Huntley, S.//Zhang, Y.//Treuner-Lange, A.//Kneip, S.//Sensen, C.W.//Sogaard-Andersen, L. 	Complete Genome Sequence of the Fruiting Myxobacterium Corallococcus coralloides  DSM 2259.	J. Bacteriol.	2012	194		3012-3013			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. 		
@D	Hunyadkurti, J.//Feltoti, Z.//Horvath, B.//Nagymihaly, M.//Voros, A.//McDowell, A.//Patrick, S.//Urban, E.//Nagy, I. 	Complete Genome Sequence of Propionibacterium acnes Type IB strain 6609.	J. Bacteriol.	2011	193		4561-4562			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). 		
@A	Huo, W. 		Enterococcus faecalis genome defense systems and their impact on conjugative antibiotic resistance plasmid transfer.			 		Ph.D. Thesis				Dallas, TEX		2017													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. 		
@D	Huo, W.//Adams, H.M.//Zhang, M.Q.//Palmer, K.L. 	Genome modification in Enterococcus faecalis OG1RF assessed by bisulfite sequencing and single molecule real time sequencing.	J. Bacteriol.	2015	197		1939-1951			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. 		
@D	Huo, Y.//Li, P. 	Separation and purification of restriction endonuclease MspI.	Shengwu Huaxue Yu Shengwu Wuli Jinzhan	1989	16		235-236			None 		
@D	Huo, Y.-Y.//Cheng, H.//Han, X.-F.//Jiang, X.-W.//Sun, C.//Zhang, X.-Q.//Zhu, X.-F.//Liu, Y.-F.//Li, P.-F.//Ni, P.-X.//Wu, M. 	Complete genome sequence of Pelagibacterium halotolerans B2T.	J. Bacteriol.	2011	194		197-198			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. 		
@D	Huo, Y.Y.//Li, Z.Y.//Cheng, H.//Wang, C.S.//Xu, X.W. 	High quality draft genome sequence of the heavy metal resistant bacterium Halomonas zincidurans type strain B6(T).	Standards in Genomic Sciences	2014	9		30			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. 		
@D	Hupfeld, M.//Fouts, D.E.//Loessner, M.J.//Klumpp, J. 	Genome Sequences of the Listeria ivanovii subsp. ivanovii Type Strain and Two Listeria ivanovii subsp. londoniensis Strains.	Genome Announcements	2015	3		e01440-14			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. 		
@D	Hupkes, M.//Azevedo, R.//Jansen, H.//van Zoelen, E.J.//Dechering, K.J. 	Identification of Novel Bacterial M.SssI DNA Methyltransferase Inhibitors.	J. Biomol. Screen.	2013	18		348-355			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. 		
@D	Hurd, P.J.//Whitmarsh, A.J.//Baldwin, G.S.//Kelly, S.M.//Waltho, J.P.//Price, N.C.//Connolly, B.A.//Hornby, D.P. 	Mechanism-based inhibition of C5-cytosine DNA methyltransferases by 2-H pyrimidinone.	J. Mol. Biol.	1999	286		389-401			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. 		
@D	Hurst, M.R.//Beattie, A.//Altermann, E.//Moraga, R.M.//Harper, L.A.//Calder, J.//Laugraud, A. 	The Draft Genome Sequence of the Yersinia entomophaga Entomopathogenic Type Strain MH96T.	Toxins (Basel)	2016	8		143			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. 		
@D	Hurst, M.R.//Glare, T.R.//Jackson, T.A. 	Cloning Serratia entomophila antifeeding genes--a putative defective prophage active against the grass grub Costelytra zealandica.	J. Bacteriol.	2004	186		5116-5128			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. 		
@D	Hurst, S.G. IV//Ghazal, S.//Morris, K.//Abebe-Akele, F.//Thomas, W.K.//Badr, U.M.//Hussein, M.A.//AbouZaied, M.A.//Khalil, K.M.//Tisa, L.S. 	Draft Genome Sequence of Photorhabdus temperata Strain Meg1, an Entomopathogenic  Bacterium Isolated from Heterorhabditis megidis Nematodes.	Genome Announcements	2014	2		e01273-14			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. 		
@D	Hurst, S.G.I.V.//Oshone, R.//Ghodhbane-Gtari, F.//Morris, K.//Abebe-Akele, F.//Thomas, W.K.//Ktari, A.//Salem, K.//Mansour, S.//Gtari, M.//Tisa, L.S. 	Draft Genome Sequence of Frankia sp. Strain Thr, a Nitrogen-Fixing Actinobacterium Isolated from the Root Nodules of Casuarina cunninghamiana Grown   in Egypt.	Genome Announcements	2014	2		e00493-14			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. 		
@D	Hurtado, U.A.//Solano, J.S.//Rodriguez, A.//Robledo, J.//Rouzaud, F. 	Draft Genome Sequence of a Mycobacterium africanum Clinical Isolate from Antioquia, Colombia.	Genome Announcements	2016	4		e00486-16			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. 		
@D	Hussain, M.//Suliman, M.//Ahmed, A.//Altayb, H.//Elneima, E. 	Draft Genome Sequence of a Multidrug-Resistant Pseudomonas aeruginosa Strain Isolated from a Patient with a Urinary Tract Infection in Khartoum, Sudan.	Genome Announcements	2017	5		e00203-17			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. 		
@D	Hutchison, C.A. III//Peterson, S.N.//Gill, S.R.//Cline, R.T.//White, O.//Fraser, C.M.//Smith, H.O.//Venter, J.C. 	Global transposon mutagenesis and a minimal mycoplasma genome.	Science	1999	286		2165			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. 		
@D	Hutt, L.P.//Huntemann, M.//Clum, A.//Pillay, M.//Palaniappan, K.//Varghese, N.//Mikhailova, N.//Stamatis, D.//Reddy, T.//Daum, C.//Shapiro, N.//Ivanova, N.//Kyrpides, N.//Woyke, T.//Boden, R. 	Permanent draft genome of Thiobacillus thioparus DSM 505T, an obligately chemolithoautotrophic member of the Betaproteobacteria.	Standards in Genomic Sciences	2017	12		10			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. 		
@D	Hwang, C. et al. 	Complete Genome Sequence of Alkaliphilus metalliredigens Strain QYMF, an Alkaliphilic and Metal-Reducing Bacterium Isolated from Borax-Contaminated  Leachate Ponds.	Genome Announcements	2016	4		e01226-16			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. 		
@D	Hwang, C. et al. 	Complete Genome Sequence of Anaeromyxobacter sp. Fw109-5, an Anaerobic, Metal-Reducing Bacterium Isolated from a Contaminated Subsurface Environment.	Genome Announcements	2015	3		e01449-14			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. 		
@D	Hwang, D.K.//Cho, J.Y.//Chae, Y.K. 	Recombinant expression and purification of functional XorII, a restriction endonuclease from Xanthomonas oryzae pv. oryzae.	J. Microbiol.	2007	45		175-178			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. 		
@D	Hwang, H.-Y.//Yim, J. 	SolI, a novel isoschizomer of BamHI isolated from Streptoverticillium olivoverticillatum.	Nucleic Acids Res.	1994	22		2197			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. 		
@D	Hwang, H.Y.//Yim, J. 	Characterization of a new type II restriction endonuclease isolated from Streptoverticillium olivoverticillatum.	Korean J. Microbiol.	1994	32		208-214			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. 		
@D	Hwang, J.Y.//Kim, S.H.//Oh, H.R.//Cho, Y.J.//Chun, J.//Chung, Y.R.//Nam, D.H. 	Draft Genome Sequence of Kitasatospora cheerisanensis KCTC 2395, Which Produces Plecomacrolide against Phytopathogenic Fungi.	Genome Announcements	2014	2		e00604-14			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. 		
@D	Hwang, S.//Song, Y.//Cho, B.K. 	Draft Genome Sequence of Acetobacterium bakii DSM 8239, a Potential Psychrophilic Chemical Producer through Syngas Fermentation.	Genome Announcements	2015	3		e01070-15			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. 		
@D	Hwang, S.B.//Lee, S.H. 	Character and function of restriction enzyme, EcoRI inhibiting substance extracted from spinach chloroplast and Chlamydomonas.	Singmul Hakhoe Chi	1990	33		217-223			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. 		
@D	Hwangbo, K.//Um, Y.//Chung, H.//Yoo, J.//Kim, K.Y.//Madhaiyan, M.//Sa, T.M.//Lee, Y. 	Complete Genome Sequence of Dyella thiooxydans ATSB10, a Thiosulfate-Oxidizing Bacterium Isolated from Sunflower Fields in South Korea.	Genome Announcements	2016	4		e00573-16			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. 		
@D	Hwangbo, K.//Um, Y.//Kim, K.Y.//Madhaiyan, M.//Sa, T.M.//Lee, Y. 	Complete Genome Sequence of Bacillus velezensis CBMB205, a Phosphate-Solubilizing Bacterium Isolated from the Rhizoplane of Rice in the Republic of Korea.	Genome Announcements	2016	4		e00654-16			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. 		
@D	Hyden, P.//Pietzka, A.//Allerberger, F.//Springer, B.//Sensen, C.//Ruppitsch, W. 	Draft Genome Sequence of a 94-Year-Old Listeria monocytogenes Isolate, SLCC208.	Genome Announcements	2016	4		e01572-15			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. 		
@D	Hyman, P.//Abedon, S.T. 	Bacteriophage Host Range and Bacterial Resistance.	Adv. Appl. Microbiol.	2010	70		217-248			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. 		
@D	Hyman, R.W.//St-Onge, R.P.//Allen, E.A.//Miranda, M.//Aparicio, A.M.//Fukushima, M.//Davis, R.W. 	Multiplex identification of microbes.	Appl. Environ. Microbiol.	2010	76		3904-3910			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. 		
@D	Hynes, R.K.//Dumonceaux, T.J.//Kangsopa, J.//Town, J.R. 	Genome Sequence of a Plant Growth-Promoting Rhizobacterium, Pseudomonas sp. Strain 31-12.	Microbiol. Resour. Announc.	2018	7		e00947-18			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. 		
@D	Hyson, P.//Shapiro, J.A.//Wien, M.W. 	Draft Genome Sequence of Exiguobacterium sp. Strain BMC-KP, an Environmental Isolate from Bryn Mawr, Pennsylvania.	Genome Announcements	2015	3		e01164-15			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. 		
@D	Hyun, D.W.//Whon, T.W.//Cho, Y.J.//Chun, J.//Kim, M.S.//Jung, M.J.//Shin, N.R.//Kim, J.Y.//Kim, P.S.//Yun, J.H.//Lee, J.//Oh, S.J.//Bae, J.W. 	Genome sequence of the moderately halophilic bacterium Salinicoccus carnicancri type strain Crm(T) (= DSM 23852(T)).	Standards in Genomic Sciences	2013	8		255-263			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. 		
@D	Iartchouk, O.//Kozyavkin, S.//Karamychev, V.//Slesarev, A. 	Complete Genome Sequence of Lactobacillus acidophilus FSI4, Isolated from Yogurt.	Genome Announcements	2015	3		e00166-15			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. 		
@D	Iatsenko, I.//Corton, C.//Pickard, D.J.//Dougan, G.//Sommer, R.J. 	Draft Genome Sequence of Highly Nematicidal Bacillus thuringiensis DB27.	Genome Announcements	2014	2		e00101-14			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. 		
@D	Ibacache-Quiroga, C.//Canales, C.//Charifeh, M.//Dinamarca, M.A. 	Genome Sequence of Cobetia sp. Strain MM1IDA2H-1, a Hydrocarbon-Degrading and Biosurfactant-Producing Marine Bacterium.	Genome Announcements	2017	5		e00132-17			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. 		
@D	Ibanez, M.//Alvarez, I.//Rodriguez-Pena, J.M.//Rotger, R. 	A ColE1-type plasmid from Salmonella enteritidis encodes a DNA cytosine methyltransferase.	Gene	1997	196		145-158			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. 		
@D	Ibanez, M.//Rotger, R. 	Characterization of small cryptic plasmid from Salmonella enteritidis that affects the growth of Escherichia coli.	FEMS Microbiol. Lett.	1993	109		225-230			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. 		
@D	Ibarra-Caballero, J.//Zerillo, M.M.//Snelling, J.//Cranshaw, W.//Boucher, C.//Tisserat, N. 	Genome Sequences of Strain ATCC 29281 and Pin and Northern Red Oak Isolates of Lonsdalea quercina subsp. quercina.	Genome Announcements	2014	2		e00584-14			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. 		
@D	Ibrahim, M.H.//Cress, B.F.//Linhardt, R.J.//Koffas, M.A.//Gross, R.A. 	Draft Genome Sequence of Bacillus subtilis Ia1a, a New Strain for Poly-gamma-Glutamic Acid and Exopolysaccharide Production.	Genome Announcements	2016	4		e01361-16			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. 		
@D	Ibryashkina, E.M.//Sasnauskas, G.//Solonin, A.S.//Zakharova, M.V.//Siksnys, V. 	Oligomeric structure diversity within the GIY-YIG nuclease family.	J. Mol. Biol.	2009	387		10-16			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. 		
@D	Ibryashkina, E.M.//Zakharova, M.V.//Baskunov, V.B.//Bogdanova, E.S.//Nagornykh, M.O.//Den'mukhamedov, M.M.//Melnik, B.S.//Kolinski, A.//Gront, D.//Feder, M.//Solonin, A.S.//Bujnicki, J.M. 	Type II restriction endonuclease R.Eco29kI is a member of the GIY-YIG nuclease superfamily.	BMC Struct. Biol.	2007	7		48			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. 		
@D	Ichida, H.//Maeda, K.//Ichise, H.//Matsuyama, T.//Abe, T.//Yoneyama, K.//Koba, T. 	In silco irestiriction landmairk genome scanning analysis of Xanthomonas oryzae pathovair oryzae MAFF 311018.	Biochem. Biophys. Res. Commun.	2007	363		852-856			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. 		
@D	Ichida, H.//Matsuyama, T.//Abe, T.//Koba, T. 	DNA adenine methylation changes dramatically during establishment of symbiosis.	FEBS J.	2007	274		951-962			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. 		
@D	Ichige, A.//Kobayashi, I. 	Stability of EcoRI Restriction-Modification Enzymes In Vivo Differentiates the EcoRI Restriction-Modification System from Other Postsegregational   Cell Killing Systems.	J. Bacteriol.	2005	187		6612-6621			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. 		
@D	Ichige, A.//Kobayashi, I. 	Stability of EcoRI restriction modification enzymes in vivo differentiates EcoRI restriction-modification system from other postsegregational cell killing systems.	Genes Genet. Syst.	2005	80		454			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. 		
@D	Ichikawa, N. et al. 	Genome Sequence of Kitasatospora setae NBRC 14216T: An Evolutionary Snapshot of the Family Streptomycetaceae.	DNA Res.	2010	17		393-406			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. 		
@D	Ichise, Y.K.//Kosuge, T.//Uwate, M.//Nakae, T.//Maseda, H. 	Complete Genome Sequence of Pseudomonas aeruginosa Strain 8380, Isolated from the Human Gut.	Genome Announcements	2015	3		e00520-15			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. 		
@D	Ichiwaki, S.//Costa, A.C.M.M.//Silva, E.G.//Rada, L.R.M.//Lima, F.R.//Ortiz-Vera, M.P.//Garrido, L.M.//Sato, M.I.Z.//Araujo, W.L.//Padilla, G. 	Genome Sequence of Micromonospora sp. NBS 11-29, an Antibiotic and Hydrolytic Enzyme Producer, Isolated from River Sediment in Brazil.	Genome Announcements	2017	5		e00552-17			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. 		
@D	Ichiyanagi, K. 	Inhibition of MspI cleavage activity by hydroxymethylation of the CpG site A concern for DNA modification studies using restriction endonucleases.	EPIGENETICS	2012	7		131-136			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. 		
@D	Ichiyanagi, K.//Ishino, Y.//Ariyoshi, M.//Komori, K.//Morikawa, K. 	Crystal structure of an archaeal intein-encoded homing endonuclease PI-PfuI.	J. Mol. Biol.	2000	300		889-901			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. 		
@D	Igbinosa, E.O.//Rathje, J.//Habermann, D.//Brinks, E.//Cho, G.S.//Franz, C.M.A.P. 	Draft Genome Sequence of Multidrug-Resistant Strain Citrobacter portucalensis MBTC-1222, Isolated from Uziza (Piper guineense) Leaves in Nigeria.	Genome Announcements	2018	6		e00123-18			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). 		
@D	Iglesias, N.G.//Valdes, La.H.D.//Olguin, N.T.//Bravo-Ferrada, B.M.//Brizuela, N.S.//Tymczyszyn, E.E.//Bibiloni, H.//Caballero, A.C.//Delfederico, L.//Semorile, L. 	Genome Sequence of Oenococcus oeni UNQOe19, the First Fully Assembled Genome Sequence of a Patagonian Psychrotrophic Oenological Strain.	Microbiol. Resour. Announc.	2018	7		e00889-18			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. 		
@D	Ignatov, A.N.//Kyrova, E.I.//Vinogradova, S.V.//Kamionskaya, A.M.//Schaad, N.W.//Luster, D.G. 	Draft Genome Sequence of Xanthomonas arboricola Strain 3004, a Causal Agent of Bacterial Disease on Barley.	Genome Announcements	2015	3		e01572-14			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. 		
@D	Iida, S.//Meyer, J.//Bachi, B.//Stalhammar-Carlemalm, M.//Schrickel, S.//Bickle, T.A.//Arber, W. 	DNA Restriction-Modification Genes of Phage P1 and Plasmid p15B.	J. Mol. Biol.	1983	165		1-18			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. 		
@D	Iida, S.//Streiff, M.B.//Bickle, T.A.//Arber, W. 	Two DNA antirestriction systems of bacteriophage P1, darA, and darB:  characterization of darA- phages.	Virology	1987	157		156-166			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. 		
@D	Iida, T.//Suetake, I.//Tajima, S.//Morioka, H.//Ohta, S.//Obuse, C.//Tsurimoto, T. 	PCNA clamp facilitates action of DNA cytosine methyltransferase 1 on hemimethylated DNA.	Genes Cells	2002	7		997-1008			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. 		
@D	Iida, Y.//Fujiwara, K.//Someya, N.//Shinohara, M. 	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.	Genome Announcements	2017	5		e00007-17			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. 		
@D	Ikawa, S.//Shibata, T.//Ando, T. 	Recognition sequence of endonuclease R. BamNx from Bacillus amyloliquefaciens N.	Agric. Biol. Chem.	1979	43		873-875			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. 		
@D	Ikawa, S.//Shibata, T.//Ando, T. 	Host-Controlled modification and restriction in Bacillus subtilis.  Bsu168-System and BsuR-System in B. subtilis 168.	Mol. Gen. Genet.	1979	170		123-127			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. 		
@D	Ikawa, S.//Shibata, T.//Ando, T. 	The Site-specific Deoxyribonuclease from Bacillus pumilus (Endonuclease R.Bpu1387).	J. Biochem. (Tokyo)	1976	80		1457-1460			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. 		
@D	Ikawa, S.//Shibata, T.//Ando, T.//Saito, H. 	Genetic studies on site-specific endodeoxyribonucleases in Bacillus subtilis:  Multiple modification and restriction systems in transformants of Bacillus subtilis 168.	Mol. Gen. Genet.	1980	177		359-368			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. 		
@D	Ikawa, S.//Shibata, T.//Matsumoto, K.//Iijima, T.//Saito, H.//Ando, T. 	Chromosomal loci of genes controlling site-specific restriction endonucleases of Bacillus subtilis.	Mol. Gen. Genet.	1981	183		1-6			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. 		
@D	Ikeda, H.//Ishikawa, J.//Hanamoto, A.//Shinose, M.//Kikuchi, H.//Shiba, T.//Sakaki, Y.//Hattori, M.//Omura, S. 	Complete genome sequence and comparative analysis of the industrial microorganism Streptomyces avermitilis.	Nat. Biotechnol.	2003	21		526-531			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. 		
@D	Ikeda, M.//Nakagawa, S. 	The Corynebacterium glutamicum genome: Features and impacts on biotechnological processes.	Appl. Microbiol. Biotechnol.	2003	62		99-109			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. 		
@D	Ikegami, K.//Aita, Y.//Shiroma, A.//Shimoji, M.//Tamotsu, H.//Ashimine, N.//Shinzato, M.//Ohki, S.//Nakano, K.//Teruya, K.//Satou, K.//Hirano, T.//Yohda, M. 	Complete Genome Sequence of Petrimonas sp. Strain IBARAKI, Assembled from the Metagenome Data of a Culture Containing Dehalococcoides spp.	Genome Announcements	2018	6		e00384-18			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. 		
@D	Ikram, H.I.//Catherine, R.//Caroline, M.//Didier, R.//Hocine, H.//Christelle, D. 	Non-contiguous finished genome sequence and description of Halopiger goleamassiliensis sp. nov.	Standards in Genomic Sciences	2014	9		956-959			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). 		
@D	Ilagan-Cruzada, M.F.C.//Rosana, A.R.R.//Montecillo, A.D.//Sabino, N.G.//Dalmacio, I.F. 	Complete Genome Sequence of Lactobacillus plantarum subsp. plantarum Strain LB1-2, Isolated from the Hindgut of European Honeybees, Apis mellifera L., from  the Philippines.	Genome Announcements	2018	6		e00209-18			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. 		
@D	Ilin, A.I.//Kulmanov, M.E.//Korotetskiy, I.S.//Akhmetova, G.K.//Lankina, M.V.//Shvidko, S.V.//Reva, O.N. 	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.	Genome Announcements	2015	3		e01272-15			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. 		
@D	Illikoud, N.//Klopp, C.//Roulet, A.//Bouchez, O.//Marsaud, N.//Jaffres, E.//Zagorec, M. 	One complete and three draft genome sequences of four Brochothrix thermosphacta strains, CD 337, TAP 175, BSAS1 3 and EBP 3070.	Standards in Genomic Sciences	2018	13		22			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. 		
@D	Imachi, H.//Sakai, S.//Lipp, J.S.//Miyazaki, M.//Saito, Y.//Yamanaka, Y.//Hinrichs, K.U.//Inagaki, F.//Takai, K. 	Pelolinea submarina gen. nov., sp. nov., an anaerobic, filamentous bacterium of the phylum Chloroflexi isolated from subseafloor sediment.	Int. J. Syst. Evol. Microbiol.	2014	64		812-818			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. 		
@D	Imagawa, T.//Nakayama, H.//Katunuma, N.//Sakuraba, H.//Ohshima, T.//Itoh, T.//Sako, Y.//Nomura, N.//Tsuge, H. 	Crystallization and preliminary X-ray diffraction analysis of homing endonuclease I-Tsp061I.	Acta Crystallogr. D Biol. Crystallogr.	2004	60		2006-2008			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. 		
@D	Imajoh, M.//Fukumoto, Y.//Yamane, J.//Sukeda, M.//Shimizu, M.//Ohnishi, K.//Oshima, S. 	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.	Genome Announcements	2015	3		e00082-15			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. 		
@D	Imajoh, M.//Sukeda, M.//Shimizu, M.//Yamane, J.//Ohnishi, K.//Oshima, S. 	Draft Genome Sequence of Erythromycin- and Oxytetracycline-Sensitive Nocardia seriolae Strain U-1 (NBRC 110359).	Genome Announcements	2016	4		e01606-15			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. 		
@D	Imajoh, M.//Tsuji, Y.//Yamashita, H.//Ohgi, M.//Monno, S.//Ohnishi, K.//Horioka, K. 	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.	Genome Announcements	2017	5		e00735-17			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. 		
@D	Imamovic, L.//Misiakou, M.A.//van der Helm, E.//Panagiotou, G.//Muniesa, M.//Sommer, M.O.A. 	Complete Genome Sequence of Escherichia coli Strain WG5.	Genome Announcements	2018	6		e01403-17			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. 		
@D	Imber, R.//Bickle, T.A. 	Purification and properties of the restriction endonuclease BglII from Bacillus globigii.	Eur. J. Biochem.	1981	117		395-399			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. 		
@D	Imhof, P.//Fischer, S.//Smith, J.C. 	Catalytic Mechanism of DNA Backbone Cleavage by the Restriction Enzyme EcoRV: A Quantum Mechanical/Molecular Mechanical Analysis.	Biochemistry	2009	48		9061-9075			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. 		
@D	Imori, P.F.M.//Campioni, F.//Cao, G.//Kastanis, G.//Leon, M.S.//Allard, M.W.//Falcao, J.P. 	Draft Genome Sequences of Yersinia frederiksenii, Yersinia intermedia, and Yersinia kristensenii Strains from Brazil.	Genome Announcements	2017	5		e00780-17			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. 		
@D	Inaba, T.//Sato, Y.//Koike, H.//Hori, T.//Kanno, M.//Kimura, N.//Kirimura, K.//Habe, H. 	Draft Genome Sequence of Pseudomonas citronellolis LA18T, a Bacterium That Uses Levulinic Acid.	Microbiol. Resour. Announc.	2018	7		e00906-18			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. 		
@D	Inada, S.//Watanabe, K. 	Draft Genome Sequence of Meiothermus ruber H328, Which Degrades Chicken Feathers, and Identification of Proteases and Peptidases Responsible for Degradation.	Genome Announcements	2013	1		e00176-13			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. 		
@D	Inagaki, K.//Dou, D.//Kita, K.//Hiraoka, N.//Kishimoto, N.//Sugio, T.//Tano, T. 	Isolation and characterization of restriction endonucleases from Acidiphilium sp. 16R and 22M.	J. Ferment. Bioeng.	1990	69		60-62			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. 		
@D	Inagaki, K.//Hikita, T.//Yanagidani, S.//Nomura, Y.//Kishimoto, N.//Tano, T.//Tanaka, H. 	Restriction endonuclease Aor13HI from Acidiphilium organovorum 13H, a new isoschizomer of BspMII: Purification and characterization.	Biosci. Biotechnol. Biochem.	1993	57		1716-1721			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. 		
@D	Inagaki, K.//Ito, T.//Sagawa, H.//Kotani, H.//Kishimoto, N.//Sugio, T.//Tano, T.//Tanaka, H. 	AcpI, a novel isoschizomer of AsuII from Acidiphilium cryptum 25H, recognizes the sequence 5'TT^CGAA3'.	Nucleic Acids Res.	1991	19		6335			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. 		
@D	Inagaki, K.//Kobayashi, F.//Dou, D.//Nomura, Y.//Kotani, H.//Kishimoto, N.//Sugio, T.//Tano, T. 	Isolation and identification of restriction endonuclease Asp35HI from Acidiphilium species 35H.	Nucleic Acids Res.	1990	18		6155			None 		
@D	Inano, K.//Suetake, I.//Ueda, T.//Miyake, Y.//Nakamura, M.//Okada, M.//Tajima, S. 	Maintenance-type DNA methyltransferase is highly expressed in post-mitotic neurons and localized in the cytoplasmic compartment.	J. Biochem. (Tokyo)	2000	128		315-321			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. 		
@D	Indiana, A.//Briand, M.//Arlat, M.//Gagnevin, L.//Koebnik, R.//Noel, L.D.//Portier, P.//Darrasse, A.//Jacques, M.A. 	Draft Genome Sequence of the Flagellated Xanthomonas fuscans subsp. fuscans Strain CFBP 4884.	Genome Announcements	2014	2		e00966-14			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. 		
@D	Inglin, R.C.//Meile, L.//Klumpp, J.//Stevens, M.J.A. 	Complete and Assembled Genome Sequence of Lactobacillus plantarum RI-113 Isolated from Salami.	Genome Announcements	2017	5		e00183-17			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. 		
@D	Inglin, R.C.//Meile, L.//Stevens, M.J.A. 	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.	Genome Announcements	2017	5		e00632-17			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. 		
@A	Inocencio, T.//Vital, J.//Vitor, J.//Falcao, A.O. 		Genome inspector: A web tool for exploring bacterial genomes.			Cachopo, J.//Sousa Santos, B. 		Proc. InForum 2013				Evora, Portugal		2013		0		5-16									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. 		
@D	Inoue, K.//Ogura, Y.//Kawano, Y.//Hayashi, T. 	Complete Genome Sequence of Geobacter sulfurreducens Strain YM18, Isolated from River Sediment in Japan.	Genome Announcements	2018	6		e00352-18			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. 		
@D	Inselburg, J. 	Phage P1 modification of bacterial DNA studied by generalized transduction.	Virology	1966	30		257-265			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. 		
@D	Inturri, R.//Ventura, M.//Ruas-Madiedo, P.//Lugli, G.A.//Blandino, G. 	Complete Genome Sequence of Bifidobacterium longum W11 (LMG P-21586), Used as a Probiotic Strain.	Genome Announcements	2017	5		e01659-16			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. 		
@D	Ioerger, T.R.//Feng, Y.//Chen, X.//Dobos, K.M.//Victor, T.C.//Streicher, E.M.//Warren, R.M.//Gey-van-Pittius, N.C.//Van Helden, P.D.//Sacchettini, J.C. 	The non-clonality of drug resistance in Beijing-genotype isolates of Mycobacterium tuberculosis from the Western Cape of South Africa.	BMC Genomics	2010	11		670			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. 		
@D	Iordanescu, S.//Surdeanu, M. 	Two restriction and modification systems in Staphylococcus aureus NCTC8325.	J. Gen. Microbiol.	1976	96		277-281			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. 		
@D	Ip, M.//Ma, H.//Li, C.//Tsui, S.//Zhou, H. 	Draft Genome Sequences of Two Streptococcus pneumoniae Serotype 19F Sequence Type 271 Clinical Isolates with Low- and High-Level Cefotaxime Resistance.	Genome Announcements	2015	3		e00605-15			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). 		
@D	Ip, M.//Wang, Z.//Lam, W.Y.//Zhou, H.//Tsui, S. 	Draft Genome Sequence of Methicillin-Resistant Staphylococcus aureus CUHK_188 (ST188), a Health Care-Associated Bacteremic Isolate from Hong Kong.	Genome Announcements	2014	2		e00255-14			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. 		
@D	Iraola, G.//Perez, R.//Naya, H.//Paolicchi, F.//Harris, D.//Lawley, T.D.//Rego, N.//Hernandez, M.//Calleros, L.//Carretto, L.//Velilla, A.//Morsella, C.//Mendez, A.//Gioffre, A. 	Complete Genome Sequence of Campylobacter fetus subsp. venerealis Biovar Intermedius, Isolated from the Prepuce of a Bull.	Genome Announcements	2013	1		e00526-13			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. 		
@D	Iriarte, A.//Giner-Lamia, J.//Silva, C.//Betancor, L.//Astocondor, L.//Cestero, J.J.//Ochoa, T.//Garcia, C.//Puente, J.L.//Chabalgoity, J.A.//Garcia-Del Portillo, F. 	Draft Genome Sequence of Salmonella enterica subsp. enterica Serovar Infantis Strain SPE101, Isolated from a Chronic Human Infection.	Genome Announcements	2017	5		e00679-17			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. 		
@D	Irisawa, T.//Oshima, K.//Suda, W.//Kitahara, M.//Sakamoto, M.//Kitamura, K.//Iida, T.//Hattori, M.//Ohkuma, M. 	Draft Genome Sequence of Lactobacillus sucicola JCM 15457T, a Motile Lactic Acid  Bacterium Isolated from Oak Sap.	Genome Announcements	2014	2		e00403-14			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. 		
@D	Irlinger, F.//Loux, V.//Bento, P.//Gibrat, J.F.//Straub, C.//Bonnarme, P.//Landaud, S.//Monnet, C. 	Genome Sequence of Staphylococcus equorum subsp. equorum Mu2, Isolated from a French Smear-Ripened Cheese.	J. Bacteriol.	2012	194		5141-5142			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. 		
@D	Irma-Syakina, M.Z.//Teh, L.K.//Salleh, M.Z. 	Draft Genome Sequence of Streptococcus agalactiae PR06.	Genome Announcements	2013	1		e00351-13			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. 		
@D	Irschik, H.//Kopp, M.//Weissman, K.J.//Buntin, K.//Piel, J.//Muller, R. 	Analysis of the sorangicin gene cluster reinforces the utility of a combined phylogenetic/retrobiosynthetic analysis for deciphering natural product assembly by trans-AT PKS.	Chembiochem	2010	11		1840-1849			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. 		
@D	Isakovic, L.//Saavedra, O.M.//Llewellyn, D.B.//Claridge, S.//Zhan, L.J.//Bernstein, N.//Vaisburg, A.//Elowe, N.//Petschner, A.J.//Rahil, J.//Beaulieu, N.//Gauthier, F.//MacLeod, A.R.//Delorme, D.//Besterman, J.M.//Wahhab, A. 	Constrained (L-)-S-adenosyl-L-homocysteine (SAH) analogues as DNA methyltransferase inhibitors.	Bioorg. Med. Chem. Lett.	2009	19		2742-2746			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. 		
@D	Isalan, M.//Choo, Y. 	Engineered Zinc Finger Proteins that Respond to DNA Modification by HaeIII and HhaI Methyltransferase Enzymes.	J. Mol. Biol.	2000	295		471-477			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. 		
@D	Isanapong, J. et al. 	High-Quality Draft Genome Sequence of the Opitutaceae Bacterium Strain TAV1, a Symbiont of the Wood-Feeding Termite Reticulitermes flavipes.	J. Bacteriol.	2012	194		2744-2745			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. 		
@D	Ishaq, M.//Kaji, A. 	Mechanism of T4 phage restriction by plasmid Rts 1. Cleavage of T4 phage DNA by Rts 1-specific enzyme.	J. Biol. Chem.	1980	255		4040-4047			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. 		
@D	Ishida, C.//Ura, K.//Hirao, A.//Sasaki, H.//Toyoda, A.//Sakaki, Y.//Niwa, H.//Li, E.//Kaneda, Y. 	Genomic organization and promoter analysis of the Dnmt3b gene.	Gene	2003	310		151-159			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. 		
@D	Ishii, S.//Amarasiri, M.//Hashiba, S.//Yang, P.//Okabe, S.//Sano, D. 	Genome Sequence of Enterobacter cloacae Strain SENG-6, a Bacterium Producing Histo-Blood Group Antigen-Like Substances That Can Bind with Human Noroviruses.	Genome Announcements	2016	4		e00893-16			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. 		
@D	Ishii, S.//Tago, K.//Nishizawa, T.//Oshima, K.//Hattori, M.//Senoo, K. 	Complete Genome Sequence of the Denitrifying and N2O-Reducing Bacterium Pseudogulbenkiania sp. Strain NH8B.	J. Bacteriol.	2011	193		6395-6396			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. 		
@D	Ishikawa, J.//Yamashita, A.//Mikami, Y.//Hoshino, Y.//Kurita, H.//Hotta, K.//Shiba, T.//Hattori, M. 	The complete genomic sequence of Nocardia farcinica IFM 10152.	Proc. Natl. Acad. Sci. U. S. A.	2004	101		14925-14930			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. 		
@D	Ishikawa, K.//Fukuda, E.//Kobayashi, I. 	Conflicts targeting epigenetic systems and their resolution by cell death: novel concepts for methyl-specific and other restriction systems.	DNA Res.	2010	17		325-342			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. 		
@D	Ishikawa, K.//Handa, N.//Kobayashi, I. 	Cleavage of a model DNA replication fork by a Type I restriction endonuclease.	Nucleic Acids Res.	2009	37		3531-3544			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. 		
@D	Ishikawa, K.//Handa, N.//Kobayashi, I. 	Coupling of DNA replication and restriction: A type I restriction enzyme cleaves branched DNAs mimicing replication forks, in vitro.	Genes Genet. Syst.	2008	83		510			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. 		
@D	Ishikawa, K.//Handa, N.//Sears, L.//Raleigh, E.A.//Kobayashi, I. 	Cleavage of a model DNA replication fork by a methyl-specific endonuclease.	Nucleic Acids Res.	2011	39		5489-5498			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. 		
@D	Ishikawa, K.//Watanabe, M.//Kuroita, T.//Uchiyama, I.//Bujnicki, J.//Kawakami, B.//Tanokura, M.//Kobayashi, I. 	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.	Genes Genet. Syst.	2005	80		454			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. 		
@D	Ishikawa, K.//Watanabe, M.//Kuroita, T.//Uchiyama, I.//Bujnicki, J.M.//Kawakami, B.//Tanokura, M.//Kobayashi, I. 	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.	Nucleic Acids Res.	2005	33		e112			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. 		
@D	Ishikawa, T.//Yamada, Y. 	Purification of restriction endonuclease from Acetobacter pasteurianus IFO 13752 (ApaORI) and its properties.	J. Gen. Appl. Microbiol.	1990	36		127-135			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). 		
@D	Ishino, Y.//Nomura, Y.//Kato, I. 	Sse8647I, a new type II restriction endonuclease from a Streptomyces species cutting at 5'-AG/GWCCT-3'.	Nucleic Acids Res.	1995	23		742-744			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. 		
@D	Ishiwata, N.//Tanimura, A.//Miyahara, M.//Mise, K. 	Studies on restriction endonucleases of bacteria causing peroral infectious diseases.  I. Characterization of Hsd plasmid in Salmonella typhi.	Shokuhin Eiseigaku Zasshi	1995	36		404-408			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. 		
@D	Ishiyama, S. et al. 	Structure of the Dnmt1 Reader Module Complexed with a Unique Two-Mono-Ubiquitin Mark on Histone H3 Reveals the Basis for DNA Methylation Maintenance.	Mol. Cell	2017	68		350-360.e7			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. 		
@D	Ishizawa, H.//Kuroda, M.//Ike, M. 	Draft Genome Sequence of Aquitalea magnusonii Strain H3, a Plant Growth-Promoting Bacterium of Duckweed (Lemna minor).	Genome Announcements	2017	5		e00812-17			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. 		
@D	Ishizawa, H.//Kuroda, M.//Morikawa, M.//Ike, M. 	Evaluation of environmental bacterial communities as a factor affecting the growth of duckweed Lemna minor.	Biotechnol. Biofuels.	2017	10		0					
@D	Iskander, M.//Hayden, K.//Van Domselaar, G.//Tsang, R. 	First Complete Genome Sequence of Haemophilus influenzae Serotype a.	Genome Announcements	2017	5		e01506-16			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. 		
@D	Ismail, A.//Teh, L.K.//Ngeow, Y.F.//Norazmi, M.N.//Zainul, Z.F.//Tang, T.H.//Najimudin, N.//Salleh, M.Z. 	Draft Genome Sequence of a Clinical Isolate of Mycobacterium tuberculosis Strain  PR05.	Genome Announcements	2013	1		e00397-13			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. 		
@D	Isojarvi, J.//Shunmugam, S.//Sivonen, K.//Allahverdiyeva, Y.//Aro, E.M.//Battchikova, N. 	Draft genome sequence of calothrix strain 336/3, a novel h2-producing cyanobacterium isolated from a finnish lake.	Genome Announcements	2015	3		e01474-14			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. 		
@D	Isokpehi, R.D.//Coker, A.O. 	Possible stepwise evolution of type II restriction-modification genes in Helicobacter pylori genome.	Int. J. Med. Microbiol.	2001	291S		94			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. 		
@D	Isokpehi, R.D.//Coker, A.O. 	In silico evidence for horizontal gene transfer of type II restriction-modification genes in Helicobacter pylori.	Biochem. Soc. Trans.	2000	28		A185			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. 		
@D	Issa, R.//Seradja, V.H.//Abdullah, M.K. 	Whole-Genome Shotgun Sequencing and Annotation of Mycobacterium tuberculosis MTB221/11 Isolated from a Cerebrospinal Fluid Sample in Malaysia.	Genome Announcements	2016	4		e00376-16			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. 		
@D	Issa, R.//Seradja, V.H.//Abdullah, M.K.//Abdul, H. 	Annotated Sequence of Mycobacterium tuberculosis MTBR3/09 Isolated from a Sputum  Sample in Malaysia.	Genome Announcements	2016	4		e00517-16			This is a report of the annotated genome sequence of Mycobacterium tuberculosis MTBR3/09. The organism was isolated from a sputum sample in Malaysia. 		
@D	Issa, R.//Seradja, V.H.//Abdullah, M.K.//Abdul, H. 	Annotated Whole-Genome Shotgun Sequence of Mycobacterium tuberculosis MTBR2/09 Isolated from a Sputum Sample in Malaysia.	Genome Announcements	2016	4		e00515-16			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. 		
@D	Issa, R.//Seradja, V.H.//Abdullah, M.K.//Abdul, H. 	Whole-Genome Shotgun Sequencing and Annotation of Mycobacterium tuberculosis MTBR1/09 Isolated from a Sputum Sample in Malaysia.	Genome Announcements	2016	4		e00513-16			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. 		
@D	Issotta, F.//Galleguillos, P.A.//Moya-Beltran, A.//Davis-Belmar, C.S.//Rautenbach, G.//Covarrubias, P.C.//Acosta, M.//Ossandon, F.J.//Contador, Y.//Holmes, D.S.//Marin-Eliantonio, S.//Quatrini, R.//Demergasso, C. 	Draft genome sequence of chloride-tolerant Leptospirillum ferriphilum Sp-Cl from  industrial bioleaching operations in northern Chile.	Standards in Genomic Sciences	2016	11		19			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. 		
@D	Ito, H.//Sadaoka, A.//Kotani, H.//Hiraoka, N.//Nakamura, T. 	Cloning, nucleotide sequence, and expression of the HincII restriction-modification system.	Nucleic Acids Res.	1990	18		3903-3911			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. 		
@D	Ito, H.//Shimato, H.//Sadaoka, A.//Kotani, H.//Kimizuka, F.//Kato, I. 	Cloning and expression of the HpaI restriction-modification genes.	Nucleic Acids Res.	1992	20		705-709			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. 		
@D	Ito, J.//Kawamura, F.//Duffy, J.J. 	Susceptibility of non-thymine containing DNA to four bacterial restriction endonucleases.	FEBS Lett.	1975	55		278-281			None 		
@D	Ito, J.//Roberts, R.J. 	Unusual base sequence arrangement in phage Phi29 DNA.	Gene	1979	5		1-7			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. 		
@D	Ito, K.//Nakajima, N.//Yamamura, S.//Tomita, M.//Suzuki, H.//Amachi, S. 	Draft Genome Sequence of Arenibacter sp. Strain C-21, an Iodine-Accumulating Bacterium Isolated from Surface Marine Sediment.	Genome Announcements	2016	4		e01155-16			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. 		
@D	Ito, S.//Shen, L.//Dai, Q.//Wu, S.C.//Collins, L.B.//Swenberg, J.A.//He, C.//Zhang, Y. 	Tet proteins can convert 5-methylcytosine to 5-formylcytosine and 5-carboxylcytosine.	Science	2011	333		1300-1303			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. 		
@D	Ito, T.//Katayama, Y.//Asada, K.//Mori, N.//Tsutsumimoto, K.//Tiensasitorn, C.//Hiramatsu, K. 	Structural comparison of three types of Staphylococcal cassette chromosome mec integrated in the chromosome in methicillin-resistant Staphylococcus aureus.	Antimicrob. Agents Chemother.	2001	45		1323-1336			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. 		
@D	Ito, T.//Ma, X.X.//Takeuchi, F.//Okuma, K.//Yuzawa, H.//Hiramatsu, K. 	Novel Type V Staphylococcal Cassette Chromosome mec Driven by a Novel Cassette Chromosome Recombinase, ccrC.	Antimicrob. Agents Chemother.	2004	48		2637-2651			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. 		
@D	Ito, T.//Maruyama, F.//Sawai, K.//Nozaki, K.//Otsu, K.//Ohya, K. 	Draft Genome Sequence of Mycobacterium virginiense Strain GF75, Isolated from the Mud of a Swine Farm in Japan.	Genome Announcements	2018	6		e00362-18			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. 		
@D	Ito, Y.//Azuma, T.//Ito, S.//Suto, H.//Miyaji, H.//Yamazaki, Y.//Kato, T.//Kohli, Y.//Keida, Y.//Kuriyama, M. 	Sequence analysis and clinical significance of the iceA gene from Helicobacter pylori strains in Japan.	J. Clin. Microbiol.	2000	38		483-488			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. 		
@D	Itoh, T. et al. 	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.	DNA Res.	1996	3		379-392			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. 		
@D	Ivancic-Bace, I.//Vlasic, I.//Cogelja-Cajo, G.//Brcic-Kostic, K.//Salaj-Smic, E. 	Roles of PriA protein and double-strand DNA break repair functions in UV-induced restriction alleviation in Escherichia coli.	Genetics	2006	174		2137-2149			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. 		
@D	Ivancic-Jelecki, J.//Baricevic, M.//Santak, M.//Forcic, D. 	Restriction enzyme cleavage of fluorescently labeled DNA fragments - Analysis of the method and its usage in examination of digestion  completeness.	Anal. Biochem.	2006	349		277-284			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. 		
@D	Ivanenko, T.//Heitman, J.//Kiss, A. 	Mutational analysis of the function of Met137 and Ile197, two amino acids implicated in sequence-specific DNA recognition by the EcoRI endonuclease.	Biol. Chem.	1998	379		459-465			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. 		
@D	Ivanova, A.A.//Naumoff, D.G.//Miroshnikov, K.K.//Liesack, W.//Dedysh, S.N. 	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.	Front. Microbiol.	2017	8		412					
@D	Ivanova, E.P.//Ng, H.J.//Webb, H.K.//Feng, G.//Oshima, K.//Hattori, M.//Ohkuma, M.//Sergeev, A.F.//Mikhailov, V.V.//Crawford, R.J.//Sawabe, T. 	Draft Genome Sequences of Marinobacter similis A3d10T and Marinobacter salarius R9SW1T.	Genome Announcements	2014	2		e00442-14			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. 		
@D	Ivanova, N. et al. 	Complete genome sequence of Sanguibacter keddieii type strain (ST-74).	Standards in Genomic Sciences	2009	1		110-118			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. 		
@D	Ivanova, N. et al. 	Complete genome sequence of Leptotrichia buccalis type strain (C-1013-b).	Standards in Genomic Sciences	2009	1		126-132			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. 		
@D	Ivanova, N. et al. 	Complete genome sequence of Gordonia bronchialis type strain (3410).	Standards in Genomic Sciences	2010	2		19-28			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. 		
@D	Ivanova, N. et al. 	Complete genome sequence of Haliangium ochraceum type strain (SMP-2).	Standards in Genomic Sciences	2010	2		96-106			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. 		
@D	Ivanova, N. et al. 	Complete genome sequence of Geodermatophilus obscurus type strain (G-20).	Standards in Genomic Sciences	2010	2		158-167			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. 		
@D	Ivanova, N. et al. 	Genome sequence of Bacillus cereus and comparative analysis with Bacillus anthracis.	Nature	2003	423		87-91			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. 		
@D	Ivanova, N. et al. 	Complete genome sequence of Truepera radiovictrix type strain (RQ-24).	Standards in Genomic Sciences	2011	4		91-99			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. 		
@D	Ivanova, N. et al. 	Complete genome sequence of the extremely halophilic Halanaerobium praevalens type strain (GSL).	Standards in Genomic Sciences	2011	4		312-321			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. 		
@D	Ivanovsky, R.N.//Keppen, O.I.//Lebedeva, N.N.//Beletsky, A.V.//Mardanov, A.V.//Grouzdev, D.S. 	Draft Genome Sequence of the Anoxygenic Phototrophic Bacterium Phaeospirillum fulvum MGU-K5.	Genome Announcements	2017	5		e00895-17			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. 		
@D	Ivarie, R. 	Thymine methyls and DNA-protein interactions.	Nucleic Acids Res.	1987	15		9975-9983			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. 		
@D	Ives, C.L.//Nathan, P.D.//Brooks, J.E. 	Regulation of the BamHI restriction-modification system by a small intergenic open reading frame, bamHIC, in both Escherichia coli and Bacillus subtilis.	J. Bacteriol.	1992	174		7194-7201			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. 		
@D	Ives, C.L.//Sohail, A.//Brooks, J.E. 	The regulatory C proteins from different restriction-modification systems can cross-complement.	J. Bacteriol.	1995	177		6313-6315			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. 		
@D	Ivic, A.//Jakeman, K.J.//Penn, C.W.//Brown, N.L. 	Type II restriction endonucleases from Helicobacter pylori include an enzyme with a novel recognition sequence.	FEMS Microbiol. Lett.	1999	179		175-180			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. 		
@D	Ivshina, I.B.//Kuyukina, M.S.//Krivoruchko, A.V.//Barbe, V.//Fischer, C. 	Draft Genome Sequence of Propane- and Butane-Oxidizing Actinobacterium Rhodococcus ruber IEGM 231.	Genome Announcements	2014	2		e01297-14			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. 		
@D	Iwabuchi, M.//Tajima, S.//Inoue, T.//Shibata, T.//Ando, T. 	A restriction enzyme, BpuI is an isoschizomer of BanII.	Nucleic Acids Res.	1992	20		5850			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. 		
@D	Iwai, M.//Katoh, H.//Katayama, M.//Ikeuchi, M. 	Improved genetic transformation of the thermophilic cyanobacterium, Thermosynechococcus elongatus BP-1.	Plant Cell Physiol.	2004	45		171-175			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. 		
@D	Iwamoto, M.//Hishiki, A.//Shimada, T.//Imasaki, T.//Tsuda, J.//Kita, K.//Shimizu, T.//Sato, M.//Hashimoto, H. 	Crystallization and X-ray diffraction studies of DNA-free and DNA-bound forms of EcoO109I DNA methyltransferase.	Acta Crystallogr. F Struct. Biol. Cryst. Commun.	2010	66		1528-1530			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. 		
@D	Iwaniec, L.M.//Kroll, J.J.//Roethel, W.M.//Maybaum, J. 	Selective inhibition of sequence-specific protein-DNA interactions by incorporation of 6-thioguanine:  Cleavage by restriction endonucleases.	Mol. Pharmacol.	1991	39		299-306			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. 		
@D	Iwase, T.//Ogura, Y.//Hayashi, T.//Mizunoe, Y. 	Complete Genome Sequence of Klebsiella oxytoca Strain JKo3.	Genome Announcements	2016	4		e01221-16			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. 		
@D	Iwase, T.//Ogura, Y.//Hayashi, T.//Mizunoe, Y. 	Complete Genome Sequence of Klebsiella pneumoniae YH43.	Genome Announcements	2016	4		e00242-16			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. 		
@D	Iyer, L.M.//Abhiman, S.//Aravind, L. 	MutL homologs in restriction-modification systems and the origin of eukaryotic MORC ATPases.	Biol. Direct	2008	3		8			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. 		
@D	Iyer, L.M.//Abhiman, S.//Aravind, L. 	Natural History of Eukaryotic DNA Methylation Systems.	Prog. Mol. Biol. Transl. Sci.	2011	101		25-104			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. 		
@D	Iyer, L.M.//Tahiliani, M.//Rao, A.//Aravind, L. 	Prediction of novel families of enzymes involved in oxidative and other complex modifications of bases in nucleic acids.	Cell Cycle	2009	8		1698-1710			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. 		
@D	Iyer, L.M.//Zhang, D.//Maxwell, B.A.//Aravind, L. 	Computational identification of novel biochemical systems involved in oxidation,  glycosylation and other complex modifications of bases in DNA.	Nucleic Acids Res.	2013	41		7635-7655			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. 		
@D	Iyer, P.R.//Geib, S.M.//Catchmark, J.//Kao, T.H.//Tien, M. 	Genome Sequence of a Cellulose Producing Bacterium, Gluconacetobacter hansenii ATCC 23769.	J. Bacteriol.	2010	192		4256-4257			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. 		
@D	Iyer, R.//Damania, A. 	Draft Genome Sequence of Rhizobium sp. GHKF11, Isolated from Farmland Soil in Pecan Grove, Texas.	Genome Announcements	2016	4		e00682-16			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. 		
@D	Iyer, R.//Damania, A. 	Draft Genome Sequence of Exiguobacterium sp. KKBO11, Isolated Downstream of a Wastewater Treatment Plant in Houston, Texas.	Genome Announcements	2016	4		e00681-16			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. 		
@D	Iyer, R.//Damania, A. 	Draft Genome Sequence of Pseudomonas putida CBF10-2, a Soil Isolate with Bioremediation Potential in Agricultural and Industrial Environmental Settings.	Genome Announcements	2016	4		e00670-16			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. 		
@D	Iyer, R.//Damania, A. 	Draft Genome Sequence of Pseudomonas stutzeri ODKF13, Isolated from Farmland Soil in Alvin, Texas.	Genome Announcements	2016	4		e00293-16			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. 		
@D	Iyer, R.//Damania, A. 	Draft Genome Sequence of Alkane-Degrading Acinetobacter venetianus JKSF02, Isolated from Contaminated Sediment of the San Jacinto River in Houston, Texas.	Genome Announcements	2016	4		e00286-16			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. 		
@D	Iyer, R.//Damania, A. 	Draft Genome Sequence of the Broad-Spectrum Xenobiotic Degrader Achromobacter xylosoxidans ADAF13.	Genome Announcements	2016	4		e00203-16			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. 		
@D	Iyer, R.//Damania, A. 	Draft Genome Sequence of Stenotrophomonas maltophilia CBF10-1, an Organophosphate-Degrading Bacterium Isolated from Ranch Soil in Fairchilds,  Texas.	Genome Announcements	2016	4		e00378-16			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. 		
@D	Iyer, R.//Damania, A. 	Draft Genome Sequence of Organophosphate-Degrading Ochrobactrum anthropi FRAF13.	Genome Announcements	2016	4		e00295-16			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. 		
@D	Izawa, K.//Kuwahara, H.//Kihara, K.//Yuki, M.//Lo, N.//Ito, T.//Ohkuma, M.//Hongoh, Y. 	Comparison of intracellular 'Ca. Endomicrobium trichonymphae' genomovars illuminates the requirement and decay of defense systems against foreign DNA.	Genome Biol. Evol.	2016	8		3099-3107			"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. 		
@D	Izquierdo, J.A. et al. 	Complete Genome Sequence of Clostridium clariflavum DSM 19732.	Standards in Genomic Sciences	2012	6		104-115			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. 		
@D	Izsvak, Z.//Duda, E. 	Star activity and complete loss of specificity of CeqI endonuclease.	Biochem. J.	1989	258		301-303			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. 		
@D	Izsvak, Z.//Jobbagy, Z.//Duda, E. 	Purification and characterization of CeqI restriction endonuclease.	Z. Naturforsch. C	1992	47		830-834			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. 		
@D	Izsvak, Z.//Jobbagy, Z.//Takacs, I.//Duda, E. 	Cloning and characterization of the genes of the CeqI restriction-modification system.	Int. J. Biochem. Cell Biol.	1997	29		895-900			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. 		
@D	Izumiya, H.//Sekizuka, T.//Nakaya, H.//Taguchi, M.//Oguchi, A.//Ichikawa, N.//Nishiko, R.//Yamazaki, S.//Fujita, N.//Watanabe, H.//Ohnishi, M.//Kuroda, M. 	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.	Antimicrob. Agents Chemother.	2011	55		623-630			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. 		
@D	Izvolsky, K.I.//Demidov, V.V.//Nielsen, P.E.//Frank-Kamenetskii, M.D. 	Sequence-specific protection of duplex DNA against restriction and methylation enzymes by pseudocomplementary PNAs.	Biochemistry	2000	39		10908-10913			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. 		
@D	Jabbar, M.A.//Snyder, L. 	Genetic and physiological studies of an Escherichia coli locus that restricts polynucleotide kinase- and RNA ligase-deficient mutants of bacteriophage T4.	J. Virol.	1984	51		522-529			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. 		
@D	Jabbari, N.//Glusman, G.//Joesch-Cohen, L.M.//Reddy, P.J.//Moritz, R.L.//Hood, L.//Lausted, C.G. 	Whole genome sequence and comparative analysis of Borrelia burgdorferi MM1.	PLoS ONE	2018	13		e0198135			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. 		
@D	Jabeen, S.//Yong, Y.H.//Abdullah, F.J.F.//Zakaria, Z.//Mat, I.N.//Tan, Y.C.//Yee, W.Y.//Omar, A.R. 	Complete Genome Sequence of Pasteurella multocida Serotype A Strain PMTB2.1 Isolated from Buffaloes That Died of Septicemia in Malaysia.	Genome Announcements	2017	5		e01190-17			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. 		
@D	Jack, W.E. 	Participation of outside DNA sequences in the EcoRI endonuclease reaction pathway.	Ph.D. Thesis	1983			1-153			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. 		
@D	Jack, W.E.//Greenough, L.//Dorner, L.F.//Xu, S.-Y.//Strzelecka, T.//Aggarwal, A.K.//Schildkraut, I. 	Overexpression, purification and crystallization of BamHI endonuclease.	Nucleic Acids Res.	1991	19		1825-1829			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. 		
@A	Jack, W.E.//Rubin, R.A.//Newman, A.//Modrich, P. 		Structures and mechanisms of EcoRI DNA restriction and modification enzymes.			Chirikjian, J.G. 		Gene Amplif. Anal.					Elsevier North Holland	1981		1		165-179									*
   I. Structural properties
  II. Catalytic properties
 III. Enzyme-substrate interactions
  IV. Cloning and the structural genes
 
 		
@D	Jack, W.E.//Terry, B.J.//Modrich, P. 	Involvement of outside DNA sequences in the major kinetic path by which EcoRI endonuclease locates and leaves its recognition sequence.	Proc. Natl. Acad. Sci. U. S. A.	1982	79		4010-4014			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. 		
@D	Jackson, A.//Humbert, M.V.//Pandey, A.//Bratcher, H.//Christodoulides, M. 	Draft Genome Sequence of Dichelobacter nodosus ATCC 25549, Strain VPI 2340 [11342], a Bacterium Causing Footrot in Sheep.	Genome Announcements	2015	3		e01002-15			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. 		
@D	Jackson, D.A.//Symons, R.H.//Berg, P. 	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.	Proc. Natl. Acad. Sci. U. S. A.	1972	69		2904-2909			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. 		
@D	Jackson, E.E.//Ogrodzki, P.//Pascoe, B.//Sheppard, S.K.//Forsythe, S.J. 	Draft Genome Sequence of an Enterobacter Species Associated with Illnesses and Powdered Infant Formula.	Genome Announcements	2016	4		e01479-15			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. 		
@D	Jackson, S.E.//Koyama, M.//Ryu, J. 	A novel use of bacterial transformation to discover new restriction enzymes in clinical E. coli strains.	J. Invest. Med.	2001	49		11A			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. 		
@D	Jacob, K.M.//Spilker, T.//LiPuma, J.J.//Dawid, S.R.//Watson, M.E. Jr. 	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).	Genome Announcements	2016	4		e00127-16			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%. 		
@D	Jacobs, D. 	Type II restriction-modification systems in Enterobacter aerogenes and Herpetosiphon giganteus.	Diss. Abstr.	1988	49		730B			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. 		
@D	Jacobs, D.//Brown, N.L. 	Isolation and characterization of the M.EaeI modification methylase.	Biochem. J.	1986	238		613-616			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. 		
@D	Jacobs, M.B.//Norris, S.J.//Phillippi-Falkenstein, K.M.//Philipp, M.T. 	Infectivity of the highly transformable BBE02(-) lp56(-) mutant of Borrelia burgdorferi, the Lyme disease spirochete, via ticks.	Infect. Immun.	2006	74		3678-3681			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. 		
@D	Jacoby, G.A.//Sutton, L. 	Restriction and modification determined by a Pseudomonas R plasmid.	Plasmid	1977	1		115-116			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. 		
@D	Jacoby, G.A.//Sutton, L. 	Restriction-modification systems determined by Pseudomonas plasmids.	Plasmid	1982	8		141-147			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. 		
@D	Jacoby, K.//Metzger, M.//Shen, B.W.//Certo, M.T.//Jarjour, J.//Stoddard, B.L.//Scharenberg, A.M. 	Expanding LAGLIDADG endonuclease scaffold diversity by rapidly surveying evolutionary sequence space.	Nucleic Acids Res.	2012	40		4954-4964			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. 		
@D	Jacques, M.A.//Bolot, S.//Charbit, E.//Darrasse, A.//Briand, M.//Arlat, M.//Gagnevin, L.//Koebnik, R.//Noel, L.D.//Portier, P.//Carrere, S.//Boureau, T. 	High-Quality Draft Genome Sequence of Xanthomonas alfalfae subsp. alfalfae Strain CFBP 3836.	Genome Announcements	2013	1		e01035-13			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. 		
@D	Jacquier, A.//Dujon, B. 	An intron-encoded protein is active in a gene conversion process that spreads an intron into a mitochondrial gene.	Cell	1985	41		383-394			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. 		
@D	Jacquier, A.//Dujon, B. 	The intron of the mitochondrial 21S rRNA gene:  distribution in different yeast species and sequence comparison between Kluyveromyces thermotolerans and Saccharomyces cerevisiae.	Mol. Gen. Genet.	1983	192		487-499			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. 		
@D	Jadhav, V.R.//Ganesh, K.N. 	Design of a combinatorial oligonucleotide library containing all possible hexamer palindromes: PCR synthesis and application for identifying restriction cleavage sites.	Biochem. Biophys. Res. Commun.	1998	242		297-302			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. 		
@D	Jaen-Luchoro, D.//Salva-Serra, F.//Aliaga-Lozano, F.//Segui, C.//Busquets, A.//Ramirez, A.//Ruiz, M.//Gomila, M.//Lalucat, J.//Bennasar-Figueras, A. 	Complete Genome Sequence of Mycobacterium chelonae Type Strain CCUG 47445, a Rapidly Growing Species of Nontuberculous Mycobacteria.	Genome Announcements	2016	4		e00550-16			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. 		
@D	Jaen-Luchoro, D.//Segui, C.//Aliaga-Lozano, F.//Salva-Serra, F.//Busquets, A.//Gomila, M.//Ramirez, A.//Ruiz, M.//Moore, E.R.//Lalucat, J.//Bennasar-Figueras, A. 	Complete Genome Sequence of the Mycobacterium immunogenum Type Strain CCUG 47286.	Genome Announcements	2016	4		e00401-16			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. 		
@D	Jaenicke, S.//Bunk, B.//Wibberg, D.//Sproer, C.//Hersemann, L.//Blom, J.//Winkler, A.//Schatschneider, S.//Albaum, S.P.//Kolliker, R.//Goesmann, A.//Puhler, A.//Overmann, J.//Vorholter, F.J. 	Complete Genome Sequence of the Barley Pathogen Xanthomonas translucens pv. translucens DSM 18974T (ATCC 19319T).	Genome Announcements	2016	4		e01334-16			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. 		
@D	Jaffe, B.//Kovacs, K.//Andras, C.//Bodi, Z.//Liu, Z.//Fray, R.G. 	Methylation of chloroplast DNA does not affect viability and maternal inheritance in tobacco and may provide a strategy towards transgene containment.	Plant Cell	2008	27		1377-1384			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. 		
@D	Jag, V.//Poehlein, A.//Bengelsdorf, F.R.//Daniel, R.//Durre, P. 	Genome Sequence of the Facultative Anaerobe Oerskovia enterophila DFA-19 (DSM 43852T).	Genome Announcements	2016	4		e00973-16			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. 		
@D	Jag, V.//Poehlein, A.//Bengelsdorf, F.R.//Daniel, R.//Durre, P. 	Genome sequencing and description of Oerskovia enterophila VJag, an agar- and cellulose-degrading bacterium.	Standards in Genomic Sciences	2017	12		30			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. 		
@D	Jager, K.//Potts, M. 	Distinct fractions of genomic DNA from cyanobacterium Nostoc commune that differ in the degree of methylation.	Gene	1988	74		197-201			Meeting Abstract 		
@D	Jaglarz, A.//Gurgul, A.//Leigh, W.J.//Costa, J.Z.//Thompson, K.D. 	Complete Genome Sequences of Three Streptococcus agalactiae Serotype Ia Isolates  Obtained from Disease Outbreaks in Nile Tilapia (Oreochromis niloticus).	Genome Announcements	2018	6		e01432-17			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. 		
@D	Jaglarz, A.//Gurgul, A.//Leigh, W.J.//Costa, J.Z.//Thompson, K.D. 	Complete Genome Sequences of Three Fish-Associated Streptococcus agalactiae Isolates.	Genome Announcements	2018	6		e00025-18			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. 		
@D	Jagoda, S.S.//Tan, E.//Arulkanthan, A.//Kinoshita, S.//Watabe, S.//Asakawa, S. 	Draft Genome Sequence of Aeromonas hydrophila Strain Ae34, Isolated from a Septicemic and Moribund Koi Carp (Cyprinus carpio koi), a Freshwater Aquarium  Fish.	Genome Announcements	2014	2		e00572-14			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. 		
@D	Jair, K.//Yen, R.-W.C.//Toyota, M.//Ho, C.//Baylin, S.B.//Issa, J.-P.J. 	De novo DNA methyltransferase activity in a lung cancer cell line.	Proc. Amer. Assoc. Cancer Res.	1998	39		95			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. 		
@D	Jaishankar, J.//Singh, P.//Srivastava, P. 	Draft Genome Sequence of a Biodesulfurizing Bacterium, Gordonia sp. Strain IITR100.	Genome Announcements	2017	5		e00230-17			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. 		
@D	Jaiswal, D.//Sengupta, A.//Sohoni, S.//Sengupta, S.//Phadnavis, A.G.//Pakrasi, H.B.//Wangikar, P.P. 	Genome Features and Biochemical Characteristics of a Robust, Fast Growing and Naturally Transformable Cyanobacterium Synechococcus elongatus PCC 11801 Isolated from India.	Sci. Rep.	2018	8		16632			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. 		
@D	Jaiswal, S.K.//Saxena, R.//Mittal, P.//Gupta, A.//Sharma, V.K. 	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.	Genome Announcements	2017	5		e01527-16			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. 		
@D	Jakobsson, H.E.//Salva-Serra, F.//Thorell, K.//Gonzales-Siles, L.//Boulund, F.//Karlsson, R.//Sikora, P.//Engstrand, L.//Kristiansson, E.//Moore, E.R. 	Draft Genome Sequence of Moraxella catarrhalis Type Strain CCUG 353T.	Genome Announcements	2016	4		e00552-16			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. 		
@D	Jakobsson, H.E.//Salva-Serra, F.//Thorell, K.//Karlsson, R.//Gonzales-Siles, L.//Boulund, F.//Engstrand, L.//Kristiansson, E.//Moore, E.R. 	Draft Genome Sequences of Six Strains of Streptococcus pneumoniae from Serotypes  5, 6A, 6B, 18C, 19A, and 23F.	Genome Announcements	2017	5		e00125-17			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. 		
@D	Jakubauskas, A. 	Domain organization analysis of Type II restriction endonucleases.	Ph.D. Thesis, Vilnius University	2007			1-42			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. 		
@D	Jakubauskas, A.//Dauksaite, V. 	Construction and analysis of chimeric enzymes between type IIs restriction endonucleases Alw26I, Eco31I and Esp3I.	Biologija	1997	1		26-30			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. 		
@D	Jakubauskas, A.//Giedriene, J.//Bujnicki, J.M.//Janulaitis, A. 	Identification of a Single HNH Active Site in Type IIS Restriction Endonuclease Eco31I.	J. Mol. Biol.	2007	370		157-169			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. 		
@D	Jakubauskas, A.//Kriukiene, E.//Trinkunaite, L.//Sapranauskas, R.//Jurenaite-Urbanaviciene, S.//Lubys, A. 	Bioinformatic and partial functional analysis of pEspA and pEspB, two plasmids from Exiguobacterium arabatum sp nov RFL1109.	Plasmid	2009	61		52-64			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. 		
@D	Jakubauskas, A.//Sasnauskas, G.//Giedriene, J.//Janulaitis, A. 	Domain organization and functional analysis of type IIS restriction endonuclease Eco31I.	Biochemistry	2008	47		8546-8556			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. 		
@D	Jalan, N.//Aritua, V.//Kumar, D.//Yu, F.//Jones, J.B.//Graham, J.H.//Setubal, J.C.//Wang, N. 	Comparative genomic analysis of Xanthomonas axonopodis pv. citrumelo F1 causing citrus bacterial spot and related strains provides insights into  virulence and host-specificity.	J. Bacteriol.	2011	193		6342-6357			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. 		
@D	Jalan, N.//Kumar, D.//Yu, F.//Jones, J.B.//Graham, J.H.//Wang, N. 	Complete Genome Sequence of Xanthomonas citri subsp. citri Strain Aw12879, a Restricted-Host-Range Citrus Canker-Causing Bacterium.	Genome Announcements	2013	1		e00235-13			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. 		
@D	Jamoussi, K.//Lazowska, J. 	Intragenic suppressors that restore the splicing and homing activities of the protein encoded by the second intron of the Saccharomyces capensis cyt b gene.	Curr. Genet.	2000	38		276-282			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. 		
@D	Jana, G.A.//Al-Yahyai, R.//Yaish, M.W. 	Genome Sequencing of Microbacterium sp. Yaish 1, a Bacterial Strain Isolated from the Rhizosphere of Date Palm Trees Affected by Salinity.	Genome Announcements	2017	5		e01247-17			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. 		
@D	Jancovich, J.K.//Bremont, M.//Touchman, J.W.//Jacobs, B.L. 	Evidence for Multiple Recent Host Species Shifts among the Ranaviruses (Family Iridoviridae).	J. Virol.	2010	84		2636-2647			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. 		
@D	Jancovich, J.K.//Mao, J.//Chinchar, V.G.//Wyatt, C.//Case, S.T.//Kumar, S.//Valente, G.//Subramanian, S.//Davidson, E.W.//Collins, J.P.//Jacobs, B.L. 	Genomic sequence of a ranavirus (family Iridoviridae) associated with salamander mortalities in North America.	Virology	2003	316		90-103			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. 		
@D	Jang, H. et al. 	Draft genomes of Cronobacter sakazakii strains isolated from dried spices bring unique insights into the diversity of plant-associated strains.	Standards in Genomic Sciences	2018	13		35			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. 		
@D	Jang, H.//Addy, N.//Ewing, L.//Jean-Gilles, B.J.//Lee, Y.//Woo, J.//Negrete, F.//Finkelstein, S.//Tall, B.D.//Lehner, A.//Eshwar, A.//Gopinath, G.R. 	Whole-Genome Sequences of Cronobacter sakazakii Isolates Obtained from Foods of Plant Origin and Dried-Food Manufacturing Environments.	Genome Announcements	2018	6		e00223-18			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%. 		
@D	Jang, J.Y.//Lim, H.I.//Park, H.W.//Choi, H.J.//Kim, T.W.//Kang, M.//Lee, J.H. 	Draft Genome Sequence of Lactobacillus plantarum wikim18, Isolated from Korean Kimchi.	Genome Announcements	2014	2		e00467-14			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. 		
@D	Jang, K.H.//Britz, M.L. 	Improved electrotransformation frequencies of Corynebacterium glutamicum using cell-surface mutantstransformation via electroporation using plasmid DNA.	Biotechnol. Lett.	2000	22		539-545			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) 		
@D	Jang, K.H.//Chambers, P.//Britz, M.L. 	Analysis of nucleotide methylation in DNA from Corynebacterium glutamicum and related species.	FEMS Microbiol. Lett.	1996	136		309-315			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. 		
@D	Jang, K.H.//Chambers, P.J.//Britz, M.L. 	Identification of a sequence containing methylated cytidine in Corynebacterium glutamicum and Brevibacterium flavum using bisulfite DNA derivatization and sequencing.	J. Microbiol. Biotechnol.	2001	11		819-824			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. 		
@D	Jang, K.J.//Lee, H.//Jin, H.L.//Park, Y.//Nam, J.M. 	Restriction-Enzyme-Coded Gold-Nanoparticle Probes for Multiplexed DNA Detection.	Small	2009	5		2665-2668			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. 		
@D	Jang, S.H.//Kim, J.//Kim, J.//Hong, S.//Lee, C. 	Genome Sequence of Cold-Adapted Pseudomonas mandelii Strain JR-1.	J. Bacteriol.	2012	194		3263			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. 		
@D	Jang, S.H.//Yoon, B.H.//Chang, H.I. 	Complete nucleotide sequence of the temperate bacteriophage LBR48, a new member of the family Myoviridae.	Arch. Virol.	2011	156		319-322			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. 		
@D	Jang, Y.//Oh, H.M.//Kang, I.//Lee, K.//Yang, S.J.//Cho, J.C. 	Genome sequence of strain IMCC3088, a proteorhodopsin-containing marine bacterium belonging to the OM60/NOR5 clade.	J. Bacteriol.	2011	193		3415-3416			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. 		
@D	Jang, Y.//Oh, H.M.//Kim, H.//Kang, I.//Cho, J.C. 	Genome Sequence of Strain IMCC1989, a Novel Member of the Marine Gammaproteobacteria.	J. Bacteriol.	2011	193		3672-3673			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. 		
@D	Jangam, A.K.//Bhuvaneswari, T.//Krishnan, A.N.//Katneni, V.K.//Avunje, S.//Grover, M.//Kumar, S.//Alavandi, S.V.//Vijayan, K.K. 	Draft Genome Sequence of Vibrio parahaemolyticus Strain VP14, Isolated from a Penaeus vannamei Culture Farm.	Genome Announcements	2018	6		e00149-18			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. 		
@D	Jangir, P.K.//Singh, A.//Shivaji, S.//Sharma, R. 	Genome Sequence of the Alkaliphilic Bacterium Nitritalea halalkaliphila Type Strain LW7, Isolated from Lonar Lake, India.	J. Bacteriol.	2012	194		5688-5689			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%. 		
@D	Jankowitsch, F.//Schwarz, J.//Ruckert, C.//Gust, B.//Szczepanowski, R.//Blom, J.//Pelzer, S.//Kalinowski, J.//Mack, M. 	The genome sequence of the bacterium Streptomyces davawensis JCM 4913 and heterologous production of the unique antibiotic roseoflavin.	J. Bacteriol.	2012	194		6818-6827			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. 		
@D	Janosi, L.//Kaji, A. 	Molecular cloning and expression of T-even phage specific restriction enzyme coded by drug resistance plasmid Rts1.	FASEB J.	1992	6		A216			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. 		
@D	Janosi, L.//Yonemitsu, H.//Hong, H.//Kaji, A. 	Molecular cloning and expression of a novel hydroxymethylcytosine-specific restriction enzyme (PvuRts1I) modulated by glucosylation of DNA.	J. Mol. Biol.	1994	242		45-61			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. 		
@D	Jans, C.//Lacroix, C.//Follador, R.//Stevens, M.J. 	Complete Genome Sequence of the Probiotic Bifidobacterium thermophilum Strain RBL67.	Genome Announcements	2013	1		e00191-13			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. 		
@D	Jans, C.//Lagler, S.//Lacroix, C.//Meile, L.//Stevens, M.J.A. 	Complete Genome Sequences of Lactobacillus curvatus KG6, L. curvatus MRS6, and Lactobacillus sakei FAM18311, Isolated from Fermented Meat Products.	Genome Announcements	2017	5		e00915-17			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%. 		
@D	Janscak, P.//Abadjieva, A.//Firman, K. 	The type I restriction endonuclease R.EcoR124I: over-production and biochemical properties.	J. Mol. Biol.	1996	257		977-991			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. 		
@D	Janscak, P.//Bickle, T.A. 	DNA supercoiling during ATP-dependent DNA translocation by the type I restriction enzyme EcoAI.	J. Mol. Biol.	2000	295		1089-1099			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. 		
@D	Janscak, P.//Bickle, T.A. 	The DNA recognition subunit of the type IB restriction-modification enzyme EcoAI tolerates circular permutations of its polypeptide chain.	J. Mol. Biol.	1998	284		937-948			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. 		
@D	Janscak, P.//Dryden, D.T.F.//Firman, K. 	Analysis of the subunit assembly of the type IC restriction-modification enzyme EcoR124I.	Nucleic Acids Res.	1998	26		4439-4445			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. 		
@D	Janscak, P.//MacWilliams, M.P.//Sandmeier, U.//Nagaraja, V.//Bickle, T.A. 	DNA translocation blockage, a general mechanism of cleavage site selection by type I restriction enzymes.	EMBO J.	1999	18		2638-2647			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. 		
@D	Janscak, P.//Sandmeier, U.//Bickle, T.A. 	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.	Nucleic Acids Res.	1999	27		2638-2643			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. 		
@D	Janscak, P.//Sandmeier, U.//Szczelkun, M.D.//Bickle, T.A. 	Subunit assembly and mode of DNA cleavage of the type III restriction endonucleases EcoP1I and EcoP15I.	J. Mol. Biol.	2001	306		417-431			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. 		
@D	Janscak, P.//Weiserova, M.//Hubacek, J.//Holubova, I.//Dutta, C.F.//Firman, K. 	Two temperature-sensitive mutations in the DNA binding subunit of EcoKI with differing properties.	FEMS Microbiol. Lett.	2000	182		99-104			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. 		
@D	Janssen, P.J.//Morin, N.//Mergeay, M.//Leroy, B.//Wattiez, R.//Vallaeys, T.//Waleron, K.//Waleron, M.//Wilmotte, A.//Quillardet, P.//de Marsac, N.T.//Talla, E.//Zhang, C.C.//Leys, N. 	Genome sequence of the edible cyanobacterium Arthrospira sp. PCC 8005.	J. Bacteriol.	2010	192		2465-2466			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. 		
@D	Janssens, T.K.S.//de Boer, T.E.//Agamennone, V.//Zaagman, N.//van Straalen, N.M.//Roelofs, D. 	Draft Genome Sequence of Bacillus toyonensis VU-DES13, Isolated from Folsomia candida (Collembola: Entomobryidae).	Genome Announcements	2017	5		e00287-17			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. 		
@D	Janto, B. et al. 	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.	Environ. Microbiol.	2011	13		3289-3309			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. 		
@D	Janulaitis, A. 	Restriction endonucleases.	Zh. Vses. Khim.	1984	29		133-138					
@D	Janulaitis, A. 	A novel approach to the study of DNA-protein interactions using related restriction endonucleases that recognize overlapping nucleotide sequences.	Biologija	1996	0		28-31			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. 		
@A	Janulaitis, A. 		Restriction Enzymes and their Applications.			Debabov, V.G. 		Trends in Science and Technology. Biotechnology series.				Moscow	Institute for Scientific and Technological Information of the USSR	1989		17		1-204											
@D	Janulaitis, A.//Bitinaite, J.//Jaskeleviciene, B. 	A new sequence-specific endonuclease from Gluconobacter suboxydans.	FEBS Lett.	1983	151		243-247			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. 		
@D	Janulaitis, A.//Kazlauskiene, R.//Lazareviciute, L.//Gilvonauskaite, R.//Steponaviciene, D.//Jagelavicius, M.//Petrusyte, M.//Bitinaite, J.//Vezeviciute, Z.//Kiuduliene, E.//Butkus, V. 	Taxonomic specificity of restriction-modification enzymes.	Gene	1988	74		229-232			Meeting Abstract 		
@D	Janulaitis, A.//Klimasauskas, S.//Petrusyte, M.//Butkus, V. 	Cytosine modification in DNA by BcnI methylase yields N4-methylcytosine.	FEBS Lett.	1983	161		131-134			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. 		
@D	Janulaitis, A.//Marcinkeviciene, L.//Petrusyte, M.//Mironov, A. 	A new sequence-specific endonuclease from Streptococcus durans.	FEBS Lett.	1981	134		172-174			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. 		
@D	Janulaitis, A.//Marcinkeviciene, L.Y.//Petrusyte, M.P. 	A specific endonuclease from Caulobacter fusiformis that cleaves only methylated DNA.	Dokl. Akad. Nauk.	1982	262		241-244			None 		
@D	Janulaitis, A.//Petrusyte, M.//Butkus, V. 	Three sequence-specific endonucleases from Escherichia coli RFL47.	FEBS Lett.	1983	161		213-216			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. 		
@D	Janulaitis, A.//Petrusyte, M.//Maneliene, Z.//Klimasauskas, S.//Butkus, V. 	Purification and properties of the Eco57I restriction endonuclease and methylase-prototypes of a new class (type IV).	Nucleic Acids Res.	1992	20		6043-6049			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. 		
@D	Janulaitis, A.//Petrusyte, M.A.//Jaskeleviciene, B.P.//Krayev, A.S.//Skryabin, K.G.//Bayev, A.A. 	A new restriction endonuclease BcnI from Bacillus centrosporus RFL 1.	FEBS Lett.	1982	137		178-180			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. 		
@D	Janulaitis, A.//Petrusyte, M.P.//Jaskeleviciene, B.P.//Krayev, A.S.//Skryabin, K.G.//Bayev, A.A. 	A new restriction endonuclease BcnI from Bacillus centrosporus RFL1.	Dokl. Akad. Nauk.	1981	257		749-750			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. 		
@D	Janulaitis, A.//Povilionis, P.//Sasnauskas, K. 	Cloning of the modification methylase gene of Bacillus centrosporus in Escherichia coli.	Gene	1982	20		197-204			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. 		
@D	Janulaitis, A.//Stakenas, P.//Jaskeleviciene, B.//Lebedenko, E.N.//Berlin, Y.A. 	A new restriction endonuclease, CfrI from Citrobacter freundii.	Bioorg. Khim.	1980	6		1746-1748			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. 		
@D	Janulaitis, A.//Stakenas, P.S.//Berlin, Y.A. 	A new site-specific endodeoxyribonuclease from Citrobacter freundii.	FEBS Lett.	1983	161		210-212			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. 		
@D	Janulaitis, A.//Stakenas, P.S.//Bitinaite, J.B.//Jaskeleviciene, B.P. 	Distribution of specific endodeoxyribonucleases in various strains of Citrobacter freundii.	Dokl. Akad. Nauk.	1983	271		483-485			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. 		
@D	Janulaitis, A.//Stakenas, P.S.//Lebedenko, E.N.//Berlin, Y.A. 	A new restriction endonuclease from Citrobacter freundii.	Nucleic Acids Res.	1982	10		6521-6530			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. 		
@D	Janulaitis, A.//Stakenas, P.S.//Petrusyte, M.P.//Bitinaite, J.B.//Klimasauskas, S.I.//Butkus, V.V. 	Specificity of new restrictases and methylases.  Unusual modification of cytosine in position 4.	Mol. Biol. (Mosk)	1983	18		115-129			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. 		
@D	Janulaitis, A.//Vaisvila, R.//Timinskas, A.//Klimasauskas, S.//Butkus, V. 	Cloning and sequence analysis of the genes coding for Eco57I type IV restriction-modification enzymes.	Nucleic Acids Res.	1992	20		6051-6056			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. 		
@D	Janulaitis, A.//Vaitkevicius, D.P. 	A spectrophotometric procedure for the determination of activity of restriction.	Anal. Biochem.	1981	116		116-122			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. 		
@D	Janulaitis, A.//Vaitkevicius, D.P. 	New methodical approach to development of technology for production of restriction endonucleases.  Development of scheme for isolation of homogeneous preparation of restrictase MvaI.	Biotekhnologiya	1985	1		39-51			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. 		
@D	Jaomanjaka, F.//Ballestra, P.//Dols-Lafargue, M.//Le Marrec, C. 	Expanding the diversity of oenococcal bacteriophages: Insights into a novel group based on the integrase sequence.	Int. J. Food Microbiol.	2013	166		331-340			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. 		
@D	Jaomanjaka, F.//Claisse, O.//Philippe, C.//Le Marrec, C. 	Complete Genome Sequence of Lytic Oenococcus oeni Bacteriophage OE33PA.	Microbiol. Resour. Announc.	2018	7		e00818-18			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. 		
@D	Jara, C.//Romero, J. 	Genome Sequences of Three Oenococcus oeni Strains Isolated from Maipo Valley, Chile.	Genome Announcements	2015	3		e00866-15			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. 		
@D	Jarjour, J.//West-Foyle, H.//Certo, M.T.//Hubert, C.G.//Doyle, L.//Getz, M.M.//Stoddard, B.L.//Scharenberg, A.M. 	High-resolution profiling of homing endonuclease binding and catalytic specificity using yeast surface display.	Nucleic Acids Res.	2009	37		6871-6880			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. 		
@D	Jarman, S.N. 	Cleaver: software for identifying taxon specific restriction endonuclease recognition sites.	Bioinformatics	2006	22		2160-2161			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. 		
@D	Jarrell, K.F.//Julseth, C.//Pearson, B.//Kuzio, J. 	Paucity of the Sau3AI recognition sequence (GATC) in the genome of Methanococcus voltae.	Mol. Gen. Genet.	1987	208		191-194			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. 		
@D	Jarvik, T.//Smillie, C.//Groisman, E.A.//Ochman, H. 	Short-term Signatures of Evolutionary Change in the Salmonella enterica serovar Typhimurium 14028 Genome.	J. Bacteriol.	2010	192		560-567			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. 		
@D	Jarvis, A.W. 	Analysis of phage resistance mechanisms encoded by lactococcal plasmid pAJ2074.	Can. J. Microbiol.	1993	39		252-258			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. 		
@D	Jarvis, A.W.//Klaenhammer, T.R. 	Bacteriophage resistance conferred on lactic Streptococci by the conjugative plasmid pTR2030: Effects on small isometric-, large Isometric-,and prolate-headed Phages.	Appl. Environ. Microbiol.	1986	51		1272-1277			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. 		
@D	Jaubert, C.//Danioux, C.//Oberto, J.//Cortez, D.//Bize, A.//Krupovic, M.//She, Q.//Forterre, P.//Prangishvili, D.//Sezonov, G. 	Genomics and genetics of Sulfolobus islandicus LAL14/1, a model hyperthermophilic archaeon.	Open Biol.	2013	3		130010			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. 		
@D	Jauregui, R.//Rodelas, B.//Geffers, R.//Boon, N.//Pieper, D.H.//Vilchez-Vargas, R. 	Draft Genome Sequence of the Naphthalene Degrader Herbaspirillum sp. Strain RV1423.	Genome Announcements	2014	2		e00188-14			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. 		
@D	Javorsky, P.//Pravdova, M.//Vanat, I.//Pristas, P.//Styriak, I. 	Gene manipulation of Streptococcus bovis: progress and problems.	Can. J. Anim. Sci.	1995	75		654-655			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. 		
@D	Jay, E.//Wu, R. 	Arthrobacter luteus restriction endonuclease recognition sequence and its cleavage map of SV40 DNA.	Biochemistry	1976	15		3612-3620			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. 		
@D	Jay, Z.J.//Beam, J.P.//Dohnalkova, A.//Lohmayer, R.//Bodle, B.//Planer-Friedrich, B.//Romine, M.//Inskeep, W.P. 	Pyrobaculum yellowstonensis str. WP30 respires on elemental sulfur and/or arsenate in circumneutral sulfidic geothermal sediments of Yellowstone National Park.	Appl. Environ. Microbiol.	2015	81		5907-5916			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. 		
@D	Jayal, A.//Johns, B.E.//Purdy, K.J.//Maddocks, S.E. 	Draft Genome Sequence of Pseudomonas aeruginosa ATCC 9027, Originally Isolated from an Outer Ear Infection.	Genome Announcements	2017	5		e01397-17			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. 		
@D	Jayapal, K.P.//Lian, W.//Glod, F.//Sherman, D.H.//Hu, W.S. 	Comparative genomic hybridizations reveal absence of large Streptomyces coelicolor genomic islands in Streptomyces lividans.	BMC Genomics	2007	8		229			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. 		
@D	Jayaraman, K.S. 	Restriction venture.	Nature	1989	341		272			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. 		
@D	Jayaraman, R. 	Phase variation and adaptation in bacteria: A 'Red Queen's Race'.	Curr. Sci.	2011	100		1163-1171			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. 		
@D	Jayashree, S.//Pooja, S.//Pushpanathan, M.//Vishnu, U.//Sankarasubramanian, J.//Rajendhran, J.//Gunasekaran, P. 	Genome Sequence of Lactobacillus fermentum Strain MTCC 8711, a Probiotic Bacterium Isolated from Yogurt.	Genome Announcements	2013	1		e00770-13			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. 		
@D	Jeddeloh, J.A.//Stokes, T.L.//Richards, E.J. 	Maintenance of genomic methylation requires a SW12/SNF2-like protein.	Nat. Genet.	1999	22		94-97			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. 		
@D	Jeffery, C.J. 	Molecular mechanisms for multitasking: recent crystal structures of moonlighting proteins.	Curr. Opin. Struct. Biol.	2004	14		663-668			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. 		
@D	Jeganathan, L.P.//Prakash, L.//Sivakumar, N.//Antony, A.//Alqarawi, S.//Prajna, L.//Devarajan, B.//Mohankumar, V. 	Draft Genome Sequence of an Invasive Multidrug-Resistant Strain, Pseudomonas aeruginosa BK1, Isolated from a Keratitis Patient.	Genome Announcements	2014	2		e00153-14			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. 		
@D	Jeltsch, A. 	Maintenance of species identity and controlling speciation of bacteria: a new function for restriction/modification systems?	Gene	2003	317		13-16			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. 		
@D	Jeltsch, A. 	The cytosine N4-methyltransferase M.PvuII also modifies adenine residues.	Biol. Chem.	2001	382		707-710			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. 		
@D	Jeltsch, A. 	Beyond Watson and Crick: DNA methylation and molecular enzymology of DNA methyltransferases.	Chembiochem	2002	3		274-293			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. 		
@D	Jeltsch, A. 	Circular permutations in the molecular evolution of DNA methyltransferase.	J. Mol. Evol.	1999	49		161-164			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. 		
@A	Jeltsch, A. 		Molecular enzymology of mammalian DNA methyltransferases.			Doerfler, W.//Bohm, P. 		Curr. Top. Microbiol. Immunol.				Berlin, Germany	Springer-Verlag	2006		301		203-225									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. 		
@D	Jeltsch, A.//Alves, J.//Maass, G.//Pingoud, A. 	On the catalytic mechanism of EcoRI and EcoRV.  A detailed proposal based on biochemical results, structural data and molecular modelling.	FEBS Lett.	1992	304		4-8			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. 		
@D	Jeltsch, A.//Alves, J.//Oelgeschlager, T.//Wolfes, H.//Maass, G.//Pingoud, A. 	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.	J. Mol. Biol.	1993	229		221-234			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. 		
@D	Jeltsch, A.//Alves, J.//Urbanke, C.//Maass, G.//Eickstein, H.//Lianshan, Z.//Bayer, E.//Pingoud, A. 	A dodecapeptide comprising the extended chain-alpha-4 region of the restriction endonuclease EcoRI specifically binds to the EcoRI recognition site.	J. Biol. Chem.	1995	270		5122-5129			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. 		
@D	Jeltsch, A.//Alves, J.//Wolfes, H.//Maass, G.//Pingoud, A. 	Substrate-assisted catalysis in the cleavage of DNA by the EcoRI and EcoRV restriction enzymes.	Proc. Natl. Acad. Sci. U. S. A.	1993	90		8499-8503			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. 		
@D	Jeltsch, A.//Alves, J.//Wolfes, H.//Maass, G.//Pingoud, A. 	Pausing of the restriction endonuclease EcoRI during linear diffusion on DNA.	Biochemistry	1994	33		10215-10219			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. 		
@D	Jeltsch, A.//Christ, F.//Fatemi, M.//Roth, M. 	On the substrate specificity of DNA methyltransferases.	J. Biol. Chem.	1999	274		19538-19544			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. 		
@D	Jeltsch, A.//Friedrich, T.//Roth, M. 	Kinetics of methylation and binding of DNA by the EcoRV adenine-N6 methyltransferase.	J. Mol. Biol.	1998	275		747-758			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. 		
@D	Jeltsch, A.//Fritz, A.//Alves, J.//Wolfes, H.//Pingoud, A. 	A fast and accurate enzyme-linked immunosorbent assay for the determination of the DNA cleavage activity of restriction endonucleases.	Anal. Biochem.	1993	213		234-240			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. 		
@D	Jeltsch, A.//Gowhar, H. 	Molecular enzymology of the DNA-(adenine-N6)-methyltransferase M.EcoRV: Kinetic mechanism, kinetics of DNA binding and bending, and linear diffusion.	Biochem. Soc. Trans.	2000	28		A312			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. 		
@A	Jeltsch, A.//Gumport, R.I. 		DNA Methyltransferases, Bacterial.			Lennarz, W.J.//Lane, D. 		Encyclopedia of Biological Chemistry					Academic Press	2004				644-651									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. 		
@D	Jeltsch, A.//Jurkowska, R.Z. 	Allosteric control of mammalian DNA methyltransferases - a new regulatory paradigm.	Nucleic Acids Res.	2016	44		8556-8575			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. 		
@D	Jeltsch, A.//Jurkowska, R.Z. 	Multimerization of the Dnmt3a DNA Methyltransferase and Its Functional Implications.	Prog. Mol. Biol. Transl. Sci.	2013	117		445-464			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. 		
@D	Jeltsch, A.//Jurkowska, R.Z.//Jurkowski, T.P.//Liebert, K.//Rathert, P.//Schlickenrieder, M. 	Application of DNA methyltransferases in targeted DNA methylation.	Appl. Microbiol. Biotechnol.	2007	75		1233-1240			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. 		
@D	Jeltsch, A.//Kroger, M.//Pingoud, A. 	Evidence for an evolutionary relationship among type-II restriction endonucleases.	Gene	1995	160		7-16			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. 		
@D	Jeltsch, A.//Maschke, H.//Selent, U.//Wenz, C.//Kohler, E.//Connolly, B.A.//Thorogood, H.//Pingoud, A. 	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.	Biochemistry	1995	34		6239-6246			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. 		
@D	Jeltsch, A.//Nellen, W.//Lyko, F. 	Two substrates are better than one: dual specificities for Dnmt2 methyltransferases.	Trends Biochem. Sci.	2006	31		306-308			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. 		
@D	Jeltsch, A.//Pingoud, A. 	Kinetic characterization of linear diffusion of the restriction endonuclease EcoRV on DNA.	Biochemistry	1998	37		2160-2169			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. 		
@D	Jeltsch, A.//Pingoud, A. 	Horizontal gene transfer contributes to the wide distribution and evolution of type II restriction-modification systems.	J. Mol. Evol.	1996	42		91-96			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. 		
@D	Jeltsch, A.//Pingoud, A.M. 	Methods for determining activity and specificity of DNA binding and DNA cleavage by class II restriction endonucleases.	Methods Mol. Biol.	2001	160		287-308			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. 		
@D	Jeltsch, A.//Pleckaityte, M.//Selent, U.//Wolfes, H.//Siksnys, V.//Pingoud, A. 	Evidence for substrate-assisted catalysis in the DNA cleavage of several restriction endonucleases.	Gene	1995	157		157-162			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. 		
@D	Jeltsch, A.//Roth, M.//Friedrich, T. 	Mutational analysis of target base flipping by the EcoRV adenine-N6 DNA methyltransferase.	J. Mol. Biol.	1999	285		1121-1130			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. 		
@D	Jeltsch, A.//Sobotta, T.//Pingoud, A. 	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.	Protein Eng.	1996	9		413-423			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. 		
@A	Jeltsch, A.//Urbanke, C. 		Sliding or hopping?  How restriction enzymes find their way on DNA.			Pingoud, A. 		Nucleic Acids Mol. Biol.				Berlin Heidelberg	Springer-Verlag	2004		14		95-110									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. 		
@D	Jeltsch, A.//Wenz, C.//Stahl, F.//Pingoud, A. 	Linear diffusion of the restriction endonuclease EcoRV on DNA is essential for the in vivo function of the enzyme.	EMBO J.	1996	15		5104-5111			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. 		
@D	Jeltsch, A.//Wenz, C.//Wende, W.//Selent, U.//Pingoud, A. 	Engineering novel restriction endonucleases: principles and applications.	Trends Biotechnol.	1996	14		235-238			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. 		
@D	Jen-Jacobson, L. 	Structural-perturbation approaches to thermodynamics of site-specific protein-DNA interactions.	Methods Enzymol.	1995	259		305-345			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. 		
@D	Jen-Jacobson, L. 	Protein-DNA recognition complexes: conservation of structure and binding energy in the transition state.	Biopolymers	1997	44		153-180			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. 		
@D	Jen-Jacobson, L.//Engler, L.E.//Ames, J.T.//Kurpiewski, M.R.//Grigorescu, A. 	Thermodynamic parameters of specific and nonspecific protein-DNA binding.	Supramol. Chem.	2000	12		143-160			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. 		
@D	Jen-Jacobson, L.//Engler, L.E.//Jacobson, L.A. 	Structural and thermodynamic strategies for site-specific DNA binding proteins.	Structure	2000	8		1015-1023			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. 		
@D	Jen-Jacobson, L.//Engler, L.E.//Lesser, D.R.//Kurpiewski, M.R.//Yee, C.//McVerry, B. 	Structural adaptations in the interaction of EcoRI endonuclease with methylated GAATTC sites.	EMBO J.	1996	15		2870-2882			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. 		
@D	Jen-Jacobson, L.//Kurpiewski, M.//Lesser, D.//Grable, J.//Boyer, H.W.//Rosenberg, J.M.//Greene, P.J. 	Coordinate ion pair formation between EcoRI endonuclease and DNA.	J. Biol. Chem.	1983	258		14638-14646			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. 		
@D	Jen-Jacobson, L.//Lesser, D.//Kurpiewski, M. 	The enfolding arms of the EcoRI Endonuclease: role in DNA binding and cleavage.	Cell	1986	45		619-629			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. 		
@A	Jen-Jacobson, L.//Lesser, D.R.//Kurpiewski, M.R. 		DNA sequence discrimination by EcoRI endonuclease.			Eckstein, F.//Lilley, D.M.J. 		Nucleic Acids and Molecular Biology					Springer-Verlag	1991		5		141-170									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. 		
@D	Jenkinson, E.//Crickmore, N. 	Identification of a novel DNA methyltransferase activity from Bacillus thuringiensis.	Curr. Microbiol.	2003	47		144-145			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. 		
@D	Jennert, K.C.//Tardif, C.//Young, D.I.//Young, M. 	Gene transfer to clostridium cellulolyticum ATCC 35319.	Microbiology	2000	146		3071-3080			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. 		
@D	Jennings, M.E.//Chia, N.//Boardman, L.A.//Metcalf, W.W. 	Draft Genome Sequence of Methanobrevibacter smithii Isolate WWM1085, Obtained from a Human Stool Sample.	Genome Announcements	2017	5		e01055-17			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. 		
@D	Jensen, R.V.//Depasquale, S.M.//Harbolick, E.A.//Hong, T.//Kernell, A.L.//Kruchko, D.H.//Modise, T.//Smith, C.E.//McCarter, L.L.//Stevens, A.M. 	Complete Genome Sequence of Prepandemic Vibrio parahaemolyticus BB22OP.	Genome Announcements	2013	1		e00002-12			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. 		
@D	Jensen, T.O.//Kvist, T.//Mikkelsen, M.J.//Westermann, P. 	Rapid and reliable method for identification of associated endonuclease cleavage and recognition sites.	Lett. Appl. Microbiol.	2014	58		576-581			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. 		
@D	Jentsch, S. 	Restriction and modification in Bacillus subtilis:  Sequence specificities of restriction/modification systems BsuM, BsuE, and BsuF.	J. Bacteriol.	1983	156		800-808			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. 		
@D	Jentsch, S.//Gunthert, U.//Trautner, T.A. 	DNA methyltransferases affecting the sequence 5'CCGG.	Nucleic Acids Res.	1981	9		2753-2759			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. 		
@A	Jentsch, S.//Pawlek, B.//Noyer-Weidner, M.//Gunthert, U.//Trautner, T.A. 		Restriction and modification in B. subtilis:  Temperate phages SPbeta and Phi3T for BsuR specific methyltransferases.			Polsinelli, M.//Mazza, G. 		Transformation 1980:  Proceedings of the Fifth European Meeting on Bacterial Transformation and Transfection				Oxford	Cotswold Press	1980		0		363-369									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. 		
@D	Jeon, S.J.//Cunha, F.//Ginn, A.//Jeong, K.C.//Galvao, K.N. 	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.	Genome Announcements	2017	5		e01511-16			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. 		
@D	Jeon, T.J. 	DNA Adenine Methylation of sams1 Gene in Symbiont-Bearing Amoeba proteus.	J. Microbiol.	2008	46		564-570			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. 		
@D	Jeon, W.//Priscilla, L.//Park, G.//Lee, H.//Lee, N.//Lee, D.//Kwon, H.//Ahn, I.//Lee, C.//Lee, H.//Ahn, J. 	Complete genome sequence of the sulfur-oxidizing chemolithoautotrophic Sulfurovum lithotrophicum 42BKTT.	Standards in Genomic Sciences	2017	12		54			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. 		
@D	Jeong, D.W.//Lee, J.H. 	Complete Genome Sequence of Staphylococcus succinus 14BME20 Isolated from a Traditional Korean Fermented Soybean Food.	Genome Announcements	2017	5		e01731-16			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. 		
@D	Jeong, H.//Barbe, V.//Lee, C.H.//Vallenet, D.//Yu, D.S.//Choi, S.H.//Couloux, A.//Lee, S.W.//Yoon, S.H.//Cattolico, L.//Hur, C.G.//Park, H.S.//Segurens, B.//Kim, S.C.//Oh, T.K.//Lenski, R.E.//Studier, F.W.//Daegelen, P.//Kim, J.F. 	Genome Sequences of Escherichia coli B strains REL606 and BL21(DE3).	J. Mol. Biol.	2009	394		644-652			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. 		
@D	Jeong, H.//Choi, S.K.//Kloepper, J.W.//Ryu, C.M. 	Genome Sequence of the Plant Endophyte Bacillus pumilus INR7, Triggering Induced  Systemic Resistance in Field Crops.	Genome Announcements	2014	2		e01093-14			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. 		
@D	Jeong, H.//Choi, S.K.//Park, S.H. 	Genome Sequences of Bacillus thuringiensis Serovar kurstaki Strain BP865 and B. thuringiensis Serovar aizawai Strain HD-133.	Genome Announcements	2017	5		e01544-16			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. 		
@D	Jeong, H.//Choi, S.K.//Park, S.Y.//Kim, S.H.//Park, S.H. 	Draft Genome Sequence of Paenibacillus peoriae Strain KCTC 3763T.	J. Bacteriol.	2012	194		1237-1238			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. 		
@D	Jeong, H.//Chun, S.J.//Srivastava, A.//Cui, Y.//Ko, S.R.//Oh, H.M.//Ahn, C.Y. 	Genome Sequences of Two Cyanobacterial Strains, Toxic Green Microcystis aeruginosa KW (KCTC 18162P) and Nontoxic Brown Microcystis sp. Strain MC19, under  Xenic Culture Conditions.	Genome Announcements	2018	6		e00378-18			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. 		
@D	Jeong, H.//Jeong, D.E.//Kim, S.H.//Song, G.C.//Park, S.Y.//Ryu, C.M.//Park, S.H.//Choi, S.K. 	Draft Genome Sequence of the Plant Growth-Promoting Bacterium Bacillus siamensis  KCTC 13613T.	J. Bacteriol.	2012	194		4148-4149			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. 		
@D	Jeong, H.//Jeong, D.E.//Sim, Y.M.//Park, S.H.//Choi, S.K. 	Genome Sequence of Lysinibacillus sphaericus Strain KCTC 3346T.	Genome Announcements	2013	1		e00625-13			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. 		
@D	Jeong, H.//Jo, S.H.//Hong, C.E.//Park, J.M. 	Genome Sequence of the Endophytic Bacterium Bacillus thuringiensis Strain KB1, a  Potential Biocontrol Agent against Phytopathogens.	Genome Announcements	2016	4		e00279-16			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. 		
@D	Jeong, H.//Kim, H.J.//Lee, S.J. 	Complete Genome Sequence of Escherichia coli Strain BL21.	Genome Announcements	2015	3		e00134-15			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. 		
@D	Jeong, H.//Kloepper, J.W.//Ryu, C.M. 	Genome Sequences of Pseudomonas amygdali pv. tabaci Strain ATCC 11528 and pv. lachrymans Strain 98A-744.	Genome Announcements	2015	3		e00683-15			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. 		
@D	Jeong, H.//Kloepper, J.W.//Ryu, C.M. 	Genome Sequence of Rhizobacterium Serratia marcescens Strain 90-166, Which Triggers Induced Systemic Resistance and Plant Growth Promotion.	Genome Announcements	2015	3		e00667-15			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. 		
@D	Jeong, H.//Park, S.H.//Choi, S.K. 	Genome Sequence of Antibiotic-Producing Bacillus amyloliquefaciens Strain KCTC 13012.	Genome Announcements	2015	3		e01121-15			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). 		
@D	Jeong, H.//Park, S.H.//Choi, S.K. 	Genome Sequence of the Acrystalliferous Bacillus thuringiensis Serovar Israelensis Strain 4Q7, Widely Used as a Recombination Host.	Genome Announcements	2014	2		e00231-14			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. 		
@D	Jeong, H.//Park, S.H.//Choi, S.K. 	Draft Genome Sequences of Four Plant Probiotic Bacillus Strains.	Genome Announcements	2016	4		e00358-16			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. 		
@D	Jeong, H.//Park, S.Y.//Chung, W.H.//Kim, S.H.//Kim, N.//Park, S.H.//Kim, J.F. 	Draft Genome Sequence of Paenibacillus polymyxa Type Strain (ATCC 842T), a Plant Growth-Promoting Bacterium.	J. Bacteriol.	2011	193		5026-5027			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. 		
@D	Jeong, H.//Sim, Y.M.//Kim, H.J.//Lee, D.W.//Lim, S.K.//Lee, S.J. 	Genome Sequence of the Vancomycin-Producing Amycolatopsis orientalis subsp. orientalis Strain KCTC 9412T.	Genome Announcements	2013	1		e00408-13			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). 		
@D	Jeong, H.//Sim, Y.M.//Kim, H.J.//Lee, Y.J.//Lee, D.W.//Lim, S.K.//Lee, S.J. 	Genome Sequences of Amycolatopsis orientalis subsp. orientalis Strains DSM 43388  and DSM 46075.	Genome Announcements	2013	1		e00545-13			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. 		
@D	Jeong, H.//Sim, Y.M.//Park, S.H.//Choi, S.K. 	Complete Genome Sequence of Bacillus subtilis Strain ATCC 6051a, a Potential Host for High-Level Secretion of Industrial Enzymes.	Genome Announcements	2015	3		e00532-15			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. 		
@D	Jeong, H.//Yim, J.H.//Lee, C.//Choi, S.H.//Park, Y.K.//Yoon, S.H.//Hur, C.G.//Kang, H.Y.//Kim, D.//Lee, H.H.//Park, K.H.//Park, S.H.//Park, H.S.//Lee, H.K.//Oh, T.K.//Kim, J.F. 	Genomic blueprint of Hahella chejuensis, a marine microbe producing an algicidal agent.	Nucleic Acids Res.	2005	33		7066-7073			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. 		
@D	Jeong, H.//Zhao, F.//Igori, D.//Oh, K.H.//Kim, S.Y.//Kang, S.G.//Kim, B.K.//Kwon, S.K.//Lee, C.H.//Song, J.Y.//Yu, D.S.//Park, M.S.//Cho, S.H.//Kim, J.F. 	Genome Sequence of the Hemolytic-Uremic Syndrome-Causing Strain Escherichia coli  NCCP15647.	J. Bacteriol.	2012	194		3747-3748			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. 		
@D	Jeong, H.W.//Bang, M.S.//Lee, Y.J.//Lee, S.J.//Lee, S.C.//Shin, J.I.//Oh, C.H. 	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.	Genome Announcements	2018	6		e00526-18			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. 		
@D	Jeong, J.J.//Lee, Y.J.//Pathiraja, D.//Park, B.//Choi, I.G.//Kim, K.D. 	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.	Genome Announcements	2018	6		e00628-18			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. 		
@D	Jeong, J.J.//Moon, H.J.//Pathiraja, D.//Park, B.//Choi, I.G.//Kim, K.D. 	Draft Genome Sequences of Bacillus megaterium KU143, Microbacterium testaceum KU313, and Pseudomonas protegens AS15, Isolated from Stored Rice Grains.	Genome Announcements	2018	6		e00468-18			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. 		
@D	Jeong, J.J.//Park, B.//Oh, J.Y.//Mannaa, M.//Kim, Y.J.//Hong, J.K.//Choi, I.G.//Kim, K.D. 	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.	Genome Announcements	2016	4		e01168-16			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. 		
@D	Jeong, J.J.//Park, B.H.//Park, H.//Choi, I.G.//Kim, K.D. 	Draft Genome Sequence of Chryseobacterium sp. Strain GSE06, a Biocontrol Endophytic Bacterium Isolated from Cucumber (Cucumis sativus).	Genome Announcements	2016	4		e00577-16			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. 		
@D	Jeong, J.J.//Park, H.//Park, B.H.//Mannaa, M.//Sang, M.K.//Choi, I.G.//Kim, K.D. 	Draft Genome Sequence of a Biocontrol Rhizobacterium, Chryseobacterium kwangjuense Strain KJ1R5, Isolated from Pepper (Capsicum annuum).	Genome Announcements	2016	4		e00301-16			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. 		
@D	Jeong, J.J.//Sang, M.K.//Pathiraja, D.//Park, B.//Choi, I.G.//Kim, K.D. 	Draft Genome Sequence of Phosphate-Solubilizing Chryseobacterium sp. Strain ISE14, a Biocontrol and Plant Growth-Promoting Rhizobacterium Isolated from Cucumber.	Genome Announcements	2018	6		e00612-18			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. 		
@D	Jeong, S.//Liang, G.N.//Sharma, S.//Lin, J.C.//Choi, S.H.//Han, H.//Yoo, C.B.//Egger, G.//Yang, A.S.//Jones, P.A. 	Selective Anchoring of DNA Methyltransferases 3A and 3B to Nucleosomes Containing Methylated DNA.	Mol. Cell. Biol.	2009	29		5366-5376			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. 		
@D	Jeong, Y.//Song, Y.//Shin, H.S.//Cho, B.K. 	Draft Genome Sequence of Acid-Tolerant Clostridium drakei SL1T, a Potential Chemical Producer through Syngas Fermentation.	Genome Announcements	2014	2		e00387-14			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. 		
@D	Jeong, Y.S.//Oh, K.B.//Park, J.S.//Kim, J.S.//Kang, Y.K. 	Cytoplasmic Localization of Oocyte-Specific Variant of Porcine DNA Methyltransferase-1 During Early Development.	Dev. Dyn.	2009	238		1666-1673			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. 		
@D	Jeraldo, P.//Cunningham, S.A.//Quest, D.//Sikkink, R.A.//O'Brien, D.//Eckloff, B.W.//Patel, R.//Chia, N. 	Draft Genome Sequences of Nine Pseudomonas aeruginosa Strains, Including Eight Clinical Isolates.	Genome Announcements	2015	3		e01154-15			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. 		
@D	Jeraldo, P.//Hernandez, A.//White, B.A.//O'Brien, D.//Ahlquist, D.//Boardman, L.//Chia, N. 	Draft genome sequences of 24 microbial strains assembled from direct sequencing from 4 stool samples.	Genome Announcements	2015	3		e00526-15			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. 		
@D	Jerke, K.//Nakatsu, C.H.//Beasley, F.//Konopka, A. 	Comparative analysis of eight Arthrobacter plasmids.	Plasmid	2008	59		73-85			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. 		
@D	Jermyn, W.S.//Boyd, E.F. 	Characterization of a novel Vibrio pathogenicity island (VPI-2) encoding neuraminidase (nanH) among toxigenic Vibrio cholerae isolates.	Microbiology	2002	148		3681-3693			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. 		
@D	Jerome, J.P.//Klahn, B.D.//Bell, J.A.//Barrick, J.E.//Brown, C.T.//Mansfield, L.S. 	Draft Genome Sequences of Two Campylobacter jejuni Clinical Isolates, NW and D2600.	J. Bacteriol.	2012	194		5707-5708			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. 		
@D	Jessen, W.J.//Dhasarathy, A.//Hoose, S.A.//Carvin, C.D.//Risinger, A.L.//Kladde, M.P. 	Mapping chromatin structure in vivo using DNA methyltransferases.	Methods	2004	33		68-80			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. 		
@D	Jett, S.D.//Bear, D.G. 	Snapshot blotting: transfer of nucleic acids and nucleoprotein complexes from electrophoresis gels to grids for electron microscopy.	Proc. Natl. Acad. Sci. U. S. A.	1994	91		6870-6874			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. 		
@D	Jeukens, J.//Boyle, B.//Bianconi, I.//Kukavica-Ibrulj, I.//Tummler, B.//Bragonzi, A.//Levesque, R.C. 	Complete Genome Sequence of Persistent Cystic Fibrosis Isolate Pseudomonas aeruginosa Strain RP73.	Genome Announcements	2013	1		e00568-13			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. 		
@D	Jeukens, J.//Freschi, L.//Kukavica-Ibrulj, I.//Nguyen, D.//Levesque, R.C. 	Draft Genome Sequence of Triclosan-Resistant Cystic Fibrosis Isolate Achromobacter xylosoxidans CF304.	Genome Announcements	2015	3		e00865-15			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. 		
@D	Jeukens, J.//Kukavica-Ibrulj, I.//Freschi, L.//Jabaji, S.//Levesque, R.C. 	Draft Genome Sequences of Two Lipopeptide-Producing Strains of Bacillus methylotrophicus.	Genome Announcements	2015	3		e01176-15			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. 		
@D	Jezewska-Frackowiak, J.//Lubys, A.//Vitkute, J.//Zakareviciene, L.//Zebrowska, J.//Krefft, D.//Skowron, M.A.//Zylicz-Stachula, A.//Skowron, P.M. 	A new prototype IIS/IIC/IIG endonuclease-methyltransferase TsoI from the thermophile Thermus scotoductus, recognising 5 '-TARCCA(N-11/9)-3 ' sequences.	J. Biotechnol.	2015	194		19-26			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. 		
@D	Jha, G.//Tyagi, I.//Kumar, R.//Ghosh, S. 	Draft Genome Sequence of Broad-Spectrum Antifungal Bacterium Burkholderia gladioli Strain NGJ1, Isolated from Healthy Rice Seeds.	Genome Announcements	2015	3		e00803-15			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. 		
@D	Jhon, N.-I.//Casas-Finet, J.R.//Maki, A.H.//Modrich, P. 	Investigation of the complexes of EcoRI endonuclease with decanucleotides containing canonical and modified recognition sequences using fluorescence and optical detection of magnetic resonance spectroscopy.	Biochim. Biophys. Acta	1988	949		189-194			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. 		
@D	Ji, B.//Gimenez, G.//Barbe, V.//Vacherie, B.//Rouy, Z.//Amrani, A.//Fardeau, M.L.//Bertin, P.//Alazard, D.//Leroy, S.//Talla, E.//Ollivier, B.//Dolla, A.//Pradel, N. 	Complete Genome Sequence of the Piezophilic, Mesophilic, Sulfate-Reducing Bacterium Desulfovibrio hydrothermalis AM13(T.).	Genome Announcements	2013	1		e00226-12			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. 		
@D	Ji, K.//Wang, W.//Zeng, B.//Chen, S.//Zhao, Q.//Chen, Y.//Li, G.//Ma, T. 	Bacterial cellulose synthesis mechanism of facultative anaerobe Enterobacter sp. FY-07.	Sci. Rep.	2016	6		21863			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. 		
@D	Jia, B.//Jin, H.M.//Lee, H.J.//Jeon, C.O. 	Draft Genome Sequence of Zhouia amylolytica AD3, Isolated from Tidal Flat Sediment.	Genome Announcements	2016	4		e00327-16			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. 		
@D	Jia, D. 	Crystallographic and biochemical studies of mammalian de novo DNA methyltransferase Dnmt3.	Ph.D. Thesis, Emory Univ., Atlanta, GA, USA	2007			1-206			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. 		
@D	Jia, D.//Jurkowska, R.Z.//Zhang, X.//Jeltsch, A.//Cheng, X. 	Structure of Dnmt3a bound to Dnmt3L suggests a model for de novo DNA methylation.	Nature	2007	449		248-251			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. 		
@D	Jia, F. 	Genome Sequence of the Oral Probiotic Streptococcus salivarius JF.	Genome Announcements	2016	4		e00971-16			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. 		
@D	Jia, F. 	Complete Genome Sequence of Lactobacillus oris J-1, a Potential Probiotic Isolated from the Human Oral Microbiome.	Genome Announcements	2016	4		e00970-16			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. 		
@D	Jia, N.//Ding, M.Z.//Du, Y.Z.//Feng, S.//Gao, F.//Yuan, Y.J. 	Complete Genome Sequence of the Industrial Bacterium Ketogulonicigenium vulgare SKV.	Genome Announcements	2016	4		e01426-16			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. 		
@D	Jia, N.//Du, J.//Ding, M.Z.//Gao, F.//Yuan, Y.J. 	Genome Sequence of Bacillus endophyticus and Analysis of Its Companion Mechanism in the Ketogulonigenium vulgare-Bacillus Strain Consortium.	PLoS ONE	2015	10		E0135104			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. 		
@D	Jia, Z.//Jin, W.//Huang, Y.//Song, S. 	Complete Genome Sequence of Bacillus subtilis J-5, a Potential Biocontrol Agent.	Genome Announcements	2017	5		e00275-17			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. 		
@D	Jiang, B.//Cui, D.//Li, A.//Gai, Z.//Ma, F.//Yang, J.//Ren, N. 	Genome Sequence of a Cold-Adaptable Sulfamethoxazole-Degrading Bacterium, Pseudomonas psychrophila HA-4.	J. Bacteriol.	2012	194		5721			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. 		
@D	Jiang, B.//Yao, H.//Tong, Y.//Yang, X.//Huang, Y.//Jiang, J.//Cao, W. 	Genome Sequence of Borrelia garinii Strain NMJW1, Isolated from China.	J. Bacteriol.	2012	194		6660-6661			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. 		
@D	Jiang, B.H.//Liu, J.L.//Hu, X.M. 	Draft Genome Sequence of the Efficient Bioflocculant-Producing Bacterium Paenibacillus sp. Strain A9.	Genome Announcements	2013	1		e00131-13			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. 		
@D	Jiang, C.//Yan, C.Y.//Huang, C.//Jiang, J.H.//Yu, R.Q. 	A bioluminescence assay for DNA methyltransferase activity based on methylation-resistant cleavage.	Anal. Biochem.	2012	423		224-228			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. 		
@D	Jiang, C.H.//Chen, Y.//Yan, F.//Fan, Z.H.//Guo, J.H. 	Whole-Genome Sequence of Bacillus cereus AR156, a Potential Biocontrol Agent with High Soilborne Disease Biocontrol Efficacy and Plant Growth Promotion.	Genome Announcements	2017	5		e00886-17			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. 		
@D	Jiang, H.//Fan, H.J.//Lu, C.P. 	Identification and distribution of putative virulent genes in strains of Streptococcus suis serotype 2.	Vet. Microbiol.	2009	133		309-316			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. 		
@D	Jiang, H.//Zou, G.//Huang, L.//Zhu, R. 	Purification of restriction endonuclease Bsp63I by two step affinity chromatography.	Xinan Shifan Daxue Xuebao, Ziran Kexueban	2000	25		74-77			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. 		
@D	Jiang, J.//Alvarez, C.//Kukutla, P.//Yu, W.//Xu, J. 	Draft Genome Sequences of Enterobacter sp. Isolate Ag1 from the Midgut of the Malaria Mosquito Anopheles gambiae.	J. Bacteriol.	2012	194		5481			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. 		
@D	Jiang, K. et al. 	Complete genome sequence of Thauera aminoaromatica strain MZ1T.	Standards in Genomic Sciences	2012	6		325-335			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. 		
@D	Jiang, K.//Xue, Y.//Ma, Y. 	Complete genome sequence of Salinicoccus halodurans H3B36, isolated from the Qaidam Basin in China.	Standards in Genomic Sciences	2015	10		116			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. 		
@D	Jiang, K.//Zheng, J.//Higgins, S.B. 	A generic algorithm for finding restriction sites within DNA sequences.	Comput. Appl. Biosci.	1991	7		249-256			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. 		
@D	Jiang, L.//L'Haridon, S.//Jebbar, M.//Xu, H.//Alain, K.//Shao, Z. 	Complete genome sequence and whole-genome phylogeny of Kosmotoga pacifica type strain SLHLJ1T from an East Pacific hydrothermal sediment.	Standards in Genomic Sciences	2017	12		3			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. 		
@D	Jiang, L.//Lin, M.//Li, X.//Cui, H.//Xu, X.//Li, S.//Huang, H. 	Genome Sequence of Thermus thermophilus ATCC 33923, a Thermostable Trehalose-Producing Strain.	Genome Announcements	2013	1		e00493-13			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. 		
@D	Jiang, L.//Long, M.//Shao, Z. 	Draft Genome Sequence of Defluviimonas indica Strain 20V17T, Isolated from a Deep-Sea Hydrothermal Vent Environment in the Southwest Indian Ocean.	Genome Announcements	2014	2		e00479-14			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%. 		
@D	Jiang, L.//Zhu, L.//Xu, X.//Li, Y.//Li, S.//Huang, H. 	Genome Sequence of Clostridium tyrobutyricum ATCC 25755, a Butyric Acid-Overproducing Strain.	Genome Announcements	2013	1		e00308-13			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. 		
@D	Jiang, S.//Zheng, B.//Ding, W.//Lv, L.//Ji, J.//Zhang, H.//Xiao, Y.//Li, L. 	Whole-Genome Sequence of Staphylococcus hominis, an Opportunistic Pathogen.	J. Bacteriol.	2012	194		4761-4762			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. 		
@D	Jiang, S.F.//Liu, Y.//Xiao, M.Y.//Ruan, C.J.//Lu, Z.J. 	Draft Genome Sequence of Klebsiella variicola Strain KV321 Isolated from Rhizosphere Soil of Pisolithus tinctorius-Eucalyptus Mycorrhiza.	Genome Announcements	2016	4		e00676-16			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. 		
@D	Jiang, T.//Gao, C.//Su, F.//Zhang, W.//Hu, C.//Dou, P.//Zheng, Z.//Tao, F.//Ma, C.//Xu, P. 	Genome Sequence of Pseudomonas stutzeri SDM-LAC, a Typical Strain for Studying the Molecular Mechanism of Lactate Utilization.	J. Bacteriol.	2012	194		894-895			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. 		
@D	Jiang, X.//Wang, S.//Cheng, H.//Huo, Y.//Zhang, X.//Zhu, X.//Han, X.//Ni, P.//Wu, M. 	Genome Sequence of Halobiforma lacisalsi AJ5, an Extremely Halophilic Archaeon Which Harbors a bop Gene.	J. Bacteriol.	2011	193		7023-7024			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. 		
@D	Jiang, X.//Xue, Y.//Wang, L.//Yu, B.//Ma, Y. 	Genome Sequence of a Novel Polymer-Grade L-Lactate-Producing Alkaliphile, Exiguobacterium sp. Strain 8-11-1.	Genome Announcements	2013	1		e00616-13			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. 		
@D	Jiang, Y.//Huang, Y.H.//Long, Z.E. 	De Novo Whole-Genome Sequence of Micromonospora carbonacea JXNU-1 with Broad-Spectrum Antimicrobial Activity, Isolated from Soil Samples.	Genome Announcements	2015	3		e00174-15			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. 		
@D	Jiang, Y.//Qu, Y.//Xu, P.//Tang, H. 	Genome Sequence of a Versatile Aromatic Hydrocarbon-Degrading Bacterium, Arthrobacter sp. W1.	Genome Announcements	2015	3		e00387-15			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. 		
@D	Jiang, Y.//Xiao, P.//Yu, G.//Sano, T.//Pan, Q.//Li, R. 	Molecular Basis and Phylogenetic Implications of Deoxycylindrospermopsin Biosynthesis in the Cyanobacterium Raphidiopsis curvata.	Appl. Environ. Microbiol.	2012	78		2256-2263			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. 		
@D	Jiang, Y.//Xu, H.//Li, Y.//Liu, H.//Yu, L.//Qiao, M.//Liu, G. 	Draft Genome Sequence of Bacillus subtilis Strain NKYL29, an Antimicrobial-Peptide-Producing Strain from Soil.	Genome Announcements	2014	2		e01140-14			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. 		
@D	Jiang, Y.//Yang, F.//Zhang, X.//Yang, J.//Chen, L.//Yan, Y.//Nie, H.//Xiong, Z.//Wang, J.//Dong, J.//Xue, Y.//Xu, X.//Zhu, Y.//Chen, S.//Jin, Q. 	The complete sequence and analysis of the large virulence plasmid pSS of Shigella sonnei.	Plasmid	2005	54		149-159			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. 		
@D	Jiang, Y.//Yu, D.L.//Wei, Z.Q.//Shen, P.//Zhou, Z.H.//Yu, Y.S. 	Complete Nucleotide Sequence of Klebsiella pneumoniae Multidrug Resistance Plasmid pKP048, Carrying bla(KPC-2), bla(DHA-1), qnrB4, and armA.	Antimicrob. Agents Chemother.	2010	54		3967-3969			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. 		
@D	Jiang, Y.L.//Zhang, M.//Jing, H.L.//Gao, L.Y. 	[Isolation and characterization of an iridovirus from sick giant salamander (Andrias davidianus)].	Bing Du Xue Bao	2011	27		274-282			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. 		
@D	Jiang, Z.F.//Xia, F.//Johnson, K.W.//Bartom, E.//Tuteja, J.H.//Stevens, R.//Grossman, R.L.//Brumin, M.//White, K.P.//Ghanim, M. 	Genome Sequences of the Primary Endosymbiont 'Candidatus Portiera aleyrodidarum'  in the Whitefly Bemisia tabaci B and Q Biotypes.	J. Bacteriol.	2012	194		6678-6679			'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. 		
@D	Jiao, J.//Paterson, J.//Busche, T.//Ruckert, C.//Kalinowski, J.//Harwani, D.//Gross, H. 	Draft Genome Sequence of Streptomyces sp. Strain DH-12, a Soilborne Isolate from  the Thar Desert with Broad-Spectrum Antibacterial Activity.	Genome Announcements	2018	6		e00108-18			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. 		
@D	Jiao, J.Y.//Carro, L.//Liu, L.//Gao, X.Y.//Zhang, X.T.//Hozzein, W.N.//Lapidus, A.//Huntemann, M.//Reddy, T.B.//Varghese, N.//Hadjithomas, M.//Ivanova, N.N.//Goker, M.//Pillay, M.//Eisen, J.A.//Woyke, T.//Klenk, H.P.//Kyrpides, N.C.//Li, W.J. 	Complete genome sequence of Jiangella gansuensis strain YIM 002T (DSM 44835T), the type species of the genus Jiangella and source of new antibiotic compounds.	Standards in Genomic Sciences	2017	12		21			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. 		
@D	Jiao, J.Y.//Liu, L.//Park, D.J.//Kim, C.J.//Xiao, M.//Chen, J.//Li, L.//Zhong, J.M.//Zhao, J.//Li, W.J. 	Draft Genome Sequence of Jiangella alkaliphila KCTC 19222T, Isolated from Cave Soil in Jeju, Republic of Korea.	Genome Announcements	2015	3		e00721-15			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.' 		
@D	Jiao, J.Y.//Liu, L.//Zhou, E.M.//Wei, D.Q.//Ming, H.//Xian, W.D.//Yuan, C.G.//Zhong, J.M.//Li, W.J. 	Actinomadura amylolytica sp. nov. and Actinomadura cellulosilytica sp. nov., isolated from geothermally heated soil.	Antonie Van Leeuwenhoek	2015	108		75-83			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. 		
@D	Jima, D.D.//Luce-Fedrow, A.//Yang, Y.//Maina, A.N.//Snesrud, E.C.//Otiang, E.//Njenga, K.//Jarman, R.G.//Richards, A.L.//Hang, J. 	Whole-Genome Sequence of 'Candidatus Rickettsia asemboensis' Strain NMRCii, Isolated from Fleas of Western Kenya.	Genome Announcements	2015	3		e00018-15			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. 		
@D	Jimenez, E.//Langa, S.//Martin, V.//Arroyo, R.//Martin, R.//Fernandez, L.//Rodriguez, J.M. 	Complete genome sequence of Lactobacillus fermentum CECT 5716, a probiotic strain isolated from human milk.	J. Bacteriol.	2010	192		4800			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. 		
@D	Jimenez, E.//Martin, R.//Maldonado, A.//Martin, V.//Gomez-de-Segura, A.//Fernandez, L.//Rodriguez, J.M. 	Complete genome sequence of Lactobacillus salivarius CECT 5713, a probiotic strain isolated from human milk and infant feces.	J. Bacteriol.	2010	192		5266-5267			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. 		
@D	Jimenez, E.//Villar-Tajadura, M.A.//Marin, M.//Fontecha, J.//Requena, T.//Arroyo, R.//Fernandez, L.//Rodriguez, J.M. 	Complete Genome Sequence of Bifidobacterium breve CECT 7263, a Strain Isolated from Human Milk.	J. Bacteriol.	2012	194		3762-3763			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. 		
@D	Jimenez, G.//Blanch, A.R.//Tamames, J.//Rossello-Mora, R. 	Complete Genome Sequence of Bacillus toyonensis BCT-7112T, the Active Ingredient  of the Feed Additive Preparation Toyocerin.	Genome Announcements	2013	1		e01080-13			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. 		
@D	Jimenez-Galisteo, G.//Villa, T.G.//Vinuesa, T.//Vinas, M.//Dominguez, A.//Munoz, E. 	Draft Genome Sequence of the Bacterium Gordonia jacobaea, a New Member of the Gordonia Genus.	Genome Announcements	2015	3		e00995-15			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. 		
@D	Jin, A.//Zhang, Y.//Xia, Y.//Traylor, E.//Nelson, M.//Van Etten, J.L. 	New restriction endonuclease CviRI cleaves DNA at TG^CA sequences.	Nucleic Acids Res.	1994	22		3928-3929			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. 		
@D	Jin, B.//Robertson, K.D. 	DNA Methyltransferases, DNA Damage Repair, and Cancer.	Adv. Exp. Med. Biol.	2013	754		3-29			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. 		
@D	Jin, D.//Chen, C.//Li, L.//Lu, S.//Li, Z.//Zhou, Z.//Jing, H.//Xu, Y.//Du, P.//Wang, H.//Xiong, Y.//Zheng, H.//Bai, X.//Sun, H.//Wang, L.//Ye, C.//Gottschalk, M.//Xu, J. 	Dynamics of fecal microbial communities in children with diarrhea of unknown etiology and genomic analysis of associated Streptococcus lutetiensis.	BMC Microbiol.	2013	13		141			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. 		
@D	Jin, D.//Zhu, Y.//Wang, X.//Kong, X.//Liu, H.//Wang, Y.//Deng, Y.//Jia, M. 	Draft Genome Sequence of Sphingobium yanoikuyae TJ, a Halotolerant Di-n-Butyl-Phthalate-Degrading Bacterium.	Genome Announcements	2016	4		e00569-16			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. 		
@D	Jin, H.//Nishizawa, T.//Guo, Y.//Nishizawa, A.//Park, H.D.//Kato, H.//Tsuji, K.//Harada, K.I. 	Complete Genome Sequence of a Microcystin-Degrading Bacterium, Sphingosinicella microcystinivorans Strain B-9.	Microbiol. Resour. Announc.	2018	7		e00898-18			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. 		
@D	Jin, H.M.//Jeong, H.//Moon, E.J.//Math, R.K.//Lee, K.//Kim, H.J.//Jeon, C.O.//Oh, T.K.//Kim, J.F. 	Complete Genome Sequence of the Polycyclic Aromatic Hydrocarbon-Degrading Bacterium Alteromonas sp. Strain SN2.	J. Bacteriol.	2011	193		4292-4293			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. 		
@D	Jin, Lu.//Ye, F.//Zhao, D.//Chen, S.//Zhu, K.//Zheng, M.//Jiang, R.-W.//Jiang, H.//Luo, C. 	Metadynamics Simulation Study on the Conformational Transformation of HhaI Methyltransferase: An Induced-Fit Base-Flipping Hypothesis.	Biomed Res. Int.	2014	2014		304563			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. 		
@D	Jin, Q. et al. 	Genome sequence of Shigella flexneri 2a: insights into pathogenicity through comparison with genomes of Escherichia coli K12 and O157.	Nucleic Acids Res.	2002	30		4432-4441			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. 		
@D	Jin, S.G.//Kadam, S.//Pfeifer, G.P. 	Examination of the specificity of DNA methylation profiling techniques towards 5-methylcytosine and 5-hydroxymethylcytosine.	Nucleic Acids Res.	2010	38		e125			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. 		
@D	Jin, Y.//Binkowski, G.//Simon, L.D.//Norris, D. 	HO endonuclease cleaves MAT DNA in vitro by an inefficient stoichiometric reaction mechanism.	J. Biol. Chem.	1997	272		7352-7359			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. 		
@D	Jindrova, E.//Schmid-Nuoffer, S.//Hamburger, F.//Janscak, P.//Bickle, T.A. 	On the DNA cleavage mechanism of Type I restriction enzymes.	FEBS J.	2005	272		552			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. 		
@D	Jindrova, E.//Schmid-Nuoffer, S.//Hamburger, F.//Janscak, P.//Bickle, T.A. 	On the DNA cleavage mechanism of Type I restriction enzymes.	Nucleic Acids Res.	2005	33		1760-1766			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. 		
@D	Jing, X.//Cao, X.//Wang, Li.//Lan, T.//Li, Y.//Xie, G. 	DNA-AuNPs based signal amplification for highly sensitive detection of DNA methylation, methyltransferase activity and inhibitor screening.	Biosensors and Bioelectronics	2014	58		40-47			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. 		
@D	Jiricny, J.//Martin, D. 	Restriction endonucleases HindII and TaqI cleave DNA with mismatched nucleotides within their recognition sequences.	Nucleic Acids Res.	1986	14		1943-1949			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. 		
@D	Jiricny, J.//Wood, S.G.//Martin, D.//Ubasawa, A. 	Oligonucleotide duplexes containing inosine, 7-deazainosine, tubercidin, nebularine and 7-deazanebularine as substrates for restriction endonucleases HindII, SalI and TaqI.	Nucleic Acids Res.	1986	14		6579-6590			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. 		
@D	Jneid, J.//Benamar, S.//Pagnier, I.//Levy, P.Y.//Lavigne, J.P.//La Scola, B. 	Draft Genome Sequence of Providencia heimbachae, Isolated from a Diabetic Foot Ulcer.	Genome Announcements	2016	4		e00276-16			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. 		
@D	Jo, J.//Choi, H.//Lee, S.G.//Oh, J.//Lee, H.G.//Park, C. 	Draft Genome Sequences of Pseudoalteromonas tetraodonis CSB01KR and Pseudoalteromonas lipolytica CSB02KR, Isolated from the Gut of the Sea Cucumber Apostichopus japonicus.	Genome Announcements	2017	5		e00627-17			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. 		
@D	Jo, K. 	Evolutionary relationship of NaeI restriction endonuclease with DNA topisomerases.	Diss. Abstr.	1996	57		889			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. 		
@D	Jo, K.//Topal, M.D. 	Step-wise DNA relaxation and decatenation by NaeI-43K.	Nucleic Acids Res.	1998	26		2380-2384			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. 		
@D	Jo, K.//Topal, M.D. 	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.	Nucleic Acids Res.	1996	24		4171-4175			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. 		
@D	Jo, K.//Topal, M.D. 	DNA topoisomerase and recombinase activities in NaeI restriction endonuclease.	Science	1995	267		1817-1820			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. 		
@D	Jo, K.//Topal, M.D. 	Changing a leucine to a lysine residue makes NaeI endonuclease hypersensitive to DNA intercalative drugs.	Biochemistry	1996	35		10014-10018			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. 		
@D	Joardar, V. et al. 	Whole-genome sequence analysis of Pseudomonas syringae pv. phaseolicola 1448A reveals divergence among pathovars in genes involved in virulence and transposition.	J. Bacteriol.	2005	187		6488			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. 		
@D	Jobbagy, Z.//Izsvak, Z.//Duda, E. 	Positive co-operative interaction between the subunits of CeqI restriction endonuclease.	Biochem. J.	1992	286		85-88			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. 		
@D	Jobling, M.G.//Raleigh, E.A.//Frank, D.N. 	Complete Genome Sequence of Escherichia coli ER1821R, a Laboratory K-12 Derivative Engineered To Be Deficient in All Methylcytosine and Methyladenine  Restriction Systems.	Genome Announcements	2016	4		e00763-16			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. 		
@D	Jogler, C.//Lin, W.//Meyerdierks, A.//Kube, M.//Katzmann, E.//Flies, C.//Pan, Y.//Amann, R.//Reinhardt, R.//Schuler, D. 	Toward cloning of the magnetotactic metagenome: identification of magnetosome island gene clusters in uncultivated magnetotactic bacteria from different aquatic sediments.	Appl. Environ. Microbiol.	2009	75		3972-3979			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. 		
@D	Jogler, C.//Niebler, M.//Lin, W.//Kube, M.//Wanner, G.//Kolinko, S.//Stief, P.//Beck, A.J.//de Beer, D.//Petersen, N.//Pan, Y.//Amann, R.//Reinhardt, R.//Schuler, D. 	Cultivation-independent characterization of 'Candidatus Magnetobacterium bavaricum' via ultrastructural, geochemical, ecological and metagenomic methods.	Environ. Microbiol.	2010	12		f2466-f2478			'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. 		
@D	Johannssen, W. 	Electron microscopy studies of DNA complexes with restriction endonuclease SalGI.	Z. Allg. Mikrobiol.	1983	23		197-201			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. 		
@D	Johannssen, W. 	Interaction of restriction endonuclease with DNA as revealed by electron microscopy.	Methods Microbiol.	1988	20		325-339			None 		
@D	Johannssen, W.//Schutte, H.//Mayer, F.//Mayer, H. 	Quaternary structure of the isolated restriction endonuclease EndoR.BglI from Bacillus globigii as revealed by electron microscopy.	J. Mol. Biol.	1979	134		707-726			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. 		
@D	Johansen, S.//Embley, T.M.//Willassen, N.P. 	A family of nuclear homing endonucleases.	Nucleic Acids Res.	1993	21		4405			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. 		
@D	Johansen, S.//Vogt, V.M. 	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.	Cell	1994	76		725-734			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. 		
@D	Johnning, A.//Jakobsson, H.E.//Boulund, F.//Salva-Serra, F.//Moore, E.R.//Ahren, C.//Karami, N.//Kristiansson, E. 	Draft Genome Sequence of Extended-Spectrum-beta-Lactamase-Producing Escherichia coli Strain CCUG 62462, Isolated from a Urine Sample.	Genome Announcements	2016	4		e01382-16			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. 		
@D	Johnson, C.M.//Grossman, A.D. 	Complete Genome Sequence of Bacillus subtilis Strain CU1050, Which Is Sensitive to Phage SPbeta.	Genome Announcements	2016	4		e00262-16			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. 		
@D	Johnson, D.L.//Reid, T.M.//Lee, M.-S.//King, C.M.//Romano, L.J. 	Preparation and characterization of a viral DNA molecule containing a site-specific 2-aminofluorene adduct:  A new probe for mutagenesis by carcinogens.	Biochemistry	1986	25		449-456			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. 		
@D	Johnson, J.//Shah, B.//Jain, K.//Parmar, N.//Hinsu, A.//Patel, N.//Joshi, C.G.//Madamwar, D. 	Draft Genome Sequence of Paenibacillus sp. Strain DMB5, Acclimatized and Enriched for Catabolizing Anthropogenic Compounds.	Genome Announcements	2016	4		e00211-16			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. 		
@D	Johnson, J.G.//Carpentier, S.//Spurbeck, R.R.//Sandhu, S.K.//Dirita, V.J. 	Genome Sequences of Campylobacter jejuni 81-176 Variants with Enhanced Fitness Relative to the Parental Strain in the Chicken Gastrointestinal Tract.	Genome Announcements	2014	2		e00006-14			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. 		
@D	Johnson, J.G.//Spurbeck, R.R.//Sandhu, S.K.//Matson, J.S. 	Genome Sequence of Klebsiella pneumoniae Respiratory Isolate IA565.	Genome Announcements	2014	2		e00896-14			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. 		
@D	Johnson, J.G.//Spurbeck, R.R.//Sandhu, S.K.//Matson, J.S. 	Genome Sequence of Klebsiella pneumoniae Urinary Tract Isolate Top52.	Genome Announcements	2014	2		e00668-14			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. 		
@D	Johnson, M.//Scheinbart, L.//Pike, M.//Richardson, B. 	Procainamide inhibits DNA methyltransferase.	Arthritis Rheum.	1989	32		S143			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. 		
@D	Johnson, P.H.//Lee, A.S.//Sinsheimer, R.L. 	Production of specific fragments of PhiX174 replicative form DNA by a restriction enzyme from Haemophilus parainfluenzae, endonuclease HP.	J. Virol.	1973	11		596-599			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. 		
@D	Johnson, S.A.//Ormsby, M.J.//Wall, D.M. 	Draft Genome Sequence of the Tumor-Targeting Salmonella enterica Serovar Typhimurium Strain SL7207.	Genome Announcements	2017	5		e01591-16			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. 		
@D	Johnson, S.L. et al. 	Complete genome sequences for 59 burkholderia isolates, both pathogenic and near  neighbor.	Genome Announcements	2015	3		e00159-15			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. 		
@D	Johnson, S.L. et al. 	Complete genome sequences for 35 biothreat assay-relevant bacillus species.	Genome Announcements	2015	3		e00151-15			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. 		
@D	Johnson, S.L. et al. 	Thirty-Two Complete Genome Assemblies of Nine Yersinia Species, Including Y. pestis, Y. pseudotuberculosis, and Y. enterocolitica.	Genome Announcements	2015	3		e00148-15			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). 		
@D	Johnson, S.L. et al. 	Genome sequencing of 18 francisella strains to aid in assay development and testing.	Genome Announcements	2015	3		e00147-15			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. 		
@D	Johnson, S.L. et al. 	Correction for Johnson et al., 'Complete Genome Sequences for 35 Biothreat Assay-Relevant Bacillus Species'.	Genome Announcements	2018	6		e01144-17					
@D	Johnson, S.L.//Baker, A.L.//Chain, P.S.//Currie, B.J.//Daligault, H.E.//Davenport, K.W.//Davis, C.B.//Inglis, T.J.//Kaestli, M.//Koren, S.//Mayo, M.//Merritt, A.J.//Price, E.P.//Sarovich, D.S.//Warner, J.//Rosovitz, M.J. 	Whole-Genome Sequences of 80 Environmental and Clinical Isolates of Burkholderia  pseudomallei.	Genome Announcements	2015	3		e01282-14			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. 		
@D	Johnson, S.L.//Khiani, A.//Bishop-Lilly, K.A.//Chapman, C.//Patel, M.//Verratti, K.//Teshima, H.//Munk, A.C.//Bruce, D.C.//Han, C.S.//Xie, G.//Davenport, K.W.//Chain, P.//Sozhamannan, S. 	Complete Genome Assemblies for Two Single-Chromosome Vibrio cholerae Isolates, Strains 1154-74 (Serogroup O49) and 10432-62 (Serogroup O27).	Genome Announcements	2015	3		e00462-15			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. 		
@D	Johnson, S.L.//Minogue, T.D.//Daligault, H.E.//Wolcott, M.J.//Teshima, H.//Coyne, S.R.//Davenport, K.W.//Jaissle, J.G.//Chain, P.S. 	Finished Genome Assembly of Warm Spring Isolate Francisella novicida DPG 3A-IS.	Genome Announcements	2015	3		e01046-15			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. 		
@D	Johnson, S.L.//Minogue, T.D.//Daligault, H.E.//Wolcott, M.J.//Teshima, H.//Coyne, S.R.//Davenport, K.W.//Jaissle, J.G.//Chain, P.S. 	Finished Genome Assembly of Yersinia pestis EV76D and KIM 10v.	Genome Announcements	2015	3		e01024-15			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. 		
@D	Johnson, S.L.//Minogue, T.D.//Teshima, H.//Davenport, K.W.//Shea, A.A.//Miner, H.L.//Wolcott, M.J.//Chain, P.S. 	Finished Genome Sequence of Bacillus cereus Strain 03BB87, a Clinical Isolate with B. anthracis Virulence Genes.	Genome Announcements	2015	3		e01446-14			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). 		
@D	Johnson, T.J.//Aziz, M.//Liu, C.M.//Sokurenko, E.//Kisiela, D.I.//Paul, S.//Andersen, P.//Johnson, J.R.//Price, L.B. 	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.	Genome Announcements	2016	4		e00334-16			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. 		
@D	Johnson, T.J.//Fernandez-Alarcon, C.//Bojesen, A.M.//Nolan, L.K.//Trampel, D.W.//Seemann, T. 	Complete Genome Sequence of Gallibacterium anatis strain UMN179, isolated from a laying hen with peritonitis.	J. Bacteriol.	2011	193		3676-3677			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. 		
@D	Johnson, T.J.//Hargreaves, M.//Shaw, K.//Snippes, P.//Lynfield, R.//Aziz, M.//Price, L.B. 	Complete Genome Sequence of a Carbapenem-Resistant Extraintestinal Pathogenic Escherichia coli Strain Belonging to the Sequence Type 131 H30R Subclade.	Genome Announcements	2015	3		e00272-15			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. 		
@D	Johnson, T.J.//Johnson, S.J.//Nolan, L.K. 	Complete DNA sequence of a ColBM plasmid from avian pathogenic Escherichia coli suggests that it evolved from closely related ColV virulence plasmids.	J. Bacteriol.	2006	188		5975-5983			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. 		
@D	Johnson, T.J.//Kariyawasam, S.//Wannemuehler, Y.//Mangiamele, P.//Johnson, S.J.//Doetkott, C.//Skyberg, J.A.//Lynne, A.M.//Johnson, J.R.//Nolan, L.K. 	The genome sequence of avian pathogenic Escherichia coli strain O1:K1:H7 shares strong similarities with human extraintestinal pathogenic E. coli  genomes.	J. Bacteriol.	2007	189		3228-3236			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. 		
@D	Johnston, C.//Martin, B.//Granadel, C.//Polard, P.//Claverys, J.P. 	Programmed Protection of Foreign DNA from Restriction Allows Pathogenicity Island Exchange during Pneumococcal Transformation.	PLoS Pathog.	2013	9		e1003178			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. 		
@D	Johnston, C.//Martin, B.//Polard, P.//Claverys, J.-P. 	Postreplication targeting of transformants by bacterial immune systems?	Trends Microbiol.	2013	21		516-521			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. 		
@D	Johnston, C.D.//Skeete, C.A.//Fomenkov, A.//Roberts, R.J.//Rittling, S.R. 	Restriction-modification mediated barriers to exogenous DNA uptake and incorporation employed by Prevotella intermedia.	PLoS ONE	2017	12		e0185234			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. 		
@D	Johnston, C.W.//Li, Y.//Magarvey, N.A. 	Draft Genome Sequence of Streptomyces silvensis ATCC 53525, a Producer of Novel Hormone Antagonists.	Genome Announcements	2016	4		e00001-16			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. 		
@D	Jois, P.S.//Madhu, N.//Rao, D.N. 	Role of histidine residues in EcoP15I DNA methyltransferase activity as probed by chemical modification and site-directed mutagenesis.	Biochem. J.	2008	410		543-553			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. 		
@D	Jomova, K.//Hegedusova, A.//Vollmannova, A. 	Restriction endonucleases - a tool for DNA cleavage.	Chem. Rozhlady	2004	4		239-245					
@D	Jonczyk, P.//Hines, R.//Smith, D.W. 	The Escherichia coli dam gene is expressed as a distal gene of a new operon.	Mol. Gen. Genet.	1989	217		85-96			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. 		
@D	Jones, A.C. et al. 	Genomic insights into the physiology and ecology of the marine filamentous cyanobacterium Lyngbya majuscula.	Proc. Natl. Acad. Sci. U. S. A.	2011	108		8815-8820			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. 		
@D	Jones, D.S.//Roepke, E.W.//Hua, A.A.//Flood, B.E.//Bailey, J.V. 	Complete Genome Sequence of Sulfuriferula sp. Strain AH1, a Sulfur-Oxidizing Autotroph Isolated from Weathered Mine Tailings from the Duluth Complex in  Minnesota.	Genome Announcements	2017	5		e00673-17			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. 		
@D	Jones, K.J.//Moore, K.//Sambles, C.//Love, J.//Studholme, D.J.//Aves, S.J. 	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.	Genome Announcements	2016	4		e01527-15			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. 		
@D	Jones, L.B.//Kunz, D.A. 	Complete Genome Sequence of a Cyanotroph, Pseudomonas fluorescens NCIMB 11764, Employing Single-Molecule Real-Time Technology.	Genome Announcements	2015	3		e01111-15			We report here the application of single-molecule real-time sequencing for determining the entire genome structure of the cyanotroph Pseudomonas fluorescens NCIMB 11764. 		
@D	Jones, M.//Wagner, R.//Radman, M. 	Mismatch repair of deaminated 5-methyl-cytosine.	J. Mol. Biol.	1987	194		155-159			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. 		
@D	Jones, P.A. 	DNA methylation errors and cancer.	Cancer Res.	1996	56		2463-2467			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. 		
@D	Jones, P.A.//Gonzalgo, M.L. 	Altered DNA methylation and genome instability: A new pathway to cancer?	Proc. Natl. Acad. Sci. U. S. A.	1997	94		2103-2105			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. 		
@D	Jones, P.A.//Takai, D. 	The role of DNA methylation in mammalian epigenetics.	Science	2001	293		1068-1070			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. 		
@D	Jones, P.L.//Veenstra, G.J.C.//Wade, P.A.//Vermaak, D.//Kass, S.U.//Landsberger, N.//Strouboulis, J.//Wolffe, A.P. 	Methylated DNA and MeCP2 recruit histone deacetylase to repress transcription.	Nat. Genet.	1998	19		187-191			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. 		
@D	Jones, W.D. Jr.//Greenberg, J. 	Host modification and restriction with a mycobacteriophage isolated from a pseudolysogenic Mycobacterium chelonei.	J. Gen. Microbiol.	1977	99		389-395			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. 		
@D	Jones-Dias, D.//Manageiro, V.//Sampaio, D.A.//Vieira, L.//Canica, M. 	Draft Genome Sequence of a Pathogenic O86:H25 Sequence Type 57 Escherichia coli Strain Isolated from Poultry and Carrying 12 Acquired Antibiotic Resistance Genes.	Genome Announcements	2015	3		e01107-15			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. 		
@D	Joo, E.J.//Park, W.S.//Kim, S.K.//Bae, Y.S.//Moon, B.J. 	Restriction endonuclease EcoRV mutants that switch metal ion requirement.	Bull. Korean Chem. Soc.	1999	20		109-111			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. 		
@D	Jordan, I.K. et al. 	Genome Sequences for Five Strains of the Emerging Pathogen Haemophilus haemolyticus.	J. Bacteriol.	2011	193		5879-5880			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. 		
@D	Jore, J.P.M.//van Luijk, N.//Luiten, R.G.M.//van der Werf, M.J.//Pouwels, P.H. 	Efficient transformation system for Propionibacterium freudenreichii based on a novel vector.	Appl. Environ. Microbiol.	2001	67		499-503			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. 		
@D	Jorgensen, S.L.//Kudirkiene, E.//Li, L.//Christensen, J.P.//Olsen, J.E.//Nolan, L.//Olsen, R.H. 	Chromosomal features of Escherichia coli serotype O2:K2, an avian pathogenic E. coli.	Standards in Genomic Sciences	2017	12		33			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. 		
@D	Jorgensen, T.S.//Xu, Z.//Hansen, M.A.//Sorensen, S.J.//Hansen, L.H. 	Hundreds of circular novel plasmids and DNA elements identified in a rat cecum metamobilome.	PLoS ONE	2014	9		E87924			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. 		
@D	Jose, T.J.//Conlan, L.H.//Dupureur, C.M. 	Quantitative evaluation of metal ion binding to PvuII restriction endonuclease.	J. Biol. Inorg. Chem.	1999	4		814-823			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. 		
@D	Joseph, B.//Schneiker-Bekel, S.//Schramm-Gluck, A.//Blom, J.//Claus, H.//Linke, B.//Schwarz, R.F.//Becker, A.//Goesmann, A.//Frosch, M.//Schoen, C. 	Comparative genome biology of a serogroup B carriage and disease strain supports a polygenic nature of meningococcal virulence.	J. Bacteriol.	2010	192		5363-5377			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. 		
@D	Joseph, T.C.//Baby, A.//Reghunathan, D.//Varghese, A.M.//Murugadas, V.//Lalitha, K.V. 	Draft Genome Sequence of the Halophilic and Highly Halotolerant Gammaproteobacteria Strain MFB021.	Genome Announcements	2014	2		e01156-14			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. 		
@D	Joseph, T.C.//Varghese, A.M.//Baby, A.//Reghunathan, D.//Murugadas, V.//Lalitha, K.V. 	First Draft Genome Sequence of a Member of the Genus Mangrovibacter, Isolated from an Aquaculture Farm in India.	Genome Announcements	2014	2		e01209-14			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. 		
@D	Josephsen, J.//Jorgen-Jensen, B.//Nyengaard, N.R. 	Determination of the recognition sequence of the type II restriction endonuclease, LlaCI, from Lactococcus lactis W15.	FEMS Microbiol. Lett.	1998	163		25-29			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. 		
@D	Josephsen, J.//Klaenhammer, T. 	Stacking of three different restriction and modification systems in Lactococcus lactis by cotransformation.	Plasmid	1990	23		71-75			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. 		
@D	Josephsen, J.//Vogensen, F.K. 	Identification of three different plasmid-encoded restriction modification systems in Streptococcus-lactis subsp cremoris W56.	FEMS Microbiol. Lett.	1989	59		161-166			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. 		
@D	Joshi, C.P.//Chiang, V.L. 	Conserved sequence motifs in plant S-adenosyl-L-methionine-dependent methyltransferases.	Plant Mol. Biol.	1998	37		663-674			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. 		
@D	Joshi, H.K.//Etzkorn, C.//Chatwell, L.//Bitinaite, J.//Horton, N.C. 	Alteration of sequence specificity of the type II restriction endonuclease HincII through an indirect readout mechanism.	J. Biol. Chem.	2006	281		23852-23869			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. 		
@D	Joshi, M.N.//Pandit, A.S.//Sharma, A.//Pandya, R.V.//Desai, S.M.//Saxena, A.K.//Bagatharia, S.B. 	Draft Genome Sequence of Arthrobacter crystallopoietes Strain BAB-32, Revealing Genes for Bioremediation.	Genome Announcements	2013	1		e00452-13			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. 		
@D	Joshi, M.N.//Pandit, A.S.//Sharma, A.//Pandya, R.V.//Saxena, A.K.//Bagatharia, S.B. 	Draft Genome Sequence of the Halophilic Bacterium Halobacillus sp. Strain BAB-2008.	Genome Announcements	2013	1		e00222-12			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. 		
@D	Joshi, M.N.//Sharma, A.//Pandit, A.S.//Pandya, R.V.//Saxena, A.K.//Bagatharia, S.B. 	Draft Genome Sequence of Brevibacillus sp. Strain BAB-2500, a Strain That Might Play an Important Role in Agriculture.	Genome Announcements	2013	1		e00021-13			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. 		
@D	Joshi, M.N.//Sharma, A.C.//Pandya, R.V.//Patel, R.P.//Saiyed, Z.M.//Saxena, A.K.//Bagatharia, S.B. 	Draft Genome Sequence of Pontibacter sp. nov. BAB1700, a Halotolerant, Industrially Important Bacterium.	J. Bacteriol.	2012	194		6329-6330			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. 		
@D	Joshi, R.//Ho, K.K.//Tenney, K.//Chen, J.H.//Golden, B.L.//Gimble, F.S. 	Evolution of I-SceI Homing Endonucleases with Increased DNA Recognition Site Specificity.	J. Mol. Biol.	2011	405		185-200			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. 		
@D	Jost, B.H.//Field, A.C.//Trinh, H.T.//Songer, J.G.//Billington, S.J. 	Tylosin Resistance in Arcanobacterium pyogenes Is Encoded by an Erm X Determinant.	Antimicrob. Agents Chemother.	2003	47		3519-3524			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. 		
@D	Jost, J.-P. 	Nuclear extracts of chicken embryos promote an active demethylation of DNA by excision repair of 5-methyldeoxycytidine.	Proc. Natl. Acad. Sci. U. S. A.	1993	90		4684-4688			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. 		
@A	Jost, J.-P. 		Mechanism of DNA demethylation in vertebrates and its biological significance.			Russo, V.E.A.//Martienssen, R.A.//Riggs, A.D. 		Epigenetic Mechanisms of Gene Regulation				Cold Spring Harbor	Cold Spring Harbor Laboratory Press	1996		0		109-125									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. 		
@D	Jost, J.-P.//Fremont, M.//Siegmann, M.//Hofsteenge, J. 	The RNA moiety of chick embryo 5-methylcytosine-DNA glycosylase targets DNA demethylation.	Nucleic Acids Res.	1997	25		4545-4550			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. 		
@D	Jost, J.-P.//Jost, Y.-C. 	Transient DNA demethylation in differentiating mouse myoblasts correlates with higher activity of 5-methyldeoxycytidine excision repair.	J. Biol. Chem.	1994	269		10040-10043			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. 		
@D	Jost, J.-P.//Siegmann, M.//Sun, L.//Leung, R. 	Mechanism of DNA demethylation in chicken embryos.	J. Biol. Chem.	1995	270		9734-9739			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. 		
@D	Jost, J.-P.//Siegmann, M.//Thiry, S.//Jost, Y.-C.//Benjamin, D.//Schwarz, S. 	A re-investigation of the ribonuclease sensitivity of a DNA demethylation reaction in chicken embryo and G8 mouse myoblasts.	FEBS Lett.	1999	449		251-254			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. 		
@D	Jothikumar, N.//Kahler, A.//Strockbine, N.//Gladney, L.//Hill, V.R. 	Draft Genome Sequence of Raoultella planticola, Isolated from River Water.	Genome Announcements	2014	2		e01061-14			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. 		
@D	Jothikumar, N.//Kahler, A.//Strockbine, N.//Gladney, L.//Hill, V.R. 	Draft Genome Sequence of Buttiauxella agrestis, Isolated from Surface Water.	Genome Announcements	2014	2		e01060-14			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. 		
@D	Jou, T.-W.//Chen, C.-S. 	Purification and characterization of restriction endonuclease CstI from Clostridium sticklandii.	Bot. Bull. Acad. Sinica	1988	29		201-208			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. 		
@D	Joung, S.M.//Jeon, S.J.//Lim, Y.J.//Lim, J.S.//Choi, B.S.//Choi, I.Y.//Yu, J.H.//Na, K.I.//Cho, E.H.//Shin, S.S.//Park, Y.K.//Kim, C.K.//Kim, H.J.//Ryoo, S.W. 	Complete Genome Sequence of Mycobacterium bovis BCG Korea, the Korean Vaccine Strain for Substantial Production.	Genome Announcements	2013	1		e0006913			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. 		
@D	Jourda, C.//Santini, S.//Rocher, C.//Le Bivic, A.//Claverie, J.M. 	Draft Genome Sequence of an Alphaproteobacterium Associated with the Mediterranean Sponge Oscarella lobularis.	Genome Announcements	2015	3		e00977-15			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.' 		
@D	Jousset, A.//Schuldes, J.//Keel, C.//Maurhofer, M.//Daniel, R.//Scheu, S.//Thuermer, A. 	Full-Genome Sequence of the Plant Growth-Promoting Bacterium Pseudomonas protegens CHA0.	Genome Announcements	2014	2		e00322-14			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. 		
@D	Jovanovic, L.//Delahunt, B.//McIver, B.//Eberhardt, N.L.//Grebe, S.K.G. 	Optimising restriction enzyme cleavage of DNA derived from archival histopathological samples: an improved HUMARA assay.	Pathology	2003	35		70-74			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. 		
@D	Juboi, H.//Basik, A.A.//Shamsul, S.S.//Arnold, P.//Schmitt, E.K.//Sanglier, J.J.//Yeo, T.C. 	Luteipulveratus halotolerans sp. nov., a novel actinobacterium (Dermacoccaceae) from Sarawak, Malaysia.	Int. J. Syst. Evol. Microbiol.	2015	65		4113-4120			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). 		
@D	Judge, N.A.//Fields, J.A.//Pajaniappan, M.//Newell, D.G.//Manning, J.//Burns, C.M.//Thompson, S.A. 	Mutation of a Campylobacter jejuni DNA methylase affects expression of multiple genes, motility, and epithelial cell adherence and invasion.	Abstr. Gen. Meet. Am. Soc. Microbiol.	2005	105		79			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. 		
@D	Jue, K.//Bestor, T.//Trasler, J.M. 	Differential expression of DNA methyltransferase in male germ cells.	Biol. Reprod.	1994	50		80			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. 		
@D	Juez, G.//Rodriguez-Valera, F.//Herrero, N.//Mojica, F.J.M. 	Evidence for salt-associated restriction pattern modifications in the Archaeobacterium Haloferax mediterranei.	J. Bacteriol.	1990	172		7278-7281			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. 		
@D	Juhala, R.J.//Ford, M.E.//Duda, R.L.//Youlton, A.//Hatfull, G.F.//Hendrix, R.W. 	Genomic sequences of bacteriophages HK97 and HK022: pervasive genetic mosaicism in the lambdoid bacteriophages.	J. Mol. Biol.	2000	299		27-51			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. 		
@D	Julio, S.M.//Heithoff, D.M.//Provenzano, D.//Klose, K.E.//Sinsheimer, R.L.//Low, D.A.//Mahan, M.J. 	DNA Adenine Methylase Is Essential for Viability and Plays a Role in the Pathogenesis of Yersinia pseudotuberculosis and Vibrio cholerae.	Infect. Immun.	2001	69		7610-7615			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. 		
@D	Julio, S.M.//Heithoff, D.M.//Sinsheimer, R.L.//Low, D.A.//Mahan, M.J. 	DNA adenine methylase overproduction in Yersinia pseudotuberculosis alters YopE expression and secretion and host immune responses to  infection.	Infect. Immun.	2002	70		1006-1009			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. 		
@D	Jullien, P.E.//Susaki, D.//Yelagandula, R.//Higashiyama, T.//Berger, F. 	DNA methylation dynamics during sexual reproduction in Arabidopsis thaliana.	Curr. Biol.	2012	22		1825-1830			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. 		
@D	Jun, H.S.//Kim, Y.S.//Choi, K.R.//Rho, H.M. 	Cloning and expression of the BdiI methylase gene in E. coli.	Korean J. Microbiol.	1987	25		40-45			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. 		
@D	Jun, J.W.//Kim, J.H.//Choresca, C.H.//Shin, S.P.//Han, J.E.//Park, S.C. 	Draft Genome Sequence of Vibrio parahaemolyticus SNUVpS-1 Isolated from Korean Seafood.	Genome Announcements	2013	1		e00132-12			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. 		
@D	Jun, X.//Lupeng, L.//Minjuan, X.//Oger, P.//Fengping, W.//Jebbar, M.//Xiang, X. 	Complete Genome Sequence of the Obligate Piezophilic Hyperthermophilic Archaeon Pyrococcus yayanosii CH1.	J. Bacteriol.	2011	193		4297-4298			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. 		
@D	Jung, J.//Baek, J.H.//Park, W. 	Complete genome sequence of the diesel-degrading Acinetobacter sp. strain DR1.	J. Bacteriol.	2010	192		4794-4795			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. 		
@D	Jung, J.//Choi, S.//Chun, J.//Park, W. 	Genome Sequence of Pectin-Degrading Alishewanella aestuarii Strain B11T, Isolated from Tidal Flat Sediment.	J. Bacteriol.	2012	194		5476			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. 		
@D	Jung, J.//Chun, J.//Park, W. 	Genome Sequence of Extracellular-Protease-Producing Alishewanella jeotgali Isolated from Traditional Korean Fermented Seafood.	J. Bacteriol.	2012	194		2097			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. 		
@D	Jung, J.H.//Holden, J.F.//Seo, D.H.//Park, K.H.//Shin, H.//Ryu, S.//Lee, J.H.//Park, C.S. 	Complete Genome Sequence of the Hyperthermophilic Archaeon Thermococcus sp. Strain CL1, Isolated from a Paralvinella sp. Polychaete Worm Collected from a  Hydrothermal Vent.	J. Bacteriol.	2012	194		4769-4770			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. 		
@D	Jung, J.H.//Joe, M.H.//Kim, D.H.//Park, H.//Choi, J.I.//Lim, S. 	Complete genome sequence of Planococcus sp. PAMC21323 isolated from Antarctica and its metabolic potential to detoxify pollutants.	Standards in Genomic Sciences	2018	13		31			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. 		
@D	Jung, J.H.//Lee, J.H.//Holden, J.F.//Seo, D.H.//Shin, H.//Kim, H.Y.//Kim, W.//Ryu, S.//Park, C.S. 	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.	J. Bacteriol.	2012	194		4434-4435			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. 		
@D	Jung, J.Y.//Ahn, Y.//Kweon, O.//LiPuma, J.J.//Hussong, D.//Marasa, B.S.//Cerniglia, C.E. 	Improved High-Quality Draft Genome Sequence and Annotation of Burkholderia contaminans LMG 23361T.	Genome Announcements	2017	5		e00245-17			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. 		
@D	Jung, J.Y.//Lee, S.H.//Jeon, C.O. 	Complete Genome Sequence of Leuconostoc carnosum Strain JB16, Isolated from Kimchi.	J. Bacteriol.	2012	194		6672-6673			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. 		
@D	Jung, J.Y.//Lee, S.H.//Jeon, C.O. 	Complete Genome Sequence of Leuconostoc gelidum Strain JB7, Isolated from Kimchi.	J. Bacteriol.	2012	194		6665			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. 		
@D	Jung, J.Y.//Lee, S.H.//Lee, S.H.//Jeon, C.O. 	Complete Genome Sequence of Leuconostoc mesenteroides subsp. mesenteroides Strain J18, Isolated from Kimchi.	J. Bacteriol.	2012	194		730-731			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. 		
@D	Jung, M.J.//Roh, S.W.//Kim, M.S.//Whon, T.W.//Bae, J.W. 	Genome Sequence of Lentibacillus jeotgali GrbiT, Isolated from Traditional Korean Salt-Fermented Seafood.	J. Bacteriol.	2011	193		6414-6415			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. 		
@D	Jung, V.//Pestka, S.B.//Pestka, S. 	Efficient cloning of PCR generated DNA containing terminal restriction endonuclease recognition sites.	Nucleic Acids Res.	1990	18		6156			None 		
@D	Jung, V.//Pestka, S.B.//Pestka, S. 	Cloning of polymerase chain reaction-generated DNA containing terminal restriction endonuclease recognition sites.	Methods Enzymol.	1993	218		357-362			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. 		
@D	Junghare, M.//Patil, Y.//Schink, B. 	Draft genome sequence of a nitrate-reducing, o-phthalate degrading bacterium, Azoarcus sp. strain PA01(T).	Standards in Genomic Sciences	2015	10		90			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. 		
@D	Juranek, S.//Wieden, H.-J.//Lipps, H.J. 	De novo cytosine methylation in the differentiating macronucleus of the stichotrichous ciliate Stylonychia lemnae.	Nucleic Acids Res.	2003	31		1387-1391			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. 		
@D	Jurenaite-Urbanaviciene, S. 	Engineering of bifunctional restriction endonucleases with novel specificities.	Ph.D. Thesis, Vilnius University	2008			1-46			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. 		
@D	Jurenaite-Urbanaviciene, S.//Kazlauskiene, R.//Urbelyte, V.//Maneliene, Z.//Petrusyte, M.//Lubys, A.//Janulaitis, A. 	Characterization of BseMII, a new type IV restriction-modification system, which recognizes the pentanucleotide sequence 5'-CTCAG(N)10/8.	Nucleic Acids Res.	2001	29		895-903			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. 		
@D	Jurenaite-Urbanaviciene, S.//Serksnaite, J.//Kriukiene, E.//Giedriene, J.//Venclovas, C.//Lubys, A. 	Generation of DNA cleavage specificities of type II restriction endonucleases by reassortment of target recognition domains.	Proc. Natl. Acad. Sci. U. S. A.	2007	104		10358-10363			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. 		
@D	Jurgaitis, A.P.//Butkus, V.V.//Klimasauskas, S.J.//Janulaitis, A. 	The effects of N4-methylcytosine and 5-methylcytosine on the thermal stability of DNA double helix.	Bioorg. Khim.	1988	14		158-165			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. 		
@A	Jurica, M.S. 		I. Structures of  intron encoded homing endonucleases and II. Allosteric regulation of pyruvate kinase.			 		Ph.D. Thesis, University of Washington				Seattle, USA		1999				1-146									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. 		
@D	Jurica, M.S.//Monnat, R.J. Jr.//Stoddard, B.L. 	DNA recognition and cleavage by the LAGLIDADG homing endonuclease I-CreI.	Mol. Cell	1998	2		469-476			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. 		
@D	Jurica, M.S.//Stoddard, B.L. 	Homing endonucleases: structure, function and evolution.	Cell. Mol. Life Sci.	1999	55		1304-1326			'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. 		
@D	Jurkowska, R.Z.//Anspach, N.//Urbanke, C.//Jia, D.//Reinhardt, R.//Nellen, W.//Cheng, X.//Jeltsch, A. 	Formation of nucleoprotein filaments by mammalian DNA methyltransferase Dnmt3a in complex with regulator Dnmt3L.	Nucleic Acids Res.	2008	36		6656-6663			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. 		
@D	Jurkowska, R.Z.//Ceccaldi, A.//Zhang, Y.//Arimondo, P.B.//Jeltsch, A. 	DNA Methyltransferase Assays.	Methods Mol. Biol.	2011	791		157-177			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. 		
@D	Jurkowska, R.Z.//Jurkowski, T.P.//Jeltsch, A. 	Structure and Function of Mammalian DNA Methyltransferases.	Chembiochem	2011	12		206-222			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. 		
@D	Jurkowska, R.Z.//Siddique, A.N.//Jurkowski, T.P.//Jeltsch, A. 	Approaches to Enzyme and Substrate Design of the Murine Dnmt3a DNA Methyltransferase.	Chembiochem	2011	12		1589-1594					
@D	Jurkowski, T.P.//Anspach, N.//Kulishova, L.//Nellen, W.//Jeltsch, A. 	The M.EcoRV DNA-(adenine N-6)-methyltransferase uses DNA bending for recognition of an expanded EcoDam recognition site.	J. Biol. Chem.	2007	282		36942-36952			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. 		
@D	Jurkowski, T.P.//Jeltsch, A. 	On the Evolutionary Origin of Eukaryotic DNA Methyltransferases and Dnmt2.	PLoS ONE	2011	6		e28104			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. 		
@D	Juste, A.//Van Trappen, S.//Verreth, C.//Cleenwerck, I.//De Vos, P.//Lievens, B.//Willems, K.A. 	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.	Int. J. Syst. Evol. Microbiol.	2012	62		129-137			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. 		
@D	Juttermann, R.//Li, E.//Jaenisch, R. 	Toxicity of 5-aza-2'-deoxycytidine to mammalian cells is mediated primarily by covalent trapping of DNA methyltransferase rather than DNA demethylation.	Proc. Natl. Acad. Sci. U. S. A.	1994	91		11797-11801			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. 		
@D	Jutur, P.P.//Hoti, S.L.//Reddy, A.R. 	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.	Mol. Biol. Rep.	2004	31		139-142			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. 		
@D	Jutur, P.P.//Reddy, A.R. 	Isolation, purification and properties of new restriction endonucleases from Bacillus badius and Bacillus lentus.	Microbiol. Res.	2007	162		378-383			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. 		
@D	Jutur, P.P.//Reddy, A.R. 	BpaI and BpnI: novel type II restriction endonucleases from Bacillus pasteurii and Bacillus pantothenticus.	Biotechnol. Lett.	2004	26		929-932			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). 		
@D	Jutur, P.P.//Reddy, A.R. 	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.	Mol. Biol. Rep.	2002	29		383-385			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. 		
@D	Kaas, R.S.//Mordhorst, H.//Leekitcharoenphon, P.//Dyring, J.J.//Haagensen, J.A.J.//Molin, S.//Pamp, S.J. 	Draft Genome Sequence of Acinetobacter johnsonii C6, an Environmental Isolate Engaging in Interspecific Metabolic Interactions.	Genome Announcements	2017	5		e00155-17			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. 		
@D	Kabisch, J.//Thurmer, A.//Hubel, T.//Popper, L.//Daniel, R.//Schweder, T. 	Characterization and optimization of Bacillus subtilis ATCC 6051 as an expression host.	J. Biotechnol.	2013	163		97-104			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. 		
@D	Kachalova, G.S.//Artyukh, R.I.//Lavrova, N.V.//Ryazanova, E.M.//Karyagina, A.S.//Kubareva, E.A.//Bartunik, H.D. 	Crystallization and preliminary crystallographic analysis of the (cytosine-5)-DNA methyltransferase NlaX from Neisseria lactamica.	Acta Crystallogr. F Struct. Biol. Cryst. Commun.	2005	61		852-854			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. 		
@D	Kachalova, G.S.//Rogulin, E.A.//Artyukh, R.I.//Perevyazova, T.A.//Zheleznaya, L.A.//Matvienko, N.I.//Bartunik, H.D. 	Crystallization and preliminary crystallographic analysis of the site-specific DNA nickase Nb.BspD6I.	Acta Crystallogr. F Struct. Biol. Cryst. Commun.	2005	61		332-334			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. 		
@D	Kachalova, G.S.//Rogulin, E.A.//Yunusova, A.K.//Artyukh, R.I.//Perevyazova, T.A.//Matvienko, N.I.//Zheleznaya, L.A.//Bartunik, H.D. 	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.	J. Mol. Biol.	2008	384		489-502			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. 		
@D	Kachalova, G.S.//Yunusova, A.K.//Artyukh, R.I.//Rogulin, E.A.//Perevyazova, T.A.//Zheleznaya, L.A.//Matvienko, N.I.//Bartunik, H.D. 	Crystallization and preliminary x-ray diffraction analysis of the small subunit of the heterodimeric restriction endonuclease R.BspD6I.	Acta Crystallogr. F Struct. Biol. Cryst. Commun.	2007	63		795-797			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. 		
@D	Kaczorowski, T.//Sektas, M.//Skowron, P.//Podhajska, A.J. 	The FokI methyltransferase from Flavobacterium okeanokoites - Purification and characterization of the enzyme and its truncated derivatives.	Mol. Biotechnol.	1999	13		1-15			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). 		
@D	Kaczorowski, T.//Skowron, P.//Podhajska, A.J. 	Purification and characterization of the FokI restriction endonuclease.	Gene	1989	80		209-216			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+. 		
@D	Kaddurah-Daouk, R.//Cho, P.//Smith, H.O. 	Catalytic properties of the HhaII restriction endonuclease.	J. Biol. Chem.	1985	260		15345-15351			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. 		
@D	Kaden, R.//Agren, J.//Ferrari, S.//Lindberg, M.//Backman, S.//Wahab, T. 	Whole-Genome Sequence of Brucella canis Strain SVA13, Isolated from an Infected Dog.	Genome Announcements	2014	2		e00700-14			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. 		
@D	Kadyrov, F.A.//Kaliman, A.V.//Kriukov, V.M. 	SegE endonuclease from phage T4. I. Cloning, expression and biochemical characteristics of endonuclease activity.	Mol. Biol. (Mosk)	1996	30		1096-1106					
@D	Kadyrov, F.A.//Kriukov, V.M.//Shliapnikov, M.G.//Baev, A.A. 	SegE-a new site-specific endodeoxyribonuclease from bacteriophage T4.	Dokl. Akad. Nauk.	1994	339		404-406					
@D	Kadyrov, F.A.//Kryukov, V.M.//Shlyapnikov, M.G.//Baev, A.A. 	SegE--a new site-specific endodeoxyribonuclease of bacteriophage T4.	Dokl. Biochem.	1994	339		145-147			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. 		
@D	Kadyrov, F.A.//Shlyapnikov, M.G.//Kryukov, V.M. 	A phage T4 site-specific endonuclease, SegE, is responsible for a non-reciprocal genetic exchange between T-even-related phages.	FEBS Lett.	1997	415		75-80			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. 		
@D	Kafka, T.A.//Geissler, A.J.//Vogel, R.F. 	Multiple Genome Sequences of Lactobacillus plantarum Strains.	Genome Announcements	2017	5		e00654-17			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. 		
@D	Kafri, T.//Hershko, A.//Razin, A. 	Probing CpG methylation at CACGTG with BbrPI restriction enzyme.	Nucleic Acids Res.	1993	21		2950			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. 		
@D	Kahng, L.S.//Shapiro, L. 	The CcrM DNA methyltransferase of Agrobacterium tumefaciens is essential, and its activity is cell cycle regulated.	J. Bacteriol.	2001	183		3065-3075			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. 		
@D	Kahramanoglou, C.//Prieto, A.I.//Khedkar, S.//Haase, B.//Gupta, A.//Benes, V.//Fraser, G.M.//Luscombe, N.M.//Seshasayee, A.S.N. 	Genomics of DNA cytosine methylation in Escherichia coli reveals its role in stationary phase transcription.	Nat. Commun.	2012	3		886			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. 		
@D	Kairov, U.//Kozhamkulov, U.//Molkenov, A.//Rakhimova, S.//Askapuli, A.//Zhabagin, M.//Akhmetova, A.//Yerezhepov, D.//Abilova, Z.//Abilmazhinova, A.//Bismilda, V.//Chingisova, L.//Zhumadilov, Z.//Akilzhanova, A. 	Draft Genome Sequences of Two Clinical Isolates of Mycobacterium tuberculosis from Sputum of Kazakh Patients.	Genome Announcements	2015	3		e00466-15			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. 		
@D	Kajala, K.//Coil, D.A.//Brady, S.M. 	Draft Genome Sequence of Rhizobium rhizogenes Strain ATCC 15834.	Genome Announcements	2014	2		e01108-14			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. 		
@D	Kakinuma, S.//Ikeda, H.//Tanaka, H.//Omura, S. 	Isolation of restriction-reduced mutants from Streptomyces.	Agric. Biol. Chem.	1990	54		2611-2617			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. 		
@D	Kakizawa, S.//Makino, A.//Ishii, Y.//Tamaki, H.//Kamagata, Y. 	Draft Genome Sequence of 'Candidatus Phytoplasma asteris' Strain OY-V, an Unculturable Plant-Pathogenic Bacterium.	Genome Announcements	2014	2		e00944-14			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. 		
@D	Kakutani, T.//Jeddeloh, J.A.//Richards, E.J. 	Characterization of an Arabidopsis thaliana DNA hypomethylation mutant.	Nucleic Acids Res.	1995	23		130-137			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. 		
@D	Kalamorz, F. et al. 	Draft Genome Sequence of the Thermoalkaliphilic Caldalkalibacillus thermarum Strain TA2.A1.	J. Bacteriol.	2011	193		4290-4291			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. 		
@D	Kalburge, S.S.//Polson, S.W.//Boyd, C.K.//Katz, L.//Turnsek, M.//Tarr, C.L.//Martinez-Urtaza, J.//Boyd, E.F. 	Complete Genome Sequence of Vibrio parahaemolyticus Environmental Strain UCM-V493.	Genome Announcements	2014	2		e00159-14			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. 		
@D	Kaldhone, P.R.//Khajanchi, B.K.//Han, J.//Nayak, R.//Ricke, S.C.//Foley, S.L. 	Draft Genome Sequences of Salmonella enterica Isolates Containing Incompatibility Group I1 Plasmids from Swine, Poultry, and Human Sources.	Genome Announcements	2017	5		e01056-17			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. 		
@D	Kaleta, P.//O'Callaghan, J.//Fitzgerald, G.F.//Beresford, T.P.//Ross, R.P. 	Crucial Role for Insertion Sequence Elements in Lactobacillus helveticus Evolution as Revealed by Interstrain Genomic Comparison.	Appl. Environ. Microbiol.	2010	76		212-220			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. 		
@D	Kalhoefer, D.//Thole, S.//Voget, S.//Lehmann, R.//Liesegang, H.//Wollher, A.//Daniel, R.//Simon, M.//Brinkhoff, T. 	Comparative genome analysis and genome-guided physiological analysis of Roseobacter litoralis.	BMC Genomics	2011	12		324			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. 		
@D	Kaliman, A.V.//Khasanova, M.A.//Kryukov, V.M.//Tanyashin, V.I.//Baev, A.A. 	Cloning and study of the structural organization of the region of inh(lip)-hoc genes of T4 bacteriophage.	Dokl. Akad. Nauk.	1988	303		1486-1489			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. 		
@D	Kaliman, A.V.//Khasanova, M.A.//Kryukov, V.M.//Tanyashin, V.I.//Bayev, A.A. 	The  nucleotide sequence of the region of bacteriophage T4 inh(lip)-hoc genes.	Nucleic Acids Res.	1990	18		4277					
@D	Kalimuddin, S.//Chen, S.L.//Lim, C.T.K.//Koh, T.H.//Tan, T.Y.//Kam, M.//Wong, C.W.//Mehershahi, K.S.//Chau, M.L.//Ng, L.C.//Tang, W.Y.//Badaruddin, H.//Teo, J.//Apisarnthanarak, A.//Suwantarat, N.//Ip, M.//Holden, M.T.G.//Hsu, L.Y.//Barkham, T. 	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.	Clin. Infect. Dis.	2017	64		S145-S152			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. 		
@D	Kalinin, V.N.//Lapaeva, I.A.//Lunin, V.G.//Skripkin, E.A.//Smirnov, V.D.//Tikchonenko, T.I. 	Isolation of HindIII isoschizomeric restriction endonuclease from Bordetella bronchiseptica.	Mol. Gen. Mikrobiol. Virusol.	1986	0		16-19			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. 		
@D	Kalinowski, J. et al. 	The complete Corynebacterium glutamicum ATCC 13032 genome sequence and its impact on the production of L-aspartate-derived amino acids and vitamins.	J. Biotechnol.	2003	104		5-25			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. 		
@D	Kalischuk, M.//Hachey, J.//Kawchuk, L. 	Complete Genome Sequence of Phytopathogenic Pectobacterium atrosepticum Bacteriophage Peat1.	Genome Announcements	2015	3		e00760-15			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. 		
@D	Kallimanis, A. et al. 	Complete genome sequence of Arthrobacter phenanthrenivorans type strain (Sphe3).	Standards in Genomic Sciences	2011	4		123-130			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. 		
@D	Kallimanis, A.//Karabika, E.//Mavromatis, K.//Lapidus, A.//Labutti, K.M.//Liolios, K.//Ivanova, N.//Goodwin, L.//Woyke, T.//Velentzas, A.D.//Perisynakis, A.//Ouzounis, C.C.//Kyrpides, N.C.//Koukkou, A.I.//Drainas, C. 	Complete genome sequence of Mycobacterium sp. strain (Spyr1) and reclassification to Mycobacterium gilvum Spyr1.	Standards in Genomic Sciences	2011	5		144-153			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. 		
@D	Kalman, S.//Mitchell, W.//Marathe, R.//Lammel, C.//Fan, J.//Hyman, R.W.//Olinger, L.//Grimwood, J.//Davis, R.W.//Stephens, R.S. 	Comparative genomes of Chlamydia pneumoniae and C. trachomatis.	Nat. Genet.	1999	21		385-389			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. 		
@D	Kalman, T.I. 	Glutathione-catalyzed hydrogen isotope exchange at position 5 of uridine.  A model for enzymic carbon alkylation reactions of pyrimidines.	Biochemistry	1971	10		2567-2573			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. 		
@D	Kaloss, W.D.//Connaughton, J.F.//Vanek, P.G.//Chirikijan, J.G. 	Characterization of overexpressed BamHII methylase.	FASEB J.	1992	6		A217			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. 		
@D	Kaloss, W.D.//Connaughton, J.F.//Vanek, P.G.//Chirikjian, J.C. 	Characterization of overexpressed BamHII methylase.	Biophys. J.	1992	61		A217			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. 		
@D	Kalugin, A.A.//Rina, M.//Eldarov, M.A.//Markaki, M.//Korolev, S.V.//Samko, O.T.//Khoroshutina, E.B.//Sikolov, N.N.//Bouriotis, V. 	Bsp153AI and BspM39I - New isoschizomers of restriction endonuclease PvuII.	Bioorg. Khim.	1996	22		108-110			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. 		
@D	Kalyuzhnaya, M.G.//Lamb, A.E.//McTaggart, T.L.//Oshkin, I.Y.//Shapiro, N.//Woyke, T.//Chistoserdova, L. 	Draft genome sequences of gammaproteobacterial methanotrophs isolated from lake washington sediment.	Genome Announcements	2015	3		e00103-15			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. 		
@D	Kamachi, K.//Sota, M.//Tamai, Y.//Nagata, N.//Konda, T.//Inoue, T.//Top, E.M.//Arakawa, Y. 	Plasmid pBP136 from Bordetella pertussis represents an ancestral form of IncP-1beta plasmids without accessory mobile elements.	Microbiology	2006	152		3477-3484			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. 		
@D	Kambarev, S.//Cate, C.//Corvec, S.//Pecorari, F. 	Draft Genome Sequence of Erythromycin-Resistant Streptococcus gallolyticus subsp. gallolyticus NTS 31106099 Isolated from a Patient with Infective Endocarditis and  Colorectal Cancer.	Genome Announcements	2015	3		e00370-15			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. 		
@D	Kambarev, S.//Corvec, S.//Chauty, A.//Marion, E.//Marsollier, L.//Pecorari, F. 	Draft Genome Sequence of Mycobacterium ulcerans S4018 Isolated from a Patient with an Active Buruli Ulcer in Benin, Africa.	Genome Announcements	2017	5		e00248-17			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. 		
@D	Kambarev, S.//Pecorari, F.//Corvec, S. 	Draft Genome Sequences of Two Highly Erythromycin-Resistant Streptococcus gallolyticus subsp. gallolyticus Isolates Containing a Novel Tn916-Like Element,   Tn6331.	Genome Announcements	2017	5		e00226-17			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. 		
@D	Kameshita, I.//Sekiguchi, M.//Hamasaki, D.//Sugiyama, Y.//Hatano, N.//Suetake, I.//Tajima, S.//Sueyoshi, N. 	Cyclin-dependent kinase-like 5 binds and phosphorylates DNA methyltransferase 1.	Biochem. Biophys. Res. Commun.	2008	377		1162-1167			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. 		
@D	Kamimura, K.//Sharmin, S.//Yoshino, E.//Tokuhisa, M.//Kanao, T. 	Draft Genome Sequence of Acidithiobacillus sp. Strain SH, a Marine Acidophilic Sulfur-Oxidizing Bacterium.	Genome Announcements	2018	6		e01603-17			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. 		
@D	Kaminska, K.H.//Kawai, M.//Boniecki, M.//Kobayashi, I.//Bujnicki, J.M. 	Type II restriction endonuclease R.Hpy188I belongs to the GIY-YIG nuclease superfamily, but exhibits an unusual active site.	BMC Struct. Biol.	2008	8		48			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. 		
@D	Kaminski, M.A.//Furmanczyk, E.M.//Dziembowski, A.//Sobczak, A.//Lipinski, L. 	Draft Genome Sequence of the Type Strain Sphingopyxis witflariensis DSM 14551.	Genome Announcements	2017	5		e00924-17			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%. 		
@D	Kaminski, M.A.//Furmanczyk, E.M.//Dziembowski, A.//Sobczak, A.//Lipinski, L. 	Draft Genome Sequence of the Type Strain Sphingopyxis bauzanensis DSM 22271.	Genome Announcements	2017	5		e01014-17			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. 		
@D	Kamps-Hughes, N.//Quimby, A.//Zhu, Z.//Johnson, E.A. 	Massively parallel characterization of restriction endonucleases.	Nucleic Acids Res.	2013	41		e119			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. 		
@D	Kan, N.C.//Lautenberger, J.A.//Edgell, M.H.//Hutchison, C.A. III 	The nucleotide sequence recognized by the Escherichia coli K12 restriction and modification enzymes.	J. Mol. Biol.	1979	130		191-209			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. 		
@D	Kan, N.C.//Lautenberger, J.A.//Edgell, M.H.//Hutchison, C.A. III 	Recognition site of the Escherichia coli K restriction enzyme.	Fed. Proc.	1978	37		1499			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. 		
@D	Kan, T.N.//Lin, L.//Chandrasegaran, S. 	Cloning, sequencing, overproduction, and purification of M.CviBI (GANTC) methyltransferase from Chlorella virus NC-1A.	Gene	1992	121		1-7			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. 		
@D	Kanada, K.//Takeshita, K.//Suetake, I.//Tajima, S.//Nakagawa, A. 	Conserved threonine 1505 in the catalytic domain stabilizes mouse DNA methyltransferase 1.	J. Biochem. (Tokyo)	2017	162		271-278			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. 		
@D	Kanaras, A.G.//Wang, Z.X.//Hussain, I.//Brust, M.//Cosstick, R.//Bates, A.D. 	Site-specific ligation of DNA-modified gold nanoparticles activated by the restriction enzyme StyI.	Small	2007	3		67-70					
@D	Kanda, K.//Nakashima, K.//Nagano, Y. 	Complete Genome Sequence of Bacillus thuringiensis Serovar Tolworthi Strain Pasteur Institute Standard.	Genome Announcements	2015	3		e00710-15			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. 		
@A	Kandavelou, K.//Mani, M.//Durai, S.//Chandrasegaran, S. 		Engineering and applications of chimeric nucleases.			Pingoud, A. 		Nucleic Acids Mol. Biol.				Berlin Heidelberg	Springer-Verlag	2004		14		413-434									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. 		
@D	Kanduri, C. 	Restriction enzyme BstZ17I is sensitive to cytosine methylation.	FEMS Microbiol. Lett.	2001	200		191-193			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. 		
@D	Kane, P.M.//Yamashiro, C.T.//Wolczyk, D.F.//Neff, N.//Goebl, M.//Stevens, T.H. 	Protein splicing converts the yeast TFP1 gene product to the 69-kD subunit of the vacuolar H+-adenosine triphosphatase.	Science	1990	250		651-657			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. 		
@D	Kane, S.R.//Chakicherla, A.Y.//Chain, P.S.//Schmidt, R.//Shin, M.W.//Legler, T.C.//Scow, K.M.//Larimer, F.W.//Lucas, S.M.//Richardson, P.M.//Hristova, K.R. 	Whole-Genome Analysis of the Methyl tert-Butyl Ether-Degrading Beta-Proteobacterium Methylibium petroleiphilum PM1.	J. Bacteriol.	2007	189		1931-1945			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. 		
@D	Kaneda, M.//Okano, M.//Hata, K.//Sado, T.//Tsujimoto, N.//Li, E.//Sasaki, H. 	Essential role for de novo DNA methyltransferase Dnmt3a in paternal and maternal imprinting.	Nature	2004	429		900-903			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. 		
@D	Kanehara, K.//Minamisawa, K. 	Complete Genome Sequence of Bradyrhizobium japonicum J5, Isolated from a Soybean  Nodule in Hokkaido, Japan.	Genome Announcements	2017	5		e01619-16			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. 		
@D	Kanekar, S.P.//Saxena, N.//Pore, S.D.//Arora, P.//Kanekar, P.P.//Dhakephalkar, P.K. 	Draft Genome Sequence of Halostagnicola sp. A56, an Extremely Halophilic Archaeon Isolated from the Andaman Islands.	Genome Announcements	2015	3		e01332-15			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. 		
@D	Kaneko, K.J.//Burke, J.M.//Kaplan, L.J. 	The action of endonucleases and methylases:  Electrophoretic analysis of DNA restriction fragments.	J. Chem. Educ.	1987	64		274-278			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. 		
@D	Kaneko, R.//Wong, S.K.//Ogura, Y.//Hayashi, T.//Yoshizawa, S.//Hamasaki, K. 	Draft Genome Sequences of Two Fabibacter sp. Strains Isolated from Coastal Surface Water of Aburatsubo Inlet, Japan.	Genome Announcements	2016	4		e01360-16			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. 		
@D	Kaneko, T. et al. 	Complete genomic sequence of the filamentous nitrogen-fixing cyanobacterium Anabaena sp. strain PCC 7120.	DNA Res.	2001	8		205-213			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. 		
@D	Kaneko, T. et al. 	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).	DNA Res.	1996	3		185-209			none 		
@D	Kaneko, T. et al. 	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.	DNA Res.	1996	3		109-136			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. 		
@D	Kaneko, T. et al. 	Complete genome structure of the nitrogen-fixing symbiotic bacterium Mesorhizobium loti.	DNA Res.	2000	7		331-338			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. 		
@D	Kaneko, T. et al. 	Complete genome structure of the Nitrogen-fixing symbiotic bacterium Mesorhizobium loti (Supplement).	DNA Res.	2000	7		381-406			none 		
@D	Kaneko, T. et al. 	Complete Genomic Structure of the Bloom-forming Toxic Cyanobacterium Microcystis aeruginosa NIES-843.	DNA Res.	2007	14		247-256			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. 		
@D	Kaneko, T.//Maita, S.//Hirakawa, H.//Uchiike, N.//Minamisawa, K.//Watanabe, A.//Sato, S. 	Complete Genome Sequence of the Soybean Symbiont Bradyrhizobium japonicum Strain USDA6T.	Genes	2011	2		763-787			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. 		
@D	Kaneko, T.//Nakamura, Y.//Sasamoto, S.//Watanabe, A.//Kohara, M.//Matsumoto, M.//Shimpo, S.//Yamada, M.//Tabata, S. 	Structural analysis of four large plasmids harboring in a unicellular cyanobacterium, Synechocystis sp. PCC 6803.	DNA Res.	2003	10		221-228			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. 		
@D	Kaneko, T.//Nakamura, Y.//Sato, S.//Minamisawa, K.//Uchiumi, T.//Sasamoto, S.//Watanabe, A.//Idesawa, K.//Iriguchi, M.//Kawashima, K.//Kohara, M.//Matsumoto, M.//Shimpo, S.//Tsuruoka, H.//Wada, T.//Yamada, M.//Tabata, S. 	Complete genomic sequence of nitrogen-fixing symbiotic bacterium Bradyrhizobium japonicum USDA110.	DNA Res.	2002	9		189-197			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. 		
@D	Kanesaki, Y.//Hirose, M.//Hirose, Y.//Fujisawa, T.//Nakamura, Y.//Watanabe, S.//Matsunaga, S.//Uchida, H.//Murakami, A. 	Draft Genome Sequence of the Nitrogen-Fixing and Hormogonia-Inducing Cyanobacterium Nostoc cycadae Strain WK-1, Isolated from the Coralloid Roots of  Cycas revoluta.	Genome Announcements	2018	6		e00021-18			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. 		
@D	Kanesaki, Y.//Ishige, T.//Sekigawa, Y.//Kobayashi, T.//Torii, Y.//Yokoyama, E.//Ishiwata, H.//Hamada, M.//Tamura, T.//Azuma, R.//Murakami, S. 	Whole-Genome Sequences of Two Closely Related Bacteria, Actinomyces sp. Strain Chiba101 and Actinomyces denticolens DSM 20671T.	Genome Announcements	2017	5		e00126-17			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. 		
@D	Kanesaki, Y.//Kubota, E.//Ohtake, R.//Higashi, Y.//Nagaoka, J.//Suzuki, T.//Akuzawa, S. 	Draft Genome Sequence of Bacillus licheniformis Heshi-B2, Isolated from Fermented Rice Bran in a Japanese Fermented Seafood Dish.	Genome Announcements	2018	6		e00118-18			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. 		
@D	Kanesaki, Y.//Masutani, H.//Sakanaka, M.//Shiwa, Y.//Fujisawa, T.//Nakamura, Y.//Yokota, A.//Fukiya, S.//Suzuki, T.//Yoshikawa, H. 	Complete Genome Sequence of Bifidobacterium longum 105-A, a Strain with High Transformation Efficiency.	Genome Announcements	2014	2		e01311-14			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. 		
@D	Kang, C.//Wu, C.-W. 	Studies on SP6 promoter using a new plasmid vector that allows gene insertion at the transcription initiation site.	Nucleic Acids Res.	1987	15		2279-2294			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. 		
@D	Kang, E.S.//Park, C.W.//Chung, J.H. 	Dnmt3b, de novo DNA methyltransferase, interacts with SUMO-1 and Ubc9 through its N-terminal region and is subject to modification by SUMO-1.	Biochem. Biophys. Res. Commun.	2001	289		862-868			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. 		
@D	Kang, H.L.//Park, Y.H.//Lee, E.J.//Kim, M.H.//Kim, J.S.//Park, S.G.//Song, J.Y.//Park, J.U.//Baik, S.C.//Ko, G.H.//Youn, H.S.//Lee, W.K.//Cho, M.J. 	Distribution of Helicobacter pylori 51-specific genes on other Korean isolates of Helicobacter pylori.	Abstr. Gen. Meet. Am. Soc. Microbiol.	2003	103		D-069			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. 		
@D	Kang, I.//Kang, D.//Oh, H.M.//Kim, H.//Kim, H.J.//Kang, T.W.//Kim, S.Y.//Cho, J.C. 	Genome sequence of strain IMCC2047, a novel marine member of the Gammaproteobacteria.	J. Bacteriol.	2011	193		3688-3689			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. 		
@D	Kang, I.//Kim, S.//Islam, M.R.//Cho, J.C. 	The first complete genome sequences of the acI lineage, the most abundant freshwater Actinobacteria, obtained by whole-genome-amplification of dilution-to-extinction cultures.	Sci. Rep.	2017	7		42252			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. 		
@D	Kang, I.//Lee, K.//Yang, S.J.//Choi, A.//Kang, D.//Lee, Y.K.//Cho, J.C. 	Genome Sequence of 'Candidatus Aquiluna' sp. Strain IMCC13023, a Marine Member of the Actinobacteria Isolated from an Arctic Fjord.	J. Bacteriol.	2012	194		3550-3551			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. 		
@D	Kang, I.//Oh, H.M.//Lim, S.I.//Ferriera, S.//Giovannoni, S.J.//Cho, J.C. 	Genome sequence of Fulvimarina pelagi HTCC2506T, a Mn(II)-oxidizing alphaproteobacterium possessing an aerobic anoxygenic photosynthetic gene  cluster and Xanthorhodopsin.	J. Bacteriol.	2010	192		4798-4799			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. 		
@D	Kang, I.//Oh, H.M.//Vergin, K.L.//Giovannoni, S.J.//Cho, J.C. 	Genome Sequence of the Marine Alphaproteobacterium HTCC2150, Assigned to the Roseobacter Clade.	J. Bacteriol.	2010	192		6315-6316			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. 		
@D	Kang, I.//Vergin, K.L.//Oh, H.M.//Choi, A.//Giovannoni, S.J.//Cho, J.C. 	Genome Sequence of strain HTCC2083, a Novel Member of the Marine Roseobacter Clade.	J. Bacteriol.	2010	193		319-320			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. 		
@D	Kang, J.//Chung, W.H.//Lim, T.J.//Lim, S.//Nam, Y.D. 	Complete genome sequence of the Bifidobacterium animalis subspecies lactis BL3, preventive probiotics for acute colitis and colon cancer.	New Microbes New Infect.	2017	19		34-37			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. 		
@D	Kang, J.//Chung, W.H.//Lim, T.J.//Whon, T.W.//Lim, S.//Nam, Y.D. 	Complete Genome Sequence of Lactobacillus casei LC5, a Potential Probiotics for Atopic Dermatitis.	Front. Immunol.	2017	8		413					
@D	Kang, J.J.S.//Meier, J.L.//Dervan, P.B. 	Design of Sequence-Specific DNA Binding Molecules for DNA Methyltransferase Inhibition.	J. Am. Chem. Soc.	2014	136		3687-3694			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. 		
@D	Kang, M.S.//Chung, J.//Kim, S.M.//Yang, K.H.//Oh, J.S. 	Effect of Weissella cibaria isolates on the formation of Streptococcus mutans biofilm.	Caries Res.	2006	40		418-425			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. 		
@D	Kang, M.S.//Yeu, J.E.//Oh, J.S.//Shin, B.A.//Kim, J.H. 	Complete Genome Sequences of Weissella cibaria Strains CMU, CMS1, CMS2, and CMS3  Isolated from Infant Saliva in South Korea.	Genome Announcements	2017	5		e01103-17			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. 		
@D	Kang, S.//Lee, H.//Han, J.S.//Hwang, D.S. 	Interaction of SeqA and Dam methylase on the hemimethylated origin of Escherichia coli chromosomal DNA replication.	J. Biol. Chem.	1999	274		11463-11468			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. 		
@D	Kang, S.C.//Choi, W.S.//Yoo, O.J. 	The effects of DNA methylation by HhaI methylase on the cleavage reactions by HaeII, AhaII and BanI endonuclease.	Biochem. Biophys. Res. Commun.	1987	145		482-487			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. 		
@D	Kang, S.C.//Yoo, O.J. 	Purification and characterization of AccI endonuclease.	Korean J. Microbiol.	1985	23		13-19			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. 		
@D	Kang, S.C.//Yoon, H.//Yoo, O.J. 	DNA protection by methylation with AluI methylase against cleavages of HindIII, SstI, PvuII and SacI endonucleases.	Korean Biochem. J.	1986	19		41-46			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. 		
@D	Kang, W.Y. et al. 	Stationary Phase Expression, Purification, and Characterization of XorKI, a Restriction Endonuclease from Xanthomonas oryzae pv. oryzae.	Protein Pept. Lett.	2010	17		381-385			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. 		
@D	Kang, X.//Ling, N.//Sun, G.//Zhou, Q.//Zhang, L.//Sheng, Q. 	Complete Genome Sequence of Streptococcus thermophilus Strain MN-ZLW-002.	J. Bacteriol.	2012	194		4428-4429			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). 		
@D	Kang, Y.//Shen, M.//Wang, H.//Zhao, Q. 	Complete Genome Sequence of Bacillus pumilus Strain WP8, an Efficient Plant Growth-Promoting Rhizobacterium.	Genome Announcements	2015	3		e01452-14			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. 		
@D	Kang, Y.K.//Lee, H.B.//Noh, M.J.//Cho, N.-Y.//Yoo, O.J. 	Different effects of base analog substitutions in BamHI restriction site on recognition by BamHI endonuclease and BamHI methylase.	Biochem. Biophys. Res. Commun.	1995	206		997-1002			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. 		
@D	Kang, Y.K.//Ryu, J.//Yoo, O.J. 	Effects of modified bases in sequence recognition by ClaI endonuclease and ClaI methylase.	Biochem. Mol. Biol. Int.	1993	29		859-865			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. 		
@D	Kania, J.//Fanning, T.G. 	Use of a Sequence-Specific DNA-Binding Ligand to probe the Environments of EcoRI Restriction Endonuclease Cleavage Sites.	Eur. J. Biochem.	1976	67		367-371			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. 		
@D	Kankel, M.W.//Ramsey, D.E.//Stokes, T.L.//Flowers, S.K.//Haag, J.R.//Jeddeloh, J.A.//Riddle, N.C.//Verbsky, M.L.//Richards, E.J. 	Arabidopsis MET1 cytosine methyltransferase mutants.	Genetics	2003	163		1109-1122			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. 		
@D	Kankia, B.I. 	A real-time assay for monitoring nucleic acid cleavage by quadruplex formation.	Nucleic Acids Res.	2006	34		e141			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. 		
@D	Kannan, P.//Cowan, G.M.//Daniel, A.S.//Gann, A.A.F.//Murray, N.E. 	Conservation of organization in the specificity polypeptides of two families of Type I restriction enzymes.	J. Mol. Biol.	1989	209		335-344			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. 		
@D	Kannan, P.R.//Dharmalingam, K. 	Restriction alleviation and enchancement of mutagenesis of the bacteriophage T4 chromosome in recBCsbcA strains of Escherichia coli.	Mol. Gen. Genet.	1987	208		413-418			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. 		
@D	Kanrar, S.//Dhar, A.K. 	Complete Genome Sequence of a Novel Mutant Strain of Vibrio parahaemolyticus from Pacific White Shrimp (Penaeus vannamei).	Genome Announcements	2018	6		e00497-18			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. 		
@D	Kanrar, S.//Dhar, A.K. 	Complete Genome Sequence of a Deletion Mutant of Vibrio parahaemolyticus from Pacific White Shrimp (Penaeus vannamei).	Genome Announcements	2018	6		e00544-18			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. 		
@D	Kant, J.A. 	DNA restriction enzymes and RFLPs in medicine.	Methods Biochem. Anal.	1992	36		129-140			*
     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
 
 		
@D	Kant, R. et al. 	Genome Sequence of 'Pedosphaera parvula' Ellin514, an Aerobic Verrucomicrobial Isolate from Pasture Soil.	J. Bacteriol.	2011	193		2900-2901			"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. 		
@D	Kant, R.//Paulin, L.//Alatalo, E.//de Vos, W.M.//Palva, A. 	Genome sequence of Lactobacillus amylovorus GRL1118, isolated from the pig ileum.	J. Bacteriol.	2011	193		3147-3148			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. 		
@D	Kant, R.//Paulin, L.//Alatalo, E.//de Vos, W.M.//Palva, A. 	Genome Sequence of Lactobacillus amylovorus GRL1112.	J. Bacteriol.	2010	193		789-790			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. 		
@D	Kant, R.//Rasinkangas, P.//Satokari, R.//Pietila, T.E.//Palva, A. 	Genome Sequence of the Butyrate-Producing Anaerobic Bacterium Anaerostipes hadrus PEL 85.	Genome Announcements	2015	3		e00224-15			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. 		
@D	Kant, R.//Taponen, S.//Koort, J.//Paulin, L.//Avall-Jaaskelainen, S.//Palva, A. 	Genome Sequences of Four Staphylococcus aureus Strains Isolated from Bovine Mastitis.	Genome Announcements	2015	3		e00334-15			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. 		
@D	Kant, R.//Uroic, K.//Hynonen, U.//Kos, B.//Suskovic, J.//Palva, A. 	Genome Sequence of Lactobacillus brevis Strain D6, Isolated from Smoked Fresh Cheese.	Genome Announcements	2016	4		e00264-16			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. 		
@D	Kanukollu, S.//Voget, S.//Pohlner, M.//Vandieken, V.//Petersen, J.//Kyrpides, N.C.//Woyke, T.//Shapiro, N.//Goker, M.//Klenk, H.P.//Cypionka, H.//Engelen, B. 	Genome sequence of Shimia str. SK013, a representative of the Roseobacter group isolated from marine sediment.	Standards in Genomic Sciences	2016	11		25			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. 		
@D	Kao, C.Y.//Chen, J.W.//Huang, Y.T.//Sheu, S.M.//Sheu, B.S.//Wu, J.J. 	Genome Sequence and Annotation of Helicobacter pylori Strain Hp238, Isolated from a Taiwanese Patient with Mucosa-Associated Lymphoid Tissue Lymphoma.	Genome Announcements	2015	3		e00006-15			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. 		
@D	Kao, C.Y.//Yan, J.J.//Lin, Y.C.//Zheng, P.X.//Wu, J.J. 	Complete Genome Sequence of Carbapenem-Resistant Klebsiella pneumoniae Strain 1756, Isolated from a Pus Specimen.	Genome Announcements	2017	5		e00066-17			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. 		
@D	Kapatral, V. et al. 	Genome sequence and analysis of the oral bacterium Fusobacterium nucleatum strain ATCC 25586.	J. Bacteriol.	2002	184		2005-2018			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. 		
@D	Kapatral, V.//Ivanova, N.//Anderson, I.//Reznik, G.//Bhattacharyya, A.//Gardner, W.L.//Mikhailova, N.//Lapidus, A.//Larsen, N.//D'Souza, M.//Walunas, T.//Haselkorn, R.//Overbeek, R.//Kyrpides, N. 	Genome Analysis of F. nucleatum sub spp vincentii and Its Comparison With the Genome of F. nucleatum ATCC 25586.	Genome Res.	2003	13		1180-1189			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. 		
@D	Kapetaniou, E.G.//Kotsifaki, D.//Providaki, M.//Rina, M.//Bouriotis, V.//Kokkinidis, M. 	Purification, crystallization and preliminary X-ray analysis of the BseCI DNA methyltransferase from Bacillus stearothermophilus in complex with its cognate DNA.	Acta Crystallogr. F Struct. Biol. Cryst. Commun.	2007	63		12-14			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. 		
@D	Kapfer, W.//Walter, J.//Trautner, T.A. 	Cloning, characterization and evolution of the BsuFI restriction endonuclease gene of Bacillus subtilis and purification of the enzyme.	Nucleic Acids Res.	1991	19		6457-6463			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. 		
@D	Kapfhammer, D.//Blass, J.//Evers, S.//Reidl, J. 	Vibrio cholerae phage K139: complete genome sequence and comparative genomics of related phages.	J. Bacteriol.	2002	184		6592-6601			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. 		
@D	Kaplan, D.A.//Nierlich, D.P. 	Cleavage of nonglucosylated bacteriophage T4 deoxyribonucleic acid by restriction endonuclease EcoRI.	J. Biol. Chem.	1975	250		2395-2397			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. 		
@D	Kaplan, D.J. 	Variation in the inhibition of restriction enzyme cleavage of lambda phage DNA produced by two covalent binding antitumor agents:  Anthramycin and Mitomycin C.	Biochem. Biophys. Res. Commun.	1982	109		639-648			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. 		
@D	Kaplan, J.B.//Lo, C.//Xie, G.//Johnson, S.L.//Chain, P.S.//Donnelly, R.//Kachlany, S.C.//Balashova, N.V. 	Genome Sequence of Kingella kingae Septic Arthritis Isolate PYKK081.	J. Bacteriol.	2012	194		3017			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. 		
@D	Kapley, A.//Sagarkar, S.//Tanksale, H.//Sharma, N.//Qureshi, A.//Khardenavis, A.//Purohit, H.J. 	Genome Sequence of Alcaligenes sp. Strain HPC1271.	Genome Announcements	2013	1		e00235-12			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. 		
@D	Kappelman, J.R.//Brady, M.//Knoche, K.//Murray, E.//Schoenfeld, T.//Williams, R.//Vesselinova, N. 	SgfI, a new type-II restriction endonuclease that recognizes the octanucleotide sequence 5'-GCGAT/CGC-3'.	Gene	1995	160		55-58			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. 		
@D	Kappler, U. et al. 	Complete genome sequence of the facultatively chemolithoautotrophic and methylotrophic alpha Proteobacterium Starkeya novella type strain (ATCC 8093(T)).	Standards in Genomic Sciences	2012	7		44-58			(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. 		
@D	Kappler, U.//Davenport, K.//Beatson, S.//Lapidus, A.//Pan, C.//Han, C.//Montero-Calasanz, M.C.//Land, M.//Hauser, L.//Rohde, M.//Goker, M.//Ivanova, N.//Woyke, T.//Klenk, H.P.//Kyrpides, N.C. 	Complete genome sequence of the haloalkaliphilic, obligately chemolithoautotrophic thiosulfate and sulfide-oxidizing gamma-proteobacterium  Thioalkalimicrobium cyclicum type strain ALM 1 (DSM 14477(T)).	Standards in Genomic Sciences	2016	11		38			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. 		
@D	Kappler, U.//Dhouib, R.//Nair, R.P.//McEwan, A.G. 	Draft Genome Sequences of Three Nontypeable Strains of Haemophilus influenzae, C188, R535, and 1200, Isolated from Different Types of Disease.	Genome Announcements	2017	5		e00035-17			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. 		
@D	Kapse, N.//Singh, P.//Roy, U.//Singh, S.M.//Dhakephalkar, P.K. 	Insights into the Psychrophilic and Sea Ice-Specific Lifestyle of Marinobacter sp. Strain AC-23: a Genomic Approach.	Genome Announcements	2017	5		e00134-17			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. 		
@D	Kaput, J.//Sneider, T.W. 	Methylation of somatic vs germ cell DNAs analyzed by restriction endonuclease digestions.	Nucleic Acids Res.	1979	7		2303-2322			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. 		
@D	Karabecov, B.P.//Oganesian, M.G.//Airumian, B.A. 	Susceptibility of the bacteriophage T5 to host-controlled restriction and modification in the Salmonella derby strain 456.	Genetika	1970	6		121-128			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. 		
@D	Karamov, E.V.//Naroditsky, B.S.//Zavizion, B.A.//Tikhonenko, T.I. 	Transformation of EcoRI restriction endonuclease substrate specificity under the influence of glycerol.	Biull. Eksp. Biol. Med.	1977	84		46-48			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. 		
@D	Karas, B.J.//Jablanovic, J.//Sun, L.//Ma, L.//Goldgof, G.M.//Stam, J.//Ramon, A.//Manary, M.J.//Winzeler, E.A.//Venter, J.C.//Weyman, P.D.//Gibson, D.G.//Glass, J.I.//Hutchison, C.A.I.I.I.//Smith, H.O.//Suzuki, Y. 	Direct transfer of whole genomes from bacteria to yeast.	Nat. Methods	2013	10		410-412			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. 		
@D	Karaseva, A.//Tsapieva, A.//Pachebat, J.//Suvorov, A. 	Draft Genome Sequence of Probiotic Enterococcus faecium Strain L-3.	Genome Announcements	2016	4		e01622-15			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. 		
@D	Karched, M.//Furgang, D.//Planet, P.J.//Desalle, R.//Fine, D.H. 	Genome Sequence of Aggregatibacter actinomycetemcomitans RHAA1, Isolated from a Rhesus Macaque, an Old World Primate.	J. Bacteriol.	2012	194		1275-1276			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. 		
@D	Karczewska-Golec, J.//Kochanowska-Lyzen, M.//Olszewski, P.//Balut, M.//Moskot, M.//Piotrowski, A.//Golec, P.//Szalewska-Palasz, A. 	Draft Genome Sequence of Flavobacterium sp. 316, a Baltic Sea Isolate Exhibiting  a High Level of Resistance to Marine Stress Conditions.	Genome Announcements	2016	4		e00180-16			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. 		
@D	Karczewska-Golec, J.//Strapagiel, D.//Sadowska, M.//Szalewska-Palasz, A.//Golec, P. 	Draft Genome Sequence of Shewanella baltica M1 Isolated from Brackish Surface Water of the Gulf of Gdansk.	Genome Announcements	2016	4		e00611-16			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. 		
@D	Karczmarczyk, M.//Wang, J.//Leonard, N.//Fanning, S. 	Complete nucleotide sequence of a conjugative IncF plasmid from an Escherichia coli isolate of equine origin containing blaCMY-2 within a novel genetic context.	FEMS Microbiol. Lett.	2014	352		123-127			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. 		
@D	Karimi, E.//Goncalves, J.M.//Reis, M.//Costa, R. 	Draft Genome Sequence of Microbacterium sp. Strain Alg239_V18, an Actinobacterium Retrieved from the Marine Sponge Spongia sp.	Genome Announcements	2017	5		e01457-16			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. 		
@D	Karl, M.M.//Poehlein, A.//Bengelsdorf, F.R.//Daniel, R.//Durre, P. 	Complete Genome Sequence of the Autotrophic Acetogen Clostridium formicaceticum DSM 92T Using Nanopore and Illumina Sequencing Data.	Genome Announcements	2017	5		e00423-17			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). 		
@D	Karlin, S.//Burge, C.//Campbell, A.M. 	Statistical analyses of counts and distributions of restriction sites in DNA sequences.	Nucleic Acids Res.	1992	20		1363-1370			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. 		
@D	Karlovsky, P. 	Mutual competitive inhibition between target sites during the restriction endonuclease digestion of DNA.	J. Theor. Biol.	1988	132		1-6			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. 		
@D	Karlovsky, P. 	Calculation of individual cleavage rates from partial digests in restriction endonuclease kinetics.	J. Theor. Biol.	1988	132		7-14			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. 		
@D	Karlovsky, P. 	Kinetics of circular DNA molecule digestion by restriction endonuclease A: Computation of kinetic constants from time dependence of fragment concentrations.	Acta Biotheor.	1986	35		279-292			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. 		
@D	Karlovsky, P. 	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.	Biochem. J.	1986	235		611-612			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. 		
@D	Karlyshev, A.V.//Abramov, V.M. 	Draft Genome Sequence of Lactobacillus plantarum 2165.	Genome Announcements	2014	2		e01179-13			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. 		
@D	Karlyshev, A.V.//Khlebnikov, V.C.//Kosarev, I.V.//Abramov, V.M. 	Draft Genome Sequence of Lactobacillus plantarum 2025.	Genome Announcements	2016	4		e01532-15			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. 		
@D	Karlyshev, A.V.//Kudryashova, E.B.//Ariskina, E.V. 	Draft Genome Sequence of 'Cohnella kolymensis' B-2846.	Genome Announcements	2016	4		e01587-15			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. 		
@D	Karlyshev, A.V.//Melnikov, V.G. 	Draft Genome Sequence of Corynebacterium pseudodiphtheriticum Strain 090104 'Sokolov'.	Genome Announcements	2013	1		e00921-13			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. 		
@D	Karlyshev, A.V.//Melnikov, V.G.//Chikindas, M.L. 	Draft Genome Sequence of Bacillus subtilis strain KATMIRA1933.	Genome Announcements	2014	2		e00619-14			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. 		
@D	Karlyshev, A.V.//Melnikov, V.G.//Chistyakov, V.A. 	Draft Genome Sequence of Bacillus amyloliquefaciens B-1895.	Genome Announcements	2014	2		e00633-14			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. 		
@D	Karlyshev, A.V.//Melnikov, V.G.//Khlebnikov, V.C.//Abramov, V.M. 	Draft Genome Sequence of Lactobacillus crispatus 2029.	Genome Announcements	2014	2		e01221-13			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. 		
@D	Karlyshev, A.V.//Melnikov, V.G.//Kosarev, I.V.//Abramov, V.M. 	Draft Genome Sequence of Lactobacillus rhamnosus 2166.	Genome Announcements	2014	2		e01222-13			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. 		
@D	Karlyshev, A.V.//Melnikov, V.G.//Kosarev, I.V.//Khlebnikov, V.C.//Sukhikh, G.T.//Abramov, V.M. 	Draft Genome Sequence of Lactobacillus gasseri Strain 2016.	Genome Announcements	2013	1		e00624-13			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. 		
@D	Karlyshev, A.V.//Nadarajah, S.//Abramov, V.M. 	Draft Genome Sequence of Lactobacillus jensenii Strain MD IIE-70(2).	Genome Announcements	2013	1		e01005-13			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. 		
@D	Karlyshev, A.V.//Raju, K.//Abramov, V.M. 	Draft Genome Sequence of Lactobacillus fermentum Strain 3872.	Genome Announcements	2013	1		e01006-13			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. 		
@D	Karlyshev, A.V.//Robyn, J.//Rasschaert, G.//Heyndrickx, M. 	Draft Genome Sequence of Enterococcus faecalis MB5259.	Genome Announcements	2014	2		e00634-14			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. 		
@D	Karlyshev, A.V.//Villena, J.//Gonzalez, C.//Albarracin, L.//Barros, J.//Garcia, A. 	Draft Genome Sequence of a Probiotic Strain, Lactobacillus fermentum UCO-979C.	Genome Announcements	2015	3		e01439-15			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. 		
@D	Karna, S.L.//Chen, T.//Chen, P.//Peacock, T.J.//Abercrombie, J.J.//Leung, K.P. 	Genome Sequence of a Virulent Pseudomonas aeruginosa Strain, 12-4-4(59), Isolated from the Blood Culture of a Burn Patient.	Genome Announcements	2016	4		e00079-16			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. 		
@D	Karpova, E.//Kubareva, E.//Petrauskene, O.//Joschimiak, A.//Van Kley, H. 	Peculiarity of the recognition and cleavage by restriction endonuclease EcoRII.	FASEB J.	1995	9		A1400			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. 		
@D	Karpova, E.A.//Kubareva, E.A.//Buryanov, Y.I.//Gromova, E.S. 	Formation of two types of enzyme-substrate complexes at the interaction of EcoRII restriction endonuclese with synthetic DNA duplexes.	Mol. Biol. (Mosk)	1992	26		993-998			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. 		
@D	Karpova, E.A.//Kubareva, E.A.//Gromova, E.S.//Buryanov, Y.I. 	Peculiaritites of the binding of restriction endonuclease EcoRII to synthetic DNA duplexes.	Biochem. Mol. Biol. Int.	1993	29		113-121			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. 		
@D	Karpova, E.A.//Kubareva, E.A.//Shabarova, Z.A. 	A model of EcoRII restriction endonuclease action: The active complex is most likely formed by one protein subunit and one DNA recognition site.	Life	1999	48		91-98			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. 		
@D	Karpova, E.A.//Meehan, E.//Pusey, M.L.//Chen, L. 	Crystallization and preliminary x-ray diffraction analysis of restriction endonuclease EcoRII.	Acta Crystallogr. D Biol. Crystallogr.	1999	55		1604-1605			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. 		
@D	Karreman, C. 	The genes for two procaryotic DNA modification methylases.	Ph.D. Thesis, State University of Leiden, Holland	1988			1-95			None 		
@D	Karreman, C.//de Waard, A. 	Isolation and characterization of the modification methylase M.SinI.	J. Bacteriol.	1988	170		2533-2536			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). 		
@D	Karreman, C.//de Waard, A. 	Agmenellum quadruplicatum M.AquI, a novel modification methylase.	J. Bacteriol.	1990	172		266-272			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. 		
@D	Karreman, C.//de Waard, A. 	Cloning and complete nucleotide sequences of the TypeII restriction-modification genes of Salmonella infantis.	J. Bacteriol.	1988	170		2527-2532			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. 		
@D	Karreman, C.//Tandeau de Marsac, N.//de Waard, A. 	Isolation of a deoxycytidylate methyl transferase capable of protecting DNA uniquely against cleavage by endonuclease R. AquI (isoschizomer of AvaI).	Nucleic Acids Res.	1986	14		5199-5205			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. 		
@D	Karrer, K.M.//VanNuland, T.A. 	Methylation of adenine in the nuclear DNA of Tetrahymena is internucleosomal and independent of histone H1.	Nucleic Acids Res.	2002	30		1364-1370			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. 		
@D	Karrer, K.M.//VanNuland, T.A. 	Position effect takes precedence over target sequence in determination of adenine methylation patterns in the nuclear genome of a eukaryote, Tetrahymena thermophila.	Nucleic Acids Res.	1998	26		4566-4573			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. 		
@A	Karska-Wysocki, B.//Hua, N.M.//Vzdornov, D.//Szatmari, G.//Mamet-Bratley, M.D. 		Detection and purification of a new restriction endonuclease, LlaMI, from Lactococcus lactis subsp. lactis M19.			none 		Sixth Symposium on Lactic Acid Bacteria Genetics, Metabolism and Applications				Veldhoven, The Netherlands	Fed. European Microbiol. Socs. and Netherlands Soc. for Microbiology	1999		0		F17									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. 		
@D	Karska-Wysocki, B.//Szatmari, G.//Barrette, B.//Mamet-Bratley, M.D. 	Characterization of a new restriction endonuclease, LlaGI, produced  by Lactococcus lactis subsp. cremoris G2.	Life Sc. Confer. Ottawa	1996	0		P088			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. 		
@A	Karska-Wysocki, B.//Szatmari, G.//Beauregard, G.//Mamet-Bratley, M.D. 		A new restriction endonuclease activity found in Lactococcus  cremoris G2.			 		Life Sc. Confer. Ottawa				Ottawa		1995		0		D2-D9									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. 		
@D	Kartashova, I.M.//Nikolskaya, I.I.//Debov, S.S. 	Separation of enzymes for modification methylases and restrictases from Shigella sonnei 47.	Mol. Gen. Mikrobiol. Virusol.	1985	4		31-35			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. 		
@D	Karunakaran, A.C.//Milton, A.A.P.//Rajendrakumar, A.M.//Sahu, A.R.//Pandey, A.//Ghatak, S.//Abhishek, N.V.K.//Gandham, R.//Agarwal, R.K. 	Draft Genome Sequences of Escherichia coli Isolates from India.	Genome Announcements	2018	6		e00047-18			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. 		
@D	Karuthedath, V.S.//Vir, S.A.//Kumar, S.P.//Garg, P.//Mohan, K.V.//Katoch, K.//Chauhan, D.S.//Scaria, V.//Sivasubbu, S. 	Draft Genome Sequence of an Extensively Drug-Resistant Mycobacterium tuberculosis Clinical Isolate of the Ural Strain OSDD493.	Genome Announcements	2013	1		e00928-13			We describe the genome sequencing and analysis of a clinical isolate of Mycobacterium tuberculosis belonging to the Ural strain OSDD493 from India. 		
@D	Karuthedath-Vellarikkal, S.//Patowary, A.//Singh, M.//Periwal, V.//Singh, A.V.//Singh, P.K.//Garg, P.//Mohan, K.V.//Katoch, K.//Jangir, P.K.//Sharma, R.//Chauhan, D.S.//Scaria, V.//Sivasubbu, S. 	Draft Genome Sequence of a Clinical Isolate of Multidrug-Resistant Mycobacterium  tuberculosis East African Indian Strain OSDD271.	Genome Announcements	2013	1		e00541-13			We describe the genome sequencing and analysis of a clinical isolate of Mycobacterium tuberculosis East African Indian (EAI) strain OSDD271 from India. 		
@D	Karyagina, A.//Shilov, I.//Tashlitskii, V.//Khodoun, M.//Vasilev, S.//Lau, P.C.K.//Nikolskaya, I. 	Specific binding of SsoII DNA methyltransferase to its promoter region provides the regulation of SsoII restriction-modification gene expression.	Nucleic Acids Res.	1997	25		2114-2120			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. 		
@D	Karyagina, A.S. 	Genetic determinants for the enzymes of bacterial restriction-modification systems.	Mol. Gen. Mikrobiol. Virusol.	1990	7		3-11			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. 		
@D	Karyagina, A.S.//Levchenko, I.Y.//Nikolskaya, I.I. 	A new method for isolation and purification of restriction endonuclease SsoII.	Biokhimiia	1993	58		908-912			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. 		
@D	Karyagina, A.S.//Lunin, V.G.//Degtyarenko, K.N.//Uvarov, V.Y.//Nikolskaya, I.I. 	Analysis of the nucleotide and derived amino acid sequences of the SsoII restriction endonuclease and methyltransferase.	Gene	1993	124		13-19			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. 		
@D	Karyagina, A.S.//Lunin, V.G.//Gruber, I.M.//Polyachenko, V.M.//Nikolskaya, I.I.//Debov, S.S. 	Activity of the restriction endonuclease SsoII in Escherichia coli cells transformed by Shigella sonnei 47 plasmids.	Mol. Gen. Mikrobiol. Virusol.	1987	12		26-29			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. 		
@D	Karyagina, A.S.//Lunin, V.G.//Levtchenko, I.Y.//Labbe, D.//Brousseau, R.//Lau, P.C.K.//Nikolskaya, I.I. 	The SsoII and NlaX DNA methyltransferases: overproduction and functional analysis.	Gene	1995	157		93-96			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. 		
@D	Karyagina, A.S.//Lunin, V.G.//Nikolskaia, I.I.//Debov, S.S. 	Functional characteristics of plasmids of Shigella sonnei 47 strains.	Mol. Gen. Mikrobiol. Virusol.	1986	10		16-21			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. 		
@D	Karyagina, A.S.//Lunin, V.G.//Nikolskaya, I.I. 	Characterization of the genetic determinants of SsoII-restriction endonuclease and modification methyltransferase.	Gene	1990	87		113-118			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. 		
@D	Karyagina, A.S.//Lunin, V.G.//Nikolskaya, I.I.//Debov, S.S. 	Localization of SsoII restriction endonuclease and methylase genes on the physical map of plasmid P4.	Mol. Gen. Mikrobiol. Virusol.	1989	3		16-20			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. 		
@D	Kas, E.//Poljak, L.//Adachi, Y.//Laemmli, K. 	A model for chromatin opening: stimulation of topoisomerase II and restriction enzyme cleavage of chromatin by distamycin.	EMBO J.	1993	12		115-126			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. 		
@D	Kasahara, Y.//Nakai, S.//Ogasawara, N.//Yata, K.//Sadaie, Y. 	Sequence analysis of the groESL-cotA region of the Bacillus subtilis genome, containing the restriction/modification system genes.	DNA Res.	1997	4		335-339			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. 		
@D	Kasarjian, J.//Kawai, S.//Ryu, J. 	Use of plasmid transformation to find new restriction enzymes.	Abstr. Gen. Meet. Am. Soc. Microbiol.	2000	100		371			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. 		
@D	Kasarjian, J.//Valinluck, V.//Ryu, J. 	Determination of the methylation sites of the type I restriction enzymes, KpnAI and KpnBI of Klebsiella species.	Abstr. Gen. Meet. Am. Soc. Microbiol.	2002	102		236			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. 		
@D	Kasarjian, J.K.A.//Burnett, A.S.//Ryu, J. 	Use of plasmid transformation to find new restriction enzymes and their recognition sequences.	J. Invest. Med.	2001	49		12A			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. 		
@D	Kasarjian, J.K.A.//Burnett, A.S.//Ryu, J. 	Identification of the recognition sequence of KpnAI, a type ID restriction enzyme, in Klebsiella pneumoniae M5a1.	Abstr. Gen. Meet. Am. Soc. Microbiol.	2001	101		403			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. 		
@D	Kasarjian, J.K.A.//Hidaka, M.//Horiuchi, T.//Iida, M.//Ryu, J. 	The recognition and modification sites for the bacterial type I restriction systems KpnAI, StySEAI, StySENI and StySGI.	Nucleic Acids Res.	2004	32		e82			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). 		
@D	Kasarjian, J.K.A.//Iida, M.//Ryu, J. 	New restriction enzymes discovered from Escherichia coli clinical strains using a plasmid transformation method.	Nucleic Acids Res.	2003	31		e22			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. 		
@D	Kasarjian, J.K.A.//Kodama, Y.//Iida, M.//Matsuda, K.//Ryu, J. 	Four new type I restriction enzymes identified in Escherichia coli clinical isolates.	Nucleic Acids Res.	2005	33		e114			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. 		
@D	Kashyap, R.S.//Bhullar, S.S.//More, R.P.//Puranik, S.//Purohit, H.J.//Taori, G.M.//Daginawala, H.F. 	Genome Sequence of Mycobacterium tuberculosis C2, a Cerebrospinal Fluid Clinical  Isolate from Central India.	Genome Announcements	2014	2		e00842-14			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. 		
@D	Kaszubska, W. 	Studies of a DNA modification methyltransferase from Rhodobacter sphaeroides.	Diss. Abstr.	1991	52		1407B			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. 		
@D	Kaszubska, W.//Aiken, C.//O'Connor, C.D.//Gumport, R.I. 	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.	Nucleic Acids Res.	1989	17		10403-10425			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). 		
@D	Kaszubska, W.//Aiken, C.R.//Gumport, R.I. 	RsrI restriction-modification enzymes from Rhodobacter sphaeroides.	Gene	1988	74		83-84			Meeting Abstract 		
@D	Kaszubska, W.//Webb, H.K.//Gumport, R. 	Purification and characterization of the M.RsrI DNA methyltransferase from Escherichia coli.	Gene	1992	118		5-11			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. 		
@D	Kataeva, I.A.//Yang, S.J.//Dam, P.//Poole, F.L.I.I.//Yin, Y.//Zhou, F.//Chou, W.C.//Xu, Y.//Goodwin, L.//Sims, D.R.//Detter, J.C.//Hauser, L.G.//Westpheling, J.//Adams, M.W. 	Genome Sequence of the Anaerobic, Thermophilic and Cellulolytic Bacterium Anaerocellum thermophilum DSM 6725.	J. Bacteriol.	2009	191		3760-3761			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. 		
@D	Katahira, K.//Ogura, Y.//Gotoh, Y.//Hayashi, T. 	Draft Genome Sequences of Five Rapidly Growing Mycobacterium Species, M. thermoresistibile, M. fortuitum subsp. acetamidolyticum, M. canariasense, M.  brisbanense, and M. novocastrense.	Genome Announcements	2016	4		e00322-16			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. 		
@D	Katani, R.//Cote, R.//Raygoza, G.J.A.//Li, L.//Arthur, T.M.//DebRoy, C.//Mwangi, M.M.//Kapur, V. 	Complete Genome Sequence of SS52, a Strain of Escherichia coli O157:H7 Recovered  from Supershedder Cattle.	Genome Announcements	2015	3		e01569-14			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. 		
@D	Katano, Y.//Fujinami, S.//Kawakoshi, A.//Nakazawa, H.//Oji, S.//Iino, T.//Oguchi, A.//Ankai, A.//Fukui, S.//Terui, Y.//Kamata, S.//Harada, T.//Tanikawa, S.//Suzuki, K.//Fujita, N. 	Complete genome sequence of Oscillibacter valericigenes Sjm18-20(T) (=NBRC 101213(T)).	Standards in Genomic Sciences	2012	6		406-414			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. 		
@D	Katiliene, Z.//Katilius, E.//Woodbury, N.W. 	Single molecule detection of DNA looping by NgoMIV restriction endonuclease.	Biophys. J.	2003	84		4053-4061			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. 		
@D	Katna, A.//Boratynski, R.//Furmanek-Blaszk, B.//Zolcinska, N.//Sektas, M. 	Unbalanced Restriction Impairs SOS-induced DNA Repair Effects.	J. Microbiol. Biotechnol.	2010	20		30-38			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. 		
@D	Kato, F. 	Isolation and characterization of restriction endonuclease from amino acid- or nucleic acid-producing bacteria.	Dojin News	1989	51		3-9			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. 		
@D	Kato, H.//Ogawa, N.//Ohtsubo, Y.//Ohshima, K.//Toyoda, A.//Yamazoe, A.//Mori, H.//Maruyama, F.//Nagata, Y.//Hattori, M.//Fujiyama, A.//Kurokawa, K.//Tsuda, M. 	Complete Genome Sequence of a Phenanthrene Degrader, Mycobacterium sp. Strain EPa45, Isolated from a Phenanthrene-Degrading Consortium.	Genome Announcements	2015	3		e00782-15			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). 		
@D	Kato, H.//Shiwa, Y.//Oshima, K.//Machii, M.//Araya-Kojima, T.//Zendo, T.//Shimizu-Kadota, M.//Hattori, M.//Sonomoto, K.//Yoshikawa, H. 	Complete Genome Sequence of Lactococcus lactis IO-1, a Lactic Acid Bacterium That Utilizes Xylose and Produces High Levels of L-Lactic Acid.	J. Bacteriol.	2012	194		2102-2103			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. 		
@D	Kato, J.//Endo, T.//Kawamura, H.//Nakashima, Y.//Furukoshi, K.//Oishi, K. 	Inhibition of restriction endonucleases by hot water extracts of spices.	Bull. Coll. Agr. Vet. Med.	1990	47		84-87			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. 		
@D	Kato, K.//Toh, H.//Sakamoto, N.//Mori, K.//Tashiro, K.//Hibi, N.//Sonomoto, K.//Nakayama, J. 	Draft Genome Sequence of Lactobacillus namurensis Chizuka 01, Isolated from Nukadoko, a Pickling Bed of Fermented Rice Bran.	Genome Announcements	2014	2		e01263-13			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. 		
@D	Kato, S.//Oikawa, T. 	Genome Sequence of Lactobacillus sakei LK-145 Isolated from a Japanese Sake Cellar as a High Producer of d-Amino Acids.	Genome Announcements	2017	5		e00656-17			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. 		
@D	Kato, S.//Oikawa, T. 	Whole-Genome Sequence of Leuconostoc mesenteroides LT-38, a Non-Spore-Forming Gram-Positive Lactic Acid Bacterium.	Genome Announcements	2017	5		e00670-17			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. 		
@D	Kato, S.//Oikawa, T. 	Whole-Genome Sequence of Lactobacillus sakei LT-13 Isolated from Moto Starter of  Sake.	Genome Announcements	2017	5		e00651-17			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. 		
@D	Kato, S.//Oikawa, T. 	Genome Sequence of Leuconostoc mesenteroides LK-151 Isolated from a Japanese Sake Cellar as a High Producer of d-Amino Acids.	Genome Announcements	2017	5		e00661-17			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. 		
@D	Katoh, H.//Miyata, S.//Inoue, H.//Iwanami, T. 	Unique features of a Japanese 'Candidatus Liberibacter asiaticus' strain revealed by whole genome sequencing.	PLoS ONE	2014	9		e106109			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. 		
@D	Katoh, T.//Maeshibu, T.//Kikkawa, K.//Gotoh, A.//Tomabechi, Y.//Nakamura, M.//Liao, W.-H.//Yamaguchi, M.//Ashida, H.//Yamamoto, K.//Katayama, T. 	Identification and characterization of a sulfoglycosidase from Bifidobacterium bifidum implicated in mucin glycan utilization.	Biosci. Biotechnol. Biochem.	2017	81		2018-2027			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. 		
@D	Katsura, S.//Harada, N.//Maeda, Y.//Komatsu, J.//Matsuura, S.//Takashima, K.//Mizuno, A. 	Activation of restriction enzyme by electrochemically released magnesium ion.	J. Biosci. Bioeng.	2004	98		293-297			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. 		
@D	Katuri, K.P.//Albertsen, M.//Saikaly, P.E. 	Draft Genome Sequence of Desulfuromonas acetexigens Strain 2873, a Novel Anode-Respiring Bacterium.	Genome Announcements	2017	5		e01522-16			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. 		
@D	Katz, J.E.//Dlakic, M.//Clarke, S. 	Automated identification of putative methyltransferases from genomic open reading frames.	Mol. Cell. Proteomics	2003	2		525-540			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. 		
@D	Katz, L.S.//Turnsek, M.//Kahler, A.//Hill, V.R.//Boyd, E.F.//Tarr, C.L. 	Draft Genome Sequence of Environmental Vibrio cholerae 2012EL-1759 with Similarities to the V. cholerae O1 Classical Biotype.	Genome Announcements	2014	2		e00617-14			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. 		
@D	Kauc, L.//Leszczynska, K. 	Identification of a new restriction endonuclease, EagI, from Enterobacter agglomerans.	Acta Microbiol. Pol.	1986	35		317-320			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. 		
@D	Kauc, L.//Piekarowicz, A. 	Purification and properties of a new restriction endonuclease from Haemophilus influenzae Rf.	Eur. J. Biochem.	1978	92		417-426			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. 		
@D	Kauc, L.//Piekarowicz, A. 	Degradation of transforming and transfecting DNA by the restriction endonucleases of Type I and Type II isolated from Haemophilus influenzae.	Acta Microbiol. Pol.	1977	26		137-148			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. 		
@A	Kauc, L.//Piekarowicz, A. 		Degradation of Transforming Deoxyribonucleic Acid by the ATP Dependent Restriction Endonuclease Isolated from Haemophilus Influenzae Rf.			Portoles, A.//Lopez, R.//Espinosa, M. 		Modern Trends in Bacterial Transformation and Transfection.				Amsterdam	Elsevier	1976		0		257-262									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. 		
@D	Kaufman, D.L.//Evans, G.A. 	Restriction endonuclease cleavage at the termini of PCR products.	Biotechniques	1990	9		304-305			None 		
@D	Kaufmann, G. 	Anticodon nucleases.	Trends Biochem. Sci.	2000	25		70-74			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. 		
@D	Kaufmann, G.//Amitsur, M.//Chapman-Shimshoni, D. 	In vivo reconstitution of latent anticodon nuclease: A tRNA restriction enzyme masked by hsd restriction-modification proteins.	J. Cell Biochem. Suppl.	1993	17C		174			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. 		
@D	Kaunietis, A.//de Jong, A.//Pranckute, R.//Buivydas, A.//Kuipers, O.P. 	Draft Genome Sequences of Two Geobacillus Species Strains, Isolated from Oil Wells and Surface Soil above Oil Pools.	Genome Announcements	2016	4		e01129-16			Here, we present the draft genome sequences of two Geobacillus species strains isolated from oil wells and surface soil above oil pools in Lithuania. 		
@D	Kaur, C.//Selvakumar, G.//Ganeshamurthy, A.N. 	Draft Genome Sequence of Phosphate-Solubilizing Bacterium Paraburkholderia tropica Strain P-31 Isolated from Pomegranate (Punica granatum) Rhizosphere.	Genome Announcements	2016	4		e00844-16			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. 		
@D	Kaur, J.//Verma, H.//Tripathi, C.//Khurana, J.P.//Lal, R. 	Draft Genome Sequence of a Hexachlorocyclohexane-Degrading Bacterium, Sphingobium baderi Strain LL03T.	Genome Announcements	2013	1		e00751-13			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%. 		
@D	Kaur, K.//Rohozinski, J.//Goorha, R. 	Identification and characterization of the frog virus 3 DNA methyltransferase gene.	J. Gen. Virol.	1995	76		1937-1943			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. 		
@D	Kaur, N.//Kumar, S.//Bala, M.//Raghava, G.P.//Mayilraj, S. 	Draft Genome Sequence of Amycolatopsis decaplanina Strain DSM 44594T.	Genome Announcements	2013	1		e0013813			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. 		
@D	Kaus-Drobek, M.//Czapinska, H.//Sokolowska, M.//Tamulaitis, G.//Szczepanowski, R.H.//Urbanke, C.//Siksnys, V.//Bochtler, M. 	Restriction endonuclease MvaI is a monomer that recognizes its target sequence asymmetrically.	Nucleic Acids Res.	2007	35		2035-2046			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. 		
@D	Kautharapu, K.B.//Jarboe, L.R. 	Genome Sequence of the Psychrophilic Deep-Sea Bacterium Moritella marina MP-1 (ATCC 15381).	J. Bacteriol.	2012	194		6296-6297			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. 		
@D	Kavamura, V.N.//Santos, S.N.//Taketani, R.G.//Vasconcellos, R.L.//Melo, I.S. 	Draft Genome Sequence of Plant Growth-Promoting Drought-Tolerant Bacillus sp. Strain CMAA 1363 Isolated from the Brazilian Caatinga Biome.	Genome Announcements	2017	5		e01534-16			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. 		
@D	Kavousi, N.//Eng, W.W.//Lee, Y.P.//Tan, L.H.//Thuraisingham, R.//Yule, C.M.//Gan, H.M. 	First High-Quality Draft Genome Sequence of Pasteurella multocida Sequence Type 128 Isolated from Infected Bone.	Genome Announcements	2016	4		e00023-16			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. 		
@D	Kaw, M.K.//Blumenthal, R.M. 	Translational independence between overlapping genes for a restriction endonuclease and its transcriptional regulator.	BMC Mol. Biol.	2010	11		87			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. 		
@D	Kawabata, H.//Norris, S.J.//Watanabe, H. 	BBE02 disruption mutants of Borrelia burgdorferi B31 have a highly transformable, infectious phenotype.	Infect. Immun.	2004	72		7147-7154			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. 		
@D	Kawai, M.//Higashiura, N.//Hayasaki, K.//Okamoto, N.//Takami, A.//Hirakawa, H.//Matsushita, K.//Azuma, Y. 	Complete genome and gene expression analyses of Asaia bogorensis reveal unique responses to culture with mammalian cells as a potential opportunistic human pathogen.	DNA Res.	2015	22		357-366			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. 		
@D	Kawaichi, S.//Yoshida, T.//Sako, Y.//Nakamura, R. 	Draft Genome Sequence of a Heterotrophic Facultative Anaerobic Thermophilic Bacterium, Ardenticatena maritima Strain 110ST.	Genome Announcements	2015	3		e01145-15			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). 		
@D	Kawakami, B. 	Application of recombinant DNA technique to the production of N-acetylneuraminate lyase and restriction enzymes.	Ph.D. Thesis, University of Kyoto University	1991			1-102			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. 		
@D	Kawakami, B.//Hilzheber, C.//Nagatomo, M.//Oka, M. 	Cloning and nucleotide sequences of the AccI restriction-modification genes in Acinetobacter calcoaceticus.	Agric. Biol. Chem.	1991	55		1553-1559			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. 		
@D	Kawakami, B.//Katsuragi, N.//Maekawa, Y.//Imanaka, T. 	Cloning and expression of the BamHI restriction-modification system in Bacillus subtilis.	J. Ferment. Bioeng.	1990	70		211-214			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. 		
@D	Kawakami, B.//Sasaki, A.//Oka, M.//Maekawa, Y. 	Nucleotide sequence of the gene coding for the BanIII DNA methyltransferase in Bacillus aneurinolyticus.	Agric. Biol. Chem.	1990	54		3227-3233			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. 		
@D	Kawalec, M.//Borsuk, P.//Piechula, S.//Stepien, P.P. 	A novel restriction endonuclease UnbI, a neoschizomer of Sau96I from an unidentified psychrofilic bacterium from Antarctica is inhibited by phosphate ions.	Acta Biochim. Pol.	1997	44		849-852			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. 		
@D	Kawamura, M.//Sakakibara, M.//Watanabe, T.//Kita, K.//Hiraoka, N.//Obayashi, A.//Takagi, M.//Yano, K. 	A new restriction endonuclease from Spirulina platensis.	Nucleic Acids Res.	1986	14		1985-1989			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. 		
@D	Kawarabayasi, Y. et al. 	Complete sequence and gene organization of the genome of a hyper-thermophilic Archaebacterium, Pyrococcus horikoshii OT3 (Supplement).	DNA Res.	1998	5		147-155			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). 		
@D	Kawarabayasi, Y. et al. 	Complete sequence and gene organization of the genome of a hyper-thermophilic Archaebacterium, Pyrococcus horikoshii OT3.	DNA Res.	1998	5		55-76			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. 		
@D	Kawarabayasi, Y. et al. 	Complete genome sequence of an aerobic thermoacidophilic crenarchaeon, Sulfolobus tokodaii strain7.	DNA Res.	2001	8		123-140			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). 		
@D	Kawarabayasi, Y. et al. 	Complete genome sequence of an aerobic hyper-thermophilic crenarchaeon, Aeropyrum pernix K1.	DNA Res.	1999	6		83-101			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). 		
@D	Kawasaki, K.//Shibata, T. 	Mitochondrial HSP70 as a subunit of eukaryotic multi-site-specific endonuclease, Endo.SceI; auto-phosphorylation and heat stability.	Mol. Biol. Cell	1995	6		135a			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. 		
@D	Kawasaki, K.//Shibata, T.//Ito, F. 	Roles of the HSP70-Subunit in a eukaryotic multi-site-specific endonuclease, Endo.SceI: Autophosphorylation and heat stability.	Biosci. Biotechnol. Biochem.	2004	68		2557-2564			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. 		
@D	Kawasaki, K.//Takahashi, M.//Ando, T.//Shibata, T. 	Sequence-specific complex formation of DNA and a eukaryotic sequence-specific endonuclease, SceI.	Eur. J. Biochem.	1991	202		665-671			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+. 		
@D	Kawasaki, K.//Takahashi, M.//Natori, M.//Shibata, T. 	DNA sequence recognition by a eukaryotic sequence-specific endonuclease, Endo.SceI, from Saccharomyces cerevisiae.	J. Biol. Chem.	1991	266		5342-5347			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. 		
@D	Kawasaki, M.//Delamare-Deboutteville, J.//Bowater, R.O.//Walker, M.J.//Beatson, S.//Ben Zakour, N.L.//Barnes, A.C. 	Microevolution of aquatic Streptococcus agalactiae ST-261 from Australia indicates dissemination via imported tilapia and ongoing adaptation to marine hosts or environment.	Appl. Environ. Microbiol.	2018	0		AEM.00859-18			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. 		
@D	Kawasaki, M.//Makino, S.-I.//Matsuzawa, H.//Satow, Y.//Ohya, Y.//Anraku, Y. 	Folding-dependent in vitro protein splicing of the Saccharomyces cerevisiae VMA1 protozyme.	Biochem. Biophys. Res. Commun.	1996	222		827-832			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. 		
@D	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. 	Archaeal adaptation to higher temperatures revealed by genomic sequence of Thermoplasma volcanium.	Proc. Natl. Acad. Sci. U. S. A.	2000	97		14257-14262			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. 		
@D	Kawashima, T.//Yamamoto, Y.//Aramaki, H.//Nunoshiba, T.//Kawamoto, T.//Watanabe, K.//Yamazaki, M.//Kanehori, K.//Amano, N.//Ohya, Y.//Makino, K.//Suzuki, M. 	Determination of the complete genomic DNA sequence of Thermoplasma volcanium GSS1.	Proc. Jpn. Acad.	1999	75		213-218			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. 		
@D	Kawata, Y.//Kawasaki, K.//Shigeri, Y. 	Draft Genome Sequence of Halomonas sp. Strain KM-1, a Moderately Halophilic Bacterium That Produces the Bioplastic Poly(3-Hydroxybutyrate).	J. Bacteriol.	2012	194		2738-2739			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. 		
@D	Kawato, S.//Nozaki, R.//Kondo, H.//Hirono, I. 	Draft Genome Sequence of Vibrio penaeicida Strain TUMSAT-NU1, Isolated from Diseased Shrimp in Japan.	Genome Announcements	2018	6		e00153-18			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. 		
@D	Kawato, Y.//Yasuike, M.//Nakamura, Y.//Shigenobu, Y.//Fujiwara, A.//Sano, M.//Nakai, T. 	Complete Genome Sequence Analysis of Two Pseudomonas plecoglossicida Phages, Potential Therapeutic Agents.	J. Appl. Environ. Microbiol.	2015	81		874-881					
@D	Kay, E.//Wren, B.W.//Parkhill, J. 	Identification of genetic differences between strains of Campylobacter jejuni using differential genomic hybridisation and comparative  genomics.	Int. J. Med. Microbiol.	2003	293		130-131			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. 		
@D	Kayansamruaj, P.//Pirarat, N.//Kondo, H.//Hirono, I.//Rodkhum, C. 	Draft Genome Sequences of Streptococcus agalactiae Strains Isolated from Nile Tilapia (Oreochromis niloticus) Farms in Thailand.	Genome Announcements	2014	2		e01300-14			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. 		
@D	Kazennova, E.V.//Tarasov, A.P.//Mileikovskaya, M.M.//Semina, I.E.//Tsvetkova, N.V. 	Isolation and purification of Bordetella pertussis restriction endonuclease BpeI.	Zh. Mikrobiol. Epidemiol. Immunobiol.	1982	0		56-57			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. 		
@D	Kazlauskiene, R.//Maneliene, Z.//Butkus, V.//Petrusyte, M.//Janulaitis, A. 	A new specific endodeoxyribonuclease from Escherichia coli RFL 72.	Bioorg. Khim.	1986	12		836-838			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. 		
@D	Kazmierczak, R.A.//Best, A.A.//Nguyen, D.//Eisenstark, A. 	Whole-Genome Shotgun Sequences of Salmonella enterica Serovar Typhimurium Lilleengen Type Strains LT1, LT18, LT19, LT20, LT21, and LT22.	Genome Announcements	2017	5		e00720-17			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. 		
@D	Kazou, M.//Alexandraki, V.//Pot, B.//Tsakalidou, E.//Papadimitriou, K. 	Complete Genome Sequence of the Dairy Isolate Lactobacillus acidipiscis ACA-DC 1533.	Genome Announcements	2017	5		e01533-16			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. 		
@D	Kazou, M.//Alexandraki, V.//Pot, B.//Tsakalidou, E.//Papadimitriou, K. 	Complete Genome Sequence of the Sourdough Isolate Lactobacillus zymae ACA-DC 3411.	Genome Announcements	2017	5		e00699-17			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. 		
@D	Kazou, M.//Alexandraki, V.//Pot, B.//Tsakalidou, E.//Papadimitriou, K. 	Whole-Genome Sequence of the Cheese Isolate Lactobacillus rennini ACA-DC 565.	Genome Announcements	2017	5		e01579-16			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. 		
@D	Kazrani, A.A.//Kowalska, M.//Czapinska, H.//Bochtler, M. 	Crystal structure of the 5hmC specific endonuclease PvuRts1I.	Nucleic Acids Res.	2014	42		5929-5936			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. 		
@D	Ke, L.//Liu, P.//Liu, S.//Gao, M. 	Complete Genome Sequence of Magnetospirillum sp. ME-1, a Novel Magnetotactic Bacterium Isolated from East Lake, Wuhan, China.	Genome Announcements	2017	5		e00485-17			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. 		
@D	Ke, Y.//Wang, Y.//Yuan, X.//Xu, J.//Zhen, Q.//Wang, Z.//Li, T.//Wang, D.//Huang, L.//Song, H.//Chen, Z. 	Complete Genome Sequence of Brucella suis Field Strain BCB025 of Sequence Type ST22.	J. Bacteriol.	2012	194		6959			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. 		
@D	Ke, Y.//Yuan, X.//Wang, Y.//Bai, Y.//Xu, J.//Song, H.//Huang, L.//Chen, Z. 	Genome Sequences of Brucella melitensis 16M and Its Two Derivatives 16M1w and 16M13w, Which Evolved In Vivo.	J. Bacteriol.	2012	194		5489			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. 		
@D	Ke, Y.//Yuan, X.//Zhen, Q.//Wang, Y.//Li, T.//Sun, Y.//Song, H.//Huang, L.//Wang, D.//Cui, B.//Mao, K.//Chen, Z. 	Genome Sequence of Brucella melitensis S66, an Isolate of Sequence Type 8, Prevalent in China.	J. Bacteriol.	2012	194		5451			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. 		
@D	Ke, Y.//Zhen, Q.//Li, T.//Wang, Y.//Yuan, X.//Xu, J.//Huang, L.//Wang, D.//Song, H.//Chen, Z. 	Complete Genome Sequence of Brucella melitensis 133, an Isolate of Biovar 1 of Sequence Type 32.	J. Bacteriol.	2012	194		6932			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. 		
@D	Keatch, S.A.//Leonard, P.G.//Ladbury, J.E.//Dryden, D.T. 	StpA protein from Escherichia coli condenses supercoiled DNA in preference to linear DNA and protects it from digestion by DNase I and EcoKI.	Nucleic Acids Res.	2005	33		6540-6546			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. 		
@D	Keatch, S.A.//Su, T.J.//Dryden, D.T. 	Alleviation of restriction by DNA condensation and non-specific DNA binding ligands.	Nucleic Acids Res.	2004	32		5841-5850			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. 		
@D	Kee, C. et al. 	Complete Genome Sequence of Pseudomonas stutzeri Type Strain SGAir0442, Isolated  from Singapore Air Samples.	Genome Announcements	2018	6		e00424-18			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. 		
@D	Kee, C. et al. 	Complete Genome Sequence of Acinetobacter schindleri SGAir0122 Isolated from Singapore Air.	Genome Announcements	2018	6		e00567-18			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. 		
@A	Keeble, A.H.//Mate, M.J.//Kleanthous, C. 		HNH Endonucleases.			Belfort, M. 		Nucleic Acids Mol. Biol.				Berlin Heidelberg	Springer-Verlag	2005		16		49-65									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. 		
@D	Keeling, P.J.//Roger, A.J. 	The selfish pursuit of sex.	Nature	1995	375		283			A letter arguing that inteins are selfish elements relevant to the evolution of sex. 		
@D	Keen, E.C.//Bliskovsky, V.V.//Adhya, S.L.//Dantas, G. 	Draft Genome Sequence of the Naturally Competent Bacillus simplex Strain WY10.	Genome Announcements	2017	5		e01295-17			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. 		
@D	Kehlet-Delgado, H.//Richards, G.P.//Hase, C.//Mueller, R.S. 	Three Draft Genome Sequences of Vibrio coralliilyticus Strains Isolated from Bivalve Hatcheries.	Genome Announcements	2017	5		e01162-17			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. 		
@D	Kehrl, J.H.//Patel, K.B.//Kahng, L.S. 	Dam methylation is essential in vibrio vulnificus and influences its interactions with host cells.	Gastroenterology	2008	134		A713			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. 		
@D	Keita, M.B.//Diene, S.M.//Robert, C.//Raoult, D.//Fournier, P.E.//Bittar, F. 	Non-contiguous finished genome sequence and description of Bacillus massiliogorillae sp. nov.	Standards in Genomic Sciences	2013	9		93-105			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. 		
@D	Keita, M.B.//Padhmanabhan, R.//Caputo, A.//Robert, C.//Delaporte, E.//Raoult, D.//Fournier, P.E.//Bittar, F. 	Non-contiguous finished genome sequence and description of Gorillibacterium massiliense gen. nov, sp. nov., a new member of the family Paenibacillaceae.	Standards in Genomic Sciences	2014	9		807-820			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. 		
@D	Keita, M.B.//Padhmananabhan, R.//Caputo, A.//Robert, C.//Delaporte, E.//Raoult, D.//Fournier, P.E.//Bittar, F. 	Non-contiguous finished genome sequence and description of Paenibacillus gorillae sp. nov.	Standards in Genomic Sciences	2014	9		1031-1045			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. 		
@D	Kejnovsky, E.//Nejedly, K.//Kypr, J. 	Factors influencing resistance of UV-irradiated DNA to the restriction endonuclease cleavage.	Int. J. Biol. Macromol.	2004	34		213-222			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. 		
@D	Kelleher, J.E. 	Defining domains of the EcoK methylase by mutational analyses and DNA sequence comparisons.	Ph.D. Thesis, University of Edinburgh	1990			1-207			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. 		
@D	Kelleher, J.E.//Daniel, A.S.//Murray, N.E. 	Mutations that confer de novo activity upon a maintenance methyltransferase.	J. Mol. Biol.	1991	221		431-440			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. 		
@D	Kelleher, J.E.//Raleigh, E.A. 	A novel activity in Escherichia coli K-12 that directs restriction of DNA modified at CG dinucleotides.	J. Bacteriol.	1991	173		5220-5223			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). 		
@D	Kelleher, J.E.//Raleigh, E.A. 	On the regulation and diversity of restriction in Escherichia coli.	Gene	1995	157		229-230			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. 		
@D	Kelleher, J.E.//Raleigh, E.A. 	Response to UV damage by four Escherichia coli K-12 restriction systems.	J. Bacteriol.	1994	176		5888-5896			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. 		
@D	Kelleher, P.//Bottacini, F.//Mahony, J.//Kilcawley, K.N.//van Sinderen, D. 	Comparative and functional genomics of the Lactococcus lactis taxon; insights into evolution and niche adaptation.	BMC Genomics	2017	18		267			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. 		
@D	Kellenberger, G.//Symonds, N.//Arber, W. 	Host specificity of DNA produced by Escherichia coli.  8.Its acquisition by phage lambda and its persistence through consecutive growth cycles.	Z. Vererbungsl.	1966	98		247-256			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. 		
@D	Keller, K.L.//Bender, K.S.//Wall, J.D. 	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.	Abstr. Gen. Meet. Am. Soc. Microbiol.	2009	109		0			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. 		
@D	Keller, K.L.//Bender, K.S.//Wall, J.D. 	Development of a markerless genetic exchange system for Desulfovibrio vulgaris Hildenborough and its use in generating a strain with increased  transformation efficiency.	Appl. Environ. Microbiol.	2009	75		7682-7691			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. 		
@D	Keller, L.E.//Thomas, J.C.//Luo, X.//Nahm, M.H.//McDaniel, L.S.//Robinson, D.A. 	Draft Genome Sequences of Five Multilocus Sequence Types of Nonencapsulated Streptococcus pneumoniae.	Genome Announcements	2013	1		e00520-13			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. 		
@D	Keller-Costa, T.//Silva, R.//Lago-Leston, A.//Costa, R. 	Genomic Insights into Aquimarina sp. Strain EL33, a Bacterial Symbiont of the Gorgonian Coral Eunicella labiata.	Genome Announcements	2016	4		e00855-16			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. 		
@D	Kelly, S. et al. 	Genome sequence of the Lotus spp. microsymbiont Mesorhizobium loti strain NZP2037.	Standards in Genomic Sciences	2014	9		7			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. 		
@D	Kelly, S.//Kaddurah-Daouk, R.//Smith, H.O. 	Purification of the HhaII restriction endonuclease from an overproducer Escherichia coli clone.	J. Biol. Chem.	1985	260		15339-15344			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. 		
@D	Kelly, S.//Sullivan, J.//Ronson, C.//Tian, R.//Brau, L.//Munk, C.//Goodwin, L.//Han, C.//Woyke, T.//Reddy, T.//Huntemann, M.//Pati, A.//Mavromatis, K.//Markowitz, V.//Ivanova, N.//Kyrpides, N.//Reeve, W. 	Genome sequence of the Lotus spp. microsymbiont Mesorhizobium loti strain R7A.	Standards in Genomic Sciences	2014	9		6			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. 		
@D	Kelly, S.A.//Megaw, J.//Gilmore, B.F. 	Draft Genome Sequence of Salinisphaera sp. Strain KSM-18, an Obligately Halophilic Bacterium Isolated from a Triassic Salt Mine.	Microbiol. Resour. Announc.	2018	7		e00897-18			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. 		
@D	Kelly, T.J. Jr.//Smith, H.O. 	A restriction enzyme from Hemophilus influenzae II.  Base sequence of the recognition site.	J. Mol. Biol.	1970	51		393-409			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. 		
@D	Kelly, T.J.//Smith, H.O. 	The nucleotide sequence of the recognition site for a restriction enzyme from H. influenzae.	Fed. Proc.	1970	29		405			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. 		
@D	Kelly, W.J.//Altermann, E.//Lambie, S.C.//Leahy, S.C. 	Interaction between the genomes of Lactococcus lactis and phages of the P335 species.	Front. Microbiol.	2013	4		257			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. 		
@D	Kelly, W.J.//Henderson, G.//Pacheco, D.M.//Li, D.//Reilly, K.//Naylor, G.E.//Janssen, P.H.//Attwood, G.T.//Altermann, E.//Leahy, S.C. 	The complete genome sequence of Eubacterium limosum SA11, a metabolically versatile rumen acetogen.	Standards in Genomic Sciences	2016	11		26			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. 		
@D	Kelly, W.J.//Leahy, S.C.//Altermann, E.//Yeoman, C.J.//Dunne, J.C.//Kong, Z.//Pacheco, D.M.//Li, D.//Noel, S.J.//Moon, C.D.//Cookson, A.L.//Attwood, G.T. 	The Glycobiome of the Rumen Bacterium Butyrivibrio proteoclasticus B316 Highlights Adaptation to a Polysaccharide-Rich Environment.	PLoS ONE	2010	5		E11942			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. 		
@D	Kelly, W.J.//Leahy, S.C.//Li, D.//Perry, R.//Lambie, S.C.//Attwood, G.T.//Altermann, E. 	The complete genome sequence of the rumen methanogen Methanobacterium formicicum  BRM9.	Standards in Genomic Sciences	2014	9		15			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. 		
@D	Kelly, W.J.//Li, D.//Lambie, S.C.//Cox, F.//Attwood, G.T.//Altermann, E.//Leahy, S.C. 	Draft Genome Sequence of the Rumen Methanogen Methanobrevibacter olleyae YLM1.	Genome Announcements	2016	4		e00232-16			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. 		
@D	Kelly, W.J.//Li, D.//Lambie, S.C.//Jeyanathan, J.//Cox, F.//Li, Y.//Attwood, G.T.//Altermann, E.//Leahy, S.C. 	Complete Genome Sequence of Methanogenic Archaeon ISO4-G1, a Member of the Methanomassiliicoccales, Isolated from a Sheep Rumen.	Genome Announcements	2016	4		e00221-16			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. 		
@D	Kelly, W.J.//Pacheco, D.M.//Li, D.//Attwood, G.T.//Altermann, E.//Leahy, S.C. 	The complete genome sequence of the rumen methanogen Methanobrevibacter millerae  SM9.	Standards in Genomic Sciences	2016	11		49			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. 		
@D	Kempf, F.//Loux, V.//Germon, P. 	Genome Sequences of Two Bovine Mastitis-Causing Escherichia coli Strains.	Genome Announcements	2015	3		e00259-15			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. 		
@D	Kemter, F.S.//Messerschmidt, S.J.//Schallopp, N.//Sobetzko, P.//Lang, E.//Bunk, B.//Sproer, C.//Teschler, J.K.//Yildiz, F.H.//Overmann, J.//Waldminghaus, T. 	Synchronous termination of replication of the two chromosomes is an evolutionary selected feature in Vibrionaceae.	PLoS Genet.	2018	14		e1007251			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. 		
@D	Keness, Y.//Bisharat, N. 	Draft Genome Sequences of Streptococcus pneumoniae with High-Level Resistance to  Respiratory Fluoroquinolones.	Genome Announcements	2016	4		e00181-16			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. 		
@D	Kennaway, C.K.//Obarska-Kosinska, A.//White, J.H.//Tuszynska, I.//Cooper, L.P.//Bujnicki, J.M.//Trinick, J.//Dryden, D.T. 	The structure of M.EcoKI Type I DNA methyltransferase with a DNA mimic antirestriction protein.	Nucleic Acids Res.	2009	37		762-770			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. 		
@D	Kennaway, C.K.//Taylor, J.E.//Song, C.F.//Potrzebowski, W.//Nicholson, W.//White, J.H.//Swiderska, A.//Obarska-Kosinska, A.//Callow, P.//Cooper, L.P.//Roberts, G.A.//Artero, J.B.//Bujnicki, J.M.//Trinick, J.//Kneale, G.G.//Dryden, D.T.F. 	Structure and operation of the DNA-translocating type I DNA restriction enzymes.	Genes Dev.	2012	26		92-104			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. 		
@D	Kennedy, V.//Van Laar, T.A.//Aleru, O.//Thomas, M.//Ganci, M.//Rawat, M. 	Genome Sequences of Three Spore-Forming Bacteria Isolated from the Feces of Organically Raised Chickens.	Genome Announcements	2016	4		e00880-16			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. 		
@D	Kennell, J.C.//Moran, J.V.//Perlman, P.S.//Butow, R.A.//Lambowitz, A.M. 	Reverse transcriptase activity associated with maturase-encoding group II introns in yeast mitochondria.	Cell	1993	73		133-146			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. 		
@D	Kenri, T.//Horino, A.//Matsui, M.//Sasaki, Y.//Suzuki, S.//Narita, M.//Ohya, H.//Okazaki, N.//Shibayama, K. 	Complete Genome Sequence of Mycoplasma pneumoniae Type 2a Strain 309, Isolated in Japan.	J. Bacteriol.	2012	194		1253-1254			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. 		
@D	Kenri, T.//Suzuki, M.//Horino, A.//Sekizuka, T.//Kuroda, M.//Fujii, H.//Hashimoto, T.//Nakajima, H.//Ohya, H.//Shibayama, K. 	Complete Genome Sequences of the p1 Gene Type 2b and 2c Strains Mycoplasma pneumoniae KCH-402 and KCH-405.	Genome Announcements	2017	5		e00513-17			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. 		
@D	Kenyon, L.J.//Meulia, T.//Sabree, Z.L. 	Habitat visualization and genomic analysis of 'Candidatus Pantoea carbekii,' the primary symbiont of the brown marmorated stink bug.	Genome Biol. Evol.	2015	7		620-635			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. 		
@D	Kenzaka, T.//Ishimoto, Y.//Tani, K. 	Draft Genome Sequence of Multidrug-Resistant Cellulosimicrobium sp. Strain KWT-B, Isolated from Feces of Hirundo rustica.	Genome Announcements	2017	5		e00641-17			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. 		
@D	Kenzaka, T.//Nakahara, M.//Higuchi, S.//Maeda, K.//Tani, K. 	Draft Genome Sequences of Amoeba-Resistant Aeromonas spp. Isolated from Aquatic Environments.	Genome Announcements	2014	2		e01115-14			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. 		
@D	Kenzaka, T.//Tani, K. 	Draft Genome Sequence of Multidrug-Resistant Stenotrophomonas pavanii BWK1, Isolated from Mareca penelope Feces.	Genome Announcements	2018	6		e00187-18			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. 		
@D	Kenzaka, T.//Tani, K. 	Draft Genome Sequence of Carbapenem-Resistant Pseudomonas fluorescens Strain BWKM6, Isolated from Feces of Mareca penelope.	Genome Announcements	2018	6		e00186-18			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. 		
@D	Kenzaka, T.//Tani, K. 	Draft Genome Sequence of Extended-Spectrum Beta-Lactamase-Producing Serratia fonticola BWK15 Isolated from Feces of Anas penelope.	Genome Announcements	2017	5		e01102-17			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. 		
@D	Kenzaka, T.//Yamada, Y.//Tani, K. 	Draft Genome Sequence of an Antifungal Bacterium Isolated from the Breeding Environment of Dorcus hopei binodulosus.	Genome Announcements	2014	2		e00424-14			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. 		
@D	Kera, Y.//Abe, K.//Kasai, D.//Fukuda, M.//Takahashi, S. 	Draft Genome Sequences of Sphingobium sp. Strain TCM1 and Sphingomonas sp. Strain TDK1, Haloalkyl Phosphate Flame Retardant- and Plasticizer-Degrading Bacteria.	Genome Announcements	2016	4		e00668-16			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. 		
@D	Kergourlay, G.//Messaoudi, S.//Dousset, X.//Prevost, H. 	Genome Sequence of Lactobacillus salivarius SMXD51, a Potential Probiotic Strain  Isolated from Chicken Cecum, Showing Anti-Campylobacter Activity.	J. Bacteriol.	2012	194		3008-3009			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. 		
@D	Kern, T.//Fischer, M.A.//Deppenmeier, U.//Schmitz, R.A.//Rother, M. 	Methanosarcina flavescens sp. nov., a methanogenic archaeon isolated from a full-scale anaerobic digester.	Int. J. Syst. Evol. Microbiol.	2016	66		1533-1538			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)). 		
@D	Kerouanton, A.//Hirchaud, E.//Rose, V.//Esnault, E.//Naquin, D.//Denis, M. 	First Complete Genome Sequence of a Salmonella enterica subsp. enterica Serovar Derby Strain Associated with Pork in France.	Genome Announcements	2015	3		e00853-15			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. 		
@D	Kerr, A.L.//Jeon, Y.J.//Svenson, C.J.//Rogers, P.L.//Neilan, B.A. 	DNA restriction-modification systems in the ethanologen, Zymomonas mobilis ZM4.	Appl. Microbiol. Biotechnol.	2011	89		761-769			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. 		
@D	Kersulyte, D.//Bertoli, M.T.//Tamma, S.//Keelan, M.//Munday, R.//Geary, J.//Veldhuyzen-van-Zanten, S.//Goodman, K.J.//Berg, D.E. 	Complete Genome Sequences of Two Helicobacter pylori Strains from a Canadian Arctic Aboriginal Community.	Genome Announcements	2015	3		e00209-15			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. 		
@D	Kersulyte, D.//Mukhopadhyay, A.K.//Shirai, M.//Nakazawa, T.//Berg, D.E. 	Functional organization and insertion specificity of IS607, a chimeric element of Helicobacter pylori.	J. Bacteriol.	2000	182		5300-5308			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. 		
@D	Kerszman, G.//Glover, S.W.//Aronovitch, J. 	The restriction of bacteriophage lambda in Escherichia coli strain W.	J. Gen. Virol.	1967	1		333-347			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. 		
@D	Kerzhner, M.A.//Shiryaev, S.A.//Zheleznaya, L.A.//Matvienko, N.I. 	Site-specific endonuclease from thermophilic Bacillus species MK strain is isoschizomer of SalI.	Biokhimiia	1997	62		1029-1036			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. 		
@D	Kesel, S.//Moormann, F.//Gumperlein, I.//Mader, A.//Morikawa, M.//Lieleg, O.//Opitz, M. 	Draft Genome Sequence of the Biofilm-Producing Bacillus subtilis Strain B-1, Isolated from an Oil Field.	Genome Announcements	2014	2		e01163-14			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. 		
@D	Keshet, E.//Cedar, H. 	Effect of CpG methylation on MspI.	Nucleic Acids Res.	1983	11		3571-3580			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. 		
@D	Kesminiene, A.//Maneliene, Z.//Vitkute, J.//Petrusyte, M.//Janulaitis, A. 	FspAI, a unique type II restriction endonuclease that recognizes the octanucleotide sequence 5'-RTGC^GCAY-3'.	Nucleic Acids Res.	2001	29		e120			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. 		
@D	Kessler, C. 	Restriction enzymes.	Chemie in unserer Zeit	1988	22		37-49			None 		
@A	Kessler, C. 		Class II restriction endonucleases.			Obe, G.//Basler, A. 		Cytogenetics					Springer-Verlag	1987		0		225-279									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). 		
@D	Kessler, C.//Bolton, B.J.//Comer, M.J. 	Screening for novel Type II restriction endonucleases.	J. Cell Biochem. Suppl.	1986	10D		101			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. 		
@D	Kessler, C.//Holtke, H.J. 	Specificity of restriction endonucleases and methylases - a review (Edition 2).	Gene	1986	47		1-153			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. 		
@D	Kessler, C.//Manta, V. 	Specificity of restriction endonucleases and DNA modification methyltransferases - a review (Edition 3) .	Gene	1990	92		1-248			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. 		
@D	Kessler, C.//Nesch, G.//Brack, R. 	SphI restriction map of bacteriophage lambda DNA.	Gene	1981	16		321-323			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. 		
@D	Kessler, C.//Neumaier, P.S.//Wolf, W. 	Recognition sequences of restriction endonucleases and methylases - a review.	Gene	1985	33		1-102			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. 		
@D	Kessner, L.//Spinard, E.//Gomez-Chiarri, M.//Rowley, D.C.//Nelson, D.R. 	Draft Genome Sequence of Aliiroseovarius crassostreae CV919-312, the Causative Agent of Roseovarius Oyster Disease (Formerly Juvenile Oyster Disease).	Genome Announcements	2016	4		e00148-16			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. 		
@D	Ketter, P.//Guentzel, M.N.//Chambers, J.P.//Jorgensen, J.//Murray, C.K.//Cap, A.P.//Yu, J.J.//Eppinger, M.//Arulanandam, B.P. 	Genome Sequences of Four Acinetobacter baumannii-A. calcoaceticus Complex Isolates from Combat-Related Infections Sustained in the Middle East.	Genome Announcements	2014	2		e00026-14			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. 		
@D	Kettler, G.C.//Martiny, A.C.//Huang, K.//Zucker, J.//Coleman, M.L.//Rodrigue, S.//Chen, F.//Lapidus, A.//Ferriera, S.//Johnson, J.//Steglich, C.//Church, G.M.//Richardson, P.//Chisholm, S.W. 	Patterns and implications of gene gain and loss in the evolution of Prochlorococcus.	PLoS Genet.	2007	3		E231			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. 		
@D	Kettling, U.//Koltermann, A.//Schwille, P.//Eigen, M. 	Real-time enzyme kinetics monitored by dual-color fluorescence cross-correlation spectroscopy.	Proc. Natl. Acad. Sci. U. S. A.	1998	95		1416-1420			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. 		
@D	Ketyi, J.//Orskov, F. 	Host-controlled modification and restriction of foreign chromosomal and plasmid DNA in Shigella flexneri strains.	Acta Path. Microbiol. Scand.	1970	78		51-58			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. 		
@D	Key, T.A.//Richmond, D.P.//Bowman, K.S.//Cho, Y.J.//Chun, J.//da Costa, M.S.//Rainey, F.A.//Moe, W.M. 	Genome sequence of the organohalide-respiring Dehalogenimonas alkenigignens type  strain (IP3-3(T)).	Standards in Genomic Sciences	2016	11		44			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. 		
@D	Khadem, A.F. et al. 	Draft Genome Sequence of the Volcano-Inhabiting Thermoacidophilic Methanotroph Methylacidiphilum fumariolicum Strain SolV.	J. Bacteriol.	2012	194		3729-3730			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. 		
@D	Khajanchi, B.K.//Han, J.//Gokulan, K.//Zhao, S.//Gies, A.//Foley, S.L. 	Draft Genome Sequences of Four Salmonella enterica Strains Isolated from Turkey-Associated Sources.	Genome Announcements	2016	4		e01122-16			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. 		
@D	Khaleque, H.N.//Ramsay, J.P.//Murphy, R.J.//Kaksonen, A.H.//Boxall, N.J.//Watkin, E.L. 	Draft Genome Sequence of the Acidophilic, Halotolerant, and Iron/Sulfur-Oxidizing Acidihalobacter prosperus DSM 14174 (Strain V6).	Genome Announcements	2017	5		e01469-16			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. 		
@D	Khaleque, H.N.//Ramsay, J.P.//Murphy, R.J.T.//Kaksonen, A.H.//Boxall, N.J.//Watkin, E.L.J. 	Draft Genome Sequence of Acidihalobacter ferrooxidans DSM 14175 (Strain V8), a New Iron- and Sulfur-Oxidizing, Halotolerant, Acidophilic Species.	Genome Announcements	2017	5		e00413-17			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). 		
@D	Khalid, M.I.//Teh, L.K.//Lee, L.S.//Zakaria, Z.A.//Salleh, M.Z. 	Genome Sequence of Proteus mirabilis Strain PR03, Isolated from a Local Hospital  in Malaysia.	Genome Announcements	2013	1		e00327-13			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. 		
@D	Khalil, A.//Sivakumar, N.//Qarawi, S. 	Genome Sequence of Anoxybacillus flavithermus Strain AK1, a Thermophile Isolated  from a Hot Spring in Saudi Arabia.	Genome Announcements	2015	3		e00604-15			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. 		
@D	Khan, A.//Khan, H.//Chung, E.J.//Hossain, M.T.//Chung, Y.R. 	Complete Genome Sequence of Martelella endophytica YC6887, Which Has Antifungal Activity Associated with a Halophyte.	Genome Announcements	2015	3		e00366-15			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. 		
@D	Khan, A.A.//Khajanchi, B.K.//Khan, S.A.//Elkins, C.A.//Foley, S.L. 	Draft Genome Sequences of Ciprofloxacin-Resistant Salmonella enterica Strains with Multiple-Antibiotic Resistance, Isolated from Imported Foods.	Genome Announcements	2017	5		e01222-17			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. 		
@D	Khan, A.U.//Beg, A.Z.//Verma, P.K. 	Draft Genome Sequence of the First NDM-4-Producing Escherichia coli Strain (AK1), Isolated from Sewage Water of a North Indian Hospital.	Genome Announcements	2017	5		e01366-17			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%. 		
@D	Khan, F.//Furuta, Y.//Kawai, M.//Kaminska, K.H.//Ishikawa, K.//Bujnicki, J.M.//Kobayashi, I. 	A putative mobile genetic element carrying a novel type IIF restriction-modification system (PluTI).	Nucleic Acids Res.	2010	38		3019-3030			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. 		
@D	Khan, M.A.//Isaacson, R.E. 	Identification of Escherichia coli genes that are specifically expressed in a murine model of septicemic infection.	Infect. Immun.	2002	70		3404-3412			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. 		
@D	Khan, M.W.//Habibi, N.//Shaheed, F.//Mustafa, A.S. 	Draft Genome Sequences of Five Clinical Strains of Brucella melitensis Isolated from Patients Residing in Kuwait.	Genome Announcements	2016	4		e01144-16			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. 		
@D	Khan, S.//Sung, K.//Iram, S.//Nawaz, M.//Xu, J.//Marasa, B. 	Draft Genome Sequences of Two Methicillin-Resistant Clinical Staphylococcus aureus Isolates.	Genome Announcements	2016	4		e01396-15			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. 		
@D	Khan, S.//Sung, K.//Marasa, B.//Min, S.//Kweon, O.//Nawaz, M.//Cerniglia, C. 	Draft Genome Sequence of Multidrug-Resistant Enterococcus faecium Clinical Isolate VRE3, with a Sequence Type 16 Pattern and Novel Structural Arrangement of  Tn1546.	Genome Announcements	2015	3		e00871-15			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. 		
@D	Khanna, N. et al. 	Complete genome sequence of Enterobacter sp. IIT-BT 08: A potential microbial strain for high rate hydrogen production.	Standards in Genomic Sciences	2013	9		359-369			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. 		
@D	Khatri, I.//Dureja, C.//Raychaudhuri, S.//Subramanian, S. 	Draft Genome Sequence of the Opportunistic Human Pathogen Morganella morganii SC01.	Genome Announcements	2013	1		e00051-12			We report the 4.1-Mb draft genome sequence of Morganella morganii SC01, a gammaproteobacterium, isolated from an Indian human fecal sample. 		
@D	Khatri, I.//Kaur, S.//Devi, U.//Kumar, N.//Sharma, D.//Subramanian, S.//Saini, A.K. 	Draft Genome Sequence of Plant Growth-Promoting Rhizobacterium Pantoea sp. Strain AS-PWVM4.	Genome Announcements	2013	1		e00947-13			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. 		
@D	Khatri, I.//Nupur, K.S.//Subramanian, S.//Pinnaka, A.K. 	Draft Genome Sequence of Rhodovulum sp. Strain PH10, a Phototrophic Alphaproteobacterium Isolated from a Soil Sample of Mangrove of Namkhana, India.	J. Bacteriol.	2012	194		6363			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. 		
@D	Khatri, I.//Singh, A.//Korpole, S.//Pinnaka, A.K.//Subramanian, S. 	Draft Genome Sequence of an Alphaproteobacterium, Caenispirillum salinarum AK4(T), Isolated from a Solar Saltern.	Genome Announcements	2013	1		e00199-12			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. 		
@D	Khayi, S.//Blin, P.//Chong, T.M.//Chan, K.G.//Faure, D. 	Complete Chromosome and Plasmid Sequences of Two Plant Pathogens, Dickeya solani  Strains D s0432-1 and PPO 9019.	Genome Announcements	2018	6		e00233-18			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. 		
@D	Khayi, S.//Blin, P.//Chong, T.M.//Chan, K.G.//Faure, D. 	Complete genome anatomy of the emerging potato pathogen Dickeya solani type strain IPO 2222T.	Standards in Genomic Sciences	2016	11		87			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. 		
@D	Khayi, S.//Blin, P.//Chong, T.M.//Robic, K.//Chan, K.G.//Faure, D. 	Complete Genome Sequences of the Plant Pathogens Dickeya solani RNS 08.23.3.1.A and Dickeya dianthicola RNS04.9.	Genome Announcements	2018	6		e01447-17			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. 		
@D	Khayi, S.//Mondy, S.//Beury-Cirou, A.//Moumni, M.//Helias, V.//Faure, D. 	Genome Sequence of the Emerging Plant Pathogen Dickeya solani Strain RNS 08.23.3.1A.	Genome Announcements	2014	2		e01270-13			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. 		
@D	Khayi, S.//Raoul-des-Essarts, Y.//Mondy, S.//Moumni, M.//Helias, V.//Beury-Cirou, A.//Faure, D. 	Draft Genome Sequences of the Three Pectobacterium-Antagonistic Bacteria Pseudomonas brassicacearum PP1-210F and PA1G7 and Bacillus simplex BA2H3.	Genome Announcements	2015	3		e01497-14			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. 		
@D	Khayi, S.//Raoul-des-Essarts, Y.//Quetu-Laurent, A.//Moumni, M.//Helias, V.//Faure, D. 	Genomic overview of the phytopathogen Pectobacterium wasabiae strain RNS 08.42.1A suggests horizontal acquisition of quorum-sensing genes.	Genetica	2015	143		241-252			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. 		
@D	Khedkar, S.//Prabhakara, S.//Loganathan, R.M.//Chandana, S.//Gowda, M.//Arakere, G.//Seshasayee, A.S.N. 	Draft Genome Sequence of Staphylococcus aureus ST672, an Emerging Disease Clone from India.	J. Bacteriol.	2012	194		6946-6947			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. 		
@D	Khelaifia, S.//Garibal, M.//Robert, C.//Raoult, D.//Drancourt, M. 	Draft Genome Sequencing of Methanobrevibacter oralis Strain JMR01, Isolated from  the Human Intestinal Microbiota.	Genome Announcements	2014	2		e00073-14			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. 		
@D	Khelaifia, S.//Garibal, M.//Robert, C.//Raoult, D.//Drancourt, M. 	Draft Genome Sequence of a Human-Associated Isolate of Methanobrevibacter arboriphilicus, the Lowest-G+C-Content Archaeon.	Genome Announcements	2014	2		e01181-13			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. 		
@D	Khemayan, K.//Prachumwat, A.//Sonthayanon, B.//Intaraprasong, A.//Sriurairatana, S.//Flegel, T.W. 	Complete Genome Sequence of Virulence-Enhancing Siphophage VHS1 from Vibrio harveyi.	Appl. Environ. Microbiol.	2012	78		2790-2796			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. 		
@D	Khesin, R.B.//Bogdanova, E.S. 	The specificity of DNA-methylase in T2-phage infected E. coli B cells.	Biokhimiia	1966	31		405-415			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. 		
@D	Khetrapal, V.//Mehershahi, K.S.//Chen, S.L. 	Complete Genome Sequence of the Original Escherichia coli Isolate, Strain NCTC86.	Genome Announcements	2017	5		e00243-17			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. 		
@D	Khmaladze, E.//Dzavashvili, G.//Chanturia, G.//Nikolich, M.P.//Chain, P.S.G.//Johnson, S.L.//Imnadze, P. 	Ten Genome Sequences of Human and Livestock Isolates of Bacillus anthracis from the Country of Georgia.	Genome Announcements	2017	5		e00256-17			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. 		
@D	Khmelenina, V.N. et al. 	Draft Genome Sequence of Methylomicrobium buryatense Strain 5G, a Haloalkaline-Tolerant Methanotrophic Bacterium.	Genome Announcements	2013	1		e00053-13			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. 		
@D	Kho, M.R.//Baker, D.J.//Laayoun, A.//Smith, S.S. 	Stalling of human DNA (cytosine-5) methyltransferase at single-strand conformers from a site of dynamic mutation.	J. Mol. Biol.	1998	275		67-79			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. 		
@D	Kholmina, G.V.//Rebentish, B.A.//Kozlovskii, Y.-E.//Sorokin, A.V.//Goldenberg, D.S.//Prozorov, A.A. 	Purification and properties of two restriction endonucleases from Bacillus subtilis.	Mol. Gen. Mikrobiol. Virusol.	1986	0		23-25			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. 		
@D	Kholmina, G.V.//Rebentish, B.A.//Skoblov, Y.S.//Mironov, A.A.//Yankovskii, N.K.//Kozlov, Y.I.//Glatmann, L.I.//Moroz, A.F.//Debabov, V.G. 	Isolation and characterization of a new site-specific endonuclease, EcoRV.	Dokl. Akad. Nauk.	1980	253		495-497			None 		
@D	Kholodii, G. 	The shuffling function of resolvases.	Gene	2001	269		121-130			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. 		
@D	Khong, W.X. et al. 	Tracking inter-institutional spread of NDM and identification of a novel NDM-positive plasmid, pSg1-NDM, using next-generation sequencing approaches.	J. Antimicrob. Chemother.	2016	71		3081-3089			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. 		
@D	Khosaka, T.//Kiwaki, M. 	Restriction endonucleases from Bifidobacterium bifidum.	FEBS Lett.	1984	177		57-60			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. 		
@D	Khosaka, T.//Kiwaki, M. 	BinI: A new site-specific endonuclease from Bifidobacterium infantis.	Gene	1984	31		251-255			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. 		
@D	Khosaka, T.//Kiwaki, M.//Rak, B. 	Two site-specific endonucleases BinSI and BinSII from Bifidobacterium infantis.	FEBS Lett.	1983	163		170-174			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. 		
@D	Khosaka, T.//Sakurai, T.//Takahashi, H.//Saito, H. 	A new site-specific endonuclease BbeI from Bifidobacterium breve.	Gene	1982	17		117-122			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. 		
@D	Khosravi, Y.//Rehvathy, V.//Wee, W.Y.//Wang, S.//Baybayan, P.//Singh, S.//Ashby, M.//Ong, J.//Amoyo, A.A.//Seow, S.W.//Choo, S.W.//Perkins, T.//Chua, E.G.//Tay, A.//Marshall, B.J.//Loke, M.F.//Goh, K.L.//Pettersson, S.//Vadivelu, J. 	Comparing the genomes of Helicobacter pylori clinical strain UM032 and Mice-adapted derivatives.	Gut Pathog.	2013	5		25			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. 		
@D	Khudyakov, I.Y.//Kirnos, M.D.//Aleksandrushkina, N.I.//Vanyushin, B.F. 	2,6-Diaminopurine - a new adenine-replacing base in the DNA of cyanophage S-2.	Dokl. Akad. Nauk.	1977	232		965-968			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. 		
@D	Khudyakov, I.Y.//Kirnos, M.D.//Alexandrushkina, N.I.//Vanyushin, B.F. 	Cyanophage S-2L contains DNA with 2,6-diaminopurine substituted for adenine.	Virology	1978	88		8-18			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. 		
@D	Kiatpapan, P.//Murooka, Y. 	Genetic manipulation system in propionibacteria.	J. Biosci. Bioeng.	2002	93		1-8			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. 		
@D	Kibret, M.//Guerrero-Garzon, J.F.//Urban, E.//Zehl, M.//Wronski, V.K.//Ruckert, C.//Busche, T.//Kalinowski, J.//Rollinger, J.M.//Abate, D.//Zotchev, S.B. 	Streptomyces spp. From Ethiopia Producing Antimicrobial Compounds: Characterization via Bioassays, Genome Analyses, and Mass Spectrometry.	Front. Microbiol.	2018	9		1270			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. 		
@D	Kidane, D.T.//Arivett, B.A.//Crigler, J.//Vick, E.J.//Farone, A.L.//Farone, M.B. 	Draft Genome Sequence of Gardnerella vaginalis Strain ATCC 49145 Associated with  Bacterial Vaginosis.	Genome Announcements	2017	5		e00286-17			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). 		
@D	Kidanemariam, G.A.//Bihon, W.//Faranani, R.//Mafofo, J.//Rees, J.//Madoroba, E. 	Complete Genome Sequence of Mannheimia haemolytica Strain Mh10517, Isolated from  Sheep in South Africa.	Genome Announcements	2015	3		e00129-15			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. 		
@D	Kienesberger, S.//Sprenger, H.//Wolfgruber, S.//Halwachs, B.//Thallinger, G.G.//Perez-Perez, G.I.//Blaser, M.J.//Zechner, E.L.//Gorkiewicz, G. 	Comparative Genome Analysis of Campylobacter fetus Subspecies Revealed Horizontally Acquired Genetic Elements Important for Virulence and Niche Specificity.	PLoS ONE	2014	9		E85491			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. 		
@D	Kieser, T.//Hopwood, D.A. 	Genetic manipulation of Streptomyces: integrating vectors and gene replacement.	Methods Enzymol.	1991	204		430-458			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. 		
@D	Kilgore, J.A.//Hoose, S.A.//Gustafson, T.L.//Porter, W.//Kladde, M.P. 	Single-molecule and population probing of chromatin structure using DNA methyltransferases.	Methods	2007	41		320-332			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. 		
@D	Kim, A.//Nguyen, T.L.//Kim, D.H. 	Complete Genome Sequence of the Virulent Aeromonas salmonicida subsp. masoucida Strain RFAS1.	Genome Announcements	2018	6		e00470-18			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. 		
@D	Kim, B.//Kim, J.//Park, H.//Park, J. 	Draft Genome Sequence of Toluene-Resistant Staphylococcus epidermidis SNUT.	Genome Announcements	2016	4		e00057-16			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. 		
@D	Kim, B.-J.//Choi, B.S.//Lim, J.S.//Choi, I.Y.//Lee, J.H.//Chun, J.//Kook, Y.H.//Kim, B.J. 	Complete Genome Sequence of Mycobacterium intracellulare Strain ATCC 13950T.	J. Bacteriol.	2012	194		2750			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. 		
@D	Kim, B.C.//Jeong, H. 	Complete Genome Sequence of Methanobrevibacter smithii Strain KB11, Isolated from a Korean Fecal Sample.	Genome Announcements	2018	6		e00038-18			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). 		
@D	Kim, B.J.//Choi, B.S.//Choi, I.Y.//Lee, J.H.//Chun, J.//Hong, S.H.//Kook, Y.H.//Kim, B.J. 	Complete Genome Sequence of Mycobacterium intracellulare Clinical Strain MOTT-36Y, Belonging to the INT5 Genotype.	J. Bacteriol.	2012	194		4141-4142			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. 		
@D	Kim, B.J.//Choi, B.S.//Lim, J.S.//Choi, I.Y.//Kook, Y.H.//Kim, B.J. 	Complete Genome Sequence of Mycobacterium intracellulare Clinical Strain MOTT-64, Belonging to the INT1 Genotype.	J. Bacteriol.	2012	194		3268			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. 		
@D	Kim, B.J.//Choi, B.S.//Lim, J.S.//Choi, I.Y.//Lee, J.H.//Chun, J.//Kook, Y.H.//Kim, B.J. 	Complete Genome Sequence of Mycobacterium intracellulare Clinical Strain MOTT-02.	J. Bacteriol.	2012	194		2771			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. 		
@D	Kim, B.J.//Kim, B.R.//Hong, S.H.//Seok, S.H.//Kook, Y.H.//Kim, B.J. 	Complete Genome Sequence of Mycobacterium massiliense Clinical Strain Asan 50594, Belonging to the Type II Genotype.	Genome Announcements	2013	1		e00429-13			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. 		
@D	Kim, B.J.//Kim, B.R.//Lee, S.Y.//Seok, S.H.//Kook, Y.H.//Kim, B.J. 	Whole-Genome Sequence of a Novel Species, Mycobacterium yongonense DSM 45126T.	Genome Announcements	2013	1		e00604-13			Here, we report the complete genome sequence of Mycobacterium yongonense DSM 45126(T), genetically closely related to the INT5 genotype of M. intracellulare. 		
@D	Kim, B.K.//Chung, J.H.//Kim, S.Y.//Jeong, H.//Kang, S.G.//Kwon, S.K.//Lee, C.H.//Song, J.Y.//Yu, D.S.//Ryu, C.M.//Kim, J.F. 	Genome Sequence of the Leaf-Colonizing Bacterium Bacillus sp. Strain 5B6, Isolated from a Cherry Tree.	J. Bacteriol.	2012	194		3758-3759			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. 		
@D	Kim, B.K.//Jung, M.Y.//Yu, D.S.//Park, S.J.//Oh, T.K.//Rhee, S.K.//Kim, J.F. 	Genome Sequence of an Ammonia-Oxidizing Soil Archaeon, 'Candidatus Nitrosoarchaeum koreensis' MY1.	J. Bacteriol.	2011	193		5539-5540			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. 		
@D	Kim, B.K.//Lee, S.H.//Kim, S.Y.//Jeong, H.//Kwon, S.K.//Lee, C.H.//Song, J.Y.//Yu, D.S.//Kang, S.G.//Kim, J.F. 	Genome Sequence of an Oligohaline Hyperthermophilic Archaeon, Thermococcus zilligii AN1, Isolated from a Terrestrial Geothermal Freshwater Spring.	J. Bacteriol.	2012	194		3765-3766			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. 		
@D	Kim, B.K.//Song, G.C.//Hong, G.H.//Seong, W.K.//Kim, S.Y.//Jeong, H.//Kang, S.G.//Kwon, S.K.//Lee, C.H.//Song, J.Y.//Yu, D.S.//Park, M.S.//Cho, S.H.//Kim, J.F. 	Genome Sequence of the Shiga Toxin-Producing Escherichia coli Strain NCCP15657.	J. Bacteriol.	2012	194		3751-3752			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. 		
@D	Kim, B.S.//Kim, C.T.//Park, B.H.//Kwon, S.//Cho, Y.J.//Kim, N.//Kim, C.J.//Chun, J.//Kwak, J.//Maeng, J.S. 	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.	J. Bacteriol.	2012	194		4441-4442			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). 		
@D	Kim, B.Y.//Kwon, O.S.//Joo, S.A.//Park, J.A.//Heo, K.Y.//Kim, M.S.//Ahn, J.S. 	A column method for determination of DNA cytosine-C-5-methyltransferase activity.	Anal. Biochem.	2004	326		21-24			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. 		
@D	Kim, B.Y.//Lee, S.Y.//Ahn, J.H.//Song, J.//Kim, W.G.//Weon, H.Y. 	Complete Genome Sequence of Bacillus amyloliquefaciens subsp. plantarum CC178, a  Phyllosphere Bacterium Antagonistic to Plant Pathogenic Fungi.	Genome Announcements	2015	3		e01368-14			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. 		
@D	Kim, C.T.//Kim, B.S.//Kim, M.J.//Park, B.H.//Kwon, S.//Maeng, H.Y.//Kwak, J.//Chun, J.//Cho, Y.J.//Kim, N.//Kim, C.J.//Maeng, J.S. 	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.	J. Bacteriol.	2012	194		7003-7004			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). 		
@D	Kim, D.-S.//Jung, M.Y.//Sin, Y.//Kim, D.W.//Paek, J.//Kim, R.N.//Park, I.S.//Kook, J.K.//Nam, S.H.//Kim, A.//Kang, A.//Park, H.S.//Choi, S.H.//Chang, Y.H. 	Genome Sequence of the Anaerobic Bacterium Clostridium arbusti SL206T.	J. Bacteriol.	2012	194		2758			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. 		
@D	Kim, D.H.//Jiang, S.//Lee, J.H.//Cho, Y.J.//Chun, J.//Choi, S.H.//Park, H.S.//Hur, H.G. 	Draft Genome Sequence of Shewanella sp. Strain HN-41, Which Produces Arsenic-Sulfide Nanotubes.	J. Bacteriol.	2011	193		5039-5040			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. 		
@D	Kim, D.S.//Choi, S.H.//Kim, D.W.//Kim, R.N.//Nam, S.H.//Kang, A.//Kim, A.//Park, H.S. 	Genome Sequence of Lactobacillus cypricasei KCTC 13900.	J. Bacteriol.	2011	193		5053-5054			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. 		
@D	Kim, D.S.//Choi, S.H.//Kim, D.W.//Kim, R.N.//Nam, S.H.//Kang, A.//Kim, A.//Park, H.S. 	Genome Sequence of Leuconostoc gelidum KCTC 3527 Isolated from Kimchi.	J. Bacteriol.	2010	193		799-800			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. 		
@D	Kim, D.S.//Choi, S.H.//Kim, D.W.//Kim, R.N.//Nam, S.H.//Kang, A.//Kim, A.//Park, H.S. 	Genome Sequence of Lactobacillus versmoldensis KCTC 3814.	J. Bacteriol.	2011	193		5589-5590			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. 		
@D	Kim, D.S.//Choi, S.H.//Kim, D.W.//Kim, R.N.//Nam, S.H.//Kang, A.//Kim, A.//Park, H.S. 	Genome Sequence of Leuconostoc inhae KCTC 3774 Isolated from Kimchi.	J. Bacteriol.	2010	193		1278-1279			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. 		
@D	Kim, D.S.//Choi, S.H.//Kim, D.W.//Nam, S.H.//Kim, R.N.//Kang, A.//Kim, A.//Park, H.S. 	Genome Sequence of Weissella cibaria KACC 11862.	J. Bacteriol.	2010	193		797-798			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). 		
@D	Kim, D.S.//Jung, M.Y.//Kang, A.//Cho, J.//Sin, Y.//Paek, J.//Kim, D.W.//Kim, R.N.//Nam, S.H.//Kim, A.//Park, H.S.//Choi, S.H.//Chang, Y.H. 	Genome Sequence of Peptoniphilus rhinitidis 1-13T, an Anaerobic Coccus Strain Isolated from Clinical Specimens.	J. Bacteriol.	2012	194		2405-2406			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. 		
@D	Kim, D.S.//Kang, Y.K.//Yoo, O.J. 	Effects of base analog substitutions in the sequence, CCGG, on the cleavage and methylation reactions of HpaII and MspI endonucleases and their cognate methylases.	Biochem. Mol. Biol. Int.	1994	32		507-514			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. 		
@D	Kim, D.S.//Paek, J.//Shin, J.H.//Kim, D.W.//Jung, M.Y.//Kim, R.N.//Sin, Y.//Kook, J.K.//Nam, S.H.//Kim, A.//Kang, A.//Park, H.S.//Choi, S.H.//Chang, Y.H. 	Genome Sequence of Myroides injenensis M09-0166T, Isolated from Clinical Specimens.	J. Bacteriol.	2012	194		2748-2749			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. 		
@D	Kim, D.S.//Sin, Y.//Kim, D.W.//Paek, J.//Kim, R.N.//Jung, M.Y.//Park, I.S.//Kim, A.//Kang, A.//Park, H.S.//Choi, S.H.//Chang, Y.H. 	Genome Sequence of the Probiotic Bacterium Sporolactobacillus vineae SL153T.	J. Bacteriol.	2012	194		3015-3016			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. 		
@D	Kim, D.W.//Choi, S.H.//Kang, A.//Nam, S.H.//Kim, D.S.//Kim, R.N.//Kim, A.//Park, H.S. 	Draft Genome Sequence of Lactobacillus mali KCTC 3596.	J. Bacteriol.	2011	193		5037			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). 		
@D	Kim, D.W.//Choi, S.H.//Kang, A.//Nam, S.H.//Kim, D.S.//Kim, R.N.//Kim, A.//Park, H.S. 	Draft Genome Sequence of Lactobacillus zeae KCTC 3804.	J. Bacteriol.	2011	193		5023			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). 		
@D	Kim, D.W.//Choi, S.H.//Kang, A.//Nam, S.H.//Kim, D.S.//Kim, R.N.//Kim, A.//Park, H.S. 	Draft Genome Sequence of Lactobacillus malefermentans KCTC 3548.	J. Bacteriol.	2011	193		5537			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). 		
@D	Kim, D.W.//Choi, S.H.//Kang, A.//Nam, S.H.//Kim, R.N.//Kim, A.//Kim, D.S.//Park, H.S. 	Genome Sequence of Leuconostoc pseudomesenteroides KCTC 3652.	J. Bacteriol.	2011	193		4299			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). 		
@D	Kim, E.//Kim, J.H.//Park, S.B.//Kim, M.J.//Kim, H.J.//Kim, C.G.//Choo, D.W.//Kim, H.Y. 	Draft Genome Sequence of Pediococcus pentosaceus Strain FBL2, a Probiotic Bacterium Isolated from Jogaejeot, a Salted Fermented Food, in the Republic of  Korea.	Genome Announcements	2017	5		e00303-17			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%. 		
@D	Kim, E.//Kim, J.H.//Yang, S.M.//Suh, S.M.//Kim, H.J.//Kim, C.G.//Choo, D.W.//Kim, H.Y. 	Draft Genome Sequence of Tetragenococcus halophilus Strain FBL3, a Probiotic Bacterium Isolated from Galchijeot, a Salted Fermented Food, in the Republic of  Korea.	Genome Announcements	2017	5		e00304-17			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%. 		
@D	Kim, E.B.//Jin, G.D.//Lee, J.Y.//Choi, Y.J. 	Draft Genome Sequence of Lactobacillus plantarum Strain SNU.Lp177 from Pig Feces  in South Korea.	Genome Announcements	2015	3		e01184-15			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). 		
@D	Kim, E.B.//Tyler, C.A.//Kopit, L.M.//Marco, M.L. 	Draft Genome Sequence of Fructophilic Lactobacillus florum.	Genome Announcements	2013	1		e00025-12			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). 		
@D	Kim, E.K.//Kim, S.H.//Nam, H.J.//Choi, M.K.//Lee, K.A.//Choi, S.H.//Seo, Y.Y.//You, H.//Kim, B.//Lee, W.J. 	Draft Genome Sequence of Gluconobacter morbifer G707T, a Pathogenic Gut Bacterium Isolated from Drosophila melanogaster Intestine.	J. Bacteriol.	2012	194		1245			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. 		
@D	Kim, E.K.//Kim, S.H.//Nam, H.J.//Choi, M.K.//Lee, K.A.//Choi, S.H.//Seo, Y.Y.//You, H.//Kim, B.//Lee, W.J. 	Draft Genome Sequence of Commensalibacter intestini A911T, a Symbiotic Bacterium  Isolated from Drosophila melanogaster Intestine.	J. Bacteriol.	2012	194		1246			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). 		
@D	Kim, E.K.//Park, Y.M.//Lee, O.Y.//Lee, W.J. 	Draft Genome Sequence of Lactobacillus plantarum Strain WJL, a Drosophila Gut Symbiont.	Genome Announcements	2013	1		e00937-13			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. 		
@D	Kim, E.L.//Makhovich, O.P.//Maliuta, S.S. 	Some differences between BamHI and BnaI, the restrictases with the same specificity.	Biopol. Kletka	1989	5		86-89			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. 		
@D	Kim, E.L.//Maliuta, S.S. 	A new isoschizomer, BnaI, of the BamHI restriction endonuclease.	Gene	1989	80		363-368			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. 		
@D	Kim, E.L.//Maliuta, S.S. 	Purification of a DNA methyltransferase from Bacillus natto B3364.	FEBS Lett.	1989	255		361-364			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. 		
@D	Kim, E.L.//Malyuta, S.S. 	BnaI a new isoshisomer of the restrictase BamHI.	Biotekhnologiya	1986	4		24-27			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. 		
@D	Kim, E.M.//Hwang, K.H.//Park, J.S. 	Complete Genome Sequence of Chryseobacterium camelliae Dolsongi-HT1, a Green Tea  Isolate with Keratinolytic Activity.	Genome Announcements	2018	6		e01421-17			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. 		
@D	Kim, G.-D.//Ni, J.//Kelesoglu, N.//Roberts, R.J.//Pradhan, S. 	Co-operation and communication between the human maintenance and de novo DNA (cytosine-5) methyltransferases.	EMBO J.	2002	21		4183-4195			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. 		
@D	Kim, H.//Jeong, W.//Jeoung, H.Y.//Song, J.Y.//Kim, J.S.//Beak, J.H.//Parisutham, V.//Lee, S.K.//Kim, J.W.//Kim, J.Y.//Jung, S.C.//Her, M.//An, D.J. 	Complete Genome Sequence of Brucella abortus A13334, a New Strain Isolated from the Fetal Gastric Fluid of Dairy Cattle.	J. Bacteriol.	2012	194		5444			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. 		
@D	Kim, H.H.//Corina, L.E.//Suh, J.K.//Herrin, D.L. 	Expression, purification, and biochemical characterization of the intron-encoded endonuclease, I-CreII.	Protein Expr. Purif.	2005	44		162-172			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. 		
@D	Kim, H.J.//Karki, S.//Kwon, S.Y.//Park, S.H.//Nahm, B.H.//Kim, Y.K.//Kwon, H.J. 	A single module type I polyketide synthase directs de novo macrolactone biogenesis during galbonolide biosynthesis in Streptomyces galbus.	J. Biol. Chem.	2014	289		34557-34568			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. 		
@D	Kim, H.J.//Kim, J.H.//Jun, J.W.//Giri, S.S.//Chi, C.//Yun, S.//Kim, S.G.//Kim, S.W.//Kang, J.W.//Jeong, D.G.//Park, S.C. 	Complete Genome Sequence of Vibrio coralliilyticus 58, Isolated from Pacific Oyster (Crassostrea gigas) Larvae.	Genome Announcements	2017	5		e00437-17			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. 		
@D	Kim, H.J.//Lee, J.H.//Kang, B.R.//Rong, X.//McSpadden, G.B.B.//Ji, H.J.//Park, C.S.//Kim, Y.C. 	Draft Genome Sequence of Pantoea ananatis B1-9, a Nonpathogenic Plant Growth-Promoting Bacterium.	J. Bacteriol.	2012	194		729			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. 		
@D	Kim, H.J.//Park, J.Y.//Han, S.H.//Lee, J.H.//Rong, X.//McSpadden, G.B.B.//Park, S.K.//Kim, Y.C. 	Draft Genome Sequence of the Biocontrol Bacterium Chromobacterium sp. Strain C-61.	J. Bacteriol.	2011	193		6803-6804			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. 		
@D	Kim, H.J.//Yano, A.//Wada, Y.//Sano, H. 	Properties of a tobacco DNA methyltransferase, NtMET1 and its involvement in chromatin movement during cell division.	Ann. Bot.	2007	99		845-856			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. 		
@D	Kim, H.S.//Cha, S.H.//Suk, H.Y.//Kwon, T.H.//Woo, J.H. 	Complete Genome Sequence of Indigo-Producing Bacterium Celeribacter sp. Strain TSPH2.	Genome Announcements	2017	5		e01124-17			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. 		
@D	Kim, H.S.//Cha, S.H.//Suk, H.Y.//Park, N.H.//Woo, J.H. 	Complete Genome Sequence of Sphingorhabdus sp. YGSMI21, Exhibiting High Enantioselective Epoxide Hydrolase Activity.	Genome Announcements	2018	6		e01441-17			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). 		
@D	Kim, J.//Jung, J.//Sung, J.S.//Chun, J.//Park, W. 	Genome Sequence of Pectin-Degrading Alishewanella agri, Isolated from Landfill Soil.	J. Bacteriol.	2012	194		5135-5136			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. 		
@D	Kim, J.//Kim, S.J.//Kim, S.H.//Kim, S.I.//Moon, Y.J.//Park, S.J.//Kahng, H.Y.//Chung, Y.H. 	Draft Genome Sequence of Sphingopyxis sp. Strain MWB1, a Crude-Oil-Degrading Marine Bacterium.	Genome Announcements	2014	2		e01256-14			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%. 		
@D	Kim, J.//Kim, S.J.//Kim, S.H.//Moon, Y.J.//Park, S.J.//Kim, S.I.//Kahng, H.Y.//Chung, Y.H. 	Genome Sequence of Arthrobacter sp. MWB30, Isolated from a Crude Oil-Contaminated Seashore.	Genome Announcements	2015	3		e00013-15			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. 		
@D	Kim, J.//Kwon, K.K.//Kim, B.K.//Hong, S.G.//Oh, H.M. 	Genome Sequence of Deinococcus marmoris PAMC 26562 Isolated from Antarctic Lichen.	Genome Announcements	2017	5		e00013-17			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. 		
@D	Kim, J.//Lindsey, R.L.//Garcia-Toledo, L.//Loparev, V.N.//Rowe, L.A.//Batra, D.//Juieng, P.//Stoneburg, D.//Martin, H.//Knipe, K.//Smith, P.//Strockbine, N. 	High-Quality Whole-Genome Sequences for 59 Historical Shigella Strains Generated  with PacBio Sequencing.	Genome Announcements	2018	6		e00282-18			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. 		
@D	Kim, J.//Roh, S.W.//Bae, J.W. 	Draft Genome Sequence of Dietzia alimentaria 72T, Belonging to the Family Dietziaceae, Isolated from a Traditional Korean Food.	J. Bacteriol.	2011	193		6791			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%. 		
@D	Kim, J.//Thorp, H.H. 	Footprinting of cytosine-5--methyltransferase by Pt2(pop)44-.	ACS Abstracts	1996	212		A290			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. 		
@D	Kim, J.-S.//DeGiovanni, A.//Jancarik, J.//Adams, P.D.//Yokota, H.//Kim, R.//Kim, S.-H. 	Crystal structure of DNA sequence specificity subunit of a type I restriction-modification enzyme and its functional implications.	Proc. Natl. Acad. Sci. U. S. A.	2005	102		3248-3253			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. 		
@D	Kim, J.F.//Jeong, H.//Lee, J.S.//Choi, S.H.//Ha, M.//Hur, C.G.//Kim, J.S.//Lee, S.//Park, H.S.//Park, Y.H.//Oh, T.K. 	The Complete Genome Sequence of Leuconostoc citreum KM20.	J. Bacteriol.	2008	190		3093-3094			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. 		
@D	Kim, J.F.//Jeong, H.//Park, S.Y.//Kim, S.B.//Park, Y.K.//Choi, S.K.//Ryu, C.M.//Hur, C.G.//Ghim, S.Y.//Oh, T.K.//Kim, J.J.//Park, C.S.//Park, S.H. 	Genome Sequence of the Polymyxin-Producing Plant-Probiotic Rhizobacterium Paenibacillus polymyxa E681.	J. Bacteriol.	2010	192		6103-6104			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. 		
@D	Kim, J.F.//Jeong, H.//Yu, D.S.//Choi, S.H.//Hur, C.G.//Park, M.S.//Yoon, S.H.//Kim, D.W.//Ji, G.E.//Park, H.S.//Oh, T.K. 	Genome sequence of the probiotic bacterium Bifidobacterium animalis subsp. lactis AD011.	J. Bacteriol.	2009	191		678-679			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. 		
@D	Kim, J.H.//Boo, Y.B.//Lee, K.Y. 	Preparation of restriction endonuclease-AluI from Arthrobacter Luteus.	Korean J. Biochem.	1985	17		149-154			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. 		
@D	Kim, J.H.//Kang, D.H. 	Draft Genome Sequence of Leptolyngbya sp. KIOST-1, a Filamentous Cyanobacterium with Biotechnological Potential for Alimentary Purposes.	Genome Announcements	2016	4		e00984-16			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. 		
@D	Kim, J.H.//Kang, D.H.//Park, S.C. 	Draft Genome Sequence of Human-Pathogenic Lactococcus garvieae LG-ilsanpaik-gs201105 That Caused Acute Acalculous Cholecystitis.	Genome Announcements	2015	3		e00464-15			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. 		
@D	Kim, J.H.//Kim, E.//Kim, C.G.//Choo, D.W.//Kim, H.Y. 	Draft Genome Sequence of Lactobacillus sakei Strain FBL1, a Probiotic Bacterium Isolated from Mukeunji, a Long-Fermented Kimchi, in South Korea.	Genome Announcements	2016	4		e00365-16			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%. 		
@D	Kim, J.J.//Koh, S.//Kim, J.S.//Lee, D.-S. 	Mode of action on EcoRI restriction endonuclease: EcoRI and EcoRI variant N199H have active monomeric forms.	J. Biochem. Mol. Biol.	1998	31		149-155			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. 		
@D	Kim, J.J.//Min, K.T.//Kim, M.H.//Augh, S.J.//Kim, B.-D.//Lee, D.-S. 	EcoRI variant N199H has enhanced specific activity.	Gene	1996	171		129-130			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. 		
@D	Kim, J.K.//Samaranayake, M.//Pradhan, S. 	Epigenetic mechanisms in mammals.	Cell. Mol. Life Sci.	2009	66		596-612			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. 		
@D	Kim, J.S.//Jeong, W.//Jeoung, H.Y.//Song, J.Y.//Kim, H.//Beak, J.H.//Parisutham, V.//Lee, S.K.//Kim, J.W.//Kim, J.Y.//Jung, S.C.//Her, M.//An, D.J. 	Complete Genome Sequence of Brucella canis Strain HSK A52141, Isolated from the Blood of an Infected Dog.	J. Bacteriol.	2012	194		5134			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. 		
@D	Kim, J.S.//Kim, J.//Jeon, S.-E.//Kim, S.-J.//Kim, N.-O.//Hong, S.//Kang, Y.-H.//Han, S.//Chung, G.T. 	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.	Int. J. Antimicrob. Agents	2014	44		533-537			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. 		
@D	Kim, J.S.//Li, J.//Barnes, I.H.A.//Thompson, S.A. 	Cj1461 DNA methyltransferase in Campylobacter jejuni 81-176 is involved in the regulation of virulence characteristics and bacterial cellular functions.	Zoonoses Public Health	2007	54		103			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. 		
@D	Kim, J.S.//Li, J.Q.//Barnes, I.H.A.//Baltzegar, D.A.//Pajaniappan, M.//Cullen, T.W.//Trent, M.S.//Burns, C.M.//Thompson, S.A. 	Role of the Campylobacter jejuni cj1461 DNA methyltransferase in regulating virulence characteristics.	J. Bacteriol.	2008	190		6524-6529			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. 		
@D	Kim, J.W.//Dutta, V.//Elhanafi, D.//Lee, S.//Osborne, J.A.//Kathariou, S. 	A Novel Restriction-Modification System Is Responsible for Temperature-Dependent Phage Resistance in Listeria monocytogenes ECII.	Appl. Environ. Microbiol.	2012	78		1995-2004			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. 		
@D	Kim, J.W.//Yoo, J.I.//Kang, G.S.//Lee, Y.S.//Yu, J.Y.//Park, C.//Kim, I.H. 	Draft Genome Sequences of Vancomycin-Intermediate Staphylococcus aureus Strains in South Korea.	Genome Announcements	2016	4		e00027-16			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. 		
@D	Kim, J.Y.//Wang, Y.//Park, M.S.//Ji, G.E. 	Improvement of Transformation Efficiency Through In Vitro Methylation and SacII Site Mutation of Plasmid Vector in Bifidobacterium longum MG1.	J. Microbiol. Biotechnol.	2010	20		1022-1026			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. 		
@D	Kim, K.//Kwon, S.K.//Yoon, J.H.//Kim, J.F. 	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).	Genome Announcements	2016	4		e00804-16			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. 		
@D	Kim, K.K.//Lee, K.C.//Jeong, H.//Stevens, D.A.//Lee, J.S. 	Draft Genome Sequence of the Human Pathogen Halomonas stevensii S18214T.	J. Bacteriol.	2012	194		5143			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. 		
@D	Kim, K.K.//Lee, K.C.//Lee, J.S. 	Draft Genome Sequence of the Extremely Halophilic Archaeon Halogranum salarium B-1T.	J. Bacteriol.	2012	194		6659			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. 		
@D	Kim, M.//Kim, S.//Ryu, S. 	Complete Genome Sequence of Bacteriophage SSU5 Specific for Salmonella enterica serovar Typhimurium Rough Strains.	J. Virol.	2012	86		10894			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. 		
@D	Kim, M.//Ryu, S. 	Antirepression System Associated with the Life Cycle Switch in the Temperate Podoviridae Phage SPC32H.	J. Virol.	2013	87		11775-11786			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. 		
@D	Kim, M.//Yi, H.//Cho, Y.J.//Jang, J.//Hur, H.G.//Chun, J. 	Draft Genome Sequence of Escherichia coli W26, an Enteric Strain Isolated from Cow Feces.	J. Bacteriol.	2012	194		5149-5150			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. 		
@D	Kim, M.J.//Ku, S.//Kim, S.Y.//Lee, H.H.//Jin, H.//Kang, S.//Li, R.//Johnston, T.V.//Park, M.S.//Ji, G.E. 	Safety Evaluations of Bifidobacterium bifidum BGN4 and Bifidobacterium longum BORI.	Int. J. Mol. Sci.	2018	19		E1422			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. 		
@D	Kim, M.S.//Whon, T.W.//Roh, S.W.//Shin, N.R.//Bae, J.W. 	Draft Genome Sequence of Bacteroides faecis MAJ27T, a Strain Isolated from Human Feces.	J. Bacteriol.	2011	193		6801-6802			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. 		
@D	Kim, N.//Jang, Y.//Kim, J.K.//Ryoo, S.//Kwon, K.H.//Kang, S.S.//Byeon, H.S.//Lee, H.S.//Lim, Y.H.//Kim, J.M. 	Complete Genome Sequence of Mycobacterium bovis Clinical Strain 1595, Isolated from the Laryngopharyngeal Lymph Node of South Korean Cattle.	Genome Announcements	2015	3		e01124-15			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. 		
@D	Kim, N.//Jang, Y.//Park, S.Y.//Song, W.S.//Kim, J.T.//Lee, H.S.//Lim, Y.H.//Kim, J.M. 	Whole-Genome Sequence of Mycobacterium bovis W-1171, Isolated from the Laryngopharyngeal Lymph Node of a Wild Boar in South Korea.	Genome Announcements	2015	3		e01464-15			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. 		
@D	Kim, R.//Modrich, P.//Kim, S.-H. 	Interactive recognition in EcoRI restriction enzyme-DNA complex.	Nucleic Acids Res.	1984	12		7285-7292			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. 		
@D	Kim, S.C.//Podhajska, A.J.//Szybalski, W. 	Cleaving DNA at any predetermined site with adapter-primers and class-IIS restriction enzymes.	Science	1988	240		504-506			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. 		
@D	Kim, S.C.//Posfai, G.//Szybalski, W. 	A novel gene-fusing vector: construction of a 5'-GGmCC-specific chimeric methyltransferase, M.BspRI/M.BsuRI.	Gene	1991	100		45-50			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. 		
@D	Kim, S.C.//Skowron, P.M.//Szybalski, W. 	Structural requirements for FokI-DNA interaction and oligodeoxyribonucleotide- instructed cleavage.	J. Mol. Biol.	1996	258		638-649			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. 		
@D	Kim, S.J.//Park, S.J.//Kim, J.G.//Jung, M.Y.//Gwak, J.H.//Rhee, S.K. 	Draft Genome Sequence of 'Candidatus Izimaplasma sp.' Strain ZiA1, Obtained from  a Toluene-Degrading and Iron-Reducing Enrichment Culture.	Microbiol. Resour. Announc.	2018	7		e00861-18			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. 		
@D	Kim, S.J.//Shin, S.C.//Hong, S.G.//Lee, Y.M.//Choi, I.G.//Park, H. 	Genome sequence of a novel member of the genus psychrobacter isolated from antarctic soil.	J. Bacteriol.	2012	194		2403			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. 		
@D	Kim, S.J.//Shin, S.C.//Hong, S.G.//Lee, Y.M.//Lee, H.//Lee, J.//Choi, I.G.//Park, H. 	Genome Sequence of Janthinobacterium sp. Strain PAMC 25724, Isolated from Alpine  Glacier Cryoconite.	J. Bacteriol.	2012	194		2096			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. 		
@D	Kim, S.K.//Chung, W.H.//Kim, S.H.//Jung, K.H.//Kim, N.//Chai, Y.G. 	Complete Genome Sequence of Bacillus anthracis HYU01, Isolated from Soil Samples  in the Korean Peninsula.	Genome Announcements	2014	2		e00769-14			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. 		
@D	Kim, S.M.//Cho, S.J.//Lee, S.B. 	Genome Sequence of the Unclassified Marine Gammaproteobacterium BDW918.	J. Bacteriol.	2012	194		3753-3754			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. 		
@D	Kim, S.W.//Haley, B.J.//Roberson, D.//Allard, M.//Hammack, T.S.//Brown, E.W.//Van Kessel, J.A. 	Genome Sequences of Four Nonhuman/Nonclinical Salmonella enterica Serovar Kentucky ST198 Isolates Recovered between 1972 and 1973.	Genome Announcements	2017	5		e01699-16			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. 		
@D	Kim, S.W.//Karns, J.S.//Van Kessel, J.A.S.//Haley, B.J. 	Genome Sequences of 30 Escherichia coli O157:H7 Isolates Recovered from a Single  Dairy Farm and Its Associated Off-Site Heifer-Raising Facility.	Genome Announcements	2017	5		e00814-17			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. 		
@D	Kim, S.W.//Karns, J.S.//Van Kessel, J.A.S.//Haley, B.J. 	Genome Sequences of Five Multidrug-Resistant Escherichia coli Sequence Type 117 Isolates Recovered from Dairy Calves.	Genome Announcements	2017	5		e00732-17			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. 		
@D	Kim, S.Y.//Hwang, S.M.//Chang, K.S. 	Correlation between Sau1 restriction and modification complex type and coagulase serotype or SCCmec type of Staphylococcus aureus.	J. Bacteriol. Virol.	2010	40		163-170			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. 		
@D	Kim, U.Y.//Jon, S.C.//Ra, S.R. 	Optimal culture condition of restriction endonuclease Bci528I producing strain by QE method.	Choson Minjujuui Inmin Konghwaguk Kwahagwon Tongbo	2008	97		42-43			In this paper we determine optimal culture condition of Bacillus circulans 528 on production of a new restriction endonuclease Bci528I by QE method. 		
@D	Kim, W.J.//Kim, Y.O.//Kim, D.G.//Nam, B.H.//Kong, H.J.//Jung, H.//Lee, S.J.//Kim, D.W.//Kim, D.S.//Chae, S.H. 	Genome Sequence of Marine Bacterium Idiomarina sp. Strain 28-8, Isolated from Korean Ark Shells.	Genome Announcements	2013	1		e00772-13			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. 		
@D	Kim, W.J.//Kim, Y.O.//Kim, D.S.//Choi, S.H.//Kim, D.W.//Lee, J.S.//Kong, H.J.//Nam, B.H.//Kim, B.S.//Lee, S.J.//Park, H.S.//Chae, S.H. 	Draft Genome Sequence of Kocuria rhizophila P7-4.	J. Bacteriol.	2011	193		4286-4287			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. 		
@D	Kim, Y.//Blasche, S.//Patil, K.R. 	Draft Genome Sequences of Three Novel Low-Abundance Species Strains Isolated from Kefir Grain.	Genome Announcements	2017	5		e00869-17			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. 		
@D	Kim, Y.//Chandrasegaran, S. 	Chimeric restriction endonuclease.	Proc. Natl. Acad. Sci. U. S. A.	1994	91		883-887			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. 		
@A	Kim, Y.//Choi, J.//Grable, J.C.//Greene, P.//Hager, P.//Rosenberg, J.M. 		Studies on the canonical DNA-EcoRI endonuclease complex and the EcoRI kink.			Sarma, R.H.//Sarma, M.H. 		Structural Biology: The State of the Art.				New York	Adenine Press	1994		0		225-246									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. 		
@D	Kim, Y.//Grable, J.C.//Love, R.//Greene, P.J.//Rosenberg, J.M. 	Refinement of EcoRI endonuclease crystal structure: A revised protein chain tracing.	Science	1990	249		1307-1309			None 		
@D	Kim, Y.-G.//Cha, J.//Chandrasegaran, S. 	Hybrid restriction enzymes: Zinc finger fusions to FokI cleavage domain.	Proc. Natl. Acad. Sci. U. S. A.	1996	93		1156-1160			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. 		
@D	Kim, Y.-G.//Kim, P.S.//Herbert, A.//Rich, A. 	Construction of a Z-DNA-specific restriction endonuclease.	Proc. Natl. Acad. Sci. U. S. A.	1997	94		12875-12879			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. 		
@D	Kim, Y.-G.//Li, L.//Chandrasegaran, S. 	Insertion and deletion mutants of FokI restriction endonuclease.	J. Biol. Chem.	1994	269		31978-31982			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. 		
@D	Kim, Y.-G.//Shi, Y.//Berg, M.//Chandrasegaran, S. 	Site-specific cleavage of DNA-RNA hybrids by zinc finger/FokI cleavage domain fusions.	Gene	1997	203		43-49			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. 		
@D	Kim, Y.-G.//Smith, J.//Durgesha, M.//Chandrasegaran, S. 	Chimeric restriction enzyme: Gal4 fusion to FokI cleavage domain.	Biol. Chem.	1998	379		489-495			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). 		
@D	Kim, Y.J.//Sukweenadhi, J.//Seok, J.W.//Kang, C.H.//Choi, E.S.//Subramaniyam, S.//Yang, D.C. 	Complete genome sequence of Paenibacillus yonginensis DCY84T, a novel plant Symbiont that promotes growth via induced systemic resistance.	Standards in Genomic Sciences	2017	12		63			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. 		
@D	Kim, Y.O.//Kim, W.J.//Choi, S.H.//Kim, D.S.//Kim, D.W.//Lee, J.S.//Kong, H.J.//Nam, B.H.//Kim, B.S.//Lee, S.J.//Park, H.S.//Chae, S.H. 	Genome Sequence of Acinetobacter sp. Strain P8-3-8, Isolated from Fistularia commersonii in Vietnam.	J. Bacteriol.	2011	193		4288-4289			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. 		
@D	Kim, Y.R.//Park, S.//Kim, T.S.//Kim, M.K.//Han, J.H.//Joung, Y.//Kim, S.B. 	Draft Genome Sequence of Streptacidiphilus oryzae TH49T, an Acidophilic Actinobacterium Isolated from Soil.	Genome Announcements	2015	3		e00703-15			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. 		
@D	Kim, Y.S.//Jeong, J.O.//Cho, S.H.//Jeong, D.Y.//Uhm, T.-B. 	Antimicrobial and Biogenic Amine-Degrading Activity of.	Misaengmul Hakhoe Chi	2012	48		163-170			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. 		
@D	Kim, Y.S.//Rho, H.M. 	Characterization of the restriction endonuclease BdiI from Brevibacterium divaricatum.	Korean J. Microbiol.	1986	24		18-23			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. 		
@D	Kim, Y.S.//Rho, H.M. 	Purification and Characterization of PstI Methylase from Providencia stuartii 164.	Korean Biochem. J.	1984	17		107-119			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. 		
@D	Kimball, M.//Linn, S. 	The release of oligonucleotides by the Escherichia coli B restriction endonuclease.	Biochem. Biophys. Res. Commun.	1976	68		585-591			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. 		
@D	Kimbrel, J.A.//Chang, J.//Arp, D.J.//Sayavedra-Soto, L.A. 	The Draft Genome Sequence of Nocardioides sp. Strain CF8 Reveals the Scope of Its Metabolic Capabilities.	Genome Announcements	2013	1		e00439-13			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. 		
@D	Kimelman, A.//Levy, A.//Sberro, H.//Kidron, S.//Leavitt, A.//Amitai, G.//Yoder-Himes, D.//Wurtzel, O.//Zhu, Y.//Rubin, E.//Sorek, R. 	A vast collection of microbial genes that are toxic to bacteria.	Genome Res.	2012	22		802-809			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. 		
@D	Kimura, B.//Takahashi, H.//Hokimoto, S.//Tanaka, Y.//Fujii, T. 	Induction of the histidine decarboxylase genes of Photobacterium damselae subsp. damselae (formally P. histaminum) at low pH.	J. Appl. Microbiol.	2009	107		485-497			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. 		
@D	Kimura, H.//Ishihara, G.//Tajima, S. 	Isolation and expression of a Xenopus laevis DNA methyltransferase cDNA.	J. Biochem. (Tokyo)	1996	120		1182-1189			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. 		
@D	Kimura, H.//Nakamura, T.//Ogawa, T.//Tanaka, S.//Shiota, K. 	Transcription of mouse DNA methyltransferase 1 (Dnmt1) is regulated by both E2F-Rb-HDAC-dependent and -independent pathways.	Nucleic Acids Res.	2003	31		3101-3113			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. 		
@D	Kimura, H.//Shiota, K. 	Methyl-CpG-binding Protein, MeCP2, Is a Target Molecule for Maintenance DNA Methyltransferase, Dnmt1.	J. Biol. Chem.	2003	278		4806-4812			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. 		
@D	Kimura, H.//Suetake, I.//Tajima, S. 	Xenopus maintenance-type DNA methyltransferase is accumulated and translocated into germinal vesicles of oocytes.	J. Biochem. (Tokyo)	1999	125		1175-1182			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. 		
@D	Kimura, H.//Takeda, T.//Tanaka, S.//Ogawa, T.//Shiota, K. 	Expression of rat DNA (cytosine-5) methyltransferase (DNA MTase) in rodent trophoblast giant cells: Molecular cloning and characterization of rat DNA MTase.	Biochem. Biophys. Res. Commun.	1998	253		495-501			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. 		
@D	Kimura, N.//Yamazoe, A.//Hosoyama, A.//Hirose, J.//Watanabe, T.//Suenaga, H.//Fujihara, H.//Futagami, T.//Goto, M.//Furukawa, K. 	Draft Genome Sequence of Pseudomonas abietaniphila KF717 (NBRC 110669), Isolated  from Biphenyl-Contaminated Soil in Japan.	Genome Announcements	2015	3		e00059-15			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. 		
@D	Kinch, L.N.//Ginalski, K.//Rychlewski, L.//Grishin, N.V. 	Identification of novel restriction endonuclease-like fold families among hypothetical proteins.	Nucleic Acids Res.	2005	33		3598-3605			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. 		
@D	Kincheloe, G.N.//Eisen, J.A.//Coil, D.A. 	Draft Genome Sequence of Arthrobacter sp. Strain UCD-GKA (Phylum Actinobacteria).	Genome Announcements	2017	5		e01599-16			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. 		
@D	Kinder, S.A.//Badger, J.L.//Bryant, G.O.//Pepe, J.C.//Miller, V.L. 	Cloning of the YenI restriction endonuclease and methyltransferase from Yersinia enterocolitica serotype O8 and construction of a transformable R-M+ mutant.	Gene	1993	136		271-275			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. 		
@D	King, G.//Murray, N.E. 	Restriction alleviation and modification enhancement by the Rac prophage of Escherichia coli K-12.	Mol. Microbiol.	1995	16		769-777			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. 		
@D	King, G.//Murray, N.E. 	Modification enhancement and restriction alleviation by bacteriophage lambda.	Gene	1995	157		225			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. 		
@D	King, G.//Murray, N.E. 	Restriction enzymes in cells, not eppendorfs.	Trends Microbiol.	1994	2		465-469			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. 		
@D	King, J.//Umezu, K.//Ryu, J. 	Complementation of type ID restriction-modification systems between KpnAI and StySBLI.	Abstr. Gen. Meet. Am. Soc. Microbiol.	2000	100		371			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. 		
@D	King, J.B.//Bowen, L.M.//Dupureur, C.M. 	Binding and conformational analysis of phosphoramidate restriction enzyme interactions.	Biochemistry	2004	43		8551-8559			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. 		
@D	King, J.S.//Valcarcel, E.R.//Rufer, J.T.//Phillps, J.W.//Morgan, W.F. 	Noncomplementary DNA double-strand-break rejoining in bacterial and human cells.	Nucleic Acids Res.	1993	21		1055-1059			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. 		
@D	King, K.//Benkovic, S.J.//Modrich, P. 	Glu-111 is required for activation of the DNA cleavage center of EcoRI endonuclease.	J. Biol. Chem.	1989	264		11807-11815			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. 		
@D	King, K.//Wright, D.//Modrich, P. 	Mutationally altered forms of EcoRI endonuclease selectively defective in DNA cleavage.	Fed. Proc.	1986	45		1913			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. 		
@A	King, K.//Wright, D.J.//Modrich, P. 		Glutamate 111 of EcoRI endonuclease is required for DNA cleavage activation.			Brew, K. 		Miami BioTechnology Winter Symposium				VA	IRL Press	1988		8		79									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. 		
@D	King, K.W.//Dybvig, K. 	Transformation of Mycoplasma capricolum and examination of DNA restriction modification in M. capricolum and Mycroplasma mycoides subsp. mycoides.	Plasmid	1994	31		308-311			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. 		
@D	King, R.A. et al. 	Genome Sequences of Subcluster K5 Mycobacteriophages AlleyCat, Edugator, and Guillsminger.	Genome Announcements	2017	5		e01122-17			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. 		
@D	Kingry, L.C.//Batra, D.//Replogle, A.//Rowe, L.A.//Pritt, B.S.//Petersen, J.M. 	Whole Genome Sequence and Comparative Genomics of the Novel Lyme Borreliosis Causing Pathogen, Borrelia mayonii.	PLoS ONE	2016	11		E0168994			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. 		
@D	Kingry, L.C.//Batra, D.//Replogle, A.//Sexton, C.//Rowe, L.//Stermole, B.M.//Christensen, A.M.//Schriefer, M.E. 	Chromosome and Linear Plasmid Sequences of a 2015 Human Isolate of the Tick-Borne Relapsing Fever Spirochete, Borrelia turicatae.	Genome Announcements	2016	4		e00655-16			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%. 		
@D	Kingry, L.C.//Replogle, A.//Batra, D.//Rowe, L.A.//Sexton, C.//Dolan, M.//Connally, N.//Petersen, J.M.//Schriefer, M.E. 	Toward a Complete North American Borrelia miyamotoi Genome.	Genome Announcements	2017	5		e01557-16			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. 		
@D	Kingry, L.C.//Replogle, A.//Dolan, M.//Sexton, C.//Padgett, K.A.//Schriefer, M.E. 	Chromosome and Large Linear Plasmid Sequences of a Borrelia miyamotoi Strain Isolated from Ixodes pacificus Ticks from California.	Genome Announcements	2017	5		e00960-17			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. 		
@D	Kingston, I.J.//Gormley, N.A.//Halford, S.E. 	DNA supercoiling enables the Type IIS restriction enzyme BspMI to recognize the relative orientation of two DNA sequences.	Nucleic Acids Res.	2003	31		5221-5228			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. 		
@D	Kinjo, M.//Nishimura, G.//Koyama, T.//Mets, U.//Rigler, R. 	Single-molecule analysis of restriction DNA fragments using fluorescence correlation spectroscopy.	Anal. Biochem.	1998	260		166-172			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. 		
@D	Kinjo, Y.//Bourguignon, T.//Tong, K.J.//Kuwahara, H.//Lim, S.J.//Yoon, K.B.//Shigenobu, S.//Park, Y.C.//Nalepa, C.A.//Hongoh, Y.//Ohkuma, M.//Lo, N.//Tokuda, G. 	Parallel and Gradual Genome Erosion in the Blattabacterium Endosymbionts of Mastotermes darwiniensis and Cryptocercus Wood Roaches.	Genome Biol. Evol.	2018	10		1622-1630			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. 		
@D	Kinney, S.R.M.//Pradhan, S. 	Regulation of Expression and Activity of DNA (Cytosine-5) Methyltransferases in Mammalian Cells.	Prog. Mol. Biol. Transl. Sci.	2011	101		311-333			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. 		
@D	Kinsella, J.M.//Shalaev, M.V.//Ivanisevic, A. 	Ligation of Nanoparticle Coated DNA Cleaved with Restriction Enzymes.	Chem. Mater.	2007	19		3586-3588			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. 		
@D	Kiran, S.//Swarnkar, M.K.//Pal, M.//Thakur, R.//Tewari, R.//Singh, A.K.//Gulati, A. 	Complete Genome Sequencing of Protease-Producing Novel Arthrobacter sp. Strain IHBB 11108 Using PacBio Single-Molecule Real-Time Sequencing Technology.	Genome Announcements	2015	3		e00346-15			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. 		
@D	Kirby, R.//Sangal, V.//Tucker, N.P.//Zakrzewska-Czerwinska, J.//Wierzbicka, K.//Herron, P.R.//Chu, C.J.//Chandra, G.//Fahal, A.H.//Goodfellow, M.//Hoskisson, P.A. 	Draft Genome Sequence of the Human Pathogen Streptomyces somaliensis, a Significant Cause of Actinomycetoma.	J. Bacteriol.	2012	194		3544-3545			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. 		
@D	Kirienko, N.V.//Lepikhov, K.A.//Zheleznaya, L.A.//Matvienko, N.I. 	Significance of codon usage and irregularities of rare codon distribution in genes for expression of BspLU11III methyltransferases.	Biokhimiia	2004	69		647-657			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). 		
@D	Kirino, H.//Kuwahara, R.//Hamasaki, N.//Oshima, T. 	Effect of unusual polyamines on cleavage of DNA by restriction enzymes.	J. Biochem. (Tokyo)	1990	107		661-665			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. 		
@D	Kirkeleite, I.O.//Bohlin, J.//Scheffer, L.//Weme, E.T.//Vestrheim, D.F. 	Draft Genome Sequence of a Potentially Novel Streptococcus Species Belonging to the Streptococcus mitis Group.	Genome Announcements	2018	6		e00620-18			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. 		
@D	Kirsanova, O.V.//Baskunov, V.B.//Gromova, E.S. 	Type IIE and IIF restriction endonucleases interacting with two recognition sites on DNA.	Mol. Biol. (Mosk)	2004	38		886-900			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. 		
@D	Kirsanova, O.V.//Cherepanova, N.A.//Gromova, E.S. 	Inhibition of C5-cytosine-DNA-methyltransferases.	Biochemistry	2009	74		1175-1186			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. 		
@D	Kirstahler, P.//Gunther, M.//Grumaz, C.//Lindemann, E.//Rupp, S.//Zibek, S.//Sohn, K. 	Draft Genome Sequence of Amantichitinum ursilacus IGB-41, a New Chitin-Degrading  Bacterium.	Genome Announcements	2015	3		e01309-15			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. 		
@D	Kiseleva, L.//Garushyants, S.K.//Briliute, J.//Simpson, D.J.//Cohen, M.F.//Goryanin, I. 	Genome Sequence of the Electrogenic Petroleum-Degrading Thalassospira sp. Strain  HJ.	Genome Announcements	2015	3		e00483-15			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. 		
@D	Kishi, L.T.//Lopes, E.M.//Fernandes, C.C.//Fernandes, G.C.//Sacco, L.P.//Carareto, A.L.M.//Lemos, E.G. 	Draft Genome Sequence of a Chitinophaga Strain Isolated from a Lignocellulose Biomass-Degrading Consortium.	Genome Announcements	2017	5		e01056-16			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. 		
@D	Kishimoto, N.//Sakai, H.//Jackson, J.//Jacobsen, S.E.//Meyerowitz, E.M.//Dennis, E.S.//Finnegan, E.J. 	Site specificity of the Arabidopsis METI DNA methyltransferase demonstrated through hypermethylation of the superman locus.	Plant Mol. Biol.	2001	46		171-183			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. 		
@D	Kishnani, P.M.//Tiwari, A.A.//Gautam, V.//Sharma, M.//Barbuddhe, S.B.//Doijad, S.P.//Chakraborty, T.//Nayak, A.R.//Bhartiya, N.M.//Daginawala, H.F.//Singh, L.R.//Kashyap, R.S. 	Draft Genome Sequence of Listeria monocytogenes Strain CIIMS-PH-1, a Serovar 4b Isolate from Infant Septicemia.	Genome Announcements	2018	6		e01320-17			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. 		
@D	Kishnani, P.M.//Tiwari, A.A.//Mangalgi, S.S.//Barbuddhe, S.B.//Daginawala, H.F.//Singh, L.R.//Kashyap, R.S. 	Whole-Genome Sequence of Brucella melitensis CIIMS-BH-2, a Biovar 2 Strain Isolated from Human Blood.	Genome Announcements	2018	6		e00079-18			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. 		
@D	Kisiala, M.//Copelas, A.//Czapinska, H.//Xu, S.Y.//Bochtler, M. 	Crystal structure of the modification-dependent SRA-HNH endonuclease TagI.	Nucleic Acids Res.	2018	46		10489-10503			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. 		
@D	Kislichkina, A.A.//Bogun, A.G.//Kadnikova, L.A.//Maiskaya, N.V.//Platonov, M.E.//Anisimov, N.V.//Galkina, E.V.//Dentovskaya, S.V.//Anisimov, A.P. 	Nineteen Whole-Genome Assemblies of Yersinia pestis subsp. microtus, Including Representatives of Biovars caucasica, talassica, hissarica, altaica,  xilingolensis, and ulegeica.	Genome Announcements	2015	3		e01342-15			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). 		
@D	Kislichkina, A.A.//Bogun, A.G.//Kadnikova, L.A.//Maiskaya, N.V.//Solomentsev, V.I.//Dentovskaya, S.V.//Balakhonov, S.V.//Anisimov, A.P. 	Nine Whole-Genome Assemblies of Yersinia pestis subsp. microtus bv. Altaica Strains Isolated from the Altai Mountain Natural Plague Focus (No. 36) in Russia.	Genome Announcements	2018	6		e01440-17			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). 		
@D	Kislichkina, A.A.//Bogun, A.G.//Kadnikova, L.A.//Maiskaya, N.V.//Solomentsev, V.I.//Platonov, M.E.//Dentovskaya, S.V.//Anisimov, A.P. 	Eight Whole-Genome Assemblies of Yersinia pestis subsp. microtus bv. caucasica Isolated from the Common Vole (Microtus arvalis) Plague Focus in Dagestan,  Russia.	Genome Announcements	2017	5		e00847-17			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). 		
@D	Kislichkina, A.A.//Bogun, A.G.//Kadnikova, L.A.//Maiskaya, N.V.//Solomentsev, V.I.//Sizova, A.A.//Dentovskaya, S.V.//Balakhonov, S.V.//Anisimov, A.P. 	Six Whole-Genome Assemblies of Yersinia pestis subsp. microtus bv. ulegeica (Phylogroup 0.PE5) Strains Isolated from Mongolian Natural Plague Foci.	Genome Announcements	2018	6		e00536-18			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. 		
@D	Kiss, A.//Baldauf, F. 	Molecular cloning and expression in Escherichia coli of two modification methylase genes of Bacillus subtilis.	Gene	1983	21		111-119			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. 		
@D	Kiss, A.//Finta, C.//Venetianer, P. 	M.KpnI is an adenine-methyltransferase.	Nucleic Acids Res.	1991	19		3460			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. 		
@D	Kiss, A.//Posfai, G.//Keller, C.C.//Venetianer, P.//Roberts, R.J. 	Nucleotide sequence of the BsuRI restriction-modification system.	Nucleic Acids Res.	1985	13		6403-6420			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. 		
@D	Kiss, A.//Posfai, G.//Zsurka, G.//Rasko, T.//Venetianer, P. 	Role of DNA minor groove interactions in substrate recognition by the M.SinI and M.EcoRII DNA (cytosine-5) methyltransferases.	Nucleic Acids Res.	2001	29		3188-3194			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. 		
@D	Kiss, A.//Sain, B.//Csordas-Toth, E.//Venetianer, P. 	A new sequence-specific endonuclease (Bsp) from Bacillus sphaericus.	Gene	1977	1		323-329			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. 		
@D	Kiss, A.//Weinhold, E. 	Functional reassembly of split enzymes on-site: a novel approach for highly sequence-specific targeted DNA methylation.	Chembiochem	2008	9		351-353			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). 		
@D	Kiss, H. et al. 	Complete genome sequence of 'Thermobaculum terrenum' type strain (YNP1).	Standards in Genomic Sciences	2010	3		153-162			'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. 		
@D	Kiss, H. et al. 	Complete genome sequence of the filamentous gliding predatory bacterium Herpetosiphon aurantiacus type strain (114-95).	Standards in Genomic Sciences	2011	5		356-370			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. 		
@D	Kiss, H. et al. 	Complete genome sequence of Denitrovibrio acetiphilus type strain (N2460).	Standards in Genomic Sciences	2010	2		270-279			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. 		
@D	Kita, A.//Iwasaki, Y.//Sakai, S.//Okuto, S.//Takaoka, K.//Suzuki, T.//Yano, S.//Sawayama, S.//Tajima, T.//Kato, J.//Nishio, N.//Murakami, K.//Nakashimada, Y. 	Development of genetic transformation and heterologous expression system in carboxydotrophic thermophilic acetogen Moorella thermoacetica.	J. Biosci. Bioeng.	2013	115		347-352			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. 		
@D	Kita, K. 	Molecular evolution of restriction endonucleases.	Baiosaiensu to Indasutori	2009	67		254-257					
@D	Kita, K. 	Type II restriction-modification gene coded by the E. coli genome. Vestiges of horizontal transfer via phages.	Kagaku To Seibutsu	2003	41		348-350					
@D	Kita, K.//Hiraoka, N.//Kimizuka, F.//Obayashi, A. 	Determination of the cleavage site of restriction enzyme, AccII, using synthetic oligonucleotide.	Agric. Biol. Chem.	1984	48		531-532			None 		
@D	Kita, K.//Hiraoka, N.//Kimizuka, F.//Obayashi, A.//Kojima, H.//Takahashi, H.//Saito, H. 	Interaction of the restriction endonuclease ScaI with its substrates.	Nucleic Acids Res.	1985	13		7015-7024			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. 		
@D	Kita, K.//Hiraoka, N.//Oshima, A.//Kadonishi, S.//Obayashi, A. 	AccIII, a new restriction endonuclease from Acinetobacter calcoaceticus.	Nucleic Acids Res.	1985	13		8685-8694			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. 		
@D	Kita, K.//Kawakami, H.//Tanaka, H. 	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.	J. Bacteriol.	2003	185		2296-2305			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. 		
@D	Kita, K.//Kotani, H.//Hiraoka, N.//Nakamura, T.//Yonaha, K. 	Overproduction and crystallization of FokI restriction endonuclease.	Nucleic Acids Res.	1989	17		8741-8753			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. 		
@D	Kita, K.//Kotani, H.//Ohta, H.//Yanase, H.//Kato, N. 	StsI, a new FokI isoschizomer from Streptococcus sanguis 54, cleaves 5' GGATG(N)10/14 3'.	Nucleic Acids Res.	1992	20		618			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. 		
@D	Kita, K.//Kotani, H.//Sugisaki, H.//Takanami, M. 	The FokI restriction-modification system  I. Organization and nucleotide sequences of the restriction and modification genes.	J. Biol. Chem.	1989	264		5751-5756			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. 		
@D	Kita, K.//Suisha, M.//Kotani, H.//Yanase, H.//Kato, N. 	Cloning and sequence analysis of the StsI restriction-modification gene: presence of homology to FokI restriction-modification enzymes.	Nucleic Acids Res.	1992	20		4167-4172			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. 		
@D	Kita, K.//Suisha, M.//Shintoh, M.//Yanase, H.//Kato, N. 	Overproduction and characterization of the StsI restriction endonuclease.	Gene	1996	169		69-73			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. 		
@D	Kita, K.//Takasaki, Y. 	Enzymology of restriction enzymes.	Seikagaku	1994	66		1237-1245			A review 		
@D	Kita, K.//Tsuda, J.//Kato, T.//Okamoto, K.//Yanase, H.//Tanaka, M. 	Evidence of horizontal transfer of the EcoO109I restriction-modification gene to Escherichia coli chromosomal DNA.	J. Bacteriol.	1999	181		6822-6827			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. 		
@D	Kita, K.//Tsuda, J.//Nakai, S.-y. 	C.EcoO109I, a regulatory protein for production of EcoO109I restriction endonuclease, specifically binds to and bends DNA upstream of its translational start site.	Nucleic Acids Res.	2002	30		3558-3565			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. 		
@D	Kita, K.//Tsuda, J.//Nishigaki, R. 	Characterization and overproduction of EcoO109I methyltransferase.	Biosci. Biotechnol. Biochem.	2001	65		2512-2518			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. 		
@D	Kitagawa, W.//Hata, M.//Sekizuka, T.//Kuroda, M.//Ishikawa, J. 	Draft Genome Sequence of Rhodococcus erythropolis JCM 6824, an Aurachin RE Antibiotic Producer.	Genome Announcements	2014	2		e01026-14			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. 		
@D	Kitajima, M.//Ishizaki, S.//Jang, J.//Ishii, S.//Okabe, S. 	Complete Genome Sequence of Klebsiella quasipneumoniae Strain S05, a Fouling-Causing Bacterium Isolated from a Membrane Bioreactor.	Genome Announcements	2018	6		e00471-18			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. 		
@D	Kits, K.D. et al. 	Genome Sequence of the Obligate Gammaproteobacterial Methanotroph Methylomicrobium album Strain BG8.	Genome Announcements	2013	1		e00170-13			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. 		
@D	Kittichotirat, W.//Good, N.M.//Hall, R.//Bringel, F.//Lajus, A.//Medigue, C.//Smalley, N.E.//Beck, D.//Bumgarner, R.//Vuilleumier, S.//Kalyuzhnaya, M.G. 	Genome Sequence of Methyloversatilis universalis FAM5T, a Methylotrophic Representative of the Order Rhodocyclales.	J. Bacteriol.	2011	193		4541			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. 		
@D	Kittler, L.//Bell, A.//Baguley, B.C.//Lober, G. 	Inhibition of restriction endonucleases by DNA sequence-reading ligands.	Biochem. Mol. Biol. Int.	1996	40		263-272			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. 		
@D	Kittler, L.//Bell, A.//Baguley, B.C.//Loeber, G. 	Sequence specific modulation of DNA restriction enzyme cleavage by minor groove binders.	Biol. Chem.	1998	379		519-525			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. 		
@D	Kivisto, A.//Larjo, A.//Ciranna, A.//Santala, V.//Roos, C.//Karp, M. 	Genome Sequence of Halanaerobium saccharolyticum subsp. saccharolyticum Strain DSM 6643T, a Halophilic Hydrogen-Producing Bacterium.	Genome Announcements	2013	1		e00187-13			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%. 		
@D	Kivisto, R.I.//Kovanen, S.//Skarp-de-Haan, A.//Schott, T.//Rahkio, M.//Rossi, M.//Hanninen, M.-L. 	Evolution and Comparative Genomics of Campylobacter jejuni ST-677 Clonal Complex.	Genome Biol. Evol.	2014	6		2424-2438			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. 		
@D	Kiwaki, M. 	Restriction enzymes.	Bifizusukin Yakurutokabu	2009	0		118-122					
@D	Kjems, J.//Garrett, R.A. 	An intron in the 23S ribosomal RNA gene of the archaebacterium Desulfurococcus mobilis.	Nature	1985	318		675-677			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). 		
@D	Kladde, M.P.//Simpson, R.T. 	Rapid detection of functional expression of C-5-DNA methytransferases in yeast.	Nucleic Acids Res.	1998	26		1354-1355			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. 		
@D	Kladde, M.P.//Simpson, R.T. 	Chromatin structure mapping in vivo using methyltransferases.	Methods Enzymol.	1996	274		214-233			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. 		
@D	Kladde, M.P.//Xu, M.//Simpson, R.T. 	DNA methyltransferases as probes of chromatin structure in vivo.	Methods Enzymol.	1999	304		431-447			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. 		
@D	Klaenhammer, T.R. 	Development of bacteriophage-resistant strains of lactic acid bacteria.	Food Biotech.	1991	19		675-682			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. 		
@D	Klaenhammer, T.R. 	Plasmid-directed mechanisms for bacteriophage defense in lactic streptococci.	FEMS Microbiol. Lett.	1987	46		313-325			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. 		
@D	Klaenhammer, T.R. 	Genetic characterization of multiple mechanisms of phage defense from a prototype phage-insensitive strain, Lactococcus lactis ME2.	J. Dairy Sci.	1989	72		3429-3443			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. 		
@A	Klaenhammer, T.R.//Fitzgerald, G.F. 		Bacteriophages and bacteriophage resistance.			Gasson, M.J.//De Vos, W.M. 		Genetics and Biotechnology of Lactic Acid Bacteria.					Blackie Academic & Professional	1994		0		106-168									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. 		
@A	Klaenhammer, T.R.//Romero, D.//Sing, W.//Hill, C. 		Molecular analysis of pTR2030 gene systems that confer bacteriophage resistance to Lactococci.			Dunny, G.M.//Cleary, P.P.//McKay, L.L. 		Genetics and Molecular Biology of Streptococci, Lactococci, and Enterococci				Washington	American Society for Microbiology	1991		8		124-130									None 		
@D	Klapatch, T.R.//Demain, A.L.//Lynd, L.R. 	Restriction endonuclease activity in Clostridium thermocellum and Clostridium thermosaccharolyticum.	Appl. Microbiol. Biotechnol.	1996	45		127-131			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. 		
@D	Klassen, J.L.//Adams, S.M.//Bramhacharya, S.//Giles, S.S.//Goodwin, L.A.//Woyke, T.//Currie, C.R. 	Draft Genome Sequence of Streptomyces sp. Strain Wigar10, Isolated from a Surface-Sterilized Garlic Bulb.	J. Bacteriol.	2011	193		6999-7000			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. 		
@D	Klassen, J.L.//Rischer, M.//Wolf, T.//Guo, H.//Shelest, E.//Clardy, J.//Beemelmanns, C. 	Genome Sequences of Three Pseudoalteromonas Strains (P1-8, P1-11, and P1-30), Isolated from the Marine Hydroid Hydractinia echinata.	Genome Announcements	2015	3		e01380-15			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. 		
@D	Klassen, J.L.//Wolf, T.//Rischer, M.//Guo, H.//Shelest, E.//Clardy, J.//Beemelmanns, C. 	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.	Genome Announcements	2015	3		e01477-15			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. 		
@D	Klasson, L.//Westberg, J.//Sapountzis, P.//Naslund, K.//Lutnaes, Y.//Darby, A.C.//Veneti, Z.//Chen, L.//Braig, H.R.//Garrett, R.//Bourtzis, K.//Andersson, S.G. 	The mosaic genome structure of the Wolbachia wRi strain infecting Drosophila simulans.	Proc. Natl. Acad. Sci. U. S. A.	2009	106		5725-5730			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. 		
@D	Klaus, S.//Hartmann, M.//Krugel, H.//Roth, M.//Walter, F.//Rautenstein, Y.I.//Solovyeva, N.Y. 	Restriction of Streptomyces phage SH5 by endonuclease ShyI from Streptomyces hygroscopicus 0477.	Mol. Gen. Genet.	1981	184		286-288			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. 		
@D	Klee, S.R.//Nassif, X.//Kusecek, B.//Merker, P.//Beretti, J.L.//Achtman, M.//Tinsley, C.R. 	Molecular and biological analysis of eight genetic islands that distinguish Neisseria meningitidis from the closely related pathogen   Neisseria gonorrhoeae.	Infect. Immun.	2000	68		2082-2095			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. 		
@D	Kleerebezem, M. et al. 	Complete genome sequence of Lactobacillus plantarum WCFS1.	Proc. Natl. Acad. Sci. U. S. A.	2003	100		1990-1995			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. 		
@D	Kleid, D.//Humayun, Z.//Jeffrey, A.//Ptashne, M. 	Novel properties of a restriction endonuclease isolated from Haemophilus parahaemolyticus.	Proc. Natl. Acad. Sci. U. S. A.	1976	73		293-297			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. 		
@D	Kleid, D.G. 	Purification and properties of the HphI endonuclease.	Methods Enzymol.	1980	65		163-166			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. 		
@D	Klein, A. 	Mechanisms of host-controlled modification of phage T1.	Z. Vererbungsl.	1965	96		346-363			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. 		
@D	Klein, A. 	Host-controlled modification.	Z. Vererbungsl.	1965	96		324-345			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. 		
@D	Klein, A.//Sauerbier, W. 	Role of methylation in host controlled modification of phage T1.	Biochem. Biophys. Res. Commun.	1965	18		440-445			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. 		
@D	Klein, B.A.//Lemon, K.P.//Faller, L.L.//Jospin, G.//Eisen, J.A.//Coil, D.A. 	Draft Genome Sequence of Curtobacterium sp. Strain UCD-KPL2560 (Phylum Actinobacteria).	Genome Announcements	2016	4		e01040-16			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. 		
@D	Klein, B.A.//Lemon, K.P.//Gajare, P.//Jospin, G.//Eisen, J.A.//Coil, D.A. 	Draft Genome Sequences of Dermacoccus nishinomiyaensis Strains UCD-KPL2534 and UCD-KPL2528 Isolated from an Indoor Track Facility.	Genome Announcements	2017	5		e01652-16			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. 		
@D	Klein, E.A.//Gitai, Z. 	Draft Genome Sequence of Uropathogenic Escherichia coli Strain J96.	Genome Announcements	2013	1		e00245-12			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. 		
@D	Klein, J.M.//Bennett, R.W.//MacFarland, L.//Abranches, Da.S.M.E.//Meza-Turner, B.M.//Dark, P.M.//Frey, M.E.//Wellappili, D.P.//Beugli, A.D.//Jue, H.J.//Mellander, J.M.//Wei, W.//Ream, W. 	Draft Genome Sequence of Erwinia billingiae OSU19-1, Isolated from a Pear Tree Canker.	Genome Announcements	2015	3		e01119-15			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. 		
@D	Klein, R.//Baranyi, U.//Rossler, N.//Greineder, B.//Scholz, H.//Witte, A. 	Natrialba magadii virus phiCh1: first complete nucleotide sequence and functional organization of a virus infecting a haloalkaliphilic archaeon.	Mol. Microbiol.	2002	45		851-863			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. 		
@D	Kleindienst, S.//Higgins, S.A.//Tsementzi, D.//Konstantinidis, K.T.//Mack, E.E.//Loffler, F.E. 	Draft Genome Sequence of a Strictly Anaerobic Dichloromethane-Degrading Bacterium.	Genome Announcements	2016	4		e00037-16			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%. 		
@D	Kleiner, G.R.//Wibberg, D.//Winkler, A.//Kalinowski, J.//Wertz, J.E.//Friehs, K. 	Complete Draft Genome Sequence of Escherichia coli JF733.	Genome Announcements	2016	4		e00298-16			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. 		
@D	Kleiner-Grote, G.R.M.//Wibberg, D.//Winkler, A.//Kalinowski, J.//Friehs, K. 	Complete Draft Genome Sequence of Escherichia coli K802.	Genome Announcements	2017	5		e00934-17			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. 		
@D	Kleinert, F.//Kallies, R.//Zweynert, A.//Bierbaum, G. 	Draft Genome Sequences of Three Northern German Epidemic Staphylococcus aureus (ST247) Strains Containing Multiple Copies of IS256.	Genome Announcements	2016	4		e00936-16			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. 		
@D	Kleinstiver, B.P.//Berube-Janzen, W.//Fernandes, A.D.//Edgell, D.R. 	Divalent Metal Ion Differentially Regulates the Sequential Nicking Reactions of the GIY-YIG Homing Endonuclease I-BmoI.	PLoS ONE	2011	6		e23804			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. 		
@D	Kleinstiver, B.P.//Fernandes, A.D.//Gloor, G.B.//Edgell, D.R. 	A unified genetic, computational and experimental framework identifies functionally relevant residues of the homing endonuclease I-BmoI.	Nucleic Acids Res.	2010	38		2411-2427			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. 		
@D	Kleinstiver, B.P.//Wolfs, J.M.//Edgell, D.R. 	The monomeric GIY-YIG homing endonuclease I-BmoI uses a molecular anchor and a flexible tether to sequentially nick DNA.	Nucleic Acids Res.	2013	41		5413-5427			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. 		
@D	Kleinstiver, B.P.//Wolfs, J.M.//Kolaczyk, T.//Roberts, A.K.//Hu, S.X.//Edgell, D.R. 	Monomeric site-specific nucleases for genome editing.	Proc. Natl. Acad. Sci. U. S. A.	2012	109		8061-8066			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. 		
@D	Kleiveland, C.R.//Hult, L.T.//Kuczkowska, K.//Jacobsen, M.//Lea, T.//Pope, P.B. 	Draft Genome Sequence of the Methane-Oxidizing Bacterium Methylococcus capsulatus (Texas).	J. Bacteriol.	2012	194		6626			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. 		
@D	Klenk, H.-P. et al. 	The complete genome sequence of the hyperthermophilic, sulphate-reducing archaeon Archaeoglobus fulgidus.	Nature	1997	390		364-370			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. 		
@D	Klenk, H.P. et al. 	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.	Standards in Genomic Sciences	2011	5		121-134			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. 		
@D	Klenk, H.P.//Held, B.//Lucas, S.//Lapidus, A.//Copeland, A.//Hammon, N.//Pitluck, S.//Goodwin, L.A.//Han, C.//Tapia, R.//Brambilla, E.M.//Potter, G.//Land, M.//Ivanova, N.//Rohde, M.//Goker, M.//Detter, J.C.//Kyrpides, N.C.//Woyke, T. 	Genome sequence of the soil bacterium Saccharomonospora azurea type strain (NA-128(T)).	Standards in Genomic Sciences	2012	6		220-229			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). 		
@D	Klenk, H.P.//Lu, M.//Lucas, S.//Lapidus, A.//Copeland, A.//Pitluck, S.//Goodwin, L.A.//Han, C.//Tapia, R.//Brambilla, E.M.//Potter, G.//Land, M.//Ivanova, N.//Rohde, M.//Goker, M.//Detter, J.C.//Li, W.J.//Kyrpides, N.C.//Woyke, T. 	Genome sequence of the ocean sediment bacterium Saccharomonospora marina type strain (XMU15(T)).	Standards in Genomic Sciences	2012	6		265-275			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). 		
@D	Klima, C.L.//Cook, S.R.//Hahn, K.R.//Amoako, K.K.//Alexander, T.W.//Hendrick, S.//McAllister, T.A. 	Draft Genome Sequence of a Mannheimia haemolytica Serotype 6 Isolate Collected from the Nasopharynx of a Beef Calf with Bovine Respiratory Disease.	Genome Announcements	2013	1		e0005113			The draft genome of a Mannheimia haemolytica serotype 6 isolate obtained from the nasopharynx of a feedlot calf with bovine respiratory disease is described. 		
@D	Klimasauskas, S.//Butkus, V.//Janulaitis, A. 	Investigation of specificity of DNA-methylases BcnI, CfrI and Cfr10I.	Mol. Biol. (Mosk)	1987	21		87-92			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. 		
@D	Klimasauskas, S.//Kumar, S.//Roberts, R.J.//Cheng, X. 	Hhal methyltransferase flips its target base out of the DNA helix.	Cell	1994	76		357-369			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. 		
@D	Klimasauskas, S.//Nelson, J.L.//Roberts, R.J. 	The sequence specificity domain of cytosine-C5 methylases.	Nucleic Acids Res.	1991	19		6183-6190			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. 		
@D	Klimasauskas, S.//Roberts, R.J. 	M.HhaI binds tightly to substrates containing mismatches at the target base.	Nucleic Acids Res.	1995	23		1388-1395			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. 		
@D	Klimasauskas, S.//Roberts, R.J. 	Disruption of the target G-C base-pair by the HhaI methyltransferase.	Gene	1995	157		163-164			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. 		
@D	Klimasauskas, S.//Steponaviciene, D.//Maneliene, Z.//Petrusyte, M.//Butkus, V.//Janulaitis, A. 	M.SmaI is an N4-methylcytosine specific DNA-methylase.	Nucleic Acids Res.	1990	18		6607-6609			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. 		
@D	Klimasauskas, S.//Szyperski, T.//Serva, S.//Wuthrich, K. 	Dynamic modes of the flipped-out cytosine during HhaI methyltransferase-DNA interactions in solution.	EMBO J.	1998	17		317-324			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. 		
@D	Klimasauskas, S.//Timinskas, A.//Menkevicius, S.//Butkiene, D.//Butkus, V.//Janulaitis, A. 	Sequence motifs characteristic of DNA[cytosine-N4]methylases:  similarity to adenine and cytosine-C5 DNA-methylases.	Nucleic Acids Res.	1989	17		9823-9832			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. 		
@D	Klimasauskas, S.//Timinskas, A.//Menkevicius, S.//Butkiene, D.//Butkus, V.//Janulaitis, A. 	Sequence motifs characteristic of DNA-cytosine-N4-methyltransferases:  The two domains of global similarity within DNA-methylases.	Eksp. Biol.	1990	0		4-12			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. 		
@D	Klimasauskas, S.//Weinhold, E. 	A new tool for biotechnology: AdoMet-dependent methyltransferases.	Trends Biotechnol.	2007	25		99-104			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. 		
@D	Klimkait, T. 	'Restriction-PCR' - a superior replacement for restriction endonucleases in DNA cloning applications.	J. Biochem. Mol. Biol.	2000	33		162-165			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. 		
@D	Klimuk, E.//Bogdanova, E.//Nagornykh, M.//Rodic, A.//Djordjevic, M.//Medvedeva, S.//Pavlova, O.//Severinov, K. 	Controller protein of restriction-modification system Kpn2I affects transcription of its gene by acting as a transcription elongation roadblock.	Nucleic Acids Res.	2018	46		10810-10826			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. 		
@D	Klingeman, D.M.//Utturkar, S.//Lu, T.Y.//Schadt, C.W.//Pelletier, D.A.//Brown, S.D. 	Draft Genome Sequences of Four Streptomyces Isolates from the Populus trichocarpa Root Endosphere and Rhizosphere.	Genome Announcements	2015	3		e01344-15			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. 		
@D	Klinzing, D.C.//Matias, R.R.//Skowronski, E.//Alvarez, M.//Liles, V.//Dimamay, M.P.//Natividad, F.F. 	Shotgun Genome Sequence of a Yersinia enterocolitica Isolate from the Philippines.	J. Bacteriol.	2012	194		542-543			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. 		
@D	Klippel, B. et al. 	Complete genome sequence of the marine cellulose- and xylan-degrading bacterium Glaciecola sp. strain 4H-3-7+YE-5.	J. Bacteriol.	2011	193		4547-4548			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. 		
@D	Klippel, B. et al. 	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.	J. Bacteriol.	2011	193		4545-4546			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. 		
@D	Klockgether, J.//Reva, O.//Larbig, K.//Tummler, B. 	Sequence Analysis of the Mobile Genome Island pKLC102 of Pseudomonas aeruginosa C.	J. Bacteriol.	2004	186		518-534			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. 		
@D	Klonowska, A.//Lopez-Lopez, A.//Moulin, L.//Ardley, J.//Gollagher, M.//Marinova, D.//Tian, R.//Huntemann, M.//Reddy, T.B.//Varghese, N.//Woyke, T.//Markowitz, V.//Ivanova, N.//Seshadri, R.//Baeshen, M.N.//Baeshen, N.A.//Kyrpides, N.//Reeve, W. 	High-quality draft genome sequence of Rhizobium mesoamericanum strain STM6155, a  Mimosa pudica microsymbiont from New Caledonia.	Standards in Genomic Sciences	2017	12		7			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. 		
@D	Klump, H. 	Codification and evolution of experimentally observed specific recognition sites for restriction enzymes on DNA.	Biosystems	1987	21		33-49			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. 		
@D	Klumpp, J.//Staubli, T.//Schmitter, S.//Hupfeld, M.//Fouts, D.E.//Loessner, M.J. 	Genome Sequences of Three Frequently Used Listeria monocytogenes and Listeria ivanovii Strains.	Genome Announcements	2014	2		e00404-14			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. 		
@D	Klysik, J.//Stirdivant, S.M.//Singleton, C.K.//Zacharias, W.//Wells, R.D. 	Effects of 5 cytosine methylation on the B-Z transition in DNA restriction fragments and recombinant plasmids.	J. Mol. Biol.	1983	168		51-71			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. 		
@D	Kneale, G.G. 	A symmetrical model for the domain structure of Type I DNA methyltransferases.	J. Mol. Biol.	1994	243		1-5			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. 		
@D	Knight, A.I.//Lilley, R.J.//Buckland, R.M.//Warner, P.J. 	Plasmid mediated restricted and modification in Acinetobacter sp.	Heredity	1988	61		284-285			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. 		
@D	Knizewski, L.//Kinch, L.N.//Grishin, N.V.//Rychlewski, L.//Ginalski, K. 	Realm of PD-(D/E)XK nuclease superfamily revisited: detection of novel families with modified transitive meta profile searches.	BMC Struct. Biol.	2007	7		40			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. 		
@D	Knoblich, I.M.//Sellmann, E.//Kaluza, K.//Frey, B.//Auer, J.//Schmitz, G.G.//Westermann, P. 	Ssp5230I, a novel isoschizomer of AatII from Streptomyces recognizing 5'-GACGT/C-3'.	Nucleic Acids Res.	1992	20		2378			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'. 		
@D	Knowle, D.//Lintner, R.E.//Touma, Y.M.//Blumenthal, R.M. 	Nature of the Promoter Activated by C.PvuII, an Unusual Regulatory Protein Conserved among Restriction-Modification Systems.	J. Bacteriol.	2005	187		488-497			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. 		
@D	Knox, J.D.//Araujo, F.D.//Bigey, P.//Slack, A.D.//Price, G.B.//Zannis-Hadjopoulos, M.//Szyf, M. 	Inhibition of DNA methyltransferase inhibits DNA replication.	J. Biol. Chem.	2000	275		17986-17990			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. 		
@D	Kobayashi, H.//Fu, Q.//Maeda, H.//Sato, K. 	Draft Genome Sequence of a Novel Coriobacteriaceae sp. Strain, EMTCatB1, Reconstructed from the Metagenome of a Thermophilic Electromethanogenic  Biocathode.	Genome Announcements	2017	5		e00022-17			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. 		
@D	Kobayashi, H.//Kawasaki, K.//Takeishi, K.//Noda, H. 	Symbiont of the stink bug Plautia stali synthesizes rough-type lipopolysaccharide.	Microbiol. Res.	2011	167		48-54			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. 		
@D	Kobayashi, H.//Sun, X.//Fu, Q.//Maeda, H.//Sato, K. 	Draft Genome Sequence of Methanothermobacter sp. Strain EMTCatA1, Reconstructed from the Metagenome of a Thermophilic Electromethanogenesis-Catalyzing  Biocathode.	Genome Announcements	2017	5		e00892-17			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. 		
@D	Kobayashi, I. 	Restriction modification systems as selfish mobile genetic elements maintaining and rearranging the genome.	Plasmid	2002	48		260-261			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. 		
@D	Kobayashi, I. 	Behavior of restriction-modification systems as selfish mobile elements and their impact on genome evolution.	Nucleic Acids Res.	2001	29		3742-3756			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. 		
@D	Kobayashi, I. 	Genome comparison: involvement of restriction modification genes in genome rearrangements.	Tanpakushitsu Kakusan Koso	2001	46		2393-2399					
@D	Kobayashi, I. 	Selfish genes for restriction-modification systems.	Saibo Kogaku	1995	14		1015-1023					
@D	Kobayashi, I. 	Selfishness and death: raison d'etre of restriction, recombination and mitochondria.	Trends Genet.	1998	14		368-374			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. 		
@D	Kobayashi, I. 	Reshaping the genome: DNA restriction-modification systems as mobile genetic elements.	Saibo Kogaku	1999	18		1846-1857					
@D	Kobayashi, I. 	Why are there restriction enzymes and genetic recombination?	Cell Struct. Funct.	1994	19		464			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.
 
 		
@D	Kobayashi, I. 	Evolution and Diversity.	Plasmid	2001	45		162-163			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. 		
@A	Kobayashi, I. 		Life cycle of restriction-modification gene complexes, powers in genome evolution.			 		Int. Congr. Ser.					Elsevier Science B.V.	2002		1246		191-200									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. 		
@A	Kobayashi, I. 		DNA modification and restriction: Selfish behavior of an epigenetic system.			Russo, V.E.A.//Martienssen, R.A.//Riggs, A.D. 		Epigenetic Mechanisms of Gene Regulation				New York	Cold Spring Harbor Laboratory Press	1996		0		155-172									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. 		
@A	Kobayashi, I. 		Restriction-modification systems as minimal forms of life.			Pingoud, A. 		Nucleic Acids Mol. Biol.				Berlin Heidelberg	Springer-Verlag	2004		14		19-62									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). 		
@A	Kobayashi, I. 		Genetic addiction: A principle of gene symbiosis in a genome.			Barbara E. Funnell and Gregory J. Phillips 		Plasmid Biology				Washington, DC	ASM Press	2004				105-144									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. 		
@A	Kobayashi, I. 		Homologous recombination and sex as a strategy against selfish genes attacking the genome.			L.H. Caporale 		Molecular Strategies in Biological Evolution				New York	Annals of the New York Academy of Sciences	1999				354-356									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. 		
@D	Kobayashi, I.//Nobusato, A.//Kobayashi-Takahashi, N.//Uchiyama, I. 	Shaping the genome--restriction-modification systems as mobile genetic elements.	Curr. Opin. Genet. Dev.	1999	9		649-656			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. 		
@D	Kobayashi, M.//Nomura, M.//Fujita, Y.//Ohmomo, S.//Okamoto, T. 	Molecular characterization of a lactococcal plasmid reducing the growth rate of host cells.	Japan Agricultural Research Quarterly	2003	37		53-57			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. 		
@D	Kobayashi, M.//Nomura, M.//Fujita, Y.//Okamoto, T.//Ohmomo, S. 	Influence of lactococcal plasmid on the specific growth rate of host cells.	Lett. Appl. Microbiol.	2002	35		403-408			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. 		
@D	Kobayashi, M.//Nomura, M.//Kimoto, H. 	Manipulation for Plasmid Elimination by Transforming Synthetic Competitors Diversifies Lactococcus lactis Starters Applicable to Food Products.	Biosci. Biotechnol. Biochem.	2007	71		2647-2654			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. 		
@D	Koberl, M.//White, R.A.I.I.I.//Erschen, S.//El-Arabi, T.F.//Jansson, J.K.//Berg, G. 	Draft Genome Sequence of Paenibacillus polymyxa Strain Mc5Re-14, an Antagonistic  Root Endophyte of Matricaria chamomilla.	Genome Announcements	2015	3		e00861-15			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. 		
@D	Koberl, M.//White, R.A.I.I.I.//Erschen, S.//El-Arabi, T.F.//Jansson, J.K.//Berg, G. 	Draft Genome Sequence of Streptomyces sp. Strain Wb2n-11, a Desert Isolate with Broad-Spectrum Antagonism against Soilborne Phytopathogens.	Genome Announcements	2015	3		e00860-15			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. 		
@D	Koberl, M.//White, R.A.I.I.I.//Erschen, S.//Spanberger, N.//El-Arabi, T.F.//Jansson, J.K.//Berg, G. 	Complete Genome Sequence of Bacillus amyloliquefaciens Strain Co1-6, a Plant Growth-Promoting Rhizobacterium of Calendula officinalis.	Genome Announcements	2015	3		e00862-15			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. 		
@D	Koblizek, M.//Janouskovec, J.//Obornik, M.//Johnson, J.H.//Ferriera, S.//Falkowski, P.G. 	Genome Sequence of the Marine Photoheterotrophic Bacterium Erythrobacter sp. Strain NAP1.	J. Bacteriol.	2011	193		5881-5882			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. 		
@D	Koch, H.//Lucker, S.//Albertsen, M.//Kitzinger, K.//Herbold, C.//Spieck, E.//Nielsen, P.H.//Wagner, M.//Daims, H. 	Expanded metabolic versatility of ubiquitous nitrite-oxidizing bacteria from the genus Nitrospira.	Proc. Natl. Acad. Sci. U. S. A.	2015	112		11371-11376			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. 		
@D	Kochanek, S.//Renz, D.//Doerfler, W. 	Probing DNA-protein interactions in vitro with the CpG DNA methyltransferase.	Nucleic Acids Res.	1993	21		2339-2342			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. 		
@D	Kodaira, K.I.//Oki, M.//Kakikawa, M.//Watanabe, N.//Hirakawa, M.//Yamada, K.//Taketo, A. 	Genome structure of the Lactobacillus temperate phage Phi g1e: the whole genome sequence and the putative promoter/repressor system.	Gene	1997	187		45-53			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. 		
@D	Koechler, S.//Plewniak, F.//Barbe, V.//Battaglia-Brunet, F.//Jost, B.//Joulian, C.//Philipps, M.//Vicaire, S.//Vincent, S.//Ye, T.//Bertin, P.N. 	Genome Sequence of Halomonas sp. Strain A3H3, Isolated from Arsenic-Rich Marine Sediments.	Genome Announcements	2013	1		e00819-13			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. 		
@D	Koeck, D.E.//Maus, I.//Wibberg, D.//Winkler, A.//Zverlov, V.V.//Liebl, W.//Puhler, A.//Schwarz, W.H.//Schluter, A. 	Complete Genome Sequence of Herbinix luporum SD1D, a New Cellulose-Degrading Bacterium Isolated from a Thermophilic Biogas Reactor.	Genome Announcements	2016	4		e00687-16			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. 		
@D	Koeck, D.E.//Maus, I.//Wibberg, D.//Winkler, A.//Zverlov, V.V.//Liebl, W.//Puhler, A.//Schwarz, W.H.//Schluter, A. 	Draft Genome Sequence of Propionispora sp. Strain 2/2-37, a New Xylan-Degrading Bacterium Isolated from a Mesophilic Biogas Reactor.	Genome Announcements	2016	4		e00609-16			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. 		
@D	Koenigsaecker, T.M.//Eisen, J.A.//Coil, D.A. 	Draft Genome Sequence of Gordonia sp. Strain UCD-TK1 (Phylum Actinobacteria).	Genome Announcements	2016	4		e01121-16			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. 		
@D	Koesters, R.//von Knebel-Doeberitz, M. 	Improved blunt-end cloning by replacing EcoRV with Eco32I.	Biotechniques	2002	32		1244-1246			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. 		
@D	Koh, H.Y.//Jung, W.//Do, H.//Lee, J.H.//Kim, H.J. 	Draft Genome Sequence of Pseudomonas pelagia CL-AP6, a Psychrotolerant Bacterium  Isolated from Culture of Antarctic Green Alga Pyramimonas gelidicola.	Genome Announcements	2013	1		e00699-13			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. 		
@D	Koh, H.Y.//Lee, S.G.//Lee, J.H.//Doyle, S.//Christner, B.C.//Kim, H.J. 	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.	J. Bacteriol.	2012	194		6656-6657			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. 		
@D	Koh, T.H.//Abdul-Rahman, N.B.//Teo, J.W.P.//La, M.V.//Periaswamy, B.//Chen, S.L. 	Draft Genome Sequence of Singapore Klebsiella pneumoniae subsp. pneumoniae Isolate DS32358_14, Which Contains the Carbapenemase Gene blaVIM-1.	Genome Announcements	2018	6		e01377-17			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. 		
@D	Kohli, P.//Dua, A.//Sangwan, N.//Oldach, P.//Khurana, J.P.//Lal, R. 	Draft Genome Sequence of Sphingobium ummariense Strain RL-3, a Hexachlorocyclohexane-Degrading Bacterium.	Genome Announcements	2013	1		e00956-13			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. 		
@D	Kohlman, M.E.//Carrillo, C.D.//Wong, A. 	Draft Genome Sequence of Hafnia paralvei Strain GTA-HAF03.	Genome Announcements	2015	3		e01592-14			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. 		
@D	Kohlmeier, M.G.//Yudistira, H.//Zhang, X.L.//Fristensky, B.//Levin, D.B.//Sparling, R.//Oresnik, I.J. 	Draft Genome Sequence of the Bacteriocin-Producing Bradyrhizobium japonicum Strain FN1.	Genome Announcements	2015	3		e00812-15			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. 		
@D	Kohn, T.//Heuer, A.//Jogler, M.//Vollmers, J.//Boedeker, C.//Bunk, B.//Rast, P.//Borchert, D.//Glockner, I.//Freese, H.M.//Klenk, H.P.//Overmann, J.//Kaster, A.K.//Rohde, M.//Wiegand, S.//Jogler, C. 	Fuerstia marisgermanicae gen. nov., sp. nov., an Unusual Member of the Phylum Planctomycetes from the German Wadden Sea.	Front. Microbiol.	2016	7		2079			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. 		
@D	Kohring, G.W.//Mayer, F. 	In situ distribution of EcoRI methylase and restriction endonuclease in cells of Escherichia coli Bs5.	FEBS Lett.	1987	216		207-210			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. 		
@D	Kohring, G.W.//Mayer, F. 	Immunoelectron microscopic localization of the restriction endonuclease EcoRI in Escherichia coli BS5.	Eur. J. Cell Biol.	1985	37		1-6			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. 		
@D	Koike, H.//Sato, S.//Morita, T.//Fukuoka, T.//Habe, H. 	Draft Genome Sequence of Acetobacter tropicalis Type Strain NBRC16470, a Producer of Optically Pure d-Glyceric Acid.	Genome Announcements	2014	2		e01329-14			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. 		
@D	Koike, H.//Yokoyama, K.//Kawashima, T.//Yamasaki, T.//Makino, S.//Clowney, L.//Suzuki, M. 	GATC Methylation by Dam methylase in archaea: its roles and possible transcription regulation by an FFRP.	Proc. Jpn. Acad., B, Phys. Biol. Sci.	2005	81		278-290			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). 		
@D	Kojima, K.K.//Furuta, Y.//Yahara, K.//Fukuyo, M.//Shiwa, Y.//Nishiumi, S.//Yoshida, M.//Azuma, T.//Yoshikawa, H.//Kobayashi, I. 	Population Evolution of Helicobacter pylori through Diversification in DNA Methylation and Interstrain Sequence Homogenization.	Mol. Biol. Evol.	2016	33		2848-2859			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. 		
@D	Kokcha, S.//Mishra, A.K.//Lagier, J.C.//Million, M.//Leroy, Q.//Raoult, D.//Fournier, P.E. 	Non contiguous-finished genome sequence and description of Bacillus timonensis sp. nov.	Standards in Genomic Sciences	2012	6		346-355			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. 		
@D	Kokcha, S.//Ramasamy, D.//Lagier, J.C.//Robert, C.//Raoult, D.//Fournier, P.E. 	Non-contiguous finished genome sequence and description of Brevibacterium senegalense sp. nov.	Standards in Genomic Sciences	2012	7		233-245			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. 		
@D	Kolek, J.//Sedlar, K.//Provaznik, I.//Patakova, P. 	Draft Genome Sequence of Clostridium pasteurianum NRRL B-598, a Potential Butanol or Hydrogen Producer.	Genome Announcements	2014	2		e00192-14			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. 		
@D	Kolesnikov, V.A.//Zinovev, V.V.//Yashina, L.N.//Karginov, V.A.//Baclanov, M.M.//Malygin, E.G. 	Relaxed specificity of endonuclease BamHI as determined by identification of recognition sites in SV40 and pBR322 DNAs.	FEBS Lett.	1981	132		101-104			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). 		
@D	Kolocheva, T.I.//Demidov, S.A.//Maksakova, G.A.//Nevinskii, G.A. 	Interaction of endonuclease EcoRI with short specific and nonspecific oligonucleotides.	Mol. Biol. (Mosk)	1998	32		1025-1033					
@D	Kolocheva, T.I.//Maksakova, G.A.//Bugreev, D.D.//Nevinsky, G.A. 	Interaction of endonuclease EcoRI with short specific and nonspecific oligonucleotides.	Life	2001	51		189-195			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. 		
@D	Kolton, M.//Green, S.J.//Harel, Y.M.//Sela, N.//Elad, Y.//Cytryn, E. 	Draft Genome Sequence of Flavobacterium sp. Strain F52, Isolated from the Rhizosphere of Bell Pepper (Capsicum annuum L. cv. Maccabi).	J. Bacteriol.	2012	194		5462-5463			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. 		
@D	Kolykhalov, A.A.//Repin, V.E.//Fish, A.M.//Rechkunova, N.I.//Degtyarev, S.K. 	Determination of substrate specificity of restriction endonuclease Vha464I.	Sib. Biol. J.	1991	19		60-61			The recognition sequence and cleavage point of restriction endonuclease Vha464I have been determined as 5'C^TTAAG. 		
@D	Komaki, H.//Hosoyama, A.//Ichikawa, N.//Igarashi, Y. 	Draft Genome Sequence of Marine-Derived Bacillus subtilis TP-B0611, a Producer of Bacilosarcins and Amicoumacins.	Genome Announcements	2016	4		e01134-16			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. 		
@D	Komaki, H.//Hosoyama, A.//Ichikawa, N.//Igarashi, Y. 	Draft Genome Sequence of Streptomyces sp. TP-A0874, a Catechoserine Producer.	Genome Announcements	2016	4		e01163-16			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. 		
@D	Komaki, H.//Hosoyama, A.//Ichikawa, N.//Panbangred, W.//Igarashi, Y. 	Draft Genome Sequence of Streptomyces sp. SPMA113, a Prajinamide Producer.	Genome Announcements	2016	4		e01126-16			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. 		
@D	Komaki, H.//Hosoyama, A.//Kimura, A.//Ichikawa, N.//Igarashi, Y. 	Draft Genome Sequence of an Anicemycin Producer, Streptomyces sp. TP-A0648.	Genome Announcements	2017	5		e01468-16			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. 		
@D	Komaki, H.//Hosoyama, A.//Yabe, S.//Yokota, A.//Uchino, Y.//Takano, H. 	Draft Genome Sequence of Thermogemmatispora onikobensis NBRC 111776T, an Aerial Mycelium- and Spore-Forming Thermophilic Bacterium Belonging to the Class  Ktedonobacteria.	Genome Announcements	2016	4		e01156-16			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. 		
@D	Komaki, H.//Ichikawa, N.//Hosoyama, A.//Fujita, N.//Harunari, E.//Igarashi, Y. 	Draft Genome Sequence of an Anthracimycin Producer, Streptomyces sp. TP-A0875.	Genome Announcements	2015	3		e01149-15			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. 		
@D	Komaki, H.//Ichikawa, N.//Hosoyama, A.//Fujita, N.//Igarashi, Y. 	Draft Genome Sequence of Marine-Derived Streptomyces sp. TP-A0873, a Producer of a Pyrrolizidine Alkaloid Bohemamine.	Genome Announcements	2015	3		e00008-15			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). 		
@D	Komaki, H.//Ichikawa, N.//Hosoyama, A.//Fujita, N.//Igarashi, Y. 	Draft genome sequence of marine-derived Streptomyces sp. TP-A0598, a producer of  anti-MRSA antibiotic lydicamycins.	Standards in Genomic Sciences	2015	10		58			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. 		
@D	Komaki, H.//Ichikawa, N.//Hosoyama, A.//Fujita, N.//Igarashi, Y. 	Draft Genome Sequence of Marine-Derived Actinomycete Nocardiopsis sp. Strain TP-A0876, a Producer of Polyketide Pyrones.	Genome Announcements	2014	2		e00665-14			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. 		
@D	Komaki, H.//Ichikawa, N.//Hosoyama, A.//Fujita, N.//Igarashi, Y. 	Draft Genome Sequence of Streptomyces sp. TP-A0356, a Producer of Yatakemycin.	Genome Announcements	2015	3		e01446-15			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. 		
@D	Komaki, H.//Ichikawa, N.//Hosoyama, A.//Fujita, N.//Igarashi, Y. 	Draft Genome Sequence of Nonomuraea sp. TP-A0861, a Producer of Myxochelin A.	Genome Announcements	2015	3		e01430-15			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. 		
@D	Komaki, H.//Ichikawa, N.//Hosoyama, A.//Fujita, N.//Igarashi, Y. 	Draft Genome Sequence of Streptomyces sp. TP-A0871, a Producer of Heronamide C.	Genome Announcements	2015	3		e01429-15			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. 		
@D	Komaki, H.//Ichikawa, N.//Hosoyama, A.//Fujita, N.//Igarashi, Y. 	Draft Genome Sequence of Streptomyces sp. TP-A0890, a Producer of FR-900452 and A-74863a.	Genome Announcements	2015	3		e01212-15			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. 		
@D	Komaki, H.//Ichikawa, N.//Hosoyama, A.//Fujita, N.//Thamchaipenet, A.//Igarashi, Y. 	Draft Genome Sequence of Linfuranone Producer Microbispora sp. GMKU 363.	Genome Announcements	2015	3		e01471-15			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. 		
@D	Komaki, H.//Ichikawa, N.//Hosoyama, A.//Hamada, M.//Harunari, E.//Ishikawa, A.//Igarashi, Y. 	Draft genome sequence of Micromonospora sp. DSW705 and distribution of biosynthetic gene clusters for depsipeptides bearing 4-amino-2,4-pentadienoate in  actinomycetes.	Standards in Genomic Sciences	2016	11		84			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. 		
@D	Komaki, H.//Ichikawa, N.//Oguchi, A.//Hamada, M.//Harunari, E.//Kodani, S.//Fujita, N.//Igarashi, Y. 	Draft genome sequence of Streptomyces sp. TP-A0867, an alchivemycin producer.	Standards in Genomic Sciences	2016	11		85			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. 		
@D	Komaki, H.//Ichikawa, N.//Oguchi, A.//Hamada, M.//Tamura, T.//Fujita, N. 	Draft Genome Sequence of Streptomyces albus Strain NBRC 13014T, the Type Species  of the Genus Streptomyces.	Genome Announcements	2015	3		e01527-14			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. 		
@D	Komaki, H.//Ichikawa, N.//Oguchi, A.//Hamada, M.//Tamura, T.//Fujita, N. 	Draft genome sequences of six type strains of the genus streptacidiphilus.	Genome Announcements	2015	3		e01387-14			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. 		
@D	Komaki, H.//Ichikawa, N.//Oguchi, A.//Hamada, M.//Tamura, T.//Suzuki, K.//Fujita, N. 	Draft Genome Sequence of Streptomyces hygroscopicus subsp. hygroscopicus NBRC 16556.	Genome Announcements	2016	4		e00139-16			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. 		
@D	Komaki, H.//Ishikawa, A.//Ichikawa, N.//Hosoyama, A.//Hamada, M.//Harunari, E.//Nihira, T.//Panbangred, W.//Igarashi, Y. 	Draft genome sequence of Streptomyces sp. MWW064 for elucidating the rakicidin biosynthetic pathway.	Standards in Genomic Sciences	2016	11		83			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. 		
@D	Komisarova, E.V.//Kislichkina, A.A.//Krasilnikova, V.M.//Bogun, A.G.//Fursova, N.K.//Volozhantsev, N.V. 	Complete Nucleotide Sequence of Klebsiella pneumoniae Bacteriophage vB_KpnM_KpV477.	Genome Announcements	2017	5		e00694-17			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. 		
@D	Komori, K.//Fujita, N.//Ichiyanagi, K.//Shinagawa, H.//Morikawa, K.//Ishino, Y. 	PI-PfuI and PI-PfuII, intein-coded homing endonucleases from Pyrococcus furiosus.  I. Purification and identification of the homing-type endonuclease activities.	Nucleic Acids Res.	1999	27		4167-4174			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. 		
@D	Komori, K.//Ichiyanagi, K.//Morikawa, K.//Ishino, Y. 	PI-PfuI and PI-PfuII, intein-coded homing endonucleases from Pyrococcus furiosus.  II. Characterization of the binding and cleavage abilities by site-directed mutagenesis.	Nucleic Acids Res.	1999	27		4175-4182			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. 		
@D	Konarev, P.V.//Kachalova, G.S.//Ryazanova, A.Y.//Kubareva, E.A.//Karyagina, A.S.//Bartunik, H.D.//Svergun, D.I. 	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.	PLoS ONE	2014	9		e93453			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. 		
@D	Koncz, C.//Kiss, A.//Venetianer, P. 	Biochemical characterization of the restriction-modification system of Bacillus sphaericus.	Eur. J. Biochem.	1978	89		523-529			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. 		
@D	Kondo, H.//Tinwongger, S.//Proespraiwong, P.//Mavichak, R.//Unajak, S.//Nozaki, R.//Hirono, I. 	Draft Genome Sequences of Six Strains of Vibrio parahaemolyticus Isolated from Early Mortality Syndrome/Acute Hepatopancreatic Necrosis Disease Shrimp in Thailand.	Genome Announcements	2014	2		e00221-14			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. 		
@D	Kondo, H.//Van, P.T.//Dang, L.T.//Hirono, I. 	Draft Genome Sequence of Non-Vibrio parahaemolyticus Acute Hepatopancreatic Necrosis Disease Strain KC13.17.5, Isolated from Diseased Shrimp in Vietnam.	Genome Announcements	2015	3		e00978-15			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. 		
@D	Kondo, Y.//Nishimata, H.//Hidaka, K.//Hasuwa, T.//Moriuchi, H.//Fujiwara, T.//Hoshino, T. 	Draft Genome Sequence of a Clinical Isolate of Streptococcus mutans Strain HM.	Genome Announcements	2017	5		e00826-17			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. 		
@D	Kondo, Y.//Ogura, Y.//Sato, K.//Imamura, K.//Hoshino, T.//Nishiguchi, M.//Hasuwa, T.//Moriuchi, H.//Hayashi, T.//Fujiwara, T. 	Complete Genome Sequence of Streptococcus sp. Strain NPS 308.	Genome Announcements	2016	4		e01349-16			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. 		
@D	Konforti, B. 	The servant with the scissors.	Nat. Struct. Biol.	2000	7		99-100			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? 		
@D	Kong, C.//Wang, L.//Li, P.//Qu, Y.//Tang, H.//Wang, J.//Zhou, H.//Ma, Q.//Zhou, J.//Xu, P. 	Genome Sequence of Dyella ginsengisoli Strain LA-4, an Efficient Degrader of Aromatic Compounds.	Genome Announcements	2013	1		e00961-13			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. 		
@D	Kong, H. 	Characterization of a new restriction-modification system, the BcgI system of Bacillus coagulans.	Ph.D. Thesis, Boston University	1998			1-130			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. 		
@D	Kong, H. 	Analyzing the functional organization of a novel restriction modification system, the BcgI system.	J. Mol. Biol.	1998	279		823-832			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. 		
@D	Kong, H.//Chen, Z. 	Isolation and identification of restriction endonuclease BstFI.	Nucleic Acids Res.	1987	15		7205			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. 		
@D	Kong, H.//Lin, L.F.//Porter, N.//Stickel, S.//Byrd, D.//Posfai, J.//Roberts, R.J. 	Functional analysis of putative restriction-modification system genes in the Helicobacter pylori J99 genome.	Nucleic Acids Res.	2000	28		3216-3223			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. 		
@D	Kong, H.//Morgan, R.D.//Chen, Z. 	A new type II restriction endonuclease, BsmAI, from Bacillus stearothermophilus.	Nucleic Acids Res.	1990	18		686			None 		
@D	Kong, H.//Morgan, R.D.//Chen, Z. 	Identification of a new type II restriction endonuclease BsaAI.	Nucleic Acids Res.	1990	18		2832			None 		
@D	Kong, H.//Morgan, R.D.//Maunus, R.E.//Schildkraut, I. 	A unique restriction endonuclease, BcgI, from Bacillus coagulans.	Nucleic Acids Res.	1993	21		987-991			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. 		
@D	Kong, H.//Roemer, S.E.//Waite-Rees, P.A.//Benner, J.S.//Wilson, G.G.//Nwankwo, D.O. 	Characterization of BcgI, a new kind of restriction-modification system.	J. Biol. Chem.	1994	269		683-690			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. 		
@D	Kong, H.//Smith, C.L. 	Does BcgI, a unique restriction endonuclease, require two recognition sites for cleavage?	Biol. Chem.	1998	379		605-609			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. 		
@D	Kong, H.//Smith, C.L. 	Substrate DNA and cofactor regulate the activities of a multi-functional restriction-modification enzyme, BcgI.	Nucleic Acids Res.	1997	25		3687-3692			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. 		
@D	Kong, J.//Gu, X.//Ma, G. 	The characterization of pJW566 from L. lactis subsp. cremoris W56.	Wei Sheng Wu Xue Bao	2001	41		542-547			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. 		
@D	Kong, J.//Jiang, H.//Li, B.//Zhao, W.//Li, Z.//Zhu, S. 	Complete Genome Sequence of Pseudomonas syringae pv. lapsa Strain ATCC 10859, Isolated from Infected Wheat.	Genome Announcements	2016	4		e00024-16			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. 		
@D	Kong, J.//Josephsen, J. 	The ability of the plasmid-encoded restriction and modification system LlaBIII to protect Lactococcus lactis against bacteriophages.	Lett. Appl. Microbiol.	2002	34		249-253			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. 		
@D	Kong, J.//Josephsen, J.//Ma, G.-R. 	The resistance conferred by the R/M system LlaBIII against bacteriophages.	Wei Sheng Wu Xue Bao	2002	42		246-250			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. 		
@D	Kong, J.//Josephsen, J.//Ma, G.R. 	Cloning and structure analysis of a restriction and modification system, LlaBIII from Lactococcus lactis subsp. cremoris W56.	Sheng Wu Gong Cheng Xue Bao	2001	17		663-668			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. 		
@D	Kong, N.//Davis, M.//Arabyan, N.//Huang, B.C.//Weis, A.M.//Chen, P.//Thao, K.//Ng, W.//Chin, N.//Foutouhi, S.//Foutouhi, A.//Kaufman, J.//Xie, Y.//Storey, D.B.//Weimer, B.C. 	Draft Genome Sequences of 1,183 Salmonella Strains from the 100K Pathogen Genome  Project.	Genome Announcements	2017	5		e00518-17			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. 		
@D	Kong, S.L.//Liu, X.Y.//Fu, L.W.//Yu, X.C.//An, C.C. 	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.	PLoS ONE	2012	7		e43738			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. 		
@D	Kong, W.J.//Yan, Y.C.//Li, X.Y.//Liu, Z.Y. 	Draft Genome Sequence of Bacillus velezensis PEBA20, a Strain with a Plant Growth-Promoting Effect and Biocontrol Potential.	Genome Announcements	2018	6		e00286-18			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. 		
@D	Konishi, K.//Kumagai, T.//Sakasegawa, S.I.//Tamura, T. 	Complete Genome Sequence of Burkholderia stabilis FERMP-21014.	Genome Announcements	2017	5		e00636-17			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. 		
@D	Konstantinidis, K.T.//DeLong, E.F. 	Genomic patterns of recombination, clonal divergence and environment in marine microbial populations.	ISME J.	2008	2		1052-1065			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. 		
@D	Kontur, W.S.//Schackwitz, W.S.//Ivanova, N.//Martin, J.//Labutti, K.//Deshpande, S.//Tice, H.N.//Pennacchio, C.//Sodergren, E.//Weinstock, G.M.//Noguera, D.R.//Donohue, T.J. 	Revised Sequence and Annotation of the Rhodobacter sphaeroides 2.4.1 Genome.	J. Bacteriol.	2012	194		7016-7017			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. 		
@D	Koo, H.//Basu, M.K.//Crowley, M.//Aislabie, J.//Bej, A.K. 	Draft Genome Sequence of Pseudomonas sp. Strain Ant30-3, a Psychrotolerant Bacterium with Biodegradative Attribute Isolated from Antarctica.	Genome Announcements	2014	2		e00522-14			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. 		
@D	Koo, H.//Ptacek, T.//Crowley, M.//Swain, A.K.//Osborne, J.D.//Bej, A.K.//Andersen, D.T. 	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.	Genome Announcements	2014	2		e00739-14			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. 		
@D	Koo, H.//Strope, B.M.//Kim, E.H.//Shabani, A.M.//Kumar, R.//Crowley, M.R.//Andersen, D.T.//Bej, A.K. 	Draft Genome Sequence of Janthinobacterium sp. Ant5-2-1, Isolated from Proglacial Lake Podprudnoye in the Schirmacher Oasis of East Antarctica.	Genome Announcements	2016	4		e01600-15			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. 		
@D	Koob, M. 	Conferring new cleavage specificities of restriction endonucleses.	Methods Enzymol.	1992	216		321-329			Detailed protocols for Achilles Heel cleavage are presented. 		
@D	Koob, M.//Burkiewicz, A.//Kur, J.//Szybalski, W. 	RecA-AC: single-site cleavage of plasmids and chromosomes at any predetermined restriction site.	Nucleic Acids Res.	1992	20		5831-5836			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. 		
@D	Koob, M.//Grimes, E.//Szybalski, W. 	Conferring operator specificity on restriction endonucleases.	Science	1988	241		1084-1086			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. 		
@D	Koob, M.//Grimes, E.//Szybalski, W. 	Conferring new specificity upon restriction endonucleases by combining repressor-operator interaction and methylation.	Gene	1988	74		165-167			Meeting Abstract 		
@D	Koob, M.D. 	Achilles' cleavage:  A general approach for conferring expanded specificities on restriction endonucleases.	Diss. Abstr.	1991	51		5161B			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. 		
@D	Koonin, E.V. 	A protein splice-junction motif in hedgehog family proteins.	Trends Biochem. Sci.	1995	20		141-142			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. 		
@D	Kopecka, H. 	A rapid purification method of restriction endonucleases from Haemophilus strains.	Biochim. Biophys. Acta	1975	391		109-120			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. 		
@D	Kopel, M.//Helbert, W.//Henrissat, B.//Doniger, T.//Banin, E. 	Draft Genome Sequence of Pseudoalteromonas sp. Strain PLSV, an Ulvan-Degrading Bacterium.	Genome Announcements	2014	2		e01257-14			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. 		
@D	Kopel, M.//Helbert, W.//Henrissat, B.//Doniger, T.//Banin, E. 	Draft Genome Sequence of Nonlabens ulvanivorans, an Ulvan-Degrading Bacterium.	Genome Announcements	2014	2		e00793-14			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. 		
@D	Kopel, M.//Helbert, W.//Henrissat, B.//Doniger, T.//Banin, E. 	Draft Genome Sequences of Two Ulvan-Degrading Isolates, Strains LTR and LOR, That Belong to the Alteromonas Genus.	Genome Announcements	2014	2		e01081-14			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. 		
@D	Kopf, M.//Klahn, S.//Voss, B.//Stuber, K.//Huettel, B.//Reinhardt, R.//Hess, W.R. 	Finished Genome Sequence of the Unicellular Cyanobacterium Synechocystis sp. Strain PCC 6714.	Genome Announcements	2014	2		e00757-14			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. 		
@D	Kopke, M.//Held, C.//Hujer, S.//Liesegang, H.//Wiezer, A.//Wollherr, A.//Ehrenreich, A.//Liebl, W.//Gottschalk, G.//Durre, P. 	Clostridium ljungdahlii represents a microbial production platform based on syngas.	Proc. Natl. Acad. Sci. U. S. A.	2010	107		13087-13092			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. 		
@D	Korba, B.E.//Hays, J.B. 	Partially deficient methylation of cytosine in DNA at CCA/TGG sites stimulates genetic recombination of bacteriophage lambda.	Cell	1982	28		531-541			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. 		
@D	Korch, C. 	Cross index for improving cloning selectivity by partially filling in 5'-extensions of DNA produced by type II restriction endonucleases.	Nucleic Acids Res.	1987	15		3199-3220			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. 		
@D	Korch, C.//Hagblom, P. 	In-vivo-modified gonococcal plasmid pJD1: A model system for analysis of restriction enzyme sensitivity to DNA modifications.	Eur. J. Biochem.	1986	161		519-524			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. 		
@D	Korch, C.//Hagblom, P.//Normark, S. 	Type III 5-methylcytosine modification of DNA in Neisseria gonorrhoeae.	J. Bacteriol.	1985	161		1236-1237			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. ] 		
@D	Korch, C.//Hagblom, P.//Normark, S. 	Sequence-specific DNA modification in Neisseria gonorrhoeae.	J. Bacteriol.	1983	155		1324-1332			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. ] 		
@D	Koren, S.//Harhay, G.P.//Smith, T.P.//Bono, J.L.//Harhay, D.M.//McVey, S.D.//Radune, D.//Bergman, N.H.//Phillippy, A.M. 	Reducing assembly complexity of microbial genomes with single-molecule sequencing.	Genome Biol.	2013	14		R101			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. 		
@D	Korlach, J.//Turner, S.W. 	Going beyond five bases in DNA sequencing.	Curr. Opin. Struct. Biol.	2012	22		251-261			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. 		
@D	Kornspan, J.D.//Lysnyansky, I.//Kahan, T.//Herrmann, R.//Rottem, S.//Nir-Paz, R. 	Genome analysis of a Mycoplasma hyorhinis strain derived from a primary human melanoma cell line.	J. Bacteriol.	2011	193		4543-4544			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. 		
@D	Korolev, S.V.//Samko, O.T.//Eldarov, M.A.//Kalugin, A.A.//Khoroshutina, E.B.//Omelyanyuk, N.M.//Sokolov, N.N.//Skryabin, K.G. 	Site-specific endonuclease BcuAI from Bacillus cereus A.	Bioorg. Khim.	1996	22		528-531			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. 		
@D	Korolev, S.V.//Sokolov, N.N.//Rina, M.//Eldarov, M.A.//Omelyanyuk, N.M.//Markaki, M.//Skryabin, K.G.//Bouriotis, V. 	Isolation and characterization of the specificity of new restriction endonucleases Bsp4009I and AsiI - isoschizomers of BamHI.	Mol. Gen. Mikrobiol. Virusol.	1998	0		32-35			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. 		
@D	Korona, R.//Korona, B.//Levin, B.R. 	Sensitivity of naturally occurring coliphages to type I and type II restriction and modification.	J. Gen. Microbiol.	1993	139		1283-1290			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. 		
@D	Korona, R.//Levin, B.R. 	Phage-mediated selection and the evolution and maintenance of restriction-modification.	Evolution	1993	47		556-575			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. 		
@D	Koryszewska-Baginska, A.//Aleksandrzak-Piekarczyk, T.//Bardowski, J. 	Complete Genome Sequence of the Probiotic Strain Lactobacillus casei (Formerly Lactobacillus paracasei) LOCK919.	Genome Announcements	2013	1		e00758-13			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. 		
@D	Koryszewska-Baginska, A.//Bardowski, J.//Aleksandrzak-Piekarczyk, T. 	Genome Sequence of the Probiotic Strain Lactobacillus rhamnosus (Formerly Lactobacillus casei) LOCK908.	Genome Announcements	2014	2		e00120-14			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). 		
@D	Korzun, V.//Balzer, H.J.//Balzer, A.//Baumlein, H.//Borner, A. 	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.	Genome	1996	39		1213-1215			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. 		
@D	Kos, V.N.//Deraspe, M.//McLaughlin, R.E.//Whiteaker, J.D.//Roy, P.H.//Alm, R.A.//Corbeil, J.//Gardner, H. 	The resistome of Pseudomonas aeruginosa in relationship to phenotypic susceptibility.	Antimicrob. Agents Chemother.	2014	59		427-436			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. 		
@D	Kosaka, T.//Toh, H.//Toyoda, A. 	Complete Genome Sequence of a Thermophilic Hydrogenotrophic Methanogen, Methanothermobacter sp. Strain CaT2.	Genome Announcements	2013	1		e00672-13			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. 		
@D	Kosaka, T.//Uchiyama, T.//Ishii, S.//Enoki, M.//Imachi, H.//Kamagata, Y.//Ohashi, A.//Harada, H.//Ikenaga, H.//Watanabe, K. 	Reconstruction and regulation of the central catabolic pathway in the thermophilic propionate-oxidizing syntroph Pelotomaculum  thermopropionicum.	J. Bacteriol.	2006	188		202-210			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. 		
@D	Kosinski, J.//Kubareva, E.//Bujnicki, J.M. 	A model of restriction endonuclease MvaI in complex with DNA: A template for interpretation of experimental data and a guide for specificity engineering.	Proteins	2007	68		324-336			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. 		
@D	Koskinen, J.P.//Laine, P.//Niemi, O.//Nykyri, J.//Harjunpaa, H.//Auvinen, P.//Paulin, L.//Pirhonen, M.//Palva, T.//Holm, L. 	Genome Sequence of Pectobacterium sp. Strain SCC3193.	J. Bacteriol.	2012	194		6004			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. 		
@D	Koskinen, P.//Deptula, P.//Smolander, O.P.//Tamene, F.//Kammonen, J.//Savijoki, K.//Paulin, L.//Piironen, V.//Auvinen, P.//Varmanen, P. 	Complete genome sequence of Propionibacterium freudenreichii DSM 20271(T).	Standards in Genomic Sciences	2015	10		83			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. 		
@D	Kossykh, V.//Repyk, A.//Kaliman, A.//Buryanov, Y. 	Nucleotide sequence of the EcoRII restriction endonuclease gene.	Biochim. Biophys. Acta	1989	1009		290-292			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. 		
@D	Kossykh, V.G.//Lloyd, R.S. 	A DNA Adenine Methyltransferase of Escherichia coli That Is Cell Cycle Regulated and Essential for Viability.	J. Bacteriol.	2004	186		2061-2067			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. 		
@D	Kossykh, V.G.//Repyk, A.V.//Hattman, S. 	Sequence motifs common to the EcoRII restriction endonuclease and the proposed sequence specificity domain of three DNA-[cytosine-C5] methyltransferases.	Gene	1993	125		65-68			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. 		
@D	Kossykh, V.G.//Schlagman, S.L.//Hattman, S. 	Function of Pro-185 in the ProCys of conserved motif IV in the EcoRII [cytosine-C5]-DNA methyltransferase.	FEBS Lett.	1995	370		75-77			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. 		
@D	Kossykh, V.G.//Schlagman, S.L.//Hattman, S. 	Conserved sequence motif DPPY in region IV of the phage T4 Dam DNA-[N6-adenine]-methyltransferase is important for S-adenosyl-L-methionine binding.	Nucleic Acids Res.	1993	21		3563-3566			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. 		
@D	Kossykh, V.G.//Schlagman, S.L.//Hattman, S. 	Phage T4 DNA [N6-adenine]Methyltransferase.	J. Biol. Chem.	1995	270		14389-14393			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). 		
@D	Kossykh, V.G.//Schlagman, S.L.//Hattman, S. 	Conserved sequence motif DPPY in region IV of the phage T4 Dam DNA-[N6-adenine]-methyltransferase is important for S-adenosyl-L-methionine binding.	Nucleic Acids Res.	1993	21		4659-4662			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. 		
@D	Kossykh, V.G.//Schlagman, S.L.//Hattman, S. 	Studies on the function of conserved sequence motifs in the T4 Dam-[N6-adenine] and EcoRII [C5-cytosine] DNA methyltransferases.	Gene	1995	157		125-126			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. 		
@D	Kossykh, V.G.//Schlagman, S.L.//Hattman, S. 	Comparative studies of the phage T2 and T4 DNA (N6-adenine) methyltransferases: Amino acid changes that affect catalytic activity.	J. Bacteriol.	1997	179		3239-3243			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. 		
@D	Kostiuk, G.//Dikic, J.//Schwarz, F.W.//Sasnauskas, G.//Seidel, R.//Siksnys, V. 	The dynamics of the monomeric restriction endonuclease BcnI during its interaction with DNA.	Nucleic Acids Res.	2017	45		5968-5979			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. 		
@D	Kostiuk, G.//Sasnauskas, G.//Tamulaitiene, G.//Siksnys, V. 	Degenerate sequence recognition by the monomeric restriction enzyme: single mutation converts BcnI into a strand-specific nicking endonuclease.	Nucleic Acids Res.	2011	39		3744-3753			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. 		
@D	Kostka, J.E.//Green, S.J.//Rishishwar, L.//Prakash, O.//Katz, L.S.//Marino-Ramirez, L.//Jordan, I.K.//Munk, C.//Ivanova, N.//Mikhailova, N.//Watson, D.B.//Brown, S.D.//Palumbo, A.V.//Brooks, S.C. 	Genome sequences for six rhodanobacter strains, isolated from soils and the terrestrial subsurface, with variable denitrification capabilities.	J. Bacteriol.	2012	194		4461-4462			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. 		
@D	Kostrewa, D.//Winkler, F.K. 	Mg2+ binding to the active site of EcoRV endonuclease: A crystallographic study of complexes with substrate and product DNA at 2 Angstrom resolution.	Biochemistry	1995	34		683-696			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. 		
@D	Kostriken, R.//Strathern, J.N.//Klar, A.J.S.//Hicks, J.B.//Heffron, F. 	A site-specific endonuclease essential for mating-type switching in Saccharomyces cerevisiae.	Cell	1983	35		167-174			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. 		
@D	Kosykh, V.G. 	Escherichia coli K-12 plasmid R245 controlling EcoRII restriction and DNA modification.	Dokl. Akad. Nauk.	1978	238		1227-1230					
@D	Kosykh, V.G.//Buryanov, Y.I.//Baev, A.A. 	Cloning the genes of EcoRII restrictase and methylase.	Dokl. Akad. Nauk.	1979	247		1269-1271					
@D	Kosykh, V.G.//Buryanov, Y.I.//Bayev, A.A. 	Molecular Cloning of EcoRII Endonuclease and Methylase Genes.	Mol. Gen. Genet.	1980	178		717-718			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. 		
@D	Kosykh, V.G.//Glinskaite, I.V.//Buryanov, J.I.//Baev, A.A. 	Mapping the EcoRII restrictase and methylase genes on recombinant plasmids.	Dokl. Akad. Nauk.	1982	265		727-730			None 		
@D	Kosykh, V.G.//Mantsygin, Y.A.//Svyatukhina, N.V.//Vitenene, I.V.//Buryanov, Y.I. 	Purification of the restriction endonuclease EcoRII using monoclonal antibodies.	Biokhimiia	1988	53		1474-1478			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. 		
@D	Kosykh, V.G.//Puntezhis, S.A.//Buryanov, Y.I.//Baev, A.A. 	Isolation, purification and properties of restriction endonuclease EcoRII.	Biokhimiia	1982	47		619-625			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. 		
@D	Kosykh, V.G.//Repik, A.V.//Kaliman, A.V.//Buryanov, Y.I.//Baev, A.A. 	Primary structure of the restriction endonuclease EcoRII gene.	Dokl. Akad. Nauk.	1989	308		1497-1499			None 		
@D	Kosykh, V.G.//Solonin, A.S.//Buryanov, Y.I.//Bayev, A.A. 	Overproduction of the EcoRII endonuclease and methylase by Escherichia coli strains carrying recombinant plasmids constructed in vitro.	Biochim. Biophys. Acta	1981	655		102-106			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. 		
@D	Kotak, M.//Isanapong, J.//Goodwin, L.//Bruce, D.//Chen, A.//Han, C.S.//Huntemann, M.//Ivanova, N.//Land, M.L.//Nolan, M.//Pati, A.//Woyke, T.//Rodrigues, J.L. 	Complete Genome Sequence of the Opitutaceae Bacterium Strain TAV5, a Potential Facultative Methylotroph of the Wood-Feeding Termite Reticulitermes flavipes.	Genome Announcements	2015	3		e00060-15			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. 		
@D	Kotani, H.//Nomura, Y.//Kawashima, Y.//Sagawa, H.//Takagi, M.//Kita, A.//Ito, H.//Kato, I. 	Sse8387I, a new type-II restriction endonuclease that recognizes the octanucleotide sequence 5'-CCTGCAGG-3'.	Nucleic Acids Res.	1990	18		5637-5640			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. 		
@D	Kothari, V.V.//Kothari, R.K.//Kothari, C.R.//Bhatt, V.D.//Nathani, N.M.//Koringa, P.G.//Joshi, C.G.//Vyas, B.R. 	Genome Sequence of Salt-Tolerant Bacillus safensis Strain VK, Isolated from Saline Desert Area of Gujarat, India.	Genome Announcements	2014	2		e00337-14					
@D	Kothari, V.V.//Kothari, R.K.//Kothari, C.R.//Bhatt, V.D.//Nathani, N.M.//Koringa, P.G.//Joshi, C.G.//Vyas, B.R. 	Genome Sequence of Salt-Tolerant Bacillus safensis Strain VK, Isolated from Saline Desert Area of Gujarat, India.	Genome Announcements	2013	1		e00671-13			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. 		
@D	Kotoky, R.//Singha, L.P.//Pandey, P. 	Draft Genome Sequence of Heavy Metal-Resistant Soil Bacterium Serratia marcescens S2I7, Which Has the Ability To Degrade Polyaromatic Hydrocarbons.	Genome Announcements	2017	5		e01338-17			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. 		
@D	Koton, Y.//Eghbaria, S.//Gordon, M.//Chalifa-Caspi, V.//Bisharat, N. 	Draft Genome Sequence of Fish Pathogenic Vibrio vulnificus Biotype 2.	Genome Announcements	2014	2		e01224-14			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. 		
@D	Kotorashvili, A.//Meparishvili, G.//Gogoladze, G.//Kotaria, N.//Muradashvili, M.//Zarandia, M.//Tsaguria, D. 	Three Draft Genome Sequences of the Bacterial Plant Pathogen Ralstonia solanacearum, Isolated in Georgia.	Genome Announcements	2017	5		e00480-17			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. 		
@D	Kotova, V.Y.//Zavilgelskii, G.B.//Belogurov, A.A. 	Weakening of the type-I restriction in the presence of plasmids of the incI group. General characteristics and molecular cloning of ard gene.	Mol. Biol. (Mosk)	1988	22		270-276			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. 		
@D	Koudan, E.V.//Brevnov, M.G.//Subach, O.M.//Rechkoblit, O.A.//Bujnicki, J.M.//Gromova, E.S. 	Probing of contacts between EcoRII DNA methyltransferase and DNA with the use of substrate analogs and molecular modeling.	Mol. Biol. (Mosk)	2007	41		806-819			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. 		
@D	Koudan, E.V.//Bujnicki, J.M.//Gromova, E.S. 	Homology modeling of the CG-specific DNA methyltransferase SssI and its complexes with DNA and AdoHcy.	J. Biomol. Struct. Dyn.	2004	22		339-345			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. 		
@D	Koudan, E.V.//Subach, O.M.//Korshunova, G.A.//Romanova, E.A.//Eritja, R.//Gromova, E.S. 	DNA duplexes containing photoactive derivatives of 2'-deoxyuridine as photocrosslinking probes for EcoRII DNA methyltransferase-substrate interaction.	J. Biomol. Struct. Dyn.	2002	20		421-428			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. 		
@D	Koufopanou, V.//Burt, A. 	Degeneration and domestication of a selfish gene in yeast: Molecular evolution versus site-directed mutagenesis.	Mol. Biol. Evol.	2005	22		1535-1538			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. 		
@D	Koufopanou, V.//Goddard, M.R.//Burt, A. 	Adaptation for horizontal transfer in a homing endonuclease.	Mol. Biol. Evol.	2002	19		239-246			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. 		
@D	Koukalova, B.//Kuhrova, V.//Reich, J. 	Protection of nonmodified phage lambda against EcoK restriction mediated by recA protein.	Folia Microbiol. (Praha)	1985	30		17-24			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. 		
@D	Kouvelis, V.N.//Davenport, K.W.//Brettin, T.S.//Bruce, D.//Detter, C.//Han, C.//Nolan, M.//Tapia, R.//Damoulaki, A.//Kyrpides, N.C.//Typas, M.A.//Pappas, K.M. 	Genome sequence of the ethanol-producing Zymomonas mobilis subsp. pomaceae lectotype strain ATCC 29192.	J. Bacteriol.	2011	193		5049-5050			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. 		
@D	Kouvelis, V.N.//Saunders, E.//Brettin, T.S.//Bruce, D.//Detter, C.//Han, C.//Typas, M.A.//Pappas, K.M. 	Complete genome sequence of ethanol producer Zymomonas mobilis NCIMB 11163.	J. Bacteriol.	2009	191		7140-7141			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. 		
@D	Kouvelis, V.N.//Teshima, H.//Bruce, D.//Detter, C.//Tapia, R.//Han, C.//Tampakopoulou, V.O.//Goodwin, L.//Woyke, T.//Kyrpides, N.C.//Typas, M.A.//Pappas, K.M. 	Finished Genome of Zymomonas mobilis subsp. mobilis Strain CP4, an Applied Ethanol Producer.	Genome Announcements	2014	2		e00845-13			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. 		
@D	Kouzminova, E.//Selker, E.U. 	dim-2 encodes a DNA methyltransferase responsible for all known cytosine methylation in Neurospora.	EMBO J.	2001	20		4309-4323			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. 		
@D	Kovalenko, N.A.//Sokolov, N.N. 	On the restriction endonucleases immobilization.	Mol. Gen. Mikrobiol. Virusol.	1988	0		13-15			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. 		
@D	Kovalenko, N.A.//Sokolov, N.N.//Chercasova, T.A.//Vonsky, V.E.//Leikin, Y.A. 	Immobilization of restriction endonucleases EcoRI, PaeI and LplI.	Bioorg. Khim.	1992	18		210-216			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. 		
@D	Kovalevskaya, N.P.//Ivanov, L.Y.//Zheleznaya, A.//Matvienko, N.I. 	Isolation and properties of the restriction endonuclease BstBSI from the thermophilic soil bacterium Bacillus stearothermophilus BS.	Mol. Gen. Mikrobiol. Virusol.	1993	3		22-25			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. 		
@D	Kovalevskaya, N.P.//Ivanov, L.Y.//Zheleznaya, L.A.//Matvienko, N.I. 	BstBSI, a restriction endonuclease from Bacillus stearothermophilus BS which recognizes 5'GTATAC3'.	Nucleic Acids Res.	1991	19		4296			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. 		
@D	Kovalevskaya, N.P.//Zelinskaya, N.V.//Zheleznaya, L.A.//Matvienko, N.I. 	Isolation and properties of the site-specific endonuclease BspTS514I from thermophilic bacterium Bacillus species TS514.	Bioorg. Khim.	1993	19		1073-1076			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. 		
@D	Kovalevskaya, N.P.//Zhelenznaya, L.A.//Zelinskaya, N.V.//Matvienko, N.I. 	A new thermophilic strain Bacillus coagulans, producing the site-specific endonuclease BcoKI.	Mikrobiologiia	1994	63		235-238			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. 		
@D	Kovalevskaya, N.P.//Zheleznaya, L.A.//Matvienko, N.I. 	BspLS21, a new site-specific endonuclease from thermophilic bacterium Bacillus species LS2.	Bioorg. Khim.	1992	18		1473-1477			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. 		
@D	Kovall, R.A.//Matthews, B.W. 	Type II restriction endonucleases: structural, functional and evolutionary relationships.	Curr. Opin. Chem. Biol.	1999	3		578-583			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. 		
@D	Kovall, R.A.//Matthews, B.W. 	Structural, functional, and evolutionary relationships between lambda-exonuclease and the type II restriction endonucleases.	Proc. Natl. Acad. Sci. U. S. A.	1998	95		7893-7897			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. 		
@D	Kovarik, A.//Koukalova, B.//Lim, L.Z.//Matyasek, R.//Lichtenstein, C.P.//Leitch, A.R.//Bezdek, M. 	Inhibition of tobacco DNA methyltransferase in vivo causes unequal hypomethylation of DNA repeated sequences.	J. Biomol. Struct. Dyn.	2000	17		1144-1145			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. 		
@D	Kowalski, J.C.//Belfort, M.//Stapleton, M.A.//Holpert, M.//Dansereau, J.T.//Pietrokovski, S.//Baxter, S.M.//Derbyshire, V. 	Configuration of the catalytic GIY-YIG domain of intron endonuclease I-TevI: coincidence of computational and molecular findings.	Nucleic Acids Res.	1999	27		2115-2125			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. 		
@D	Kowalski, J.C.//Derbyshire, V. 	Characterization of homing endonucleases.	Methods	2002	28		365-373			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. 		
@D	Kozak, N.A.//Buss, M.//Lucas, C.E.//Frace, M.//Govil, D.//Travis, T.//Olsen-Rasmussen, M.//Benson, R.F.//Fields, B.S. 	Virulence factors encoded by Legionella longbeachae identified on the basis of the genome sequence analysis of clinical isolate D-4968.	J. Bacteriol.	2010	192		1030-1044			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. 		
@D	Kozak-Muiznieks, N.A.//Morrison, S.S.//Mercante, J.W.//Ishaq, M.K.//Johnson, T.//Caravas, J.//Lucas, C.E.//Brown, E.//Raphael, B.H.//Winchell, J.M. 	Comparative genome analysis reveals a complex population structure of Legionella pneumophila subspecies.	Infect. Genet. Evol.	2018	59		172-185			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. 		
@D	Kozak-Muiznieks, N.A.//Morrison, S.S.//Sammons, S.//Rowe, L.A.//Sheth, M.//Frace, M.//Lucas, C.E.//Loparev, V.N.//Raphael, B.H.//Winchell, J.M. 	Three Genome Sequences of Legionella pneumophila subsp. pascullei Associated with Colonization of a Health Care Facility.	Genome Announcements	2016	4		e00335-16			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. 		
@D	Kozbial, P.Z.//Mushegian, A.R. 	Natural history of S-adenosylmethionine-binding proteins.	BMC Struct. Biol.	2005	5		19			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. 		
@D	Kozdon, J.B.//Melfi, M.D.//Luong, K.//Clark, T.A.//Boitano, M.//Wang, S.//Zhou, B.//Gonzalez, D.//Collier, J.//Turner, S.W.//Korlach, J.//Shapiro, L.//McAdams, H.H. 	Global methylation state at base-pair resolution of the Caulobacter genome throughout the cell cycle.	Proc. Natl. Acad. Sci. U. S. A.	2013	110		E4658-E4667			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. 		
@D	Kozhakhmetov, S.S.//Kushugulova, A.R.//Saduakhasova, S.A.//Shakhabayeva, G.S.//Khassenbekova, Z.R.//Molkenov, A.B.//Kairov, U.E.//Issayeva, R.B.//Nurgozhin, T.S.//Zhumadilov, Z.S. 	Draft Genome Sequence of Lactobacillus rhamnosus CLS17.	Genome Announcements	2015	3		e00478-15			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. 		
@D	Koziaeva, V.V.//Dziuba, M.V.//Ivanov, T.M.//Kuznetsov, B.B.//Skryabin, K.G.//Grouzdev, D.S. 	Draft Genome Sequences of Two Magnetotactic Bacteria, Magnetospirillum moscoviense BB-1 and Magnetospirillum marisnigri SP-1.	Genome Announcements	2016	4		e00814-16			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. 		
@D	Koziel, M.//Lucid, A.//Bullman, S.//Corcoran, G.D.//Lucey, B.//Sleator, R.D. 	Draft Genome Sequence of Campylobacter corcagiensis Strain CIT045T, a Representative of a Novel Campylobacter Species Isolated from Lion-Tailed Macaques (Macaca silenus).	Genome Announcements	2014	2		e00248-14			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. 		
@D	Koziolkiewicz, M. 	Interactions between EcoRI restriction endonuclease and DNA.	Postepy Biochem.	1991	37		23-32			*
 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
 
 		
@D	Koziolkiewicz, M.//Stec, W.J. 	Application of phosphate-backbone-modified oligonucleotides in the studies on EcoRI endonuclease mechanism of action.	Biochemistry	1992	31		9460-9466			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. 		
@D	Kozlowski, J.A.//Kits, K.D.//Stein, L.Y. 	Genome Sequence of Nitrosomonas communis Strain Nm2, a Mesophilic Ammonia-Oxidizing Bacterium Isolated from Mediterranean Soil.	Genome Announcements	2016	4		e01541-15			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. 		
@D	Kozlowski, J.A.//Kits, K.D.//Stein, L.Y. 	Complete Genome Sequence of Nitrosomonas ureae Strain Nm10, an Oligotrophic Group 6a Nitrosomonad.	Genome Announcements	2016	4		e00094-16			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. 		
@D	Krabbe, M.//Carlson, K. 	Squence and structure of endonuclease II-dependent cleavage sites in bacteriophage T4 DNA.	J. Biol. Chem.	1991	266		23407-23415			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. 		
@D	Kraev, A.S.//Kravets, A.N.//Chernov, B.K.//Skryabin, K.G.//Baev, A.A. 	The EcoRV restriction-modification system:  genes, enzymes, synthetic substrates.	Mol. Biol. (Mosk)	1985	19		278-284			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. 		
@D	Kraev, A.S.//Zimin, A.A.//Mironova, M.V.//Janulaitis, A.//Tanyashin, V.I.//Skryabin, K.G.//Bayev, A.A. 	The DNA ligase gene of bacteriophage T4.	Dokl. Akad. Nauk.	1983	270		1495-1500			note: This paper shows that GAGCT^C is a site for SduI.  This is the missing sequence from the earlier paper in FEBS Lett. 		
@D	Kraft, C.//Stack, A.//Josenhans, C.//Niehus, E.//Dietrich, G.//Correa, P.//Fox, J.G.//Falush, D.//Suerbaum, S. 	Genomic Changes during Chronic Helicobacter pylori Infection.	J. Bacteriol.	2006	188		249-254			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. 		
@D	Krahn, T.//Wibberg, D.//Maus, I.//Winkler, A.//Nordmann, P.//Puhler, A.//Poirel, L.//Schluter, A. 	Complete Genome Sequence of the Clinical Strain Acinetobacter baumannii R2090 Carrying the Chromosomally Encoded Metallo-beta-Lactamase Gene blaNDM-1.	Genome Announcements	2015	3		e01008-15			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. 		
@D	Krahn, T.//Wibberg, D.//Maus, I.//Winkler, A.//Puhler, A.//Poirel, L.//Schluter, A. 	Complete Genome Sequence of Acinetobacter baumannii CIP 70.10, a Susceptible Reference Strain for Comparative Genome Analyses.	Genome Announcements	2015	3		e00850-15			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. 		
@D	Kramarov, V.M.//Fomenkov, A.I.//Matvienko, N.I. 	A new type of cleavage of the recognition sequence by a site-specific endonuclease Bst4.4I from Bacillus stearothermophilus 4.4.	Bioorg. Khim.	1988	14		916-920			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. 		
@D	Kramarov, V.M.//Fomenkov, A.I.//Matvienko, N.I.//Ubieta, R.H.//Smolianinov, V.V.//Gorlenko, V.M. 	A new sequence-specific endonuclease CauB3I from Chloroflexus aurantiacus B3.	Bioorg. Khim.	1987	13		773-776			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. 		
@D	Kramarov, V.M.//Mazanov, A.L.//Pachkunov, D.M.//Smolyaninov, V.V.//Matvienko, N.I. 	Another site-specific endonuclease from Rhodopseudomonas sphaeroides.	Bioorg. Khim.	1984	10		46-49			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'. 		
@D	Kramarov, V.M.//Mazanov, A.L.//Smolyaninov, V.V. 	Isolation of a second site-specific endonuclease from Xanthomonas holcicola and its characterization.	Bioorg. Khim.	1982	8		220-223			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+. 		
@A	Kramarov, V.M.//Pachkunov, D.M.//Matvienko, N.I. 		Site-specific endonucleases BmeI and RshII.			Gaziev, A.I. 		Nek. Aspekty Fiziol. Mikroorg. Akad. Nauk. SSR.				Pushchino, USSR.	Nauchn. Tsentr Biol. Issled.	1983		0		22-26									None 		
@D	Kramarov, V.M.//Skrypina, N.A.//Smolyaninov, V.V.//Smirnov, V.V.//Resnik, S.R.//Sorokulova, I.B.//Matvienko, N.I. 	New site-specific endonuclease producer strains of Bacillus genera.	Mol. Gen. Mikrobiol. Virusol.	1989	0		42-45			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. 		
@D	Kramarov, V.M.//Smolyaninov, V.V. 	DNA methylase from Arthrobacter luteus screens DNA from the action of site-specific endonuclease AluI.	Biokhimiia	1981	46		1526-1529			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. 		
@D	Krasilnikova, M.M.//Izvolskii, K.I.//Krupnik, O.V.//Lazurkin, Y.S. 	Use of specific binding of peptide nucleic acids to DNA in the "Achilles heel" method.	Dokl. Akad. Nauk.	1995	344		552-555					
@D	Krasnoslobodtsev, A.V.//Shlyakhtenko, L.S.//Lyubchenko, Y.L. 	Probing Interactions within the Synaptic DNA-SfiI Complex by AFM Force Spectroscopy.	J. Mol. Biol.	2006	365		1407-1416			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. 		
@D	Krause, A. et al. 	Complete genome of the mutualistic, N2-fixing grass endophyte Azoarcus sp. strain BH72.	Nat. Biotechnol.	2006	24		1385-1391			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. 		
@D	Krause, D.O.//Little, A.C.//Dowd, S.E.//Bernstein, C.N. 	Complete genome sequence of adherent invasive Escherichia coli UM146 isolated from ileal Crohn's disease biopsy tissue.	J. Bacteriol.	2010	193		583			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. 		
@D	Krause, K.L.//Miller, M.D. 	A new engine for cleaving nucleic acid.	ACS Symp. Ser.	2002	827		270-293			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. 		
@D	Kravets, A.N.//Pertsev, A.V.//Tarutina, Z.E.//Solonin, A.S. 	High homology of plasmids carrying class II restriction modification systems, EcoRV isoschizomers, and their prevalence in natural Escherichia coli strains.	Mol. Gen. Mikrobiol. Virusol.	1998	3		20-22			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. 		
@D	Kravets, A.N.//Pertsev, A.V.//Tarutina, Z.Y.//Krendelev, Y.D.//Zakharova, M.V.//Beletskaya, I.V.//Solonin, A.S. 	New isoschizomers of restriction endonucleases in Pseudomonas aeruginosa strains.	Mol. Gen. Mikrobiol. Virusol.	1998	0		14-17			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. 		
@D	Kravets, A.N.//Solonin, A.S.//Zakharova, M.V.//Tarutina, Z.E. 	Plasmid localization and cloning of restriction-modification genes from Citrobacter freundii 4111 strain.	Mol. Gen. Mikrobiol. Virusol.	1992	7		4-7			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. 		
@D	Kravets, A.N.//Zakharova, M.V.//Solonin, A.S.//Kuzmin, N.P.//Tanyushin, V.I.//Glatman, L.I.//Moroz, A.F.//Baev, A.A. 	Cloning of genes of the EcoRV restriction-modification system and regulation of their expression.	Mol. Biol. (Mosk)	1990	24		438-447			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. 		
@D	Kravetz, A.N.//Tarutina, Z.E.//Solonin, A.S. 	Two novel restriction endonucleases from Pseudomonas aeruginosa.	Nucleic Acids Res.	1991	19		4781			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). 		
@D	Kravetz, A.N.//Zakharova, M.V.//Beletskaya, I.V.//Sineva, E.V.//Denjmuchametov, M.M.//Petrov, S.I.//Glatman, L.I.//Solonin, A.S. 	The cleavage sites and localization of genes encoding the restriction endonuclease Eco1831I and EcoHI.	Gene	1993	129		153-154			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. 		
@D	Kravetz, A.N.//Zakharova, M.V.//Beljetzkaja, I.V.//Pertzev, A.V.//Spivak, O.I.//Solonin, A.S. 	Two novel restriction endonucleases from Klebsiella pneumoniae.	Nucleic Acids Res.	1993	21		1501			Kpn49kI and Kpn49kII, type II restriction endonucleases have been isolated from the clinical strain Klebsiella pneumoniae 49k. 		
@D	Krawczyk, A.O.//Berendsen, E.M.//Eijlander, R.T.//de Jong, A.//Wells-Bennik, M.H.//Kuipers, O.P. 	Draft Genome Sequences of Four Bacillus thermoamylovorans Strains Isolated from Milk and Acacia Gum, a Food Ingredient.	Genome Announcements	2015	3		e00165-15			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. 		
@D	Krawczyk, A.O.//de Jong, A.//Eijlander, R.T.//Berendsen, E.M.//Holsappel, S.//Wells-Bennik, M.H.//Kuipers, O.P. 	Next-Generation Whole-Genome Sequencing of Eight Strains of Bacillus cereus, Isolated from Food.	Genome Announcements	2015	3		e01480-15			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. 		
@D	Krawczyk, A.O.//de Jong, A.//Holsappel, S.//Eijlander, R.T.//van Heel, A.//Berendsen, E.M.//Wells-Bennik, M.H.//Kuipers, O.P. 	Genome Sequences of 12 Spore-Forming Bacillus Species, Comprising Bacillus coagulans, Bacillus licheniformis, Bacillus amyloliquefaciens, Bacillus  sporothermodurans, and Bacillus vallismortis, Isolated from Foods.	Genome Announcements	2016	4		e00103-16			Here, we report the draft genomes of twelve isolates of five different Bacillus species, all spore-forming, Gram-positive bacteria. 		
@D	Krebes, J.//Morgan, R.D.//Bunk, B.//Sproeer, C.//Luong, K.//Parusel, R.//Anton, B.P.//Koenig, C.//Josenhans, C.//Overmann, J.//Roberts, R.J.//Korlach, J.//Suerbaum, S. 	The complex methylome of the human gastric pathogen Helicobacter pylori.	Nucleic Acids Res.	2014	42		2415-2432			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. 		
@D	Krefft, D.//Zylicz-Stachula, A.//Mulkiewicz, E.//Papkov, A.//Jezewska-Frackowiak, J.//Skowron, P.M. 	Two-stage gene assembly/cloning of a member of the TspDTI subfamily of bifunctional restriction endonucleases, TthHB27I.	J. Biotechnol.	2015	194		67-80			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. 		
@D	Kremer, F.S.//Eslabao, M.R.//Provisor, M.//Woloski, R.D.//Ramires, O.V.//Moreno, L.Z.//Moreno, A.M.//Hamond, C.//Lilenbaum, W.//Dellagostin, O.A. 	Draft Genome Sequences of Leptospira santarosai Strains U160, U164, and U233, Isolated from Asymptomatic Cattle.	Genome Announcements	2015	3		e00910-15			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. 		
@D	Krempl, P.M.//Mairhofer, J.//Striedner, G.//Thallinger, G.G. 	Finished Genome Sequence of the Laboratory Strain Escherichia coli K-12 RV308 (ATCC 31608).	Genome Announcements	2014	2		e00971-14			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). 		
@D	Kresge, N.//Simoni, R.D.//Hill, R.L. 	The Characterization of Restriction Endonucleases: the Work of Hamilton Smith.	J. Biol. Chem.	2010	285		e2-3			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. 		
@D	Kretchmar, S.A.//Chiu, H.S.//Srinivasan, A. 	Interaction of caffeine with DNA:  an evaluation with restriction endonucleases.	Microbios Lett.	1986	31		31-38			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. 		
@D	Kretz, P.L.//Kohler, S.W.//Short, J.M. 	Identification and characterization of a gene responsible for inhibiting propagation of methylated DNA sequences in mcrA mcrB1 Escherichia coli strains.	J. Bacteriol.	1991	173		4707-4716			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. 		
@D	Kretz, P.L.//Reid, C.H.//Greener, A.//Short, J.M. 	Effect of lambda packaging extract mcr restriction activity on DNA cloning.	Nucleic Acids Res.	1989	17		5409			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. 		
@D	Kriebardis, A.//Guschlbauer, W. 	dam methylase from E. coli: Circular dichroism investigations of the secondary structure and influence of S-adenosylmethionine.	FEBS Lett.	1987	213		297-300			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. 		
@D	Krishnakumar, R.//Assad-Garcia, N.//Benders, G.A.//Phan, Q.//Montague, M.G.//Glass, J.I. 	Targeted Chromosomal Knockouts in Mycoplasma pneumoniae.	Appl. Environ. Microbiol.	2010	76		5297-5299			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. 		
@D	Krishnamurthy, V.//Rao, D.N. 	Interaction of EcoPI modification methylase with S-adenosyl-L-methionine: a UV-crosslinking study.	Biochem. Mol. Biol. Int.	1994	32		623-632			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. 		
@D	Krishnaswamy, T.D.S. 	Structure-based sequence alignment of type-II restriction endonucleases.	Biochim. Biophys. Acta	2001	1544		217-228			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. 		
@D	Kriss, J.//Herrin, G.//Forman, L.//Cotton, R. 	Digestion conditions resulting in altered cut site specificity for HinfI.	Nucleic Acids Res.	1990	18		3665			None 		
@D	Kristiansen, R.//Dueholm, M.S.//Bank, S.//Nielsen, P.H.//Karst, S.M.//Cattoir, V.//Lienhard, R.//Grisold, A.J.//Olsen, A.B.//Reinhard, M.//Soby, K.M.//Christensen, J.J.//Prag, J.//Thomsen, T.R. 	Complete Genome Sequence of Actinobaculum schaalii Strain CCUG 27420.	Genome Announcements	2014	2		e00880-14			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. 		
@D	Kriszt, B.//Tancsics, A.//Cserhati, M.//Toth, A.//Nagy, I.//Horvath, B.//Nagy, I.//Tamura, T.//Kukolya, J.//Szoboszlay, S. 	De Novo Genome Project for the Aromatic Degrader Rhodococcus pyridinivorans Strain AK37.	J. Bacteriol.	2012	194		1247-1248			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. 		
@D	Kriukiene, E. 	Domain organization and metal ion requirement of the Type IIS restriction endonuclease MnlI.	FEBS Lett.	2006	580		6115-6122			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. 		
@D	Kriukiene, E. 	Restriction endonuclease MnlI - A member of the HNH family of endonucleases.	Ph.D. Thesis, Vilnius University	2007			1-45			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. 		
@D	Kriukiene, E.//Lubiene, J.//Lagunavicius, A.//Lubys, A. 	MnlI - The member of H-N-H subtype of Type IIS restriction endonucleases.	Biochim. Biophys. Acta	2005	1751		194-204			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. 		
@D	Kriukiene, E.//Lubys, A. 	Cloning and analysis of DNA regions adjacent to methyltransferase Lsp1109I of restriction-modification system Lsp1109I, type IIs.	Biologija	1998	2		62-65			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. 		
@D	Kriukiene, E.//Lubys, A. 	Comparison of two restriction-modification systems recognizing the same GGATCC sequence.	Biologija	1998	1		55-59			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. 		
@D	Kroft, B.S.//Brown, E.W.//Meng, J.//Gonzalez-Escalona, N. 	Draft Genome Sequences of Two Salmonella Strains from the SARA Collection, SARA64 (Muenchen) and SARA33 (Heidelberg), Provide Insight into Their Antibiotic  Resistance.	Genome Announcements	2013	1		e00806-13			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). 		
@D	Kroger, M.//Blum, E.//Deppe, E.//Dusterhoft, A.//Erdmann, D.//Kilz, S.//Meyer-Rogge, S.//Mostl, D. 	Organization and gene expression within restriction-modification systems of Herpetosiphon giganteus.	Gene	1995	157		43-47			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. 		
@D	Kroger, M.//Hobom, G. 	Restriction enzyme HgiCI characterization of the 6-nucleotide staggered cut sequence and its application in mismatch cloning.	Methods Enzymol.	1987	155		3-10			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. 		
@D	Kroger, M.//Hobom, G. 	The nucleotide sequence recognized by the Escherichia coli A restriction and modification enzyme.	Nucleic Acids Res.	1984	12		887-899			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. 		
@D	Kroger, M.//Hobom, G.//Schutte, H.//Mayer, H. 	Eight new restriction endonucleases from Herpetosiphon giganteus - divergent evolution in a family of enzymes.	Nucleic Acids Res.	1984	12		3127-3141			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. 		
@D	Krogh, T.J.//Agergaard, C.N.//Moller-Jensen, J.//Justesen, U.S. 	Draft Genome Sequence of Parabacteroides goldsteinii with Putative Novel Metallo-beta-Lactamases Isolated from a Blood Culture from a Human Patient.	Genome Announcements	2015	3		e00937-15			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. 		
@D	Kroon, A.M.//Bakker, H.//Holtrop, M.//Terpstra, P. 	The restriction endonuclease cleavage map of rat liver mitochondrial DNA.	Biochim. Biophys. Acta	1977	474		61-68			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. 		
@D	Kropinski, A.M.//Arutyunov, D.//Foss, M.//Cunningham, A.//Ding, W.//Singh, A.//Pavlov, A.R.//Henry, M.//Evoy, S.//Kelly, J.//Szymanski, C.M. 	Genome and Proteome of Campylobacter jejuni Bacteriophage NCTC 12673.	Appl. Environ. Microbiol.	2011	77		8265-8271			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. 		
@D	Kropinski, A.M.//Kovalyova, I.V.//Billington, S.J.//Patrick, A.N.//Butts, B.D.//Guichard, J.A.//Pitcher, T.J.//Guthrie, C.C.//Sydlaske, A.D.//Barnhill, L.M.//Havens, K.A.//Day, K.R.//Falk, D.R.//McConnell, M.R. 	The genome of epsilon 15, a serotype-converting, group E1 Salmonella enterica-specific bacteriophage.	Virology	2007	369		234-244			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. 		
@D	Kropp, K.A.//Lucid, A.//Carroll, J.//Belgrudov, V.//Walsh, P.//Kelly, B.//Smith, C.//Dickinson, P.//O'Driscoll, A.//Templeton, K.//Ghazal, P.//Sleator, R.D. 	Draft Genome Sequence of a Serratia marcescens Strain Isolated from a Preterm Neonatal Blood Sepsis Patient at the Royal Infirmary, Edinburgh, Scotland, United  Kingdom.	Genome Announcements	2014	2		e00908-14			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. 		
@D	Kropp, K.A.//Lucid, A.//Carroll, J.//Belgrudov, V.//Walsh, P.//Kelly, B.//Smith, C.//Dickinson, P.//O'Driscoll, A.//Templeton, K.//Ghazal, P.//Sleator, R.D. 	Draft Genome Sequence of an Enterococcus faecalis Strain Isolated from a Neonatal Blood Sepsis Patient.	Genome Announcements	2014	2		e00907-14			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. 		
@D	Kropp, K.A.//Lucid, A.//Carroll, J.//Belgrudov, V.//Walsh, P.//Kelly, B.//Smith, C.//Dickinson, P.//O'Driscoll, A.//Templeton, K.//Ghazal, P.//Sleator, R.D. 	Draft Genome Sequence of a Staphylococcus warneri Strain Isolated from a Preterm  Neonate Blood Sepsis Patient at the Royal Infirmary, Edinburgh, Scotland.	Genome Announcements	2014	2		e00877-14			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. 		
@D	Kropp, K.A.//Lucid, A.//Carroll, J.//Belgrudov, V.//Walsh, P.//Kelly, B.//Smith, C.//Dickinson, P.//O'Driscoll, A.//Templeton, K.//Ghazal, P.//Sleator, R.D. 	Draft Genome Sequence of a Streptococcus agalactiae Strain Isolated from a Preterm Neonate Blood Sepsis Patient at the Royal Infirmary, Edinburgh, Scotland.	Genome Announcements	2014	2		e00875-14			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. 		
@D	Kropp, K.A.//Lucid, A.//Carroll, J.//Belgrudov, V.//Walsh, P.//Kelly, B.//Templeton, K.//Smith, C.//Dickinson, P.//O'Driscoll, A.//Ghazal, P.//Sleator, R.D. 	Draft Genome Sequence of a Staphylococcus aureus Isolate Taken from the Blood of  a Preterm Neonatal Blood Sepsis Patient.	Genome Announcements	2014	2		e00906-14			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. 		
@D	Kropp, K.A.//Lucid, A.//Carroll, J.//Belgrudov, V.//Walsh, P.//Kelly, B.//Templeton, K.//Smith, C.//Dickinson, P.//O'Driscoll, A.//Ghazal, P.//Sleator, R.D. 	Draft Genome Sequence of a Pantoea sp. Isolated from a Preterm Neonatal Blood Sepsis Patient.	Genome Announcements	2014	2		e00904-14			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. 		
@D	Kruasuwan, W.//Hoskisson, P.A.//Thamchaipenet, A. 	Draft Genome Sequence of Root-Associated Sugarcane Growth-Promoting Microbispora  sp. Strain GKU 823.	Genome Announcements	2017	5		e00647-17			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. 		
@D	Kruasuwan, W.//Salih, T.S.//Brozio, S.//Hoskisson, P.A.//Thamchaipenet, A. 	Draft Genome Sequence of Plant Growth-Promoting Endophytic Streptomyces sp. GKU 895 Isolated from the Roots of Sugarcane.	Genome Announcements	2017	5		e00358-17			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. 		
@D	Krueger, D.H.//Kupper, D.//Meisel, A.//Reuter, M.//Schroeder, C. 	The significance of distance and orientation of restriction endonuclease recognition sites in viral DNA genomes.	FEMS Microbiol. Rev.	1995	17		177-184			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. 		
@D	Krueger, D.H.//Kupper, D.//Meisel, A.//Tierlich, M.//Reuter, M.//Schroeder, C. 	Restriction endonucleases functionally interacting with two DNA sites.	Gene	1995	157		165			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. 		
@D	Krueger, D.H.//Presber, W.//Hansen, S.//Rosenthal, H.A. 	Biological functions of the bacteriophage T3 SAMase gene.	J. Virol.	1975	16		453-455			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. 		
@D	Krueger, D.H.//Reuter, M. 	Reliable detection of DNA cytosine methylation at CpNpG sites using the engineered restriction enzyme EcoRII-C.	Biotechniques	2005	38		855-856			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. 		
@D	Krueger, M.//Meyerdierks, A.//Gloeckner, F.O.//Amann, R.//Widdel, F.//Kube, M.//Reinhardt, R.//Kahnt, J.//Boecher, R.//Thauer, R.K.//Shima, S. 	A conspicuous nickel protein in microbial mats that oxidize methane anaerobically.	Nature	2003	426		878-881			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. 		
@D	Kruger, D.H. 	Methylases as regulators of gene activity.	Wiss. Fortsch.	1987	37		268-270			None 		
@D	Kruger, D.H. 	Methylation of DNA as a molecular biological regulatory signal.	Biol. Zentralbl.	1988	107		257-266			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. 		
@A	Kruger, D.H. 		Host-controlled modification and restriction.			Webster, R.G//Granoff, A 		Encyclop. Virol.					Academic Press	1994		0		669-674									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.
 
 		
@D	Kruger, D.H.//Barcak, G.J.//Reuter, M.//Smith, H.O. 	EcoRII can be activated to cleave refractory DNA recognition sites.	Nucleic Acids Res.	1988	16		3997-4008			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. 		
@D	Kruger, D.H.//Barcak, G.J.//Smith, H.O. 	Abolition of DNA recognition site resistance to the restriction endonuclease EcoRII.	Biomed. Biochim. Acta	1988	47		K1-K5			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. 		
@D	Kruger, D.H.//Bickle, T.A. 	Bacteriophage Survival:  Multiple mechanisms for avoiding the deoxyribonucleic acid restriction systems of their hosts.	Microbiol. Rev.	1983	47		345-360			None 		
@A	Kruger, D.H.//Bickle, T.A.//Reuter, M.//Pein, C.-D.//Schroeder, C. 		DNA methylation and restriction processes in Escherichia coli: Insights by use of bacterial viruses T3 and T7.			Clawson, G.A.//Willis, D.B.//Weissbach, A.//Jones, P.A. 		Nucleic Acid Methylation					Alan R. Liss, Inc.	1990		0		113-124									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. 		
@D	Kruger, D.H.//Bickle, T.A.//Reuter, M.//Pein, C.D.//Schroeder, C. 	Studies on DNA methylation and restriction processes by use of bacterial virus T7.	J. Cell Biochem. Suppl.	1989	13D		200			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. 		
@D	Kruger, D.H.//Chernin, L.S.//Hansen, S.//Rosenthal, H.A.//Goldfarb, D.M. 	Protection of foreign DNA against host-controlled restriction in bacterial cells.	Mol. Gen. Genet.	1978	159		107-110			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. 		
@D	Kruger, D.H.//Gola, G.//Weisshuhn, I.//Hansen, S. 	The ocr gene function of bacterial viruses T3 and T7 prevents host-controlled modification.	J. Gen. Virol.	1978	41		189-192			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. 		
@D	Kruger, D.H.//Hansen, S.//Presber, W. 	Host-controlled modification and restriction of bacteriophage T7 by various Escherichia coli B strains in vivo.	Z. Allg. Mikrobiol.	1976	16		73-76			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. 		
@D	Kruger, D.H.//Hansen, S.//Reuter, M. 	The ocr+ gene function of bacteriophages T3 and T7 counteracts the Salmonella typhimurium DNA restriction systems SA and SB.	J. Virol.	1983	45		1147-1149			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. 		
@D	Kruger, D.H.//Presber, W.//Hansen, S.//Rosenthal, H.A. 	Different restriction of bacteriophages T3 and T7 by P1-lysogenic cells and the role of the T3-coded SAMase.	Z. Allg. Mikrobiol.	1977	17		581-591			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. 		
@D	Kruger, D.H.//Prosch, S.//Reuter, M.//Goebel, W. 	Cloning of the resistant EcoRII recognition site of phage T7 into an EcoRII-sensitive plasmid makes the site susceptible to the restriction enzyme.	J. Basic Microbiol.	1990	9		679-683			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. 		
@D	Kruger, D.H.//Reuter, M.//Hansen, S.//Schroeder, C. 	Influence of phage T3 and T7 gene functions on a Type III (EcoP1) DNA restriction-modification system in vivo.	Mol. Gen. Genet.	1982	185		457-461			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. 		
@D	Kruger, D.H.//Reuter, M.//Schroeder, C.//Glatman, L.I.//Chernin, L.S. 	Restriction of bacteriophage T3 and T7 ocr+ strains by the type II restriction endonuclease EcoRV.	Mol. Gen. Genet.	1983	190		349-351			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. 		
@D	Kruger, D.H.//Schroeder, C.//Hansen, S.//Rosenthal, H.A. 	Active protection by bacteriophages T3 and T7 against E. coli B- and K-specific restriction of their DNA.	Mol. Gen. Genet.	1977	153		99-106			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. 		
@D	Kruger, D.H.//Schroeder, C.//Reuter, M.//Bickle, T.A.//Bogdarina, I.G.//Buryanov, Y.I. 	Use of bacterial virus T7 as a tool for the study of DNA methylation.	Gene	1988	74		85-87			Meeting Abstract 		
@D	Kruger, D.H.//Schroeder, C.//Reuter, M.//Bogdarina, I.G.//Buryanov, Y.I.//Bickle, T.A. 	DNA methylation of bacterial viruses T3 and T7 by different DNA methylases in Escherichia coli K12 cells.	Eur. J. Biochem.	1985	150		323-330			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. 		
@D	Kruger, D.H.//Schroeder, C.//Santibanez-Koref, M.//Reuter, M. 	Avoidance of DNA methylation:  A virus-encoded methylase inhibitor and evidence for counterselection of methylase recognition sites in viral genomes.	Cell Biophys.	1989	15		87-95			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. 		
@D	Kruger, H.//Kirch, H. 	A nuclear protein from HeLa cells containing a methyltransferase specific domain binds to an intragenic region of the adenovirus 12 CS-1 E1A oncogene.	Biol. Chem. Hoppe Seyler	1992	373		789			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. 		
@D	Kruger, T.//Grund, C.//Wild, C.//Noyer-Weidner, M. 	Characterization of the mcrBC region of Escherichia coli K-12 wild-type and mutant strains.	Gene	1992	114		1-12			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. 		
@D	Kruger, T.//Wild, C.//Noyer-Weidner, M. 	McrB: a prokaryotic protein specifically recognizing DNA containing modified cytosine residues.	EMBO J.	1995	14		2661-2669			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. 		
@D	Kruger, V.D.H.//Reuter, M.//Chernin, L.S.//Gachechiladze, K.K.//Chanishvili, T.G.//Schroeder, C. 	Biological functions of restriction endonucleases.	Biol. Zentralbl.	1990	109		257-266			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. 		
@D	Krukov, V.M.//Shlyapnikov, M.G.//Kadyrov, F.A. 	Endonuclease SegE phage T4.  II. Determination and characterization of recognition site.	Mol. Biol. (Mosk)	1996	30		1307-1315					
@D	Kruse, T. et al. 	Complete genome sequence of Dehalobacter restrictus PER-K23(T.).	Standards in Genomic Sciences	2013	8		375-388			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. 		
@D	Krylov, V.N.//Karapetian, A.T. 	Discovery of new type of restriction and modification in enterobacteriaceae.	Genetika	1977	13		1079-1088			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. 		
@D	Krynetskaya, N.F.//Kubareva, E.A.//Timchenko, M.A.//Belkov, V.M.//Shabarova, Z.A. 	Transition-metal complexes as inhibitors of proteins recognizing double-stranded fragments of nucleic acids.	Biokhimiia	1998	63		1251-1257			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. 		
@D	Krzyzanowska, D.M.//Iwanicki, A.//Ossowicki, A.//Obuchowski, M.//Jafra, S. 	Genome Sequence of Bacillus subtilis MB73/2, a Soil Isolate Inhibiting the Growth of Plant Pathogens Dickeya spp. and Rhizoctonia solani.	Genome Announcements	2013	1		e00238-13			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. 		
@D	Ktari, A.//Nouioui, I.//Furnholm, T.//Swanson, E.//Ghodhbane-Gtari, F.//Tisa, L.S.//Gtari, M. 	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.	Standards in Genomic Sciences	2017	12		51			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. 		
@D	Ku, C.//Lo, W.S.//Chen, L.L.//Kuo, C.H. 	Complete Genome Sequence of Spiroplasma apis B31T (ATCC 33834), a Bacterium Associated with May Disease of Honeybees (Apis mellifera).	Genome Announcements	2014	2		e01151-13			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. 		
@D	Ku, C.//Lo, W.S.//Chen, L.L.//Kuo, C.H. 	Complete genomes of two dipteran-associated spiroplasmas provided insights into the origin, dynamics, and impacts of viral invasion in Spiroplasma.	Genome Biol. Evol.	2013	5		1151-1164			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. 		
@D	Kubareva, E.A.//Gromova, E.S.//Ortskaya, T.S.//Shabarova, Z.A. 	Interaction of EcoRII restriction and modification enzymes with synthetic DNA fragments.  X. Hydrolysis of substrates with structural anomalies.	Bioorg. Khim.	1987	13		1205-1211			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. 		
@D	Kubareva, E.A.//Gromova, E.S.//Pein, C.-D.//Krug, A.//Oretskaya, T.S.//Cech, D.//Shabarova, Z.A. 	Oligonucleotide cleavage by restriction endonucleases MvaI and EcoRII: a comprehensive study on the influence of structural parameters on the enzyme-substrate interaction.	Biochim. Biophys. Acta	1991	1088		395-400			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. 		
@D	Kubareva, E.A.//Gromova, E.S.//Romanova, E.A.//Oretskaya, T.S.//Shabarova, Z.A. 	Cleavage of substrates containing modified amino groups in heterocyclic bases by MvaI and EcoRII restriction endonucleases.	Bioorg. Khim.	1990	16		501-506			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. 		
@D	Kubareva, E.A.//Kuznetsova, S.A.//Kanevsky, I.A.//Karyagina, A.S.//Nikolskaya, I.I.//Shabarova, Z.A. 	DNA dumbbells as substrates for studying restriction-modification and repair enzymes.	FASEB J.	1997	11		A1309			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. 		
@D	Kubareva, E.A.//Pein, C.-D.//Gromova, E.S.//Kuznezova, S.A.//Tashlitzki, V.N.//Chech, D.//Shabarova, Z.A. 	The role of modifications in oligonucleotides in sequence recognition by MvaI restriction endonuclease.	Eur. J. Biochem.	1988	175		615-618			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. 		
@D	Kubareva, E.A.//Petrauskene, O.V.//Karyagina, A.S.//Nikolskaya, I.I.//Gromova, E.S. 	DNA duplexes with non-nucleotide inserts: interaction with restriction endonucleases.	Nucleic Acids Symp. Ser.	1991	24		308			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. 		
@D	Kubareva, E.A.//Petrauskene, O.V.//Karyagina, A.S.//Nikolskaya, I.I.//Gromova, E.S. 	Change of cleavage site of synthetic substrates by SsoII restriction endonuclease due to non-nucleotide inserts into the recognition sequence.	Bioorg. Khim.	1992	18		1131-1134			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. 		
@D	Kubareva, E.A.//Petrauskiene, O.V.//Karyagina, A.S.//Tashlitsky, V.N.//Nikolskaya, I.I.//Gromova, E.S. 	Cleavage of synthetic substrates containing non-nucleotide inserts by restriction endonucleases. Change in the cleavage specificity of endonuclease SsoII.	Nucleic Acids Res.	1992	20		4533-4538			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. 		
@D	Kubareva, E.A.//Thole, H.//Karyagina, A.S.//Oretskaya, T.S.//Pingoud, A.//Pingoud, V. 	Identification of a base-specific contact between the restriction endonuclease SsoII and its recognition sequence by photocross-linking.	Nucleic Acids Res.	2000	28		1085-1091			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. 		
@D	Kubareva, E.A.//Walter, J.//Karyagina, A.S.//Vorobeva, O.V.//Lau, P.C.//Trautner, T. 	Determination of methylation site of DNA-methyltransferase NlaX by a hybrid method.	Biotechniques	2002	33		526-531			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. 		
@D	Kubareva, E.A.//Walter, J.//Vorobeva, O.V.//Razumikhin, M.V.//Karyagina, A.S.//Lau, P.C.K.//Trautner, T. 	Determination of a non-methylated deoxycytidine desidue in the decognition site of DNA-methyltransferases.	Biokhimiia	2001	66		1356-1360			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. 		
@D	Kube, M.//Beck, A.//Zinder, S.H.//Kuhl, H.//Reinhardt, R.//Adrian, L. 	Genome sequence of the chlorinated compound-respiring bacterium Dehalococcoides species strain CBDB1.	Nat. Biotechnol.	2005	23		1269-1273			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. 		
@D	Kube, M.//Migdoll, A.M.//Gehring, I.//Heitmann, K.//Mayer, Y.//Kuhl, H.//Knaust, F.//Geider, K.//Reinhardt, R. 	Genome comparison of the epiphytic bacteria Erwinia billingiae and E. tasmaniensis with the pear pathogen E. pyrifoliae.	BMC Genomics	2010	11		393			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. 		
@D	Kube, M.//Schneider, B.//Kuhl, H.//Dandekar, T.//Heitmann, K.//Migdoll, A.M.//Reinhardt, R.//Seemuller, E. 	The linear chromosome of the plant-pathogenic mycoplasma 'Candidatus Phytoplasma mali'.	BMC Genomics	2008	9		306			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. 		
@D	Kube, M.//Siewert, C.//Migdoll, A.M.//Duduk, B.//Holz, S.//Rabus, R.//Seemuller, E.//Mitrovic, J.//Muller, I.//Buttner, C.//Reinhardt, R. 	Analysis of the Complete Genomes of Acholeplasma brassicae, A. palmae and A. laidlawii and Their Comparison to the Obligate Parasites from ' Candidatus Phytoplasma'.	J. Mol. Microbiol. Biotechnol.	2013	24		19-36			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. 		
@D	Kubiak, A.M.//Poehlein, A.//Budd, P.//Kuehne, S.A.//Winzer, K.//Theys, J.//Lambin, P.//Daniel, R.//Minton, N.P. 	Complete Genome Sequence of the Nonpathogenic Soil-Dwelling Bacterium Clostridium sporogenes Strain NCIMB 10696.	Genome Announcements	2015	3		e00942-15			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. 		
@D	Kubicek-Sutherland, J.Z.//Heithoff, D.M.//Ersoy, S.C.//Shimp, W.R.//Mahan, M.J. 	Immunization with a DNA adenine methylase over-producing Yersinia pseudotuberculosis vaccine confers robust cross-protection against heterologous pathogenic serotypes.	Vaccine	2014	32		1451-1459			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. 		
@D	Kubota, T. 	DNA methylase 3B (DNMT3B).	Seitai Kagaku	2005	56		378-379					
@D	Kuch, D.//Schermelleh, L.//Manetto, S.//Leonhardt, H.//Carell, T. 	Synthesis of DNA dumbbell based inhibitors for the human DNA methyltransferase Dnmt1.	Angew. Chem. Int. Ed. Engl.	2008	47		1515-1518			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. 		
@D	Kuck, D.//Singh, N.//Lyko, F.//Medina-Franco, J.L. 	Novel and selective DNA methyltransferase inhibitors: Docking-based virtual screening and experimental evaluation.	Bioorg. Med. Chem.	2010	18		822-829			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. 		
@D	Kudirkiene, E.//Christensen, H.//Bojesen, A.M. 	Draft Genome Sequence of Gallibacterium anatis bv. haemolytica 12656-12 Liver, an Isolate Obtained from the Liver of a Septicemic Chicken.	Genome Announcements	2013	1		e00810-13			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. 		
@D	Kudirkiene, E.//Hansen, M.J.//Bojesen, A.M. 	Draft Genome Sequence of Chelonobacter oris Strain 1662T, Associated with Respiratory Disease in Hermann's Tortoises.	Genome Announcements	2014	2		e01322-14			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%. 		
@D	Kudo, T. et al. 	Draft Genome Sequences of Psychrobacter Strains JCM 18900, JCM 18901, JCM 18902,  and JCM 18903, Isolated Preferentially from Frozen Aquatic Organisms.	Genome Announcements	2014	2		e00280-14			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. 		
@D	Kudo, T.//Kawauchi, A.//Nakahara, T.//Zhang, X.//Taniyama, S.//Takatani, T.//Arakawa, O.//Oshima, K.//Suda, W.//Kitamura, K.//Iida, T.//Iino, T.//Inoue, T.//Hongoh, Y.//Hattori, M.//Ohkuma, M. 	Draft Genome Sequences of Vibrio sp. Strains Isolated from Tetrodotoxin-Bearing Scavenging Gastropod.	Genome Announcements	2014	2		e00623-14			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. 		
@D	Kudo, T.//Nakahara, T.//Zhang, X.//Taniyama, S.//Arakawa, O.//Murase, S.//Nakata, H.//Oshima, K.//Suda, W.//Kitamura, K.//Iida, T.//Oshida, Y.//Inoue, T.//Hongoh, Y.//Hattori, M.//Ohkuma, M. 	Draft Genome Sequences of Geomicrobium sp. Strains JCM 19037, JCM 19038, JCM 19039, and JCM 19055, Isolated from Aquatic Samples.	Genome Announcements	2014	2		e00622-14			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. 		
@D	Kudo, T.//Sakamoto, K.//Akinaga, M.//Kawauchi, A.//Nakahara, T.//Zhang, X.//Yamada, A.//Oshima, K.//Suda, W.//Kuwahara, H.//Nakamura, N.//Nogi, Y.//Kitamura, K.//Yuki, M.//Iida, T.//Moriya, S.//Inoue, T.//Hongoh, Y.//Hattori, M.//Ohkuma, M. 	Draft Genome Sequences of Cyclodextrin-Producing Alkaliphilic Bacillus Strains JCM 19045, JCM 19046, and JCM 19047.	Genome Announcements	2014	2		e00211-14			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. 		
@D	Kuebbing, D.//Blakesley, R.J. 	A New Restriction Endonuclease from Streptomyces Stanford.	Fed. Proc.	1979	38		780			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. 		
@D	Kuehn, J.S.//Register, K.B.//Phillips, G.J. 	Draft Genome Sequences for 10 Isolates of the Swine Pathogen Haemophilus parasuis.	Genome Announcements	2013	1		e00739-13			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. 		
@D	Kuester, W.//Alves, J. 	Mutational analysis of the function of Ile197 in the EcoRI restriction endonuclease.	Biol. Chem. Hoppe Seyler	1995	376		S122			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. 		
@D	Kuever, J. et al. 	Genome analysis of Desulfotomaculum gibsoniae strain Groll(T) a highly versatile  Gram-positive sulfate-reducing bacterium.	Standards in Genomic Sciences	2014	9		821-839			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. 		
@D	Kugadas, A.//Humann, J.L.//Pierle, S.A.//Srikumaran, S.//Brayton, K.A. 	Genome Sequence of Bibersteinia trehalosi Strain Y31 Isolated from the Pneumonic  Lung of a Bighorn Sheep.	Genome Announcements	2016	4		e00722-16			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. 		
@D	Kuhlmann, U.C.//Moore, G.R.//James, R.//Kleanthous, C.//Hemmings, A.M. 	Structural parsimony in endonuclease active sites: should the number of homing endonuclease families be redefined?	FEBS Lett.	1999	463		1-2			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. 		
@D	Kuhn, H.//Frank-Kamenetskii, M.D.//Demidov, V.V. 	Site-specific nicking of duplex DNA using PNAs and restriction endonucleases.	J. Biomol. Struct. Dyn.	2003	20		916-917			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. 		
@D	Kuhn, H.//Hu, Y.//Frank-Kamenetskii, M.D.//Demidov, V.V. 	Artificial site-specific DNA-nicking system based on common restriction enzymes assisted by PNA openers.	Biochemistry	2003	42		4985-4992			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. 		
@D	Kuhn, I.//Stephenson, F.//Boyer, H.//Greene, P. 	Positive-selection vectors utilizing lethality of the EcoRI endonuclease.	Gene	1986	42		253-263			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. 		
@D	Kuhnlein, U.//Arber, W. 	Host specificity of DNA produced by Escherichia coli. XV.  The role of nucleotide methylation in in vitro B-specific modification.	J. Mol. Biol.	1972	63		9-19			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. 		
@D	Kuhnlein, U.//Linn, S.//Arber, W. 	Host specificity of DNA produced by Escherichia coli, XI.  In vitro modification of phage fd replicative form.	Proc. Natl. Acad. Sci. U. S. A.	1969	63		556-562			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. 		
@D	Kuhnlein, U.//Linn, S.//Arber, W. 	In vitro modifikation der replikativen form des bakteriophagen fd.	Pathol. Microbiol. (Basel)	1969	34		136			None 		
@D	Kulakauskas, S.//Barsomian, J.M.//Lubys, A.//Roberts, R.J.//Wilson, G.G. 	Organization and sequence of the HpaII restriction-modification system and adjacent genes.	Gene	1994	142		9-15			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). 		
@D	Kulakauskas, S.//Lubys, A.//Ehrlich, S.D. 	DNA restriction-modification systems mediate plasmid maintenance.	J. Bacteriol.	1995	177		3451-3454			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. 		
@D	Kulandai, L.T.//Lakshmipathy, D.//Ramasubban, G.//Vetrivel, U.//Rao, M.H.//Rathinam, S.//Narasimhan, M. 	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.	Genome Announcements	2014	2		e01173-14			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. 		
@D	Kulasekara, B.R. et al. 	Analysis of the genome of the Escherichia coli O157:H7 2006 spinach-associated outbreak isolate indicates candidate genes that may enhance virulence.	Infect. Immun.	2009	77		3713-3721			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. 		
@D	Kulba, A.M.//Abdel-Sabur, M.S.//Butkus, V.V.//Janulaitis, A.//Fomichev, Y.K. 	New type-II restrictase from cells of Erwinia herbicola.	Mol. Biol. (Mosk)	1987	21		250-254			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. 		
@D	Kulba, A.M.//Elgammudi, A.A. 	Detection of restriction endonucleases in Aeromonas bacteria.	Vestn. Beloruss. Gos. Univ.	1997	2		47-49					
@D	Kuleshov, K.V.//Koetsveld, J.//Goptar, I.A.//Markelov, M.L.//Kolyasnikova, N.M.//Sarksyan, D.S.//Toporkova, M.G.//Kirdyashkina, N.P.//Shipulin, G.A.//Hovius, J.W.//Platonov, A.E. 	Whole-Genome Sequencing of Six Borrelia miyamotoi Clinical Strains Isolated in Russia.	Genome Announcements	2018	6		e01424-17			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. 		
@D	Kuleshov, K.V.//Vodop'ianov, S.O.//Dedkov, V.G.//Markelov, M.L.//Kermanov, A.V.//Kruglikov, V.D.//Vodop'ianov, A.S.//Pisanov, R.V.//Chemisova, O.S.//Mazrukho, A.B.//Titova, S.V.//Shipulin, G.A. 	Draft Genome Sequencing of Vibrio cholerae O1 El Tor Isolates Collected in the Russian Federation from Imported Cholera Cases.	Genome Announcements	2014	2		e00624-14			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. 		
@D	Kuleshov, K.V.//Vodop'ianov, S.O.//Markelov, M.L.//Dedkov, V.G.//Kermanov, A.V.//Kruglikov, V.D.//Vodop'ianov, A.S.//Pisanov, R.V.//Mazrukho, A.B.//Shipulin, G.A. 	Draft Genome Sequences of Vibrio cholerae O1 ElTor Strains 2011EL-301 and P-18785, Isolated in Russia.	Genome Announcements	2013	1		e00659-13			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. 		
@D	Kuley, R.//Kuijt, E.//Smits, M.A.//Roest, H.I.J.//Smith, H.E.//Bossers, A. 	Genome Plasticity and Polymorphisms in Critical Genes Correlate with Increased Virulence of Dutch Outbreak-Related Coxiella burnetii Strains.	Front. Microbiol.	2017	8		1526			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. 		
@D	Kulik, E.M.//Bickle, T.A. 	Regulation of the activity of the type IC EcoR124I restriction enzyme.	J. Mol. Biol.	1996	264		891-906			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. 		
@D	Kulkarni, M.//Nirwan, N.//van Aelst, K.//Szczelkun, M.D.//Saikrishnan, K. 	Structural insights into DNA sequence recognition by Type ISP restriction-modification enzymes.	Nucleic Acids Res.	2016	44		4396-4408			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. 		
@D	Kumagai, Y.//Yoshizawa, S.//Nakamura, K.//Ogura, Y.//Hayashi, T.//Kogure, K. 	Complete and Draft Genome Sequences of Eight Oceanic Pseudomonas aeruginosa Strains.	Genome Announcements	2017	5		e01255-17			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. 		
@D	Kumagai, Y.//Yoshizawa, S.//Oshima, K.//Hattori, M.//Iwasaki, W.//Kogure, K. 	Complete Genome Sequence of Winogradskyella sp. Strain PG-2, a Proteorhodopsin-Containing Marine Flavobacterium.	Genome Announcements	2014	2		e00490-14			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. 		
@D	Kumano, M.//Sakakibara, M. 	Recombination of DNA in blue-green algae - restriction enzyme systems and transfection vectors.	Baiosaiensu to Indasutori	1988	46		38-41			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. 		
@D	Kumar, A.//Garg, N. 	Restriction endonucleases.	Genet. Eng. (N Y)	2005	0		55-74			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. 		
@D	Kumar, A.//Munjal, V.//Sheoran, N.//Prameela, T.P.//Suseelabhai, R.//Aggarwal, R.//Jain, R.K.//Eapen, S.J. 	Draft Genome Sequence of Highly Virulent Race 4/Biovar 3 of Ralstonia solanacearum CaRs_Mep Causing Bacterial Wilt in Zingiberaceae Plants in India.	Genome Announcements	2017	5		e01420-16			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. 		
@D	Kumar, B.K.//Deekshit, V.K.//Rai, P.//Gurtler, V.//Karunasagar, I.//Karunasagar, I. 	Draft Genome Sequence of trh+ Vibrio parahaemolyticus VP-49, Isolated from Seafood Harvested along the Mangalore Coast, India.	Genome Announcements	2014	2		e00607-14			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. 		
@D	Kumar, M.//Gazara, R.K.//Verma, S.//Kumar, M.//Verma, P.K.//Thakur, I.S. 	Genome Sequence of Pandoraea sp. ISTKB, a Lignin-Degrading Betaproteobacterium, Isolated from Rhizospheric Soil.	Genome Announcements	2016	4		e01240-16			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. 		
@D	Kumar, M.//Gazara, R.K.//Verma, S.//Kumar, M.//Verma, P.K.//Thakur, I.S. 	Genome Sequence of Carbon Dioxide-Sequestering Serratia sp. Strain ISTD04 Isolated from Marble Mining Rocks.	Genome Announcements	2016	4		e01141-16			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. 		
@D	Kumar, M.//Khanna, S. 	Diversity of 16S rRNA and dioxygenase genes detected in coal-tar-contaminated site undergoing active bioremediation.	J. Appl. Microbiol.	2010	108		1252-1262			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. 		
@D	Kumar, M.R.//Hosur, R.V.//Roy, K.B.//Miles, H.T.//Govil, G. 	Resonance assignment of the 500-MHz proton NMR spectrum of self-complementary dodecanucleotide d-GGATCCGGATCC:  altered conformations at BamHI cleavage sites.	Biochemistry	1985	24		7703-7711			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. 		
@D	Kumar, N.//Mukhopadhyay, A.K.//Patra, R.//De, R.//Baddam, R.//Shaik, S.//Alam, J.//Tiruvayipati, S.//Ahmed, N. 	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.	J. Bacteriol.	2012	194		5963-5964			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. 		
@D	Kumar, R.//Acharya, V.//Singh, D.//Kumar, S. 	Strategies for high-altitude adaptation revealed from high-quality draft genome of non-violacein producing Janthinobacterium lividum ERGS5:01.	Standards in Genomic Sciences	2018	13		11			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. 		
@D	Kumar, R.//Chang, C.C.//Ng, T.H.//Ding, J.Y.//Tseng, T.C.//Lo, C.F.//Wang, H.C. 	Draft Genome Sequence of Vibrio parahaemolyticus Strain M1-1, Which Causes Acute  Hepatopancreatic Necrosis Disease in Shrimp in Vietnam.	Genome Announcements	2018	6		e01468-17			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. 		
@D	Kumar, R.//Dwivedi, V.//Negi, V.//Khurana, J.P.//Lal, R. 	Draft Genome Sequence of Sphingobium lactosutens Strain DS20T, Isolated from a Hexachlorocyclohexane Dumpsite.	Genome Announcements	2013	1		e00753-13			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%. 		
@D	Kumar, R.//Mukhopadhyay, A.K.//Ghosh, P.//Rao, D.N. 	Comparative Transcriptomics of H. pylori Strains AM5, SS1 and Their hpyAVIBM Deletion Mutants: Possible Roles of Cytosine Methylation.	PLoS ONE	2012	7		e42303			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. 		
@D	Kumar, R.//Mukhopadhyay, A.K.//Rao, D.N. 	Characterization of an N6 adenine methyltransferase from Helicobacter pylori strain 26695 which methylates adjacent adenines on the same strand.	FEBS J.	2010	277		1666-1683			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. 		
@D	Kumar, R.//Prasad, Y.//Rao, D.N. 	Helicobacter pylori Restriction Modification systems: Role beyond genome protection.	Helicobacter	2014	19		0					
@D	Kumar, R.//Rao, D.N. 	A nucleotide insertion between two adjacent methyltransferases in Helicobacter pylori results in a bifunctional DNA methyltransferase.	Biochem. J.	2011	433		487-495			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. 		
@D	Kumar, R.//Rao, D.N. 	Role of DNA methyltransferases in epigenetic regulation in bacteria.	Subcell. Biochem.	2012	61		81-102			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. 		
@D	Kumar, R.//Sabareesh, V.//Mukhopadhyay, A.K.//Rao, D.N. 	Mutations in hpyAVIBM, C5 cytosine DNA methyltransferase from Helicobacter pylori result in relaxed specificity.	FEBS J.	2012	279		1080-1092			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. 		
@D	Kumar, R.//Singh, D.//Swarnkar, M.K.//Singh, A.K.//Kumar, S. 	Genome Assembly of Chryseobacterium polytrichastri ERMR1:04, a Psychrotolerant Bacterium with Cold Active Proteases, Isolated from East Rathong Glacier in  India.	Genome Announcements	2015	3		e01305-15			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. 		
@D	Kumar, R.//Srivastava, R.//Singh, R.K.//Surolia, A.//Rao, D.N. 	Activation and inhibition of DNA methyltransferases by S-adenosyl-L-homocysteine analogues.	Bioorg. Med. Chem.	2008	16		2276-2285			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. 		
@D	Kumar, R.A.//Vaze, M.B.//Chandra, N.R.//Vijayan, M.//Muniyappa, K. 	Functional characterization of the precursor and spliced forms of RecA protein of Mycobacterium tuberculosis.	Biochemistry	1996	35		1793-1802			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. 		
@D	Kumar, S.//Bala, M.//Raghava, G.P.//Mayilraj, S. 	Draft Genome Sequence of Rhodococcus triatomae Strain BKS 15-14.	Genome Announcements	2013	1		e0012913			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. 		
@D	Kumar, S.//Cheng, X.//Klimasauskas, S.//Sha, M.//Posfai, J.//Roberts, R.J.//Wilson, G.G. 	The DNA (cytosine-5) methyltransferases.	Nucleic Acids Res.	1994	22		1-10			A review of the m5C-methyltransferases relating sequence to structure and function. 		
@D	Kumar, S.//Cheng, X.//Pflugrath, J.W.//Roberts, R.J. 	Purification, crystallization, and preliminary X-ray diffraction analysis of an M.HhaI-AdoMet complex.	Biochemistry	1992	31		8648-8653			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. 		
@D	Kumar, S.//Horton, J.R.//Jones, G.D.//Walker, R.T.//Roberts, R.J.//Cheng, X. 	DNA containing 4'-thio-2'-deoxycytidine inhibits methylation by HhaI methyltransferase.	Nucleic Acids Res.	1997	25		2773-2783			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. 		
@D	Kumar, S.//Jangam, A.K.//Akhil, V.//Rajendran, V.//Katneni, V.K.//Sahaya, R.J.J.//Grover, M.//Nagaleekar, V.K.//Alavandi, S.V.//Vijayan, K.K. 	Draft Genome Sequence of the Luminescent Strain Vibrio campbellii LB102, Isolated from a Black Tiger Shrimp (Penaeus monodon) Broodstock Rearing System.	Genome Announcements	2017	5		e00342-17			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. 		
@D	Kumar, S.//Johnson, W.S.//Tomasz, M. 	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.	Biochemistry	1993	32		1364-1372			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. 		
@D	Kumar, S.//Karmakar, B.C.//Nagarajan, D.//Mukhopadhyay, A.K.//Morgan, R.D.//Rao, D.N. 	N4-cytosine DNA methylation regulates transcription and pathogenesis in Helicobacter pylori.	Nucleic Acids Res.	2018	46		3429-3445			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. 		
@D	Kumar, S.//Kaur, C.//Kimura, K.//Takeo, M.//Raghava, G.P.//Mayilraj, S. 	Draft Genome Sequence of the Type Species of the Genus Citrobacter, Citrobacter freundii MTCC 1658.	Genome Announcements	2013	1		e00120-12			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. 		
@D	Kumar, S.//Kaur, N.//Singh, N.K.//Raghava, G.P.//Mayilraj, S. 	Draft Genome Sequence of Streptomyces gancidicus Strain BKS 13-15.	Genome Announcements	2013	1		e00150-13			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. 		
@D	Kumar, S.//Lindquist, I.E.//Sundararajan, A.//Rajanna, C.//Floyd, J.T.//Smith, K.P.//Andersen, J.L.//He, G.//Ayers, R.M.//Johnson, J.A.//Werdann, J.J.//Sandoval, A.A.//Mojica, N.M.//Schilkey, F.D.//Mudge, J.//Varela, M.F. 	Genome Sequence of Non-O1 Vibrio cholerae PS15.	Genome Announcements	2013	1		e00227-12			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. 		
@D	Kumar, S.//Patil, P.P.//Midha, S.//Ray, P.//Patil, P.B.//Gautam, V. 	Genome Sequence of Acinetobacter baumannii Strain 10441_14 Belonging to ST451, Isolated from India.	Genome Announcements	2015	3		e01322-15			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. 		
@D	Kumar, S.//Patil, P.P.//Midha, S.//Ray, P.//Patil, P.B.//Gautam, V. 	Genome Sequence of Acinetobacter baumannii Strain 5021_13, Isolated from Cerebrospinal Fluid.	Genome Announcements	2015	3		e01213-15			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. 		
@D	Kumar, S.//Subramanian, S.//Raghava, G.P.//Pinnaka, A.K. 	Genome Sequence of the Marine Bacterium Marinilabilia salmonicolor JCM 21150T.	J. Bacteriol.	2012	194		3746			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. 		
@D	Kumar, S.//Vikram, S.//Raghava, G.P. 	Genome Sequence of the Nitroaromatic Compound-Degrading Bacterium Burkholderia sp. Strain SJ98.	J. Bacteriol.	2012	194		3286			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. 		
@D	Kumar, S.//Vikram, S.//Subramanian, S.//Raghava, G.P.//Pinnaka, A.K. 	Genome Sequence of the Halotolerant Bacterium Imtechella halotolerans K1T.	J. Bacteriol.	2012	194		3731			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. 		
@D	Kumar-Pinnaka, P.A.//Ara, S.//Singh, A.//Shivaji, S. 	Draft Genome Sequence of Winogradskyella psychrotolerans RS-3T, Isolated from the Marine Transect of Kongsfjorden, Ny-Alesund, Svalbard, Arctic Ocean.	Genome Announcements	2013	1		e00630-13			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. 		
@D	Kumar-Pinnaka, P.A.//Singh, A.//Ara, S.//Begum, Z.//Reddy, G.S.//Shivaji, S. 	Draft Genome Sequence of Leifsonia rubra Strain CMS 76RT, Isolated from a Cyanobacterial Mat Sample from a Pond in Wright Valley, McMurdo, Antarctica.	Genome Announcements	2013	1		e00633-13			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. 		
@D	Kumaravel, S.//Thankappan, S.//Raghupathi, S.//Uthandi, S. 	Draft Genome Sequence of Plant Growth-Promoting and Drought-Tolerant Bacillus altitudinis FD48, Isolated from Rice Phylloplane.	Genome Announcements	2018	6		e00019-18			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. 		
@D	Kumaresan, D.//Wischer, D.//Hillebrand-Voiculescu, A.M.//Murrell, J.C. 	Draft Genome Sequences of Facultative Methylotrophs, Gemmobacter sp. Strain LW1 and Mesorhizobium sp. Strain 1M-11, Isolated from Movile Cave, Romania.	Genome Announcements	2015	3		e01266-15			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. 		
@D	Kumari, M.//Swarnkar, M.K.//Kumar, S.//Singh, A.K.//Gupta, M. 	Complete Genome Sequence of Potential Probiotic Lactobacillus sp. HFC8, Isolated  from Human Gut Using PacBio SMRT Sequencing.	Genome Announcements	2015	3		e01337-15			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. 		
@D	Kumari, M.//Swarnkar, M.K.//Kumar, S.//Singh, A.K.//Gupta, M. 	Genome Sequence of a Potential Probiotic Strain, Lactobacillus fermentum HFB3, Isolated from a Human Gut.	Genome Announcements	2015	3		e01296-15			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. 		
@D	Kumari, P.//Badhai, J.//Das, S.K. 	Draft Genome Sequence of Marinomonas fungiae Strain AN44(T) (JCM 18476(T)), Isolated from the Coral Fungia echinata from the Andaman Sea.	Genome Announcements	2018	6		e00112-18			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. 		
@D	Kumru, S.//Tekedar, H.C.//Griffin, M.J.//Waldbieser, G.C.//Liles, M.R.//Sonstegard, T.//Schroeder, S.G.//Lawrence, M.L.//Karsi, A. 	Draft Genome Sequence of Fish Pathogen Aeromonas bestiarum GA97-22.	Genome Announcements	2018	6		e00524-18			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. 		
@D	Kumru, S.//Tekedar, H.C.//Waldbieser, G.C.//Karsi, A.//Lawrence, M.L. 	Genome Sequence of the Fish Pathogen Flavobacterium columnare Genomovar II Strain 94-081.	Genome Announcements	2016	4		e00430-16			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. 		
@D	Kunadia, K.//Nathani, N.M.//Kothari, V.//Kotadia, R.J.//Kothari, C.R.//Joshi, A.//Rank, J.K.//Faldu, P.R.//Shekar, M.C.//Viroja, M.J.//Patel, P.A.//Jadeja, D.//Reddy, B.//Pal, S.R.//Koringa, P.G.//Joshi, C.G.//Kothari, R.K. 	Draft Genome Sequence of Commercial Textile Dye-Decolorizing and -Degrading Bacillus subtilis Strain C3 Isolated in India.	Genome Announcements	2016	4		e00104-16			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. 		
@D	Kunert, N. 	Identification and characterization of IPOD, a novel interaction partner of the DNA methyltransferase Dnmt2 from Drosophila melanogaster.	Ph.D. Thesis, Germany	2005			1-142					
@D	Kunkel, L.M.//Silberklang, M.//McCarthy, B.J. 	A third restriction endonuclease from Xanthomonas malvacearum.	J. Mol. Biol.	1979	132		133-139			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. 		
@D	Kunne, C.//Billion, A.//Mshana, S.E.//Schmiedel, J.//Domann, E.//Hossain, H.//Hain, T.//Imirzalioglu, C.//Chakraborty, T. 	Complete Sequences of Plasmids from the Hemolytic-Uremic Syndrome-Associated Escherichia coli Strain HUSEC41.	J. Bacteriol.	2012	194		532-533			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. 		
@D	Kunst, F. et al. 	The complete genome sequence of the Gram-positive bacterium Bacillus subtilis.	Nature	1997	390		249-256			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. 		
@D	Kunta, M.//Zheng, Z.//Wu, F.//da Graca, J.V.//Park, J.W.//Deng, X.//Chen, J. 	Draft Whole-Genome Sequence of 'Candidatus Liberibacter asiaticus' Strain TX2351  Isolated from Asian Citrus Psyllids in Texas, USA.	Genome Announcements	2017	5		e00170-17			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. 		
@D	Kunz, A.//Mackeldanz, P.//Mucke, M.//Meisel, A.//Reuter, M.//Schroeder, C.//Kruger, D.H. 	Mutual activation of two restriction endonucleases: interaction of EcoPI and EcoP15.	Biol. Chem.	1998	379		617-620			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. 		
@D	Kunz, A.//Meisel, A.//Mackeldanz, P.//Reuter, M.//Kruger, D.H. 	An experimental selection system to identify bacterial cells exhibiting a new DNA host specificity.	Biol. Chem.	1998	379		563-566			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. 		
@D	Kuo, V.//Shoemaker, W.R.//Muscarella, M.E.//Lennon, J.T. 	Whole-Genome Sequence of the Soil Bacterium Micrococcus sp. KBS0714.<jour_book>Genome Announc.		2017	5		e00697-17			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. 		
@D	Kuosmanen, M.//Poso, H. 	Inhibition of the activity of restriction endonucleases by spermidine and spermine.	FEBS Lett.	1985	179		17-20			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. 		
@D	Kupper, D.//Moncke-Buchner, E.//Reuter, M.//Kruger, D.H. 	Oligonucleotide stimulators allow complete cleavage of agarose-embedded DNA by particular type II restriction endonucleases.	Anal. Biochem.	1999	272		275-277			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. 		
@D	Kupper, D.//Reuter, M.//Kruger, D.H. 	Overproduction of His-tagged EcoRII restriction endonuclease and terminally deleted mutant proteins.	Gene	1995	157		97-98			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. 		
@D	Kupper, D.//Reuter, M.//Mackeldanz, P.//Meisel, A.//Alves, J.//Schroeder, C.//Kruger, D.H. 	Hyperexpressed EcoRII renatured from inclusion bodies and native enzyme both exhibit essential cooperativity with two DNA sites.	Protein Expr. Purif.	1995	6		1-9			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. 		
@D	Kupper, D.//Reuter, M.//Meisel, A.//Kruger, D.H. 	Reliable detection of DNA CpG methylation profiles by the isoschizomers MspI/HpaII using oligonucleotide stimulators.	Biotechniques	1997	23		843-846			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. 		
@D	Kupper, D.//Zhou, J.-G.//Kiss, A.//Venetianer, P. 	Cloning and structure of the M.BepI modification methyltransferase.	Gene	1988	74		33			Meeting abstract 		
@D	Kupper, D.//Zhou, J.-G.//Venetianer, P.//Kiss, A. 	Cloning and structure of the BepI modification methylase.	Nucleic Acids Res.	1989	17		1077-1088			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. 		
@D	Kupriyanova, N.S.//Kirilenko, P.M.//Netchvolodov, K.K.//Ryskov, A.P. 	Preferential cleavage sites for Sau3A restriction endonuclease in human ribosomal DNA.	Biochem. Biophys. Res. Commun.	2000	274		11-15			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. 		
@D	Kur, J. 	Integration host factor (IHF) applied for partial digestion by restriction endonucleases in large DNA molecules (IARC procedure).	Acta Microbiol. Pol.	1993	42		145-150			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. 		
@D	Kur, J. 	Use of IHF mediated achilles' heel cleavage (IHF-AC) method for mapping ihf sites.	Acta Microbiol. Pol.	1993	42		137-144			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. 		
@D	Kur, J.//Koob, M.//Burkiewicz, A.//Szybalski, W. 	A novel method for converting common restriction enzymes into rare cutters:  integration host factor-mediated Achilles' cleavage (IHF-AC).	Gene	1992	110		1-7			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. 		
@D	Kurakin, A.V.//Zaritskaya, L.S.//Metliskaya, A.Z.//Volodin, A.A.//Cherny, D.I. 	BspRI methyltransferase as a marker for electron microscopic physical mapping.	Micron and Microscopica Acta	1991	22		213-221			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. 		
@D	Kurata, A.//Hirose, Y.//Misawa, N.//Hurunaka, K.//Kishimoto, N. 	Draft Genome Sequence of the Ionic Liquid-Tolerant Bacterium Bacillus amyloliquefaciens CMW1.	Genome Announcements	2014	2		e01051-14			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. 		
@D	Kurata, A.//Nishimura, M.//Kishimoto, N.//Kobayashi, T. 	Draft Genome Sequence of a Deep-Sea Bacterium, Bacillus niacini Strain JAM F8, Involved in the Degradation of Glycosaminoglycans.	Genome Announcements	2014	2		e00983-14			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. 		
@D	Kurilshikov, A.M.//Fomenko, N.V.//Stronin, O.V.//Tikunov, A.Y.//Kabilov, M.R.//Tupikin, A.E.//Tikunova, N.V. 	Complete Genome Sequencing of Borrelia valaisiana and Borrelia afzelii Isolated from Ixodes persulcatus Ticks in Western Siberia.	Genome Announcements	2014	2		e01315-14			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. 		
@D	Kurilung, A.//Keeratipusana, C.//Suriyaphol, P.//Prapasarakul, N. 	Draft Genome Sequence of a Leptospira interrogans Strain Isolated from the Urine  of an Asymptomatic Dog in Thailand.	Genome Announcements	2018	6		e01140-17			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. 		
@D	Kuroda, M. et al. 	Whole genome sequencing of meticillin-resistant Staphylococcus aureus.	Lancet	2001	357		1225-1240			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. 		
@D	Kuroda, M.//Ayano, H.//Sei, K.//Yamashita, M.//Ike, M. 	Draft Genome Sequence of Bacillus selenatarsenatis SF-1T, a Promising Agent for Bioremediation of Environments Contaminated with Selenium and Arsenic.	Genome Announcements	2015	3		e01466-14			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. 		
@D	Kuroda, M.//Ogata, Y.//Yahara, T.//Yokoyama, T.//Ishizawa, H.//Takada, K.//Inoue, D.//Sei, K.//Ike, M. 	Draft Genome Sequence of Sphingobium fuliginis OMI, a Bacterium That Degrades Alkylphenols and Bisphenols.	Genome Announcements	2017	5		e01323-17			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. 		
@D	Kuroda, M.//Yamashita, A.//Hirakawa, H.//Kumano, M.//Morikawa, K.//Higashide, M.//Maruyama, A.//Inose, Y.//Matoba, K.//Toh, H.//Kuhara, S.//Hattori, M.//Ohta, T. 	Whole genome sequence of Staphylococcus saprophyticus reveals the pathogenesis of uncomplicated urinary tract infection.	Proc. Natl. Acad. Sci. U. S. A.	2005	102		13272-13277			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. 		
@D	Kurokawa, S.//Bessho, Y.//Higashijima, K.//Shirouzu, M.//Yokoyama, S.//Watanabe, K.I.//Ohama, T. 	Adaptation of intronic homing endonuclease for successful horizontal transmission.	FEBS J.	2005	272		2487-2496			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. 		
@D	Kurokawa, S.//Kabayama, J.//Nho, S.W.//Hwang, S.D.//Hikima, J.//Jung, T.S.//Kondo, H.//Hirono, I.//Takeyama, H.//Aoki, T. 	Whole-Genome Sequence of Fish-Pathogenic Mycobacterium sp. Strain 012931, Isolated from Yellowtail (Seriola quinqueradiata).	Genome Announcements	2013	1		e00534-13			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). 		
@D	Kuroyedov, A.A.//Grokhovsky, S.L.//Zhuze, A.L.//Nosikov, V.V.//Polyanovsky, O.L. 	Distamycin A and its analogs as agents for blocking of endo R. EcoRI activity.	Gene	1977	1		389-395			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. 		
@D	Kurpiewski, M.R.//Engler, L.E.//Wozniak, L.A.//Kobylanska, A.//Koziolkiewicz, M.//Stec, W.J.//Jen-Jacobson, L. 	Mechanisms of Coupling between DNA Recognition Specificity and Catalysis in EcoRI Endonuclease.	Structure	2004	12		1775-1788			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. 		
@D	Kurpiewski, M.R.//Koziolkiewicz, M.//Wilk, A.//Stec, W.J.//Jen-Jacobson, L. 	Chiral phosphorothioates as probes of protein interactions with individual DNA phosphoryl oxygens:  Essential interactions of EcoRI endonuclease with the phosphate at pGAATTC.	Biochemistry	1996	35		8846-8854			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. 		
@D	Kurth, D.//Romero, C.M.//Fernandez, P.M.//Ferrero, M.A.//Martinez, M.A. 	Draft Genome Sequence of Achromobacter sp. Strain AR476-2, Isolated from a Cellulolytic Consortium.	Genome Announcements	2016	4		e00587-16			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. 		
@D	Kurylo, C.M.//Alexander, N.//Dass, R.A.//Parks, M.M.//Altman, R.A.//Vincent, C.T.//Mason, C.E.//Blanchard, S.C. 	Genome sequence and analysis of Escherichia coli MRE600, a colicinogenic, nonmotile strain that lacks RNase I and the type I methyltransferase, EcoKI.	Genome Biol. Evol.	2016	8		742-752			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. 		
@D	Kusano, K.//Asami, Y.//Fujita, A.//Tanokura, M.//Kobayashi, I. 	Type I restriction enzyme with RecA protein promotes illegitimate recombination.	Plasmid	2003	50		202-212			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. 		
@D	Kusano, K.//Naito, T.//Handa, N.//Kobayashi, I. 	Restriction-modification systems as genomic parasites in competition for specific sequences.	Proc. Natl. Acad. Sci. U. S. A.	1995	92		11095-11099			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. 		
@D	Kusano, K.//Sakagami, K.//Yokochi, T.//Naito, T.//Tokinaga, Y.//Euda, E.//Kobayashi, I. 	A new type of illegitimate recombination is dependent on restriction and homologous interaction.	J. Bacteriol.	1997	179		5380-5390			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. 		
@D	Kusiak, M.//Price, C.//Rice, D.//Hornby, D.P. 	The HsdS polypeptide of the Type IC restriction enzyme EcoR124 is a sequence-specific DNA-binding protein.	Mol. Microbiol.	1992	6		3251-3256			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. 		
@D	Kuspa, A.//Loomis, W.F. 	Tagging developmental genes in Dictyostelium by restriction enzyme-mediated integration of plasmid DNA.	Proc. Natl. Acad. Sci. U. S. A.	1992	89		8803-8807			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. 		
@D	Kusumoto, M.//Fukamizu, D.//Ogura, Y.//Yoshida, E.//Yamamoto, F.//Iwata, T.//Ooka, T.//Akiba, M.//Hayashi, T. 	The lineage-specific distribution of IS-excision enhancer in enterotoxigenic Escherichia coli isolated from swine.	Appl. Environ. Microbiol.	2014	80		1394-1402			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. 		
@D	Kutish, G.F.//Li, Y.//Lu, Z.//Furuta, M.//Rock, D.L.//Van Etten, J.L. 	Analysis of 76 kb of the Chlorella virus PBCV-1 330-kb genome: Map positions 182 to 258.	Virology	1996	223		303-317			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. 		
@A	Kutter, E.//Rueger, W. 		Structure, organization, and manipulation of the genome.			Mathews, C.K.//Kutter, E.M.//Mosig, G.//Berget, P.B. 		Bacteriophage T4				Washington, D.C.	American Society for Microbiology	1983		0		277-290									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. 		
@A	Kutter, E.//Stidham, T.//Guttman, B.//Kutter, E.//Batts, D.//Peterson, S.//Javakhishvili, T.D.//Arisaka, F.//Mesyanzhinov, V.//Rueger, W.//Mosig, G. 		Genomic map of bacteriophage T4.			Karam, J.D.//Drake, J.W.//Kreuzer, K.N.//Mosig, G.//Hall, D.H.//Eiserling, F.A. 		Molecular Biology of Bacteriophage T4				Washington, D.C.	American Society for Microbiology	1994		0		491-519									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. 		
@D	Kutueva, L.I.//Ashapkin, V.V.//Vanyushin, B.F. 	The methylation pattern of a cytosine DNA-methyltransferase gene in Arabidopsis thaliana plants.	Biochem. Mol. Biol. Int.	1996	40		347-353			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. 		
@D	Kutumbaka, K.K.//Han, S.//Mategko, J.//Nadala, C.//Buser, G.L.//Cassidy, M.P.//Beldavs, Z.G.//Weissman, S.J.//Morey, K.E.//Vega, R.//Samadpour, M. 	Draft Genome Sequence of blaNDM-1-Positive Escherichia coli O25b-ST131 Clone Isolated from an Environmental Sample.	Genome Announcements	2014	2		e00462-14			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. 		
@D	Kutumbaka, K.K.//Pasmowitz, J.//Mategko, J.//Reyes, D.//Friedrich, A.//Han, S.//Martens-Habbena, W.//Neal-McKinney, J.//Janagama, H.K.//Nadala, C.//Samadpour, M. 	Draft Genome Sequence of the Beer Spoilage Bacterium Megasphaera cerevisiae Strain PAT 1T.	Genome Announcements	2015	3		e01045-15			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). 		
@D	Kuwahara, H.//Yuki, M.//Izawa, K.//Ohkuma, M.//Hongoh, Y. 	Genome of 'Ca. Desulfovibrio trichonymphae', an H2-oxidizing bacterium in a tripartite symbiotic system within a protist cell in the termite gut.	ISME J.	2017	11		766-776			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. 		
@D	Kuwahara, T.//Ogura, Y.//Oshima, K.//Kurokawa, K.//Ooka, T.//Hirakawa, H.//Itoh, T.//Nakayama-Imaohji, H.//Ichimura, M.//Itoh, K.//Ishifune, C.//Maekawa, Y.//Yasutomo, K.//Hattori, M.//Hayashi, T. 	The lifestyle of the segmented filamentous bacterium: a non-culturable gut-associated immunostimulating microbe inferred by whole-genome sequencing.	DNA Res.	2011	18		291-303			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. 		
@D	Kuwahara, T.//Yamashita, A.//Hirakawa, H.//Nakayama, H.//Toh, H.//Okada, N.//Kuhara, S.//Hattori, M.//Hayashi, T.//Ohnishi, Y. 	Genomic analysis of Bacteroides fragilis reveals extensive DNA inversions regulating cell surface adaptation.	Proc. Natl. Acad. Sci. U. S. A.	2004	101		14919-14924			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. 		
@D	Kuzin, A.I.//Bolesnin, M.I.//Smolyaninov, V.V.//Azizbekyan, R.R. 	Site specific restriction endonuclease BtcI from Bacillus thuringiensis var. canadensis.	Mol. Gen. Mikrobiol. Virusol.	1989	0		36-39			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. 		
@D	Kuzmanovic, N.//Pulawska, J.//Prokic, A.//Ivanovic, M.//Zlatkovic, N.//Gasic, K.//Obradovic, A. 	Draft Genome Sequences of Agrobacterium nepotum Strain 39/7T and Agrobacterium sp. Strain KFB 330.	Genome Announcements	2015	3		e00331-15			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. 		
@D	Kuzmin, N.P.//Fodor, I.//Baev, A.A. 	A specific endonuclease in Klebsiella pneumoniae OK8.	Dokl. Akad. Nauk.	1977	236		477-480			None 		
@D	Kuzmin, N.P.//Loseva, S.P.//Belyaeva, R.K.//Kravets, A.N.//Solonin, A.S.//Tanyashin, V.I.//Baev, A.A. 	Physical and catalytic properties of homogeneous restriction endonuclease EcoRV.	Mol. Biol. (Mosk)	1984	18		166-173			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. 		
@D	Kuznetsov, B.B.//Ivanovsky, R.N.//Keppen, O.I.//Sukhacheva, M.V.//Bumazhkin, B.K.//Patutina, E.O.//Beletsky, A.V.//Mardanov, A.V.//Baslerov, R.V.//Panteleeva, A.N.//Kolganova, T.V.//Ravin, N.V.//Skryabin, K.G. 	Draft genome sequence of the anoxygenic filamentous phototrophic bacterium Oscillochloris trichoides ssp. DG-6.	J. Bacteriol.	2010	193		321-322			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. 		
@D	Kuznetsova, S.A.//Kubareva, E.A.//Oretskaya, T.S.//Dolinnaya, N.G.//Krynetskaya, N.F.//Gromova, E.S.//Shabarova, Z.A.//Cech, D. 	Interaction between EcoRII restriction/modification enzymes and synthetic DNA fragments. Synthesis of substrates containing a single recognition site.	Biopol. Kletka	1987	3		283-289			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. 		
@D	Kvachadze, L.I.//Andriashvili, I.A.//Chanishvili, T.G.//Arutyunyan, E.E.//Nikolskaia, I.I.//Debov, S.S. 	Identification of the system modification-restriction in Staphylococci.	Vopr. Med. Khim.	1985	31		121-125			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. 		
@D	Kwak, J.//Jiang, H.//Kendrick, K.E. 	Transformation using in vivo and in vitro methylation in Streptomyces griseus.	FEMS Microbiol. Lett.	2002	209		243-248			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. 		
@D	Kwak, M.J.//Jeong, H.//Madhaiyan, M.//Lee, Y.//Sa, T.M.//Oh, T.K.//Kim, J.F. 	Genome Information of Methylobacterium oryzae, a Plant-Probiotic Methylotroph in the Phyllosphere.	PLoS ONE	2014	9		E106704			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. 		
@D	Kwak, M.J.//Kwon, S.K.//Kim, J.F. 	Complete genome sequence of the sand-sediment actinobacterium Nocardioides dokdonensis FR1436T.	Standards in Genomic Sciences	2017	12		44			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. 		
@D	Kwak, M.J.//Kwon, S.K.//Yoon, J.H.//Kim, J.F. 	Genome sequence of Lysobacter dokdonensis DS-58(T), a gliding bacterium isolated  from soil in Dokdo, Korea.	Standards in Genomic Sciences	2015	10		123			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. 		
@D	Kwak, M.J.//Song, J.Y.//Kim, S.Y.//Jeong, H.//Kang, S.G.//Kim, B.K.//Kwon, S.K.//Lee, C.H.//Yu, D.S.//Park, S.H.//Kim, J.F. 	Complete Genome Sequence of the Endophytic Bacterium Burkholderia sp. Strain KJ006.	J. Bacteriol.	2012	194		4432-4433			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. 		
@D	Kwak, Y.//Li, Q.X.//Shin, J.H. 	Draft genome sequence of Mycobacterium rufum JS14(T), a polycyclic-aromatic-hydrocarbon-degrading bacterium from petroleum-contaminated  soil in Hawaii.	Standards in Genomic Sciences	2016	11		47			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. 		
@D	Kwak, Y.//Park, G.S.//Shin, J.H. 	High quality draft genome sequence of the type strain of Pseudomonas lutea OK2(T), a phosphate-solubilizing rhizospheric bacterium.	Standards in Genomic Sciences	2016	11		51			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. 		
@D	Kwan, T.//Liu, J.//Dubow, M.//Gros, P.//Pelletier, J. 	The complete genomes and proteomes of 27 Staphylococcus aureus bacteriophages.	Proc. Natl. Acad. Sci. U. S. A.	2005	102		5174-5179			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. 		
@D	Kwasiborski, A.//Mondy, S.//Beury-Cirou, A.//Faure, D. 	Genome Sequence of the Quorum-Quenching Rhodococcus erythropolis Strain R138.	Genome Announcements	2014	2		e00224-14			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. 		
@D	Kwasiborski, A.//Mondy, S.//Beury-Cirou, A.//Faure, D. 	Genome Sequence of the Pectobacterium atrosepticum Strain CFBP6276, Causing Blackleg and Soft Rot Diseases on Potato Plants and Tubers.	Genome Announcements	2013	1		e00374-13			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. 		
@D	Kwiatek, A.//Bacal, P.//Wasiluk, A.//Trybunko, A.//Adamczyk-Poplawska, M. 	The dam replacing gene product enhances Neisseria gonorrhoeae FA1090 viability and biofilm formation.	Front. Microbiol.	2014	5		712			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. 		
@D	Kwiatek, A.//Kobes, M.//Olejnik, K.//Piekarowicz, A. 	DNA methyltransferases from Neisseria meningitidis and Neisseria gonorrhoeae FA1090 associated with mismatch nicking endonucleases.	Microbiology	2004	150		1713-1722			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. 		
@D	Kwiatek, A.//Luczkiewicz, M.//Bandyra, K.//Stein, D.C.//Piekarowicz, A. 	Neisseria gonorrhoeae FA1090 encodes two classes of Vsr endonucleases.	J. Bacteriol.	2010	192		3951-3960			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. 		
@D	Kwiatek, A.//Piekarowicz, A. 	The restriction endonuclease R.NmeDI from Neisseria meningitidis that recognizes a palindromic sequence and cuts the DNA on both sides of the  recognition sequence.	Nucleic Acids Res.	2007	35		6539-6546			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. 		
@D	Kwiatkowski, B.//Boschek, B.//Thiele, H.//Stirm, S. 	Substrate specificity of two bacteriophage-associated endo-N-acetylneuraminidases.	J. Virol.	1983	45		367-374			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. 		
@D	Kwoh, T.J.//Kwoh, D.Y.//McCue, A.W.//Davis, G.R.//Patrick, D.//Gingeras, T.R. 	Introduction and expression of the bacterial PaeR7 methylase gene in mammalian cells.	Proc. Natl. Acad. Sci. U. S. A.	1986	83		7713-7717			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. 		
@D	Kwoh, T.J.//Obermiller, P.S.//McCue, A.W.//Kwoh, D.Y.//Sullivan, S.A.//Gingeras, T.R. 	Introduction and expression of the bacterial PaeR7I restriction endonuclease gene in mouse cells containing the PaeR7I methylase.	Nucleic Acids Res.	1988	16		11489-11506			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. 		
@D	Kwok, J.S.//Ip, M.//Chan, T.F.//Lam, W.Y.//Tsui, S.K. 	Draft Genome Sequence of Clostridium butyricum Strain NOR 33234, Isolated from an Elderly Patient with Diarrhea.	Genome Announcements	2014	2		e01356-14			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. 		
@D	Kwon, S.K.//Kim, B.K.//Song, J.Y.//Kwak, M.J.//Lee, C.H.//Yoon, J.H.//Oh, T.K.//Kim, J.F. 	Genomic makeup of the marine flavobacterium Nonlabens (Donghaeana) dokdonensis DSW-6 and identification of a novel class of rhodopsins.	Genome Biol. Evol.	2013	5		187-199			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. 		
@D	Kwon, T.//Cho, S.H. 	Draft Genome Sequence of Enterohemorrhagic Escherichia coli O157 NCCP15739, Isolated in the Republic of Korea.	Genome Announcements	2015	3		e00522-15			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. 		
@D	Kwon, T.//Han, S.J.//Yoo, W.G.//Yun, M.R.//Lee, S.//Lee, J.S.//Kim, D.W. 	Draft Genome Sequence of Mycobacterium tuberculosis KT-0184, Isolated in South Korea.	Genome Announcements	2016	4		e01755-15			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. 		
@D	Kwon, T.//Han, S.J.//Yoo, W.G.//Yun, M.R.//Lee, S.//Lee, J.S.//Kim, D.W. 	Draft Genome Sequence of Mycobacterium tuberculosis KT-0133, Isolated in South Korea.	Genome Announcements	2016	4		e01731-15			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. 		
@D	Kwon, T.//Yang, J.W.//Lee, S.//Yun, M.R.//Yoo, W.G.//Kim, H.S.//Cha, J.O.//Kim, D.W. 	Complete Genome Sequence of Klebsiella pneumoniae subsp. pneumoniae KP617, Coproducing OXA-232 and NDM-1 Carbapenemases, Isolated in South Korea.	Genome Announcements	2016	4		e01550-15			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. 		
@D	Kwon, Y.K.//Kim, J.J.//Kim, J.H.//Jeon, S.M.//Ye, B.R.//Jang, J.//Heo, S.J.//Park, S.C.//Kang, D.H.//Oh, C. 	Draft genome sequence of the xylan-degrading marine bacterium strain s124, representing a novel species of the genus oceanicola.	J. Bacteriol.	2012	194		6325			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. 		
@D	Kwon, Y.M.//Kim, S.J. 	Complete Genome Sequence of the Proteorhodopsin-Containing Marine Bacterium Sediminicola sp. YIK13.	Genome Announcements	2016	4		e01635-15			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. 		
@D	Kwon, Y.T.//Jun, H.S.//Rho, H.M. 	Characterization of BmaI methylase from Bacillus macerans.	Korean J. Microbiol.	1988	26		88-92			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. 		
@D	Kwon, Y.T.//Jun, H.S.//Rho, H.M. 	Characterization of BmaI endonuclease from Bacillus macerans ATCC 8244.	Korean J. Microbiol.	1988	26		1-5			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. 		
@D	Kwong, S.M.//Yeo, C.C.//Suwanto, A.//Poh, C.L. 	Characterization of the endogenous plasmid from Pseudomonas alcaligenes NCIB 9867: DNA sequence and mechanism of transfer.	J. Bacteriol.	2000	182		81-90			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. 		
@D	Kwong, W.K.//Engel, P.//Koch, H.//Moran, N.A. 	Genomics and host specialization of honey bee and bumble bee gut symbionts.	Proc. Natl. Acad. Sci. U. S. A.	2014	111		11509-11514			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. 		
@D	Kwong, W.K.//Mancenido, A.L.//Moran, N.A. 	Genome Sequences of Lactobacillus sp. Strains wkB8 and wkB10, Members of the Firm-5 Clade, from Honey Bee Guts.	Genome Announcements	2014	2		e01176-14			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. 		
@D	Kwun, M.J.//Cheng, J.//Yang, S.H.//Lee, D.R.//Suh, J.W.//Hong, H.J. 	Draft Genome Sequence of Ristocetin-Producing Strain Amycolatopsis sp. Strain MJM2582 Isolated in South Korea.	Genome Announcements	2014	2		e01091-14			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. 		
@D	Kwun, M.J.//Hong, H.J. 	Draft Genome Sequence of Amycolatopsis lurida NRRL 2430, Producer of the Glycopeptide Family Antibiotic Ristocetin.	Genome Announcements	2014	2		e01050-14			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. 		
@D	Kwun, M.J.//Hong, H.J. 	Genome Sequence of Streptomyces toyocaensis NRRL 15009, Producer of the Glycopeptide Antibiotic A47934.	Genome Announcements	2014	2		e00749-14			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. 		
@D	Kyle, J.L.//Cummings, C.A.//Parker, C.T.//Quinones, B.//Vatta, P.//Newton, E.//Huynh, S.//Swimley, M.//Degoricija, L.//Barker, M.//Fontanoz, S.//Nguyen, K.//Patel, R.//Fang, R.//Tebbs, R.//Petrauskene, O.//Furtado, M.//Mandrell, R.E. 	Escherichia coli Serotype O55:H7 Diversity Supports Parallel Acquisition of Bacteriophage at Shiga Toxin Phage Insertion Sites during Evolution of the O157:H7 Lineage.	J. Bacteriol.	2012	194		1885-1896			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. 		
@D	L'abee-Lund, T.M.//Jorgensen, H.J.//O'Sullivan, K.//Bohlin, J.//Ligard, G.//Granum, P.E.//Lindback, T. 	The Highly Virulent 2006 Norwegian EHEC O103:H25 Outbreak Strain Is Related to the 2011 German O104:H4 Outbreak Strain.	PLoS ONE	2012	7		E31413			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. 		
@D	L'Haridon, S.//Corre, E.//Guan, Y.//Vinu, M.//La Cono, V.//Yakimov, M.//Stingl, U.//Toffin, L.//Jebbar, M. 	Complete Genome Sequence of the Halophilic Methylotrophic Methanogen Archaeon Methanohalophilus portucalensis Strain FDF-1(T).	Genome Announcements	2018	6		e01482-17			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. 		
@D	L'Haridon, S.//Corre, E.//Guan, Y.//Vinu, M.//La Cono, V.//Yakimov, M.//Stingl, U.//Toffin, L.//Jebbar, M. 	Complete Genome Sequence of Methanohalophilus halophilus DSM 3094T, Isolated from a Cyanobacterial Mat and Bottom Deposits at Hamelin Pool, Shark Bay, Northwestern  Australia.	Genome Announcements	2017	5		e01604-16			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. 		
@D	La Torre, A.//Bassi, D.//Zotta, T.//Orru, L.//Lamontanara, A.//Cocconcelli, P.S. 	Draft Genome Sequence of Clostridium sporogenes Strain UC9000 Isolated from Raw Milk.	Genome Announcements	2016	4		e00244-16			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. 		
@D	Laayoun, A.//Baker, D.J.//Riley, J.//Smith, S.S. 	The response of M.HpaII to heteroduplexes.	Gene	1994	150		195-196			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. 		
@D	Laayoun, A.//Smith, S.S. 	Methylation of slipped duplexes, snapbacks and cruciforms by human DNA(cytosine-5)methyltransferase.	Nucleic Acids Res.	1995	23		1584-1589			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. 		
@D	Labahn, J.//Granzin, J.//Schluckebier, G.//Robinson, D.P.//Jack, W.E.//Schildkraut, I.//Saenger, W. 	Three-dimensional structure of the adenine-specific DNA methyltransferase M.TaqI in complex with the cofactor S-adenosylmethionine.	Proc. Natl. Acad. Sci. U. S. A.	1994	91		10957-10961			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. 		
@D	Labbe, D.//Holtke, H.J.//Lau, P.C.K. 	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.	1990	224		101-110			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. 		
@D	Labbe, G.//Edirmanasinghe, R.//Ziebell, K.//Nash, J.H.//Bekal, S.//Parmley, E.J.//Mulvey, M.R.//Johnson, R.P. 	Complete Genome and Plasmid Sequences of Three Canadian Isolates of Salmonella enterica subsp. enterica Serovar Heidelberg from Human and Food Sources.	Genome Announcements	2016	4		e01526-15			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. 		
@D	Labbe, G.//Ziebell, K.//Bekal, S.//Macdonald, K.A.//Parmley, E.J.//Agunos, A.//Desruisseau, A.//Daignault, D.//Slavic, D.//Hoang, L.//Ramsay, D.//Pollari, F.//Robertson, J.//Nash, J.H.//Johnson, R.P. 	Complete Genome Sequences of 17 Canadian Isolates of Salmonella enterica subsp. enterica Serovar Heidelberg from Human, Animal, and Food Sources.	Genome Announcements	2016	4		e00990-16			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. 		
@D	Labbe, S.//Xia, Y.//Roy, P.H. 	BspMII and AccIII are an isoschizomer pair which differ in their sensitivity to cytosine methylation.	Nucleic Acids Res.	1988	16		7184			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. 		
@D	Labeots, L.A. 	Structure and function of DNA phosphotriester substrates of the restriction endonuclease AluI.	Diss. Abstr.	1993	53		2842			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. 		
@D	Laborda, P.R.//Fonseca, F.S.//Angolini, C.F.//Oliveira, V.M.//Souza, A.P.//Marsaioli, A.J. 	Genome Sequence of Bacillus safensis CFA06, Isolated from Biodegraded Petroleum in Brazil.	Genome Announcements	2014	2		e00642-14			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. 		
@D	Labrador-Herrera, G.//Alvarez, R.//Lopez-Rojas, R.//Smani, Y.//Cebrero-Cangueiro, T.//Rueda, A.//Perez, F.J.//Pachon, J.//Pachon-Ibanez, M.E. 	Draft Genome Sequences of Seven Multidrug-Resistant Acinetobacter baumannii Strains, Isolated from Respiratory Samples in Spain.	Genome Announcements	2016	4		e00083-16			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. 		
@D	Labrie, S.J.//El Haddad, L.//Tremblay, D.M.//Plante, P.L.//Wasserscheid, J.//Dumaresq, J.//Dewar, K.//Corbeil, J.//Moineau, S. 	First Complete Genome Sequence of Staphylococcus xylosus, a Meat Starter Culture  and a Host to Propagate Staphylococcus aureus Phages.	Genome Announcements	2014	2		e00671-14			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. 		
@D	Labrie, S.J.//Samson, J.E.//Moineau, S. 	Bacteriophage resistance mechanisms.	Nat. Rev. Microbiol.	2010	8		317-327			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. 		
@D	Labrie, S.J.//Tremblay, D.M.//Plante, P.L.//Wasserscheid, J.//Dewar, K.//Corbeil, J.//Moineau, S. 	Complete Genome Sequence of Streptococcus thermophilus SMQ-301, a Model Strain for Phage-Host Interactions.	Genome Announcements	2015	3		e00480-15			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. 		
@D	Labudda, L.//Strapagiel, D.//Karczewska-Golec, J.//Golec, P. 	Complete Annotated Genome Sequences of Four Klebsiella pneumoniae Phages Isolated from Sewage in Poland.	Genome Announcements	2017	5		e00919-17			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. 		
@D	Labutti, K. et al. 	Complete genome sequence of Anaerococcus prevotii type strain (PC1).	Standards in Genomic Sciences	2009	1		159-165			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. 		
@D	Labutti, K. et al. 	Permanent draft genome sequence of Dethiosulfovibrio peptidovorans type strain (SEBR 4207).	Standards in Genomic Sciences	2010	3		85-92			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. 		
@D	Labutti, K. et al. 	Complete genome sequence of Planctomyces limnophilus type strain (Mu 290).	Standards in Genomic Sciences	2010	3		47-56			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. 		
@D	Lacap-Bugler, D.C.//Jiang, J.//Huo, Y.B.//Chan, Y.//Leung, F.C.//Watt, R.M. 	Complete Genome Sequence of the Oral Spirochete Bacterium Treponema putidum Strain OMZ 758T (ATCC 700334T).	Genome Announcements	2014	2		e01076-14			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. 		
@D	Lacey, J.A.//Allnutt, T.R.//Vezina, B.//Van, T.T.//Stent, T.//Han, X.//Rood, J.I.//Wade, B.//Keyburn, A.L.//Seemann, T.//Chen, H.//Haring, V.//Johanesen, P.A.//Lyras, D.//Moore, R.J. 	Whole genome analysis reveals the diversity and evolutionary relationships between necrotic enteritis-causing strains of Clostridium perfringens.	BMC Genomics	2018	19		379			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. 		
@D	Lackner, G.//Moebius, N.//Partida-Martinez, L.//Hertweck, C. 	Complete Genome Sequence of Burkholderia rhizoxinica, the Endosymbiont of Rhizopus microsporus.	J. Bacteriol.	2010	193		783-784			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. 		
@D	Lacks, S.//Greenberg, B. 	A deoxyribonuclease of Diplococcus pneumoniae specific for methylated DNA.	J. Biol. Chem.	1975	250		4060-4066			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. 		
@D	Lacks, S.//Greenberg, B. 	Complementary specificity of restriction endonucleases of Diplococcus pneumoniae with respect to DNA methylation.	J. Mol. Biol.	1977	114		153-168			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. 		
@D	Lacks, S.//Neuberger, M. 	Membrane location of a deoxyribonuclease implicated in the genetic transformation of Diplococcus pneumoniae.	J. Bacteriol.	1975	124		1321-1329			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. 		
@D	Lacks, S.A. 	Purification and properties of the complementary endonucleases DpnI and DpnII.	Methods Enzymol.	1980	65		138-146			None 		
@D	Lacks, S.A.//Ayalew, S.//de la Campa, A.G.//Greenberg, B. 	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.	Mol. Microbiol.	2000	35		1089-1098			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. 		
@D	Lacks, S.A.//Dunn, J.J.//Greenberg, B. 	Identification of base mismatches recognized by the heteroduplex-DNA-repair system of Streptococcus pneumoniae.	Cell	1982	31		327-336			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. 		
@D	Lacks, S.A.//Greenberg, B. 	Atypical ribosome binding sites and regulation of gene expression in the DpnII restriction enzyme system of S. pneumoniae.	FASEB J.	1993	7		A1082			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. 		
@D	Lacks, S.A.//Greenberg, B.//Sabelnikov, A.G. 	Possible regulation of DNA methyltransferase expression by RNA processing in Streptococcus pneumoniae.	Gene	1995	157		209-212			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. 		
@D	Lacks, S.A.//Mannarelli, B.M.//Springhorn, S.S.//Greenberg, B. 	Genetic basis of the complementary DpnI and DpnII restriction systems of S. pneumoniae:  An intercellular cassette mechanism.	Cell	1986	46		993-1000			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. 		
@A	Lacks, S.A.//Mannarelli, B.M.//Springhorn, S.S.//Greenberg, B.//de la Campa, A. 		Genetics of the complementary restriction systems DpnI and DpnII revealed by cloning and recombination in Streptococcus pneumoniae.			Ferretti, J.J.//Curtiss, R.//III 		Streptococcal Genetics				Washington, DC	American Society for Microbiology	1987		0		31-41									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. 		
@A	Lacks, S.A.//Sabelnikov, A.G.//Chen, J.-D.//Greenberg, B. 		Gene expression in the DpnI and DpnII restriction enzyme systems of Streptococcus pneumoniae.			Balla, E.//Berencsi, G.//Szentirmai, A. 		DNA Transfer and Gene Expression in Microorganisms				Andover	Intercept	1993		0		169-178									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. 		
@D	Lacks, S.A.//Springhorn, S.S. 	Transfer of recombinant plasmids containing the gene for DpnII DNA methylase into strains of Streptococcus pneumoniae that produce DpnI or DpnII restriction endonucleases.	J. Bacteriol.	1984	158		905-909			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. 		
@D	Lacks, S.A.//Springhorn, S.S. 	Cloning in Streptococcus pneumoniae of the gene for DpnII DNA methylase.	J. Bacteriol.	1984	157		934-936			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. 		
@A	Lacks, S.A.//Springhorn, S.S.//Cerritelli, S. 		Restriction/Modification systems of Pneumococci:  Why two methylases in the DpnII system?			Dunny, G.M.//Cleary, P.P.//McKay, L.L. 		Genetics and Molecular Biology of Streptococci, Lactococci, and Enterococci				Washington	American Society for Microbiology	1991		8		71-76									None 		
@D	Ladero, V.//Alvarez-Sieiro, P.//Redruello, B.//Del Rio, B.//Linares, D.M.//Martin, M.C.//Fernandez, M.//Alvarez, M.A. 	Draft Genome Sequence of Lactobacillus plantarum Strain IPLA 88.	Genome Announcements	2013	1		e00524-13			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. 		
@D	Ladero, V.//Del Rio, B.//Linares, D.M.//Fernandez, M.//Mayo, B.//Martin, M.C.//Alvarez, M.A. 	Draft Genome Sequence of the Putrescine-Producing Strain Lactococcus lactis subsp. lactis 1AA59.	Genome Announcements	2015	3		e00669-15			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. 		
@D	Ladero, V.//Del Rio, B.//Linares, D.M.//Fernandez, M.//Mayo, B.//Martin, M.C.//Alvarez, M.A. 	Genome Sequence Analysis of the Biogenic Amine-Producing Strain Lactococcus lactis subsp. cremoris CECT 8666 (Formerly GE2-14).	Genome Announcements	2014	2		e01088-14			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. 		
@D	Ladero, V.//Herrero-Fresno, A.//Martinez, N.//Del Rio, B.//Linares, D.M.//Fernandez, M.//Martin, M.C.//Alvarez, M.A. 	Genome Sequence Analysis of the Biogenic Amine-Degrading Strain Lactobacillus casei 5b.	Genome Announcements	2014	2		e01199-13			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. 		
@D	Ladero, V.//Linares, D.M.//Del Rio, B.//Fernandez, M.//Martin, M.C.//Alvarez, M.A. 	Draft Genome Sequence of the Tyramine Producer Enterococcus durans Strain IPLA 655.	Genome Announcements	2013	1		e00265-13			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. 		
@D	Ladner, J.T.//Welch, T.J.//Whitehouse, C.A.//Palacios, G.F. 	Genome Sequence of Weissella ceti NC36, an Emerging Pathogen of Farmed Rainbow Trout in the United States.	Genome Announcements	2013	1		e00187-12			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. 		
@D	Ladner, J.T.//Whitehouse, C.A.//Koroleva, G.I.//Palacios, G.F. 	Genome Sequence of Moraxella macacae 0408225, a Novel Bacterial Species Isolated  from a Cynomolgus Macaque with Epistaxis.	Genome Announcements	2013	1		e00188-12			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. 		
@D	Lafi, F.F.//Alam, I.//Bisseling, T.//Geurts, R.//Bajic, V.B.//Hirt, H.//Saad, M.M. 	Draft Genome Sequence of the Plant Growth-Promoting Rhizobacterium Acinetobacter  radioresistens Strain SA188 Isolated from the Desert Plant Indigofera argentea.	Genome Announcements	2017	5		e01708-16			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. 		
@D	Lafi, F.F.//Alam, I.//Geurts, R.//Bisseling, T.//Bajic, V.B.//Hirt, H.//Saad, M.M. 	Draft Genome Sequence of the Phosphate-Solubilizing Bacterium Pseudomonas argentinensis Strain SA190 Isolated from the Desert Plant Indigofera argentea.	Genome Announcements	2016	4		e01431-16			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. 		
@D	Lafi, F.F.//Alam, I.//Geurts, R.//Bisseling, T.//Bajic, V.B.//Hirt, H.//Saad, M.M. 	Draft Genome Sequence of Ochrobactrum intermedium Strain SA148, a Plant Growth-Promoting Desert Rhizobacterium.	Genome Announcements	2017	5		e01707-16			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. 		
@D	Lafi, F.F.//Alam, I.//Geurts, R.//Bisseling, T.//Bajic, V.B.//Hirt, H.//Saad, M.M. 	Draft Genome Sequence of Enterobacter sp. Sa187, an Endophytic Bacterium Isolated from the Desert Plant Indigofera argentea.	Genome Announcements	2017	5		e01638-16			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. 		
@D	Lafi, F.F.//AlBladi, M.L.//Salem, N.M.//Al-Banna, L.//Alam, I.//Bajic, V.B.//Hirt, H.//Saad, M.M. 	Draft Genome Sequence of the Plant Growth-Promoting Pseudomonas punonensis Strain D1-6 Isolated from the Desert Plant Erodium hirtum in Jordan.	Genome Announcements	2017	5		e01437-16			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. 		
@D	Lafi, F.F.//Bokhari, A.//Alam, I.//Bajic, V.B.//Hirt, H.//Saad, M.M. 	Draft Genome Sequence of the Plant Growth-Promoting Cupriavidus gilardii Strain JZ4 Isolated from the Desert Plant Tribulus terrestris.	Genome Announcements	2016	4		e00678-16			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. 		
@D	Lafi, F.F.//Ramirez-Prado, J.S.//Alam, I.//Bajic, V.B.//Hirt, H.//Saad, M.M. 	Draft Genome Sequence of Halomonas elongata Strain K4, an Endophytic Growth-Promoting Bacterium Enhancing Salinity Tolerance In Planta.	Genome Announcements	2016	4		e01214-16			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. 		
@D	Lafi, F.F.//Ramirez-Prado, J.S.//Alam, I.//Bajic, V.B.//Hirt, H.//Saad, M.M. 	Draft Genome Sequence of Plant Growth-Promoting Micrococcus luteus Strain K39 Isolated from Cyperus conglomeratus in Saudi Arabia.	Genome Announcements	2017	5		e01520-16			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. 		
@D	Lafleur, J.E.//Costa, S.K.//Bitzer, A.S.//Silby, M.W. 	Draft Genome Sequence of Cellulophaga sp. E6, a Marine Algal Epibiont That Produces a Quorum-Sensing Inhibitory Compound Active against Pseudomonas  aeruginosa.	Genome Announcements	2015	3		e01565-14			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. 		
@D	Laganeckas, M.//Margelevicius, M.//Venclovas, C. 	Identification of new homologs of PD-(D/E)XK nucleases by support vector machines trained on data derived from profile-profile alignments.	Nucleic Acids Res.	2011	39		1187-1196			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/. 		
@D	Lagier, J.C.//Armougom, F.//Mishra, A.K.//Nguyen, T.T.//Raoult, D.//Fournier, P.E. 	Non-contiguous finished genome sequence and description of Alistipes timonensis sp. nov.	Standards in Genomic Sciences	2012	6		315-324			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. 		
@D	Lagier, J.C.//Bibi, F.//Ramasamy, D.//Azhar, E.I.//Robert, C.//Yasir, M.//Jiman-Fatani, A.A.//Alshali, K.Z.//Fournier, P.E.//Raoult, D. 	Non contiguous-finished genome sequence and description of Clostridium jeddahense sp. nov.	Standards in Genomic Sciences	2014	9		1003-1019			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. 		
@D	Lagier, J.C.//El Karkouri, K.//Mishra, A.K.//Robert, C.//Raoult, D.//Fournier, P.E. 	Non contiguous-finished genome sequence and description of Enterobacter massiliensis sp. nov.	Standards in Genomic Sciences	2013	7		399-412			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. 		
@D	Lagier, J.C.//El Karkouri, K.//Nguyen, T.T.//Armougom, F.//Raoult, D.//Fournier, P.E. 	Non-contiguous finished genome sequence and description of Anaerococcus senegalensis sp. nov.	Standards in Genomic Sciences	2012	6		116-125			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. 		
@D	Lagier, J.C.//Elkarkouri, K.//Rivet, R.//Couderc, C.//Raoult, D.//Fournier, P.E. 	Non contiguous-finished genome sequence and description of Senegalemassilia anaerobia gen. nov., sp. nov.	Standards in Genomic Sciences	2013	7		343-356			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. 		
@D	Lagier, J.C.//Gimenez, G.//Robert, C.//Raoult, D.//Fournier, P.E. 	Non-contiguous finished genome sequence and description of Herbaspirillum massiliense sp. nov.	Standards in Genomic Sciences	2012	7		200-209			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. 		
@D	Lagier, J.C.//Khelaifia, S.//Azhar, E.I.//Croce, O.//Bibi, F.//Jiman-Fatani, A.A.//Yasir, M.//Helaby, H.B.//Robert, C.//Fournier, P.E.//Raoult, D. 	Genome sequence of Oceanobacillus picturae strain S1, an halophilic bacterium first isolated in human gut.	Standards in Genomic Sciences	2015	10		91			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. 		
@D	Lagier, J.C.//Ramasamy, D.//Rivet, R.//Raoult, D.//Fournier, P.E. 	Non contiguous-finished genome sequence and description of Cellulomonas massiliensis sp. nov.	Standards in Genomic Sciences	2012	7		258-270			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. 		
@D	Laging, M.//Lindner, E.//Fritz, H.-J.//Kramer, W. 	Repair of hydrolytic DNA deamination damage in thermophilic bacteria: cloning and characterization of a Vsr endonuclease homolog from Bacillus stearothermophilus.	Nucleic Acids Res.	2003	31		1913-1920			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. 		
@D	Lagonenko, A.L.//Komardina, V.S.//Nikolaichik, Y.A.//Evtushenkov, A.N. 	First Report of Erwinia amylovora Fire Blight in Belarus.	J. Phytopathol.	2008	156		638-640					
@D	Laguerre, S.//Amari, M.//Vuillemin, M.//Robert, H.//Loux, V.//Klopp, C.//Morel, S.//Gabriel, B.//Remaud-Simeon, M.//Gabriel, V.//Moulis, C.//Fontagne-Faucher, C. 	Genome Sequences of Three Leuconostoc citreum Strains, LBAE C10, LBAE C11, and LBAE E16, Isolated from Wheat Sourdoughs.	J. Bacteriol.	2012	194		1610-1611			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. 		
@D	Lagunavicius, A. 	DNA binding by MunI restriction endonuclease.	Biologija	1997	1		13-20			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. 		
@D	Lagunavicius, A.//Grazulis, S.//Balciunaite, E.//Vainius, D.//Siksnys, V. 	DNA binding specificity of MunI restriction endonuclease is controlled by pH and calcium ions: Involvement of active site carboxylate residues.	Biochemistry	1997	36		11093-11099			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. 		
@D	Lagunavicius, A.//Sasnauskas, G.//Halford, S.E.//Siksnys, V. 	The metal-independent type IIS restriction enzyme BfiI is a dimer that binds two DNA sites but has only one catalytic centre.	J. Mol. Biol.	2003	326		1051-1064			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. 		
@D	Lagunavicius, A.//Siksnys, V. 	Mutational analysis of MunI restriction endonuclease.	Biologija	1996	0		35-38			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. 		
@D	Lagunavicius, A.//Siksnys, V. 	Site-directed mutagenesis of putative active site residues of MunI restriction endonuclease: replacement of catalytically essential carboxylate residues triggers DNA binding specificity.	Biochemistry	1997	36		11086-11092			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. 		
@D	Lahav, T.//Zchori-Fein, E.//Naor, V.//Freilich, S.//Iasur-Kruh, L. 	Draft Genome Sequence of a Dyella-Like Bacterium from the Planthopper Hyalesthes  obsoletus.	Genome Announcements	2016	4		e00686-16			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. 		
@D	Lahlou, L.//El Mrimar, N.//Alouane, T.//Laamarti, M.//Karti, S.//Benhrif, O.//El Mesbahi, H.//Lemriss, H.//Bssaibis, F.//Maleb, A.//El Rarit, S.//Zegmout, A.//El Jaoudi, R.//Frikh, M.//Lemnouar, A.//Dakka, T.//Elouennass, M.//Ibrahimi, A. 	Annotated Whole-Genome Shotgun Sequence of Multidrug-Resistant Mycobacterium tuberculosis MTB13_M Isolated from Morocco.	Genome Announcements	2017	5		e01756-16			Here, we describe the annotated genome sequence of Mycobacterium tuberculosis MTB13_M. The organism was isolated from a sputum sample in Morocco. 		
@D	Lahlou, L.//El Mrimar, N.//Laamarti, M.//Alouane, T.//Bendahou, M.A.//Bssaibis, F.//Ben Lahlou, Y.//Zegmout, A.//El Hafidi, N.//ElJaoudi, R.//Frikh, M.//Lemnouar, A.//Elouennass, M.//Ibrahimi, A. 	Whole-Genome Shotgun Sequences of Three Multidrug-Resistant Mycobacterium tuberculosis Strains Isolated from Morocco.	Genome Announcements	2017	5		e01275-17			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. 		
@D	Lai, C.//Wu, X.//Chen, C.//Huang, T.//Xiong, X.//Wu, S.//Gu, M.//Deng, Z.//Chen, Xi.//Chen, S.//Wang, L. 	In Vivo Mutational Characterization of DndE Involved in DNA Phosphorothioate Modification.	PLoS ONE	2014	9		e107981			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. 		
@D	Lai, J.Y.//Zhang, H.//Chiang, M.H.//Yu, M.//Zhang, R.//Lau, S.C. 	Draft Genome Sequence of Escherichia coli E1728 Isolated from Marine Sediment in  Hong Kong.	Genome Announcements	2014	2		e00430-14			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. 		
@D	Lai, J.Y.//Zhang, H.//Chiang, M.H.//Yu, M.//Zhang, R.//Lau, S.C. 	Draft Genome Sequences of Three Escherichia coli Strains Investigated for the Effects of Lysogeny on Niche Diversification.	Genome Announcements	2014	2		e00955-14			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. 		
@D	Lai, Q.//Cao, J.//Yuan, J.//Li, F.//Shao, Z. 	Celeribacter indicus sp. nov. a polycyclic aromatic hydrocarbon-degrading bacterium from deep-sea sediment and reclassification of Huaishuia halophila as Celeribacter halophilus comb. nov.	Int. J. Syst. Evol. Microbiol.	2014	64		4160-4167			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)). 		
@D	Lai, Q.//Li, C.//Shao, Z. 	Genome Sequence of Galbibacter marinum Type Strain ck-I2-15.	J. Bacteriol.	2012	194		6973			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. 		
@D	Lai, Q.//Li, G.//Shao, Z. 	Genome Sequence of Nitratireductor pacificus Type Strain pht-3B.	J. Bacteriol.	2012	194		6958			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. 		
@D	Lai, Q.//Li, G.//Yu, Z.//Shao, Z. 	Genome Sequence of Nitratireductor indicus Type Strain C115.	J. Bacteriol.	2012	194		6990			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. 		
@D	Lai, Q.//Li, W.//Shao, Z. 	Complete Genome Sequence of Alcanivorax dieselolei Type Strain B5.	J. Bacteriol.	2012	194		6674			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. 		
@D	Lai, Q.//Li, W.//Wang, B.//Yu, Z.//Shao, Z. 	Complete Genome Sequence of the Pyrene-Degrading Bacterium Cycloclasticus sp. Strain P1.	J. Bacteriol.	2012	194		6677			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. 		
@D	Lai, Q.//Liu, Y.//Shao, Z. 	Genome Sequence of Bacillus sp. Strain HYC-10, Isolated from Intestinal Tract Contents from a Marine Fish (Mugil cephalus).	J. Bacteriol.	2012	194		6991			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. 		
@D	Lai, Q.//Shao, Z. 	Genome Sequence of an Alkane-Degrading Bacterium, Alcanivorax pacificus Type Strain W11-5, Isolated from Deep Sea Sediment.	J. Bacteriol.	2012	194		6936			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. 		
@D	Lai, Q.//Shao, Z. 	Genome Sequence of Oceanibaculum indicum Type Strain P24.	J. Bacteriol.	2012	194		6942			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. 		
@D	Lai, Q.//Shao, Z. 	Genome Sequence of Thalassospira profundimaris Type Strain WP0211.	J. Bacteriol.	2012	194		6956			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. 		
@D	Lai, Q.//Shao, Z. 	Genome Sequence of Thalassospira xiamenensis Type Strain M-5.	J. Bacteriol.	2012	194		6957			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. 		
@D	Lai, Q.//Shao, Z. 	Genome Sequence of the Alkane-Degrading Bacterium Alcanivorax hongdengensis Type  Strain A-11-3.	J. Bacteriol.	2012	194		6972			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. 		
@D	Lai, Q.//Wang, L.//Wang, W.//Shao, Z. 	Genome Sequence of Gallaecimonas xiamenensis Type Strain 3-C-1.	J. Bacteriol.	2012	194		6937			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. 		
@D	Lai, Q.//Wang, L.//Wang, W.//Shao, Z. 	Genome Sequence of Idiomarina xiamenensis Type Strain 10-D-4.	J. Bacteriol.	2012	194		6938			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. 		
@D	Lai, W.X.//Gan, H.M.//Hudson, A.O.//Savka, M.A. 	Whole-Genome Sequencing Reveals a New Genospecies of Methylobacterium sp. GXS13,  Isolated from Vitis vinifera L. Xylem Sap.	Genome Announcements	2016	4		e01695-15			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. 		
@D	Lai, Y.C.//Yang, S.L.//Peng, H.L.//Chang, H.Y. 	Identification of genes present specifically in a virulent strain of Klebsiella pneumoniae.	Infect. Immun.	2000	68		7149-7151			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. 		
@D	Laigret, F.//Gaurivaud, P.//Bove, J.-M. 	The unique organization of the rpoB region of Spiroplasma citri: a restriction and modification system gene is adjacent to rpoB.	Gene	1996	171		95-98			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. 		
@D	Lail, K. et al. 	Complete genome sequence of Spirosoma linguale type strain (1).	Standards in Genomic Sciences	2010	2		176-185			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. 		
@D	Laino, J.E.//Hebert, E.M.//Savoy-de-Giori, G.//LeBlanc, J.G. 	Draft Genome Sequence of Lactobacillus delbrueckii subsp. bulgaricus CRL871, a Folate-Producing Strain Isolated from a Northwestern Argentinian Yogurt.	Genome Announcements	2015	3		e00693-15			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. 		
@D	Lainson, F.A.//Dagleish, M.P.//Fontaine, M.//Bayne, C.//Hodgson, J.C. 	Draft Genome Sequences of Strains of Pasteurella multocida Isolated from the United Kingdom and the United States.	Genome Announcements	2013	1		e00773-13			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. 		
@D	Lainson, F.A.//Dagleish, M.P.//Fontaine, M.C.//Bayne, C.//Hodgson, J.C. 	Draft Genome Sequence of Pasteurella multocida A:3 Strain 671/90.	Genome Announcements	2013	1		e00803-13			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. 		
@D	Laird, P.W.//Jackson-Grusby, L.//Fazeli, A.//Dickinson, S.L.//Jung, W.E.//Li, E.//Weinberg, R.A.//Jaenisch, R. 	Suppression of intestinal neoplasia by DNA hypomethylation.	Cell	1995	81		197-205			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. 		
@D	Laird, P.W.//Jaenisch, R. 	The role of DNA methylation in cancer genetics and epigenetics.	Annu. Rev. Genet.	1996	30		441-464			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. 		
@D	Laity, C.//Chater, K.F.//Lewis, C.G.//Buttner, M.J. 	Genetic analysis of the phi C31-specific phage growth limitation (Pgl) system of  Streptomyces coelicolor A3(2).	Mol. Microbiol.	1993	7		329-336			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. 		
@D	Lajoie, M.J.//Rovner, A.J.//Goodman, D.B.//Aerni, H.-R.//Haimovich, A.D.//Kuznetsov, G.//Mercer, J.A.//Wang, H.H.//Carr, P.A.//Mosberg, J.A.//Rohland, N.//Schultz, P.G.//Jacobson, J.M.//Rinehart, J.//Church, G.M.//Isaacs, F.J. 	Genomically Recoded Organisms Expand Biological Functions.	Science	2013	342		357-360			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. 		
@D	Laksanalamai, P.//Steyert, S.R.//Burall, L.S.//Datta, A.R. 	Genome Sequences of Listeria monocytogenes Serotype 4b Variant Strains Isolated from Clinical and Environmental Sources.	Genome Announcements	2013	1		e00771-13			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. 		
@D	Lakshmipathy, D.//Vetrivel, U.//Irudayam, L.T.//Ramasubban, G.//Madhavan, H.N.//Sridhar, R.//Meenakshi, N. 	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.	Genome Announcements	2014	2		e00475-14			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. 		
@D	Lakshmipathy, D.//Vetrivel, U.//Ramasubban, G.//Kulandai, L.T.//Madhavan, H.N.//Sridhar, R.//Meenakshi, N. 	Whole Genome Sequence of Polyresistant Mycobacterium tuberculosis CWCFVRF PRTB 19 Sputum Isolate from Chennai, India, Closely Clustering with East African Indian 5  Genogroup.	Genome Announcements	2014	2		e00702-14			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. 		
@D	Lal, S.//Ramachandran, U.//Zhang, X.//Munir, R.//Sparling, R.//Levin, D.B. 	Draft Genome Sequence of the Cellulolytic, Mesophilic, Anaerobic Bacterium Clostridium termitidis Strain CT1112 (DSM 5398).	Genome Announcements	2013	1		e00281-13			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. 		
@D	Lal, S.//Ramachandran, U.//Zhang, X.//Sparling, R.//Levin, D.B. 	Draft Genome Sequence of the Hydrogen- and Ethanol-Producing Bacterium Clostridium intestinale Strain URNW.	Genome Announcements	2013	1		e00871-13			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. 		
@D	Lallement, A.//Besaury, L.//Eyheraguibel, B.//Amato, P.//Sancelme, M.//Mailhot, G.//Delort, A.M. 	Draft Genome Sequence of Rhodococcus enclensis 23b-28, a Model Strain Isolated from Cloud Water.	Genome Announcements	2017	5		e01199-17			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. 		
@D	Lam, M.C.//Seemann, T.//Bulach, D.M.//Gladman, S.L.//Chen, H.//Haring, V.//Moore, R.J.//Ballard, S.//Grayson, M.L.//Johnson, P.D.//Howden, B.P.//Stinear, T.P. 	Comparative Analysis of the First Complete Enterococcus faecium Genome.	J. Bacteriol.	2012	194		2334			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. 		
@D	Lam, W.C.//Tsao, D.H.H.//Maki, A.H.//Maegley, K.A.//Reich, N.O. 	Spectroscopic studies of arsenic(III) binding to Escherichia coli RI methyltransferase and to two mutants, C223S and W183F.	Biochemistry	1992	31		10438-10442			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. 		
@D	Lambert, A.R.//Hallinan, J.P.//Shen, B.W.//Chik, J.K.//Bolduc, J.M.//Kulshina, N.//Robins, L.I.//Kaiser, B.K.//Jarjour, J.//Havens, K.//Scharenberg, A.M.//Stoddard, B.L. 	Indirect DNA Sequence Recognition and Its Impact on Nuclease Cleavage Activity.	Structure	2016	24		862-873			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. 		
@D	Lambert, A.R.//Sussman, D.//Shen, B.//Maunus, R.//Nix, J.//Samuelson, J.//Xu, S.Y.//Stoddard, B.L. 	Structures of the Rare-Cutting Restriction Endonuclease NotI Reveal a Unique Metal Binding Fold Involved in DNA Binding.	Structure	2008	16		558-569			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. 		
@D	Lambert, G.R.//Carr, N.G. 	Resistance of DNA from filamentous and unicellular cyanobacteria to restriction endonuclease cleavage.	Biochim. Biophys. Acta	1984	781		45-55			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. 		
@D	Lambert, J.N. 	The chemistry of biology: Molecular evolution, the total synthesis of proteins, and DNA restriction and modification.	Aust. J. Chem.	1996	49		1179-1196			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. 		
@D	Lambie, S.C.//Altermann, E.//Leahy, S.C.//Kelly, W.J. 	Draft Genome Sequence of Lactococcus lactis subsp. cremoris HPT, the First Defined-Strain Dairy Starter Culture Bacterium.	Genome Announcements	2014	2		e00107-14			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. 		
@D	Lambie, S.C.//Kelly, W.J.//Leahy, S.C.//Li, D.//Reilly, K.//McAllister, T.A.//Valle, E.R.//Attwood, G.T.//Altermann, E. 	The complete genome sequence of the rumen methanogen Methanosarcina barkeri CM1.	Standards in Genomic Sciences	2015	10		57			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. 		
@D	Lambowitz, A.M. 	Infectious introns.	Cell	1989	56		323-326			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. 		
@D	Lambowitz, A.M.//Belfort, M. 	Introns as mobile genetic elements.	Annu. Rev. Biochem.	1993	62		587-622			*
 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
 
 		
@A	Lambowitz, A.M.//Caprara, M.G.//Zimmerly, S.//Perlman, P.S. 		Group I and Group II ribozymes as RNPs: Clues to the past and guides to the future.			Gesteland, R.F.//Cech, T.R.//Atkins, J.F. 		The RNA World				Cold Spring Harbor	Cold Spring Harbor Laboratory Press	1999				451-485									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. 		
@D	Lambowitz, A.M.//Mohr, G.//Zimmerly, S. 	Group II intron homing endonucleases: ribonucleoprotein complexes with programmable target specificity.	Nucleic Acids Mol. Biol.	2005	16		121-145			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. 		
@D	Lamontanara, A.//Caggianiello, G.//Orru, L.//Capozzi, V.//Michelotti, V.//Bayjanov, J.R.//Renckens, B.//van Hijum, S.A.//Cattivelli, L.//Spano, G. 	Draft Genome Sequence of Lactobacillus plantarum Lp90 Isolated from Wine.	Genome Announcements	2015	3		e00097-15			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. 		
@D	Lamontanara, A.//Orru, L.//Cattivelli, L.//Russo, P.//Spano, G.//Capozzi, V. 	Genome Sequence of Oenococcus oeni OM27, the First Fully Assembled Genome of a Strain Isolated from an Italian Wine.	Genome Announcements	2014	2		e00658-14			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. 		
@D	Lan, H.//Yang, H.//Li, P.//Wang, C.//Zhou, H.//Zhou, H.//Pan, H.//Yu, Y.//Lu, X.//Tian, Y. 	Complete Genome Sequence of Enterobacter sp. Strain ODB01, a Bacterium That Degrades Crude Oil.	Genome Announcements	2017	5		e01763-16			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. 		
@D	Lan, J.//Hua, S.//He, X.N.//Zhang, Y. 	DNA methyltransferases and methyl-binding proteins of mammals.	Acta Biochim. Biophys. Sin.	2010	42		243-252			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. 		
@D	Lan, J.//Hua, S.//Liu, J.//Zhang, Y. 	cDNA Cloning of Goat DNA Methyltransferase 1, Screening of shRNA Vectors and Influences to Development of Nuclear Transfer Embryos.	Agric. Sci. China	2010	9		1035-1040			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. 		
@D	Lan, S.F.//Huang, C.H.//Chang, C.H.//Liao, W.C.//Lin, I.H.//Jian, W.N.//Wu, Y.G.//Chen, S.Y.//Wong, H.C. 	Characterization of a New Plasmid-Like Prophage in a Pandemic Vibrio parahaemolyticus O3:K6 Strain.	Appl. Environ. Microbiol.	2009	75		2659-2667			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. 		
@D	Lancaster, W.A.//Utturkar, S.M.//Poole, F.L.//Klingeman, D.M.//Elias, D.A.//Adams, M.W.//Brown, S.D. 	Near-Complete Genome Sequence of Clostridium paradoxum Strain JW-YL-7.	Genome Announcements	2016	4		e00229-16			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. 		
@D	Lanclos, V.C.//Henson, M.W.//Pitre, D.M.//Thrash, J.C. 	Draft Genome Sequence of Strain LSUCC0135, an Early Diverging Member of the Order Methylophilales in the Phylum Betaproteobacteria.	Genome Announcements	2016	4		e01231-16			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. 		
@D	Land, M. et al. 	Complete genome sequence of Beutenbergia cavernae type strain (HKI 0122).	Standards in Genomic Sciences	2009	1		21-28			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. 		
@D	Land, M. et al. 	Complete genome sequence of Actinosynnema mirum type strain (101).	Standards in Genomic Sciences	2009	1		46-53			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. 		
@D	Land, M. et al. 	Non-contiguous finished genome sequence of Bacteroides coprosuis type strain (PC139).	Standards in Genomic Sciences	2011	4		233-243			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. 		
@D	Landry, D.//Barsomian, J.M.//Feehery, G.R.//Wilson, G.G. 	Characterization of Type II DNA-Methyltransferases.	Methods Enzymol.	1992	216		244-259					
@D	Landry, D.//Looney, M.C.//Feehery, G.R.//Slatko, B.E.//Jack, W.E.//Schildkraut, I.//Wilson, G.G. 	M.FokI methylates adenine in both strands of its asymmetric recognition sequence.	Gene	1989	77		1-10			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. 		
@D	Landthaler, M.//Begley, U.//Lau, N.C.//Shub, D.A. 	Two self-splicing group I introns in the ribonucleotide reductase large subunit gene of Staphylococcus aureus phage Twort.	Nucleic Acids Res.	2002	30		1935-1943			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. 		
@D	Landthaler, M.//Lau, N.C.//Shub, D.A. 	Group I intron homing in Bacillus phages SPO1 and SP82: A gene conversion event initiated by a nicking homing endonuclease.	J. Bacteriol.	2004	186		4307-4314			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. 		
@D	Landthaler, M.//Shen, B.W.//Stoddard, B.L.//Shub, D.A. 	I-Basl and I-Hmul: Two phage intron-encoded endonucleases with homologous DNA recognition sequences but distinct DNA Specificities.	J. Mol. Biol.	2006	358		1137-1151			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. 		
@D	Landthaler, M.//Shub, D.A. 	The nicking homing endonuclease I-BasI is encoded by a group I intron in the DNA polymerase gene of the Bacillus thuringiensis phage Bastille.	Nucleic Acids Res.	2003	31		3071-3077			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. 		
@D	Landy, A.//Foeller, C.//Ross, W. 	DNA fragments carrying genes for tRNATyrI.	Nature	1974	249		738-742			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. 		
@D	Landy, A.//Olchowski, E.//Ross, W.//Reiness, G. 	Isolation of a functional lac regulatory region.	Mol. Gen. Genet.	1974	133		273-281			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. 		
@D	Landy, A.//Ruedisueli, E.//Robinson, L.//Foeller, C.//Ross, W. 	Digestion of deoxyribonucleic acids from bacteriophage T7, lambda, and Phi80h with site-specific nucleases from Hemophilus influenzae strain Rc and strain Rd.	Biochemistry	1974	13		2134-2142			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. 		
@D	Lang, E. et al. 	Complete genome sequence of Dyadobacter fermentans type strain (NS114).	Standards in Genomic Sciences	2009	1		133-140			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. 		
@D	Lang, E. et al. 	Complete genome sequence of Weeksella virosa type strain (9751).	Standards in Genomic Sciences	2011	4		81-90			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. 		
@D	Lange, C.//Jugel, A.//Walter, J.//Noyer-Weidner, M.//Trautner, T.A. 	Pseudo domains in phage-encoded DNA methyltransferases.	Nature	1991	352		645-648			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. 		
@D	Lange, C.//Noyer-Weidner, M.//Trautner, T.A.//Weiner, M.//Zahler, S.A. 	M.H2I, a multispecific 5C-DNA methyltransferase encoded by Bacillus amyloliquefaciens phage H2.	Gene	1991	100		213-218			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. 		
@D	Lange, C.//Wild, C.//Trautner, T.A. 	Altered sequence recognition specificity of a C5-DNA methyltransferase carrying a chimeric 'target recognizing domain'.	Gene	1995	157		127-128			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). 		
@D	Lange, C.//Wild, C.//Trautner, T.A. 	Identification of a subdomain within DNA-(cytosine-C5)-methyltransferases responsible for the recognition of the 5' part of their DNA target.	EMBO J.	1996	15		1443-1450			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. 		
@D	Lange, C.//Wild, C.//Trautner, T.A. 	Colinearity between amino acids of the target recognizing domains of a C5-DNA-methyltransferase and the nucleotide sequence of its target.	FASEB J.	1995	9		A1391			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. 		
@D	Langella, P.//Chopin, A. 	Effect of restriction-modification systems on transfer of foreign DNA into Lactococcus lactis subsp. lactis.	FEMS Microbiol. Lett.	1989	59		301-306			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. 		
@D	Langhans, M.T.//Palladino, M.J. 	Cleavage of mispaired heteroduplex DNA substrates by numerous restriction enzymes.	Curr. Issues Mol. Biol.	2008	11		1-12			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. 		
@D	Langowski, J.//Alves, J.//Pingoud, A.//Maass, G. 	Does the specific recognition of DNA by the restriction endonuclease EcoRI involve a linear diffusion step?  Investigation of the processivity of the EcoRI endonuclease.	Nucleic Acids Res.	1983	11		501-513			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. 		
@D	Langowski, J.//Pingoud, A.//Goppelt, M.//Maass, G. 	Inhibition of EcoRI action by polynucleotides.  A characterization of the non-specific binding of the enzyme to DNA.	Nucleic Acids Res.	1980	8		4727-4736			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. 		
@D	Langowski, J.//Urbanke, C.//Pingoud, A.//Maass, G. 	Transient cleavage kinetics of the EcoRI restriction endonuclease measured in a pulsed quench-flow apparatus:  enzyme concentration-dependent activity change.	Nucleic Acids Res.	1981	9		3483-3490			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. 		
@D	Lanie, J.A.//Ng, W.L.//Kazmierczak, K.M.//Andrzejewski, T.M.//Davidsen, T.M.//Wayne, K.J.//Tettelin, H.//Glass, J.I.//Winkler, M.E. 	Genome Sequence of Avery's Virulent Serotype 2 Strain D39 of Streptococcus pneumoniae and Comparison with That of Unencapsulated Laboratory Strain  R6.	J. Bacteriol.	2007	189		38-51			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. 		
@D	Lanio, T.//Jeltsch, A. 	PCR-based random mutagenesis method using spiked oligonucleotides to randomize selected parts of a gene without any wild-type background.	Biotechniques	1998	25		958-965			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. 		
@D	Lanio, T.//Jeltsch, A.//Pingoud, A. 	Automated purification of His6-tagged proteins allows exhaustive screening of libraries generated by random mutagenesis.	Biotechniques	2000	29		338-342			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. 		
@D	Lanio, T.//Jeltsch, A.//Pingoud, A. 	On the possibilities and limitations of rational protein design to expand the specificity of restriction enzymes: a case study employing EcoRV as the target.	Protein Eng.	2000	13		275-281			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. 		
@D	Lanio, T.//Jeltsch, A.//Pingoud, A. 	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.	J. Mol. Biol.	1998	283		59-69			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. 		
@D	Lanio, T.//Selent, U.//Wenz, C.//Wende, W.//Schulz, A.//Adiraj, M.//Katti, S.B.//Pingoud, A. 	EcoRV-T94V: a mutant restriction endonucleaase with an altered substrate specificity towards modified oligodeoxynucleotides.	Protein Eng.	1996	9		1005-1010			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. 		
@D	Lannoy, N.N.//Hoet, P.P.//Cocito, C.G. 	Cloning of DNA segments of phage 2C, which allows autonomous plasmid replication in Bacillus subtilis.	Eur. J. Biochem.	1985	152		137-142			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. 		
@D	Lanois, A.//Ogier, J.C.//Gouzy, J.//Laroui, C.//Rouy, Z.//Givaudan, A.//Gaudriault, S. 	Draft Genome Sequence and Annotation of the Entomopathogenic Bacterium Xenorhabdus nematophila Strain F1.	Genome Announcements	2013	1		e00342-13			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. 		
@D	Lanzarotti, E.//Pellizza, L.//Bercovich, A.//Foti, M.//Coria, S.H.//Vazquez, S.C.//Ruberto, L.//Hernandez, E.A.//Dias, R.L.//Mac, C.W.P.//Cicero, D.O.//Smal, C.//Nicolas, M.F.//Vasconcelos, A.T.//Marti, M.A.//Turjanski, A.G. 	Draft Genome Sequence of Bizionia argentinensis, Isolated from Antarctic Surface Water.	J. Bacteriol.	2011	193		6797-6798			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. 		
@D	Lao, W.//Chen, S. 	HsaI:  A restriction enzyme from human being.	Sci. Sin.	1986	29		947-953			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. 		
@D	Lapidus, A. et al. 	Genome sequence of the moderately thermophilic halophile Flexistipes sinusarabici strain (MAS10).	Standards in Genomic Sciences	2011	5		86-96			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. 		
@D	Lapidus, A. et al. 	Complete genome sequence of Brachybacterium faecium type strain (Schefferle 6-10).	Standards in Genomic Sciences	2009	1		3-11			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. 		
@D	Lapidus, A. et al. 	Genome sequence of the filamentous, gliding Thiothrix nivea neotype strain (JP2(T)).	Standards in Genomic Sciences	2011	5		398-406			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. 		
@D	Lapidus, A.//Clum, A.//Labutti, K.//Kaluzhnaya, M.G.//Lim, S.//Beck, D.A.//Glavina del Rio, T.//Nolan, M.//Mavromatis, K.//Huntemann, M.//Lucas, S.//Lidstrom, M.E.//Ivanova, N.//Chistoserdova, L. 	Genomes of three methylotrophs from a single niche reveal the genetic and metabolic divergence of the Methylophilaceae.	J. Bacteriol.	2011	193		3757-3764			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. 		
@D	Lapierre, P.//Halse, T.A.//Shea, J.//Escuyer, V.E.//Musser, K.A. 	Draft Genome Sequence of Branchiibius sp. NY16-3462-2, Isolated from a Mixed Clinical Sample.	Genome Announcements	2016	4		e00368-16			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. 		
@D	Lapkouski, M.//Panjikar, S.//Janscak, P.//Smatanova, I.K.//Carey, J.//Ettrich, R.//Csefalvay, E. 	Structure of the motor subunit of type I restriction-modification complex EcoR124I.	Nat. Struct. Mol. Biol.	2009	16		94-95			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. 		
@D	Lapkouski, M.//Panjikar, S.//Smatanova, I.K.//Csefalvay, E. 	Purification, crystallization and preliminary X-ray analysis of the HsdR subunit of the EcoR124I endonuclease from Escherichia coli.	Acta Crystallogr. F Struct. Biol. Cryst. Commun.	2007	63		582-585			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. 		
@D	LaPorte, J.P.//Spinard, E.J.//Gomez-Chiarri, M.//Rowley, D.C.//Mekalanos, J.J.//Nelson, D.R. 	Draft Genome Sequence of Bowmanella denitrificans JL63, a Bacterium Isolated from Whiteleg Shrimp (Litopenaeus vannamei) That Can Inhibit the Growth of Vibrio  parahaemolyticus.	Genome Announcements	2018	6		e00215-18			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. 		
@D	Lappalainen, I.//Vihinen, M. 	Structural basis of ICF-causing mutations in the methyltransferase domain of DNMT3B.	Protein Eng.	2002	15		1005-1014			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. 		
@D	Lara, Y.//Durieu, B.//Cornet, L.//Verlaine, O.//Rippka, R.//Pessi, I.S.//Misztak, A.//Joris, B.//Javaux, E.J.//Baurain, D.//Wilmotte, A. 	Draft Genome Sequence of the Axenic Strain Phormidesmispriestleyi ULC007, a Cyanobacterium Isolated from Lake Bruehwiler (Larsemann Hills, Antarctica).	Genome Announcements	2017	5		e01546-16			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. 		
@D	Larbi, D.//Decaris, B.//Simonet, J.M. 	Different bacteriophage resistance mechanisms in Streptococcus salivarius subsp. thermophilus.	J. Dairy Res.	1992	59		349-357			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. 		
@D	Larimer, F.W. 	Cleavage by ApaI is inhibited by overlapping dcm methylation.	Nucleic Acids Res.	1987	15		9087					
@D	Lark, C.//Arber, W. 	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.	J. Mol. Biol.	1970	52		337-348			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. 		
@D	Larner-Svensson, H.//Worning, P.//Bartels, M.D.//Hestbjerg, H.L.//Boye, K.//Westh, H. 	Complete Genome Sequence of Staphylococcus aureus Strain M1, a Unique t024-ST8-IVa Danish Methicillin-Resistant S. aureus Clone.	Genome Announcements	2013	1		e00336-13			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. 		
@D	Larson, M.A.//Nalbantoglu, U.//Sayood, K.//Zentz, E.B.//Bartling, A.M.//Francesconi, S.C.//Fey, P.D.//Dempsey, M.P.//Hinrichs, S.H. 	Francisella tularensis Subtype A.II Genomic Plasticity in Comparison with Subtype A.I.	PLoS ONE	2015	10		E0124906			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. 		
@D	Larsson, P.//Elfsmark, D.//Svensson, K.//Wikstrom, P.//Forsman, M.//Brettin, T.//Keim, P.//Johansson, A. 	Molecular evolutionary consequences of niche restriction in Francisella tularensis, a facultative intracellular pathogen.	PLoS Pathog.	2009	5		e1000472			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. 		
@D	Lartigue, C.//Vashee, S.//Algire, M.A.//Chuang, R.Y.//Benders, G.A.//Ma, L.//Noskov, V.N.//Denisova, E.A.//Gibson, D.G.//Assad-Garcia, N.//Alperovich, N.//Thomas, D.W.//Merryman, C.//Hutchison, C.A.I.I.I.//Smith, H.O.//Venter, J.C.//Glass, J.I. 	Creating bacterial strains from genomes that have been cloned and engineered in yeast.	Science	2009	325		1693-1696			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. 		
@D	Lasa, A.//Gibas, C.J.//Romalde, J.L. 	Draft Genome Sequence of Vibrio toranzoniae Strain CECT 7225T.	Genome Announcements	2016	4		e00212-16			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. 		
@D	Lasek, R.//Dziewit, L.//Bartosik, D. 	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.	Extremophiles	2012	16		363-376			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. 		
@D	Lasko, D.D.//Basu, A.K.//Kadlubar, F.F.//Evans, F.E.//Lay, J.O.//Essigmann, J.M. 	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.	Biochemistry	1987	26		3072-3081			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. 		
@D	Lassen, S.B.//Lomholt, H.B.//Bruggemann, H. 	Complete Genome Sequence of a Staphylococcus epidermidis Strain with Exceptional  Antimicrobial Activity.	Genome Announcements	2017	5		e00004-17			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. 		
@D	Lasserre, M.//Berna, L.//Greif, G.//Diaz-Viraque, F.//Iraola, G.//Naya, H.//Castro-Ramos, M.//Juambeltz, A.//Robello, C. 	Whole-Genome Sequences of Mycobacterium bovis Strain MbURU-001, Isolated from Fresh Bovine Infected Samples.	Genome Announcements	2015	3		e01237-15			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. 		
@D	Laszlo, V.G.//Rimanoczy, I. 	Restriction and modification of Shigella flexneri phages by R factors.	Acta Microbiol. Acad. Sci. Hung.	1976	23		259-270			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. 		
@D	Lata, P.//Govindarajan, S.S.//Qi, F.//Li, J.L.//Maurya, S.K.//Sahoo, M.K. 	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.	Genome Announcements	2017	5		e00500-17			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. 		
@D	Lata, P.//Govindarajan, S.S.//Qi, F.//Li, J.L.//Maurya, S.K.//Sahoo, M.K. 	Draft Genome Sequences of Extended-Spectrum-Beta-Lactamase-Producing Morganella morganii Strains AA1 and AV1, Isolated from a Freshwater Lake and  Eicchorniacrassipes Roots.	Genome Announcements	2017	5		e00527-17			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. 		
@D	Lata, P.//Govindarajan, S.S.//Qi, F.//Li, J.L.//Maurya, S.K.//Sahoo, M.K. 	Whole-Genome Sequence of Pantoea americana Strain VS1, an Extended-Spectrum beta-Lactamase-Producing Epibiont Isolated from Magnolia grandiflora.	Genome Announcements	2017	5		e01285-17			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. 		
@D	Lata, P.//Govindarajan, S.S.//Qi, F.//Li, J.L.//Maurya, S.K.//Sahoo, M.K. 	De Novo Whole-Genome Sequence of Pantoea latae Strain AS1, Isolated from Zamia floridana Rhizosphere in Central Florida, USA.	Genome Announcements	2017	5		e00640-17			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. 		
@D	Lata, P.//Govindarajan, S.S.//Qi, F.//Li, J.L.//Sahoo, M.K. 	Deep Sequencing-Identified Kanamycin-Resistant Paenibacillus sp. Strain KS1 Isolated from Epiphyte Tillandsia usneoides (Spanish Moss) in Central Florida,  USA.	Genome Announcements	2017	5		e01523-16			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. 		
@D	Latif, H.//Lerman, J.A.//Portnoy, V.A.//Tarasova, Y.//Nagarajan, H.//Schrimpe-Rutledge, A.C.//Smith, R.D.//Adkins, J.N.//Lee, D.H.//Qiu, Y.//Zengler, K. 	The Genome Organization of Thermotoga maritima Reflects Its Lifestyle.	PLoS Genet.	2013	9		E1003485			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. 		
@D	Latif, H.//Li, H.J.//Charusanti, P.//Palsson, B.O.//Aziz, R.K. 	A Gapless, Unambiguous Genome Sequence of the Enterohemorrhagic Escherichia coli  O157:H7 Strain EDL933.	Genome Announcements	2014	2		e00821-14			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. 		
@D	Lau, E.Y.//Bruice, T.C. 	Active site dynamics of the HhaI methyltransferase: Insights from computer simulation.	J. Mol. Biol.	1999	293		9-18			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. 		
@D	Lau, N.S.//Sam, K.K.//Amirul, A.A. 	Genome features of moderately halophilic polyhydroxyalkanoate-producing Yangia sp. CCB-MM3.	Standards in Genomic Sciences	2017	12		12			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. 		
@D	Lau, P.C.K.//Forghani, F.//Labbe, D.//Bergeron, H.//Brousseau, R.//Holtke, H.J. 	The NlaIV restriction and modification genes of Neisseria lactamica are flanked by leucine biosynthesis genes.	Mol. Gen. Genet.	1994	243		24-31			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. 		
@D	Lau, R.H.//Doolittle, W.F. 	AquI: a more easily purified isoschizomer of AvaI.	FEBS Lett.	1980	121		200-202			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. 		
@D	Lau, R.H.//Visentin, L.P.//Martin, S.M.//Hofman, J.D.//Doolittle, W.F. 	Site-specific restriction endonuclease from the filamentous cyanobacterium Nostoc sp. MAC PCC 8009.	FEBS Lett.	1985	179		129-132			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. 		
@D	Lau, S.C.//Riedel, T.//Fiebig, A.//Han, J.//Huntemann, M.//Petersen, J.//Ivanova, N.N.//Markowitz, V.//Woyke, T.//Goker, M.//Kyrpides, N.C.//Klenk, H.P.//Qian, P.Y. 	Genome sequence of the pink-pigmented marine bacterium Loktanella hongkongensis type strain (UST950701-009P(T)), a representative of the Roseobacter group.	Standards in Genomic Sciences	2015	10		51			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. 		
@D	Lau, S.K.//Teng, J.L.//Huang, Y.//Curreem, S.O.//Tsui, S.K.//Woo, P.C. 	Draft Genome Sequence of Catabacter hongkongensis Type Strain HKU16T, Isolated from a Patient with Bacteremia and Intestinal Obstruction.	Genome Announcements	2015	3		e00531-15			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. 		
@D	Laue, F.//Ankenbauer, W.//Schmitz, G.G.//Kessler, C. 	The selective inhibitory effect of netropsin on relaxation of sequence specificity of restriction endonuclease SgrAI recognizing 5'-CR^CCGGYG-3'.	Nucleic Acids Res.	1990	18		3421			None 		
@D	Laue, F.//Evans, L.R.//Jarsch, M.//Brown, N.L.//Kessler, C. 	A complex family of class-II restriction endonucleases, DsaI-VI, in Dactylococcopsis salina.	Gene	1991	97		87-95			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. 		
@D	Lauer, A.C.//Humrighouse, B.W.//Loparev, V.//Shewmaker, P.L.//Whitney, A.M.//McQuiston, J.R.//McLaughlin, R.W. 	Complete Genome Sequences of Enterococcus rotai LMG 26678T and Enterococcus silesiacus LMG 23085T.	Genome Announcements	2016	4		e01387-16			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. 		
@D	Lauer, A.C.//Nicholson, A.C.//Humrighouse, B.W.//Emery, B.//Drobish, A.//Juieng, P.//Loparev, V.//McQuiston, J.R. 	Genome Sequences of Oblitimonas alkaliphila gen. nov. sp. nov. (Proposed), a Novel Bacterium of the Pseudomonadaceae Family.	Genome Announcements	2015	3		e01474-15			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. 		
@D	Laugraud, A.//Young, S.//Gerard, E.//O'Callaghan, M.//Wakelin, S. 	Draft Genome Sequence of the Clover (Trifolium repens L.) Root Endophyte Paraburkholderia sp. Strain A27.	Genome Announcements	2017	5		e00466-17			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. 		
@D	Laugraud, A.//Young, S.//Gerard, E.//O'Callaghan, M.//Wakelin, S. 	Draft Genome Sequence of a Kale (Brassica oleracea L.) Root Endophyte, Pseudomonas sp. Strain C9.	Genome Announcements	2017	5		e00163-17			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. 		
@D	Laurens, N.//Bellamy, S.R.//Harms, A.F.//Kovacheva, Y.S.//Halford, S.E.//Wuite, G.J. 	Dissecting protein-induced DNA looping dynamics in real time.	Nucleic Acids Res.	2009	37		5454-5464			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. 		
@D	Laurens, N.//Rusling, D.A.//Pernstich, C.//Brouwer, I.//Halford, S.E.//Wuite, G.J. 	DNA looping by FokI: the impact of twisting and bending rigidity on protein-induced looping dynamics.	Nucleic Acids Res.	2012	40		4988-4997			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. 		
@D	Laurent, J.P.//Faske, S.//Cangelosi, G.A. 	Characterization of IS999, an unstable genetic element in Mycobacterium avium.	Gene	2002	294		249-257			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. 		
@D	Laurino, P.//Tawfik, D. 	Engineering DNA methyltransferases for a novel cofactor.	FEBS J.	2013	280		173-174			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. 		
@D	Lauro, F.M.//Chastain, R.A.//Ferriera, S.//Johnson, J.//Yayanos, A.A.//Bartlett, D.H. 	Draft Genome Sequence of the Deep-Sea Bacterium Shewanella benthica Strain KT99.	Genome Announcements	2013	1		e00210-13			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. 		
@D	Lauro, F.M.//Stratton, T.K.//Chastain, R.A.//Ferriera, S.//Johnson, J.//Goldberg, S.M.//Yayanos, A.A.//Bartlett, D.H. 	Complete Genome Sequence of the Deep-Sea Bacterium Psychromonas Strain CNPT3.	Genome Announcements	2013	1		e00304-13			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. 		
@D	Lauster, R. 	Duplication and variation as a phylogenetic principle of Type II DNA methyltransferases.	Gene	1988	74		243			Meeting Abstract 		
@D	Lauster, R. 	Evolution of type II DNA methyltransferases:  A gene duplication model.	J. Mol. Biol.	1989	206		313-321			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. 		
@D	Lauster, R. 	Close relationship between the HinfI and DpnA DNA-methyltransferase.	Nucleic Acids Res.	1989	17		4402			None 		
@D	Lauster, R.//Kriebardis, A.//Guschlbauer, W. 	The GATATC-modification enzyme EcoRV is closely related to the GATC-recognizing methyltransferases DpnII and dam from E. coli and phage T4.	FEBS Lett.	1987	220		167-176			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. 		
@D	Lauster, R.//Trautner, T.A.//Noyer-Weidner, M. 	Cytosine-specific type II DNA methyltransferases:  A conserved enzyme core with variable target-recognizing domains.	J. Mol. Biol.	1989	206		305-312			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. 		
@D	Lautenberger, J.//Eskin, B.//Linn, S. 	The DNA modification methylase and restriction endonuclease of Escherichia coli B.	Fed. Proc.	1972	31		474			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. 		
@D	Lautenberger, J.A.//Edgell, M.H.//Hutchison, C.A. III 	The nucleotide sequence recognized by the BstEII restriction endonuclease.	Gene	1980	12		171-174			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. 		
@D	Lautenberger, J.A.//Edgell, M.H.//Hutchison, C.A. III 	The DNA sequence on bacteriophage G4 recognized by the Escherichia coli B restriction enzyme.	J. Mol. Biol.	1979	131		871-875			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. 		
@D	Lautenberger, J.A.//Kan, N.C.//Lackey, D.//Linn, S.//Edgell, M.H.//Hutchison, C.A. III 	Recognition site of Escherichia coli B restriction enzyme on PhiXsB1 and simian virus 40 DNAs: An interrupted sequence.	Proc. Natl. Acad. Sci. U. S. A.	1978	75		2271-2275			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. 		
@D	Lautenberger, J.A.//Linn, S. 	The deoxyribonucleic acid modification and restriction enzymes of Escherichia coli B. I. Purification, subunit structure, and catalytic properties of the modification methylase.	J. Biol. Chem.	1972	247		6176-6182			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. 		
@D	Lautenberger, J.A.//White, C.T.//Haigwood, N.L.//Edgell, M.H.//Hutchison, C.A. 	The recognition site of Type II restriction enzyme BglI is interrupted.	Gene	1980	9		213-231			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. 		
@D	Laverde-Gomez, J.A.//van Schaik, W.//Freitas, A.R.//Coque, T.M.//Weaver, K.E.//Francia, M.V.//Witte, W.//Werner, G. 	A multiresistance megaplasmid pLG1 bearing a hylEfm genomic island in hospital Enterococcus faecium isolates.	Int. J. Med. Microbiol.	2011	301		165-175			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. 		
@D	Lavezzo, E.//Toppo, S.//Barzon, L.//Cobelli, C.//Di Camillo, B.//Finotello, F.//Franchin, E.//Peruzzo, D.//Toffolo, G.M.//Trevisan, M.//Palu, G. 	Draft genome sequences of two Neisseria meningitidis serogroup C clinical isolates.	J. Bacteriol.	2010	192		5270-5271			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. 		
@D	Laviad, S.//Lapidus, A.//Copeland, A.//Reddy, T.//Huntemann, M.//Pati, A.//Ivanova, N.N.//Markowitz, V.M.//Pukall, R.//Klenk, H.P.//Woyke, T.//Kyrpides, N.C.//Halpern, M. 	High quality draft genome sequence of Leucobacter chironomi strain MM2LB(T) (DSM  19883(T)) isolated from a Chironomus sp. egg mass.	Standards in Genomic Sciences	2015	10		21			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. 		
@D	Laviad, S.//Lapidus, A.//Han, J.//Haynes, M.//Reddy, T.//Huntemann, M.//Pati, A.//Ivanova, N.N.//Mavromatis, K.//Lang, E.//Rohde, M.//Markowitz, V.//Woyke, T.//Klenk, H.P.//Kyrpides, N.C.//Halpern, M. 	High quality draft genome sequence of Brachymonas chironomi AIMA4(T) (DSM 19884(T)) isolated from a Chironomus sp. egg mass.	Standards in Genomic Sciences	2015	10		29			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. 		
@D	Laviad-Shitrit, S. et al. 	High quality permanent draft genome sequence of Chryseobacterium bovis DSM 19482T, isolated from raw cow milk.	Standards in Genomic Sciences	2017	12		31			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. 		
@D	Law, J.A.//Jacobsen, S.E. 	Establishing, maintaining and modifying DNA methylation patterns in plants and animals.	Nat. Rev. Genet.	2010	11		204-220			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. 		
@D	Lawrence, P.K.//Bey, R.F.//Wiener, B.//Kittichotirat, W.//Bumgarner, R.E. 	Genome Sequence of a Presumptive Mannheimia haemolytica Strain with an A1/A6-Cross-Reactive Serotype from a White-Tailed Deer (Odocoileus virginianus).	Genome Announcements	2014	2		e00114-14			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. 		
@D	Lawrence, P.K.//Kittichotirat, W.//Bumgarner, R.E.//McDermott, J.E.//Herndon, D.R.//Knowles, D.P.//Srikumaran, S. 	Genome sequences of Mannheimia haemolytica serotype A2: ovine and bovine isolates.	J. Bacteriol.	2010	192		1167-1168			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). 		
@D	Lawrence, P.K.//Wiener, B.L.//Kolander-Bremer, T.//Bey, R.F.//Stine, D.L.//Kittichotirat, W.//Bumgarner, R.E. 	Genome-Wide Association Studies of Virulent and Avirulent Haemophilus parasuis Serotype 4 Strains.	Genome Announcements	2014	2		e00884-14			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. 		
@D	Lawrenz, M.B.//Kawabata, H.//Norris, S.J. 	Plasmid content determines the ability to transform Borrelia burgdorferi.	Abstr. Gen. Meet. Am. Soc. Microbiol.	2002	102		179			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. 		
@D	Lawrenz, M.B.//Kawabata, H.//Purser, J.E.//Norris, S.J. 	Decreased electroporation efficiency in Borrelia burgdorferi containing linear plasmids lp25 and lp56: impact on transformation of infectious  B. burgdorferi.	Infect. Immun.	2002	70		4798-4804			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. 		
@D	Lazarev, V.N. et al. 	Complete Genome and Proteome of Acholeplasma laidlawii.	J. Bacteriol.	2011	193		4943-4953			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. 		
@D	Lazarevic, V.//Dusterhoft, A.//Soldo, B.//Hilbert, H.//Mauel, C.//Karamata, D. 	Nucleotide sequence of the Bacillus subtilis temperate bacteriophage SPbetaetac2.	Microbiology	1999	145		1055-1067			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. 		
@D	Lazarevic, V.//Soldo, B.//Dusterhoft, A.//Hilbert, H.//Mauel, C.//Karamata, D. 	Introns and intein coding sequence in the ribonucleotide reductase genes of Bacillus subtilis temperate bacteriophage SPbeta.	Proc. Natl. Acad. Sci. U. S. A.	1998	95		1692-1697			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. 		
@D	Lazareviciute, L.//Maneliene, Z.//Padegimiene, A.//Kiuduliene, L.//Laucys, V.//Bitinaite, J.//Gruber, I.M.//Polyachenko, V.M.//Butkus, V.//Janulaitus, A. 	Isolation and characteristics of new restriction endonucleases from Haemophilus influenzae.	Bioorg. Khim.	1990	16		889-897			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. 		
@D	Lazaro-Diez, M.//Acosta, F.//Remuzgo-Martinez, S.//Ocampo-Sosa, A.//Ocejo-Vinyals, J.G.//Bravo, J.//El Aamri, F.//Escuela, O.//Martinez-Martinez, L.//Ramos-Vivas, J. 	Whole-Genome Sequence of Serratia liquefaciens HUMV-21, a Cytotoxic, Quorum-Sensing, and Biofilm-Producing Clinical Isolate.	Genome Announcements	2015	3		e00533-15			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. 		
@D	Lazaro-Diez, M.//Redondo-Salvo, S.//Arboleya-Agudo, A.//Ocejo-Vinyals, J.G.//Chapartegui-Gonzalez, I.//Ocampo-Sosa, A.A.//Acosta, F.//Martinez-Martinez, L.//Ramos-Vivas, J. 	Whole-Genome Sequence of Hafnia alvei HUMV-5920, a Human Isolate.	Genome Announcements	2016	4		e00556-16			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. 		
@D	Lazaro-Perona, F.//Sotillo, A.//Troyano-Hernaez, P.//Gomez-Gil, R.//Vega-Bueno, A.//Mingorance, J. 	Genomic path to panresistance in a clinical isolate of Klebsiella pneumoniae.	Int. J. Antimicrob. Agents	2018	52		713-718			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. 		
@D	Lazarte, J.N.//Lopez, R.P.//Ghiringhelli, P.D.//Beron, C.M. 	Bacillus wiedmannii biovar thuringiensis: A Specialized Mosquitocidal Pathogen with Plasmids from Diverse Origins.	Genome Biol. Evol.	2018	10		2823-2833			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. 		
@D	Lazim, H.//Josephsen, J.//Ben Hassen, A.//Belhadj, O.//Limam, R. 	Eco1524I, a type II restriction endonuclease - Isolation, partial purification, and characterization.	Appl. Biochem. Biotechnol.	2005	125		189-199			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. 		
@D	Lazowska, J.//Meunier, B.//Macadre, C. 	Homing of a group II intron in yeast mitochondrial DNA is accompanied by unidirectional co-conversion of upstream-located markers.	EMBO J.	1994	13		4963-4972			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. 		
@D	Lazowska, J.//Szczepanek, T.//Macadre, C.//Dakova, M. 	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.	C.R. Acad. Sci. III	1992	315		37-41			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. 		
@D	Le Bars, H.//Bousarghin, L.//Bonnaure-Mallet, M.//Jolivet-Gougeon, A.//Barloy-Hubler, F. 	Complete Genome Sequence of the Strong Mutator Salmonella enterica subsp. enterica Serotype Heidelberg Strain B182.	J. Bacteriol.	2012	194		3537-3538			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%). 		
@D	Le Gac, G.//Esteve, P.-O.//Ferec, C.//Pradhan, S. 	DNA damage-induced down-regulation of human Cdc25C and Cdc2 is mediated by cooperation between p53 and maintenance DNA (Cytosine-5) methyltransferase 1.	J. Biol. Chem.	2006	281		24161-24170			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. 		
@D	Le Guen, L.//Santos, R.//Camadro, J.-M. 	Functional analaysis of the hemK gene product involvement in protoporphyrinogen oxidase activity in yeast.	FEMS Microbiol. Lett.	1999	173		175-182			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. 		
@D	Le Guern, R.//Grandjean, T.//Faure, K.//Bauduin, M.//Kipnis, E.//Dessein, R. 	Draft Genome Sequences of Two Carbapenemase-Producing Klebsiella pneumoniae Strains Isolated from Blood Cultures.	Microbiol. Resour. Announc.	2018	7		e01057-18			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. 		
@D	Le Marechal, C.//Hernandez, D.//Schrenzel, J.//Even, S.//Berkova, N.//Thiery, R.//Vautor, E.//Fitzgerald, J.R.//Francois, P.//Le Loir, Y. 	Genome Sequence of two Staphylococcus aureus ovine strains that induce severe (strain O11) and mild (strain O46) mastitis.	J. Bacteriol.	2011	193		2353-2354			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. 		
@D	le Roux, W.J.//Chan, W.Y.//De Maayer, P.//Venter, S.N. 	Genome Sequence of Vibrio cholerae G4222, a South African Clinical Isolate.	Genome Announcements	2013	1		e0004013			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. 		
@D	Le, Y.//Zhu, S. 	Purification of restriction endonuclease MspI.	Huaxue Shiji	1988	10		35-37			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. 		
@D	Leahy, S.C.//Kelly, W.J.//Altermann, E.//Ronimus, R.S.//Yeoman, C.J.//Pacheco, D.M.//Li, D.//Kong, Z.//McTavish, S.//Sang, C.//Lambie, S.C.//Janssen, P.H.//Attwood, G.T. 	The genome sequence of the rumen methanogen Methanobrevibacter ruminantium M1.	PLoS ONE	2010	5		e8926			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. 		
@D	Leahy, S.C.//Kelly, W.J.//Li, D.//Li, Y.//Altermann, E.//Lambie, S.C.//Cox, F.//Attwood, G.T. 	The Complete genome sequence of Methanobrevibacter sp. AbM4.	Standards in Genomic Sciences	2013	8		215-227			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. 		
@D	Lean, S.S.//Yeo, C.C.//Suhaili, Z.//Thong, K.L. 	Comparative Genomics of Two ST 195 Carbapenem-Resistant Acinetobacter baumannii with Different Susceptibility to Polymyxin Revealed Underlying Resistance  Mechanism.	Front. Microbiol.	2015	6		1445			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. 		
@D	Leandro, T.//da Costa, M.S.//Sanz, J.L.//Amils, R. 	Complete Genome Sequence of Tessaracoccus sp. Strain T2.5-30 Isolated from 139.5  Meters Deep on the Subsurface of the Iberian Pyritic Belt.	Genome Announcements	2017	5		e00238-17			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). 		
@D	Leao, S.C.//Matsumoto, C.K.//Viana-Niero, C.//Ramos, R.T.//Carneiro, A.R.//Barbosa, M.S.//Lima, K.V.//Lopes, M.L.//Azevedo, V.//Silva, A. 	Draft Genome Sequence of Mycobacterium abscessus subsp. bolletii INCQS 00594.	Genome Announcements	2013	1		e00896-13			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. 		
@D	Leao, T.//Guimaraes, P.I.//de Melo, A.G.//Ramos, R.T.//Leao, P.N.//Silva, A.//Fiore, M.F.//Schneider, M.P. 	Draft Genome Sequence of the N2-Fixing Cyanobacterium Nostoc piscinale CENA21, Isolated from the Brazilian Amazon Floodplain.	Genome Announcements	2016	4		e00189-16			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. 		
@D	Lebedev, L.R.//Afinogenova, G.N.//Andreeva, I.S.//Pustoshilova, N.M.//Pozdnyakov, S.G.//Chizhikov, V.E. 	Determination of substrate specificity of a site-specific deoxyribonuclease RtrI.	Bioorg. Khim.	1991	17		277-279			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. 		
@D	Lebedev, L.R.//Pustoshilova, N.M.//Repin, V.E.//Degtyarev, S.K. 	Isolation of restriction endonuclease RsaI from Rhodopseudomonas sphaeroides and study of its properties.	Prikl. Biokhim. Mikrobiol.	1991	27		330-337			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. 		
@D	Lebenka, A.I.//Melvidas, V.I. 	The sensitivity of E. coli and C. freundii strains to 5-azacytidine.	Vopr. Med. Khim.	2001	47		477-482			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. 		
@D	Lebenka, A.Y.//Chitavichyus, D.B. 	Enzymes of DNA restriction-modification from Caulobacter fusiformis BC-25.	Biokhimiia	1988	53		1895-1899			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. 		
@D	Lebenka, A.Y.//Kanopkaite, S.I.//Buryanov, Y.I. 	DNA methylation in the cells of Escherichia coli MRE 600 in the presence of S-methylmethionine.	Biokhimiia	1981	46		2160-2163			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. 		
@D	Lebenka, A.Y.//Rackus, Y.A. 	DNA methylase Sau3AI:  isolation and properties.	Biokhimiia	1989	54		1009-1014			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. 		
@D	Lebert, B.M.//Sanford, S.A.//Reisinger, L.M.//Forsman, A.M.//Savage, A.E. 	Draft Genome Sequence of Xenophilus sp., a Novel Bacterium Isolated from the Skin of a Southern Leopard Frog (Rana sphenocephala) in Florida, USA.	Genome Announcements	2017	5		e01067-17			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. 		
@D	Lebionka, A.Y.//Melvidas, V.I. 	The ability of bacterial DNA methyltransferases to use methylcobalamine as a cofactor in DNA methylation reactions.	Bioorg. Khim.	2007	53		159-163			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. 		
@D	LeBon, J.M.//Kado, C.I.//Rosenthal, L.J.//Chirikjian, J.G. 	DNA modifying enzymes of Agrobacterium tumefaciens: Effect of DNA topoisomerase, restriction endonuclease, and unique DNA endonuclease on plasmid and plant DNA.	Proc. Natl. Acad. Sci. U. S. A.	1978	75		4097-4101			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. 		
@D	Lebreton, F.//Valentino, M.D.//Duncan, L.B.//Zeng, Q.//Manson, Mc.G.A.//Earl, A.M.//Gilmore, M.S. 	High-Quality Draft Genome Sequence of Vagococcus lutrae Strain LBD1, Isolated from the Largemouth Bass Micropterus salmoides.	Genome Announcements	2013	1		e01087-13			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. 		
@D	Lebreton, F.//van Schaik, W.//McGuire, A.M.//Godfrey, P.//Griggs, A.//Mazumdar, V.//Corander, J.//Cheng, L.//Saif, S.//Young, S.//Zeng, Q.//Wortman, J.//Birren, B.//Willems, R.J.//Earl, A.M.//Gilmore, M.S. 	Emergence of epidemic multidrug-resistant Enterococcus faecium from animal and commensal strains.	MBio	2013	4		e00534-13			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. 		
@D	Lechner, M.//Frey, B.//Laue, F.//Ankenbauer, W.//Schmitz, G. 	SwaI, a unique restriction endonuclease from Staphylococcus warneri, which recognizes 5'-ATTTAAAT-3'.	Fresenius Z. Anal. Chem.	1992	343		121-122			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. 		
@D	Lechner, M.//Frey, B.//Laue, F.//Anton-Botella, J.//Smith, C.L.//Ankenbauer, W.//Schmitz, G.G. 	SwaI, a unique restriction endonuclease from Staphylococcus warneri, which recognizes 5'-ATTTAAAT-3'.	Nucleic Acids Res.	1992	20		2293-2296			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. 		
@D	Leclercq, S.//Dittmer, J.//Bouchon, D.//Cordaux, R. 	Phylogenomics of 'Candidatus Hepatoplasma crinochetorum,' a Lineage of Mollicutes Associated with Noninsect Arthropods.	Genome Biol. Evol.	2014	6		407-415			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. 		
@D	Lederberg, S. 	Genetics of host-controlled restriction anad modification of deoxyribonucleic acid in Escherichia coli.	J. Bacteriol.	1966	91		1029-1036			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. 		
@D	Lederberg, S. 	Host-controlled restriction and modification of deoxyribonucleic acid in Eschericia coli.	Virology	1965	27		378-387			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. 		
@D	Ledwaba, B.//Mafofo, J.//van Heerden, H. 	Genome Sequences of Brucella abortus and Brucella suis Strains Isolated from Bovine in Zimbabwe.	Genome Announcements	2014	2		e01063-14			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. 		
@D	Lee, A.S.//Sinsheimer, R.L. 	A cleavage map of bacteriophage PhiX174 genome.	Proc. Natl. Acad. Sci. U. S. A.	1974	71		2882-2886			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. 		
@D	Lee, B.//Muller, M.T. 	SUMOylation enhances DNA methyltransferase 1 activity.	Biochem. J.	2009	421		449-461			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. 		
@D	Lee, B.H.//Yegnasubramanian, S.//Lin, X.H.//Nelson, W.G. 	Procainamide is a specific inhibitor of DNA methyltransferase 1.	J. Biol. Chem.	2005	280		40749-40756			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. 		
@D	Lee, B.M.//Park, Y.J.//Park, D.S.//Kang, H.W.//Kim, J.G.//Song, E.S.//Park, I.C.//Yoon, U.H.//Hahn, J.H.//Koo, B.S.//Lee, G.B.//Kim, H.//Park, H.S.//Yoon, K.O.//Kim, J.H.//Jung, C.H.//Koh, N.H.//Seo, J.S.//Go, S.J. 	The genome sequence of Xanthomonas oryzae pathovar oryzae KACC10331, the bacterial blight pathogen of rice.	Nucleic Acids Res.	2005	33		577-586			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. 		
@D	Lee, C.//Peters, V.//Melefors, O.//Romling, U. 	Draft Genome Sequence of Pseudomonas aeruginosa SG17M, an Environmental Isolate Belonging to Clone C, Prevalent in Patients and Aquatic Habitats.	Genome Announcements	2014	2		e00186-14			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. 		
@D	Lee, C.G.//Yuki, M.//Iida, T.//Nakaho, K.//Ohkuma, M. 	Draft Genome Sequence of Tepidibacter mesophilus Strain JCM 16806T Isolated from  Soil Polluted by Crude Oil in China.	Genome Announcements	2017	5		e01308-17			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. 		
@D	Lee, D.//Kim, Y.K.//Kim, Y.S.//Kim, T.J. 	Complete Genome Sequence of Elizabethkingia sp. BM10, a Symbiotic Bacterium of the Wood-Feeding Termite Reticulitermes speratus KMT1.	Genome Announcements	2015	3		e01181-15			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. 		
@D	Lee, D.//Seo, H.//Park, C.//Park, K. 	WeGAS: a web-based microbial genome annotation system.	Biosci. Biotechnol. Biochem.	2009	73		213-216			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. 		
@D	Lee, D.G.//Urbach, J.M.//Wu, G.//Liberati, N.T.//Feinbaum, R.L.//Miyata, S.//Diggins, L.T.//He, J.//Saucier, M.//Deziel, E.//Friedman, L.//Li, L.//Grills, G.//Montgomery, K.//Kucherlapati, R.//Rahme, L.G.//Ausubel, F.M. 	Genomic analysis reveals that Pseudomonas aeruginosa virulence is combinatorial.	Genome Biol.	2006	7		R90			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. 		
@D	Lee, D.H.//Jin, S.G.//Cai, S.//Chen, Y.//Pfeifer, G.P.//O'Connor, T.R. 	Repair of methylation damage in DNA and RNA by mammalian AlkB homologues.	J. Biol. Chem.	2005	280		39448-39459			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. 		
@D	Lee, D.H.//Kim, H.R.//Chung, H.Y.//Lim, J.G.//Kim, S.//Kim, S.K.//Ku, H.J.//Kim, H.//Ryu, S.//Choi, S.H.//Lee, J.H. 	Complete genome sequence of Bacillus cereus FORC_005, a food-borne pathogen from  the soy sauce braised fish-cake with quail-egg.	Standards in Genomic Sciences	2015	10		97			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. 		
@D	Lee, G.H.//Kumar, S.//Lee, J.H.//Chang, D.H.//Kim, D.S.//Choi, S.H.//Rhee, M.S.//Lee, D.W.//Yoon, M.H.//Kim, B.C. 	Genome Sequence of Oscillibacter ruminantium Strain GH1, Isolated from Rumen of Korean Native Cattle.	J. Bacteriol.	2012	194		6362			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. 		
@D	Lee, G.W.//Lee, K.J.//Chae, J.C. 	Genome Sequence of Herbaspirillum sp. Strain GW103, a Plant Growth-Promoting Bacterium.	J. Bacteriol.	2012	194		4150			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. 		
@D	Lee, H.//Kang, S.//Yim, J.-B.//Hwang, D.S. 	Identification of hemimethylated DNA binding activity in the seqA mutant.	Korean J. Biol. Sci.	1998	2		351-353			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. 		
@D	Lee, H.//Kim, B.J.//Kim, K.//Hong, S.H.//Kook, Y.H.//Kim, B.J. 	Whole-Genome Sequence of Mycobacterium intracellulare Clinical Strain MOTT-H4Y, Belonging to INT5 Genotype.	Genome Announcements	2013	1		e00006-13			Here, we report the draft genome sequence of the clinical strain MOTT-H4Y, grouped previously into the INT5 genotype of the 5 genotypes of . 		
@D	Lee, H.//Shin, S.C.//Lee, J.//Kim, S.J.//Kim, B.K.//Hong, S.G.//Kim, E.H.//Park, H. 	Genome Sequence of Sphingomonas sp. Strain PAMC 26621, an Arctic-Lichen-Associated Bacterium Isolated from a Cetraria sp.	J. Bacteriol.	2012	194		3030			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. 		
@D	Lee, H.J.//Chun, B.H.//Jeon, H.H.//Kim, Y.B.//Lee, S.H. 	Complete Genome Sequence of Bacillus velezensis YJ11-1-4, a Strain with Broad-Spectrum Antimicrobial Activity, Isolated from Traditional Korean Fermented  Soybean Paste.	Genome Announcements	2017	5		e01352-17			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. 		
@D	Lee, H.J.//Lee, S.H.//Lee, S.S.//Lee, J.S.//Kim, Y.//Kim, S.C.//Jeon, C.O. 	Ramlibacter solisilvae sp. nov., isolated from forest soil, and emended description of the genus Ramlibacter.	Int. J. Syst. Evol. Microbiol.	2014	64		1317-1322			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. 		
@D	Lee, H.J.//Nishi, K.//Song, J.M.//Kim, J.S. 	Expression, crystallization and preliminary X-ray diffraction analysis of a modification subunit of a putative type I restriction enzyme from Vibrio vulnificus YJ016.	Acta Crystallogr. F Struct. Biol. Cryst. Commun.	2009	65		1271-1273			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%. 		
@D	Lee, H.S.//Bae, S.S.//Kim, M.S.//Kwon, K.K.//Kang, S.G.//Lee, J.H. 	Complete Genome Sequence of Hyperthermophilic Pyrococcus sp. Strain NA2, Isolated from Deep-Sea Hydrothermal Vent Area.	J. Bacteriol.	2011	193		3666-3667			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. 		
@D	Lee, H.S.//Kang, S.G.//Bae, S.S.//Lim, J.K.//Cho, Y.//Kim, Y.J.//Jeon, J.H.//Cha, S.S.//Kwon, K.K.//Kim, H.T.//Park, C.J.//Lee, H.W.//Kim, S.I.//Chun, J.//Colwell, R.R.//Kim, S.J.//Lee, J.H. 	The complete genome sequence of Thermococcus onnurineus NA1 reveals a mixed heterotrophic and carboxydotrophic metabolism.	J. Bacteriol.	2008	190		7491-7499			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. 		
@D	Lee, H.S.//Kang, S.G.//Kwon, K.K.//Lee, J.H.//Kim, S.J. 	Genome Sequence of the Algicidal Bacterium Kordia algicida OT-1.	J. Bacteriol.	2011	193		4031-4032			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. 		
@D	Lee, H.W.//Kim, D.W.//Lee, M.H.//Kim, B.Y.//Cho, Y.J.//Yim, K.J.//Song, H.S.//Rhee, J.K.//Seo, M.J.//Choi, H.J.//Choi, J.S.//Lee, D.G.//Yoon, C.//Nam, Y.D.//Roh, S.W. 	Draft genome sequence of the extremely halophilic archaeon Haladaptatus cibarius  type strain D43(T) isolated from fermented seafood.	Standards in Genomic Sciences	2015	10		53			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 %. 		
@D	Lee, I.M.//Shao, J.//Bottner-Parker, K.D.//Gundersen-Rindal, D.E.//Zhao, Y.//Davis, R.E. 	Draft Genome Sequence of 'Candidatus Phytoplasma pruni' Strain CX, a Plant-Pathogenic Bacterium.	Genome Announcements	2015	3		e01117-15			'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%. 		
@D	Lee, J.//Cho, A.//Yang, J.Y.//Woo, J.//Lee, H.K.//Hong, S.G.//Kim, O.S. 	Complete Genome Sequence of Cryobacterium arcticum Strain PAMC 27867, Isolated from a Sedimentary Rock Sample in Northern Victoria Land, Antarctica.	Genome Announcements	2016	4		e00885-16			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. 		
@D	Lee, J.//Jang, Y.-S.//Han, M.-J.//Kim, J.Y.//Lee, S.Y. 	Deciphering Clostridium tyrobutyricum metabolism based on the whole genome sequence and proteome analyses.	MBio	2016	7		e00743-16			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. 		
@D	Lee, J.//Kwon, M.//Yang, J.Y.//Woo, J.//Lee, H.K.//Hong, S.G.//Kim, O.S. 	Complete Genome Sequence of Psychrobacter alimentarius PAMC 27889, a Psychrophile Isolated from an Antarctic Rock Sample.	Genome Announcements	2016	4		e00704-16			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. 		
@D	Lee, J.//Roh, S.W.//Whon, T.W.//Shin, N.R.//Kim, Y.O.//Bae, J.W. 	Genome Sequence of Strain TW15, a Novel Member of the Genus Ruegeria Belonging to the Marine Roseobacter Clade.	J. Bacteriol.	2011	193		3401-3402			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. 		
@D	Lee, J.//Shin, S.C.//Kim, S.J.//Kim, B.K.//Hong, S.G.//Kim, E.H.//Park, H.//Lee, H. 	Draft Genome Sequence of a Sphingomonas sp., an Endosymbiotic Bacterium Isolated  from an Arctic Lichen Umbilicaria sp.	J. Bacteriol.	2012	194		3010-3011			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. 		
@D	Lee, J.-H.//Shin, H.//Kim, H.//Ryu, S. 	Complete Genome Sequence of Salmonella Bacteriophage SPN3US.	J. Virol.	2011	85		13470-13471			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. 		
@D	Lee, J.-I.//Yang, C.-H. 	The purification and characterization of PvuII, restriction endonuclease.	Korean Biochem. J.	1984	17		357-364			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. 		
@D	Lee, J.-T.//Cho, T.-J.//Lim, J.-Y. 	Characterization of a restriction endonuclease AspJI from Alcaligenes sp. J-482.	Korean J. Microbiol.	1994	32		285-290			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. 		
@D	Lee, J.C.//Kim, D.S.//Moon, D.C.//Lee, J.H.//Kim, M.J.//Lee, S.M.//Lee, Y.S.//Kang, S.W.//Lee, E.J.//Kang, S.S.//Lee, E.//Hyun, S.H. 	Prediction of bacterial proteins carrying a nuclear localization signal and nuclear targeting of HsdM from Klebsiella pneumoniae.	J. Microbiol.	2009	47		641-645			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. 		
@D	Lee, J.H.//Bae, J.W.//Chun, J. 	Draft Genome Sequence of Weissella koreensis KCTC 3621T.	J. Bacteriol.	2012	194		5711-5712			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. 		
@D	Lee, J.H.//Chae, J.P.//Lee, J.Y.//Lim, J.S.//Kim, G.B.//Ham, J.S.//Chun, J.//Kang, D.K. 	Genome Sequence of Lactobacillus johnsonii PF01, Isolated from Piglet Feces.	J. Bacteriol.	2011	193		5030-5031			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. 		
@D	Lee, J.H.//Cheon, I.S.//Shim, B.S.//Kim, D.W.//Kim, S.W.//Chun, J.//Song, M. 	Draft Genome Sequence of Klebsiella pneumoniae subsp. pneumoniae DSM 30104T.	J. Bacteriol.	2012	194		5722-5723			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. 		
@D	Lee, J.H.//Choi, Y.//Shin, H.//Lee, J.//Ryu, S. 	Complete Genome Sequence of Cronobacter sakazakii Temperate Bacteriophage phiES15.	J. Virol.	2012	86		7713-7714			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. 		
@D	Lee, J.H.//Karamychev, V.N.//Kozyavkin, S.A.//Mills, D.//Pavlov, A.R.//Pavlova, N.V.//Polouchine, N.N.//Richardson, P.M.//Shakhova, V.V.//Slesarev, A.I.//Weimer, B.//O'Sullivan, D.J. 	Comparative genomic analysis of the gut bacterium Bifidobacterium longum reveals loci susceptible to deletion during pure culture growth.	BMC Genomics	2008	9		247			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. 		
@D	Lee, J.H.//Koh, H.Y.//Lee, S.G.//Doyle, S.//Christner, B.C.//Kim, H.J. 	Draft Genome Sequence of Paenisporosarcina sp. Strain TG-20, a Psychrophilic Bacterium Isolated from the Basal Ice of Taylor Glacier.	J. Bacteriol.	2012	194		6636			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. 		
@D	Lee, J.H.//Rhee, M.S.//Kumar, S.//Lee, G.H.//Chang, D.H.//Kim, D.S.//Choi, S.H.//Lee, D.W.//Yoon, M.H.//Kim, B.C. 	Genome Sequence of Methanobrevibacter sp. Strain JH1, Isolated from Rumen of Korean Native Cattle.	Genome Announcements	2013	1		e00002-13			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. 		
@D	Lee, J.H.//Shin, H.//Choi, Y.//Ryu, S. 	Complete genome sequence analysis of bacterial-flagellum-targeting bacteriophage chi.	Arch. Virol.	2013	158		2179-2183			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. 		
@D	Lee, J.H.//Valeriano, V.D.//Shin, Y.R.//Chae, J.P.//Kim, G.B.//Ham, J.S.//Chun, J.//Kang, D.K. 	Genome Sequence of Lactobacillus mucosae LM1, Isolated from Piglet Feces.	J. Bacteriol.	2012	194		4766			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. 		
@D	Lee, J.J.//Srinivasan, S.//Lim, S.//Joe, M.//Im, S.//Bae, S.I.//Park, K.R.//Han, J.H.//Park, S.H.//Joo, B.M.//Park, S.J.//Kim, M.K. 	Spirosoma radiotolerans sp. nov., a gamma-radiation-resistant bacterium isolated from gamma ray-irradiated soil.	Curr. Microbiol.	2014	69		286-291			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)). 		
@D	Lee, J.Y.H.//Monk, I.R.//Pidot, S.J.//Singh, S.//Chua, K.Y.L.//Seemann, T.//Stinear, T.P.//Howden, B.P. 	Functional analysis of the first complete genome sequence of a multidrug resistant sequence type 2 Staphylococcus epidermidis.	Microbial Genomics	2016	2		e000077			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. 		
@D	Lee, K.//Yi, H.//Cho, Y.J.//Jang, J.//Hur, H.G.//Chun, J. 	Draft Genome Sequence of Escherichia coli AI27, a Porcine Isolate Belonging to Phylogenetic Group B1.	J. Bacteriol.	2012	194		6640-6641			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. 		
@D	Lee, K.-F.//Kam, K.-M.//Shaw, P.-C. 	A bacterial methyltransferase M.EcoHK31I requires two proteins for in vitro methylation.	Nucleic Acids Res.	1995	23		103-108			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. 		
@D	Lee, K.-F.//Liaw, Y.-C.//Shaw, P.-C. 	Overproduction, purification and characterization of M.EcoHK31I, a bacterial methyltransferase with two polypeptides.	Biochem. J.	1996	314		321-326			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. 		
@D	Lee, K.-F.//Shaw, P.-C.//Picone, S.J.//Wilson, G.G.//Lunnen, K.D. 	Sequence comparison of the EcoHK31I and EaeI restriction-modification systems suggests an intergenic transfer of genetic material.	Biol. Chem.	1998	379		437-441			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. 		
@D	Lee, K.-F.//Shi, S.-D.//Kam, K.-M.//Shaw, P.-C. 	Restriction endonuclease from thermophilic bacterial species III.  Isolation and characterization of BsiHKAI.	Nucleic Acids Res.	1992	20		921			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. 		
@D	Lee, K.C.//Morgan, X.C.//Power, J.F.//Dunfield, P.F.//Huttenhower, C.//Stott, M.B. 	Complete genome sequence of the thermophilic Acidobacteria, Pyrinomonas methylaliphatogenes type strain K22(T).	Standards in Genomic Sciences	2015	10		101			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. 		
@D	Lee, K.F.//Ling, J.M.-L.//Kam, K.-M.//Clark, D.R.//Shaw, P.-C. 	Restriction endonucleases in clinical isolates of Shigella spp.	J. Med. Microbiol.	1997	46		949-952			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. 		
@D	Lee, K.S. 	Cytotoxicity of patulin and its effect on lambda DNA cleavage by restriction endonuclease.	Korean J. Toxicol.	1991	7		157-163			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. 		
@D	Lee, K.S.//Seo, S.Y.//Lee, S.W.//Rho, H.M. 	Cloning and Expression of the Pst I Restriction Endonuclease Gene.	Korean Biochem. J.	1982	15		315-329			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. 		
@D	Lee, K.W.//Arumugam, K.//Purbojati, R.W.//Tay, Q.X.//Williams, R.B.//Kjelleberg, S.//Rice, S.A. 	Draft Genome Sequence of Klebsiella pneumoniae Strain KP-1.	Genome Announcements	2013	1		e01082-13			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. 		
@D	Lee, L.//Teh, L.//Zainuddin, Z.//Salleh, M. 	The Genome Sequence of a Type ST239 Methicillin-Resistant Staphylococcus aureus Isolate from a Malaysian Hospital.	Standards in Genomic Sciences	2014	9		933-939			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. 		
@D	Lee, L.L. et al. 	Complete Genome Sequences of Caldicellulosiruptor sp. Strain Rt8.B8, Caldicellulosiruptor sp. Strain Wai35.B1, and 'Thermoanaerobacter  cellulolyticus'.	Genome Announcements	2015	3		e00440-15			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). 		
@D	Lee, M.//Roh, S.W.//Lee, H.W.//Yim, K.J.//Kim, K.N.//Bae, J.W.//Choi, K.S.//Jeon, Y.J.//Jung, W.K.//Kang, H.//Hyun, C.G.//Kim, D. 	Draft Genome Sequence of Pedobacter agri PB92T, Which Belongs to the Family Sphingobacteriaceae.	J. Bacteriol.	2012	194		3738			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. 		
@D	Lee, N.//Valinluck, B.//Randriamahefa, A.//Rutebuka, O.//Ryu, J. 	Cloning and mapping of the hsdR genes of KpnAI and KpnBI restriction-modification systems of Klebsiella pneumoniae.	Abstr. Gen. Meet. Am. Soc. Microbiol.	1993	93		199			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.
 
 		
@D	Lee, N.S.//Rutebuka, O.//Arakawa, T.//Bickle, T.A.//Ryu, J. 	KpnAI, a new type I restriction-modification system in Klebsiella pneumoniae.	J. Mol. Biol.	1997	271		342-348			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. 		
@D	Lee, N.S.//Ryu, J. 	DNA sequence of the hsdR region of KpnBI R-M system of Klebsiella pneumoniae GM236.	Abstr. Gen. Meet. Am. Soc. Microbiol.	1994	94		237			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.
 
 		
@D	Lee, R.D.//Jospin, G.//Coil, D.A.//Eisen, J.A. 	Draft Genome Sequence of the Endosymbiont 'Candidatus Ruthia magnifica' UCD-CM (Phylum Proteobacteria).	Genome Announcements	2014	2		e00717-14			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. 		
@D	Lee, R.D.//Jospin, G.//Lang, J.M.//Eisen, J.A.//Coil, D.A. 	Draft Genome Sequence of Pseudoalteromonas tetraodonis Strain UCD-SED8 (Phylum Gammaproteobacteria).	Genome Announcements	2015	3		e01276-15			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. 		
@D	Lee, R.D.//Jospin, G.//Lang, J.M.//Eisen, J.A.//Coil, D.A. 	Draft Genome Sequences of Two Pseudoalteromonas porphyrae Strains Isolated from Seagrass Sediment.	Genome Announcements	2016	4		e00092-16			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. 		
@D	Lee, R.D.//Jospin, G.//Lang, J.M.//Eisen, J.A.//Coil, D.A. 	Draft Genome Sequences of Two Vibrio splendidus Strains, Isolated from Seagrass Sediment.	Genome Announcements	2016	4		e01769-15			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. 		
@D	Lee, R.D.//Jospin, G.//Lang, J.M.//Eisen, J.A.//Coil, D.A. 	Draft Genome Sequence of Bacillus vietnamensis Strain UCD-SED5 (Phylum Firmicutes).	Genome Announcements	2015	3		e01376-15			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. 		
@D	Lee, S.//Cho, Y.J.//Lee, A.H.//Chun, J.//Ha, N.J.//Ko, G. 	Genomic sequence of Lactobacillus ruminis SPM0211, isolated from a fecal sample from a healthy Korean.	J. Bacteriol.	2011	193		5034			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. 		
@D	Lee, S.//Han, S.J.//Kwon, T.//Yoo, W.G.//Yun, M.R.//Lee, J.S.//Kim, D.W. 	Draft Genome Sequence of Mycobacterium tuberculosis KT-0192, Isolated in South Korea.	Genome Announcements	2016	4		e01601-15			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. 		
@D	Lee, S.//Ward, T.J.//Siletzky, R.M.//Kathariou, S. 	Two Novel Type II Restriction-Modification Systems Occupying Genomically Equivalent Locations on the Chromosomes of Listeria monocytogenes Strains.	Appl. Environ. Microbiol.	2012	78		2623-2630			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. 		
@D	Lee, S.//You, H.J.//Kwon, B.//Ko, G. 	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.	Genome Announcements	2017	5		e00045-17			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. 		
@D	Lee, S.//You, H.J.//Kwon, B.//Ko, G. 	Complete Genome Sequence of Lactobacillus jensenii Strain SNUV360, a Probiotic for Treatment of Bacterial Vaginosis Isolated from the Vagina of a Healthy Korean  Woman.	Genome Announcements	2017	5		e01757-16			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. 		
@D	Lee, S.F.//Forsberg, C.W.//Gibbins, A.M. 	Type II DNA restriction-modification system and an endonuclease from the ruminal bacterium Fibrobacter succinogenes S85.	J. Bacteriol.	1992	174		5275-5283			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. 		
@D	Lee, S.G.//Koh, H.Y.//Lee, J.H.//Kang, S.H.//Kim, H.J. 	Draft Genome Sequence of Moritella dasanensis Strain ArB 0140, a Psychrophilic Bacterium Isolated from the Arctic Ocean.	J. Bacteriol.	2012	194		5452-5453			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. 		
@D	Lee, S.H.//Choe, H.//Nasir, A.//Park, D.S.//Kim, K.M. 	Complete Genome Sequence of Nitrilotriacetate-Degrading Aminobacter aminovorans KCTC 2477T.	Genome Announcements	2016	4		e01363-16			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. 		
@D	Lee, S.H.//Jin, H.M.//Lee, H.J.//Kim, J.M.//Jeon, C.O. 	Complete Genome Sequence of the BTEX-Degrading Bacterium Pseudoxanthomonas spadix BD-a59.	J. Bacteriol.	2012	194		544			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. 		
@D	Lee, S.H.//Jung, J.Y.//Jeon, C.O. 	Draft Genome Sequence of Salimicrobium sp. Strain MJ3, Isolated from Myulchi-Jeot, Korean Fermented Seafood.	J. Bacteriol.	2012	194		6695			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. 		
@D	Lee, S.H.//Jung, J.Y.//Lee, S.H.//Jeon, C.O. 	Complete Genome Sequence of Leuconostoc kimchii Strain C2, Isolated from Kimchi.	J. Bacteriol.	2011	193		5548			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. 		
@D	Lee, S.H.//Jung, M.Y.//Park, B.//Sung-Oh, S.//Park, H.W.//Choi, H.J.//Lee, J.H. 	Complete Genome Sequence of Pediococcus pentosaceus Strain wikim 20, Isolated from Korean Kimchi.	Genome Announcements	2016	4		e01233-16			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. 		
@D	Lee, S.H.//Jung, M.Y.//Song, J.H.//Lee, M.//Chang, J.Y. 	Complete Genome Sequence of Lactobacillus curvatus Strain WiKim38 Isolated from Kimchi.	Genome Announcements	2017	5		e00273-17			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%. 		
@D	Lee, S.H.//Rho, H.M. 	Cloning of PstI methylase gene.	Korean J. Genet.	1985	7		42-48			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. 		
@D	Lee, S.J.//Lee, Y.J.//Jeong, H.//Lee, S.J.//Lee, H.S.//Pan, J.G.//Kim, B.C.//Lee, D.W. 	Draft Genome Sequence of Virgibacillus halodenitrificans 1806.	J. Bacteriol.	2012	194		6332-6333			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. 		
@D	Lee, S.J.//Lee, Y.J.//Park, G.S.//Kim, B.C.//Lee, S.J.//Shin, J.H.//Lee, D.W. 	Draft Genome Sequence of an Anaerobic and Extremophilic Bacterium, Caldanaerobacter yonseiensis, Isolated from a Geothermal Hot Stream.	Genome Announcements	2013	1		e00923-13			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. 		
@D	Lee, S.J.//Lee, Y.J.//Ryu, N.//Park, S.//Jeong, H.//Lee, S.J.//Kim, B.C.//Lee, D.W.//Lee, H.S. 	Draft Genome Sequence of the Thermophilic Bacterium Anoxybacillus kamchatkensis G10.	J. Bacteriol.	2012	194		6684-6685			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. 		
@D	Lee, S.P.//Porter, D.//Chirikjian, J.G.//Knutson, J.R.//Han, M.K. 	A fluorometric assay for DNA cleavage reactions characterized with BamHI restriction endonuclease.	Anal. Biochem.	1994	220		377-383			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. 		
@D	Lee, S.P.//Porter, D.K.//Chirikjian, J.G.//Knutson, J.R.//Han, M.K. 	The development of a fluorescence assay for the BamHI restriction endonuclease utilizing modified oligonucleotides.	Biophys. J.	1994	66		A163			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. 		
@D	Lee, S.S.//Kongari, R.R.//Hernandez, A.C.//Kuty, E.G.F. 	Complete Genome Sequence of Bacillus megaterium Siphophage Stills.	Genome Announcements	2015	3		e00855-15			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. 		
@D	Lee, S.Y.//Kim, B.Y.//Ahn, J.H.//Song, J.//Seol, Y.J.//Kim, W.G.//Weon, H.Y. 	Draft Genome Sequence of the Biocontrol Bacterium Bacillus amyloliquefaciens Strain M27.	J. Bacteriol.	2012	194		6934-6935			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. 		
@D	Lee, S.Y.//Kim, S.H.//Lee, D.G.//Shin, S.//Yun, S.H.//Choi, C.W.//Chung, Y.H.//Choi, J.S.//Kahng, H.Y.//Kim, S.I. 	Draft Genome Sequence of Petroleum Oil-Degrading Marine Bacterium Pseudomonas taeanensis Strain MS-3, Isolated from a Crude Oil-Contaminated Seashore.	Genome Announcements	2014	2		e00818-13			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%. 		
@D	Lee, S.Y.//Mermelstein, L.D.//Bennett, G.N.//Papoutsakis, E.T. 	Vector construction, transformation, and gene amplification in Clostridium acetobutylicum ATCC 824.	Ann. NY Acad. Sci.	1992	665		39-51			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. 		
@D	Lee, S.Y.//Yun, S.H.//Choi, C.W.//Lee, D.G.//Choi, J.S.//Kahng, H.Y.//Kim, S.I. 	Draft Genome Sequence of an Aniline-Degrading Bacterium, Burkholderia sp. K24.	Genome Announcements	2014	2		e01250-14			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%. 		
@D	Lee, W.-K.//An, Y.-S.//Kim, K.-H.//Kim, S.-H.//Song, J.-Y.//Ryu, B.-D.//Choi, Y.-J.//Yoon, Y.-H.//Baik, S.-C.//Rhee, K.-H.//Cho, M.-J. 	Construction of a Helicobacter pylori-Escherichia coli shuttle vector for gene transfer in Helicobacter pylori.	Appl. Environ. Microbiol.	1997	63		4866-4871			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. 		
@D	Lee, W.C.//Anton, B.P.//Wang, S.//Baybayan, P.//Singh, S.//Ashby, M.//Chua, E.G.//Tay, C.Y.//Thirriot, F.//Loke, M.F.//Goh, K.L.//Marshall, B.J.//Roberts, R.J.//Vadivelu, J. 	The complete methylome of Helicobacter pylori UM032.	BMC Genomics	2015	16		424			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. 		
@D	Lee, Y. 	Prediction of putative resistance islands in a carbapenem-resistant Acinetobacter baumannii global clone 2 clinical isolate.	Ann. Lab. Med.	2016	36		320-324			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. 		
@D	Lee, Y.//Jang, S. 	Draft Genome Sequence of the Environmentally Isolated Acinetobacter pittii Strain IPK_TSA6.1.	Genome Announcements	2016	4		e01028-16			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. 		
@D	Lee, Y.//Nguyen, T.L.//Kim, A.//Kim, N.//Roh, H.J.//Han, H.J.//Jung, S.H.//Cho, M.Y.//Kang, H.Y.//Kim, D.H. 	Complete Genome Sequence of Multiple-Antibiotic-Resistant Streptococcus parauberis Strain SPOF3K, Isolated from Diseased Olive Flounder (Paralichthys  olivaceus).	Genome Announcements	2018	6		e00248-18			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. 		
@D	Lee, Y.-F.//Tawfik, D.S.//Griffiths, A.D. 	Investigating the target recognition of DNA cytosine-5 methyltransferase HhaI by library selection using in vitro compartmentalization.	Nucleic Acids Res.	2002	30		4937-4944			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. 		
@D	Lee, Y.-H.//Blakesley, R.W.//Smith, L.A.//Chirikjian, J.G. 	Preparation and properties of insolubilized restriction endonucleases.	Nucleic Acids Res.	1978	5		679-689			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. 		
@D	Lee, Y.-W.//Broday, L.//Costa, M. 	Effects of nickel on DNA methyltransferase activity and genomic DNA methylation levels.	Mutat. Res.	1998	415		213-218			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. 		
@D	Lee, Y.D.//Chang, H.I.//Park, J.H. 	Complete genomic sequence of virulent Cronobacter sakazakii phage ESSI-2 isolated from swine feces.	Arch. Virol.	2011	156		721-724			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. 		
@D	Lee, Y.H.//Blakesley, R.//Smith, L.A.//Chirikjian, G. 	Preparation and properties of immobilized sequence specific endonucleases.	Methods Enzymol.	1980	65		173-182			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. 		
@D	Lee, Y.H.//Chirikjian, J.G. 	Sequence-specific endonuclease BglI.	J. Biol. Chem.	1979	254		6838-6841			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. 		
@D	Lee, Y.H.//Smith, L.A.//Blakesley, R.W. 	Preparation and properties of matrix-bound restriction endonucleases.	Fed. Proc.	1978	37		1414			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. 		
@D	Lee, Y.J.//Jeong, H.//Park, G.S.//Kwak, Y.//Lee, S.J.//Lee, S.J.//Park, M.K.//Kim, J.Y.//Kang, H.K.//Shin, J.H.//Lee, D.W. 	Genome sequence of a native-feather degrading extremely thermophilic Eubacterium, Fervidobacterium islandicum AW-1.	Standards in Genomic Sciences	2015	10		71			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. 		
@D	Lee, Y.J.//Lee, S.J.//Jeong, H.//Kim, H.J.//Ryu, N.//Kim, B.C.//Lee, H.S.//Lee, D.W.//Lee, S.J. 	Draft Genome Sequence of Bacillus oceanisediminis 2691.	J. Bacteriol.	2012	194		6351-6352			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. 		
@D	Lee, Y.J.//Lee, S.J.//Kim, S.H.//Lee, S.J.//Kim, B.C.//Lee, H.S.//Jeong, H.//Lee, D.W. 	Draft Genome Sequence of Bacillus endophyticus 2102.	J. Bacteriol.	2012	194		5705-5706			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. 		
@D	Lee, Y.W.//Clanton, D.//Chirikjian, J.G. 	Subpalindromic sequences as inhibitors for restriction endonucleases.	Fed. Proc.	1979	38		294			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. 		
@D	Lees, J.//Gladstone, R.A. 	R-M systems go on the offensive.	Nat. Rev. Microbiol.	2015	13		131			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. 		
@D	Lees, N.D.//Welker, N.E. 	Restriction and modification of bacteriophage in Bacillus stearothermophilus.	J. Virol.	1973	11		606-609			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. 		
@D	Lees-Murdock, D.J.//McLoughlin, G.A.//McDaid, J.R.//Quinn, L.M.//O'Doherty, A.//Hiripi, L.//Hack, C.J.//Walsh, C.P. 	Identification of 11 pseudogenes in the DNA methyltransferase gene family in rodents and humans and implications for the functional loci.	Genomics	2004	84		193-204			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. 		
@D	Lefebure, T.//Richards, V.P.//Lang, P.//Pavinski-Bitar, P.//Stanhope, M.J. 	Gene Repertoire Evolution of Streptococcus pyogenes Inferred from Phylogenomic Analysis with Streptococcus canis and Streptococcus dysgalactiae.	PLoS ONE	2012	7		E37607			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). 		
@D	Lefort, F.//Calmin, G.//Crovadore, J.//Falquet, J.//Hurni, J.P.//Osteras, M.//Haldemann, F.//Farinelli, L. 	Whole-Genome Shotgun Sequence of Arthrospira platensis Strain Paraca, a Cultivated and Edible Cyanobacterium.	Genome Announcements	2014	2		e00751-14			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. 		
@D	Lefort, F.//Calmin, G.//Crovadore, J.//Osteras, M.//Farinelli, L. 	Whole-Genome Shotgun Sequence of Pseudomonas viridiflava, a Bacterium Species Pathogenic to Ararabidopsis thaliana.	Genome Announcements	2013	1		e00116-12			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. 		
@D	Lefort, F.//Calmin, G.//Pelleteret, P.//Farinelli, L.//Osteras, M.//Crovadore, J. 	Whole-Genome Shotgun Sequence of Bacillus amyloliquefaciens Strain UASWS BA1, a Bacterium Antagonistic to Plant Pathogenic Fungi.	Genome Announcements	2014	2		e00016-14			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. 		
@D	LeFrancois, J.//Gasc, A.-M.//Sicard, M. 	Electrotransformation of Streptococcus pneumoniae: Evidence for restriction of the DNA on entry.	Microb. Drug Resist.	1997	3		101-104			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. 		
@D	Lefrancois, J.//Sicard, A.M. 	Electrotransformation of Streptococcus pneumoniae: evidence for restriction of DNA on entry.	Microbiology	1997	143		523-526			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. 		
@D	Leguizamon, M.//Draghi, W.O.//Montanaro, P.//Schneider, A.//Prieto, C.I.//Martina, P.//Lagares, A.//Lasch, P.//Bosch, A. 	Draft Genome Sequence of Burkholderia puraquae Type Strain CAMPA 1040, Isolated from Hospital Settings in Cordoba, Argentina.	Genome Announcements	2017	5		e01302-17			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. 		
@D	Lehours, P.//Chaineux, J.//Dupouy, S.//Menard, A.//Morgner, A.//Megraud, F. 	Identification of a new restriction modification system in Helicobacter pylori.	Int. J. Antimicrob. Agents	2004	24		S211			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. 		
@D	Lehours, P.//Dupouy, S.//Chaineux, J.//Ruskone-Fourmestraux, A.//Delchier, J.C.//Morgner, A.//Megraud, F.//Menard, A. 	Genetic diversity of the HpyC1I restriction modification system in Helicobacter pylori.	Res. Microbiol.	2007	158		265-271			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. 		
@D	Lehours, P.//Vale, F.F.//Bjursell, M.K.//Melefors, O.//Advani, R.//Glavas, S.//Guegueniat, J.//Gontier, E.//Lacomme, S.//Alves, M.A.//Menard, A.//Megraud, F.//Engstrand, L.//Andersson, A.F. 	Genome sequencing reveals a phage in Helicobacter pylori.	MBio	2011	2		e00239-11			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. 		
@D	Lehri, B.//Seddon, A.M.//Karlyshev, A.V. 	Potential probiotic-associated traits revealed from completed high quality genome sequence of Lactobacillus fermentum 3872.	Standards in Genomic Sciences	2017	12		19			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. 		
@D	Lei, H.//Oh, S.P.//Okano, M.//Juttermann, R.//Goss, K.A.//Jaenisch, R.//Li, E. 	De novo DNA cytosine methyltransferase activities in mouse embryonic stem cells.	Development	1996	122		3195-3205			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. 		
@D	Lei, M.//Lu, P.//Jin, L.//Wang, Y.//Qin, J.//Xu, X.//Zhang, L.//Wang, Y. 	Complete Genome Sequence of Paenibacillus polymyxa CF05, a Strain of Plant Growth-Promoting Rhizobacterium with Elicitation of Induced Systemic Resistance.	Genome Announcements	2015	3		e00198-15			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. 		
@D	Lei, X.//Yuan, F.//Shi, Y.//Li, X.//Wang, L.//Hong, B. 	Draft Genome Sequence of Norvancomycin-Producing Strain Amycolatopsis orientalis  CPCC200066.	Genome Announcements	2015	3		e00296-15			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. 		
@D	Lei, X.Y.//Ou, T.//Zhu, R.L.//Zhang, Q.Y. 	Sequencing and analysis of the complete genome of Rana grylio virus (RGV).	Arch. Virol.	2012	157		1559-1564			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. 		
@D	Leimbach, A.//Poehlein, A.//Witten, A.//Scheutz, F.//Schukken, Y.//Daniel, R.//Dobrindt, U. 	Complete Genome Sequences of Escherichia coli Strains 1303 and ECC-1470 Isolated  from Bovine Mastitis.	Genome Announcements	2015	3		e00182-15			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. 		
@D	Leimbach, A.//Poehlein, A.//Witten, A.//Wellnitz, O.//Shpigel, N.//Petzl, W.//Zerbe, H.//Daniel, R.//Dobrindt, U. 	Whole-Genome Draft Sequences of Six Commensal Fecal and Six Mastitis-Associated Escherichia coli Strains of Bovine Origin.	Genome Announcements	2016	4		e00753-16			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. 		
@D	Leismann, O.//Roth, M.//Friedrich, T.//Wende, W.//Jeltsch, A. 	The Flavobacterium okeanokoites adenine-N6-specific DNA-methyltransferase M.FokI is a tandem enzyme of two independent domains with very different kinetic properties.	Eur. J. Biochem.	1998	251		899-906			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. 		
@D	Leite, L.R.//Medeiros, J.D.//Fernandes, G.R.//Araujo, F.//Pylro, V.S.//Salim, A.C.//Volpini, A.//Oliveira, G.//Cuadros-Orellana, S. 	Draft Genome Sequence of Hydrotalea flava Strain CCUG 51397T.	Genome Announcements	2016	4		e00527-16			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. 		
@D	Lekota, K.E.//Mafofo, J.//Madoroba, E.//Rees, J.//van Heerden, H.//Muchadeyi, F.C. 	Draft Genome Sequences of Two South African Bacillus anthracis Strains.	Genome Announcements	2015	3		e01313-15			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. 		
@D	Lemieux, C.//Lee, R.W. 	Nonreciprocal recombination between alleles of the chloroplast 23S rRNA gene in interspecific Chlamydomonas crosses.	Proc. Natl. Acad. Sci. U. S. A.	1987	84		4166-4170			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. 		
@D	Lemriss, H.//Dumont, Y.//Lemriss, S.//Martins-Simoes, P.//Butin, M.//Lahlou, L.//Rasigade, J.P.//El Kabbaj, S.//Laurent, F.//Ibrahimi, A. 	Genome Sequences of Multiresistant Staphylococcus capitis Pulsotype NRCS-A and Methicillin-Susceptible S. capitis Pulsotype NRCS-C.	Genome Announcements	2016	4		e00541-16			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). 		
@D	Lemriss, H.//Lemriss, S.//Butin, M.//Ibrahimi, A.//El Kabbaj, S.//Rasigade, J.//Laurent, F. 	Non-contiguous finished genome sequence of Staphylococcus capitis CR01 (pulsetype NRCS-A).	Standards in Genomic Sciences	2014	9		1118-1127			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. 		
@D	Lemriss, H.//Lemriss, S.//Martins-Simoes, P.//Butin, M.//Lahlou, L.//Rasigade, J.P.//Kearns, A.//Denis, O.//Deighton, M.//Ibrahimi, A.//Laurent, F.//El Kabbaj, S. 	Genome Sequences of Four Staphylococcus capitis NRCS-A Isolates from Geographically Distant Neonatal Intensive Care Units.	Genome Announcements	2015	3		e00501-15			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. 		
@D	Lenneman, E.M.//Barney, B.M. 	Draft Genome Sequences of the Alga-Degrading Bacteria Aeromonas hydrophila Strain AD9 and Pseudomonas pseudoalcaligenes Strain AD6.	Genome Announcements	2014	2		e00709-14			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. 		
@D	Lennen, R.M.//Nilsson, W.A.I.//Pedersen, M.//Bonde, M.//Luo, H.//Herrgard, M.J.//Sommer, M.O. 	Transient overexpression of DNA adenine methylase enables efficient and mobile genome engineering with reduced off-target effects.	Nucleic Acids Res.	2016	44		e36			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. 		
@D	Lentini, A.//Lagerwall, C.//Vikingsson, S.//Mjoseng, H.K.//Douvlataniotis, K.//Vogt, H.//Green, H.//Meehan, R.R.//Benson, M.//Nestor, C.E. 	A reassessment of DNA-immunoprecipitation-based genomic profiling.	Nat. Methods	2018	15		499-504			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. 		
@D	Lenz, A.//Tomkins, J.//Fabich, A.J. 	Draft Genome Sequence of Citrobacter rodentium DBS100 (ATCC 51459), a Primary Model of Enterohemorrhagic Escherichia coli Virulence.	Genome Announcements	2015	3		e00415-15			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. 		
@D	Lenz, T.//Bonnist, E.Y.M.//Pljevaljcic, G.//Neely, R.K.//Dryden, D.T.F.//Scheidig, A.J.//Jones, A.C.//Weinhold, E. 	2-Aminopurine Flipped into the Active Site of the Adenine-Specific DNA Methyltransferase M.TaqI: Crystal Structures and Time-Resolved Fluorescence.	J. Am. Chem. Soc.	2007	129		6240-6248			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. 		
@D	Leon, M.J.//Ghai, R.//Fernandez, A.B.//Sanchez-Porro, C.//Rodriguez-Valera, F.//Ventosa, A. 	Draft Genome of Spiribacter salinus M19-40, an Abundant Gammaproteobacterium in Aquatic Hypersaline Environments.	Genome Announcements	2013	1		e00179-12			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. 		
@D	Leonard, M.T.//Davis-Richardson, A.G.//Ardissone, A.N.//Kemppainen, K.M.//Drew, J.C.//Ilonen, J.//Knip, M.//Simell, O.//Toppari, J.//Veijola, R.//Hyoty, H.//Triplett, E.W. 	The methylome of the gut microbiome: disparate Dam methylation patterns in intestinal Bacteroides dorei.	Front. Microbiol.	2014	5		361			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. 		
@D	Leonard, M.T.//Fagen, J.R.//Davis-Richardson, A.G.//Davis, M.J.//Triplett, E.W. 	Complete genome sequence of Liberibacter crescens BT-1.	Standards in Genomic Sciences	2012	7		271-283					
@D	Leonard, M.T.//Panayotova, N.//Farmerie, W.G.//Triplett, E.W.//Nicholson, W.L. 	Complete Genome Sequence of Carnobacterium gilichinskyi Strain WN1359T (DSM 27470T).	Genome Announcements	2013	1		e00985-13			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. 		
@D	Leonard, M.T.//Valladares, R.B.//Ardissone, A.//Gonzalez, C.F.//Lorca, G.L.//Triplett, E.W. 	Complete Genome Sequences of Lactobacillus johnsonii Strain N6.2 and Lactobacillus reuteri Strain TD1.	Genome Announcements	2014	2		e00397-14			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. 		
@D	Leonard, S.R.//Lacher, D.W.//Elkins, C.A.//Jung, C.M. 	Draft Genome Sequence of the Multidrug-Resistant Escherichia coli Strain LR09, Isolated from a Wastewater Treatment Plant.	Genome Announcements	2014	2		e00272-14			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. 		
@D	Leonard, S.R.//Lacher, D.W.//Lampel, K.A. 	Draft Genome Sequences of the Enteroinvasive Escherichia coli Strains M4163 and 4608-58.	Genome Announcements	2015	3		e01395-14			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. 		
@D	Leong, K.W.C.//Cooley, L.A.//O'Toole, R.F. 	Draft Genome Sequence of New Vancomycin-Resistant Enterococcus faecium Sequence Type 1421.	Genome Announcements	2018	6		e00438-18			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). 		
@D	Leong, L.E.X.//Shaw, D.//Papanicolas, L.//Lagana, D.//Bastian, I.//Rogers, G.B. 	Draft Genome Sequences of Two Enterobacter cloacae subsp. cloacae Strains Isolated from Australian Hematology Patients with Bacteremia.	Genome Announcements	2017	5		e00756-17			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. 		
@D	Leonhardt, H.//Page, A.W.//Weier, H.U.//Bestor, T.H. 	A targeting sequence directs DNA methyltransferase to sites of DNA replication in mammalian nuclei.	Cell	1992	71		865-873			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. 		
@D	Leopold, S.R.//Magrini, V.//Holt, N.J.//Shaikh, N.//Mardis, E.R.//Cagno, J.//Ogura, Y.//Iguchi, A.//Hayashi, T.//Mellmann, A.//Karch, H.//Besser, T.E.//Sawyer, S.A.//Whittam, T.S.//Tarr, P.I. 	A precise reconstruction of the emergence and constrained radiations of Escherichia coli O157 portrayed by backbone concatenomic analysis.	Proc. Natl. Acad. Sci. U. S. A.	2009	106		8713-8718			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. 		
@D	Lepcha, R.T.//Poddar, A.//Whitman, W.B.//Das, S.K. 	Draft Genome Sequence of Idiomarina woesei Strain W11T (DSM 27808T) Isolated from the Andaman Sea.	Genome Announcements	2016	4		e00831-16			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. 		
@D	Lephoto, T.E.//Featherston, J.//Gray, V.M. 	Draft Whole-Genome Sequence of Serratia sp. Strain TEL, Associated with Oscheius  sp. TEL-2014 (Nematoda: Rhabditidae) Isolated from a Grassland in South Africa.	Genome Announcements	2015	3		e00747-15			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%. 		
@D	Lepikhov, K.//Tchernov, A.//Zheleznaja, L.//Matvienko, N.//Walter, J.//Trautner, T.A. 	Characterization of the type IV restriction modification system BspLU11III from Bacillus sp. LU11.	Nucleic Acids Res.	2001	29		4691-4698			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. 		
@D	Lepp, D.//Roxas, B.//Parreira, V.R.//Marri, P.R.//Rosey, E.L.//Gong, J.//Songer, J.G.//Vedantam, G.//Prescott, J.F. 	Identification of novel pathogenicity loci in Clostridium perfringens strains that cause avian necrotic enteritis.	PLoS ONE	2010	5		E10795			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. 		
@D	Lepuschitz, S.//Mach, R.//Springer, B.//Allerberger, F.//Ruppitsch, W. 	Draft Genome Sequence of a Community-Acquired Methicillin-Resistant Staphylococcus aureus USA300 Isolate from a River Sample.	Genome Announcements	2017	5		e01166-17			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. 		
@D	Lepuschitz, S.//Pekard-Amenitsch, S.//Haunold, R.//Schill, S.//Schriebl, A.//Mach, R.//Allerberger, F.//Ruppitsch, W.//Forsythe, S.J. 	Draft Genome Sequence of the First Documented Clinical Siccibacter turicensis Isolate in Austria.	Genome Announcements	2018	6		e00380-18			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. 		
@D	Lepuschitz, S.//Sorschag, S.//Springer, B.//Allerberger, F.//Ruppitsch, W. 	Draft Genome Sequence of Carbapenemase-Producing Serratia marcescens Isolated from a Patient with Chronic Obstructive Pulmonary Disease.	Genome Announcements	2017	5		e01288-17			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). 		
@D	Lesaulnier, C.//Papamichail, D.//McCorkle, S.//Ollivier, B.//Skiena, S.//Taghavi, S.//Zak, D.//van der Lelie, D. 	Elevated atmospheric CO2 affects soil microbial diversity associated with trembling aspen.	Environ. Microbiol.	2008	10		926-941			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. 		
@D	Lescot, M.//Audic, S.//Robert, C.//Nguyen, T.T.//Blanc, G.//Cutler, S.J.//Wincker, P.//Couloux, A.//Claverie, J.M.//Raoult, D.//Drancourt, M. 	The genome of Borrelia recurrentis, the agent of deadly louse-borne relapsing fever, is a degraded subset of tick-borne Borrelia duttonii.	PLoS Genet.	2008	4		e1000185			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. 		
@D	Lesiak, J.M.//Liebl, W.//Ehrenreich, A. 	Development of an in vivo methylation system for the solventogen Clostridium saccharobutylicum NCP 262 and analysis of two endonuclease mutants.	J. Biotechnol.	2014	188		97-99			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. 		
@D	Leski, T.A.//Taitt, C.R.//Bangura, U.//Ansumana, R.//Stenger, D.A.//Wang, Z.//Vora, G.J. 	Finished Genome Sequence of the Highly Multidrug-Resistant Human Urine Isolate Citrobacter freundii Strain SL151.	Genome Announcements	2016	4		e01225-16			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. 		
@D	Lesnik, E.A.//Beschetnikova, Z.A.//Maslova, R.N.//Varshavsky, J.M. 	The inhibition of restriction endonucleases due to Z-DNA in negatively supercoiled plasmids.	FEBS Lett.	1991	280		91-93			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. 		
@D	Lesnik, E.A.//Beschetnikova, Z.A.//Maslova, R.N.//Varshavsky, J.M. 	The influence of Z-DNA formation on the activity of restriction endonucleases.	J. Biomol. Struct. Dyn.	1991	8		A118			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. 		
@D	Lesnik, E.A.//Khalimullina, Z.A. 	The influence of Z-conformation of the enzyme activity of restriction endonucleases.	Mol. Biol. (Mosk)	1989	23		1638-1644			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. 		
@D	Lesser, D.R.//Grajkowski, A.//Kurpiewski, M.R.//Koziolkiewicz, M.//Stec, W.J.//Jacobson, L.J. 	Steroselective interaction with chiral phosphorothioates at the central DNA kink of the EcoRI endonuclease-GAATTC Complex.	J. Biol. Chem.	1992	267		24810-24818			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. 		
@D	Lesser, D.R.//Kurpiewski, M.R.//Jen-Jacobson, L. 	The energetic basis of specificity in the EcoRI endonuclease-DNA interaction.	Science	1990	250		776-786			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. 		
@D	Lesser, D.R.//Kurpiewski, M.R.//Waters, T.//Connolly, B.A.//Jen-Jacobson, L. 	Facilitated distortion of the DNA site enhances EcoRI endonuclease-DNA recognition.	Proc. Natl. Acad. Sci. U. S. A.	1993	90		7548-7552			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. 		
@D	Letek, M. et al. 	The genome of a pathogenic rhodococcus: cooptive virulence underpinned by key gene acquisitions.	PLoS Genet.	2010	6		e1001145			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. 		
@D	Leung, D.W.//Lui, A.C.P.//Merilees, H.//McBride, B.C.//Smith, M. 	A restriction enzyme from Fusobacterium nucleatum 4H which recognizes GCNGC.	Nucleic Acids Res.	1979	6		17-25			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. 		
@D	Leung, K.S.//Siu, G.K.//Tam, K.K.//To, S.W.//Rajwani, R.//Ho, P.L.//Wong, S.S.//Zhao, W.W.//Ma, O.C.//Yam, W.C. 	Comparative Genomic Analysis of Two Clonally Related Multidrug Resistant Mycobacterium tuberculosis by Single Molecule Real Time Sequencing.	Front Cell Infect Microbiol	2017	7		478			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. 		
@D	Leung, S.M.//Chan, K.Y.//Suen, Y.K.//Shaw, P.C. 	Screening and characterization of restriction endonucleases from a bacterial culture collection in Hong Kong.	Nucleic Acids Res.	1989	17		10133			None 		
@D	Leung, S.M.//Kam, K.M.//Chan, K.Y.//Shaw, P.C. 	Purification and characterization of restriction endonuclease BcoI from a soil isolate of Bacillus coagulans.	FEMS Microbiol. Lett.	1990	66		153-156			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. 		
@D	Levasseur, A.//Asmar, S.//Robert, C.//Drancourt, M. 	Draft Genome Sequence of Mycobacterium interjectum Strain ATCC 51457T.	Genome Announcements	2016	4		e00452-16			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. 		
@D	Levasseur, A.//Asmar, S.//Robert, C.//Drancourt, M. 	Draft Genome Sequence of Mycobacterium houstonense Strain ATCC 49403T.	Genome Announcements	2016	4		e00443-16			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. 		
@D	Leveau, J.H.//Gerards, S.//de Boer, W.//van Veen, J.A. 	Phylogeny-function analysis of (meta)genomic libraries: screening for expression of ribosomal RNA genes by large-insert library fluorescent in situ hybridization (LIL-FISH).	Environ. Microbiol.	2004	6		990-998			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. 		
@A	Levin, B.R. 		Restriction-modification immunity and the maintenance of genetic diversity in bacterial populations.			S. Karlin//E. Nero 		Evolutionary Processes and Theory				New York	Academic Press	1986		0		669-688									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. 		
@D	Levine, J.D.//Cech, C.L. 	Low frequency restriction enzymes in pulsed field electrophoresis.	Biotechnology	1989	7		1033-1036			None 		
@D	Levine, S.M.//Lin, E.A.//Emara, W.//Kang, J.//DiBenedetto, M.//Ando, T.//Falush, D.//Blaser, M.J. 	Plastic cells and populations: DNA substrate characteristics in Helicobacter pylori transformation define a flexible but conservative system for genomic variation.	FASEB J.	2007	21		3458-3467			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. 		
@D	Levitz, R.//Chapman, D.//Amitsur, M.//Green, R.//Snyder, L.//Kaufmann, G. 	The optional E. coli prr locus encodes a latent form of phage T4-induced anticodon nuclease.	EMBO J.	1990	9		1383-1389			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. 		
@D	Levy, W.P.//Welker, N.E. 	Deoxyribonucleic acid modification methylase from Bacillus stearothermophilus.	Biochemistry	1981	20		1120-1127			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. 		
@D	Levy, W.P.//Welker, N.E. 	Purification and properties of a modification methylase from Bacillus stearothermophilus (Meth M.Bst 1503).	Fed. Proc.	1978	37		1414			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. 		
@D	Lewis, A.L.//Deitzler, G.E.//Ruiz, M.J.//Weimer, C.//Park, S.//Robinson, L.S.//Hallsworth-Pepin, K.//Wollam, A.//Mitreva, M.//Lewis, W.G. 	Genome Sequences of 11 Human Vaginal Actinobacteria Strains.	Genome Announcements	2016	4		e00887-16			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. 		
@D	Lewis, L.K.//Lobachev, K.//Westmoreland, J.W.//Karthikeyan, G.//Williamson, K.M.J.J.J.//Resnick, M.A. 	Use of a restriction endonuclease cytotoxicity assay to identify inducible GAL1 promoter variants with reduced basal activity - for use  in fucntional genomics.	Gene	2005	363		183-192			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. 		
@D	Lewis, Z.A.//Adhvaryu, K.K.//Honda, S.//Shiver, A.L.//Knip, M.//Sack, R.//Selker, E.U. 	DNA Methylation and Normal Chromosome Behavior in Neurospora Depend on Five Components of a Histone Methyltransferase Complex, DCDC.	PLoS Genet.	2010	6		e1001196			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. 		
@D	Li, A.//Gai, Z.//Cui, D.//Ma, F.//Yang, J.//Zhang, X.//Sun, Y.//Ren, N. 	Genome Sequence of a Highly Efficient Aerobic Denitrifying Bacterium, Pseudomonas stutzeri T13.	J. Bacteriol.	2012	194		5720			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. 		
@D	Li, A.//Geng, J.//Cui, D.//Shu, C.//Zhang, S.//Yang, J.//Xing, J.//Wang, J.//Ma, F.//Hu, S. 	Genome Sequence of Agrobacterium tumefaciens Strain F2, a Bioflocculant-Producing Bacterium.	J. Bacteriol.	2011	193		5531			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. 		
@D	Li, B.//Brinks, E.//Franz, C.M.A.P.//Cho, G.S. 	Draft Genome Sequence of Staphylococcus fleurettii Strain MBTS-1 Isolated from Cucumber.	Genome Announcements	2017	5		e00335-17			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. 		
@D	Li, B.//Chen, Y.//Liu, Q.//Hu, S.//Chen, X. 	Complete Genome Analysis of Sulfobacillus acidophilus Strain TPY, Isolated from a Hydrothermal Vent in the Pacific Ocean.	J. Bacteriol.	2011	193		5555-5556			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. 		
@D	Li, B.//Shi, Y.//Ibrahim, M.//Liu, H.//Shan, C.//Wang, Y.//Kube, M.//Xie, G.L.//Sun, G. 	Genome Sequence of the Rice Pathogen Dickeya zeae Strain ZJU1202.	J. Bacteriol.	2012	194		4452-4453			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. 		
@D	Li, B.//Ye, M.//Guo, Q.//Zhang, Z.//Yang, S.//Ma, W.//Yu, F.//Chu, H. 	Determination of MIC Distribution and Mechanisms of Decreased Susceptibility to Bedaquiline Among Clinical Isolates of Mycobacterium abscessus.	Antimicrob. Agents Chemother.	2018	0		AAC.00175-18			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. 		
@D	Li, C.//Li, Y.H.//Zhang, X.M.//Stafford, P.//Dinu, V. 	ICRPfinder: a fast pattern design algorithm for coding sequences and its application in finding potential restriction enzyme recognition sites.	BMC Bioinformatics	2009	10		286			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. 		
@D	Li, C.//Yan, X.//Lillehoj, H.S. 	Complete Genome Sequence of Clostridium perfringens LLY_N11, a Necrotic Enteritis-Inducing Strain Isolated from a Healthy Chicken Intestine.	Genome Announcements	2017	5		e01225-17			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. 		
@D	Li, D.//Greenfield, P.//Rosewarne, C.P.//Midgley, D.J. 	Draft Genome Sequence of Thermoanaerobacter sp. Strain A7A, Reconstructed from a  Metagenome Obtained from a High-Temperature Hydrocarbon Reservoir in the Bass  Strait, Australia.	Genome Announcements	2013	1		e00701-13			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. 		
@D	Li, E.//Beard, C.//Jaenisch, R. 	Role for DNA methylation in genomic imprinting.	Nature	1993	366		362-366			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. 		
@D	Li, E.//Bestor, T.H.//Jaenisch, R. 	Targeted mutation of the DNA methyltransferase gene results in embryonic lethality.	Cell	1992	69		915-926			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. 		
@D	Li, F.//Jiang, P.//Zheng, H.//Wang, S.//Zhao, G.//Qin, S.//Liu, Z. 	Draft Genome Sequence of Marine bacterium Streptomyces griseoaurantiacus M045, which produces Novel Manumycin-type Antibiotics with a pABA Core Component.	J. Bacteriol.	2011	193		3417-3418			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. 		
@D	Li, F.//Papworth, M.//Minczuk, M.//Rohde, C.//Zhang, Y.//Ragozin, S.//Jeltsch, A. 	Chimeric DNA methyltransferases target DNA methylation to specific DNA sequences and repress expression of target genes.	Nucleic Acids Res.	2007	35		100-112			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. 		
@D	Li, G.//Hu, F.Z.//Yang, X.//Cui, Y.//Yang, J.//Qu, F.//Gao, G.F.//Zhang, J.R. 	Complete Genome Sequence of Streptococcus pneumoniae Strain ST556, a Multidrug-Resistant Isolate from an Otitis Media Patient.	J. Bacteriol.	2012	194		3294-3295			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. 		
@D	Li, G.//Lu, S.//Shen, M.//Le, S.//Tan, Y.//Li, M.//Zhao, X.//Wang, J.//Shen, W.//Guo, K.//Yang, Y.//Zhu, H.//Li, S.//Zhu, J.//Rao, X.//Hu, F. 	Complete Genome Sequence of Pseudomonas aeruginosa Phage-Resistant Variant PA1RG.	Genome Announcements	2016	4		e01761-15			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. 		
@D	Li, G.//Mo, Z.//Li, J.//Xiao, P.//Hao, B. 	Complete Genome Sequence of Vibrio anguillarum M3, a Serotype O1 Strain Isolated  from Japanese Flounder in China.	Genome Announcements	2013	1		e00769-13			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. 		
@D	Li, G.//Xie, F.//Zhang, Y.//Wang, C. 	Draft Genome Sequence of Actinobacillus pleuropneumoniae Serotype 7 Strain S-8.	J. Bacteriol.	2012	194		6606-6607			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. 		
@D	Li, H.//Feng, Z.M.//Sun, Y.J.//Zhou, W.L.//Jiao, X.//Zhu, H. 	Draft Genome Sequence of Sphingomonas sp. WG, a Welan Gum-Producing Strain.	Genome Announcements	2016	4		e01709-15			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. 		
@D	Li, H.//Pellenz, S.//Ulge, U.//Stoddard, B.L.//Monnat, R.J. Jr. 	Generation of single-chain LAGLIDADG homing endonucleases from native homodimeric precursor proteins.	Nucleic Acids Res.	2009	37		1650-1662			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. 		
@D	Li, H.//Tong, Y.//Huang, Y.//Bai, J.//Yang, H.//Liu, W.//Cao, W. 	Complete Genome Sequence of Bartonella quintana, a Bacterium Isolated from Rhesus Macaques.	J. Bacteriol.	2012	194		6347			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. 		
@D	Li, H.//Ulge, U.Y.//Hovde, B.T.//Doyle, L.A.//Monnat, R.J. Jr. 	Comprehensive homing endonuclease target site specificity profiling reveals evolutionary constraints and enables genome engineering applications.	Nucleic Acids Res.	2012	40		2587-2598			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. 		
@D	Li, H.//Zhou, S.//Johnson, T.//Vercruysse, K.//Ropelewski, A.J.//Thannhauser, T.W. 	Draft Genome Sequence of New Bacillus cereus Strain tsu1.	Genome Announcements	2014	2		e01294-14			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). 		
@D	Li, J.//Cheng, Y.//Wang, D.//Li, J.//Wang, Y.//Han, W.//Li, F. 	Draft Genome Sequence of the Polysaccharide-Degrading Marine Bacterium Pseudoalteromonas sp. Strain A601.	Genome Announcements	2017	5		e00590-17			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. 		
@D	Li, J.//Guo, W.//Shi, M.//Cao, Y.//Wang, G. 	High-quality-draft genomic sequence of Paenibacillus ferrarius CY1T with the potential to bioremediate Cd, Cr and Se contamination.	Standards in Genomic Sciences	2017	12		60			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. 		
@D	Li, J.//Lan, R.//Xiong, Y.//Ye, C.//Yuan, M.//Liu, X.//Chen, X.//Yu, D.//Liu, B.//Lin, W.//Bai, X.//Wang, Y.//Sun, Q.//Wang, Y.//Zhao, H.//Meng, Q.//Chen, Q.//Zhao, A.//Xu, J. 	Sequential Isolation in a Patient of Raoultella planticola and Escherichia coli Bearing a Novel ISCR1 Element Carrying blaNDM-1.	PLoS ONE	2014	9		E89893			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. 		
@D	Li, J.//Li, J.W.//Feng, Z.//Wang, J.//An, H.//Liu, Y.//Wang, Y.//Wang, K.//Zhang, X.//Miao, Z.//Liang, W.//Sebra, R.//Wang, G.//Wang, W.C.//Zhang, J.R. 	Epigenetic Switch Driven by DNA Inversions Dictates Phase Variation in Streptococcus pneumoniae.	PLoS Pathog.	2016	12		e1005762			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. 		
@D	Li, J.//Peng, H.//Xu, L.G.//Xie, Y.Z.//Xuan, X.B.//Ma, C.X.//Hu, S.//Chen, Z.X.//Yang, W.//Xie, Y.P.//Pan, Y.//Tao, L. 	Draft Genome Sequence of Haemophilus parasuis gx033, a Serotype 4 Strain Isolated from the Swine Lower Respiratory Tract.	Genome Announcements	2013	1		e00224-13			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. 		
@D	Li, J.//Yan, H.F.//Wang, K.M.//Tan, W.H.//Zhou, X.W. 	Hairpin fluorescence DNA probe for real-time monitoring of DNA methylation.	Anal. Chem.	2007	79		1050-1056			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. 		
@D	Li, J.-K.//Tu, J. 	Ssp RFI, a novel class-II restriction endonuclease from Synechococcus RF-1 recognizing 5'TT/CGAA-3' .	Nucleic Acids Res.	1991	19		4770			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. 		
@D	Li, J.Y.//Pu, M.T.//Hirasawa, R.//Li, B.Z.//Huang, Y.N.//Zeng, R.//Jing, N.H.//Chen, T.//Li, E.//Sasaki, H.//Xu, G.L. 	Synergistic function of DNA Methyltransferases dnmt3a and dnrnt3b in the methylation of Oct4 and Nanog.	Mol. Cell. Biol.	2007	27		8748-8759			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. 		
@D	Li, K.//Wang, S.//Shi, Y.//Qu, J.//Zhai, Y.//Xu, L.//Xu, Y.//Song, J.//Liu, L.//Rahman, M.A.//Yan, Y. 	Genome Sequence of Paracoccus sp.TRP, a Chlorpyrifos Biodegrader.	J. Bacteriol.	2011	193		1786-1787			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. 		
@D	Li, L. 	Studies on FokI (a type IIS) restriction endonuclease.	Diss. Abstr.	1994	55		877B-878B			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. 		
@D	Li, L.//Bannantine, J.P.//Zhang, Q.//Amonsin, A.//May, B.J.//Alt, D.//Banerji, N.//Kanjilal, S.//Kapur, V. 	The complete genome sequence of Mycobacterium avium subspecies paratuberculosis.	Proc. Natl. Acad. Sci. U. S. A.	2005	102		12344-12349			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. 		
@D	Li, L.//Chandrasegaran, S. 	Alteration of the cleavage distance of Fok I restriction endonuclease by insertion mutagenesis.	Proc. Natl. Acad. Sci. U. S. A.	1993	90		2764-2768			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. 		
@D	Li, L.//Cheng, C.K.//Cheung, M.K.//Law, P.T.//Ling, J.M.//Kam, K.M.//Cheung, W.M.//Kwan, H.S. 	Draft Genome Sequence of Salmonella enterica Serovar Typhimurium ST1660/06, a Multidrug-Resistant Clinical Strain Isolated from a Diarrheic Patient.	J. Bacteriol.	2012	194		6319-6320			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. 		
@D	Li, L.//Su, F.//Wang, Y.//Zhang, L.//Liu, C.//Li, J.//Ma, C.//Xu, P. 	Genome Sequences of Two Thermophilic Bacillus licheniformis Strains, Efficient Producers of Platform Chemical 2,3-Butanediol.	J. Bacteriol.	2012	194		4133-4134			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. 		
@D	Li, L.//Wang, Y.//Li, K.//Su, F.//Ma, C.//Xu, P. 	Genome Sequence of meso-2,3-Butanediol-Producing Strain Serratia marcescens ATCC  14041.	Genome Announcements	2014	2		e00590-14			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. 		
@D	Li, L.//Wang, Y.//Wang, K.//Li, K.//Ma, C.//Xu, P. 	Genome Sequence of Thermophilic Bacillus licheniformis Strain 3F-3, an Efficient  Pentose-Utilizing Producer of 2,3-Butanediol.	Genome Announcements	2014	2		e00615-14			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. 		
@D	Li, L.//Wu, L.P.//Chandrasegaran, S. 	Functional domains in FokI restriction endonuclease.	Proc. Natl. Acad. Sci. U. S. A.	1992	89		4275-4279			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. 		
@D	Li, L.//Wu, L.P.//Clarke, R.//Chandrasegaran, S. 	C-terminal deletion mutants of the FokI restriction endonuclease.	Gene	1993	133		79-84			*
 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.
 
 		
@D	Li, L.G.//Cai, L.//Zhang, T. 	Genome of Cupriavidus sp. HMR-1, a Heavy Metal-Resistant Bacterium.	Genome Announcements	2013	1		e00202-12			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. 		
@D	Li, L.I.//Tanyashin, V.I.//Matvienko, N.I.//Bayev, A.A. 	Production of Specific Fragments of T4 DNA by Endonuclease EcoRI.	Dokl. Akad. Nauk.	1975	223		1262-1265			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-. 		
@D	Li, L.L.//Taghavi, S.//Izquierdo, J.A.//van der Lelie, D. 	Complete Genome Sequence of Clostridium sp. Strain BNL1100, a Cellulolytic Mesophile Isolated from Corn Stover.	J. Bacteriol.	2012	194		6982-6983			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. 		
@D	Li, M.//Yang, S.//Lai, Q.//Shao, Z. 	Draft Genome Sequence of Thalassospira xiamenensis Strain MCCC 1A03042T.	Genome Announcements	2017	5		e01702-16			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. 		
@D	Li, M.Z.//Elledge, S.J. 	MAGIC, an in vivo genetic method for the rapid construction of recombinant DNA molecules.	Nat. Genet.	2005	37		311-319			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. 		
@D	Li, N.//Zhang, J.//Zhang, L.Q.//Nie, P. 	Difference in genes between a high virulence strain G4 and a low virulence strain G18 of Flavobacterium columnare by using suppression subtractive hybridization.	J. Fish Dis.	2010	33		403-412			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. 		
@D	Li, N.//Zhang, L.Q.//Zhang, J.//Liu, Z.X.//Huang, B.//Zhang, S.H.//Nie, P. 	Type I restriction-modification system and its resistance in electroporation efficiency in Flavobacterium columnare.	Vet. Microbiol.	2012	160		61-68			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. 		
@D	Li, N.Z.//Xia, T.//Xu, Y.L.//Qiu, R.R.//Xiang, H.//He, D.//Peng, Y.Y. 	Genome Sequence of Paenibacillus sp. Strain Aloe-11, an Endophytic Bacterium with Broad Antimicrobial Activity and Intestinal Colonization Ability.	J. Bacteriol.	2012	194		2117-2118			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. 		
@D	Li, P.//Yang, C.//Wang, J.//Yi, S.//Li, H.//Wang, Y.//Qiu, S.//Song, H. 	Draft Genome Sequence of a New Shigella flexneri Subserotype, 4S BJ10610.	Genome Announcements	2014	2		e00715-14			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. 		
@D	Li, P.Y.//Xie, B.B.//Zhang, X.Y.//Qin, Q.L.//Dang, H.Y.//Wang, X.M.//Chen, X.L.//Yu, J.//Zhang, Y.Z. 	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.	Environ. Microbiol.	2012	14		467-479			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. 		
@D	Li, Q.//Hu, Y.//Xu, L.//Xie, X.//Tao, M.//Jiao, X. 	Complete Genome Sequence of Salmonella enterica Serovar Choleraesuis Vaccine Strain C500 Attenuated by Chemical Mutation.	Genome Announcements	2014	2		e01022-14			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. 		
@D	Li, Q.//Pan, Y.//Ding, L.//Hong, H.//Yan, S.//Wu, B.//Liang, Y. 	Draft Genome Sequence of Lactobacillus brevis Strain 3M004, a Probiotic with Potential Quorum-Sensing Regulation.	Genome Announcements	2017	5		e00675-17			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%. 		
@D	Li, Q.//Xu, L.Z.//Zou, T.//Ai, P.//Huang, G.H.//Li, P.//Zheng, A.P. 	Complete genome sequence of Bacillus thuringiensis strain HD521.	Standards in Genomic Sciences	2015	10		62			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. 		
@D	Li, S.//Liu, F.//Sun, H.//Zhu, B.//Lv, N.//Xue, G. 	Whole-Genome Sequencing of Macrolide-Resistant Mycoplasma pneumoniae Strain S355, Isolated in China.	Genome Announcements	2016	4		e00087-16			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. 		
@D	Li, S.//Skov, R.L.//Han, X.//Larsen, A.R.//Larsen, J.//Sorum, M.//Wulf, M.//Voss, A.//Hiramatsu, K.//Ito, T. 	Novel types of staphylococcal cassette chromosome mec elements identified in clonal complex 398 methicillin-resistant Staphylococcus aureus strains.	Antimicrob. Agents Chemother.	2011	55		3046-3050			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. 		
@D	Li, S.//Sun, H.//Liu, F.//Zhao, H.//Zhu, B.//Lv, N. 	Complete Genome Sequence of the Macrolide-Resistant Mycoplasma pneumoniae Strain  C267 in China.	Genome Announcements	2016	4		e00236-16			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. 		
@D	Li, S.//Yang, D.//Qiu, M.//Shao, J.//Guo, R.//Shen, B.//Yin, X.//Zhang, R.//Zhang, N.//Shen, Q. 	Complete Genome Sequence of Paenibacillus polymyxa SQR-21, a Plant Growth-Promoting Rhizobacterium with Antifungal Activity and Rhizosphere Colonization Ability.	Genome Announcements	2014	2		e00281-14			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. 		
@D	Li, S.//Zhao, H.//Li, Y.//Niu, S.//Cai, B. 	Complete Genome Sequence of the Naphthalene-Degrading Pseudomonas putida Strain ND6.	J. Bacteriol.	2012	194		5154-5155			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. 		
@D	Li, T.//Chen, J.//Chang, D.//Fang, X.//Wang, J.//Guo, Y.//Su, L.//Xu, G.//Wang, Y.//Chen, Z.//Liu, C. 	Draft Genome Sequence of Escherichia coli Strain LCT-EC59.	Genome Announcements	2013	1		e00242-12			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. 		
@D	Li, T.//Huang, S.//Jiang, W.Z.//Wright, D.//Spalding, M.H.//Weeks, D.P.//Yang, B. 	TAL nucleases (TALNs): hybrid proteins composed of TAL effectors and FokI DNA-cleavage domain.	Nucleic Acids Res.	2010	39		359-372			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. 		
@D	Li, T.//Pu, F.//Yang, R.//Fang, X.//Wang, J.//Guo, Y.//Chang, D.//Su, L.//Guo, N.//Jiang, X.//Zhao, J.//Liu, C. 	Draft Genome Sequence of Escherichia coli LCT-EC106.	J. Bacteriol.	2012	194		4443-4444			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. 		
@D	Li, W.//Liu, L.//Qiu, D.//Chen, H.//Zhou, R. 	Identification of Streptococcus suis serotype 2 genes preferentially expressed in the natural host.	Int. J. Med. Microbiol.	2010	300		482-488			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. 		
@D	Li, W.//Shi, J.//Wang, X.//Han, Y.//Tong, W.//Ma, L.//Liu, B.//Cai, B. 	Complete nucleotide sequence and organization of the naphthalene catabolic plasmid pND6-1 from Pseudomonas sp. strain ND6.	Gene	2004	336		231-240			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. 		
@D	Li, W.//Wu, P.//Zhang, H.//Cai, C.X. 	Signal Amplification of Graphene Oxide Combining with Restriction Endonuclease for Site-Specific Determination of DNA Methylation and Assay of Methyltransferase Activity.	Anal. Chem.	2012	84		7583-7590			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. 		
@D	Li, X.//Gong, J.//Hu, Y.//Cai, L.//Johnstone, L.//Grass, G.//Rensing, C.//Wang, G. 	Genome Sequence of the Moderately Halotolerant, Arsenite-Oxidizing Bacterium Pseudomonas stutzeri TS44.	J. Bacteriol.	2012	194		4473-4474			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. 		
@D	Li, X.//Gu, Q.//Lou, X.//Zhang, X.//Song, D.//Shen, L.//Zhao, Y. 	Complete Genome Sequence of the Probiotic Lactobacillus plantarum Strain ZJ316.	Genome Announcements	2013	1		e0009413			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. 		
@D	Li, X.//Hojberg, O.//Noel, S.J.//Canibe, N.//Jensen, B.B. 	Draft Genome Sequence of Olsenella scatoligenes SK9K4T, a Producer of 3-Methylindole (Skatole) and 4-Methylphenol (p-Cresol), Isolated from Pig Feces.	Genome Announcements	2016	4		e00042-16			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. 		
@D	Li, X.//Hu, Y.//Gong, J.//Lin, Y.//Johnstone, L.//Rensiing, C.//Wang, G. 	Genome sequence of the highly efficient arsenite-oxidizing bacterium Achromobacter arsenitoxydans SY8.	J. Bacteriol.	2012	194		1243-1244			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. 		
@D	Li, X.//Hu, Y.//Gong, J.//Lin, Y.//Johnstone, L.//Rensing, C.//Wang, G. 	Genome Sequence of the Highly Efficient Arsenite-Oxidizing Bacterium Achromobacter arsenitoxydans SY8.	J. Bacteriol.	2012	194		1243-1244			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. 		
@D	Li, X.//Koblizek, M.//Feng, F.//Li, Y.//Jian, J.//Zeng, Y. 	Whole-Genome Sequence of a Freshwater Aerobic Anoxygenic Phototroph, Porphyrobacter sp. Strain AAP82, Isolated from the Huguangyan Maar Lake in  Southern China.	Genome Announcements	2013	1		e0007213			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. 		
@D	Li, X.//Kot, W.//Wang, D.//Zheng, S.//Wang, G.//Hansen, L.H.//Rensing, C. 	Draft Genome Sequence of Se(IV)-Reducing Bacterium Pseudomonas migulae ES3-33.	Genome Announcements	2015	3		e00406-15			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. 		
@D	Li, X.//Liu, F.//Hu, Y.//Mi, K. 	Draft Genome Sequence of mc251, a Highly Hydrogen Peroxide-Resistant Mycobacterium smegmatis Mutant Strain.	Genome Announcements	2014	2		e00092-14			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). 		
@D	Li, X.//Marshall, I.P.//Schreiber, L.//Hojberg, O.//Canibe, N.//Jensen, B.B. 	Draft Genome Sequence of Megasphaera sp. Strain DJF_B143, an Isolate from Pig Hindgut Unable to Produce Skatole.	Genome Announcements	2016	4		e00007-16			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. 		
@D	Li, X.//Song, C.//Zhao, M.//Li, Y. 	Continuous monitoring of restriction endonuclease cleavage activity by universal molecular beacon light quenching coupled with real-time polymerase chain reaction.	Anal. Biochem.	2008	381		1-7			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. 		
@D	Li, X.//Yuan, H.//Yang, J.//Li, B. 	Genome Sequence of the Polyphosphate-Accumulating Organism Arthrobacter sp. Strain PAO19 Isolated from Maize Rhizosphere Soil.	Genome Announcements	2013	1		e00566-13			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. 		
@D	Li, X.F.//Liao, X.Y.//Liu, Y.F.//Guo, L.Q.//Ye, Z.W.//Lin, J.F. 	Complete Genome Sequence of Probiotic Lactobacillus plantarum Strain FMNP01, Isolated from Mango Fruit.	Genome Announcements	2014	2		e01207-14			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. 		
@D	Li, X.R.//Gong, F.M.//Zheng, H.J.//Zhang, Z.H.//Luo, Y.Y.//Liu, C.J. 	Draft Genome Sequence of Lactobacillus plantarum Strain AY01, Isolated from the Raw Material of Fermented Goat Milk Cheese.	Genome Announcements	2013	1		e00737-13			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%. 		
@D	Li, X.S.//Yuan, K.X.//Cullis, J.//Levesque, C.A.//Chen, W.//Lewis, C.T.//De Boer, S.H. 	Draft Genome Sequences for Canadian Isolates of Pectobacterium carotovorum subsp. brasiliense with Weak Virulence on Potato.	Genome Announcements	2015	3		e00240-15			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. 		
@D	Li, X.S.//Yuan, X.K. 	Genome Sequences for Multiple Clavibacter Strains from Different Subspecies.	Genome Announcements	2017	5		e00721-17			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. 		
@D	Li, Y.//Cao, B.//Zhang, Y.//Zhou, J.//Yang, B.//Wang, L. 	Complete Genome Sequence of Staphylococcus aureus T0131, an ST239-MRSA-SCCmec type III Clone isolated in China.	J. Bacteriol.	2011	193		3411-3412			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. 		
@D	Li, Y.//Fu, P.//Shi, L.-Y. 	Study on a type II restriction endonuclease NcrI.	Chinese Biochem. J.	1990	6		309-313			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'. 		
@D	Li, Y.//Guo, X.H.//Dang, Y.R.//Sun, L.L.//Zhang, X.Y.//Chen, X.L.//Qin, Q.L.//Wang, P. 	Complete genome sequence of Arcticibacterium luteifluviistationis SM1504(T), a cytophagaceae bacterium isolated from Arctic surface seawater.	Standards in Genomic Sciences	2018	13		33			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. 		
@D	Li, Y.//Huang, C.C.//Zheng, J.B.//Qi, H.L. 	Electrogenerated chemiluminescence biosensing method for the detection of DNA methylation and assay of the methyltransferase activity.	Biosensors and Bioelectronics	2012	38		407-410			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. 		
@D	Li, Y.//Leahy, S.C.//Jeyanathan, J.//Henderson, G.//Cox, F.//Altermann, E.//Kelly, W.J.//Lambie, S.C.//Janssen, P.H.//Rakonjac, J.//Attwood, G.T. 	The complete genome sequence of the methanogenic archaeon ISO4-H5 provides insights into the methylotrophic lifestyle of a ruminal representative of the  Methanomassiliicoccales.	Standards in Genomic Sciences	2016	11		59			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. 		
@D	Li, Y.//Li, Q.//Li, Y.//Gao, J.//Fan, X. 	Draft Genome Sequence of Paenibacillus polymyxa KF-1, an Excellent Producer of Microbicides.	Genome Announcements	2016	4		e00727-16			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. 		
@D	Li, Y.//Li, S.//Chen, M.//Peng, G.//Tan, Z.//An, Q. 	Complete genome sequence of Kosakonia oryzae type strain Ola 51T.	Standards in Genomic Sciences	2017	12		28			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. 		
@D	Li, Y.//Lin, Y.//Garvey, C.J.//Birch, D.//Corkery, R.W.//Loughlin, P.C.//Scheer, H.//Willows, R.D.//Chen, M. 	Characterization of red-shifted phycobilisomes isolated from the chlorophyll f-containing cyanobacterium Halomicronema hongdechloris.	Biochim. Biophys. Acta	2016	1857		107-114			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. 		
@D	Li, Y.//Liu, Y.//Zhou, Z.//Huang, H.//Ren, Y.//Zhang, Y.//Li, G.//Zhou, Z.//Wang, L. 	Complete Genome Sequence of Aeromonas Veronii Strain B565.	J. Bacteriol.	2011	193		3389-3390			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. 		
@D	Li, Y.//Lu, Z.//Sun, L.//Ropp, S.//Kutish, G.F.//Rock, D.L.//Van Etten, J.L. 	Analysis of 74 kb of DNA located at the right end of the 330-kb chlorella virus PBCV-1 genome.	Virology	1997	237		360-377			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. 		
@D	Li, Y.//Ng, I.S.//Zhang, X.//Wang, N. 	Draft Genome Sequence of the Dye-Decolorizing and Nanowire-Producing Bacterium Shewanella xiamenensis BC01.	Genome Announcements	2014	2		e00721-14			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. 		
@D	Li, Y.//Wang, Y.//Wang, R.//Zhu, Y.//Liu, S.//Wang, Q.//Shao, J.//Chen, Y.//Gao, L.//Zhou, C.//Liu, H.//Wang, X.//Zheng, H.//Xin, J. 	Changes in pathogenicity and immunogenicity of Mycoplasma mycoides subsp. mycoides strains revealed by comparative genomics analysis.	Sci. Rep.	2016	6		19081			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. 		
@D	Li, Y.//Yan, Z.//Zheng, J.//Qi, H. 	Label-free and amplified electrogenerated chemiluminescence biosensing method for the determination of DNA methyltransferase activity using signal reagent-assembled graphene oxide.	Electrochim. Acta.	2014	137		454-461			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. 		
@D	Li, Y.//Zhang, C.//Liu, C.//Ju, J.//Ma, J. 	Genome Sequencing of Streptomyces atratus SCSIOZH16 and Activation Production of Nocardamine via Metabolic Engineering.	Front. Microbiol.	2018	9		1269			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. 		
@D	Li, Y.//Zheng, H.//Liu, Y.//Jiang, Y.//Xin, J.//Chen, W.//Song, Z. 	The Complete Genome Sequence of Mycoplasma bovis Strain Hubei-1.	PLoS ONE	2011	6		e20999			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. 		
@D	Li, Y.//Zhu, H.//Li, C.//Zhang, H.//Chen, Z.//Zheng, W.//Xu, H.//Zheng, T. 	Draft Genome Sequence of the Algicidal Bacterium Mangrovimonas yunxiaonensis Strain LY01.	Genome Announcements	2014	2		e01234-14			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. 		
@D	Li, Y.Q.//Zhou, P.Z.//Zheng, X.D.//Walsh, C.P.//Xu, G.L. 	Association of Dnmt3a and thymine DNA glycosylase links DNA methylation with base-excision repair.	Nucleic Acids Res.	2007	35		390-400			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. 		
@D	Li, Z.//Cai, J.//Cao, X.//Lou, Z.//Chao, Y.//Kan, W.//Zhou, J. 	Whole-Genome Sequence of Chlamydia abortus Strain GN6 Isolated from Aborted Yak Fetus.	Genome Announcements	2017	5		e00893-17			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. 		
@D	Li, Z.//Chen, H.//Chen, X.//Zhou, T.//Zhao, L.//Zhang, C.//Jin, W. 	Genome Sequence of the Human-Pathogenic Bacterium Vibrio vulnificus Type Strain ATCC 27562.	J. Bacteriol.	2012	194		6954-6955			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. 		
@D	Li, Z.//Chen, M.//Ran, K.//Wang, J.//Zeng, Q.//Song, F. 	Draft Genome Sequence of Bacillus velezensis Lzh-a42, a Plant Growth-Promoting Rhizobacterium Isolated from Tomato Rhizosphere.	Genome Announcements	2018	6		e00161-18			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. 		
@D	Li, Z.//Li, X.//Zeng, Q.//Chen, M.//Liu, D.//Wang, J.//Shen, L.//Song, F. 	Genome Sequence of Pseudomonas chlororaphis Lzh-T5, a Plant Growth-Promoting Rhizobacterium with Antimicrobial Activity.	Genome Announcements	2018	6		e00328-18			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. 		
@D	Li, Z.//Ma, Z.//Hao, X.//Wei, G. 	Draft Genome Sequence of Sinorhizobium meliloti CCNWSX0020, a Nitrogen-Fixing Symbiont with Copper Tolerance Capability Isolated from Lead-Zinc Mine Tailings.	J. Bacteriol.	2012	194		1267-1268			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. 		
@D	Li, Z.//Marsland, P.A.//Meek, R.T.//Eckmann, K.//Allard, M.W.//Perez-Osorio, A.C. 	Draft Genome Sequences of Listeria monocytogenes Strains from Listeriosis Outbreaks Linked to Soft Cheese in Washington State.	Genome Announcements	2017	5		e00936-17			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. 		
@D	Li, Z.//Song, N.//Li, W.//Hardwidge, P.R.//Bu, Z.//Liu, S. 	Complete Genome Sequences of Two Porcine Enterotoxigenic Escherichia coli Strains.	Genome Announcements	2018	6		e00059-18			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. 		
@D	Li, Z.//Wu, S.//Bai, X.//Liu, Y.//Lu, J.//Liu, Y.//Xiao, B.//Lu, X.//Fan, L. 	Genome Sequence of the Tobacco Bacterial Wilt Pathogen Ralstonia solanacearum.	J. Bacteriol.	2011	193		6088-6089			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. 		
@D	Li, Z.F.//Li, X.//Liu, H.//Liu, X.//Han, K.//Wu, Z.H.//Hu, W.//Li, F.F.//Li, Y.Z. 	Genome Sequence of the Halotolerant Marine Bacterium Myxococcus fulvus HW-1.	J. Bacteriol.	2011	193		5015-5016			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. 		
@D	Liakopoulos, A.//Oikonomou, O.//Wareham, D.W. 	Draft Genome Sequence of Providencia stuartii PS71, a Multidrug-Resistant Strain  Associated with Nosocomial Infections in Greece.	Genome Announcements	2017	5		e00056-17			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. 		
@D	Liang, G.//Chan, M.F.//Tomigahara, Y.//Tsai, Y.C.//Gonzales, F.A.//Li, E.//Laird, P.W.//Jones, P.A. 	Cooperativity between DNA methyltransferases in the maintenance methylation of repetitive elements.	Mol. Cell. Biol.	2002	22		480-491			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. 		
@D	Liang, J.//Blumenthal, R.M. 	Naturally-occurring, dually-functional fusions between restriction endonucleases  and regulatory proteins.	BMC Evol. Biol.	2013	13		218			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. 		
@D	Liang, J.//Hoffrichter, A.//Brachmann, A.//Marin, M. 	Complete genome of Rhizobium leguminosarum Norway, an ineffective Lotus micro-symbiont.	Standards in Genomic Sciences	2018	13		36			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. 		
@D	Liang, J.//Wang, Z.//He, X.//Li, J.//Zhou, X.//Deng, Z. 	DNA modification by sulfur: analysis of the sequence recognition specificity surrounding the modification sites.	Nucleic Acids Res.	2007	35		2944-2954			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. 		
@D	Liang, J.X.//Blumenthal, R.M. 	Naturally-occurring, dually-functional fusions between restriction endonucleases and regulatory proteins.	BMC Evol. Biol.	2013	13		0			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. 		
@D	Liang, K.//Orata, F.D.//Winkjer, N.S.//Rowe, L.A.//Tarr, C.L.//Boucher, Y. 	Complete Genome Sequence of Vibrio sp. Strain 2521-89, a Close Relative of Vibrio cholerae Isolated from Lake Water in New Mexico, USA.	Genome Announcements	2017	5		e00905-17			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. 		
@D	Liang, R.//Liu, H.//Tao, F.//Liu, Y.//Ma, C.//Liu, X.//Liu, J. 	Genome Sequence of Pseudomonas putida Strain SJTE-1, a Bacterium Capable of Degrading Estrogens and Persistent Organic Pollutants.	J. Bacteriol.	2012	194		4781-4782			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. 		
@D	Liang, S.//Jin, D.//Wang, X.//Fan, H.//Bai, Z. 	Draft Genome Sequence of Paenibacillus polymyxa EBL06, a Plant Growth-Promoting Bacterium Isolated from Wheat Phyllosphere.	Genome Announcements	2015	3		e00414-15			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). 		
@D	Liang, X.//Jensen, K.//Frank-Kamenetskii, M.D. 	Acceleration of de novo DNA synthesis by restriction enzymes.	J. Biomol. Struct. Dyn.	2005	22		766-767			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. 		
@D	Liang, X.G.//Jensen, K.//Frank-Kamenetskii, M.D. 	Very efficient template/primer-independent DNA synthesis by thermophilic DNA polymerase in the presence of a thermophilic  restriction endonuclease.	Biochemistry	2004	43		13459-13466			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. 		
@D	Liang, Z.//Li, G.//An, T.//Das, R. 	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.	Genome Announcements	2016	4		e00474-16			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. 		
@D	Liang, Z.//Li, G.//An, T.//Zhang, G.//Das, R. 	Draft Genome Sequence of a Tetrabromobisphenol A-Degrading Strain, Ochrobactrum sp. T, Isolated from an Electronic Waste Recycling Site.	Genome Announcements	2016	4		e00680-16			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. 		
@D	Liang, Z.//Stephens, M.//Ploplis, V.A.//Lee, S.W.//Castellino, F.J. 	Draft Genome Sequences of Six Skin Isolates of Streptococcus pyogenes.	Genome Announcements	2018	6		e00592-18			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. 		
@D	Liao, H.M.//Chao, C.C.//Lei, H.//Li, B.//Tsai, S.//Hung, G.C.//Ching, W.M.//Lo, S.C. 	Genomic Sequencing of Orientia tsutsugamushi Strain Karp, an Assembly Comparable  to the Genome Size of the Strain Ikeda.	Genome Announcements	2016	4		e00702-16			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. 		
@D	Liao, J.//Karnik, R.//Gu, H.//Ziller, M.J.//Clement, K.//Tsankov, A.M.//Akopian, V.//Gifford, C.A.//Donaghey, J.//Galonska, C.//Pop, R.//Reyon, D.//Tsai, S.Q.//Mallard, W.//Joung, J.K.//Rinn, J.L.//Gnirke, A.//Meissner, A. 	Targeted disruption of DNMT1, DNMT3A and DNMT3B in human embryonic stem cells.	Nat. Genet.	2015	47		469-478			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. 		
@D	Liao, T.L.//Lin, A.C.//Chen, E.//Huang, T.W.//Liu, Y.M.//Chang, Y.H.//Lai, J.F.//Lauderdale, T.L.//Wang, J.T.//Chang, S.C.//Tsai, S.F.//Chen, Y.T. 	Complete Genome Sequence of Klebsiella oxytoca E718, a New Delhi Metallo-beta-Lactamase-1-Producing Nosocomial Strain.	J. Bacteriol.	2012	194		5454			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. 		
@D	Liao, Y.C.//Chen, Y.H.//Lin, H.H.//Mu, J.J.//Wu, H.S.//Chen, F.C.//Hsiung, C.A. 	Draft Genome Sequence of NDM-1-Producing Klebsiella pneumoniae Clinical Isolate 303K.	Genome Announcements	2013	1		e01069-13			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. 		
@D	Liao, Y.C.//Chen, Y.Y.//Lin, H.H.//Chang, J.R.//Su, I.J.//Huang, T.S.//Dou, H.Y. 	Draft Genome Sequences of the Mycobacterium tuberculosis Clinical Strains A2 and  A4, Isolated from a Relapse Patient in Taiwan.	Genome Announcements	2014	2		e00672-14			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. 		
@D	Liao, Y.C.//Chen, Y.Y.//Lin, H.H.//Chang, J.R.//Su, I.J.//Huang, T.S.//Dou, H.Y. 	Draft Genome Sequence of the Mycobacterium tuberculosis Clinical Isolate C2, Belonging to the Latin American-Mediterranean Family.	Genome Announcements	2014	2		e00536-14			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. 		
@D	Liao, Y.C.//Liu, T.T.//Chang, J.R.//Chen, Y.Y.//Lin, H.H.//Hsu, C.H.//Lin, C.Y.//Lo, Y.C.//Dou, H.Y. 	Draft Genome Sequence of Mycobacterium tuberculosis Clinical Strain W06, a Prevalent Beijing Genotype Isolated in Taiwan.	Genome Announcements	2015	3		e01460-15			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. 		
@D	Liao, Z.//Ren, C.//Guo, X.//Yan, Y.//Li, J.//Zhao, B. 	Draft Genome Sequence of Bacillus urumqiensis BZ-SZ-XJ18(T), a Moderately Haloalkaliphilic Bacterium Isolated from a Saline-Alkaline Lake.	Genome Announcements	2018	6		e00460-18			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. 		
@D	Libuit, K.G.//Turner, L. 	Draft Genome Sequences of Two Salmonella Strains Isolated from Wild Animals on the Eastern Shore of Virginia.	Genome Announcements	2018	6		e00329-18			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. 		
@D	Licciardello, G.//Bella, P.//Devescovi, G.//Strano, C.P.//Sarris, P.F.//Catara, A.F.//Venturi, V.//Catara, V. 	Draft Genome Sequence of Pseudomonas mediterranea Strain CFBP 5447T, a Producer of Filmable Medium-Chain-Length Polyhydroxyalkanoates.	Genome Announcements	2014	2		e01260-14			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. 		
@D	Lieb, M. 	Bacterial genes mutL, mutS, and dcm participate in repair of mismatches at 5-methylcytosine sites.	J. Bacteriol.	1987	169		5241-5246			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. 		
@D	Lieb, M. 	Specific mismatch correction in bacteriophage lambda crosses by very short patch repair.	Mol. Gen. Genet.	1983	191		118-125			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. 		
@D	Lieb, M. 	Spontaneous Mutation at a 5-methylcytosine hotspot is prevented by very short patch (VSP) mismatch repair.	Genetics	1991	128		23-27			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. 		
@D	Lieb, M.//Allen, E.//Read, D. 	Very short patch mismatch repair in phage lambda: repair sites and length of repair tracts.	Genetics	1986	114		1041-1060			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. 		
@D	Lieb, M.//Bhagwat, A.S. 	Very short patch repair: reducing the cost of cytosine methylation.	Mol. Microbiol.	1996	20		467-473			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. 		
@D	Lieb, M.//Bhagwat, A.S. 	Very short patch mismatch repair activity associated with gene dcm is not conferred by a plasmid coding for EcoRII methylase.	J. Bacteriol.	1988	170		4967-4968			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. 		
@D	Lieb, M.//Rehmat, S. 	5-Methylcytosine is not a mutation hot spot in nondividing Escherichia coli.	Proc. Natl. Acad. Sci. U. S. A.	1997	94		940-945			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. 		
@D	Lieb, M.//Rehmat, S. 	Very short patch repair of T:G mismatches in vivo: importance of context and accessory proteins.	J. Bacteriol.	1995	177		660-666			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. 		
@D	Lieb, M.//Rehmat, S.//Bhagwat, A.S. 	Interaction of MutS and Vsr: Some Dominant-Negative mutS Mutations That Disable Methyladenine-Directed Mismatch Repair Are Active in Very-Short-Patch Repair.	J. Bacteriol.	2001	183		6487-6490			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. 		
@D	Liebert, K.//Hermann, A.//Schlickenrieder, M.//Jeltsch, A. 	Stopped-flow and mutational analysis of base flipping by the Escherichia coli dam DNA-(adenine-N6)-methyltransferase.	J. Mol. Biol.	2004	341		443-454			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. 		
@D	Liebert, K.//Horton, J.R.//Chahar, S.//Orwick, M.//Cheng, X.D.//Jeltsch, A. 	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.	J. Biol. Chem.	2007	282		22848-22855			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)). 		
@D	Lienau, E.K.//Strain, E.//Wang, C.//Zheng, J.//Ottesen, A.R.//Keys, C.E.//Hammack, T.S.//Musser, S.M.//Brown, E.W.//Allard, M.W.//Cao, G.//Meng, J.//Stones, R. 	Identification of a salmonellosis outbreak by means of molecular sequencing.	N. Engl. J. Med.	2011	364		981-982					
@D	Liesegang, H.//Kaster, A.K.//Wiezer, A.//Goenrich, M.//Wollherr, A.//Seedorf, H.//Gottschalk, G.//Thauer, R.K. 	Complete Genome Sequence of Methanothermobacter marburgensis, a Methanoarchaeon Model Organism.	J. Bacteriol.	2010	192		5850-5851			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. 		
@D	Liljeqvist, M.//Valdes, J.//Holmes, D.S.//Dopson, M. 	Draft Genome of the Psychrotolerant Acidophile Acidithiobacillus ferrivorans SS3.	J. Bacteriol.	2011	193		4304-4305			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. 		
@D	Lilley, D.M.J. 	Cisplatin adducts in DNA: distortion and recognition.	J. Biol. Inorg. Chem.	1996	1		189-191			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. 		
@D	Lim, H.I.//Lee, J.//Jang, J.Y.//Park, H.W.//Choi, H.J.//Kim, T.W.//Kang, M.R.//Lee, J.H. 	Draft Genome Sequence of Lactobacillus sakei Strain wikim 22, Isolated from Kimchi in Chungcheong Province, South Korea.	Genome Announcements	2014	2		e01296-14			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%. 		
@D	Lim, J.//Lee, T.H.//Nahm, B.H.//Choi, Y.D.//Kim, M.//Hwang, I. 	Complete Genome Sequence of Burkholderia glumae BGR1.	J. Bacteriol.	2009	191		3758-3759			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. 		
@D	Lim, J.S.//Choi, B.S.//Choi, A.Y.//Kim, K.D.//Kim, D.I.//Choi, I.Y.//Ka, J.O. 	Complete Genome Sequence of the Fenitrothion-Degrading Burkholderia sp. Strain YI23.	J. Bacteriol.	2012	194		896			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. 		
@D	Lim, J.Y.//Hwang, I.//Ganzorig, M.//Huang, S.L.//Cho, G.S.//Franz, C.M.A.P.//Lee, K. 	Complete Genome Sequences of Three Moraxella osloensis Strains Isolated from Human Skin.	Genome Announcements	2018	6		e01509-17			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. 		
@D	Lim, J.Y.//Hwang, I.//Ganzorig, M.//Pokhriyal, S.//Singh, R.//Lee, K. 	Complete Genome Sequence of Paracoccus yeei TT13, Isolated from Human Skin.	Genome Announcements	2018	6		e01514-17			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. 		
@D	Lim, S.//Chang, D.H.//Ahn, S.//Kim, B.C. 	Whole genome sequencing of 'Faecalibaculum rodentium' ALO17, isolated from C57BL/6J laboratory mouse feces.	Gut Pathog.	2016	8		3			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. 		
@D	Lim, S.B.Y. et al. 	Genome Sequence of Bacillus velezensis SGAir0473, Isolated from Tropical Air Collected in Singapore.	Genome Announcements	2018	6		e00642-18			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. 		
@D	Lim, S.K.//Kim, S.J.//Cha, S.H.//Oh, Y.K.//Rhee, H.J.//Kim, M.S.//Lee, J.K. 	Complete genome sequence of Rhodobacter sphaeroides KD131.	J. Bacteriol.	2009	191		1118-1119			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. 		
@D	Lim, S.R.//Jeong, D.G.//Chi, W.J.//Kim, J.H. 	Complete Genome Sequence of Lacinutrix venerupis DOK2-8 Isolated from Marine Sediment from the East Sea, Republic of Korea.	Genome Announcements	2018	6		e01485-17			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. 		
@D	Lim, Y.L.//Ee, R.//Yong, D.//Yu, C.Y.//Ang, G.Y.//Tee, K.K.//Yin, W.F.//Chan, K.G. 	Complete Genome Sequence Analysis of Pandoraea pnomenusa Type Strain DSM 16536T Isolated from a Cystic Fibrosis Patient.	Front. Microbiol.	2016	7		109			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. 		
@D	Lim, Y.L.//Roberts, R.J.//Ee, R.//Yin, W.F.//Chan, K.G. 	Complete Genome Sequence and Methylome Analysis of Aeromonas hydrophila Strain YL17, Isolated from a Compost Pile.	Genome Announcements	2016	4		e00060-16			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. 		
@D	Lima, A.C.//de Moura, V.A.//Pinheiro, K.D.//Paixao, C.T.//da Costa, W.L.//Folador, A.R.//Guaraldi, A.L.//Ramos, R.T.//Silva, A.//Marques, J.M. 	Draft Genome Sequence of Corynebacterium pseudotuberculosis Strain PA05 Isolated  from an Ovine Host in Para State, Brazil.	Genome Announcements	2017	5		e00082-17			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. 		
@D	Lima, A.O.//Cabral, A.//Andreote, F.D.//Cavalett, A.//Pessatti, M.L.//Dini-Andreote, F.//da Silva, M.A. 	Draft Genome Sequence of Bacillus stratosphericus LAMA 585, Isolated from the Atlantic Deep Sea.	Genome Announcements	2013	1		e00204-13			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). 		
@D	Lima, A.R.//Siqueira, A.S.//Dos Santos, B.G.//da Silva, F.D.//Inada, D.T.//Lima, C.P.//Cardoso, J.F.//Vianez-Junior, J.L.//Nunes, M.R.//Goncalves, E.C. 	Draft Genome Sequence of Rhodobacter sp. Strain CACIA 14H1, a Heterotrophic Bacterium Obtained from a Nonaxenic Culture of a Cyanobium Species.	Genome Announcements	2014	2		e01116-13			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. 		
@D	Lima, A.R.//Siqueira, A.S.//Dos Santos, B.G.//da Silva, F.D.//Lima, C.P.//Cardoso, J.F.//Vianez, J.J.L.//Dall'Agnol, L.T.//McCulloch, J.A.//Nunes, M.R.//Goncalves, E.C. 	Draft Genome Sequence of the Brazilian Cyanobium sp. Strain CACIAM 14.	Genome Announcements	2014	2		e00669-14			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. 		
@D	Lima, A.R.//Siqueira, A.S.//Dos Santos, B.G.//da Silva, F.D.//Lima, C.P.//Cardoso, J.F.//Vianez-Junior, J.L.//Nunes, M.R.//Goncalves, E.C. 	Draft Genome Sequence of Blastomonas sp. Strain CACIA 14H2, a Heterotrophic Bacterium Associated with Cyanobacteria.	Genome Announcements	2014	2		e01200-13			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. 		
@D	Lima, A.R.J.//Castro, W.O.//Moraes, P.H.G.//Siqueira, A.S.//Aguiar, D.C.F.//de Lima, C.P.S.//Vianez-Junior, J.L.S.G.//Nunes, M.R.T.//Dall'Agnol, L.T.//Goncalves, E.C. 	Draft Genome Sequence of Alkalinema sp. Strain CACIAM 70d, a Cyanobacterium Isolated from an Amazonian Freshwater Environment.	Genome Announcements	2017	5		e00635-17			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. 		
@D	Lima, N.B.//Gama, M.A.S.//Mariano, R.L.R.//Silva, W.J. Jr.//Farias, A.R.G.//Falcao, R.M.//Sousa-Paula, L.C.//Benko-Iseppon, A.M.//Paiva, S.S.L. Jr.//Balbino, V.Q.//Souza, E.B. 	Complete Genome Sequence of Xanthomonas campestris pv. viticola Strain CCRMXCV 80 from Brazil.	Genome Announcements	2017	5		e01263-17			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. 		
@D	Limsowtin, G.K.Y.//Heap, H.A.//Lawrence, R.C. 	Heterogeneity among strains of lactic streptococci.	New Zealand J. Dairy Sci. Techn.	1978	13		1-8			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. 		
@D	Lin, A.C.//Liao, T.L.//Lin, Y.C.//Lai, Y.C.//Lu, M.C.//Chen, Y.T. 	Complete Genome Sequence of Klebsiella pneumoniae 1084, a Hypermucoviscosity-Negative K1 Clinical Strain.	J. Bacteriol.	2012	194		6316			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. 		
@D	Lin, B.//Lu, G.//Li, S.//Hu, Z.//Chen, H. 	Draft Genome Sequence of the Novel Agarolytic Bacterium Aquimarina agarilytica ZC1.	J. Bacteriol.	2012	194		2769			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. 		
@D	Lin, B.-C.//Chien, M.-C.//Lou, S.-Y. 	A sequence-specific endonuclease (XmnI) from Xanthomonas manihotis.	Nucleic Acids Res.	1980	8		6189-6198			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'. 		
@D	Lin, C.//den Bakker, H.C.//Suzuki, H.//Lefebure, T.//Ponnala, L.//Sun, Q.//Stanhope, M.J.//Wiedmann, M.//Duhamel, G.E. 	Complete Genome Sequence of the Porcine Strain Brachyspira pilosicoli P43/6/78(T.).	Genome Announcements	2013	1		e00215-12			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. 		
@D	Lin, D.//Guo, Y.//Chen, C.//Fuzhu, Y.//Xiao, S.//Zhu, D.//Wang, M.//Xu, X. 	Draft Genome Sequence of Linezolid-Resistant Enterococcus faecalis Clinical Isolate HS0914.	Genome Announcements	2014	2		e00782-14			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. 		
@D	Lin, H.//Coletta-Filho, H.D.//Han, C.S.//Lou, B.//Civerolo, E.L.//Machado, M.A.//Gupta, G. 	Draft Genome Sequence of 'Candidatus Liberibacter americanus' Bacterium Associated with Citrus Huanglongbing in Brazil.	Genome Announcements	2013	1		e00275-13			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. 		
@D	Lin, H.//Han, C.S.//Liu, B.//Lou, B.//Bai, X.//Deng, C.//Civerolo, E.L.//Gupta, G. 	Complete Genome Sequence of a Chinese Strain of 'Candidatus Liberibacter asiaticus'.	Genome Announcements	2013	1		e00184-13			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. 		
@D	Lin, H.//Pietersen, G.//Han, C.//Read, D.A.//Lou, B.//Gupta, G.//Civerolo, E.L. 	Complete Genome Sequence of 'Candidatus Liberibacter africanus,' a Bacterium Associated with Citrus Huanglongbing.	Genome Announcements	2015	3		e00733-15			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. 		
@D	Lin, H.H.//Chen, Y.S.//Hsiao, H.W.//Hsueh, P.T.//Ni, W.F.//Chen, Y.L. 	Two Genome Sequences of Klebsiella pneumoniae Strains with Sequence Type 23 and Capsular Serotype K1.	Genome Announcements	2016	4		e01097-16			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. 		
@D	Lin, I.-H.//Liu, T.-T.//Teng, Y.-T.//Wu, H.-L.//Liu, Y.-M.//Wu, K.-M.//Chang, C.-H.//Hsu, M.-T. 	Sequencing and Comparative Genome Analysis of Two Pathogenic Streptococcus gallolyticus Subspecies: Genome Plasticity, Adaptation and Virulence.	PLoS ONE	2011	6		e20519			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. 		
@D	Lin, I.G.//Han, L.//Taghva, A.//O'Brien, L.E.//Hsieh, C.L. 	Murine de novo methyltransferase Dnmt3a demonstrates strand asymmetry and site preference in the methylation of DNA in vitro.	Mol. Cell. Biol.	2002	22		704-723			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. 		
@D	Lin, J.//Vogt, V.M. 	I-PpoI, the endonuclease encoded by the group I intron PpLSU3, is expressed from an RNA polymerase I transcript.	Mol. Cell. Biol.	1998	18		5809-5817			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. 		
@D	Lin, J.//Zhao, F.//Feng, Y.//Zong, Z. 	Draft Genome Sequence of a High-Level Colistin-Resistant Clinical Strain of the Enterobacter cloacae Complex.	Genome Announcements	2017	5		e00131-17			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. 		
@D	Lin, J.N.//Lai, C.H.//Yang, C.H.//Huang, Y.H.//Lin, H.H. 	Complete Genome Sequence of Elizabethkingia miricola Strain EM798-26 Isolated from the Blood of a Cancer Patient.	Genome Announcements	2018	6		e01408-17			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. 		
@D	Lin, J.N.//Yang, C.H.//Lai, C.H.//Huang, Y.H.//Lin, H.H. 	Draft Genome Sequence of Elizabethkingia anophelis Strain EM361-97 Isolated from  the Blood of a Cancer Patient.	Genome Announcements	2016	4		e01215-16			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. 		
@D	Lin, L.//Wei, C.//Chen, M.//Wang, H.//Li, Y.//Li, Y.//Yang, L.//An, Q. 	Complete genome sequence of endophytic nitrogen-fixing Klebsiella variicola strain DX120E.	Standards in Genomic Sciences	2015	10		22			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. 		
@D	Lin, L.//Xu, Q.//Zhang, Y.//Yin, B.//Fan, Y.//Luo, Y.//Han, S.//Zhang, Z.//Wu, G.//Shen, Y. 	Alternative splicing of de novo methyltransferase gene 3b in adult and newborn mice.	Zhongguo Yixue Kexueyuan Xuebao	2000	22		312-316			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. 		
@D	Lin, L.C.//Lin, G.H.//Tseng, Y.H.//Yu, M.S. 	Draft Genome Sequence of Vibrio owensii GRA50-12, Isolated from Green Algae in the Intertidal Zone of Eastern Taiwan.	Genome Announcements	2015	3		e01438-14			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. 		
@D	Lin, L.F.//Posfai, J.//Roberts, R.J.//Kong, H.M. 	Comparative genomics of the restriction-modification systems in Helicobacter pylori.	Proc. Natl. Acad. Sci. U. S. A.	2001	98		2740-2745			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. 		
@D	Lin, M.J.//Lee, T.L.//Hsu, D.W.//Shen, C.K. 	One-codon alternative splicing of the CpG MTase dnmt1 transcript in mouse somatic cells.	FEBS Lett.	2000	469		101-104			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. 		
@D	Lin, M.J.//Tang, L.Y.//Reddy, M.N.//Shen, C.K.J. 	DNA methyltransferase gene dDnmt2 and longevity of Drosophila.	J. Biol. Chem.	2005	280		861-864			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. 		
@D	Lin, N.//Liu, Z.//Zhou, J.//Wang, S.//Fleming, J. 	Draft Genome Sequences of Two Super-XDR Isolates of M. tuberculosis from China.	FEMS Microbiol. Lett.	2013	347		93-96			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. 		
@D	Lin, P.M.//Lee, C.H.//Roberts, R.J. 	Cloning and characterization of the genes encoding the MspI restriction modification system.	Nucleic Acids Res.	1989	17		3001-3011			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. 		
@D	Lin, S.Y.//Shieh, W.Y.//Chen, J.S.//Tang, S.L. 	Complete Genome Sequence of Simiduia agarivorans SA1(T), a Marine Bacterium Able  To Degrade a Variety of Polysaccharides.	Genome Announcements	2013	1		e00039-12			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. 		
@D	Lin, T.L.//Shun, C.T.//Chang, K.C.//Wang, J.T. 	Isolation and characterization of a HpyC1I restriction-modification system in Helicobacter pylori.	J. Biol. Chem.	2004	279		11156-11162			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. 		
@D	Lin, W.H.//Zheng, P.X.//Liu, T.//Tseng, C.C.//Chen, W.C.//Wang, M.C.//Wu, J.J. 	Complete Genome Sequence of Community-Acquired Klebsiella pneumoniae KP36, a Strain Isolated from a Patient with an Upper Urinary Tract Infection.	Genome Announcements	2016	4		e01403-16			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. 		
@D	Lin, X.//Wang, Z.//Li, Y. 	Draft Genome Sequence of Pseudoalteromonas sp. Strain A2, an Isolate with High Antioxidative Activity from Arctic Seawater.	Genome Announcements	2014	2		e00885-14			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. 		
@D	Lin, Y.//Fan, H.//Hao, X.//Johnstone, L.//Hu, Y.//Wei, G.//Alwathnani, H.A.//Wang, G.//Rensing, C. 	Draft genome sequence of Halomonas sp. Strain HAL1, a moderately halophilic arsenite-oxidizing bacterium isolated from gold-mine soil.	J. Bacteriol.	2011	194		199-200			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. 		
@D	Lin, Y.//Hao, X.//Johnstone, L.//Miller, S.J.//Baltrus, D.A.//Rensing, C.//Wei, G. 	Draft Genome of Streptomyces zinciresistens K42, a Novel Metal-Resistant Species Isolated from Copper-Zinc Mine Tailings.	J. Bacteriol.	2011	193		6408-6409			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. 		
@D	Lin, Y.T.//Tsai, J.C.//Chen, H.J.//Hung, W.C.//Hsueh, P.R.//Teng, L.J. 	A Novel Staphylococcal Cassette Chromosomal Element, SCCfusC, Carrying fusC and speG in Fusidic Acid-Resistant Methicillin-Resistant Staphylococcus aureus.	Antimicrob. Agents Chemother.	2014	58		1224-1227			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. 		
@D	Lin, Z.//Liu, Z.//Yang, R.//Zou, Y.//Wan, D.//Chen, J.//Guo, M.//Zhao, J.//Fang, C.//Yang, R.//Liu, F. 	Whole-Genome Sequencing of Lactobacillus shenzhenensis Strain LY-73T.	Genome Announcements	2013	1		e00972-13			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. 		
@D	Linares, D.M.//Arboleya, S.//Ross, R.P.//Stanton, C. 	Complete Genome Sequence of the Gamma-Aminobutyric Acid-Producing Strain Streptococcus thermophilus APC151.	Genome Announcements	2017	5		e00205-17			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%. 		
@D	Linares, D.M.//Kok, J.//Poolman, B. 	Genome Sequences of Lactococcus lactis MG1363 (Revised) and NZ9000 and Comparative Physiological Studies.	J. Bacteriol.	2010	192		5806-5812			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. 		
@D	Lincoln, S.A.//Hamilton, T.L.//Valladares, J.A.G.//Schedler, M.//Macalady, J.L.//Muller, R.//Freeman, K.H. 	Draft Genome Sequence of the Piezotolerant and Crude Oil-Degrading Bacterium Rhodococcus qingshengii Strain TUHH-12.	Genome Announcements	2015	3		e00268-15			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. 		
@D	Lindahl, T. 	Enzymatic methylation of DNA - Roles and prospects.	Biol. Chem.	1998	379		375-376			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. 		
@D	Linder, P.//Doelz, R.//Gubler, M.//Bickle, T.A. 	An anticodon nuclease gene inserted into a hsd region encoding a type I DNA restriction system.	Nucleic Acids Res.	1990	18		7170			None 		
@D	Lindler, L.E.//Plano, G.V.//Burland, V.//Mayhew, G.F.//Blattner, F.R. 	Complete DNA sequence and detailed analysis of the Yersinia pestis KIM5 plasmid encoding murine toxin and capsular antigen.	Infect. Immun.	1998	66		5731-5742			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. 		
@D	Lindroth, A.M.//Cao, X.//Jackson, J.P.//Zilberman, D.//McCallum, C.M.//Henikoff, S.//Jacobsen, S.E. 	Requirement of CHROMOMETHYLASE3 for maintenance of CpXpG methylation.	Science	2001	292		2077-2080			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. 		
@D	Lindsay, J.A. 	Genomic variation and evolution of Staphylococcus aureus.	Int. J. Med. Microbiol.	2010	300		98-103			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. 		
@D	Lindsay, J.A. 	Staphylococcus aureus genomics and the impact of horizontal gene transfer.	Int. J. Med. Microbiol.	2014	304		103-109			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. 		
@D	Lindsey, R.L.//Batra, D.//Rowe, L.//Loparev, V.N.//Juieng, P.//Garcia-Toledo, L.//Bicknese, A.//Stripling, D.//Martin, H.//Chen, J.//Strockbine, N.//Trees, E. 	High-Quality Draft Genome Sequences for Four Drug-Resistant or Outbreak-Associated Shigella sonnei Strains Generated with PacBio Sequencing and   Whole-Genome Maps.	Genome Announcements	2017	5		e00906-17			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. 		
@D	Lindsey, R.L.//Batra, D.//Rowe, L.//Loparev, V.N.//Stripling, D.//Garcia-Toledo, L.//Knipe, K.//Juieng, P.//Sheth, M.//Martin, H.//Laufer, H.A. 	High-Quality Genome Sequence of an Escherichia coli O157 Strain Carrying an mcr-1 Resistance Gene Isolated from a Patient in the United States.	Genome Announcements	2017	5		e01725-16			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. 		
@D	Lindsey, R.L.//Batra, D.//Smith, P.//Patel, P.N.//Tagg, K.A.//Garcia-Toledo, L.//Loparev, V.N.//Juieng, P.//Sheth, M.//Joung, Y.J.//Rowe, L.A. 	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.	Microbiol. Resour. Announc.	2018	7		e01025-18			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. 		
@D	Lindsey, R.L.//Knipe, K.//Rowe, L.//Garcia-Toledo, L.//Loparev, V.//Juieng, P.//Trees, E.//Strockbine, N.//Stripling, D.//Gerner-Smidt, P. 	Complete Genome Sequences of Two Shiga Toxin-Producing Escherichia coli Strains from Serotypes O119:H4 and O165:H25.	Genome Announcements	2015	3		e01496-15			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. 		
@D	Lindsey, R.L.//Rowe, L.//Garcia-Toledo, L.//Loparev, V.//Knipe, K.//Stripling, D.//Martin, H.//Trees, E.//Juieng, P.//Batra, D.//Strockbine, N. 	High-Quality Draft Genome Sequences for Five Non-O157 Shiga Toxin-Producing Escherichia coli Strains Generated with PacBio Sequencing and Optical Maps.	Genome Announcements	2016	4		e00626-16			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. 		
@D	Lindsey, R.L.//Trees, E.//Sammons, S.//Loparev, V.//Frace, M.//Strockbine, N.//Sabol, A.L.//Sowers, E.//Stripling, D.//Martin, H.//Knipe, K.//Rowe, L.//Gerner-Smidt, P. 	Draft Whole-Genome Sequences of Nine Non-O157 Shiga Toxin-Producing Escherichia coli Strains.	Genome Announcements	2014	2		e00501-14			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. 		
@D	Lindstrom, W.M. Jr. 	The enzymology of bacterial dna methyltransferases.	Ph.D. Thesis, Univ. of California, Santa Barbara	2000			109			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. 		
@D	Lindstrom, W.M. Jr.//Flynn, J.//Reich, N.O. 	HhaI DNA cytosine-C5 methyltransferase: Reconciling function and structure.	FASEB J.	1999	13		A1443			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. 		
@D	Lindstrom, W.M. Jr.//Malygin, E.G.//Ovechkina, L.G.//Zinoviv, V.V.//Reich, N.O. 	Functional analysis of BamHI DNA cytosine-N4 methyltransferase.	J. Mol. Biol.	2003	325		711-720			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. 		
@D	Lindstrom, W.M.//Flynn, J.//Reich, N.O. 	Reconciling structure and function in HhaI DNA cytosine-C-5 methyltransferase.	J. Biol. Chem.	2000	275		4912-4919			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. 		
@D	Ling, J.//Lin, L.//Zhang, Y.//Lin, X.//Ahamad, M.//Zhou, W.//Dong, J. 	Draft Genome Sequence of Marinobacter hydrocarbonoclasticus Strain STW2, a Polycyclic Aromatic Hydrocarbon-Degrading and Denitrifying Bacterium from the  Rhizosphere of Seagrass Enhalus acodoides.	Genome Announcements	2017	5		e01412-16			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. 		
@D	Ling, Y.//Sankpal, U.T.//Robertson, A.K.//McNally, J.G.//Karpova, T.//Robertson, K.D. 	Modification of de novo DNA methyltransferase 3a (Dnmt3a) by SUMO-1 modulates its interaction with histone deacetylases (HDACs) and its capacity to repress transcription.	Nucleic Acids Res.	2004	32		598-610			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. 		
@D	Ling, Y.H.//Nelson, J.A.//Chan, J.Y.//Beattie, K.L. 	6-Thioguanine substituted DNA as a substrate for restriction endonucleases and ligases.	Proc. Amer. Assoc. Cancer Res.	1992	33		543					
@D	Linn, S. 	The 1978 Nobel prize in physiology or medicine.	Science	1978	202		1069-1071			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. 		
@D	Linn, S.//Arber, W. 	Host specificity of DNA produced by Escherichia coli, X.  In vitro restriction of phage fd replicative form.	Proc. Natl. Acad. Sci. U. S. A.	1968	59		1300-1306			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. 		
@D	Linn, S.//Lautenberger, J.A.//Eskin, B.//Lackey, D. 	Host-controlled restriction and modification enzymes of Escherichia coli B1,2.	Fed. Proc.	1974	33		1128-1134			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. 		
@D	Linz, B.//Windsor, H.M.//Gajewski, J.P.//Hake, C.M.//Drautz, D.I.//Schuster, S.C.//Marshall, B.J. 	Helicobacter pylori genomic microevolution during naturally occurring transmission between adults.	PLoS ONE	2013	8		e82187			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. 		
@D	Linz, B.//Windsor, H.M.//McGraw, J.J.//Hansen, L.M.//Gajewski, J.P.//Tomsho, L.P.//Hake, C.M.//Solnick, J.V.//Schuster, S.C.//Marshall, B.J. 	A mutation burst during the acute phase of Helicobacter pylori infection in humans and rhesus macaques.	Nat. Commun.	2014	5		4165			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. 		
@D	Lio, P.//Vannucci, M. 	Finding pathogenicity islands and gene transfer events in genome data.	Bioinformatics	2000	16		932-940			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. 		
@D	Liolios, K. et al. 	Complete genome sequence of the gliding, heparinolytic Pedobacter saltans type strain (113).	Standards in Genomic Sciences	2011	5		30-40			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. 		
@D	Liolios, K. et al. 	Complete genome sequence of Thermobispora bispora type strain (R51).	Standards in Genomic Sciences	2010	2		318-326			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. 		
@D	Liolos, K. et al. 	Complete genome sequence of the halophilic bacterium Spirochaeta africana type strain (Z-7692(T)) from the alkaline Lake Magadi in the East African Rift.	Standards in Genomic Sciences	2013	8		165-176			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. 		
@D	Liou, M.L.//Liu, C.C.//Lu, C.W.//Hsieh, M.F.//Chang, K.C.//Kuo, H.Y.//Lee, C.C.//Chang, C.T.//Yang, C.Y.//Tang, C.Y. 	Genome Sequence of Acinetobacter baumannii TYTH-1.	J. Bacteriol.	2012	194		6974			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. 		
@D	Lippmann, J.E.//Wu, H.//Fives-Taylor, P.M. 	Directed mutagenesis of the DNA-adenine-methyltransferase (DAM) gene in Actinobacillus actinomycetemcomitans (Aa) by conjugation.	J. Dent. Res.	2002	81		A-145			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. 		
@D	Lippow, S.M.//Aha, P.M.//Parker, M.H.//Blake, W.J.//Baynes, B.M.//Lipovsek, D. 	Creation of a type IIS restriction endonuclease with a long recognition sequence.	Nucleic Acids Res.	2009	37		3061-3073			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. 		
@D	Lippow, S.M.//Aha, P.M.//Parker, M.H.//Blake, W.J.//Baynes, B.M.//Lipovsek, D. 	BIOT 7-Creation of a type IIS restriction endonuclease with a long recognition sequence.	ACS Abstracts	2008	236		0			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. 		
@D	Lipus, D.//Ross, D.//Bibby, K.//Gulliver, D. 	Draft Genome Sequence of Pseudomonas sp. BDAL1 Reconstructed from a Bakken Shale  Hydraulic Fracturing-Produced Water Storage Tank Metagenome.	Genome Announcements	2017	5		e00033-17			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. 		
@D	Lipus, D.//Vikram, A.//Ross, D.E.//Bibby, K. 	Draft Genome Sequence of Methanohalophilus mahii Strain DAL1 Reconstructed from a Hydraulic Fracturing-Produced Water Metagenome.	Genome Announcements	2016	4		e00899-16			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. 		
@D	Lira, F.//Garcia-Leon, G.//Oliver, A.//Martinez, J.L. 	Draft Genome Sequences of Four Pseudomonas aeruginosa Isolates Obtained from Patients with Chronic Obstructive Pulmonary Disease.	Genome Announcements	2017	5		e00147-17			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. 		
@D	Lira, F.//Hernandez, A.//Belda, E.//Sanchez, M.B.//Moya, A.//Silva, F.J.//Martinez, J.L. 	Whole-Genome Sequence of Stenotrophomonas maltophilia D457, a Clinical Isolate and a Model Strain.	J. Bacteriol.	2012	194		3563-3564			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. 		
@D	Lisle, W.//Dutta, C.F.//Penner, M.//Amitsur, M.//Kaufmann, G.//Firman, K. 	Phage T4-ancoded Stp alleviates the DNA restriction activity of EcoR124I endonuclease by affecting a critical step in the subunit assembly pathway.	Mol. Biol. Today	2000	1		57-64			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. 		
@D	Little, E.J.//Babic, A.C.//Horton, N.C. 	Early interrogation and recognition of DNA sequence by indirect readout.	Structure	2008	16		1828-1837			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. 		
@D	Little, E.J.//Horton, N.C. 	DNA-induced conformational changes in type II restriction endonucleases: The structure of unliganded HincII.	J. Mol. Biol.	2005	351		76-88			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. 		
@D	Little, G.T.//Winzer, K.//Minton, N.P. 	Genome Sequence of the Solvent-Producing Clostridium beijerinckii Strain 59B, Isolated from Staffordshire Garden Soil.	Genome Announcements	2015	3		e00108-15			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. 		
@D	Little, J.W.//Mount, D.W. 	Creating new restriction sites by silent changes in coding sequences.	Gene	1984	32		67-73			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. 		
@D	Liu, B.//Bian, C.//Huang, H.//Yin, Z.//Shi, Q.//Deng, X. 	Complete Genome Sequence of a Marine Bacterium, Pseudomonas pseudoalcaligenes Strain S1, with High Mercury Resistance and Bioaccumulation Capacity.	Genome Announcements	2016	4		e00381-16			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. 		
@D	Liu, B.//Frostegard, A.//Shapleigh, J.P. 	Draft genome sequences of five strains in the genus thauera.	Genome Announcements	2013	1		e00052-12			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. 		
@D	Liu, B.//Ge, B.//Azhar, N.//Zhao, W.//Cui, H.//Zhang, K. 	Complete Genome Sequence of Bacillus methylotrophicus Strain NKG-1, Isolated from the Changbai Mountains, China.	Genome Announcements	2018	6		e01454-17			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%. 		
@D	Liu, B.//Hu, B.//Zhou, Z.//Guo, D.//Guo, X.//Ding, P.//Feng, L.//Wang, L. 	A novel non-homologous recombination-mediated mechanism for Escherichia coli unilateral flagellar phase variation.	Nucleic Acids Res.	2012	40		4530-4538			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. 		
@D	Liu, B.//Liu, G.H.//Cetin, S.//Schumann, P.//Pan, Z.Z.//Chen, Q.Q. 	Bacillus gobiensis sp. nov., isolated from a soil sample.	Int. J. Syst. Evol. Microbiol.	2016	66		379-384			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). 		
@D	Liu, B.//Liu, G.H.//Zhu, Y.J.//Wang, J.P.//Che, J.M.//Chen, Q.Q.//Chen, Z. 	Draft Genome Sequences of Type Strains Bacillus drentensis DSM 15600T and Bacillus novalis DSM 15603T.	Genome Announcements	2016	4		e01423-16			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. 		
@D	Liu, C.//Hu, J.//Fang, X.//Zhang, D.//Chang, D.//Wang, J.//Li, T.//Guo, Y.//Dai, W.//Liu, C. 	Genome Sequence of Pseudomonas aeruginosa Strain LCT-PA41, with Changed Metabolism after Space Flight.	Genome Announcements	2014	2		e01124-13			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. 		
@D	Liu, C.//Zheng, H.//Yang, M.//Xu, Z.//Wang, X.//Wei, L.//Tang, B.//Liu, F.//Zhang, Y.//Ding, Y.//Tang, X.//Wu, B.//Johnson, T.J.//Chen, H.//Tan, C. 	Genome analysis and in vivo virulence of porcine extraintestinal pathogenic Escherichia coli strain PCN033.	BMC Genomics	2015	16		717			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. 		
@D	Liu, D.//Zhou, Y.//Naito, M.//Yumoto, H.//Li, Q.//Miyake, Y.//Liang, J.//Shu, R. 	Draft Genome Sequence of Porphyromonas gingivalis Strain SJD2, Isolated from the  Periodontal Pocket of a Patient with Periodontitis in China.	Genome Announcements	2014	2		e01091-13			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. 		
@D	Liu, D.Y.//Li, Y.//Magarvey, N.A. 	Draft Genome Sequence of Streptomyces canus ATCC 12647, a Producer of Telomycin.	Genome Announcements	2016	4		e00173-16			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. 		
@D	Liu, F.//Li, J.//Li, Z. 	Draft Genome Sequence of 'Candidatus Synechococcus spongiarum' m9, Binned from a  Metagenome of South China Sea Sponge Theonella swinhoei.	Genome Announcements	2017	5		e01307-16			'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. 		
@D	Liu, F.//Ma, R.//Tay, C.Y.A.//Octavia, S.//Lan, R.//Chung, H.K.L.//Riordan, S.M.//Grimm, M.C.//Leong, R.W.//Tanaka, M.M.//Connor, S.//Zhang, L. 	Genomic analysis of oral Campylobacter concisus strains identified a potential bacterial molecular marker associated with active Crohn's disease.	Emerg. Microbes Infect.	2018	7		64			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. 		
@D	Liu, F.//Yang, J.//Xiao, Y.//Li, L.//Yang, F.//Jin, Q. 	Complete Genome Sequence of a Clinical Isolate of Enterobacter asburiae.	Genome Announcements	2016	4		e00523-16			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. 		
@D	Liu, G.//Deng, C.//Song, L.//Peng, Q.//Zhang, J.//Lereclus, D.//Song, F. 	Draft Genome Sequence of Bacillus thuringiensis Strain LM1212, Isolated from the  Cadaver of an Oryctes gigas Larva in Madagascar.	Genome Announcements	2014	2		e00516-14			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. 		
@D	Liu, G.//Liu, B.//Lin, N.//Tang, W.//Tang, J.//Lin, Y. 	Genome Sequence of the Aerobic Bacterium Bacillus sp. Strain FJAT-13831.	J. Bacteriol.	2012	194		6633			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%. 		
@D	Liu, G.//Liu, B.//Tang, W.//Che, J.//Lin, Y.//Zhu, Y.//Su, M.//Tang, J. 	Genome Sequence of Bacillus sp. Strain FJAT-14515.	Genome Announcements	2014	2		e01123-13			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. 		
@D	Liu, G.//Ou, H.Y.//Wang, T.//Li, L.//Tan, H.//Zhou, X.//Rajakumar, K.//Deng, Z.//He, X. 	Cleavage of Phosphorothioated DNA and Methylated DNA by the Type IV Restriction Endonuclease ScoMcrA.	PLoS Genet.	2010	6		e1001253			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. 		
@D	Liu, G.//Song, L.//Shu, C.//Wang, P.//Deng, C.//Peng, Q.//Lereclus, D.//Wang, X.//Huang, D.//Zhang, J.//Song, F. 	Complete Genome Sequence of Bacillus thuringiensis subsp. kurstaki Strain HD73.	Genome Announcements	2013	1		e0008013			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. 		
@D	Liu, G.//Zhang, W.//Lu, C. 	Complete Genome Sequence of Streptococcus agalactiae GD201008-001, Isolated in China from Tilapia with Meningoencephalitis.	J. Bacteriol.	2012	194		6653			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. 		
@D	Liu, G.H.//Liu, B.//Tang, J.Y.//Che, J.M.//Zhu, Y.J.//Su, M.X.//Wang, J.P.//Chen, Q.Q. 	Draft Genome Sequence of Bacillus fengqiuensis FJAT-14578, Isolated from a Soil Sample in China.	Genome Announcements	2014	2		e01126-14			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). 		
@D	Liu, G.H.//Liu, B.//Wang, J.P.//Che, J.M.//Chen, Q.Q. 	Complete Genome Sequence of a Potential Novel Bacillus sp. Strain, FJAT-18017, Isolated from a Potato Field.	Genome Announcements	2017	5		e01424-16			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%. 		
@D	Liu, G.H.//Liu, B.//Wang, J.P.//Che, J.M.//Chen, Q.Q.//Chen, Z. 	High-Quality Genome Sequence of Bacillus vireti DSM 15602T for Setting Up Phylogenomics for the Genomic Taxonomy of Bacillus-Like Bacteria.	Genome Announcements	2015	3		e00864-15			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. 		
@D	Liu, G.H.//Liu, B.//Wang, J.P.//Che, J.M.//Chen, Q.Q.//Chen, Z. 	Draft Genome Sequence of Bacillus simplex DSM 1321 for Setting Up Phylogenomics in Genomic Taxonomy of the Bacillus-Like Bacteria.	Genome Announcements	2016	4		e00574-16			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. 		
@D	Liu, G.H.//Liu, B.//Wang, J.P.//Che, J.M.//Chen, Q.Q.//Chen, Z.//Ge, C.B. 	Genome Sequence of Type Strain Lysinibacillus macroides DSM 54T.	Genome Announcements	2015	3		e01271-15			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. 		
@D	Liu, G.H.//Liu, B.//Wang, J.P.//Che, J.M.//Chen, Q.Q.//Zhu, Y.J. 	Draft Genome Sequence of Bacillus sp. FJAT-27238 for Setting up Phylogenomic Analysis of Genomic Taxonomy of Bacillus-Like Bacteria.	Genome Announcements	2015	3		e00985-15			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%. 		
@D	Liu, G.H.//Liu, B.//Wang, J.P.//Che, J.M.//Zheng, X.F.//Chen, Q.Q.//Ge, C.B. 	Draft Genome Sequence of Type Strain Lysinibacillus xylanilyticus DSM 23493T.	Genome Announcements	2015	3		e01037-15			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. 		
@D	Liu, G.H.//Liu, B.//Wang, J.P.//Che, J.M.//Zhu, Y.J.//Chen, Q.Q.//Ruan, C.Q. 	Genome Sequence of Paenibacillus sp. Strain FJAT-28004 for the Genome Sequencing  Project for Genomic Taxonomy and Phylogenomics of Bacillus-Like Bacteria.	Genome Announcements	2015	3		e00863-15			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. 		
@D	Liu, G.H.//Liu, B.//Wang, J.P.//Chen, Q.Q.//Che, J.M.//Zheng, X.F.//Ge, C.B. 	Genome Sequence of Type Strain Bacillus decisifrondis E5HC-32T (DSM 11725T), Isolated from Soil Underlying the Decaying Leaf Litter of a Slash Pine Forest.	Genome Announcements	2015	3		e01249-15			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. 		
@D	Liu, G.H.//Liu, B.//Zhu, Y.J.//Wang, J.P.//Che, J.M.//Chen, Q.Q.//Chen, Z. 	Draft Genome Sequence of Bacillus mesonae FJAT-13985T (=DSM 25968T) for Setting Up Phylogenomics in Genomic Taxonomy of the Bacillus-Like Bacteria.	Genome Announcements	2016	4		e00575-16			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). 		
@D	Liu, H.//Cheng, Y.//Gu, J.//Wang, Y.//Li, J.//Li, F.//Han, W. 	Draft Genome Sequence of Paenibacillus sp. Strain MY03, a Terrestrial Bacterium Capable of Degrading Multiple Marine-Derived Polysaccharides.	Genome Announcements	2017	5		e00678-17			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. 		
@D	Liu, H.//Liu, K.//Li, Y.//Wang, C.//Hou, Q.//Xu, W.//Fan, L.//Zhao, J.//Gou, J.//Du, B.//Ding, Y. 	Complete Genome Sequence of Paenibacillus polymyxa YC0136, a Plant Growth-Promoting Rhizobacterium Isolated from Tobacco Rhizosphere.	Genome Announcements	2017	5		e01635-16			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. 		
@D	Liu, H.//Qiu, H.//Zhao, W.//Cui, Z.//Ibrahim, M.//Jin, G.//Li, B.//Zhu, B.//Xie, G.L. 	Genome Sequence of the Plant Pathogen Pseudomonas syringae pv. panici LMG 2367.	J. Bacteriol.	2012	194		5693-5694			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. 		
@D	Liu, H.//Shan, W.//Zhou, Y.//Yu, X. 	Draft Genome Sequence of Paenibacillus sp. XY044, a Potential Plant Growth Promoter Isolated from a Tea Plant.	Genome Announcements	2017	5		e01016-17			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. 		
@D	Liu, H.//Song, L.//Cai, Y.//Wang, Y.//Yu, L. 	Draft Genome Sequence of Escherichia coli Strain SEC470, Isolated from a Piglet Experiencing Diarrhea.	Genome Announcements	2016	4		e00088-16			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. 		
@D	Liu, H.//Wang, C.//Li, Y.//Liu, K.//Hou, Q.//Xu, W.//Fan, L.//Zhao, J.//Gou, J.//Du, B.//Ding, Y. 	Complete Genome Sequence of Paenibacillus polymyxa YC0573, a Plant Growth-Promoting Rhizobacterium with Antimicrobial Activity.	Genome Announcements	2017	5		e01636-16			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. 		
@D	Liu, H.//Wu, Z.//Li, M.//Zhang, F.//Zheng, H.//Han, J.//Liu, J.//Zhou, J.//Wang, S.//Xiang, H. 	Complete Genome Sequence of Haloarcula hispanica, a Model Haloarchaeon for Studying Genetics, Metabolism, and Virus-Host Interaction.	J. Bacteriol.	2011	193		6086-6087			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. 		
@D	Liu, J.//Cheng, A.//Bangayan, N.J.//Barnard, E.//Curd, E.//Craft, N.//Li, H. 	Draft Genome Sequences of Propionibacterium acnes Type Strain ATCC6919 and Antibiotic-Resistant Strain HL411PA1.	Genome Announcements	2014	2		e00740-14			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. 		
@D	Liu, J.//Li, L.//Peters, B.M.//Li, B.//Chen, D.//Xu, Z.//Shirtliff, M.E. 	Complete genome sequence and bioinformatics analyses of Bacillus thuringiensis strain BM-BT15426.	Microb. Pathog.	2017	108		55-60			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. 		
@D	Liu, J.//Xue, Y.//Meng, Y.//Zhao, X.//Cai, Y. 	Expression detection and location analysis of BstNI isoschizomer restriction-modification system gene.	Wei Sheng Wu Xue Bao	1999	39		209-214			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. 		
@D	Liu, J.//Zhao, X.//Meng, Y.//Shen, J.//Xue, Y.//Shi, S.//Cai, Y. 	Expression and deletion analysis of EcoRII endonuclease and methylase gene.	Zhongguo Yi Xue Ke Xue Yuan Xue Bao	2000	22		111-114			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. 		
@D	Liu, J.//Zhao, X.//Meng, Y.//Shen, J.//Xue, Y.//Shi, S.//Cai, Y. 	Expression and deletion analysis of EcoRII endonuclease and methylase gene.	Chin. Med. Sci. J.	2001	16		200-203			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. 		
@D	Liu, J.//Zhou, Q.//Ibrahim, M.//Liu, H.//Jin, G.//Zhu, B.//Xie, G. 	Genome Sequence of the Biocontrol Agent Microbacterium barkeri Strain 2011-R4.	J. Bacteriol.	2012	194		6666-6667			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. 		
@D	Liu, J.-Y.//Zhao, X.-J.//Cai, Y.Y.//Shen, J.//Meng, Y. 	High expression and purification of EcoRII restriction endonuclease.	Chin. J. Biochem. Mol. Biol.	2000	16		417-420			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). 		
@D	Liu, K.//Wang, Y.F.//Cantemir, C.//Muller, M.T. 	Endogenous assays of DNA methyltransferases: Evidence for differential activities of DNMT1, DNMT2, and DNMT3 in mammalian cells in vivo.	Mol. Cell. Biol.	2003	23		2709-2719			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. 		
@D	Liu, L.//Gao, P.//Chen, G.//Wang, L. 	Draft Genome Sequence of Cellulose-Digesting Bacterium Sporocytophaga myxococcoides PG-01.	Genome Announcements	2014	2		e01154-14			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. 		
@D	Liu, L.//Li, N.//Zhang, D.//Fu, X.//Shi, C.//Lin, Q. 	Complete Genome Sequence of the Type Strain of Aeromonas schubertii, ATCC 43700.	Genome Announcements	2016	4		e00012-16			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. 		
@D	Liu, L.//Li, N.//Zhang, D.//Fu, X.//Shi, C.//Lin, Q.//Hao, G. 	Complete Genome Sequence of the Highly Virulent Aeromonas schubertii Strain WL1483, Isolated from Diseased Snakehead Fish (Channa argus) in China.	Genome Announcements	2016	4		e01567-15			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. 		
@D	Liu, L.//Li, Y.//Zhang, J.//Zhou, Z.//Liu, J.//Li, X.//Zhou, J.//Du, G.//Wang, L.//Chen, J. 	Complete Genome Sequence of the Industrial Strain Ketogulonicigenium vulgare WSH-001.	J. Bacteriol.	2011	193		6108-6109			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. 		
@D	Liu, L.//Li, Y.//Zhang, J.//Zou, W.//Zhou, Z.//Liu, J.//Li, X.//Wang, L.//Chen, J. 	Complete Genome Sequence of the Industrial Strain Bacillus megaterium WSH-002.	J. Bacteriol.	2011	193		6389-6390			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. 		
@D	Liu, L.//Santi, D.V. 	Mutation of asparagine 229 to aspartate in thymidylate synthase converts the enzyme to a deoxycytidylate methylase.	Biochemistry	1992	31		5100-5104			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. 		
@D	Liu, L.//Xiao, J.//Xia, X.//Pan, Y.//Yan, S.//Wang, Y. 	Draft Genome Sequence of Vibrio owensii Strain SH-14, Which Causes Shrimp Acute Hepatopancreatic Necrosis Disease.	Genome Announcements	2015	3		e01395-15			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. 		
@D	Liu, L.//Yang, F.//Li, X.//Luo, J.//Zhang, Z.//Li, H. 	Whole-Genome Sequence of Streptococcus parauberis Strain SP-llh, Isolated from Cows with Mastitis in Western China.	Genome Announcements	2017	5		e01389-16			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%. 		
@D	Liu, L.//Zhang, S.//Luo, M.//Wang, G. 	Genomic information of the arsenic-resistant bacterium Lysobacter arseniciresistens type strain ZS79(T) and comparison of Lysobacter draft genomes.	Standards in Genomic Sciences	2015	10		88			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. 		
@D	Liu, L.J.//You, X.Y.//Zheng, H.J.//Wang, S.Y.//Jiang, C.Y.//Liu, S.J. 	Complete genome sequence of Metallosphaera cuprina, a metal sulfide-oxidizing archaeon from hot spring.	J. Bacteriol.	2011	193		3387-3388			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. 		
@D	Liu, L.N.//Faulkner, M.//Liu, X.//Huang, F.//Darby, A.C.//Hall, N. 	Revised Genome Sequence of the Purple Photosynthetic Bacterium Blastochloris viridis.	Genome Announcements	2016	4		e01520-15			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. 		
@D	Liu, M.//Chen, S. 	Draft Genome Sequence of Vibrio parahaemolyticus V110, Isolated from Shrimp in Hong Kong.	Genome Announcements	2013	1		e00300-13			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. 		
@D	Liu, M.S.//Gingery, M.//Doulatov, S.R.//Liu, Y.C.//Hodes, A.//Baker, S.//Davis, P.//Simmonds, M.//Churcher, C.//Mungall, K.//Quail, M.A.//Preston, A.//Harvill, E.T.//Maskell, D.J.//Eiserling, F.A.//Parkhill, J.//Miller, J.F. 	Genomic and genetic analysis of Bordetella bacteriophages encoding reverse transcriptase-mediated tropism-switching cassettes.	J. Bacteriol.	2004	186		1503-1517			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. 		
@D	Liu, P.//Li, P.//Jiang, X.//Bi, D.//Xie, Y.//Tai, C.//Deng, Z.//Rajakumar, K.//Ou, H.Y. 	Complete Genome Sequence of Klebsiella pneumoniae subsp. pneumoniae HS11286, a Multidrug-Resistant Strain Isolated from Human Sputum.	J. Bacteriol.	2012	194		1841-1842			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). 		
@D	Liu, P.//Yang, X.-Hai.//Wang, Q.//Huang, J.//Liu, J.-Bo.//Zhu, Y.//He, L.-L.//Wang, Ke.-Min. 	Sensitive detection of DNA methyltransferase activity based on rolling circle amplification technology.	Chin. Chem. Lett.	2014	25		1047-1051			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. 		
@D	Liu, P.//Zheng, H.//Meng, Q.//Terahara, N.//Gu, W.//Wang, S.//Zhao, G.//Nakane, D.//Wang, W.//Miyata, M. 	Chemotaxis without Conventional Two-Component System, Based on Cell Polarity and Aerobic Conditions in Helicity-Switching Swimming of Spiroplasma eriocheiris.	Front. Microbiol.	2017	8		58			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. 		
@D	Liu, P.P.//Liu, Y.//Wang, L.H.//Wei, D.D.//Wan, L.G. 	Draft Genome Sequence of an NDM-5-Producing Klebsiella pneumoniae Sequence Type 14 Strain of Serotype K2.	Genome Announcements	2016	4		e01610-15			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. 		
@D	Liu, P.Y.//Huang, Y.T.//Lin, S.Y.//Chang, G.C.//Chen, J.W. 	Draft Genome Sequence of the Serratia marcescens Strain VGH107, a Taiwanese Clinical Isolate.	Genome Announcements	2013	1		e00249-13			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. 		
@D	Liu, Q.//Chen, X.//Zhao, X.//Chen, Y.//Chen, D. 	The effect of methylation outside the recognition sequence of restriction endonuclease PvuII on its cleavage efficiency.	Gene	1992	113		89-93			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. 		
@D	Liu, Q.//Derbyshire, V.//Balfort, M.//Edgell, D.R. 	Distance determination by GIY-YIG intron endonucleases: Discrimination between repression and cleavage functions.	Nucleic Acids Res.	2006	34		1755			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. 		
@D	Liu, Q.//Wu, Y.H.//Cheng, H.//Xu, L.//Wang, C.S.//Xu, X.W. 	Complete genome sequence of bacteriochlorophyll-synthesizing bacterium Porphyrobacter neustonensis DSM 9434.	Standards in Genomic Sciences	2017	12		32			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. 		
@D	Liu, Q.Q.//Dansereau, J.T.//Puttamadappa, S.S.//Shekhtman, A.//Derbyshire, V.//Belfort, M. 	Role of the interdomain linker in distance determination for remote cleavage by homing endonuclease I-TevI.	J. Mol. Biol.	2008	379		1094-1106			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. 		
@D	Liu, S.//Wang, Y.//Xu, J.//Li, Y.//Guo, J.//Ke, Y.//Yuan, X.//Wang, L.//Du, X.//Wang, Z.//Huang, L.//Zhang, N.//Chen, Z. 	Genome Sequence of an OXA23-Producing, Carbapenem-Resistant Acinetobacter baumannii Strain of Sequence Type ST75.	J. Bacteriol.	2012	194		6000-6001			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. 		
@D	Liu, S.L.//Hessel, A.//Sanderson, K.E. 	Genomic mapping with I-CeuI, an intron-encoded endonuclease specific for genes for ribosomal RNA, in Salmonella ssp., Escherichia coli, and other bacteria.	Proc. Natl. Acad. Sci. U. S. A.	1993	90		6874-6878			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. 		
@D	Liu, T.//Zhu, L.//Zhang, Z.//Jiang, L.//Huang, H. 	Draft Genome Sequence of Myroides sp. N17-2, a Multidrug-Resistant Bacterium Isolated from Radiation-Polluted Soils.	Genome Announcements	2017	5		e01301-17			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. 		
@D	Liu, T.-T.//Liu, J.-F.//Wang, W.-X.//Wang, H.//Wang, Z.-L.//Zeng, Z.-J.//Yan, W.-Y. 	Cloning and expression profiling of the DNA methyltransferase Dnmt3 gene in the Chinese honeybee, Apis cerana cerana (Hymenoptera: Apidae).	Acta Entomologica Sinica	2012	55		284-290			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. 		
@D	Liu, W. 	Fluorescence studies of EcoRI restriction endonuclease structure and dynamics.	Diss. Abstr.	1997	58		681			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. 		
@D	Liu, W.//Chen, Y.//Watrob, H.//Bartlett, S.G.//Jen-Jacobson, L.//Barkley, M.D. 	N-termini of EcoRI restriction endonuclease dimer are in close proximity on the protein surface.	Biochemistry	1998	37		15457-15465			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. 		
@D	Liu, W.//Fang, L.//Li, S.//Li, Q.//Zhou, Z.//Feng, Z.//Luo, R.//Shao, G.//Wang, L.//Chen, H.//Xiao, S. 	Complete Genome Sequence of Mycoplasma hyorhinis Strain HUB-1.	J. Bacteriol.	2010	192		5844-5845			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. 		
@D	Liu, W.//Feng, Z.//Fang, L.//Zhou, Z.//Li, Q.//Li, S.//Luo, R.//Wang, L.//Chen, H.//Shao, G.//Xiao, S. 	Complete Genome Sequence of Mycoplasma hyopneumoniae Strain 168.	J. Bacteriol.	2011	193		1016-1017			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. 		
@D	Liu, W.//Jing, Z.//Ou, Q.//Cui, B.//He, Y.//Wu, Q. 	Complete Genome Sequence of Brucella melitensis Biovar 3 Strain NI, Isolated from an Aborted Bovine Fetus.	J. Bacteriol.	2012	194		6321			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. 		
@D	Liu, W.//Liu, C.//Sun, D. 	Complete Genome Sequence of a Novel Bioflocculant-Producing Strain, Microbacterium paludicola CC3.	Genome Announcements	2017	5		e01008-17			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. 		
@D	Liu, W.//Xiao, S.//Li, M.//Guo, S.//Li, S.//Luo, R.//Feng, Z.//Li, B.//Zhou, Z.//Shao, G.//Chen, H.//Fang, L. 	Comparative genomic analyses of Mycoplasma hyopneumoniae pathogenic 168 strain and its high-passaged attenuated strain.	BMC Genomics	2013	14		80			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. 		
@D	Liu, W.//Yang, M.//Xu, Z.//Zheng, H.//Liang, W.//Zhou, R.//Wu, B.//Chen, H. 	Complete Genome Sequence of Pasteurella multocida HN06, a Toxigenic Strain of Serogroup D.	J. Bacteriol.	2012	194		3292-3293			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. 		
@D	Liu, W.B.//Yu, W.B.//Gao, S.H.//Ye, B.C. 	Genome Sequence of Saccharopolyspora erythraea D, a Hyperproducer of Erythromycin.	Genome Announcements	2013	1		e00718-13			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. 		
@D	Liu, W.Q.//Feng, Y.//Wang, Y.//Zou, Q.H.//Chen, F.//Guo, J.T.//Peng, Y.H.//Jin, Y.//Li, Y.G.//Hu, S.N.//Johnston, R.N.//Liu, G.R.//Liu, S.L. 	Salmonella paratyphi C: genetic divergence from Salmonella choleraesuis and pathogenic convergence with Salmonella typhi.	PLoS ONE	2009	4		E4510			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. 		
@D	Liu, W.Y.//Chung, K.M.//Wong, C.F.//Jiang, J.W.//Hui, R.K.//Leung, F.C. 	Complete Genome Sequence of the Endophytic Enterobacter cloacae subsp. cloacae Strain ENHKU01.	J. Bacteriol.	2012	194		5965			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. 		
@D	Liu, X.//Arumugam, K.//Natarajan, G.//Seviour, T.W.//Drautz-Moses, D.I.//Wuertz, S.//Law, Y.//Williams, R.B.H. 	Draft Genome Sequence of a 'Candidatus Brocadia' Bacterium Enriched from Activated Sludge Collected in a Tropical Climate.	Genome Announcements	2018	6		e00406-18			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. 		
@D	Liu, X.//Gai, Z.//Tao, F.//Yu, H.//Tang, H.//Xu, P. 	Genome Sequences of Pseudomonas luteola XLDN4-9 and Pseudomonas stutzeri XLDN-R,  Two Efficient Carbazole-Degrading Strains.	J. Bacteriol.	2012	194		5701-5702			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. 		
@D	Liu, X.//Huang, D.//Wu, J.//Yu, C.//Zhou, R.//Liu, C.//Zhang, W.//Yao, J.//Cheng, M.//Guo, S. 	The Genome Sequence of Alcaligenes faecalis NBIB-017 Contains Genes with Potentially High Activities against Erwinia carotovora.	Genome Announcements	2016	4		e00222-16			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. 		
@D	Liu, X.//Huang, Y.//Xu, X.//Zhao, Y.//Sun, Q.//Zhang, Z.//Zhang, X.//Wu, Y.//Wang, J.//Zhou, D.//An, X.//Pei, G.//Wang, Y.//Mi, Z.//Yin, Z.//Tong, Y. 	Complete Genome Sequence of Multidrug-Resistant Citrobacter freundii Strain P10159, Isolated from Urine Samples from a Patient with Esophageal Carcinoma.	Genome Announcements	2016	4		e01754-15			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%. 		
@D	Liu, X.//Min, Y.//Huang, D.//Zhou, R.//Fang, W.//Liu, C.//Rao, B.//Zhang, G.//Wang, K.//Yang, Z. 	Complete Genome Sequence of Bacillus vallismortis NBIF-001, a Novel Strain from Shangri-La, China, That Has High Activity against Fusarium oxysporum.	Genome Announcements	2017	5		e01305-17			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. 		
@D	Liu, X.//Zhou, R.//Fu, G.//Zhang, W.//Min, Y.//Tian, Y.//Huang, D.//Wang, K.//Wan, Z.//Yao, J.//Yang, Z. 	Draft Genome Sequence of Bacillus thuringiensis NBIN-866 with High Nematocidal Activity.	Genome Announcements	2014	2		e00429-14			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. 		
@D	Liu, X.-Q. 	Protein-splicing intein: Genetic mobility, origin, and evolution.	Annu. Rev. Genet.	2000	34		61-76			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. 		
@D	Liu, X.-Q.//Hu, Z. 	A DnaB intein in Rhodothermus marinus: Indication of recent intein homing across remotely related organisms.	Proc. Natl. Acad. Sci. U. S. A.	1997	94		7851-7856			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. 		
@D	Liu, X.F.//Cao, Y.//Zhang, H.L.//Chen, Y.J.//Hu, C.J. 	Complete Genome Sequence of Vibrio alginolyticus ATCC 17749T.	Genome Announcements	2015	3		e01500-14			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. 		
@D	Liu, X.Y.//Luo, X.J.//Li, C.X.//Lai, Q.L.//Xu, J.H. 	Draft Genome Sequence of Burkholderia sp. Strain MP-1, a Methyl Parathion (MP)-Degrading Bacterium from MP-Contaminated Soil.	Genome Announcements	2014	2		e00344-14			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. 		
@D	Liu, X.Y.//Min, Y.//Wang, K.M.//Wan, Z.Y.//Zhang, Z.G.//Cao, C.X.//Zhou, R.H.//Jiang, A.B.//Liu, C.J.//Zhang, G.Y.//Cheng, X.L.//Zhang, W.//Yang, Z.W. 	Draft genome sequence of Bacillus amyloliquefaciens HB-26.	Standards in Genomic Sciences	2014	9		775-782			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. 		
@D	Liu, Y.//Hu, A.//Shen, L.//Yao, T.//Jiao, N.//Wang, N.//Xu, B. 	Draft genome sequence of Dyadobacter tibetensis type strain (Y620-1) isolated from glacial ice.	Standards in Genomic Sciences	2014	9		883-892			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. 		
@D	Liu, Y.//Ichige, A.//Kobayashi, I. 	Regulation of the EcoRI restriction-modification system: Identification of ecoRIM gene promoters and their upstream negative regulators in the ecoRIR gene.	Gene	2007	400		140-149			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. 		
@D	Liu, Y.//Lu, S.E.//Baird, S.M.//Qiao, J.//Du, Y. 	Draft Genome Sequence of Pseudomonas chlororaphis YL-1, a Biocontrol Strain Suppressing Plant Microbial Pathogens.	Genome Announcements	2014	2		e01225-13			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%. 		
@D	Liu, Y.//Oakeley, E.J.//Sun, L.//Jost, J.-P. 	Multiple domains are involved in the targeting of the mouse DNA methyltransferase to the DNA replication foci.	Nucleic Acids Res.	1998	26		1038-1045			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. 		
@D	Liu, Y.//Santi, D.V. 	m5C RNA and m5C DNA methyl transferases use different cysteine residues as catalysts.	Proc. Natl. Acad. Sci. U. S. A.	2000	97		8263-8265			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. 		
@D	Liu, Y.//Shen, W.//Shi, G.//Wang, Z. 	Cloning, expression and nucleotide sequence analysis of gene encoding for BamHI methyltransferase from Bacillus amyloliquefaciens CICIM B2125.	Shengwu Jishu Tongbao	2009	11		65-68			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. 		
@D	Liu, Y.//Sun, L.//Jost, J.-P. 	In differentiating mouse myoblasts DNA methyltransferase is posttranscriptionally and posttranslationally regulated.	Nucleic Acids Res.	1996	24		2718-2722			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. 		
@D	Liu, Y.//Sun, L.//Jost, J.-P. 	In differentiating mouse myoblasts DNA methyltransferase is posttranscriptionally and posttranslationally regulated.	Mol. Biol. Cell	1996	7		8a			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. 		
@D	Liu, Y.//Wang, Y.//Schwarz, S.//Wang, S.//Chen, L.//Wu, C.//Shen, J. 	Investigation of a multiresistance gene cfr that fails to mediate resistance to phenicols and oxazolidinones in Enterococcus faecalis.	J. Antimicrob. Chemother.	2014	69		892-898			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. 		
@D	Liu, Y.//Yao, S.//Liu, Y.//Xu, Y.//Cheng, C. 	Genome Sequence of Luteimonas huabeiensis HB-2, a Novel Species of Luteimonas with High Oil Displacement Efficiency.	Genome Announcements	2014	2		e00152-14			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. 		
@D	Liu, Y.//Ye, W.//Zheng, J.//Fang, L.//Peng, D.//Ruan, L.//Sun, M. 	High-quality draft genome sequence of nematocidal Bacillus thuringiensis Sbt003.	Standards in Genomic Sciences	2014	9		624-631			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. 		
@D	Liu, Y.//Yi, Z.//Zeng, R. 	Draft Genome Sequence of a Symbiotic Bacterium, Rhizobium vignae CCBAU 05176T.	Genome Announcements	2014	2		e00657-14			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. 		
@D	Liu, Y.//Zeng, R.//Weng, B.//Luo, T.//Luo, Q.//Xu, L. 	Draft Genome Sequence of Streptococcus sp. X13SY08, Isolated from Murray Cod (Maccullochella peelii peelii).	Genome Announcements	2016	4		e01470-15			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. 		
@D	Liu, Y.//Zheng, H.//Zhan, G.H.//Qin, W.//Tian, L.//Li, W.L. 	Establishment of an efficient transformation protocol and its application in marine-derived Bacillus strain.	Sci. China C Life Sci.	2014	57		627-635			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. 		
@D	Liu, Y.C.//Wang, S.C.//Yu, Y.J.//Fung, K.M.//Yang, M.T.//Tseng, Y.H.//Tsai, S.F.//Sun, H.S.//Lyu, P.C.//Chou, S.H. 	Complete Genome Sequence of Xanthomonas campestris pv. campestris Strain 17 from  Taiwan.	Genome Announcements	2015	3		e01466-15			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. 		
@D	Liu, Y.P.//Kobayashi, I. 	Negative regulation of the EcoRI restriction enzyme gene is associated with intragenic reverse promoters.	J. Bacteriol.	2007	189		6928-6935			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. 		
@D	Liu, Y.P.//Tang, Q.//Zhang, J.Z.//Tian, L.F.//Gao, P.//Yan, X.X. 	Structural basis underlying complex assembly and conformational transition of the type I R-M system.	Proc. Natl. Acad. Sci. U. S. A.	2017	114		11151-11156			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. 		
@D	Liu, Z.//Muller, J.//Li, T.//Alvey, R.M.//Vogl, K.//Frigaard, N.U.//Rockwell, N.C.//Boyd, E.S.//Tomsho, L.P.//Schuster, S.C.//Henke, P.//Rohde, M.//Overmann, J.//Bryant, D.A. 	Genomic analysis reveals key aspects of prokaryotic symbiosis in the phototrophic consortium 'Chlorochromatium aggregatum'.	Genome Biol.	2013	14		R127			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. 		
@D	Liutkeviciute, Z.//Kriukiene, E.//Grigaityte, I.//Masevicius, V.//Klimasauskas, S. 	Methyltransferase-Directed Derivatization of 5-Hydroxymethylcytosine in DNA.	Angew. Chem. Int. Ed. Engl.	2011	50		2090-2093			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. 		
@D	Liutkeviciute, Z.//Kriukiene, E.//Grigaityte, I.//Vainorius, G.//Masevicius, V.//Klimasauskas, S. 	Catalytic versatility of DNA cytosine-5 methyltransferases: reactions involving non-cofactor-like substrates.	FEBS J.	2012	279		540			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. 		
@D	Liutkeviciute, Z.//Lukinavicius, G.//Masevicius, V.//Daujotyte, D.//Klimasauskas, S. 	Cytosine-5-methyltransferases add aldehydes to DNA.	Nat. Chem. Biol.	2009	5		400-402			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. 		
@D	Llado, S.//Xu, Z.//Sorensen, S.J.//Baldrian, P. 	Draft Genome Sequence of Burkholderia sordidicola S170, a Potential Plant Growth  Promoter Isolated from Coniferous Forest Soil in the Czech Republic.	Genome Announcements	2014	2		e00810-14			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. 		
@D	Lloyd, K.G.//Schreiber, L.//Petersen, D.G.//Kjeldsen, K.U.//Lever, M.A.//Steen, A.D.//Stepanauskas, R.//Richter, M.//Kleindienst, S.//Lenk, S.//Schramm, A.//Jorgensen, B.B. 	Predominant archaea in marine sediments degrade detrital proteins.	Nature	2013	496		215-218			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. 		
@D	Lloyd, R.S.//Cheng, X. 	Mechanistic link between DNA methyltransferases and DNA repair enzymes by base flipping.	Biopolymers	1997	44		139-151			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. 		
@D	Lluch-Senar, M.//Luong, K.//Llorens-Rico, V.//Delgado, J.//Fang, G.//Spittle, K.//Clark, T.A.//Schadt, E.//Turner, S.W.//Korlach, J.//Serrano, L. 	Comprehensive Methylome Characterization of Mycoplasma genitalium and Mycoplasma  pneumoniae at Single-Base Resolution.	PLoS Genet.	2013	9		e1003191			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. 		
@D	Lo, A.S.//Merrell, D.S.//Lei, H.//Sardi, A.//McAvoy, T.//Testerman, T.L. 	A Novel Member of Chitinophagaceae Isolated from a Human Peritoneal Tumor.	Genome Announcements	2015	3		e01297-15			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. 		
@D	Lo, C.I.//Mishra, A.K.//Padhmanabhan, R.//Samb, B.//Sow, A.G.//Robert, C.//Couderc, C.//Faye, N.//Raoult, D.//Fournier, P.E.//Fenollar, F. 	Non-contiguous finished genome sequence and description of Clostridium dakarense  sp. nov.	Standards in Genomic Sciences	2013	9		14-27			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. 		
@D	Lo, C.I.//Padhmanabhan, R.//Mediannikov, O.//Nguyen, T.T.//Raoult, D.//Fournier, P.E.//Fenollar, F. 	Genome sequence and description of Pantoea septica strain FF5.	Standards in Genomic Sciences	2015	10		103			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. 		
@D	Lo, C.I.//Padhmanabhan, R.//Mediannikov, O.//Terras, J.//Robert, C.//Faye, N.//Raoult, D.//Fournier, P.E.//Fenollar, F. 	High-quality genome sequence and description of Bacillus dielmoensis strain FF4(T) sp. nov.	Standards in Genomic Sciences	2015	10		41			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. 		
@D	Lo, C.I.//Sankar, S.A.//Fall, B.//Sambe-Ba, B.//Diawara, S.//Gueye, M.W.//Mediannikov, O.//Blanc-Tailleur, C.//Wade, B.//Raoult, D.//Fournier, P.E.//Fenollar, F. 	High-quality draft genome sequence and description of Haemophilus massiliensis sp. nov.	Standards in Genomic Sciences	2016	11		31			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. 		
@D	Lo, I.//Denef, V.J.//Verberkmoes, N.C.//Shah, M.B.//Goltsman, D.//Dibartolo, G.//Tyson, G.W.//Allen, E.E.//Ram, R.J.//Detter, J.C.//Richardson, P.//Thelen, M.P.//Hettich, R.L.//Banfield, J.F. 	Strain-resolved community proteomics reveals recombining genomes of acidophilic bacteria.	Nature	2007	446		537-541			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. 		
@D	Lo, J.R.//Lang, J.M.//Darling, A.E.//Eisen, J.A.//Coil, D.A. 	Draft Genome Sequence of an Actinobacterium, Brachybacterium muris Strain UCD-AY4.	Genome Announcements	2013	1		e0008613			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. 		
@D	Lo, R.//Stanton-Cook, M.J.//Beatson, S.A.//Turner, M.S.//Bansal, N. 	Draft Genome Sequence of Pseudomonas fluorescens SRM1, an Isolate from Spoiled Raw Milk.	Genome Announcements	2015	3		e00138-15			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. 		
@D	Lo, W.-S.//Ku, C.//Chen, L.-L.//Chang, T.-H.//Kuo, C.-H. 	Comparison of metabolic capacities and inference of gene content evolution in mosquito-associated Spiroplasma diminutum and S. taiwanense.	Genome Biol. Evol.	2013	5		1512-1523			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. 		
@D	Lo, W.S.//Chen, H.//Chen, C.Y.//Kuo, C.H. 	Complete Genome Sequence of Vibrio vulnificus 93U204, a Bacterium Isolated from Diseased Tilapia in Taiwan.	Genome Announcements	2014	2		e01005-14			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. 		
@D	Lo, W.S.//Gasparich, G.E.//Kuo, C.H. 	Complete Genome Sequence of Spiroplasma turonicum Tab4cT, a Bacterium Isolated from Horse Flies (Haematopota sp.).	Genome Announcements	2016	4		e01010-16			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. 		
@D	Lo, W.S.//Haryono, M.//Gasparich, G.E.//Kuo, C.H. 	Complete Genome Sequence of Spiroplasma sp. TU-14.	Genome Announcements	2017	5		e01465-16			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. 		
@D	Lo, W.S.//Lai, Y.C.//Lien, Y.W.//Wang, T.H.//Kuo, C.H. 	Complete Genome Sequence of Spiroplasma litorale TN-1T (DSM 21781), a Bacterium Isolated from a Green-Eyed Horsefly (Tabanus nigrovittatus).	Genome Announcements	2015	3		e01116-15			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. 		
@D	Lo, W.S.//Liu, P.Y.//Kuo, C.H. 	Complete Genome Sequence of Spiroplasma cantharicola CC-1T (DSM 21588), a Bacterium Isolated from Soldier Beetle (Cantharis carolinus).	Genome Announcements	2015	3		e01253-15			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. 		
@D	Lobner-Olesen, A.//Boye, E.//Marinus, M.G. 	Expression of the Escherichia coli dam gene.	Mol. Microbiol.	1992	6		1841-1851			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. 		
@D	Lobner-Olesen, A.//Skovgaard, O.//Marinus, M.G. 	Dam methylation: coordinating cellular processes.	Curr. Opin. Microbiol.	2005	8		154-160			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. 		
@D	Lobner-Olesen, A.//von Freiesleben, U. 	Chromosomal replication incompatibility in Dam methyltransferase deficient Escherichia coli cells.	EMBO J.	1996	15		5999-6008			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. 		
@D	Lobocka, M.B.//Rose, D.J.//Rusin, M.//Plunkett, G. III//Samojedny, A.//Lehnherr, H.//Yarmolinsky, M.B.//Blattner, F.R. 	Genome of bacteriophage P1.	J. Bacteriol.	2004	186		7032-7068			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. 		
@D	Lobos, C.//Vasquez, C. 	Purification and characterisation of BstLVI restriction endonuclease, a thermostable isoschizomer of ClaI from Bacillus stearothermophilus LV.	Biochim. Biophys. Acta	1993	1171		295-298			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. 		
@D	Lodwick, D.//Ross, H.N.M.//Harris, J.E.//Almond, J.W.//Grant, W.D. 	dam Methylation in the archaebacteria.	J. Gen. Microbiol.	1986	132		3055-3059			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. 		
@D	Loeffler, J.M.//Fischetti, V.A. 	Lysogeny of Streptococcus pneumoniae with MM1 Phage: Improved Adherence and Other Phenotypic Changes.	Infect. Immun.	2006	74		4486-4495			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. 		
@D	Loenen, W.//Murray, N. 	Modification Enhancement by Restriction Alleviation Protein (Ral) of Bacteriophage lambda.	J. Mol. Biol.	1986	190		11-22			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. 		
@D	Loenen, W.A.//Dryden, D.T.//Raleigh, E.A.//Wilson, G.G. 	Type I restriction enzymes and their relatives.	Nucleic Acids Res.	2014	42		20-44			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. 		
@D	Loenen, W.A.//Dryden, D.T.//Raleigh, E.A.//Wilson, G.G.//Murray, N.E. 	Highlights of the DNA cutters: a short history of the restriction enzymes.	Nucleic Acids Res.	2014	42		3-19			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. 		
@D	Loenen, W.A.//Raleigh, E.A. 	The other face of restriction: modification-dependent enzymes.	Nucleic Acids Res.	2014	42		56-69			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. 		
@D	Loenen, W.A.M. 	Tracking EcoKI and DNA fifty years on: a golden story full of surprises.	Nucleic Acids Res.	2003	31		7059-7069			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. 		
@D	Loenen, W.A.M.//Daniel, A.S.//Braymer, H.D.//Murray, N.E. 	Organization and sequence of the hsd genes of Escherichia coli K12.	J. Mol. Biol.	1987	198		159-170			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. 		
@D	Loessner, M.J.//Wendlinger, G.//Scherer, S. 	Heterogeneous endolysins in Listeria monocytogenes bacteriophages: a new class of enzymes and evidence for conserved holin genes within the siphoviral lysis cassettes.	Mol. Microbiol.	1995	16		1231-1241			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. 		
@D	Loewen, P.C.//Alsaadi, Y.//Fernando, D.//Kumar, A. 	Genome Sequence of a Tigecycline-Resistant Clinical Isolate of Acinetobacter baumannii Strain AB031 Obtained from a Bloodstream Infection.	Genome Announcements	2014	2		e01036-14			We report here the 3.8-Mbp genome sequence of a blood isolate of Acinetobacter baumannii strain AB031. 		
@D	Loewen, P.C.//Alsaadi, Y.//Fernando, D.//Kumar, A. 	Genome Sequence of an Extremely Drug-Resistant Clinical Isolate of Acinetobacter  baumannii Strain AB030.	Genome Announcements	2014	2		e01035-14			We report the 4.3-Mbp genome sequence of a blood isolate of Acinetobacter baumannii strain AB030. 		
@D	Loewen, P.C.//Switala, J.//Fernando, W.G.//de Kievit, T. 	Genome Sequence of Pseudomonas brassicacearum DF41.	Genome Announcements	2014	2		e00390-14			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. 		
@D	Loewen, P.C.//Villenueva, J.//Fernando, W.G.//de Kievit, T. 	Genome Sequence of Pseudomonas chlororaphis Strain PA23.	Genome Announcements	2014	2		e00689-14			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. 		
@D	Loftie-Eaton, W.//Suzuki, H.//Bashford, K.//Heuer, H.//Stragier, P.//De Vos, P.//Settles, M.L.//Top, E.M. 	Draft Genome Sequence of Pseudomonas sp. nov. H2.	Genome Announcements	2015	3		e00241-15			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. 		
@D	Loftus, B. et al. 	The genome of the protist parasite Entamoeba histolytica.	Nature	2005	433		865-868			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. 		
@D	Loizos, N.//Silva, G.H.//Belfort, M. 	Intron-encoded endonuclease I-TevII binds across the minor groove and induces two distinct conformational changes in its DNA substrate.	J. Mol. Biol.	1996	255		412-424			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. 		
@D	Loizos, N.//Tillier, E.R.M.//Belfort, M. 	Evolution of mobile group I introns: recognition of intron sequences by an intron-encoded endonuclease.	Proc. Natl. Acad. Sci. U. S. A.	1994	91		11983-11987			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. 		
@D	Loman, N.J.//Snyder, L.A.//Linton, J.D.//Langdon, R.//Lawson, A.J.//Weinstock, G.M.//Wren, B.W.//Pallen, M.J. 	Genome sequence of the emerging pathogen Helicobacter canadensis.	J. Bacteriol.	2009	191		5566-5567			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. 		
@D	Lomonaco, S.//Gallina, S.//Filipello, V.//Sanchez, L.M.//Kastanis, G.J.//Allard, M.//Brown, E.//Amato, E.//Pontello, M.//Decastelli, L. 	Draft Genome Sequences of 510 Listeria monocytogenes Strains from Food Isolates and Human Listeriosis Cases from Northern Italy.	Genome Announcements	2018	6		e01276-17			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. 		
@D	Lomovskaya, N.D.//Chater, K.F.//Mkrtumian, N.M. 	Genetics and Molecular Biology of Streptomyces Bacteriophages.	Microbiol. Rev.	1980	44		206-229			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. 		
@D	Long, M.//Ruan, L.//Yu, Z.//Xu, X. 	Genome sequence of Pseudomonas sp. S9, an extracellular arylsulfatase producing bacterium isolated from the mangrove soil.	J. Bacteriol.	2011	193		4041			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. 		
@D	Long, S.W.//Kachroo, P.//Musser, J.M.//Olsen, R.J. 	Whole-Genome Sequencing of a Human Clinical Isolate of emm28 Streptococcus pyogenes Causing Necrotizing Fasciitis Acquired Contemporaneously with Hurricane   Harvey.	Genome Announcements	2017	5		e01269-17			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. 		
@D	Long, S.W.//Linson, S.E.//Ojeda, S.M.//Cantu, C.//Davis, J.J.//Brettin, T.//Olsen, R.J. 	Whole-Genome Sequencing of a Human Clinical Isolate of the Novel Species Klebsiella quasivariicola sp. nov.	Genome Announcements	2017	5		e01057-17			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. 		
@D	Long, S.W.//Olsen, R.J.//Eagar, T.N.//Beres, S.B.//Zhao, P.//Davis, J.J.//Brettin, T.//Xia, F.//Musser, J.M. 	Population Genomic Analysis of 1,777 Extended-Spectrum Beta-Lactamase-Producing Klebsiella pneumoniae Isolates, Houston, Texas: Unexpected Abundance of Clonal Group 307.	MBio	2017	8		e00489-17			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. 		
@D	Longley, M.J.//Mosbaugh, D.W. 	Characterization of DNA metabolizing enzymes in situ following polyacrylamide gel electrophoresis.	Biochemistry	1991	30		2655-2664			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. 		
@D	Longo, M.//De Jode, M.//Plainvert, C.//Weckel, A.//Hua, A.//Chateau, A.//Glaser, P.//Poyart, C.//Fouet, A. 	Complete Genome Sequence of Streptococcus pyogenes emm28 Clinical Isolate M28PF1, Responsible for a Puerperal Fever.	Genome Announcements	2015	3		e00750-15			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. 		
@D	Looft, T.//Bayles, D.O.//Alt, D.P.//Stanton, T.B. 	Complete Genome Sequence of Coriobacteriaceae Strain 68-1-3, a Novel Mucus-Degrading Isolate from the Swine Intestinal Tract.	Genome Announcements	2015	3		e01143-15			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. 		
@D	Looney, M.C.//Moran, L.S.//Jack, W.E.//Feehery, G.R.//Benner, J.S.//Slatko, B.E.//Wilson, G.G. 	Nucleotide sequence of the FokI restriction-modification system:  separate strand-specificity domains in the methyltransferase.	Gene	1989	80		193-208			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. 		
@D	Lopatina, N.//Haskell, J.F.//Andrews, L.G.//Poole, J.C.//Saldanha, S.//Tollefsbol, T. 	Differential maintenance and de novo methylating activity by three DNA methyltransferases in aging and immortalized fibroblasts.	J. Cell. Biochem.	2002	84		324-334			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. 		
@D	Lopatina, N.G.//Kirnos, M.D.//Suchkov, S.V.//Vanyushin, B.F.//Nikolskaya, I.I.//Debov, S.S. 	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.	Biokhimiia	1985	50		495-502			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. 		
@D	Lopatina, N.G.//Lopareva, E.N.//Posypanova, A.M.//Nikolskaya, A.//Debov, S.S. 	Cytosine DNA-methylase SsoII from Shigella sonnei 47 cells.	Biokhimiia	1988	53		1265-1269			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. 		
@D	Lopatina, N.G.//Nikolskaya, I.I.//Buryanov, Y.I.//Debov, S.S. 	Presence of 2 DNA-methylases of cytosine in Escherichia coli CK cells.	Dokl. Akad. Nauk.	1978	240		1475-1477					
@D	Lopatina, N.G.//Nikolskaya, I.I.//Sverdiov, E.D.//Debov, S.S. 	Determination of the recognition sites of adenine DNA-methylases from Escherichia coli CK.	Vopr. Med. Khim.	1981	27		220-223			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'. 		
@D	Lopatina, N.G.//Suchkov, S.V.//Kulikov, S.M.//Nikolskaya, I.I.//Debov, S.S. 	Site-specificity of DNA methylases from Shigella sonnei 47 cells.	Biokhimiia	1985	50		1694-1701			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. 		
@D	Loper, J.E. et al. 	Comparative Genomics of Plant-Associated Pseudomonas spp.: Insights into Diversity and Inheritance of Traits Involved in Multitrophic Interactions.	PLoS Genet.	2012	8		E1002784			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. 		
@D	Lopes, E.F.//Da Costa, J.G.//Wolf, I.R.//Lima, J.P.A.//Astolfi-Filho, S. 	Draft Genome Sequence of Burkholderia gladioli Coa14, a Bacterium with Petroleum  Bioremediation Potential Isolated from Coari Lake, Amazonas, Brazil.	Genome Announcements	2018	6		e00301-18			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. 		
@D	Lopes, E.M.//Kishi, L.T.//Fernandes, C.C.//Paganelli, F.L.//Alves, L.M.//Lemos, E.G.//de Souza, J.A. 	Draft Genome Sequence of Bradyrhizobium elkanii TnphoA 33, a Producer of Polyhydroxyalkanoates.	Genome Announcements	2017	5		e01502-16			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. 		
@D	Lopes, T. et al. 	Complete Genome Sequence of Corynebacterium pseudotuberculosis Strain Cp267, Isolated from a Llama.	J. Bacteriol.	2012	194		3567-3568			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. 		
@D	Lopes-Santos, L.//Castro, D.B.//Ottoboni, L.M.//Park, D.//Weir, B.S.//Destefano, S.A. 	Draft Genome Sequence of Burkholderia andropogonis Type Strain ICMP2807, Isolated from Sorghum bicolor.	Genome Announcements	2015	3		e00455-15			Here, we report the draft genome sequence of Burkholderia andropogonis ICMP2807,  a phytopathogenic bacterium isolated from Sorghum bicolor plants in the United States. 		
@D	Lopez, G.//Diaz-Cardenas, C.//Shapiro, N.//Woyke, T.//Kyrpides, N.C.//David, A.J.//Gonzalez, L.N.//Restrepo, S.//Baena, S. 	Draft genome sequence of Pseudomonas extremaustralis strain USBA-GBX 515 isolated from Superparamo soil samples in Colombian Andes.	Standards in Genomic Sciences	2017	12		78			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. 		
@D	Lopez, L.L.//Rusconi, B.//Gildersleeve, H.//Qi, C.//McLaughlin, M.//Scheetz, M.H.//Seshu, J.//Eppinger, M. 	Genome Sequences of Five Clinical Isolates of Klebsiella pneumoniae.	Genome Announcements	2016	4		e00040-16			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. 		
@D	Lopez, M.//Alvarez-Fraga, L.//Gato, E.//Blasco, L.//Poza, M.//Fernandez-Garcia, L.//Bou, G.//Tomas, M. 	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.	Genome Announcements	2016	4		e00962-16			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. 		
@D	Lopez, M.//Rueda, A.//Florido, J.P.//Blasco, L.//Gato, E.//Fernandez-Garcia, L.//Martinez-Martinez, L.//Fernandez-Cuenca, F.//Pachon, J.//Cisneros, J.M.//Garnacho-Montero, J.//Vila, J.//Rodriguez-Bano, J.//Pascual, A.//Bou, G.//Tomas, M. 	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).	Genome Announcements	2016	4		e01182-16			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. 		
@D	Lopez, O.J.//Quintanar, A.//Padhye, N.V.//Nelson, M. 	Genotyping of DNA using sequence-specific methyltransferases followed by immunochemical detection.	J. Immunoassay Immunochem.	2003	24		11-28			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. 		
@D	Lopez-Alonso, V.//Ortiz, S.//Martinez-Suarez, J.V. 	Genome Sequences of Five Disinfectant-Resistant Listeria monocytogenes Strains from Two Iberian Pork-Processing Plants.	Genome Announcements	2015	3		e00077-15			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. 		
@D	Lopez-Garrido, J.//Casadesus, J. 	Regulation of Salmonella enterica Pathogenicity Island 1 by DNA Adenine Methylation.	Genetics	2010	184		637-649			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. 		
@D	Lopez-Hermoso, C.//de la Haba, R.R.//Sanchez-Porro, C.//Bayliss, S.C.//Feil, E.J.//Ventosa, A. 	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.	Genome Announcements	2017	5		e00244-17			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). 		
@D	Lopez-Lopez, A.//Richter, M.//Pena, A.//Tamames, J.//Rossello-Mora, R. 	New insights into the archaeal diversity of a hypersaline microbial mat obtained by a metagenomic approach.	Syst. Appl. Microbiol.	2013	36		205-214			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. 		
@D	Lopez-Perez, M.//Gonzaga, A.//Rodriguez-Valera, F. 	Genomic Diversity of 'Deep Ecotype' Alteromonas macleodii Isolates: Evidence for Pan-Mediterranean Clonal Frames.	Genome Biol. Evol.	2013	5		1220-1232			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. 		
@D	Lopez-Perez, M.//Rodriguez-Valera, F.//Webb, H.K.//Crawford, R.J.//Ivanova, E.P. 	Genome Sequence of 'Thalassospira australica' NP3b2T Isolated from St. Kilda Beach, Tasman Sea.	Genome Announcements	2014	2		e01139-14			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. 		
@D	Lorenz, S.C.//Kotewicz, M.L.//Hoffmann, M.//Gonzalez-Escalona, N.//Fischer, M.//Kase, J.A. 	Complete Genome Sequences of Four Enterohemolysin-Positive (ehxA) Enterocyte Effacement-Negative Shiga Toxin-Producing Escherichia coli Strains.	Genome Announcements	2016	4		e00846-16			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. 		
@D	Lorenzi, A.S.//Silva, G.G.//Lopes, F.A.//Chia, M.A.//Edwards, R.A.//Bittencourt-Oliveira, M.C. 	Draft Genome Sequence of Cylindrospermopsis raciborskii (Cyanobacteria) Strain ITEP-A1 Isolated from a Brazilian Semiarid Freshwater Body: Evidence of Saxitoxin  and Cylindrospermopsin Synthetase Genes.	Genome Announcements	2016	4		e00228-16			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). 		
@D	Lorincz, M.C.//Groudine, M. 	CmC(a/t)GG methylation: a new epigenetic mark in mammalian DNA?	Proc. Natl. Acad. Sci. U. S. A.	2001	98		10034-10036			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. 		
@D	Lorincz, M.C.//Schubeler, D.//Hutchinson, S.R.//Dickerson, D.R.//Groudine, M. 	DNA methylation density influences the stability of an epigenetic imprint and Dnmt3a/b-independent de novo methylation.	Mol. Cell. Biol.	2002	22		7572-7580			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. 		
@D	Loscar, M.E.//Huptas, C.//Wenning, M.//Sieber, V.//Schmid, J. 	Draft Genome Sequence of Lysinibacillus xylanilyticus SR-86.	Genome Announcements	2016	4		e01317-16			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. 		
@D	Lou, S.//Wu, L. 	Isolation of thermostable restriction endonuclease from thermophilic Synechococcus elongatus T3.	J. Xiamen Univ.	1997	36		272-275			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. 		
@D	Loucif, L.//Michelle, C.//Terras, J.//Rolain, J.M.//Raoult, D.//Fournier, P.E. 	Draft Genome Sequence of Streptomyces specialis Type Strain GW41-1564 (DSM 41924).	Genome Announcements	2017	5		e00101-17			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. 		
@D	Louie, T.S.//Giovannelli, D.//Yee, N.//Narasingarao, P.//Starovoytov, V.//Goker, M.//Klenk, H.P.//Lang, E.//Kyrpides, N.C.//Woyke, T.//Bini, E.//Haggblom, M.M. 	High-quality draft genome sequence of Sedimenticola selenatireducens strain AK4OH1T, a gammaproteobacterium isolated from estuarine sediment.	Standards in Genomic Sciences	2016	11		66			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. 		
@D	Loureiro, D.//Portela, R.W.//Sousa, T.J.//Rocha, F.//Pereira, F.L.//Dorella, F.A.//Carvalho, A.F.//Menezes, N.//Macedo, E.S.//Moura-Costa, L.F.//Meyer, R.//Leal, C.A.//Figueiredo, H.C.//Azevedo, V. 	Complete Genome Sequence of Corynebacterium pseudotuberculosis Viscerotropic Strain N1.	Genome Announcements	2016	4		e01673-15			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. 		
@D	Loux, V.//Coeuret, G.//Zagorec, M.//Champomier, V.M.C.//Chaillou, S. 	Complete and Draft Genome Sequences of Nine Lactobacillus sakei Strains Selected  from the Three Known Phylogenetic Lineages and Their Main Clonal Complexes.	Genome Announcements	2018	6		e00082-18			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. 		
@D	Loux, V.//Mariadassou, M.//Almeida, S.//Chiapello, H.//Hammani, A.//Buratti, J.//Gendrault, A.//Barbe, V.//Aury, J.M.//Deutsch, S.M.//Parayre, S.//Madec, M.N.//Chuat, V.//Jan, G.//Peterlongo, P.//Azevedo, V.//Le Loir, Y.//Falentin, H. 	Mutations and genomic islands can explain the strain dependency of sugar utilization in 21 strains of Propionibacterium freudenreichii.	BMC Genomics	2015	16		296			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. 		
@D	Lovett, S.//Chase, K.//Koroleva, G.//Palacios, G.//Rozak, D.//Ladner, J.T. 	Complete Genome Sequence of Pigmentation-Negative Yersinia pestis Strain Cadman.	Genome Announcements	2016	4		e01207-16			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. 		
@D	Low, D.A.//Casadesus, J. 	Clocks and switches: bacterial gene regulation by DNA adenine methylation.	Curr. Opin. Microbiol.	2008	11		106-112			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. 		
@D	Low, D.A.//Weyand, N.J.//Mahan, M.J. 	Roles of DNA adenine methylation in regulating bacterial gene expression and virulence.	Infect. Immun.	2001	69		7197-7204			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. 		
@D	Loy, J.D.//Dickey, A.M.//Clawson, M.L. 	Complete Genome Sequence of Moraxella bovis Strain Epp-63 (300), an Etiologic Agent of Infectious Bovine Keratoconjunctivitis.	Microbiol. Resour. Announc.	2018	7		e01004-18			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. 		
@D	Loyola, C.//Saavedra, C.//Gomez, I.//Vasquez, C. 	The amino acidic substitution of cysteine 167 by serine (C167S) in BstVI restriction endonuclease of Bacillus stearothermophilus V affects its conformation and thermostability.	Biochimie	1999	81		261-266			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. 		
@D	Lozano, G.L.//Bravo, J.I.//Handelsman, J. 	Draft Genome Sequence of Pseudomonas koreensis CI12, a Bacillus cereus 'Hitchhiker' from the Soybean Rhizosphere.	Genome Announcements	2017	5		e00570-17			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. 		
@D	Lozano, G.L.//Holt, J.//Ravel, J.//Rasko, D.A.//Thomas, M.G.//Handelsman, J. 	Draft Genome Sequence of Biocontrol Agent Bacillus cereus UW85.	Genome Announcements	2016	4		e00910-16			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. 		
@D	Lu, A.-L.//Jack, W.E.//Modrich, P. 	DNA determinants important in sequence recognition by EcoRI endonuclease.	J. Biol. Chem.	1981	256		13200-13206			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. 		
@D	Lu, A.L.//Cheng, S.C.//Jack, W.E.//Modrich, P. 	DNA contacts and mechanism of specific site location of EcoRI endonuclease, and effects of modification methylation on DNA helix conformation.	Fed. Proc.	1982	41		1199			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. 		
@D	Lu, C.//Marjanovic, O.//Morales, C.//Kiang, D. 	Genome Sequences of Two Listeria monocytogenes Strains from Nectarines Associated with Listeriosis in 2014.	Genome Announcements	2017	5		e00389-17			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. 		
@D	Lu, H.//Graham, D.//Xiao, S.D.//Gutierrez, O.//Yamaoka, Y. 	Relationship between Helicobacter pylori restriction endonuclease-replacing gene, Hrga and clinical outcome.	Gastroenterology	2003	124		A270			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. 		
@D	Lu, J.J.//Wang, J.F.//Hu, X.F. 	Genome Sequence of Growth-Improving Paenibacillus mucilaginosus Strain KNP414.	Genome Announcements	2013	1		e00881-13			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. 		
@D	Lu, L.//Patel, H.//Bissler, J.J. 	Optimizing DpnI digestion conditions to detect replicated DNA.	Biotechniques	2002	33		316-318			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. 		
@D	Lu, L.//Zhou, S.Y.//Chen, C.//Weng, S.P.//Chan, S.M.//He, J.G. 	Complete genome sequence analysis of an iridovirus isolated from the orange-spotted grouper, Epinephelus coioides.	Virology	2005	339		81-100			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. 		
@D	Lu, M.G.//Jiang, J.//Liu, L.//Ma, A.P.//Leung, F.C. 	Complete Genome Sequence of Klebsiella variicola Strain HKUOPLA, a Cellulose-Degrading Bacterium Isolated from Giant Panda Feces.	Genome Announcements	2015	3		e01200-15			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. 		
@D	Lu, M.G.//Jiang, J.//Liu, L.//Ma, A.P.//Leung, F.C. 	Complete Genome Sequence of Klebsiella pneumoniae Strain HKUOPLC, a Cellulose-Degrading Bacterium Isolated from Giant Panda Feces.	Genome Announcements	2015	3		e01318-15			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. 		
@D	Lu, P.//Lei, M.//Xiao, F.//Zhang, L.//Wang, Y. 	Complete Genome Sequence of Terribacillus aidingensis Strain MP602, a Moderately  Halophilic Bacterium Isolated from Cryptomeria fortunei in Tianmu Mountain in  China.	Genome Announcements	2015	3		e00126-15			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. 		
@D	Lu, S.//Le, S.//Li, G.//Shen, M.//Tan, Y.//Zhao, X.//Wang, J.//Shen, W.//Guo, K.//Yang, Y.//Zhu, H.//Li, S.//Li, M.//Zhu, J.//Rao, X.//Hu, F. 	Complete Genome Sequence of Pseudomonas aeruginosa PA1, Isolated from a Patient with a Respiratory Tract Infection.	Genome Announcements	2015	3		e01453-15			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. 		
@D	Lu, S.//Zhang, X.//Zhu, Y.//Kim, K.S.//Yang, J.//Jin, Q. 	Complete Genome Sequence of the Neonatal-Meningitis-Associated Escherichia coli Strain CE10.	J. Bacteriol.	2011	193		7005			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. 		
@D	Lu, W.//Wise, M.J.//Tay, C.Y.//Windsor, H.M.//Marshall, B.J.//Peacock, C.//Perkins, T. 	Comparative analysis of the full genome of the Helicobacter pylori isolate, Sahul64, identifies genes of high divergence.	J. Bacteriol.	2013	196		1073-1083			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. 		
@D	Lu, W.D.//Pang, H.Q.//Guo, L.Z. 	Genome Sequence of the Fructan-Degrading Organism Marinimicrobium sp. Strain LS-A18, Isolated from a Marine Solar Saltern.	Genome Announcements	2013	1		e00776-13			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. 		
@D	Lu, Y.//Samac, D.A.//Glazebrook, J.//Ishimaru, C.A. 	Complete Genome Sequence of Clavibacter michiganensis subsp. insidiosus R1-1 Using PacBio Single-Molecule Real-Time Technology.	Genome Announcements	2015	3		e00396-15			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. 		
@D	Lu, Z.//Li, Y.//Que, Q.//Kutish, G.F.//Rock, D.L.//Van Etten, J.L. 	Analysis of 94 kb of the chlorella virus PBCV-1 330-kb genome: Map positions 88 to 182.	Virology	1996	216		102-123			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. 		
@D	Lu, Z.//Lu, Y. 	Complete Genome Sequence of a Thermophilic Methanogen, Methanocella conradii HZ254, Isolated from Chinese Rice Field Soil.	J. Bacteriol.	2012	194		2398-2399			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. 		
@D	Luan, X.//Cui, Z.//Gao, W.//Li, Q.//Yin, X.//Zheng, L. 	Genome Sequence of the Petroleum Hydrocarbon-Degrading Bacterium Alcanivorax sp.  Strain 97CO-5.	Genome Announcements	2014	2		e01277-14			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. 		
@D	Lubys, A.//Janulaitis, A. 	Cloning and analysis of the plasmid-borne genes encoding the Bsp6I restriction and modification enzymes.	Gene	1995	157		25-29			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. 		
@D	Lubys, A.//Jurenaite, S.//Janulaitis, A. 	Structural organization and regulation of the plasmid-borne type II restriction-modification system Kpn21 from Klebsiella pneumoniae RFL2.	Nucleic Acids Res.	1999	27		4228-4234			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. 		
@D	Lubys, A.//Lubiene, J. 	Cloning of the genes encoding type IIS restriction-modification system HphI from Haemophilus parahaemolyticus.	Biologija	1996	0		39-41			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. 		
@D	Lubys, A.//Lubiene, J.//Kulakauskas, S.//Stankevicius, K.//Timinskas, A.//Janulaitis, A. 	Cloning and analysis of the genes encoding the type IIS restriction-modification system HphI from Haemophilus parahaemolyticus.	Nucleic Acids Res.	1996	24		2760-2766			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. 		
@D	Lubys, A.//Menkevicius, S.//Timinskas, A.//Butkus, V.//Janulaitis, A. 	Cloning and analysis of translational control for genes encoding the Cfr9I restriction-modification system.	Gene	1994	141		85-89			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. 		
@D	Lucas, P.//Jouy, E.//Le Devendec, L.//de Boisseson, C.//Perrin-Guyomard, A.//Jove, T.//Blanchard, Y.//Touzain, F.//Kempf, I. 	Characterization of plasmids harboring blaCTX-M genes in Escherichia coli from French pigs.	Vet. Microbiol.	2018	224		100-106			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. 		
@D	Lucas, P.//Otis, C.//Mercier, J.-P.//Turmel, M.//Lemieux, C. 	Rapid evolution of the DNA-binding site in LAGLIDADG homing endonucleases.	Nucleic Acids Res.	2001	29		960-969			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. 		
@D	Lucas, S. et al. 	Complete Genome Sequence of the Thermophilic, Piezophilic, Heterotrophic Bacterium Marinitoga piezophila KA3.	J. Bacteriol.	2012	194		5974-5975			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. 		
@D	Lucas-Elio, P.//Goodwin, L.//Woyke, T.//Pitluck, S.//Nolan, M.//Kyrpides, N.C.//Detter, J.C.//Copeland, A.//Lu, M.//Bruce, D.//Detter, C.//Tapia, R.//Han, S.//Land, M.L.//Ivanova, N.//Mikhailova, N.//Johnston, A.W.//Sanchez-Amat, A. 	Complete genome sequence of Marinomonas posidonica type strain (IVIA-Po-181(T)).	Standards in Genomic Sciences	2012	7		31-43			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. 		
@D	Lucas-Elio, P.//Goodwin, L.//Woyke, T.//Pitluck, S.//Nolan, M.//Kyrpides, N.C.//Detter, J.C.//Copeland, A.//Teshima, H.//Bruce, D.//Detter, C.//Tapia, R.//Han, S.//Land, M.L.//Ivanova, N.//Mikhailova, N.//Johnston, A.W.//Sanchez-Amat, A. 	Complete genome sequence of the melanogenic marine bacterium Marinomonas mediterranea type strain (MMB-1(T)).	Standards in Genomic Sciences	2012	6		63-73			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. 		
@D	Lucas-Elio, P.//Goodwin, L.//Woyke, T.//Pitluck, S.//Nolan, M.//Kyrpides, N.C.//Detter, J.C.//Copeland, A.//Teshima, H.//Bruce, D.//Detter, C.//Tapia, R.//Han, S.//Land, M.L.//Ivanova, N.//Mikhailova, N.//Johnston, A.W.B.//Sanchez-Amat, A. 	Complete genome sequence of the melanogenic marine bacterium Marinomonas mediterranea type strain (MMB-1T).	Standards in Genomic Sciences	2012	5		63-73					
@D	Lucchini, S.//Sidoti, J.//Brussow, H. 	Broad-range bacteriophage resistance in Streptococcus thermophilus by insertional mutagenesis.	Virology	2000	275		267-277			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. 		
@D	Lucid, A.//Bullman, S.//Koziel, M.//Corcoran, G.D.//Cotter, P.D.//Sleator, R.D.//Lucey, B. 	Draft Genome Sequence of Campylobacter ureolyticus Strain CIT007, the First Whole-Genome Sequence of a Clinical Isolate.	Genome Announcements	2014	2		e00262-14			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. 		
@D	Lucker, S.//Wagner, M.//Maixner, F.//Pelletier, E.//Koch, H.//Vacherie, B.//Rattei, T.//Damste, J.S.//Spieck, E.//Le Paslier, D.//Daims, H. 	A Nitrospira metagenome illuminates the physiology and evolution of globally important nitrite-oxidizing bacteria.	Proc. Natl. Acad. Sci. U. S. A.	2010	107		13479-13484			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. 		
@D	Luckwu-de-Lucena, B.T.//Silva, G.G.//Manoel-Dos-Santos, B.//Dias, G.M.//Amaral, G.R.//Moreira, A.P.//de Morais, J.M.A.//Dutilh, B.E.//Edwards, R.A.//Balbino, V.//Thompson, C.C.//Thompson, F.L. 	Genome Sequences of the Ethanol-Tolerant Lactobacillus vini Strains LMG 23202T and JP7.8.9.	J. Bacteriol.	2012	194		3018			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. 		
@D	Ludannyy, R.//Alvarez, F.M.//Levi, D.//Markelov, M.//Dedkov, V.//Aleksandrova, N.//Shipulin, G. 	Whole-Genome Sequence of Mycobacterium bovis BCG-1 (Russia).	Genome Announcements	2015	3		e01320-15			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. 		
@D	Ludeke, C.H.//Kong, N.//Weimer, B.C.//Fischer, M.//Jones, J.L. 	Complete Genome Sequences of a Clinical Isolate and an Environmental Isolate of Vibrio parahaemolyticus.	Genome Announcements	2015	3		e00216-15			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. 		
@D	Luedin, S.M.//Pothier, J.F.//Danza, F.//Storelli, N.//Frigaard, N.U.//Wittwer, M.//Tonolla, M. 	Complete genome sequence of 'Thiodictyon syntrophicum' sp. nov. strain Cad16(T),  a photolithoautotrophic purple sulfur bacterium isolated from the alpine meromictic Lake Cadagno.	Standards in Genomic Sciences	2018	13		14			'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. 		
@D	Lugli, G.A.//Duranti, S.//Milani, C.//Turroni, F.//Viappiani, A.//Mangifesta, M.//van Sinderen, D.//Ventura, M. 	The Genome Sequence of Bifidobacterium moukalabense DSM 27321 Highlights the Close Phylogenetic Relatedness with the Bifidobacterium dentium Taxon.	Genome Announcements	2014	2		e00048-14			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. 		
@D	Luhtanen, A.M.//Eronen-Rasimus, E.//Kaartokallio, H.//Rintala, J.M.//Autio, R.//Roine, E. 	Isolation and characterization of phage-host systems from the Baltic Sea ice.	Extremophiles	2014	18		121-130			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. 		
@D	Luhung, I. et al. 	Genome Sequence of Pantoea ananatis SGAir0210, Isolated from Outdoor Air in Singapore.	Genome Announcements	2018	6		e00643-18			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. 		
@D	Lui, A.C.P.//McBride, B.C.//Vovis, G.F.//Smith, M. 	Site specific endonuclease from Fusobacterium nucleatum.	Nucleic Acids Res.	1979	6		1-15			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. 		
@D	Lujan, A.M.//Feliziani, S.//Smania, A.M. 	Draft Genome Sequence of Pseudomonas aeruginosa Strain Hex1T Isolated from Soils  Contaminated with Used Lubricating Oil in Argentina.	Genome Announcements	2017	5		e01473-16			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. 		
@D	Lujan, K.M.//Eisen, J.A.//Coil, D.A. 	Draft Genome Sequence of Tenacibaculum soleae UCD-KL19.	Genome Announcements	2016	4		e01120-16			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. 		
@D	Lujan, K.M.//Eisen, J.A.//Coil, D.A. 	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.	Genome Announcements	2017	5		e00023-17			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. 		
@D	Lukacs, C.M.//Aggarwal, A.K. 	BglII and MunI: what a difference a base makes.	Curr. Opin. Struct. Biol.	2001	11		14-18			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. 		
@D	Lukacs, C.M.//Kucera, R.//Schildkraut, I.//Aggarwal, A.K. 	Understanding the immutability of restriction enzymes: crystal structure of BglII and its DNA substrate at 1.5A resolution.	Nat. Struct. Biol.	2000	7		134-140			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. 		
@D	Luke, P.A.//Halford, S.E. 	Fluorescent labelling of EcoRI and EcoRV.	Biochem. Soc. Trans.	1986	14		259-260			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. 		
@D	Luke, P.A.//Halford, S.E. 	Solubility of the EcoRI restriction endonuclease and its purification from an over-producing strain.	Gene	1985	37		241-246			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. 		
@A	Luke, P.A.//McCallum, S.A.//Halford, S.E. 		The EcoRV restriction endonuclease.			Chirikjian, J.G. 		Gene Amplif. Anal.					Elsevier North Holland	1987		5		185-207									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. 		
@D	Lukinavicius, G.//Klimasauskas, S.//Dalhoff, C.//Weinhold, E. 	Conversion of DNA methyltransferases to alkyltransferases via cofactor engineering.	FEBS Lett.	2006	273		336-337			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. 		
@D	Lukinavicius, G.//Lapiene, V.//Stasevskij, Z.//Dalhoff, C.//Weinhold, E.//Klimasauskas, S. 	Targeted labeling of DNA by methyltransferase-directed transfer of activated groups (mTAG).	J. Am. Chem. Soc.	2007	129		2758-2759			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. 		
@D	Lukinavicius, G.//Lapinaite, A.//Urbanaviciute, G.//Gerasimaite, R.//Klimasauskas, S. 	Engineering the DNA cytosine-5 methyltransferase reaction for sequence-specific labeling of DNA.	Nucleic Acids Res.	2012	40		11594-11602			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. 		
@D	Lukinavicius, G.//Tomkuviene, M.//Masevicius, V.//Klimasauskas, S. 	Enhanced Chemical Stability of AdoMet Analogues for Improved Methyltransferase-Directed Labeling of DNA.	ACS Chem. Biol.	2013	8		1134-1139			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. 		
@D	Lukyanchuk, V.//Reva, O.//Polishchuk, L. 	Restriction endonucleases of type II from two endophytic strains of Bacillus.	Biochem. Soc. Trans.	2000	28		A181			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. 		
@D	Lukyanchuk, V.V.//Polishchuk, L.V.//Strizhkova, G.M.//Kopieiko, O.P.//Matselyukh, B.P. 	Determination of site-specificity of the II type restriction endonuclease in Streptomyces sp. 48.	Mikrobiol. Zh.	1999	61		80-83			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. 		
@D	Lukyanchuk, V.V.//Reva, O.M.//Polishchuk, L.V. 	Type-II site-specific restriction endonucleases in endophytic strains of the genus Bacillus.	Mikrobiol. Zh.	1999	61		28-30			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. 		
@D	Lukyanchuk, V.V.//Reva, O.N.//Polishchuk, L.V. 	Endophytic bacilli producing type II restriction endonucleases.	Mikrobiologiia	2002	71		491-493			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. 		
@D	Lukyanchuk, V.V.//Strizhkova, G.M.//Polishchuk, L.V.//Kopeyko, O.P.//Matselyukh, B.P. 	Search for site-specific endonucleases of the II type restriction among Streptomycetes.	Mikrobiol. Zh.	1998	60		33-35			Three Streptomycetes strains producing endonucleases of restriction of II type have been found using the modified method of Belavin. 		
@D	Lukyanchuk, V.V.//Suchanoff, S.M.//Polishchuk, L.V.//Matselyukh, B.P. 	Isolation of site-specific endonuclease of Streptomyces sp. 48.	Biopol. Kletka	2000	16		559-561			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. 		
@D	Lulitanond, A.//Ito, T.//Li, S.//Han, X.//Ma, X.X.//Engchanil, C.//Chanawong, A.//Wilailuckana, C.//Jiwakanon, N.//Hiramatsu, K. 	ST9 MRSA strains carrying a variant of type IX SCCmec identified in the Thai community.	BMC Infect. Dis.	2013	13		214			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. 		
@D	Lumactud, R.//Fulthorpe, R.//Sentchilo, V.//van der Meer, J.R. 	Draft Genome Sequence of Microbacterium foliorum Strain 122 Isolated from a Plant Growing in a Chronically Hydrocarbon-Contaminated Site.	Genome Announcements	2017	5		e00434-17			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. 		
@D	Lumactud, R.//Fulthorpe, R.//Sentchilo, V.//van der Meer, J.R. 	Draft Genome Sequence of Plantibacterflavus Strain 251 Isolated from a Plant Growing in a Chronically Hydrocarbon-Contaminated Site.	Genome Announcements	2017	5		e00276-17			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. 		
@D	Luna-Flores, C.H.//Nielsen, L.K.//Marcellin, E. 	Genome Sequence of Propionibacterium acidipropionici ATCC 55737.	Genome Announcements	2016	4		e00248-16			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. 		
@D	Luna-Flores, C.H.//Palfreyman, R.W.//Kromer, J.O.//Nielsen, L.K.//Marcellin, E. 	Improved production of propionic acid using genome shuffling.	Biotechnol. J.	2017	12		0			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. 		
@D	Lund, L.C.//Sydenham, T.V.//Hogh, S.V.//Skov, M.//Kemp, M.//Justesen, U.S. 	Draft Genome Sequence of 'Terrisporobacter othiniensis' Isolated from a Blood Culture from a Human Patient.	Genome Announcements	2015	3		e00042-15			'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. 		
@D	Lundin, A.//Bjorkholm, B.//Kupershmidt, I.//Unemo, M.//Nilsson, P.//Andersson, D.I.//Engstrand, L. 	Slow genetic divergence of Helicobacter pylori strains during long-term colonization.	Infect. Immun.	2005	73		4818-4822			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. 		
@D	Lunnen, K.D.//Barsomian, J.M.//Camp, R.R.//Card, C.O.//Chen, S.-Z.//Croft, R.//Looney, M.C.//Meda, M.M.//Moran, L.S.//Nwankwo, D.O.//Slatko, B.E.//Van Cott, E.M.//Wilson, G.G. 	Cloning Type II restriction and modification genes.	Gene	1988	74		25-32			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. 		
@D	Lunnen, K.D.//Morgan, R.D.//Timan, C.J.//Krzycki, J.A.//Reeve, J.N.//Wilson, G.G. 	Characterization and cloning of MwoI (GCN7GC), a new type-II restriction-modification system from Methanobacterium wolfei.	Gene	1989	77		11-19			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. 		
@D	Luo, C.//Walk, S.T.//Gordon, D.M.//Feldgarden, M.//Tiedje, J.M.//Konstantinidis, K.T. 	Genome sequencing of environmental Escherichia coli expands understanding of the ecology and speciation of the model bacterial species.	Proc. Natl. Acad. Sci. U. S. A.	2011	108		7200-7205			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. 		
@D	Luo, F.//Zou, Y.//Huang, T.//Lin, S. 	Draft Genome Sequence of Streptomyces sp. B9173, a Producer of Indole Diketopiperazine Maremycins.	Genome Announcements	2017	5		e00447-17			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%. 		
@D	Luo, G.Z.//Wang, F.//Weng, X.//Chen, K.//Hao, Z.//Yu, M.//Deng, X.//Liu, J.//He, C. 	Characterization of eukaryotic DNA N6-methyladenine by a highly sensitive restriction enzyme-assisted sequencing.	Nat. Commun.	2016	7		11301			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. 		
@D	Luo, J.//Bruice, T.C. 	Low-frequency normal mode in DNA HhaI methyltransferase and motions of residues involved in the base flipping.	Proc. Natl. Acad. Sci. U. S. A.	2005	102		16194-16198			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. 		
@D	Luo, W.Y.//Tu, A.H.T.//Cao, Z.H.//Yu, H.L.//Dybvig, K. 	Identification of an isoschizomer of the HhaI DNA methyltransferase in Mycoplasma arthritidis.	FEMS Microbiol. Lett.	2009	290		195-198			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. 		
@D	Luo, X.//Wan, C.//Zhang, L. 	Draft Genome Sequence of Streptomyces mutabilis TRM45540, Isolated from a Hypersaline Soil Sample.	Genome Announcements	2015	3		e01465-15			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. 		
@D	Luo, Y.//Kong, Q.//Yang, J.//Golden, G.//Wanda, S.Y.//Jensen, R.V.//Ernst, P.B.//Curtiss, R.I.I.I. 	Complete Genome Sequence of the Universal Killer, Salmonella enterica serovar Typhimurium UK-1 (ATCC 68169).	J. Bacteriol.	2011	193		4035-4036			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. 		
@D	Luo, Y.//Wang, C.//Allard, S.//Strain, E.//Allard, M.W.//Brown, E.W.//Zheng, J. 	Draft Genome Sequences of Paenibacillus alvei A6-6i and TS-15.	Genome Announcements	2013	1		e00673-13			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. 		
@D	Luo, Y.//Xu, X.//Ding, Z.//Liu, Z.//Zhang, B.//Yan, Z.//Sun, J.//Hu, S.//Hu, X. 	Complete genome of Phenylobacterium zucineum - a novel facultative intracellular bacterium isolated from human erythroleukemia cell line  K562.	BMC Genomics	2008	9		386			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. 		
@D	Luo, Y.R.//Kang, S.G.//Kim, S.J.//Kim, M.R.//Li, N.//Lee, J.H.//Kwon, K.K. 	Genome Sequence of Benzo(a)pyrene-Degrading Bacterium Novosphingobium pentaromativorans US6-1.	J. Bacteriol.	2012	194		907			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. 		
@D	Lupker, H.S.C.//Dekker, B.M.M. 	Purification of the sequence-specific endonuclease SinI from Salmonella infantis.	Biochim. Biophys. Acta	1981	654		297-299			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. 		
@D	Luria, S.E. 	Host-induced modifications of viruses.	Cold Spring Harb. Symp. Quant. Biol.	1953	18		237-244			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. 		
@D	Luria, S.E. 	The recognition of DNA in Bacteria.	Sci. Am.	1970	222		88-102			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. 		
@D	Luria, S.E.//Human, M.L. 	A nonhereditary, host-induced variation of bacterial viruses.	J. Bacteriol.	1952	64		557-569			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). 		
@D	Lushnikov, A.Y.//Potaman, V.N.//Oussatcheva, E.A.//Sinden, R.R.//Lyubchenko, Y.L. 	DNA strand arrangement within the SfiI-DNA complex: atomic force microscopy analysis.	Biochemistry	2006	45		152-158			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. 		
@D	Lusk, B.G.//Badalamenti, J.P.//Parameswaran, P.//Bond, D.R.//Torres, C.I. 	Draft Genome Sequence of the Gram-Positive Thermophilic Iron Reducer Thermincola  ferriacetica Strain Z-0001T.	Genome Announcements	2015	3		e01072-15			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. 		
@D	Luthje, F.L.//Hasman, H.//Aarestrup, F.M.//Alwathnani, H.A.//Rensing, C. 	Genome Sequences of Two Copper-Resistant Escherichia coli Strains Isolated from Copper-Fed Pigs.	Genome Announcements	2014	2		e01341-14			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. 		
@D	Lutsenko, E.//Bhagwat, A.S. 	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.	Mutat. Res.	1999	437		11-20			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. 		
@D	Lutz, C.//Martin, T.Q.X.//Sun, S.//McDougald, D. 	Draft Genome Sequence of Shewanella sp. Strain CP20.	Genome Announcements	2015	3		e00256-15			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. 		
@D	Lux, T.M.//Lee, R.//Love, J. 	Complete Genome Sequence of a Free-Living Vibrio furnissii sp. nov. Strain (NCTC 11218).	J. Bacteriol.	2011	193		1487-1488			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. 		
@D	Lv, R.//Yang, X.//Fang, N.//Song, Y.//Luo, X.//Guo, J.//Peng, F.//Yang, R.//Cui, Y.//Fang, C.//Song, Y. 	Draft Genome Sequence of 'Paramesorhizobium deserti' A-3-ET, a Strain Highly Resistant to Diverse beta-Lactam Antibiotics.	Genome Announcements	2016	4		e00311-16			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. 		
@D	Lv, Y.//Liao, J.//Wu, Z.//Han, S.//Lin, Y.//Zheng, S. 	Genome Sequence of Corynebacterium glutamicum ATCC 14067, Which Provides Insight into Amino Acid Biosynthesis in Coryneform Bacteria.	J. Bacteriol.	2012	194		742-743			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. 		
@D	Lv, Y.//Wu, Z.//Han, S.//Lin, Y.//Zheng, S. 	Genome Sequence of Corynebacterium glutamicum S9114, a Strain for Industrial Production of Glutamate.	J. Bacteriol.	2011	193		6096-6097			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. 		
@D	Ly, L.K.//Underwood, G.E.//McCully, L.M.//Bitzer, A.S.//Godino, A.//Bucci, V.//Brigham, C.J.//Principe, A.//Fischer, S.E.//Silby, M.W. 	Draft Genome Sequences of Pseudomonas fluorescens Strains SF39a and SF4c, Potential Plant Growth Promotion and Biocontrol Agents.	Genome Announcements	2015	3		e00219-15			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. 		
@D	Lycksell, P.O.//Graslund, A.//Claesens, F.//McLaughlin, L.W.//Larsson, U.//Rigler, R. 	Base pair opening dynamics of a 2-aminopurine substituted EcoRI restriction sequence and its unsubstituted counterpart in oligonucleotides.	Nucleic Acids Res.	1987	15		9011-9025			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. 		
@D	Lykidis, A.//Mavromatis, K.//Ivanova, N.//Anderson, I.//Land, M.//DiBartolo, G.//Martinez, M.//Lapidus, A.//Lucas, S.//Copeland, A.//Richardson, P.//Wilson, D.B.//Kyrpides, N. 	Genome sequence and analysis of the soil cellulolytic actinomycete Thermobifida fusca YX.	J. Bacteriol.	2007	189		2477-2486			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. 		
@D	Lykke-Andersen, J.//Garrett, R.A.//Kjems, J. 	Protein footprinting approach to mapping DNA binding sites of two archaeal homing enzymes: evidence for a two-domain protein structure.	Nucleic Acids Res.	1996	24		3982-3989			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. 		
@D	Lykke-Andersen, J.//Garrett, R.A.//Kjems, J. 	Mapping metal ions at the catalytic centres of two intron-encoded endonucleases.	EMBO J.	1997	16		3272-3281			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+. 		
@D	Lykke-Andersen, J.//Thi-Ngoc, H.P.//Garrett, R.A. 	DNA substrate specificity and cleavage kinetics of an archaeal homing-type endonuclease from Pyrobaculum organotrophum.	Nucleic Acids Res.	1994	22		4583-4590			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. 		
@D	Lyko, F.//Brown, R. 	DNA methyltransferase inhibitors and the development of epigenetic cancer therapies.	J. Natl. Cancer Inst.	2005	97		1498-1506			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. 		
@D	Lyko, F.//Ramsahoye, B.H.//Jaenisch, R. 	DNA methylation in Drosophila melanogaster.	Nature	2000	408		538-540			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. 		
@D	Lyko, F.//Ramsahoye, B.H.//Kashevsky, H.//Tudor, M.//Mastrangelo, M.A.//Orr-Weaver, T.L.//Jaenisch, R. 	Mammalian (cytosine-5) methyltransferases cause genomic DNA methylation and lethality in drosophila.	Nat. Genet.	1999	23		363-366			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. 		
@D	Lyko, F.//Whittaker, A.J.//Orr-Weaver, T.L.//Jaenisch, R. 	The putative Drosophila methyltransferase gene dDnmt2 is contained in a transposon-like element and is expressed specifically in ovaries.	Mech. Dev.	2000	95		215-217			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. 		
@D	Lylloff, J.E.//Hansen, L.B.//Jepsen, M.//Hallin, P.F.//Sorensen, S.J.//Stougaard, P.//Glaring, M.A. 	Draft genome sequences of two protease-producing strains of arsukibacterium, isolated from two cold and alkaline environments.	Genome Announcements	2015	3		e00585-15			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. 		
@D	Lymperopoulou, D.S.//Coil, D.A.//Schichnes, D.//Lindow, S.E.//Jospin, G.//Eisen, J.A.//Adams, R.I. 	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.	Standards in Genomic Sciences	2017	12		17			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. 		
@D	Lynch, K.H.//Stothard, P.//Dennis, J.J. 	Genomic analysis and relatedness of P2-like phages of the Burkholderia cepacia complex.	BMC Genomics	2010	11		599			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. 		
@D	Lynch, K.H.//Stothard, P.//Dennis, J.J. 	Comparative analysis of two phenotypically-similar but genomically-distinct Burkholderia cenocepacia-specific bacteriophages.	BMC Genomics	2012	13		223			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. 		
@D	Lynch, K.H.//Stothard, P.//Dennis, J.J. 	Characterization of DC1, a broad-host-range Bcep22-like podovirus.	Appl. Environ. Microbiol.	2012	78		889-891			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. 		
@D	Lynch, T.W.//Sligar, S.G. 	Macromolecular Hydration Changes Associated with BamHI Binding and Catalysis.	J. Biol. Chem.	2000	275		30561-30565			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. 		
@D	Lyngstadaas, A.//Lobner-Olesen, A.//Boye, E. 	Characterization of three genes in the dam-containing operon of Escherichia coli.	Mol. Gen. Genet.	1995	247		546-554			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. 		
@D	Lynn, S.P.//Cohen, L.K.//Gardner, J.F.//Kaplan, S. 	Characterization of a site-specific restriction endonuclease from Rhodopseudomonas sphaeroides.	J. Bacteriol.	1979	138		505-509			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. 		
@D	Lynn, S.P.//Cohen, L.K.//Kaplan, S.//Gardner, J.F. 	RsaI: a new sequence-specific endonuclease activity from Rhodopseudomonas sphaeroides.	J. Bacteriol.	1980	142		380-383			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. 		
@D	Lyra, C.//Halme, T.//Torsti, A.-M.//Tenkanen, T.//Sivonen, K. 	Site-specific restriction endonucleases in cyanobacteria.	J. Appl. Microbiol.	2000	89		979-991			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. 		
@D	Lyu, W.//Wu, Y.//Liu, Y.//Lyu, Z. 	Draft Genome Sequence of Bacillus litoralis C44, Isolated from Chinese Scholar Tree (Sophora japonica) Forest Soil.	Genome Announcements	2016	4		e01059-16			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. 		
@D	Lyumkis, D.//Talley, H.//Stewart, A.//Shah, S.//Park, C.K.//Tama, F.//Potter, C.S.//Carragher, B.//Horton, N.C. 	Allosteric Regulation of DNA Cleavage and Sequence-Specificity through Run-On Oligomerization.	Structure	2013	21		1848-1858			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. 		
@D	Lyutzkanova, D.//Stoilova-Disheva, M.//Peltekova, V. 	The restriction-modification system in Streptomyces flavopersicus.	Folia Microbiol. (Praha)	2001	46		119-122			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. 		
@D	Ma, A.P.//Jiang, J.//Tun, H.M.//Mauroo, N.F.//Yuen, C.S.//Leung, F.C. 	Complete Genome Sequence of Staphylococcus xylosus HKUOPL8, a Potential Opportunistic Pathogen of Mammals.	Genome Announcements	2014	2		e00653-14			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. 		
@D	Ma, B.//Ma, J.//Liu, D.//Guo, L.//Chen, H.//Ding, J.//Liu, W.//Zhang, H. 	Biochemical and structural characterization of a DNA N6-adenine methyltransferase from Helicobacter pylori.	Oncotarget	2016	7		40965-40977			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. 		
@D	Ma, B.C.//Wang, J.//Fang, X.H. 	Fluorescence study of DNA binding and bending by EcoRI DNA methyltransferase.	J. Phys. Chem. B	2006	110		19647-19651			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. 		
@D	Ma, C.B.//Tang, Z.W.//Wang, K.M.//Tan, W.H.//Yang, X.H.//Li, W.//Li, Z.H.//Lv, X.Y. 	Real-time monitoring of restriction endonuclease activity using molecular beacon.	Anal. Biochem.	2007	363		294-296			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. 		
@D	Ma, D.//Bai, J.//Deng, G.//Li, S. 	Sequence analysis of DNA methyltransferase gene from Largemouth bass ulcerative syndrome virus and its expression in prokaryote.	Nong Ye Sheng Wu Ji Shu Xue Bao	2011	19		342-349			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. 		
@D	Ma, D.//Hao, Z.//Sun, R.//Bartlam, M.//Wang, Y. 	Genome Sequence of a Typical Ultramicrobacterium, Curvibacter sp. Strain PAE-UM,  Capable of Phthalate Ester Degradation.	Genome Announcements	2016	4		e01510-15			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. 		
@D	Ma, D.P.//King, Y.T.//Kim, Y.//Luckett, S. 	The group I intron of apocytochrome b gene from Chlamydomonas smithii encodes a site-specific endonuclease.	Plant Mol. Biol.	1992	18		1001-1004			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. 		
@D	Ma, J.//He, Y.//Hu, B.//Luo, Z.Q. 	Genome Sequence of an Environmental Isolate of the Bacterial Pathogen Legionella  pneumophila.	Genome Announcements	2013	1		e00320-13			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. 		
@D	Ma, J.//Liu, H.//Liu, K.//Wang, C.//Li, Y.//Hou, Q.//Yao, L.//Cui, Y.//Zhang, T.//Wang, H.//Wang, B.//Wang, Y.//Ge, R.//Xu, B.//Yao, G.//Xu, W.//Fan, L.//Ding, Y.//Du, B. 	Complete Genome Sequence of Bacillus velezensis GQJK49, a Plant Growth-Promoting  Rhizobacterium with Antifungal Activity.	Genome Announcements	2017	5		e00922-17			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. 		
@D	Ma, J.//Liu, H.//Wang, C.//Xia, Z.//Liu, K.//Hou, Q.//Li, Y.//Zhang, T.//Wang, H.//Wang, B.//Wang, Y.//Ge, R.//Xu, B.//Yao, G.//Jiang, Z.//Hou, W.//Ding, Y.//Du, B. 	Complete Genome Sequence of Bacillus subtilis GQJK2, a Plant Growth-Promoting Rhizobacterium with Antifungal Activity.	Genome Announcements	2017	5		e00467-17			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. 		
@D	Ma, L.//Chen, K.//Clarke, D.J.//Nortcliffe, C.P.//Wilson, G.G.//Edwardson, J.M.//Morton, A.J.//Jones, A.C.//Dryden, D.T.F. 	Resriction endonuclease TseI cleaves A:A and T:T mismatches in CAG and CTG repeats.	Nucleic Acids Res.	2013	41		4999-5009			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). 		
@D	Ma, L.//Wu, X.//Wilson, G.G.//Jones, A.C.//Dryden, D.T.F. 	Time-resolved fluorescence of 2-aminopurine in DNA duplexes in the presence of the EcoP15I Type III restriction-modification enzyme.	Biochem. Biophys. Res. Commun.	2014	449		120-125			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. 		
@D	Ma, L.//Zhu, Z.//Li, T.//Wang, Z. 	Assaying multiple restriction endonucleases functionalities and inhibitions on DNA microarray with multifunctional gold nanoparticle probes.	Biosensors and Bioelectronics	2014	52		118			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. 		
@D	Ma, M.//Wang, C.//Ding, Y.//Li, L.//Shen, D.//Jiang, X.//Guan, D.//Cao, F.//Chen, H.//Feng, R.//Wang, X.//Ge, Y.//Yao, L.//Bing, X.//Yang, X.//Li, J.//Du, B. 	Complete Genome Sequence of Paenibacillus polymyxa SC2, a Strain of Plant Growth Promoting Rhizobacteria with Broad-Spectrum Antimicrobial Activity.	J. Bacteriol.	2010	193		311-312			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. 		
@D	Ma, Q.//Qu, Y.//Tang, H.//Yu, H.//Ma, F.//Shi, S.//Zhang, X.//Zhou, H.//Zhou, J.//Xu, P. 	Genome Sequence of a Novel Indigo-Producing Strain, Pseudomonas monteilii QM.	J. Bacteriol.	2012	194		4459-4460			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. 		
@D	Ma, Q.//Qu, Y.//Zhang, Z.//Li, P.//Tang, H. 	Genome Sequence of an Efficient Indole-Degrading Bacterium, Cupriavidus sp. Strain IDO, with Potential Polyhydroxyalkanoate Production Applications.	Genome Announcements	2015	3		e00102-15			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. 		
@D	Ma, R.//Wang, J.//Wang, Q.//Ma, Z.//Li, J.//Chen, L. 	Draft Genome Sequence of Loktanella cinnabarina Strain XM1 Isolated from Coastal  Surface Water.	Genome Announcements	2017	5		e01310-17			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%. 		
@D	Ma, X.X.//Ito, T.//Tiensasitorn, C.//Jamklang, M.//Chongtrakool, P.//Boyle-Vavra, S.//Daum, R.S.//Hiramatsu, K. 	Novel Type of Staphylococcal Cassette Chromosome mec Identified in Community-Acquired Methicillin-Resistant Staphylococcus aureus Strains.	Antimicrob. Agents Chemother.	2002	46		1147-1152			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. 		
@D	Ma, Y.F.//Zhang, Y.//Zhang, J.Y.//Chen, D.W.//Zhu, Y.//Zheng, H.//Wang, S.Y.//Jiang, C.Y.//Zhao, G.P.//Liu, S.J. 	The Complete Genome of Comamonas testosteroni Reveals Its Genetic Adaptations to Changing Environments.	Appl. Environ. Microbiol.	2009	75		6812-6819			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. 		
@D	Ma, Y.L.//Xia, J.L.//Yang, Y.//Nie, Z.Y.//Liu, H.C.//Liu, L.Z. 	Complete Genome Sequence of the Extremely Thermoacidophilic Archaeon Acidianus manzaensis YN-25.	Genome Announcements	2017	5		e00438-17			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. 		
@D	Ma, Z.//Geng, J.//Zhang, H.//Yu, H.//Yi, L.//Lei, M.//Lu, C.P.//Fan, H.J.//Hu, S. 	Complete Genome Sequence of Streptococcus equi subsp. zooepidemicus Strain ATCC 35246.	J. Bacteriol.	2011	193		5583-5584			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. 		
@D	Ma, Z.//Geng, J.N.//Yi, L.//Xu, B.//Jia, R.Y.//Li, Y.//Meng, Q.S.//Fan, H.J.//Hu, S.N. 	Insight into the specific virulence related genes and toxin-antitoxin virulent pathogenicity islands in swine streptococcosis pathogen Streptococcus equi ssp zooepidemicus strain ATCC35246.	BMC Genomics	2013	14		377			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. 		
@D	Ma, Z.//Shen, X.//Hu, H.//Wang, W.//Peng, H.//Xu, P.//Zhang, X. 	Genome Sequence of Sphingomonas wittichii DP58, the First Reported Phenazine-1-Carboxylic Acid-Degrading Strain.	J. Bacteriol.	2012	194		3535-3536			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. 		
@D	Maaloum, M.//Diop, A.//Ndongo, S.//Nguyen, T.T.//Cadoret, F.//Raoult, D.//Fournier, P.E. 	Draft Genome Sequence of Megamonas funiformis Strain Marseille-P3344, Isolated from a Human Fecal Microbiota.	Genome Announcements	2018	6		e01459-17			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. 		
@D	Maas, R. 	Change in plasmid DNA structure, hypermethylation, and lon-proteolysis as steps in a replicative cascade.	Cell	2001	105		945-955			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. 		
@D	Maass, G. 	Recognition of DNA sequences by restriction endonucleases.	NATO ASI Ser.	1987	137		225-237			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. 		
@D	Maass, G.//Alves, J.//Fliess, A.//Pingoud, A.//Wolfes, H. 	Recognition of DNA-sequences by restriction endonucleases.	Hoppe Seylers Z. Physiol. Chem.	1986	367		47			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. 		
@D	Maass, G.//Ruter, T.//Oelgeschlager, T.//Alves, J.//Wolfes, H.//Pingoud, A. 	Site-directed mutagenesis studies suggest that Asp91 is part of the catalytic center of the restriction endonuclease EcoRI.	J. Biomol. Struct. Dyn.	1991	8		A126			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. 		
@D	Mac Aogain, M.//Bower, J.E.//Basu, I.//Freeman, J.T.//O'Toole, R.F. 	Draft Genome Sequence of a Drug-Susceptible New Zealand Isolate of Mycobacterium  tuberculosis Lineage 3.	Genome Announcements	2015	3		e00499-15			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. 		
@D	Mac Aogain, M.//Fennelly, N.//Walsh, A.//Lynagh, Y.//Bekaert, M.//Lawlor, B.//Walsh, P.//Kelly, B.//Rogers, T.R.//Crowley, B. 	Fourteen Draft Genome Sequences for the First Reported Cases of Azithromycin-Resistant Neisseria gonorrhoeae in Ireland.	Genome Announcements	2017	5		e00403-17			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. 		
@D	Mac Aogain, M.//Gautam, S.S.//Bower, J.E.//Basu, I.//O'Toole, R.F. 	Draft Genome Sequence of a New Zealand Rangipo Strain of Mycobacterium tuberculosis.	Genome Announcements	2016	4		e00657-16			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. 		
@D	Mac, A.M.//Roycroft, E.//Raftery, P.//Mok, S.//Fitzgibbon, M.//Rogers, T.R. 	Draft Genome Sequences of Three Mycobacterium chimaera Respiratory Isolates.	Genome Announcements	2015	3		e01409-15			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. 		
@D	Macaluso, A.//Mettus, A.-M. 	Efficient transformation of Bacillus thuringiensis requires nonmethylated plasmid DNA.	J. Bacteriol.	1991	173		1353-1356			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. 		
@D	MacAogain, M.//Johari, B.M.//Bower, J.E.//O'Toole, R.F. 	Draft Genome Sequence of a Multidrug-Resistant New Zealand Isolate of Mycobacterium tuberculosis Lineage 3.	Genome Announcements	2014	2		e01017-14			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. 		
@D	Macdonald, P.M.//Mosig, G. 	Regulation of a new bacteriophage T4 gene, 69, that spans an origin of DNA replication.	EMBO J.	1984	3		2863-2871			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. 		
@D	Macdonald, S.E.//Gundogdu, O.//Dorrell, N.//Wren, B.W.//Blake, D.//Stabler, R. 	Draft Genome Sequence of Campylobacter jejuni 11168H.	Genome Announcements	2017	5		e01556-16			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. 		
@D	Macey, M.C.//Pratscher, J.//Crombie, A.//Murrell, J.C. 	Draft Genome Sequences of Obligate Methylotrophs Methylovorus sp. Strain MM2 and  Methylobacillus sp. Strain MM3, Isolated from Grassland Soil.	Microbiol. Resour. Announc.	2018	7		e00824-18			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. 		
@D	MacGregor, B.J.//Biddle, J.F.//Siebert, J.R.//Staunton, E.//Hegg, E.L.//Matthysse, A.G.//Teske, A. 	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.	Appl. Environ. Microbiol.	2013	79		1183-1190			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. 		
@D	MacGregor, B.J.//Biddle, J.F.//Teske, A. 	Mobile Elements in a Single-Filament Orange Guaymas Basin Beggiatoa ('Candidatus Maribeggiatoa') sp Draft Genome: Evidence for Genetic Exchange with Cyanobacteria.	Appl. Environ. Microbiol.	2013	79		3974-3985			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. 		
@D	Macgregor, R.B. 	Reversible inhibition of EcoRI with elevated pressure.	Biochem. Biophys. Res. Commun.	1990	170		775-778			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. 		
@D	Machado, H.//Mansson, M.//Gram, L. 	Draft Genome Sequence of Photobacterium halotolerans S2753, Producer of Bioactive Secondary Metabolites.	Genome Announcements	2014	2		e00535-14			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. 		
@D	Machado, V.S.//Bicalho, R.C. 	Complete Genome Sequence of Trueperella pyogenes, an Important Opportunistic Pathogen of Livestock.	Genome Announcements	2014	2		e00400-14			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. 		
@D	Machnicka, M.A.//Kaminska, K.H.//Dunin-Horkawicz, S.//Bujnicki, J.M. 	Phylogenomics and sequence-structure-function relationships in the GmrSD family of Type IV restriction enzymes.	BMC Bioinformatics	2015	16		336			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. 		
@D	Macickova-Cahova, H.//Hocek, M. 	Cleavage of adenine-modified functionalized DNA by type II restriction endonucleases.	Nucleic Acids Res.	2009	37		7612-7622			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. 		
@D	Macickova-Cahova, H.//Pohl, R.//Hocek, M. 	Cleavage of Functionalized DNA Containing 5-Modified Pyrimidines by Type II Restriction Endonucleases.	Chembiochem	2011	12		431-438			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. 		
@D	Macinnes, J.I.//Mackinnon, J.//Bujold, A.R.//Ziebell, K.//Kropinski, A.M.//Nash, J.H. 	Complete Genome Sequence of Actinobacillus suis H91-0380, a Virulent Serotype O2  Strain.	J. Bacteriol.	2012	194		6686-6687			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. 		
@D	Macintyre, G.//Atwood, C.V.//Cupples, C.G. 	Lowering S-adenosylmethionine levels in Escherichia coli modulates C-to-T transition mutations.	J. Bacteriol.	2001	183		921-927			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. 		
@D	Macintyre, G.//Doiron, K.//Cupples, G. 	Analysis of the levels of Dcm and Vsr in E. coli.	Abstr. Gen. Meet. Am. Soc. Microbiol.	1997	97		294			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. 		
@D	Macintyre, G.//Doiron, K.M.J.//Cupples, C.G. 	The Vsr endonuclease of Escherichia coli: an efficient DNA repair enzyme and a potent mutagen.	J. Bacteriol.	1997	179		6048-6052			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. 		
@D	Macintyre, G.//Pitsikas, P.//Cupples, C.G. 	Growth phase-dependent regulation of Vsr endonuclease may contribute to 5-methylcytosine mutational hot spots in Escherichia coli.	J. Bacteriol.	1999	181		4435-4436			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. 		
@D	Mackeldanz, P.//Alves, J.//Moncke-Buchner, E.//Wyszomirski, K.H.//Kruger, D.H.//Reuter, M. 	Functional consequences of mutating conserved SF2 helicase motifs in the Type III restriction endonuclease EcoP15I translocase domain.	Biochimie	2013	95		817-823			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. 		
@D	Mackenzie, D.A.//McLay, K.//Roos, S.//Walter, J.//Swarbreck, D.//Drou, N.//Crossman, L.C.//Juge, N. 	Draft Genome Sequence of a Novel Lactobacillus salivarius Strain Isolated from Piglet.	Genome Announcements	2014	2		e01231-13			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. 		
@D	Macklaim, J.M.//Gloor, G.B.//Anukam, K.C.//Cribby, S.//Reid, G. 	At the crossroads of vaginal health and disease, the genome sequence of Lactobacillus iners AB-1.	Proc. Natl. Acad. Sci. U. S. A.	2011	108		4688-4695			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. 		
@D	Mackova, M.//Pohl, R.//Hocek, M. 	Polymerase Synthesis of DNAs Bearing Vinyl Groups in the Major Groove and their Cleavage by Restriction Endonucleases.	Chembiochem	2014	15		2306-2312			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. 		
@D	MacLea, K.S.//Trachtenberg, A.M. 	Complete Genome Sequence of Staphylococcus epidermidis ATCC 12228 Chromosome and  Plasmids, Generated by Long-Read Sequencing.	Genome Announcements	2017	5		e00954-17			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%. 		
@D	MacLeod, A.R.//Szyf, M. 	Expression of antisense to DNA methyltransferase mRNA induces DNA demethylation and inhibits tumorigenesis.	J. Biol. Chem.	1995	270		8037-8043			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. 		
@D	MacMillan, A.M.//Chen, L.//Verdine, G.L. 	Synthesis of an oligonucleotide suicide substrate for DNA methyltransferases.	J. Org. Chem.	1992	57		2989-2991			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. 		
@D	MacNeil, D. 	Characterization of a unique methyl-specific restriction system in Streptomyces avermitilis.	Abstr. Gen. Meet. Am. Soc. Microbiol.	1988	88		156			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. 		
@D	MacNeil, D.J. 	Characterization of a unique methyl-specific restriction system in Streptomyces avermitilis.	J. Bacteriol.	1988	170		5607-5612			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. 		
@D	Macori, G.//Romano, A.//Adriano, D.//Razzuoli, E.//Bianchi, D.M.//Gallina, S.//Bellio, A.//Decastelli, L. 	Draft Genome Sequences of Four Yersinia enterocolitica Strains, Isolated from Wild Ungulate Carcasses.	Genome Announcements	2017	5		e00192-17			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%. 		
@D	Macreadie, I.G.//Scott, R.M.//Zinn, A.R.//Butow, R.A. 	Transposition of an intron in yeast mitochondria requires a protein encoded by that intron.	Cell	1985	41		395-402			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. 		
@D	MacWilliams, M.//Meister, J.//Jutte, H.//Bickle, T. 	Generation of a new type-I restriction-modification specificity by transposition.	J. Cell Biochem. Suppl.	1994	18C		136			*
 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.
 
 		
@D	MacWilliams, M.P.//Bickle, T.A. 	Generation of new DNA binding specificity by truncation of the type IC EcoDXXI hsdS gene.	EMBO J.	1996	15		4775-4783			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. 		
@D	Madani, N.//Giraud, P.//Mendy, C.//Colaneri, C.//Cherchame, E.//Cherfa, M.A.//Richomme, C.//Decors, A.//Girault, G. 	First Draft Genome Sequences of Three Strains of Francisella tularensis subsp. holarctica, Isolated from Hares and a Tick in France.	Genome Announcements	2017	5		e00993-17			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. 		
@D	Madhaiyan, M.//Chan, K.L.//Ji, L. 	Draft Genome Sequence of Methylobacterium sp. Strain L2-4, a Leaf-Associated Endophytic N-Fixing Bacterium Isolated from Jatropha curcas L.	Genome Announcements	2014	2		e01306-14			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. 		
@D	Madhaiyan, M.//Peng, N.//Ji, L. 	Complete Genome Sequence of Enterobacter sp. Strain R4-368, an Endophytic N-Fixing Gammaproteobacterium Isolated from Surface-Sterilized Roots of Jatropha   curcas L.	Genome Announcements	2013	1		e00544-13			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. 		
@D	Madhavan, T.P.//Steen, J.A.//Hugenholtz, P.//Sakellaris, H. 	Genome Sequence of Enterotoxigenic Escherichia coli Strain B2C.	Genome Announcements	2014	2		e00247-14			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. 		
@D	Madhavilatha, G.K.//Joseph, B.V.//Paul, L.K.//Kumar, R.A.//Hariharan, R.//Mundayoor, S. 	Whole-Genome Sequences of Two Clinical Isolates of Mycobacterium tuberculosis from Kerala, South India.	J. Bacteriol.	2012	194		4430			We report the annotated genome sequence of two clinical isolates of Mycobacterium tuberculosis isolated from Kerala, India. 		
@D	Madhusoodanan, J.//Seo, K.S.//Remortel, B.//Park, J.Y.//Hwang, S.Y.//Fox, L.K.//Park, Y.H.//Deobald, C.F.//Wang, D.//Liu, S.//Daugherty, S.C.//Gill, A.L.//Bohach, G.A.//Gill, S.R. 	An Enterotoxin-Bearing Pathogenicity Island in Staphylococcus epidermidis.	J. Bacteriol.	2011	193		1854-1862			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. 		
@D	Madhusoodanan, U.K.//Rao, D.N. 	Diversity of DNA methyltransferases that recognize asymmetric target sequences.	Crit. Rev. Biochem. Mol. Biol.	2010	45		125-145			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.</. 		
@D	Madsen, A.//Josephsen, J. 	The LlaGI restriction and modification system of Lactococcus lactis W10 consists of only one single polypeptide.	FEMS Microbiol. Lett.	2001	200		91-96			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. 		
@D	Madsen, A.//Josephsen, J. 	Characterization of LlaCI, a new restriction-modification system from Lactococcus lactis subsp. cremoris W15.	Biol. Chem.	1998	379		443-449			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. 		
@D	Madsen, A.//Josephsen, J. 	Cloning and characterization of the lactococcal plasmid-encoded type II restriction/modification system, LlaDII.	Appl. Environ. Microbiol.	1998	64		2424-2431			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. 		
@D	Madsen, A.//Nellemann, L.J.//Josephsen, J. 	The restriction and modification system LlaCI and its use in the development of phage resistant lactococcal starter cultures.	FASEB J.	1997	11		A1035			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. 		
@D	Madsen, A.//Westphal, C.//Josephsen, J. 	Characterization of a novel plasmid-encoded HsdS subunit, S.LlaW12I, from Lactococcus lactis W12.	Plasmid	2000	44		196-200			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. 		
@D	Madueno, L.//Macchi, M.//Morelli, I.S.//Coppotelli, B.M. 	Draft Whole-Genome Sequence of Sphingobium sp. 22B, a Polycyclic Aromatic Hydrocarbon-Degrading Bacterium from Semiarid Patagonia, Argentina.	Genome Announcements	2016	4		e00488-16			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. 		
@D	Maeda, A.H.//Nishi, S.//Ishii, S.//Shimane, Y.//Kobayashi, H.//Ichikawa, J.//Kurosawa, K.//Arai, W.//Takami, H.//Ohta, Y. 	Complete Genome Sequence of Altererythrobacter sp. Strain B11, an Aromatic Monomer-Degrading Bacterium, Isolated from Deep-Sea Sediment under the Seabed off  Kashima, Japan.	Genome Announcements	2018	6		e00200-18			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. 		
@D	Maeda, A.H.//Nishi, S.//Ozeki, Y.//Ohta, Y.//Hatada, Y.//Kanaly, R.A. 	Draft Genome Sequence of Sphingobium sp. Strain KK22, a High-Molecular-Weight Polycyclic Aromatic Hydrocarbon-Degrading Bacterium Isolated from Cattle Pasture   Soil.	Genome Announcements	2013	1		e00911-13			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. 		
@D	Maeder, D.L.//Anderson, I.//Brettin, T.S.//Bruce, D.C.//Gilna, P.//Han, C.S.//Lapidus, A.//Metcalf, W.W.//Saunders, E.//Tapia, R.//Sowers, K.R. 	The Methanosarcina barkeri genome: comparative analysis with Methanosarcina acetivorans and Methanosarcina mazei reveals extensive  rearrangement within methanosarcinal genomes.	J. Bacteriol.	2006	188		7922-7931			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. 		
@D	Maeder, D.L.//Weiss, R.B.//Dunn, D.M.//Cherry, J.L.//Gonzalez, J.M.//DiRuggiero, J.//Robb, F.T. 	Divergence of the hyperthermophilic archaea Pyrococcus furiosus and P. horikoshii inferred from complete genomic sequences.	Genetics	1999	152		1299-1305			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. 		
@D	Maegley, K.//Reich, N.O. 	Enhanced substrate specificity observed in EcoRI DNA methyltransferase upon mutagenesis of cysteine 223.	FASEB J.	1992	6		A61			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. 		
@D	Maegley, K.//Reich, N.O. 	Enhanced substrate specificity observed in EcoRI DNA methyltransferase upon mutagenesis of cysteine 223.	Biophys. J.	1992	61		A61			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. 		
@D	Maegley, K.//Reich, N.O. 	Enhanced substrate specificity observed in EcoRI DNA methyltransferase upon mutagenesis of cysteine 223.	Biochemistry	1992	31		2197			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. 		
@D	Maegley, K.//Reich, N.O. 	Enhanced substrate specificity observed in EcoRI DNA methyltransferase upon mutagenesis of cysteine 223.	ACS Abstracts	1992	203		57-BIOL			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. 		
@D	Maegley, K.//Reich, N.O. 	Enhanced substrate discriminiation and identification of an essential catalytic residue of the EcoRI DNA methyltransferase by site directed mutagenesis.	FASEB J.	1993	7		A1197			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. 		
@D	Maegley, K.//Shoemaker, D.//Everett, B.//Reich, N.O. 	Limited proteolysis of EcoRI DNA methylase.	FASEB J.	1990	4		A1793			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. 		
@D	Maegley, K.//Shoemaker, D.//Reich, N.O. 	Covalent intermediate in EcoRI DNA methyltransferase investigated by site directed mutagenesis.	J. Cell. Biochem.	1991	15G		175			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. 		
@D	Maegley, K.A. 	Structural and functional characterization of the EcoRI DNA methyltransferase.	Diss. Abstr.	1995	55		3293B			*
 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.
 
 		
@D	Maegley, K.A.//Gonzalez, L.//Smith, D.W.//Reich, N.O. 	Cofactor and DNA interactions in EcoRI DNA methyltransferase.	J. Biol. Chem.	1992	267		18527-18532			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). 		
@D	Maehara, T.//Itaya, M.//Ogura, M.//Tanaka, T. 	Effect of Bacillus subtilis BsuM restriction-modification on plasmid transfer by polyethylene glycol-induced protoplast fusion.	FEMS Microbiol. Lett.	2011	325		49-55			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. 		
@D	Maekawa, Y.//Kawakami, B. 	The relaxation of specificity of BanI restriction endonuclease from Bacillus aneurinolyticus IAM 1077.	J. Ferment. Bioeng.	1990	69		57-59			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. 		
@D	Maekawa, Y.//Kawakami, B. 	Cloning and expression in Escherichia coli of the BanI and BanIII restriction-modification systems from Bacillus aneurinolyticus.	J. Ferment. Bioeng.	1990	69		195-198			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. 		
@D	Maekawa, Y.//Yasukawa, H.//Kawakami, B. 	Cloning and nucleotide sequences of the BanI restriction-modification genes in Bacillus aneurinolyticus.	J. Biochem. (Tokyo)	1990	107		645-649			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. 		
@D	Magana-Lizarraga, J.A.//Ahumada-Santos, Y.P.//Parra-Unda, J.R.//Uribe-Beltran, M.J.//Gomez-Gil, B.//Baez-Flores, M.E. 	Draft Genome Sequence of Escherichia coli Strain M15-4, a Typical Enteropathogenic E. coli Strain Isolated in Mexico.	Genome Announcements	2018	6		e01522-17			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. 		
@D	Magana-Lizarraga, J.A.//Hernandez-Peinado, J.V.//Ahumada-Santos, Y.P.//Parra-Unda, J.R.//Uribe-Beltran, M.J.//Gomez-Gil, B.//Baez-Flores, M.E. 	Draft Genome Sequence of a Mexican Community-Associated Methicillin-Resistant Staphylococcus epidermidis Strain.	Genome Announcements	2017	5		e01236-17			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. 		
@D	Maggini, V.//Presta, L.//Miceli, E.//Fondi, M.//Bosi, E.//Chiellini, C.//Fagorzi, C.//Bogani, P.//Di Pilato, V.//Rossolini, G.M.//Mengoni, A.//Firenzuoli, F.//Perrin, E.//Fani, R. 	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.	Genome Announcements	2017	5		e00351-17			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. 		
@D	Magni, C.//Espeche, C.//Repizo, G.D.//Saavedra, L.//Suarez, C.A.//Blancato, V.S.//Espariz, M.//Esteban, L.//Raya, R.R.//Font-de-Valdez, G.//Vignolo, G.//Mozzi, F.//Taranto, M.P.//Hebert, E.M.//Nader-Macias, M.E.//Sesma, F. 	Draft Genome Sequence of Enterococcus mundtii CRL1656.	J. Bacteriol.	2012	194		550			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. 		
@D	Magno-Perez-Bryan, M.C.//Martinez-Garcia, P.M.//Hierrezuelo, J.//Rodriguez-Palenzuela, P.//Arrebola, E.//Ramos, C.//de Vicente, A.//Perez-Garcia, A.//Romero, D. 	Comparative Genomics Within the Bacillus Genus Reveal the Singularities of Two Robust Bacillus amyloliquefaciens Biocontrol Strains.	Mol. Plant Microbe Interact.	2015	28		1102-1116			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. 		
@D	Magrini, V.//Salmi, D.//Thomas, D.//Herbert, S.K.//Hartzell, P.L.//Youderian, P. 	Temperate Myxococcus xanthus phage Mx8 encodes a DNA adenine methylase, Mox.	J. Bacteriol.	1997	179		4254-4263			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. 		
@D	Mahalingam, N.//Manivannan, B.//Jadhao, S.//Mishra, G.//Nilawe, P.//Pradeep, B.E. 	Draft Genome Sequences of Two Extensively Drug-Resistant Acinetobacter baumannii  Strains Isolated from Pus Samples.	Genome Announcements	2016	4		e00161-16			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. 		
@D	Mahan, K.M.//Klingeman, D.M.//Hettich, R.L.//Parry, R.J.//Graham, D.E. 	Draft Genome Sequence of Streptomyces vitaminophilus ATCC 31673, a Producer of Pyrrolomycin Antibiotics, Some of Which Contain a Nitro Group.	Genome Announcements	2016	4		e01582-15			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. 		
@D	Mahan, M.J.//Low, D.A. 	DNA methylation regulates bacterial gene expression and virulence.	ASM News	2001	67		356-361			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. 		
@D	Mahato, N.K.//Tripathi, C.//Verma, H.//Singh, N.//Lal, R. 	Draft Genome Sequence of Deinococcus sp. Strain RL Isolated from Sediments of a Hot Water Spring.	Genome Announcements	2014	2		e00703-14			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%. 		
@D	Maher, L.J. III 	DNA triple-helix formation: an approach to artificial gene repressors?	Bioessays	1992	14		807-815			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. 		
@D	Maher, L.J.//Wold, B.//Dervan, P.B. 	Inhibition of DNA binding proteins by oligonucleotide-directed triple helix formation.	Science	1989	245		725-733			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. 		
@D	Maheux, A.F.//Berube, E.//Boudreau, D.K.//Raymond, F.//Corbeil, J.//Roy, P.H.//Boissinot, M.//Omar, R.F. 	Draft Genome Sequence of Criibacterium bergeronii gen. nov., sp. nov., Strain CCRI-22567T, Isolated from a Vaginal Sample from a Woman with Bacterial  Vaginosis.	Genome Announcements	2016	4		e00959-16			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. 		
@D	Maheux, A.F.//Boudreau, D.K.//Berube, E.//Boissinot, M.//Cantin, P.//Raymond, F.//Corbeil, J.//Omar, R.F.//Bergeron, M.G. 	Draft Genome Sequence of Romboutsia weinsteinii sp. nov. Strain CCRI-19649T Isolated from Surface Water.	Genome Announcements	2017	5		e00901-17			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. 		
@D	Maheux, A.F.//Boudreau, D.K.//Berube, E.//Boissinot, M.//Raymond, F.//Brodeur, S.//Corbeil, J.//Brightwell, G.//Broda, D.//Omar, R.F.//Bergeron, M.G. 	Draft Genome Sequence of Romboutsia maritimum sp. nov. Strain CCRI-22766T, Isolated from Coastal Estuarine Mud.	Genome Announcements	2017	5		e01044-17			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. 		
@D	Maheux, A.F.//Boudreau, D.K.//Berube, E.//Boissinot, M.//Raymond, F.//Brodeur, S.//Corbeil, J.//Isabel, S.//Omar, R.F.//Bergeron, M.G. 	Draft Genome Sequence of a Sporulating and Motile Strain of Lachnotalea glycerini Isolated from Water in Quebec City, Canada.	Genome Announcements	2017	5		e01059-17			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. 		
@D	Mahony, J.//Bottacini, F.//van Sinderen, D.//Fitzgerald, G.F. 	Progress in lactic acid bacterial phage research.	Microb. Cell Fact.	2014	13		S1			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. 		
@D	Mahowald, M.A. et al. 	Characterizing a model human gut microbiota composed of members of its two dominant bacterial phyla.	Proc. Natl. Acad. Sci. U. S. A.	2009	106		5859-5864			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. 		
@D	Mai-Prochnow, A.//Bradbury, M.//Murphy, A.B. 	Draft Genome Sequence of Pseudomonas aeruginosa ATCC 9027 (DSM 1128), an Important Rhamnolipid Surfactant Producer and Sterility Testing Strain.	Genome Announcements	2015	3		e01259-15			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. 		
@D	Maida, I.//Bosi, E.//Perrin, E.//Papaleo, M.C.//Orlandini, V.//Fondi, M.//Fani, R.//Wiegel, J.//Bianconi, G.//Canganella, F. 	Draft Genome Sequence of the Fast-Growing Bacterium Vibrio natriegens Strain DSMZ 759.	Genome Announcements	2013	1		e00648-13			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. 		
@D	Mainardi, R.M.//Lima, J.E.A.//Ribeiro, J.J.C.//Beloti, V.//Carmo, A.O.//Kalapothakis, E.//Goncalves, D.D.//Padua, S.B.//Pereira, U.P. 	Complete Genome Sequence of Streptococcus agalactiae Strain S25 Isolated from Peritoneal Liquid of Nile Tilapia.	Genome Announcements	2016	4		e00784-16			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. 		
@D	Mairhofer, J.//Krempl, P.M.//Thallinger, G.G.//Striedner, G. 	Finished Genome Sequence of Escherichia coli K-12 Strain HMS174 (ATCC 47011).	Genome Announcements	2014	2		e00975-14			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). 		
@D	Maita, C.//Matushita, M.//Okubo, T.//Matsuo, J.//Miyake, M.//Nagai, H.//Yamaguchi, H. 	Draft Genome Sequences of Legionella pneumophila JR32 and Lp01 Laboratory Strains Domesticated in Japan.	Genome Announcements	2016	4		e00791-16			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. 		
@D	Maitra, N.//Whitman, W.B.//Ayyampalayam, S.//Samanta, S.//Sarkar, K.//Bandopadhyay, C.//Aftabuddin, M.//Sharma, A.P.//Manna, S.K. 	Draft Genome Sequence of the Aquatic Phosphorus-Solubilizing and -Mineralizing Bacterium Bacillus sp. Strain CPSM8.	Genome Announcements	2014	2		e01265-13			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. 		
@D	Maizel, D.//Utturkar, S.M.//Brown, S.D.//Ferrero, M.A.//Rosen, B.P. 	Draft Genome Sequence of Brevibacterium linens AE038-8, an Extremely Arsenic-Resistant Bacterium.	Genome Announcements	2015	3		e00316-15			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. 		
@D	Majid, M.//Kumar, N.//Qureshi, A.//Yerra, P.//Kumar, A.//Kumar, M.K.//Tiruvayipati, S.//Baddam, R.//Shaik, S.//Srikantam, A.//Ahmed, N. 	Genomes of Two Clinical Isolates of Mycobacterium tuberculosis from Odisha, India.	Genome Announcements	2014	2		e00199-14			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. 		
@D	Majumder, K. 	The importance of flanking sequences in the sequence specific cleavage by the restriction endonucleases RsaI, AluI and HaeIII.	Biophys. J.	1989	55		48a			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. 		
@D	Mak, A.N.//Lambert, A.R.//Stoddard, B.L. 	Folding, DNA Recognition, and Function of GIY-YIG Endonucleases: Crystal Structures of R.Eco29kI.	Structure	2010	18		1321-1331			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. 		
@D	Mak, A.N.S.//Fung, W.T.//Kong, K.P.S.//Poon, A.W.S.//Ngai, S.M.//Shaw, P.C. 	Characterization of the large subunit of EcoHK31I methyltransferase by structural modeling and mutagenesis.	Biol. Chem.	2007	388		265-271			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. 		
@D	Mak, T.N.//Sfanos, K.S.//Bruggemann, H. 	Draft Genome Sequences of Two Strains of Propionibacterium acnes Isolated from Radical Prostatectomy Specimens.	Genome Announcements	2013	1		e01071-13			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. 		
@D	Makarova, K. et al. 	Comparative genomics of the lactic acid bacteria.	Proc. Natl. Acad. Sci. U. S. A.	2006	103		15611-15616			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. 		
@D	Makarova, K.S.//Wolf, Y.I.//Koonin, E.V. 	Comparative genomics of defense systems in archaea and bacteria.	Nucleic Acids Res.	2013	41		4360-4377			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. 		
@D	Makarova, K.S.//Wolf, Y.I.//Snir, S.//Koonin, E.V. 	Defense islands in bacterial and archaeal genomes and prediction of novel defense systems.	J. Bacteriol.	2011	193		6039-6056			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. 		
@D	Makarova, O.//Johnston, P.//Walther, B.//Rolff, J.//Roesler, U. 	Complete Genome Sequence of the Livestock-Associated Methicillin-Resistant Strain Staphylococcus aureus subsp. aureus 08S00974 (Sequence Type 398).	Genome Announcements	2017	5		e00294-17			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. 		
@D	Makarova, O.//Johnston, P.//Walther, B.//Rolff, J.//Roesler, U. 	Complete Genome Sequence of the Disinfectant Susceptibility Testing Reference Strain Staphylococcus aureus subsp. aureus ATCC 6538.	Genome Announcements	2017	5		e00293-17			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). 		
@D	Maker, A.//Hemp, J.//Pace, L.A.//Ward, L.M.//Fischer, W.W. 	Draft Genome Sequence of Hydrogenibacillus schlegelii MA48, a Deep-Branching Member of the Bacilli Class of Firmicutes.	Genome Announcements	2017	5		e00380-16			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. 		
@D	Maki, A.H.//Tsao, D.H.H. 	Microwave-optical study of an As(III) derivative of EcoRI methylase.	Biomol. Spectroscopy II	1991	1432		119-128			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. 		
@D	Makino, K.//Ishii, K.//Yasunaga, T.//Hattori, M.//Yokoyama, K.//Yutsudo, H.C.//Kubota, Y.//Yamaichi, Y.//Iida, T.//Yamamoto, K.//Honda, T.//Han, C.G.//Ohtsubo, E.//Kasamatsu, M.//Hayashi, T.//Kuhara, S.//Shinagawa, H. 	Complete nucleotide sequences of 93-kb and 3.3-kb plasmids of an enterohemorrhagic Escherichia coli O157:H7 derived from Sakai outbreak.	DNA Res.	1998	5		1-9			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. 		
@D	Makino, K.//Oshima, K.//Kurokawa, K.//Yokoyama, K.//Uda, T.//Tagomori, K.//Iijima, Y.//Najima, M.//Nakano, M.//Yamashita, A.//Kubota, Y.//Kimura, S.//Yasunaga, T.//Honda, T.//Shinagawa, H.//Hattori, M.//Iida, T. 	Genome sequence of Vibrio parahaemolyticus: a pathogenic mechanism distinct from that of V cholerae.	Lancet	2003	361		743-749			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. 		
@D	Makino, K.//Yokoyama, K.//Kubota, Y.//Watanabe, M.//Kimura, S.//Yutsudo, C.H.//Kurokawa, K.//Ishii, K.//Hattori, M.//Abe, H.//Yamamoto, K.//Hayashi, T.//Yasunaga, T.//Honda, T.//Sasakawa, C.//Shinagawa, H. 	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.	Genes Genet. Syst.	1999	74		227-239			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. 		
@D	Makino, O.//Kawamura, F.//Saito, H.//Ikeda, Y. 	Inactivation of restriction endonuclease BamNx after infection with phage UNR2.	Nature	1979	277		64-65			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. 		
@D	Makino, O.//Saito, H.//Ando, T. 	Bacillus subtilis-Phage Phi1 overcomes host-controlled restriction by producing BamNx inhibitor protein.	Mol. Gen. Genet.	1980	179		463-468			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. 		
@D	Makita, H.//Nishi, S.//Takaki, Y.//Tanaka, E.//Nunoura, T.//Mitsunobu, S.//Takai, K. 	Draft Genome Sequence of Mariprofundus micogutta Strain ET2.	Genome Announcements	2018	6		e00342-18			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. 		
@D	Makovets, S.//Doronina, V.A.//Murray, N.E. 	Regulation of endonuclease activity by proteolysis prevents breakage of unmodified bacterial chromosomes by type I restriction enzymes.	Proc. Natl. Acad. Sci. U. S. A.	1999	96		9757-9762			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. 		
@D	Makovets, S.//Powell, L.M.//Titheradge, A.J.B.//Blakely, G.W.//Murray, N.E. 	Is modification sufficient to protect a bacterial chromosome from a resident restriction endonuclease?	Mol. Microbiol.	2004	51		135-147			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. 		
@D	Makovets, S.//Titheradge, A.J.B.//Murray, N.E. 	ClpX and ClpP are essential for the efficient acquisition of genes specifying type IA and IB restriction systems.	Mol. Microbiol.	1998	28		25-35			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. 		
@D	Maksimenko, A.//Gottikh, M.B.//Kubareva, E.A.//Fedorova, O.A.//Shabarova, Z.A. 	Restriction endonucleases can be used to confirm a structure of unusual DNA duplexes.	Biol. Chem.	1998	379		625-630			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. 		
@D	Makula, R.A.//Meagher, R.B. 	A new restriction endonuclease from the anaerobic bacterium, Desulfovibrio desulfuricans, Norway.	Nucleic Acids Res.	1980	8		3125-3131			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. 		
@D	Malagnac, F.//Gregoire, A.//Goyon, C.//Rossignol, J.-L.//Faugeron, G. 	Masc2, a gene from Ascobolus encoding a protein with a DNA-methyltransferase activity in vitro, is dispensable for in vivo methylation.	Mol. Microbiol.	1999	31		331-338			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. 		
@D	Malagnac, F.//Wendel, B.//Goyon, C.//Faugeron, G.//Zickler, D.//Rossignol, J.-L.//Noyer-Weidner, M.//Vollmayr, P.//Trautner, T.A.//Walter, J. 	A gene essential for de novo methylation and development in Ascobolus reveals a novel type of eukaryotic DNA methyltransferase structure.	Cell	1997	91		281-290			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. 		
@D	Malathi, J.//Murugan, N.//Umashankar, V.//Bagyalakshmi, R.//Madhavan, H.N. 	Draft Genome Sequence of Multidrug-Resistant Pseudomonas aeruginosa Strain VRFPA02, Isolated from a Septicemic Patient in India.	Genome Announcements	2013	1		e00425-13			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. 		
@D	Malcolm, A.D.B. 	Binding sites of restriction endonucleases.	Biochem. Soc. Trans.	1986	14		202-204			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. 		
@A	Malcolm, A.D.B. 		The use of restriction enzymes in genetic engineering.			R. Williamson 		Genet. Eng. (N Y)				New York	Academic Press	1981		2		129-173									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). 		
@D	Malcolm, A.D.B.//Mofatt, J.R. 	Measurement of differential reactivities at restriction endonuclease sites.	Biochem. Soc. Trans.	1980	8		734-735			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. 		
@D	Malcolm, A.D.B.//Moffat, J.R. 	Differential reactivities at restriction enzyme sites.	Biochim. Biophys. Acta	1981	655		128-135			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. 		
@D	Malcolm, A.D.B.//Moffatt, J.R.//Fox, K.R.//Waring, M.J. 	Differential inhibition of a restriction enzyme by quinoxaline antibiotics.	Biochim. Biophys. Acta	1982	699		211-216			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. 		
@D	Malcolm, A.D.B.//Snounou, G. 	Restriction enzymes and DNA.	Top. Mol. Struct. Biol.	1987	9		193-222			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. 		
@D	Maldonado-Barragan, A.//Caballero-Guerrero, B.//Lucena-Padros, H.//Ruiz-Barba, J.L. 	Genome Sequence of Lactobacillus pentosus IG1, a Strain Isolated from Spanish-Style Green Olive Fermentations.	J. Bacteriol.	2011	193		5605			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. 		
@D	Maldonado-Contreras, A.//Mane, S.P.//Zhang, X.-S.//Pericchi, L.//Alarcon, T.//Contreras, M.//Linz, B.//Blaser, M.J.//Dominguez-Bello, M.G. 	Phylogeographic evidence of cognate recognition site patterns and transformation efficiency differences in H. pylori: theory of strain dominance.	BMC Microbiol.	2013	13		14			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. 		
@D	Maldonado-Contreras, A.L.//Olagibel, L.//Dominguez-Bello, M.G. 	Geographical differences in restriction-modification system cognate recognition sites in Helicobacter pylori.	Abstr. Gen. Meet. Am. Soc. Microbiol.	2007	107		656			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. 		
@D	Malfatti, S. et al. 	Complete genome sequence of Halogeometricum borinquense type strain (PR3).	Standards in Genomic Sciences	2009	1		150-159			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. 		
@D	Malhotra, J.//Dua, A.//Saxena, A.//Sangwan, N.//Mukherjee, U.//Pandey, N.//Rajagopal, R.//Khurana, P.//Khurana, J.P.//Lal, R. 	Genome Sequence of Acinetobacter sp. Strain HA, Isolated from the Gut of the Polyphagous Insect Pest Helicoverpa armigera.	J. Bacteriol.	2012	194		5156			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%. 		
@D	Malik, G.//Dangwal, M.//Kapoor, S.//Kapoor, M. 	Role of DNA methylation in growth and differentiation in Physcomitrella patens and characterization of cytosine DNA methyltransferases.	FEBS J.	2012	279		4081-4094			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. 		
@D	Malik, S.//Siezen, R.J.//Renckens, B.//Vaneechoutte, M.//Vanderleyden, J.//Lebeer, S. 	Draft Genome Sequence of Lactobacillus plantarum CMPG5300, a Human Vaginal Isolate.	Genome Announcements	2014	2		e01149-14			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. 		
@D	Malin, G.//Iakobashvili, R.//Lapidot, A. 	Effect of tetrahydropyrimidine derivatives on protein-nucleic acids interaction.	J. Biol. Chem.	1999	274		6920-6929			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. 		
@D	Malinga, L.A.//Abeel, T.//Desjardins, C.A.//Dlamini, T.C.//Cassell, G.//Chapman, S.B.//Birren, B.W.//Earl, A.M.//van der Walt, M. 	Draft Genome Sequences of Two Extensively Drug-Resistant Strains of Mycobacterium tuberculosis Belonging to the Euro-American S Lineage.	Genome Announcements	2016	4		e01771-15			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. 		
@D	Mallamaci, M.A.//Bascoy, M.L.//Brown, J.//Combates, N.J.//Winkle, S.A. 	Locating binding sites for the carcinogen N-acetoxy-N-acetyl-2-aminofluorene using restriction enzyme inhibition assays.	J. Biomol. Struct. Dyn.	1992	10		83-96			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). 		
@D	Malone, C.S.//Miner, M.D.//Doerr, J.R.//Jackson, J.P.//Jacobsen, S.E.//Wall, R.//Teitell, M. 	CmC(A/T)GG DNA methylation in mature B cell lymphoma gene silencing.	Proc. Natl. Acad. Sci. U. S. A.	2001	98		10404-10409			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. 		
@D	Malone, K.M.//Farrell, D.//Stuber, T.P.//Schubert, O.T.//Aebersold, R.//Robbe-Austerman, S.//Gordon, S.V. 	Updated Reference Genome Sequence and Annotation of Mycobacterium bovis AF2122/97.	Genome Announcements	2017	5		e00157-17			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. 		
@D	Malone, T.//Blumenthal, R.M.//Cheng, X. 	Structure-guided analysis reveals nine sequence motifs conserved among DNA amino-methyl-transferases, and suggests a catalytic mechanism for these enzymes.	J. Mol. Biol.	1995	253		618-632			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. 		
@D	Maltchenko, S. 	The target recognition domains from the methyltransferases of II class have common subdomains.	Protein Engineering Suppl.	1993	6		46			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. 		
@D	Maltseva, D.V.//Baykov, A.A.//Jeltsch, A.//Gromova, E.S. 	Impact of 7,8-Dihydro-8-oxoguanine on Methylation of the CpG Site by Dnmt3a (dagger).	Biochemistry	2009	48		1361-1368			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. 		
@D	Maluta, R.P.//Nicholson, B.//Logue, C.M.//Nolan, L.K.//Rojas, T.C.//Dias-da-Silveira, W. 	Complete Genomic Sequence of an Avian Pathogenic Escherichia coli Strain of Serotype O7:HNT.	Genome Announcements	2016	4		e01611-15			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. 		
@D	Malygin, E.G.//Evdokimov, A.A.//Hattman, S. 	Dimeric/oligomeric DNA methyltransferases: an unfinished story.	Biol. Chem.	2009	390		835-844			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. 		
@D	Malygin, E.G.//Evdokimov, A.A.//Zinoviev, V.V.//Ovechkina, L.G.//Lindstrom, W.M.//Reich, N.O.//Schlagman, S.L.//Hattman, S. 	A dual role for substrate S-adenosyl-L-methionine in the methylation reaction with bacteriophage T4 Dam DNA-[N6-adenine]-methyltransferase.	Nucleic Acids Res.	2001	29		2361-2369			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. 		
@D	Malygin, E.G.//Hattman, S. 	DNA methyltransferases: Mechanistic models derived from kinetic analysis.	Crit. Rev. Biochem. Mol. Biol.	2012	47		97-193			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. 		
@D	Malygin, E.G.//Lindstrom, W.M. Jr.//Schlagman, S.L.//Hattman, S.//Reich, N.O. 	Pre-steady state kinetics of bacteriophage T4 Dam DNA-[N6-adenine] methyltransferase: interaction with native (GATC) or modified sites.	Nucleic Acids Res.	2000	28		4207-4211			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. 		
@D	Malygin, E.G.//Lindstrom, W.M.//Zinoviev, V.V.//Evdokimov, A.A.//Schlagman, S.L.//Reich, N.O.//Hattman, S. 	Bacteriophage T4Dam (DNA-(adenine-N6)-methyltransferase). Evidence for two distinct stages of methylation under single turnover conditions.	J. Biol. Chem.	2003	278		41749-41755			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. 		
@D	Malygin, E.G.//Ovechkina, L.G.//Evdokimov, A.A.//Zinoviev, V.V. 	Single turnover kinetics of methylation by T4 DNA-(N6-adenine)-methyltransferase.	Mol. Biol. (Mosk)	2001	35		65-78			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. 		
@D	Malygin, E.G.//Ovechkina, L.G.//Zinoviev, V.V.//Linstrem, U.M.//Reich, N.O. 	DNA-(N4-cytosine)-methyltransferase from Bacillus amyloliquefaciens: kinetic and substrate-binding properties.	Mol. Biol. (Mosk)	2001	35		42-51			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. 		
@D	Malygin, E.G.//Petrov, N.A.//Gorbunov, Y.A.//Kossykh, V.G.//Hattman, S. 	Interaction of the phage T4 Dam DNA-[N6-adenine] methyltransferase with oligonucleotides containing native or modified (defective) recognition sites.	Nucleic Acids Res.	1997	25		4393-4399			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. 		
@D	Malygin, E.G.//Sclavi, B.//Zinoviev, V.V.//Evdokimov, A.A.//Hattman, S.//Buckle, M. 	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.	J. Biol. Chem.	2004	279		50012-50018			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. 		
@D	Malygin, E.G.//Zinovev, V.V. 	Studies of the role of symmetry in the specific recognition of natural and synthetic DNA by type II restriction and modification enzymes.	Sov. Sci. Rev. D. Physiochem. Biol.	1989	9		87-142			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. 		
@D	Malygin, E.G.//Zinovev, V.V.//Gorbunov, Y.A.//Popov, S.G.//Rechkunova, N.I.//Buryanov, Y.I.//Nesternko, V.F.//Baev, A.A. 	Influence of the structure of oligonucleotide substrates on the interaction with Eco dam methylase.	Biokhimiia	1988	53		1639-1647			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. 		
@D	Malygin, E.G.//Zinoviev, V.V.//Evdokimov, A.A.//Lindstrom, W.M. Jr.//Reich, N.O.//Hattman, S. 	DNA (cytosine-N4-)- and -(adenine-N6-)-methyltransferases have different kinetic mechanisms but the same reaction route. A comparison of M.BamHI and T4 Dam.	J. Biol. Chem.	2003	278		15713-15719			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. 		
@D	Malygin, E.G.//Zinoviev, V.V.//Petrov, N.A.//Evdokimov, A.A.//Jen-Jacobson, L.//Kossykh, V.G.//Hattman, S. 	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.	Nucleic Acids Res.	1999	27		1135-1144			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). 		
@D	Malyguine, E.//Vannier, P.//Yot, P. 	Alteration of the specificity of restriction endonucleases in the presence of organic solvents.	Gene	1980	8		163-177			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. 		
@D	Mamelak, L.//Boyer, H.W. 	Genetic control of the secondary modification of deoxyribonucleic acid in Escherichia coli.	J. Bacteriol.	1970	104		57-62			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. 		
@D	Manachini, P.L.//Parini, C.//Fortina, M.G.//Benazzi, L. 	BliI, a restriction endonuclease from Bacillus licheniformis.	FEBS Lett.	1987	214		305-307			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. 		
@D	Manageiro, V.//Clemente, L.//Duarte, S.//Vieira, L.//Canica, M. 	Draft Genome Sequence of an Escherichia coli Strain Isolated from a Gallus gallus Broiler Producing the Novel CTX-M-166 Variant.	Genome Announcements	2016	4		e01029-16			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. 		
@D	Manageiro, V.//Sampaio, D.A.//Pereira, P.//Rodrigues, P.//Vieira, L.//Palos, C.//Canica, M. 	Draft Genome Sequence of the First NDM-1-Producing Providencia stuartii Strain Isolated in Portugal.	Genome Announcements	2015	3		e01077-15			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. 		
@D	Manakova, E.//Golovenko, D.//Grazulis, S.//Zaremba, M.//Siksnys, V. 	Structural mechanism of cognate DNA recognition by the BfiI restriction enzyme.	FEBS J.	2012	279		446-447			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. 		
@D	Manakova, E.//Grazulis, S.//Zaremba, M.//Tamulaitiene, G.//Golovenko, D.//Siksnys, V. 	Structural mechanisms of the degenerate sequence recognition by Bse634I restriction endonuclease.	Nucleic Acids Res.	2012	40		6741-6751			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. 		
@D	Manavalan, P.//Johnson, W.C. Jr.//Modrich, P. 	Prediction of secondary structure for EcoRI endonuclease.	J. Biol. Chem.	1984	259		11666-11667			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. 		
@D	Mancini, S.//Abicht, H.K.//Karnachuk, O.V.//Solioz, M. 	Genome Sequence of Desulfovibrio sp. A2, a Highly Copper Resistant, Sulfate-Reducing Bacterium Isolated from Effluents of a Zinc Smelter at  the Urals.	J. Bacteriol.	2011	193		6793-6794			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. 		
@D	Mandape, S.N.//Marshall, D.R.//Dent, L.L.//Pratap, S. 	Draft Genome Sequence of Multidrug-Resistant Acinetobacter baumannii Strain MMC4, Isolated from a Patient in Tennessee.	Genome Announcements	2014	2		e00051-14			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. 		
@D	Mandelli, F.//Oliveira, R.B.//Couger, M.B.//Paixao, D.A.//Camilo, C.M.//Polikarpov, I.//Prade, R.//Riano-Pachon, D.M.//Squina, F.M. 	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.	Genome Announcements	2015	3		e00475-15			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. 		
@D	Mane, S.P. et al. 	Host-interactive genes in amerindian Helicobacter pylori diverge from their old world homologs and mediate inflammatory responses.	J. Bacteriol.	2010	192		3078-3092			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. 		
@D	Manfredi, P.//Pagni, M.//Cornelis, G.R. 	Complete Genome Sequence of the Dog Commensal and Human Pathogen Capnocytophaga canimorsus Strain 5.	J. Bacteriol.	2011	193		5558-5559			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). 		
@D	Manfredi, P.//Renzi, F.//Cornelis, G.R. 	Draft Genome Sequences of Three Capnocytophaga cynodegmi Strains Isolated from the Oral Cavity of Healthy Dogs.	Genome Announcements	2015	3		e00200-15			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. 		
@D	Manfredi, P.//Renzi, F.//Cornelis, G.R. 	Draft Genome Sequences of Three Capnocytophaga canimorsus Strains Isolated from Healthy Canine Oral Cavities.	Genome Announcements	2015	3		e00199-15			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. 		
@D	Manfredi, P.//Renzi, F.//Cornelis, G.R. 	Draft Genome Sequences of Three Capnocytophaga canimorsus Strains Isolated from Septic Patients.	Genome Announcements	2015	3		e00193-15			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. 		
@D	Mangiamele, P.//Nicholson, B.//Wannemuehler, Y.//Seemann, T.//Logue, C.M.//Li, G.//Tivendale, K.A.//Nolan, L.K. 	Complete Genome Sequence of the Avian Pathogenic Escherichia coli Strain APEC O78.	Genome Announcements	2013	1		e0002613			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. 		
@D	Manichanh, C.//Chapple, C.E.//Frangeul, L.//Gloux, K.//Guigo, R.//Dore, J. 	A comparison of random sequence reads versus 16S rDNA sequences for estimating the biodiversity of a metagenomic library.	Nucleic Acids Res.	2008	36		5180-5188			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. 		
@A	Maniloff, J.//Dybvig, K.//Sladek, T.L. 		Mycoplasma DNA Restriction and Modification.			Maniloff, J. 		Mycoplasmas: Molecular Biology and Pathogenesis				Rochester, NY	American Society for Microbiology	1992		0		325-330									*
 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
 
 		
@D	Manivannan, B.//Mahalingam, N.//Jadhao, S.//Mishra, A.//Nilawe, P.//Pradeep, B.E. 	Draft Genome Sequence of a Clinically Isolated Extensively Drug-Resistant Pseudomonas aeruginosa Strain.	Genome Announcements	2016	4		e00162-16			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. 		
@D	Manivasakam, P.//Aubrecht, J.//Sidhom, S.//Schiestl, R.H. 	Restriction enzymes increase efficiencies of illegitimate DNA integration but decrease homologous integration in mammalian cells.	Nucleic Acids Res.	2001	29		4826-4833			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. 		
@D	Manivasakam, P.//Schiestl, R.H. 	Nonhomologous end joining during restriction enzyme-mediated DNA integration in Saccharomyces cerevisiae.	Mol. Cell. Biol.	1998	18		1736-1745			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. 		
@D	Mann, A.J.//Hahnke, R.L.//Huang, S.//Werner, J.//Xing, P.//Barbeyron, T.//Huettel, B.//Stueber, K.//Reinhardt, R.//Harder, J.//Gloeckner, F.O.//Amann, R.I.//Teeling, H. 	The genome of the algae-associated marine flavobacterium Formosa agariphila KMM 3901T reveals a broad potential for the degradation of algal polysaccharides.	Appl. Environ. Microbiol.	2013	79		6813			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. 		
@A	Mann, M.B. 		The cloned HhaII restriction-modification system.			Chirikjian, J.G. 		Gene Amplif. Anal.					Elsevier North Holland	1981		1		229-237									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. 		
@D	Mann, M.B.//Rao, R.N.//Smith, H.O. 	Cloning of restriction and modification genes in E. coli: the HhaII system from Haemophilus haemolyticus.	Gene	1978	3		97-112			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. 		
@D	Mann, M.B.//Smith, H.O. 	Specificity of HpaII and HaeIII DNA methylases.	Nucleic Acids Res.	1977	4		4211-4221			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. 		
@A	Mann, M.B.//Smith, H.O. 		Specificity of DNA Methylases from Haemophilus Sp.			Usdin, E.//Borchardt, R.T.//Creveling, C.R. 		Proceedings of the Conference on Transmethylation				New York	Elsevier North Holland	1979		0		483-492									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. 		
@A	Mann, M.B.//Smith, H.O. 		Size of 5'-terminal fragments cleaved from poly(dG-dC) by EndoR.HhaI.			Vogel, H.J. 		Nucleic Acid - Protein Recognition				New York	Academic Press	1977		0		269-271									None 		
@D	Mannala, G.K.//Hain, T.//Sproer, C.//Bunk, B.//Overmann, J.//Alt, V.//Domann, E. 	Complete Genome and Plasmid Sequences of Staphylococcus aureus EDCC 5055 (DSM 28763), Used To Study Implant-Associated Infections.	Genome Announcements	2017	5		e01698-16			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. 		
@D	Mannarelli, B.M.//Balganesh, T.S.//Greenberg, B.//Springhorn, S.S.//Lacks, S.A. 	Nucleotide sequence of the DpnII DNA methylase gene of Streptococcus pneumoniae and its relationship to the dam gene of Escherichia coli.	Proc. Natl. Acad. Sci. U. S. A.	1985	82		4468-4472			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. 		
@D	Manninger, P.//Koziol, A.//Carrillo, C.D. 	Draft Whole-Genome Sequences of Escherichia fergusonii Strains Isolated from Beef Trim (GTA-EF02), Ground Beef (GTA-EF03), and Chopped Kale (GTA-EF04).	Genome Announcements	2016	4		e00185-16			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). 		
@D	Mannino, S.J.//Jenkins, C.L.//Raines, R.T. 	Chemical mechanism of DNA cleavage by the homing endonuclease I-PpoI.	Biochemistry	1999	38		16178-16186			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. 		
@D	Mannion, A.//Shen, Z.//Feng, Y.//Garcia, A.//Fox, J.G. 	Draft Genome Sequences of Five Novel Polyketide Synthetase-Containing Mouse Escherichia coli Strains.	Genome Announcements	2016	4		e01082-16			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. 		
@D	Mansilla, S.//Garcia-Ferrer, I.//Mendez, C.//Salas, J.A.//Portugal, J. 	Differential inhibition of restriction enzyme cleavage by chromophore-modified analogues of the antitumour antibiotics mithramycin and chromomycin reveals structure-activity relationships.	Biochem. Pharmacol.	2010	79		1418-1427			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. 		
@D	Manso, A.S.//Chai, M.H.//Atack, J.M.//Furi, L.//De Ste, C.M.//Haigh, R.//Trappetti, C.//Ogunniyi, A.D.//Shewell, L.K.//Boitano, M.//Clark, T.A.//Korlach, J.//Blades, M.//Mirkes, E.//Gorban, A.N.//Paton, J.C.//Jennings, M.P.//Oggioni, M.R. 	A random six-phase switch regulates pneumococcal virulence via global epigenetic  changes.	Nat. Commun.	2014	5		5055			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. 		
@D	Manso-Silvan, L. et al. 	Draft Genome Sequences of Mycoplasma alkalescens, Mycoplasma arginini, and Mycoplasma bovigenitalium, Three Species with Equivocal Pathogenic Status for  Cattle.	Genome Announcements	2013	1		e00348-13			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. 		
@D	Mansor, M.//Macalady, J.L. 	Draft Genome Sequence of Lampenflora Chlorobium limicola Strain Frasassi in a Sulfidic Cave System.	Genome Announcements	2016	4		e00357-16			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. 		
@D	Mansour, C.A.//Doiron, K.M.//Cupples, C.G. 	Characterization of functional interactions among the Escherichia coli mismatch repair proteins using a bacterial two-hybrid assay.	Mutat. Res.	2001	485		331-338			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. 		
@D	Mansour, S.R.//Oshone, R.//Hurst, S.G.I.V.//Morris, K.//Thomas, W.K.//Tisa, L.S. 	Draft Genome Sequence of Frankia sp. Strain CcI6, a Salt-Tolerant Nitrogen-Fixing Actinobacterium Isolated from the Root Nodule of Casuarina cunninghamiana.	Genome Announcements	2014	2		e01205-13			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. 		
@D	Manwaring, N.P.//Skurray, R.A.//Firth, N. 	Nucleotide sequence of the F plasmid leading region.	Plasmid	1999	41		219-225			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. 		
@D	Manzanera, M.//Garcia-Fontana, C.//Vilchez, J.I.//Gonzalez-Lopez, J. 	Genome Sequence of Rhodococcus sp. 4J2A2, a Desiccation-Tolerant Bacterium Involved in Biodegradation of Aromatic Hydrocarbons.	Genome Announcements	2015	3		e00592-15			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. 		
@D	Manzanera, M.//Garcia-Fontana, C.//Vilchez, J.I.//Narvaez-Reinaldo, J.J.//Gonzalez-Lopez, J. 	Genome Sequence of Microbacterium sp. Strain 3J1, a Highly Desiccation-Tolerant Bacterium That Promotes Plant Growth.	Genome Announcements	2015	3		e00713-15			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. 		
@D	Manzanera, M.//Narvaez-Reinaldo, J.J.//Garcia-Fontana, C.//Vilchez, J.I.//Gonzalez-Lopez, J. 	Genome Sequence of Arthrobacter koreensis 5J12A, a Plant Growth-Promoting and Desiccation-Tolerant Strain.	Genome Announcements	2015	3		e00648-15			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. 		
@D	Manzanera, M.//Santa-Cruz-Calvo, L.//Vilchez, J.I.//Garcia-Fontana, C.//Silva-Castro, G.A.//Calvo, C.//Gonzalez-Lopez, J. 	Genome Sequence of Arthrobacter siccitolerans 4J27, a Xeroprotectant-Producing Desiccation-Tolerant Microorganism.	Genome Announcements	2014	2		e00526-14			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). 		
@D	Manzanera, M.//Vilchez, J.I.//Garcia-Fontana, C.//Calvo, C.//Gonzalez-Lopez, J. 	Genome Sequence of Leucobacter sp. 4J7B1, a Plant-Osmoprotectant Soil Microorganism.	Genome Announcements	2015	3		e00398-15			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. 		
@D	Manzano-Marin, A.//Latorre, A. 	Settling down: the genome of Serratia symbiotica from the aphid Cinara tujafilina zooms in on the process of accommodation to a cooperative intracellular life.	Genome Biol. Evol.	2014	6		1683-1698			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. 		
@D	Manzella, M.P.//Holmes, D.E.//Rocheleau, J.M.//Chung, A.//Reguera, G.//Kashefi, K. 	The complete genome sequence and emendation of the hyperthermophilic, obligate iron-reducing archaeon 'Geoglobus ahangari' strain 234(T).	Standards in Genomic Sciences	2015	10		77			'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. 		
@D	Manzoor, S.//Bongcam-Rudloff, E.//Schnurer, A.//Muller, B. 	First Genome Sequence of a Syntrophic Acetate-Oxidizing Bacterium, Tepidanaerobacter acetatoxydans Strain Re1.	Genome Announcements	2013	1		e00213-12			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. 		
@D	Manzoor, S.//Muller, B.//Niazi, A.//Bongcam-Rudloff, E.//Schnurer, A. 	Draft Genome Sequence of Clostridium ultunense Strain Esp, a Syntrophic Acetate-Oxidizing Bacterium.	Genome Announcements	2013	1		e0010713			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. 		
@D	Manzoor, S.//Muller, B.//Niazi, A.//Schnurer, A.//Bongcam-Rudloff, E. 	Working draft genome sequence of the mesophilic acetate oxidizing bacterium Syntrophaceticus schinkii strain Sp3.	Standards in Genomic Sciences	2015	10		99			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. 		
@D	Manzoor, S.//Niazi, A.//Bejai, S.//Meijer, J.//Bongcam-Rudloff, E. 	Genome Sequence of a Plant-Associated Bacterium, Bacillus amyloliquefaciens Strain UCMB5036.	Genome Announcements	2013	1		e0011113			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. 		
@D	Manzoor, S.//Schnurer, A.//Bongcam-Rudloff, E.//Muller, B. 	Complete genome sequence of Methanoculleus bourgensis strain MAB1, the syntrophic partner of mesophilic acetate-oxidising bacteria (SAOB).	Standards in Genomic Sciences	2016	11		80			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. 		
@D	Mao, D.//Grogan, D. 	Genomic evidence of rapid, global-scale gene flow in a Sulfolobus species.	ISME J.	2012	6		1613-1616			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. 		
@D	Mao, M.//Yang, X.//Poff, K.//Bennett, G. 	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.	Genome Biol. Evol.	2017	9		1803-1815					
@D	Mao, X.H.//Wei, M.//Zhu, C.F.//Lu, J.X.//Gao, J.M.//Simon, A.J.//Shi, J.Y.//Huang, Q.//Fan, C.H. 	Real Time in Vitro Regulation of DNA Methylation Using a 5-Fluorouracil Conjugated DNA-Based Stimuli-Responsive Platform.	ACS Appl. Mater. Inter.	2013	5		2604-2609			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. 		
@D	Mao, Y.//Chen, M.//Horvath, P. 	Draft Genome Sequence of Lactobacillus sp. Strain TCF032-E4, Isolated from Fermented Radish.	Genome Announcements	2015	3		e00821-15			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). 		
@D	Mao, Z.//Li, M.//Chen, J. 	Draft Genome Sequence of Pseudomonas plecoglossicida Strain NB2011, the Causative Agent of White Nodules in Large Yellow Croaker (Larimichthys crocea).	Genome Announcements	2013	1		e00586-13			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. 		
@D	Mappley, L.J.//Black, M.L.//Abuoun, M.//Darby, A.C.//Woodward, M.J.//Parkhill, J.//Turner, A.K.//Bellgard, M.I.//La, T.//Phillips, N.D.//La Ragione, R.M.//Hampson, D.J. 	Comparative genomics of Brachyspira pilosicoli strains: genome rearrangements, reductions and correlation of genetic compliment with phenotypic diversity.	BMC Genomics	2012	13		454			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. 		
@D	Marasa, B.S.//Khan, S.//Iram, S.//Sung, K.//Xu, J. 	Draft Genome Sequence of Methicillin-Resistant Clinical Staphylococcus aureus Isolate 51S (Sequence Type 291).	Genome Announcements	2015	3		e01050-15			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. 		
@D	Marasa, B.S.//Revollo, J.//Iram, S.//Sung, K.//Xu, J.//Khan, S. 	Draft Genome Sequence of a Methicillin-Resistant Staphylococcus aureus ST1413 Strain for Studying Genetic Mechanisms of Antibiotic Resistance.	Genome Announcements	2014	2		e00162-14			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. 		
@D	Marasini, D.//Abo-Shama, U.H.//Fakhr, M.K. 	Complete Genome Sequences of Salmonella enterica Serovars Anatum and Anatum var.  15+, Isolated from Retail Ground Turkey.	Genome Announcements	2016	4		e01619-15			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). 		
@D	Marasini, D.//Abo-Shama, U.H.//Fakhr, M.K. 	Whole-Genome Sequencing of Salmonella enterica subsp. enterica Serovar Ouakam Isolated from Ground Turkey.	Genome Announcements	2016	4		e01618-15			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. 		
@D	Marasini, D.//Cornell, C.R.//Oyewole, O.//Sheaff, R.J.//Fakhr, M.K. 	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.	Genome Announcements	2017	5		e01343-17			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. 		
@D	Marasini, D.//Fakhr, M.K. 	Complete Genome Sequences of the Plasmid-Bearing Campylobacter coli Strains HC2-48, CF2-75, and CO2-160 Isolated from Retail Beef Liver.	Genome Announcements	2016	4		e01004-16			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. 		
@D	Marasini, D.//Fakhr, M.K. 	Complete Genome Sequences of Plasmid-Bearing Campylobacter coli and Campylobacter jejuni Strains Isolated from Retail Chicken Liver.	Genome Announcements	2017	5		e01350-17			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. 		
@D	Marasini, D.//Fakhr, M.K. 	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.	Genome Announcements	2016	4		e01060-16			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. 		
@D	Marasini, D.//Fakhr, M.K. 	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.	Genome Announcements	2016	4		e00460-16			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. 		
@D	Marasini, D.//Fakhr, M.K. 	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.	Genome Announcements	2017	5		e01360-17			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. 		
@D	Marasini, D.//Fakhr, M.K. 	Complete Genome Sequences of Campylobacter jejuni Strains Isolated from Retail Chicken and Chicken Gizzards.	Genome Announcements	2017	5		e01351-17			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. 		
@D	Marcaida, M.J. et al. 	Homing endonucleases: from basics to therapeutic applications.	Cell. Mol. Life Sci.	2010	67		727-748			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. 		
@D	Marcaida, M.J.//Prieto, J.//Redondo, P.//Nadra, A.D.//Alibes, A.//Serrano, L.//Grizot, S.//Duchateau, P.//Paques, F.//Blanco, F.J.//Montoya, G. 	Crystal structure of I-DmoI in complex with its target DNA provides new insights into meganuclease engineering.	Proc. Natl. Acad. Sci. U. S. A.	2008	105		16888-16893			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. 		
@D	March, J.B.//Clark, J. 	Enzymes by post-restriction enzyme stability.	Nat. Biotechnol.	2000	18		243			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. 		
@D	Marche, L.//Saraoui, T.//Remenant, B.//Zagorec, M.//Prevost, H.//Delbarre-Ladrat, C.//Leroi, F.//Pilet, M.F. 	Complete Genome Sequence of Lactococcus piscium CNCM I-4031, a Bioprotective Strain for Seafood Products.	Genome Announcements	2017	5		e01510-16			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. 		
@D	Marchionni, M.A.//Roufa, D.J. 	Digestion of 5-bromodeoxyuridine-substituted lambda-DNA by restriction endonucleases.	J. Biol. Chem.	1978	253		9075-9081			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. 		
@D	Marcial-Coba, M.S.//Marshall, I.P.G.//Schreiber, L.//Nielsen, D.S. 	High-Quality Draft Genome Sequence of Lactobacillus casei Strain Z11, Isolated from a Human Adult Intestinal Biopsy Sample.	Genome Announcements	2017	5		e00634-17			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. 		
@D	Marcoleta, A.//Gutierrez-Cortez, S.//Maturana, D.//Monasterio, O.//Lagos, R. 	Whole-Genome Sequence of the Microcin E492-Producing Strain Klebsiella pneumoniae RYC492.	Genome Announcements	2013	1		e00178-13			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. 		
@D	Marcon, J.//Taketani, R.G.//Dini-Andreote, F.//Mazzero, G.I.//Soares, F.L.J.//Melo, I.S.//Azevedo, J.L.//Andreote, F.D. 	Draft Genome Sequence of Bacillus thuringiensis Strain BrMgv02-JM63, a Chitinolytic Bacterium Isolated from Oil-Contaminated Mangrove Soil in Brazil.	Genome Announcements	2014	2		e01264-13			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. 		
@D	Marczynski, G.T. 	Chromosome methylation and measurement of faithful, once and only once per cell cycle chromosome replication in Caulobacter crescentus.	J. Bacteriol.	1999	181		1984-1993			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. 		
@D	Mardanov, A.V.//Beletskii, A.V.//Gumerov, V.M.//Karbysheva, E.A.//Mikheeva, L.E. 	New low-copy plasmid in cyanobacterium Anabaena variabilis.	Genetika	2013	49		798-805			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). 		
@D	Mardanov, A.V.//Eldarov, M.A.//Sklyarenko, A.V.//Dumina, M.V.//Beletsky, A.V.//Yarotsky, S.V.//Ravin, N.V. 	Draft Genome Sequence of Escherichia coli Strain VKPM B-10182, Producing the Enzyme for Synthesis of Cephalosporin Acids.	Genome Announcements	2014	2		e01222-14			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. 		
@D	Mardanov, A.V.//Gumerov, V.M.//Beletsky, A.V.//Prokofeva, M.I.//Bonch-Osmolovskaya, E.A.//Ravin, N.V.//Skryabin, K.G. 	Complete genome sequence of the thermoacidophilic crenarchaeon Thermoproteus uzoniensis 768-20.	J. Bacteriol.	2011	193		3156-3157			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. 		
@D	Mardanov, A.V.//Gumerov, V.M.//Slobodkina, G.B.//Beletsky, A.V.//Bonch-Osmolovskaya, E.A.//Ravin, N.V.//Skryabin, K.G. 	Complete genome sequence of strain 1860, a crenarchaeon of the genus pyrobaculum able to grow with various electron acceptors.	J. Bacteriol.	2012	194		727-728			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. 		
@D	Mardanov, A.V.//Kochetkova, T.V.//Beletsky, A.V.//Bonch-Osmolovskaya, E.A.//Ravin, N.V.//Skryabin, K.G. 	Complete Genome Sequence of the Hyperthermophilic Cellulolytic Crenarchaeon 'Thermogladius cellulolyticus' 1633.	J. Bacteriol.	2012	194		4446-4447			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. 		
@D	Mardanov, A.V.//Ravin, N.V.//Svetlitchnyi, V.A.//Beletsky, A.V.//Miroshnichenko, M.L.//Bonch-Osmolovskaya, E.A.//Skryabin, K.G. 	Metabolic versatility and indigenous origin of the archaeon Thermococcus sibiricus, isolated from a siberian oil reservoir, as revealed by genome analysis.	Appl. Environ. Microbiol.	2009	75		4580-4588			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. 		
@D	Mardanov, A.V.//Slododkina, G.B.//Slobodkin, A.I.//Beletsky, A.V.//Gavrilov, S.N.//Kublanov, I.V.//Bonch-Osmolovskaya, E.A.//Skryabin, K.G.//Ravin, N.V. 	The genome of Geoglobus acetivorans: Fe(III) reduction, acetate utilization, autotrophic growth and degradation of aromatic compounds in a hyperthermophilic archaeon.	Appl. Environ. Microbiol.	2015	81		1003-1012			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. 		
@D	Mardanov, A.V.//Svetlitchnyi, V.A.//Beletsky, A.V.//Prokofeva, M.I.//Bonch-Osmolovskaya, E.A.//Ravin, N.V.//Skryabin, K.G. 	The Genome Sequence of the Crenarchaeon Acidilobus saccharovorans Supports a New Order, Acidilobales, and Suggests an Important Ecological Role in Terrestrial Acidic Hot Springs.	Appl. Environ. Microbiol.	2010	76		5652-5657			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. 		
@D	Mardanova, A.M.//Toymentseva, A.A.//Gilyazeva, A.G.//Kazakov, S.V.//Shagimardanova, E.I.//Khaitlina, S.Y.//Sharipova, M.R. 	Draft Genome Sequence of Serratia grimesii Strain A2.	Genome Announcements	2014	2		e00937-14			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. 		
@D	Marenda, M.S.//Sagne, E.//Poumarat, F.//Citti, C. 	Suppression subtractive hybridization as a basis to assess Mycoplasma agalactiae and Mycoplasma bovis genomic diversity and species-specific sequences.	Microbiology	2005	151		475-489			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. 		
@D	Maresca, D.//De Filippis, F.//Tytgat, H.L.P.//de Vos, W.M.//Mauriello, G. 	Draft Genome Sequences of the Aerobic Strains Lactobacillus gasseri AL3 and AL5.	Genome Announcements	2017	5		e00213-17			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. 		
@D	Margolles, A.//Gueimonde, M.//Sanchez, B. 	Genome Sequence of the Antarctic Psychrophile Bacterium Planococcus antarcticus DSM 14505.	J. Bacteriol.	2012	194		4465			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. 		
@D	Margos, G.//Hepner, S.//Mang, C.//Sing, A.//Liebl, B.//Fingerle, V. 	Completed Genome Sequences of Borrelia burgdorferi Sensu Stricto B31(NRZ) and Closely Related Patient Isolates from Europe.	Genome Announcements	2017	5		e00637-17			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. 		
@D	Margot, J.B.//Aguirre-Arteta, A.M.//Di Giacco, B.V.//Pradhan, S.//Roberts, R.J.//Cardoso, M.C.//Leonhardt, H. 	Structure and Function of the Mouse DNA Methyltransferase Gene: Dnmt1 shows a Tripartite Structure.	J. Mol. Biol.	2000	297		293-300			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. 		
@D	Margot, J.B.//Cardoso, M.C.//Leonhardt, H. 	Mammalian DNA methyltransferases show different subnuclear distributions.	J. Cell. Biochem.	2001	83		373-379			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. 		
@D	Margot, J.B.//Ehrenhofer-Murray, A.E.//Leonhardt, H. 	Interactions within the mammalian DNA methyltransferase family.	BMC Mol. Biol.	2003	4		7			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. 		
@D	Margulies, M. et al. 	Genome sequencing in microfabricated high-density picolitre reactors.	Nature	2005	437		376-380			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. 		
@D	Mariita, R.M.//Bhatnagar, S.//Hanselmann, K.//Hossain, M.J.//Korlach, J.//Boitano, M.//Roberts, R.J.//Liles, M.R.//Moss, A.G.//Leadbetter, J.R.//Newman, D.K.//Dawson, S.C. 	Complete Genome Sequence of Streptomyces sp. Strain CCM_MD2014, Isolated from Topsoil in Woods Hole, Massachusetts.	Genome Announcements	2015	3		e01506-15			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. 		
@D	Mariita, R.M.//Bhatnagar, S.//Hanselmann, K.//Hossain, M.J.//Korlach, J.//Boitano, M.//Roberts, R.J.//Liles, M.R.//Moss, A.G.//Leadbetter, J.R.//Newman, D.K.//Dawson, S.C. 	Complete Genome Sequence of Curtobacterium sp. Strain MR_MD2014, Isolated from Topsoil in Woods Hole, Massachusetts.	Genome Announcements	2015	3		e01504-15			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. 		
@D	Marin, M.A.//Fonseca, E.L.//Andrade, B.N.//Cabral, A.C.//Vicente, A.C. 	Worldwide Occurrence of Integrative Conjugative Element Encoding Multidrug Resistance Determinants in Epidemic Vibrio cholerae O1.	PLoS ONE	2014	9		E108728			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. 		
@D	Marinho-Almeida, D.//Dini-Andreote, F.//Camargo-Neves, A.A.//Juca-Ramos, R.T.//Andreote, F.D.//Carneiro, A.R.//Oliveira-de-Souza, L.A.//Caracciolo-Gomes-de-Sa, P.H.//Ribeiro-Barbosa, M.S.//Araujo, W.L.//Silva, A. 	Draft Genome Sequence of Methylobacterium mesophilicum Strain SR1.6/6, Isolated from Citrus sinensis.	Genome Announcements	2013	1		e00356-13			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. 		
@D	Marinus, M.G. 	Recombination is essential for viability of an Escherichia coli dam (DNA adenine methyltransferase) mutant.	J. Bacteriol.	2000	182		463-468			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. 		
@D	Marinus, M.G. 	DNA methylation in Escherichia coli.	Annu. Rev. Genet.	1987	21		113-131			None 		
@D	Marinus, M.G. 	DNA methylation influences trpR promoter activity in Escherichia coli K-12.	Mol. Gen. Genet.	1985	200		185-186			Methylation of adenine in the GATC-sequence of the -35 region of the trpR promoter decreases activity by 2-3 fold. 		
@D	Marinus, M.G. 	Location of DNA methylase genes on the Escherichia coli K-12 genetic map.	Mol. Gen. Genet.	1973	127		47-55			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. 		
@D	Marinus, M.G. 	Adenine methylation of Okazaki fragments in Escherichia coli.	J. Bacteriol.	1976	128		853-854			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. 		
@D	Marinus, M.G. 	Influence of uvrD3, uvrE502, and recL152 mutations on the phenotypes of Escherichia coli K-12 dam mutants.	J. Bacteriol.	1980	141		223-226			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. 		
@A	Marinus, M.G. 		DNA Methylation.			Neidhardt, F.C.//Ingraham, J.L.//Low, K.B.//Magasanik, B.//Schaechter, M.//Umbarger, H.E. 		Methylation of DNA in Escherichia coli and Salmonella typhimurium: Cellular and Molecular Biology				Washington, DC	Am. Soc. Microbiol.	1996		0		782-791									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. 		
@A	Marinus, M.G. 		Methylation of DNA.			Neidhardt, F.C. 		Escherichia coli and Salmonella typhimurium: Cellular and molecular biology.				Washington, D.C.	ASM Publications	1987		0		697-702									None 		
@A	Marinus, M.G. 		Methylation of prokaryotic DNA.			Razin, A.//Cedar, H.//Riggs, A.D. 		DNA Methylation. Biochemistry and Biological Significance.				New York	Springer-Verlag	1984		0		81-109									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). 		
@D	Marinus, M.G.//Carraway, M.//Frey, A.Z.//Brown, L.//Arraj, J.A. 	Insertion mutations in the dam gene of Escherichia coli K-12.	Mol. Gen. Genet.	1983	192		288-289			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. 		
@D	Marinus, M.G.//Casadesus, J. 	Roles of DNA adenine methylation in host-pathogen interactions: mismatch repair, transcriptional regulation, and more.	FEMS Microbiol. Rev.	2009	33		488-503			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. 		
@D	Marinus, M.G.//Konrad, E.B. 	Hyper-recombination in dam mutants of Escherichia coli K-12.	Mol. Gen. Genet.	1976	149		273-277			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. 		
@A	Marinus, M.G.//Lobner-Olesen, A. 		DNA Methylation.			Boeck, A.//Curtiss, R. III//Kaper, J.B.//Karp, P.D.//Neidhardt, F.C.//Nystroem, T.//Slauch, J.M.//Squires, C.L.//Ussery, D. 		EcoSal-Escherichia coli and Salmonella: Cellular and Molecular Biology				Washington, DC	ASM Press	2009				1-51									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. 		
@D	Marinus, M.G.//Morris, N.R. 	Biological function for 6-methyladenine residues in the DNA of Escherichia coli K12.	J. Mol. Biol.	1974	85		309-322			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. 		
@D	Marinus, M.G.//Morris, N.R. 	Pleiotropic effects of a DNA adenine methylation mutation (dam-3) in Escherichia coli K12.	Mutat. Res.	1975	28		15-26			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. 		
@D	Marinus, M.G.//Morris, N.R. 	Isolation of deoxyribonucleic acid methylase mutants of Escherichia coli K-12.	J. Bacteriol.	1973	114		1143-1150			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. 		
@D	Marinus, M.G.//Poteete, A.//Arraj, J.A. 	Correlation of DNA adenine methylase activity with spontaneous mutability in Escherichia coli K-12.	Gene	1984	28		123-125			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. 		
@D	Mark, K.-K.//Studier, F.W. 	Purification of the gene 0.3 protein of bacteriophage T7, an inhibitor of the DNA restriction system of Escherichia coli.	J. Biol. Chem.	1981	256		2573-2578			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. 		
@D	Markell, J.A.//Koziol, A.G.//Lambert, D. 	Draft Genome Sequence of Escherichia coli O157:H7 ATCC 35150 and a Nalidixic Acid-Resistant Mutant Derivative.	Genome Announcements	2015	3		e00734-15			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. 		
@D	Markie, D.//Tvrdeich, G.//Hill, D.F.//Poulter, R. 	The response of Type II restriction endonucleases to single base pair mismatches in heteroduplex DNA.	Proc. Univ. Otago Med. Sch.	1986	64		13-14			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. 		
@D	Marks, P.//McGeehan, J.//Kneale, G. 	A novel strategy for the expression and purification of the DNA methyltransferase, M.AhdI.	Protein Expr. Purif.	2004	37		236-242			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. 		
@D	Marks, P.//McGeehan, J.//Wilson, G.//Errington, N.//Kneale, G. 	Purification and characterization of a novel DNA methyltransferase, M.AhdI.	Nucleic Acids Res.	2003	31		2803-2810			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. 		
@D	Marques, C.//Franceschi, C.//Collin, V.//Laurent, F.//Chatellier, S.//Forestier, C. 	Genome Sequence of a Clinical Staphylococcus aureus Strain from a Prosthetic Joint Infection.	Genome Announcements	2016	4		e00198-16			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. 		
@D	Marques, J.M.//de Moura, V.A.//Lima, A.C.//Paixao, C.T.//Lobato, A.R.//Alves, J.T.//Guaraldi, A.L.//Folador, A.R.//Ramos, R.T.//Silva, A. 	Draft Genome Sequence of Corynebacterium pseudotuberculosis Strain PA06 Isolated  from a Subauricular Abscess in an Ovine Host.	Genome Announcements	2017	5		e00083-17			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. 		
@D	Marques, L.M.//Guimaraes, A.M.//Martins, H.B.//Rezende, I.S.//Barbosa, M.S.//Campos, G.B.//do Nascimento, N.C.//Dos Santos, A.P.//Amorim, A.T.//Santos, V.M.//Messick, J.B.//Timenetsky, J. 	Genome Sequence of Ureaplasma diversum Strain ATCC 49782.	Genome Announcements	2015	3		e00314-15			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. 		
@D	Marquez, V.E.//Eritja, R.//Kelley, J.A.//Vanbemmel, D.//Christman, J. 	Potent inhibition of HhaI DNA methylase by the aglycon of 2-(1H)-pyrimidinone riboside (Zebularine) at the G(C)under-barGC recognition domain.	Therapeutic Oligonucleotides	2003	1002		154-164			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. 		
@D	Marquez, V.E.//Eritja, R.//Kelley, J.A.//Vanbemmel, D.//Christman, J.K. 	Potent inhibition of HhaI DNA methylase by the aglycon of 2-(1H)-pyrimidinone riboside (Zebularine) at the GCGC recognition domain.	Ann. NY Acad. Sci.	2003	1002		154-164			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. 		
@D	Marquez, V.E.//Goddard, A.//Alvarez, E.//Ford, H. Jr.//Christman, J.K.//Sheikhnejad, G.//Brank, A.//Marasco, C.J.//Suffrin, J.R.//O'Gara, M.//Cheng, X. 	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.	Antisense Nucleic Acid Drug Dev.	1999	9		415-421			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. 		
@D	Marquez, V.E.//Wang, P.Y.//Nicklaus, M.C.//Maier, M.//Manoharan, M.//Christman, J.K.//Banavali, N.K.//Mackerell, A.D. 	Inhibition of (cytosine C5)-methyltransferase by oligonucleotides containing flexible (cyclopentane) and conformationally constrained  (bicyclo[3.1.0]hexane) abasic sites.	Nucleosides Nucleotides Nucleic Acids	2001	20		451-459			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. 		
@D	Marquez-Ortiz, R.A.//Haggerty, L.//Sim, E.M.//Duarte, C.//Castro-Cardozo, B.E.//Beltran, M.//Saavedra, S.//Vanegas, N.//Escobar-Perez, J.//Petty, N.K. 	First Complete Providencia rettgeri Genome Sequence, the NDM-1-Producing Clinical Strain RB151.	Genome Announcements	2017	5		e01472-16			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. 		
@D	Marra, A.//Shuman, H.A. 	Isolation of a Legionella pneumophila restriction mutant with increased ability to act as a recipient in heterospecific matings.	J. Bacteriol.	1989	171		2238-2240			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. 		
@D	Marrero, R.//Welkos, S.L. 	The transformation frequency of plasmids into Bacillus anthracis is affected by adenine methylation.	Gene	1995	152		75-78			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. 		
@D	Marsan, D.//Wommack, K.E.//Ravel, J.//Chen, F. 	Draft Genome Sequence of Synechococcus sp. Strain CB0101, Isolated From the Chesapeake Bay Estuary.	Genome Announcements	2014	2		e01111-13			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. 		
@D	Marsh, J.W.//Krauland, M.G.//Nelson, J.S.//Schlackman, J.L.//Brooks, A.M.//Pasculle, A.W.//Shutt, K.A.//Doi, Y.//Querry, A.M.//Muto, C.A.//Harrison, L.H. 	Genomic Epidemiology of an Endoscope-Associated Outbreak of Klebsiella pneumoniae Carbapenemase (KPC)-Producing K. pneumoniae.	PLoS ONE	2015	10		E0144310			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. 		
@D	Marshall, J.J.//Gowers, D.M.//Halford, S.E. 	Restriction Endonucleases that Bridge and Excise Two Recognition Sites from DNA.	J. Mol. Biol.	2007	367		419-431			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. 		
@D	Marshall, J.J.//Smith, R.M.//Ganguly, S.//Halford, S.E. 	Concerted action at eight phosphodiester bonds by the BcgI restriction endonuclease.	Nucleic Acids Res.	2011	39		7630-7640			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. 		
@D	Marshall, J.J.T.//Halford, S.E. 	The Type IIB restriction endonucleases.	Biochem. Soc. Trans.	2010	38		410-416			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. 		
@D	Marshall, K.T.//Morris, R.M. 	Genome Sequence of 'Candidatus Thioglobus singularis' Strain PS1, a Mixotroph from the SUP05 Clade of Marine Gammaproteobacteria.	Genome Announcements	2015	3		e01155-15			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. 		
@D	Marshall, P.//Davis, T.B.//Lemieux, C. 	The I-CeuI endonuclease: purification and potential role in the evolution of Chlamydomonas group I introns.	Eur. J. Biochem.	1994	220		855-859			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. 		
@D	Marshall, P.//Lemieux, C. 	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.	Nucleic Acids Res.	1992	20		6401-6407			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. 		
@D	Marshall, P.//Lemieux, C. 	Cleavage pattern of the homing endonuclease encoded by the fifth intron in the chloroplast large subunit rRNA-encoding gene of Chlamydomonas eugametos.	Gene	1991	104		241-245			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. 		
@D	Marston, M.F.//Pierciey, F.J. Jr.//Shepard, A.//Gearin, G.//Qi, J.//Yandava, C.//Schuster, S.C.//Henn, M.R.//Martiny, J.B. 	Rapid diversification of coevolving marine Synechococcus and a virus.	Proc. Natl. Acad. Sci. U. S. A.	2012	109		4544-4549			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. 		
@D	Marti, R.//Hagens, S.//Loessner, M.J.//Klumpp, J. 	Genome Sequence of Salmonella bongori Strain N268-08.	Genome Announcements	2013	1		e01018-13			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. 		
@D	Marti, R.//Hagens, S.//Loessner, M.J.//Klumpp, J. 	Genome Sequence of Salmonella bongori Strain N268-08, a Rare Clinical Isolate.	Genome Announcements	2013	1		e00580-13			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. 		
@D	Marti, R.//Schmid, M.//Kulli, S.//Schneeberger, K.//Naskova, J.//Knochel, S.//Ahrens, C.H.//Hummerjohann, J. 	Biofilm Formation Potential of Heat-Resistant Escherichia coli Dairy Isolates and the Complete Genome of Multidrug-Resistant, Heat-Resistant Strain FAM21845.	Appl. Environ. Microbiol.	2017	83		e00628-17			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. 		
@D	Marti, R.//Stephan, R.//Klumpp, J.//Nuesch-Inderbinen, M.//Hummerjohann, J.//Bagutti, C.//Zurfluh, K. 	Draft Genome Sequence of Klebsiella pneumoniae 704SK6, an OXA-48- and CTX-M-15-Encoding Wastewater Isolate.	Genome Announcements	2017	5		e00831-17			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. 		
@D	Marti, R.//Stephan, R.//Klumpp, J.//Nuesch-Inderbinen, M.//Hummerjohann, J.//Bagutti, C.//Zurfluh, K. 	Complete Genome Sequence of Enterobacter cloacae 704SK10, an OXA-48-Encoding Wastewater Isolate.	Genome Announcements	2017	5		e00830-17			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. 		
@D	Martienssen, R. 	Chipping away at chromatin.	Nat. Genet.	2001	27		240-241			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. 		
@D	Martienssen, R.A.//Colot, V. 	DNA methylation and epigenetic inheritance in plants and filamentous fungi.	Science	2001	293		1070-1074			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. 		
@D	Martienssen, R.A.//Richards, E.J. 	DNA methylation in eukaryotes.	Curr. Opin. Genet. Dev.	1995	5		234-242			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. 		
@D	Martin, A.M.//Horton, N.C.//Luseti, S.//Reich, N.O.//Perona, J.J. 	Divalent metal dependence of site-specific DNA binding by EcoRV endonuclease.	Biochemistry	1999	38		8430-8439			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. 		
@D	Martin, A.M.//Sam, M.D.//Reich, N.O.//Perona, J.J. 	Structural and energetic origins of indirect readout in site-specific DNA cleavage by a restriction endonuclease.	Nat. Struct. Biol.	1999	6		269-277			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. 		
@D	Martin, J.L.//McMillan, F.M. 	SAM (dependent) I AM: the S-adenosylmethionine-dependent methyltransferase fold.	Curr. Opin. Struct. Biol.	2002	12		783-793			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. 		
@D	Martin, P.//Boulukos, K.E.//Pognonec, P. 	REtools: a laboratory program for restriction enzyme work: enzyme selection and reaction condition assistance.	BMC Bioinformatics	2006	7		98			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. 		
@D	Martin, R.N.A.//McGeehan, J.E.//Ball, N.J.//Streeter, S.D.//Thresh, S.J.//Kneale, G.G. 	Structural analysis of DNA-protein complexes regulating the restriction-modification system Esp1396I.	Acta Crystallogr. F Struct. Biol. Cryst. Commun.	2013	69		962-966			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. 		
@D	Martin, R.N.A.//McGeehan, J.E.//Kneale, G. 	Structural and Mutagenic Analysis of the RM Controller Protein C.Esp1396I.	PLoS ONE	2014	9		e98365			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. 		
@D	Martin, V.//Cardenas, N.//Jimenez, E.//Maldonado, A.//Rodriguez, J.M.//Fernandez, L. 	Genome Sequence of Lactobacillus gastricus PS3, a Strain Isolated from Human Milk.	Genome Announcements	2013	1		e00489-13			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. 		
@D	Martin, V.//Maldonado-Barragan, A.//Jimenez, E.//Ruas-Madiedo, P.//Fernandez, L.//Rodriguez, J.M. 	Complete Genome Sequence of Streptococcus salivarius PS4, a Strain Isolated from  Human Milk.	J. Bacteriol.	2012	194		4466-4467			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. 		
@D	Martin-Cuadrado, A.B.//Lopez-Garcia, P.//Alba, J.C.//Moreira, D.//Monticelli, L.//Strittmatter, A.//Gottschalk, G.//Rodriguez-Valera, F. 	Metagenomics of the deep mediterranean, a warm bathypelagic habitat.	PLoS ONE	2007	2		e914			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. 		
@D	Martin-Cuadrado, A.B.//Rodriguez-Valera, F.//Moreira, D.//Alba, J.C.//Ivars-Martinez, E.//Henn, M.R.//Talla, E.//Lopez-Garcia, P. 	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.	ISME J.	2008	2		865-886			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. 		
@D	Martin-Laurent, F.//Marti, R.//Waglechner, N.//Wright, G.D.//Topp, E. 	Draft Genome Sequence of the Sulfonamide Antibiotic-Degrading Microbacterium sp.  Strain C448.	Genome Announcements	2014	2		e01113-13			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. 		
@D	Martineau, C.//Villeneuve, C.//Mauffrey, F.//Villemur, R. 	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.	Genome Announcements	2014	2		e01165-13			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. 		
@D	Martinet, N.//Michel, B.Y.//Bertrand, P.//Benhida, R. 	Small molecules DNA methyltransferases inhibitors.	MedChemComm	2012	3		263-273			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. 		
@D	Martinez, N.//Luque, R.//Olivares, M.M.//Margolles, A.//Banuelos, O. 	Resequencing the Genome of Bifidobacterium breve Strain CECT7263.	Genome Announcements	2017	5		e00299-17			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. 		
@D	Martinez, R.J.//Bruce, D.//Detter, C.//Goodwin, L.A.//Han, J.//Han, C.S.//Held, B.//Land, M.L.//Mikhailova, N.//Nolan, M.//Pennacchio, L.//Pitluck, S.//Tapia, R.//Woyke, T.//Sobecky, P.A. 	Complete Genome Sequence of Rahnella sp. Strain Y9602, a Gammaproteobacterium Isolate from Metal- and Radionuclide-Contaminated Soil.	J. Bacteriol.	2012	194		2113-2114			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. 		
@D	Martinez, R.J.//Bruce, D.//Detter, C.//Goodwin, L.A.//Han, J.//Han, C.S.//Held, B.//Land, M.L.//Mikhailova, N.//Nolan, M.//Pennacchio, L.//Pitluck, S.//Tapia, R.//Woyke, T.//Sobecky, P.A. 	Complete Genome Sequence of Rahnella aquatilis CIP 78.65.	J. Bacteriol.	2012	194		3020-3021			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. 		
@D	Martinez, T.//Ropelewski, A.J.//Gonzalez-Mendez, R.//Vazquez, G.J.//Robledo, I.E. 	Draft Genome Sequence of Klebsiella pneumoniae Carbapenemase-Producing Acinetobacter baumannii Strain M3AC9-7, Isolated from Puerto Rico.	Genome Announcements	2015	3		e00274-15			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%. 		
@D	Martinez, T.//Ropelewski, A.J.//Gonzalez-Mendez, R.//Vazquez, G.J.//Robledo, I.E. 	Draft Genome Sequence of a Multidrug-Resistant Klebsiella pneumoniae Carbapenemase-Producing Acinetobacter baumannii Sequence Type 2 Isolate from  Puerto Rico.	Genome Announcements	2016	4		e00758-16			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%. 		
@D	Martinez, V.//Hormigo, D.//Del Cerro, C.//Gomez-de-Santos, P.//Garcia-Hidalgo, J.//Arroyo, M.//Prieto, A.//Garcia, J.L.//de la Mata, I. 	Genome Sequence of Streptomyces exfoliatus DSMZ 41693, a Source of Poly(3-Hydroxyalkanoate)-Degrading Enzymes.	Genome Announcements	2014	2		e01272-13			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. 		
@D	Martinez-Abarca, F.//Garcia-Rodriguez, F.M.//Toro, N. 	Homing of a bacterial group II intron with an intron-encoded protein lacking a recognizable endonuclease domain.	Mol. Microbiol.	2000	35		1405-1412			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. 		
@D	Martinez-Abarca, F.//Martinez-Rodriguez, L.//Lopez-Contreras, J.A.//Jimenez-Zurdo, J.I.//Toro, N. 	Complete Genome Sequence of the Alfalfa Symbiont Sinorhizobium/Ensifer meliloti Strain GR4.	Genome Announcements	2013	1		e00174-12			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). 		
@D	Martinez-Ballesteros, I.//Arizaga, Y.//Bikandi, J.//Garaizar, J.//Ganau, G.//Paglietti, B.//Murgia, M.//Deligios, M.//Rubino, S. 	Draft Genome Sequence of an Oceanobacillus sp. Strain Isolated from Soil in a Burial Crypt.	Genome Announcements	2016	4		e00701-16			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. 		
@D	Martinez-Blanch, J.F.//Ramon, D.//Beltran, D.//Romo-Vaquero, M.//Garcia-Villalba, R.//Espin, J.C.//Tomas-Barberan, F.A.//Codoner, F.M.//Selma, M.V. 	Complete Genome Sequence of the New Urolithin-Producing Bacterium Gordonibacter urolithinfaciens DSM 27213(T).	Genome Announcements	2017	5		e01120-17			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. 		
@D	Martinez-Garcia, P.M.//Rodriguez-Palenzuela, P.//Arrebola, E.//Carrion, V.J.//Gutierrez-Barranquero, J.A.//Perez-Garcia, A.//Ramos, C.//Cazorla, F.M.//Vicente, Ad. 	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.	PLoS ONE	2015	10		E0136101			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. 		
@D	Martinez-Garcia, P.M.//Ruano-Rosa, D.//Schiliro, E.//Prieto, P.//Ramos, C.//Rodriguez-Palenzuela, P.//Mercado-Blanco, J. 	Complete genome sequence of Pseudomonas fluorescens strain PICF7, an indigenous root endophyte from olive (Olea europaea L.) and effective biocontrol agent  against Verticillium dahliae.	Standards in Genomic Sciences	2015	10		10			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. 		
@D	Martinez-Ocampo, F.//Fernandez, L.M.G.//Lozano-Aguirre, B.L.F.//Popoca-Ursino, E.C.//Ortiz-Hernandez, M.L.//Sanchez-Salinas, E.//Ramos, Q.F.//Villalobos-Lopez, M.A.//Dantan-Gonzalez, E. 	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.	Genome Announcements	2016	4		e00220-16			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. 		
@D	Martinez-Ocampo, F.//Lozano-Aguirre, B.L.F.//Hernandez-Mendoza, A.//Rojas-Espinoza, L.E.//Popoca-Ursino, E.C.//Ortiz-Hernandez, M.L.//Sanchez-Salinas, E.//Ramos, Q.F.//Dantan-Gonzalez, E. 	Burkholderia cenocepacia Strain CEIB S5-1, a Rhizosphere-Inhabiting Bacterium with Potential in Bioremediation.	Genome Announcements	2015	3		e00056-15			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. 		
@D	Martinez-Ocampo, F.//Rodriguez-Camarillo, S.D.//Amaro-Estrada, I.//Quiroz-Castaneda, R.E. 	Draft Genome Sequence of 'Candidatus Mycoplasma haemobos,' a Hemotropic Mycoplasma Identified in Cattle in Mexico.	Genome Announcements	2016	4		e00656-16			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. 		
@D	Martinez-Penafiel, E.//Fernandez-Ramirez, F.//Ishida, C.//Reyes-Cortes, R.//Sepulveda-Robles, O.//Guarneros-Pena, G.//Bermudez-Cruz, R.M.//Kameyama, L. 	Overexpression of Ipe protein from the coliphage mEp021 induces pleiotropic effects involving hemolysis by HlyE-containing vesicles and cell death.	Biochimie	2012	94		1262-1273			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. 		
@D	Martinez-Raudales, I.//De La Cruz-Rodriguez, Y.//Alvarado-Gutierrez, A.//Vega-Arreguin, J.//Fraire-Mayorga, A.//Alvarado-Rodriguez, M.//Balderas-Hernandez, V.//Fraire-Velazquez, S. 	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.	Standards in Genomic Sciences	2017	12		73			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. 		
@D	Martinez-Raudales, I.//De La Cruz-Rodriguez, Y.//Vega-Arreguin, J.//Alvarado-Gutierrez, A.//Fraire-Mayorga, A.//Alvarado-Rodriguez, M.//Balderas-Hernandez, V.//Gomez-Soto, J.M.//Fraire-Velazquez, S. 	Draft Genome Sequence of Bacillus velezensis 3A-25B, a Strain with Biocontrol Activity against Fungal and Oomycete Root Plant Phytopathogens, Isolated from  Grassland Soil.	Genome Announcements	2017	5		e01021-17			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. 		
@D	Martinez-Romero, E.//Silva-Sanchez, J.//Barrios, H.//Rodriguez-Medina, N.//Martinez-Barnetche, J.//Tellez-Sosa, J.//Gomez-Barreto, R.E.//Garza-Ramos, U. 	Draft Genome Sequences of Klebsiella variicola Plant Isolates.	Genome Announcements	2015	3		e01015-15			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. 		
@D	Martinez-Steele, L.//Lowe, C.G.//Okihiro, M.S.//Berlemont, R. 	Draft Genome Sequences of Nine New Carnobacterium maltaromaticum Strains Isolated from Diseased Sharks.	Genome Announcements	2018	6		e00354-18			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). 		
@D	Martino, G.P.//Quintana, I.M.//Espariz, M.//Blancato, V.S.//Gallina, N.G.//Esteban, L.//Magni, C. 	Draft Genome Sequences of Four Enterococcus faecium Strains Isolated from Argentine Cheese.	Genome Announcements	2016	4		e01576-15			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. 		
@D	Martino, M.E.//Bayjanov, J.R.//Joncour, P.//Hughes, S.//Gillet, B.//Kleerebezem, M.//Siezen, R.//van Hijum, S.A.//Leulier, F. 	Resequencing of the Lactobacillus plantarum Strain WJL Genome.	Genome Announcements	2015	3		e01382-15			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. 		
@D	Martino, M.E.//Bayjanov, J.R.//Joncour, P.//Hughes, S.//Gillet, B.//Kleerebezem, M.//Siezen, R.//van Hijum, S.A.//Leulier, F. 	Nearly Complete Genome Sequence of Lactobacillus plantarum Strain NIZO2877.	Genome Announcements	2015	3		e01370-15			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. 		
@D	Maruyama, F.//Kobata, M.//Kurokawa, K.//Nishida, K.//Sakurai, A.//Nakano, K.//Nomura, R.//Kawabata, S.//Ooshima, T.//Nakai, K.//Hattori, M.//Hamada, S.//Nakagawa, I. 	Comparative genomic analyses of Streptococcus mutans provide insights into chromosomal shuffling and species-specific content.	BMC Genomics	2009	10		358			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. 		
@D	Marvig, R.L.//Jochumsen, N.//Johansen, H.K.//Hoiby, N.//Molin, S.//Sommer, M.O.//Jelsbak, L.//Folkesson, A. 	Draft Genome Sequences of Pseudomonas aeruginosa B3 Strains Isolated from a Cystic Fibrosis Patient Undergoing Antibiotic Chemotherapy.	Genome Announcements	2013	1		e00804-13			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. 		
@D	Marx, C.J. et al. 	Complete genome sequences of six strains of the genus methylobacterium.	J. Bacteriol.	2012	194		4746-4748			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. 		
@D	Marx, H.//Graf, A.B.//Tatto, N.E.//Thallinger, G.G.//Mattanovich, D.//Sauer, M. 	Genome Sequence of the Ruminal Bacterium Megasphaera elsdenii.	J. Bacteriol.	2011	193		5578-5579			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. 		
@D	Marx, J.L. 	Restriction enzymes:  new tools for studying DNA.	Science	1973	180		482-485			None 		
@D	Marzabal, S.//DuBois, S.//Thielking, V.//Cano, A.//Eritja, R.//Guschlbauer, W. 	Dam methylase from Escherichia coli: kinetic studies using modified DNA oligomers: hemimethylated substrates.	Nucleic Acids Res.	1995	23		3648-3655			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. 		
@D	Mas-Llado, M.//Pina-Villalonga, J.M.//Brunet-Galmes, I.//Nogales, B.//Bosch, R. 	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.	Genome Announcements	2015	3		e00041-15			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. 		
@D	Mas-Llado, M.//Pina-Villalonga, J.M.//Brunet-Galmes, I.//Nogales, B.//Bosch, R. 	Draft Genome Sequences of Two Isolates of the Roseobacter Group, Sulfitobacter sp. Strains 3SOLIMAR09 and 1FIGIMAR09, from Harbors of Mallorca Island  (Mediterranean Sea).	Genome Announcements	2014	2		e00350-14			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. 		
@D	Masai, E.//Kamimura, N.//Kasai, D.//Oguchi, A.//Ankai, A.//Fukui, S.//Takahashi, M.//Yashiro, I.//Sasaki, H.//Harada, T.//Nakamura, S.//Katano, Y.//Narita-Yamada, S.//Nakazawa, H.//Hara, H.//Katayama, Y.//Fukuda, M.//Yamazaki, S.//Fujita, N. 	Complete Genome Sequence of Sphingobium sp. Strain SYK-6, a Degrader of Lignin-Derived Biaryls and Monoaryls.	J. Bacteriol.	2012	194		534-535			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. 		
@D	Mascarenhas, D.S.A.C.//Jie, R.//Antunes, G.H.//Alves, M.//Pombert, J.F. 	Complete Genome Sequences of the Potential Zoonotic Pathogens Staphylococcus felis and Staphylococcus kloosii.	Genome Announcements	2018	6		e00404-18			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). 		
@D	Mashhoon, N. 	Kinetic and chemical mechanisms of the EcoRI DNA (N6-adenine) methyltransferase.	Diss. Abstr.	1994	54		5132B-5133B			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. 		
@D	Mashhoon, N.//Carroll, M.//Pruss, C.//Eberhard, J.//Ishikawa, S.//Estabrook, R.A.//Reich, N. 	Functional Characterization of Escherichia coli DNA Adenine Methyltransferase, a Novel Target for Antibiotics.	J. Biol. Chem.	2004	279		52075-52081			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. 		
@D	Mashhoon, N.//Pruss, C.//Carroll, M.//Johnson, P.H.//Reich, N.O. 	Selective inhibitors of bacterial DNA adenine methyltransferases.	J. Biomol. Screen.	2006	11		497-510			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. 		
@D	Mashhoon, N.//Reich, N.O. 	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.	Biochemistry	1994	33		7113-7119			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. 		
@D	Mashhoon, N.//Reich, N.O. 	A kinetic study of DNA methylation by EcoRI methylase.	J. Cell Biol.	1988	107		838a			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. 		
@D	Mashhoon, N.//Reich, N.O. 	An investigation of the chemical mechanism of the EcoRI DNA methyltransferase.	FASEB J.	1992	6		A333			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. 		
@D	Mashhoon, N.//Reich, N.O. 	Analysis of the kinetic and chemical mechanisms of EcoRI methylase.	FASEB J.	1990	4		A1979			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. 		
@D	Mashhoon, N.//Reich, N.O. 	A kinetic study of DNA methylation by EcoRI methylase.	ACS Abstracts	1988	196		96			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. 		
@D	Mashima, I.//Liao, Y.C.//Sabharwal, A.//Haase, E.M.//Nakazawa, F.//Scannapieco, F.A. 	Draft Genome Sequences of Four Strains of Recently Established Novel Veillonella  Species Isolated from Human Oral Cavities.	Genome Announcements	2018	6		e00259-18			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. 		
@D	Mashima, I.//Nakazawa, F. 	Draft Genome Sequence of Veillonella tobetsuensis ATCC BAA-2400T Isolated from Human Tongue Biofilm.	Genome Announcements	2015	3		e00808-15			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. 		
@D	Mashimo, C.//Yamane, K.//Yamanaka, T.//Maruyama, H.//Wang, P.L.//Komasa, S.//Okazaki, J.//Nambu, T. 	Genome Sequence of Actinomyces naeslundii Strain ATCC 27039, Isolated from an Abdominal Wound Abscess.	Genome Announcements	2016	4		e01443-16			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. 		
@D	Maslov, A.//Metrikin, M.//Vijg, J. 	A dual-activation, adenoviral-based system for the controlled induction of DNa double-strand breaks by the restriction endonuclease SacI.	Biotechniques	2009	47		847-854			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. 		
@D	Maslov, D.A.//Shur, K.V.//Bekker, O.B.//Zakharevich, N.V.//Zaichikova, M.V.//Klimina, K.M.//Smirnova, T.G.//Zhang, Y.//Chernousova, L.N.//Danilenko, V.N. 	Draft Genome Sequences of Two Pyrazinamide-Resistant Clinical Isolates, Mycobacterium tuberculosis 13-4152 and 13-2459.	Genome Announcements	2015	3		e00758-15			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. 		
@D	Masood, N.//Jackson, E.//Moore, K.//Farbos, A.//Paszkiewicz, K.//Dickins, B.//McNally, A.//Forsythe, S. 	Draft Genome Sequence of 'Candidatus Cronobacter colletis' NCTC 14934T, a New Species in the Genus Cronobacter.	Genome Announcements	2014	2		e00585-14			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. 		
@D	Masood, N.//Moore, K.//Farbos, A.//Hariri, S.//Block, C.//Paszkiewicz, K.//Dickins, B.//McNally, A.//Forsythe, S. 	Draft Genome Sequence of a Meningitic Isolate of Cronobacter sakazakii Clonal Complex 4, Strain 8399.	Genome Announcements	2013	1		e00833-13			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. 		
@D	Masood, N.//Moore, K.//Farbos, A.//Hariri, S.//Paszkiewicz, K.//Dickins, B.//McNally, A.//Forsythe, S. 	Draft Genome Sequences of Three Newly Identified Species in the Genus Cronobacter, C. helveticus LMG23732T, C. pulveris LMG24059, and C. zurichensis  LMG23730T.	Genome Announcements	2013	1		e00783-13			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. 		
@D	Masood, N.//Moore, K.//Farbos, A.//Hariri, S.//Paszkiewicz, K.//Dickins, B.//McNally, A.//Forsythe, S. 	Draft Genome Sequence of the Earliest Cronobacter sakazakii Sequence Type 4 Strain, NCIMB 8272.	Genome Announcements	2013	1		e00782-13			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. 		
@D	Master, S.S. 	What is the origin and role of the large variable region in the M-AluI DNA-(cytosine c5) methyltransferase?	Diss. Abstr.	1996	57		1626			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. 		
@D	Master, S.S.//Blumenthal, R.M. 	A genetic and functional analysis of the unusually large variable region in the M.AluI DNA-(cytosine C5)-methyltransferase.	Mol. Gen. Genet.	1997	257		14-22			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. 		
@D	Master, S.S.//Blumenthal, R.M. 	Is the M.AluI DNA-(cytosine C5)-methyltransferase monospecific or multispecific?	FASEB J.	1995	9		A1399			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. 		
@D	Masuda, H.//Shiwa, Y.//Yoshikawa, H.//Zylstra, G.J. 	Draft Genome Sequence of the Versatile Alkane-Degrading Bacterium Aquabacterium sp. Strain NJ1.	Genome Announcements	2014	2		e01271-14			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. 		
@D	Masuda, S.//Hori, K.//Maruyama, F.//Ren, S.//Sugimoto, S.//Yamamoto, N.//Mori, H.//Yamada, T.//Sato, S.//Tabata, S.//Ohta, H.//Kurokawa, K. 	Whole-Genome Sequence of the Purple Photosynthetic Bacterium Rhodovulum sulfidophilum Strain W4.	Genome Announcements	2013	1		e00577-13			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. 		
@D	Matejkova, P.//Strouhal, M.//Smajs, D.//Norris, S.J.//Palzkill, T.//Petrosino, J.F.//Sodergren, E.//Norton, J.E.//Singh, J.//Richmond, T.A.//Molla, M.N.//Albert, T.J.//Weinstock, G.M. 	Complete genome sequence of Treponema pallidum ssp. pallidum strain SS14 determined with oligonucleotide arrays.	BMC Microbiol.	2008	8		76			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. 		
@D	Mateos-Rivera, A.//Islam, T.//Marshall, I.P.G.//Schreiber, L.//Ovreas, L. 	High-quality draft genome of the methanotroph Methylovulum psychrotolerans Str. HV10-M2 isolated from plant material at a high-altitude environment.	Standards in Genomic Sciences	2018	13		10			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%. 		
@D	Mather, A.E. et al. 	Distinguishable epidemics of multidrug-resistant Salmonella Typhimurium DT104 in different hosts.	Science	2013	341		1514-1517			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. 		
@D	Mathers, A.J.//Stoesser, N.//Sheppard, A.E.//Pankhurst, L.//Giess, A.//Yeh, A.J.//Didelot, X.//Turner, S.D.//Sebra, R.//Kasarskis, A.//Peto, T.//Crook, D.//Sifri, C.D. 	Klebsiella pneumoniae carbapenemase (KPC)-producing K. pneumoniae at a single institution: insights into endemicity from whole-genome sequencing.	Antimicrob. Agents Chemother.	2015	59		1656-1663			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. 		
@D	Mathew, D.C.//Lo, S.C.//Mathew, G.M.//Chang, K.H.//Huang, C.C. 	Genomic sequence analysis of a plant-associated Photobacterium halotolerans MELD1: from marine to terrestrial environment?	Standards in Genomic Sciences	2016	11		56			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. 		
@D	Mathew, D.C.//Mathew, G.M.//Gicana, R.G.//Huang, C.C. 	Genome Sequence of Photobacterium halotolerans MELD1, with Mercury Reductase (merA), Isolated from Phragmites australis.	Genome Announcements	2015	3		e00530-15			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. 		
@D	Mathew, M.J.//Subramanian, G.//Nguyen, T.T.//Robert, C.//Mediannikov, O.//Fournier, P.E.//Raoult, D. 	Genome Sequence of Diplorickettsia massiliensis, an Emerging Ixodes ricinus-Associated Human Pathogen.	J. Bacteriol.	2012	194		3287			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. 		
@D	Mathews, S.L.//Pawlak, J.//Grunden, A.M. 	Draft Genome Sequences of Two Strains of Paenibacillus glucanolyticus with the Ability To Degrade Lignocellulose.	Genome Announcements	2016	4		e00423-16			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. 		
@D	Mathimaran, N.//Srivastava, R.//Wiemken, A.//Sharma, A.K.//Boller, T. 	Genome sequences of two plant growth-promoting fluorescent pseudomonas strains, r62 and r81.	J. Bacteriol.	2012	194		3272-3273			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. 		
@D	Mathur, P.//Veeraraghavan, B.//Devanga, R.N.K.//Inbanathan, F.Y.//Khurana, S.//Bhardwaj, N.//Kumar, S.//Sagar, S.//Gupta, A. 	First Report on a Cluster of Colistin-Resistant Klebsiella pneumoniae Strains Isolated from a Tertiary Care Center in India: Whole-Genome Shotgun Sequencing.	Genome Announcements	2017	5		e01466-16			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. 		
@D	Matic, I.//Taddei, F.//Radman, M. 	Genetic barriers among bacteria.	Trends Microbiol.	1996	4		69-73			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. 		
@D	Matilla, M.A.//Drew, A.//Udaondo, Z.//Krell, T.//Salmond, G.P. 	Genome Sequence of Serratia plymuthica A153, a Model Rhizobacterium for the Investigation of the Synthesis and Regulation of Haterumalides, Zeamine, and  Andrimid.	Genome Announcements	2016	4		e00373-16			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. 		
@D	Matilla, M.A.//Pizarro-Tobias, P.//Roca, A.//Fernandez, M.//Duque, E.//Molina, L.//Wu, X.//van der Lelie, D.//Gomez, M.J.//Segura, A.//Ramos, J.L. 	Complete genome of the plant-growth promoting rhizobacterium Pseudomonas putida BIRD-1.	J. Bacteriol.	2010	193		1290			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. 		
@D	Matilla, M.A.//Udaondo, Z.//Krell, T.//Salmond, G.P. 	Genome Sequence of Serratia marcescens MSU97, a Plant-Associated Bacterium That Makes Multiple Antibiotics.	Genome Announcements	2017	5		e01752-16			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. 		
@D	Matin, M.M.//Hornby, D.P. 	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).	Anal. Biochem.	2000	278		46-51			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. 		
@D	Matin, M.M.//Hornby, D.P. 	Exploring the structural flexibility of 5m-cytosine-DNA methyltransferases.	Biochem. Soc. Trans.	1998	26		S394			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. 		
@D	Matje, D.M.//Coughlin, D.F.//Connolly, B.A.//Dahlquist, F.W.//Reich, N.O. 	Determinants of Precatalytic Conformational Transitions in the DNA Cytosine Methyltransferase M.HhaI.	Biochemistry	2011	50		1465-1473			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. 		
@D	Matje, D.M.//Zhou, H.//Smith, D.A.//Neely, R.K.//Dryden, D.T.//Jones, A.C.//Dahlquist, F.W.//Reich, N.O. 	Enzyme-Promoted Base Flipping Controls DNA Methylation Fidelity.	Biochemistry	2013	52		1677-1685			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. 		
@D	Matney, T.S.//MacDougall, N.L.T.//Butler, M.A.//Suit, J.C. 	Host-induced modification/restriction and the utilization of 5-bromouracil by thymineless mutants of Escherichia coli.	J. Bacteriol.	1970	104		606-607			An mk-rk- mutation exerted no measurable effect on 5-bromouracil incorporation by a thymineless derivative of Escherichia coli K. 		
@D	Matrosova, V.Y. et al. 	High-quality genome sequence of the radioresistant bacterium Deinococcus ficus KS 0460.	Standards in Genomic Sciences	2017	12		46			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. 		
@D	Matselyukh, A.B. 	Genetic transformation of Streptomyces globisporus 1912 strains: restriction barrier and plasmid compatibility.	Mikrobiol. Zh.	2001	63		15-21			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. 		
@D	Matson, E.G.//Zhang, X.//Leadbetter, J.R. 	Selenium controls transcription of paralogous formate dehydrogenase genes in the termite gut acetogen, Treponema primitia.	Environ. Microbiol.	2010	12		2245-2258			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. 		
@D	Matsui, H.//Takahashi, T.//Murayama, S.Y.//Uchiyama, I.//Yamaguchi, K.//Shigenobu, S.//Suzuki, M.//Rimbara, E.//Shibayama, K.//Overby, A.//Nakamura, M. 	Draft Genome Sequence of Helicobacter suis Strain SNTW101, Isolated from a Japanese Patient with Nodular Gastritis.	Genome Announcements	2016	4		e00934-16			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. 		
@D	Matsui, M.//Mise, K.//Yoshida, Y.//Ishidate, M. 	Production of restriction endonucleases from various Salmonella strains of human origin.	Eisei Shikenjo Hokoku	1986	104		92-96			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. 		
@D	Matsumoto, A.//Igo, M.M. 	Species-Specific Type II Restriction-Modification System of Xylella fastidiosa Temecula1.	Appl. Environ. Microbiol.	2010	76		4092-4095			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. 		
@D	Matsumura, H.//Takahashi, H.//Inoue, T.//Yamamoto, T.//Hashimoto, H.//Nishioka, M.//Fujiwara, S.//Takagi, M.//Imanaka, T.//Kai, Y. 	Crystal structure of intein homing endonuclease II encoded in DNA polymerase gene from hyperthermophilic archaeon Thermococcus kodakaraensis strain KOD1.	Proteins	2006	63		711-715					
@D	Matsumura, Y.//Peirano, G.//Pitout, J.D.D. 	Complete Genome Sequence of Escherichia coli J53, an Azide-Resistant Laboratory Strain Used for Conjugation Experiments.	Genome Announcements	2018	6		e00433-18			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. 		
@D	Matsumura, Y.//Yamamoto, M.//Nakano, S.//Nagao, M. 	Complete Genome Sequence of Escherichia coli ME8067, an Azide-Resistant Laboratory Strain Used for Conjugation Experiments.	Genome Announcements	2018	6		e00515-18			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. 		
@D	Matsunaga, E.//Higuchi, Y.//Mori, K.//Tashiro, K.//Kuhara, S.//Takegawa, K. 	Draft Genome Sequence of Streptomyces sp. JHA19, a Strain That Possesses beta-d-Galactofuranosidase Activity.	Genome Announcements	2015	3		e01171-15			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. 		
@D	Matsunaga, E.//Higuchi, Y.//Mori, K.//Tashiro, K.//Takegawa, K. 	Draft Genome Sequence of Streptomyces sp. JHA26, a Strain That Harbors a PA14 Domain Containing beta-d-Galactofuranosidase.	Genome Announcements	2017	5		e00190-17			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. 		
@D	Matsunaga, T.//Okamura, Y.//Fukuda, Y.//Wahyudi, A.T.//Murase, Y.//Takeyama, H. 	Complete Genome Sequence of the Facultative Anaerobic Magnetotactic Bacterium Magnetospirillum sp. strain AMB-1.	DNA Res.	2005	12		157-166			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. 		
@D	Matsuo, K.//Silke, J.//Gramatikoff, K.//Schaffner, W. 	The CpG-specific methylase SssI has topoisomerase activity in the presence of Mg2+.	Nucleic Acids Res.	1994	22		5354-5359			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. 		
@D	Matsuoka, S.//Asai, K.//Sadaie, Y. 	Restriction and modification of SP10 phage by BsuM of Bacillus subtilis Marburg.	FEMS Microbiol. Lett.	2005	244		335-339			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. 		
@D	Matsushima, P.//Baltz, R.H. 	Streptomyces lipmanii expresses two restriction systems that inhibit plasmid transformation and bacteriophage plaque formation.	J. Bacteriol.	1989	171		3128-3132			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. 		
@D	Matsushima, P.//Baltz, R.H. 	Restriction and modification in Streptomyces lipmanii.	Abstr. Gen. Meet. Am. Soc. Microbiol.	1989	89		361			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. 		
@D	Matsushima, P.//Cox, K.L.//Baltz, R.H. 	Highly transformable mutants of Streptomyces fradiae defective in several restriction systems.	Mol. Gen. Genet.	1987	206		393-400			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. 		
@D	Matsushima, P.//McHenney, M.A.//Baltz, R.H. 	Efficient transformation of Amycolatopsis orientalis (Nocardia orientalis) protoplasts by Streptomyces plasmids.	J. Bacteriol.	1987	169		2298-2300			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. 		
@D	Matsushima, P.//McHenney, M.A.//Baltz, R.H. 	Transduction and transformation of plasmid DNA in Streptomyces fradiae strains that express different levels of restriction.	J. Bacteriol.	1989	171		3080-3084			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. 		
@D	Matsushita, S.//Nakano, M.//Aoi, Y.//Kindaichi, T.//Ozaki, N.//Ohashi, A. 	Draft Genome Sequence of Mn(II)-Oxidizing Pseudomonas resinovorans Strain MO-1.	Genome Announcements	2018	6		e00088-18			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. 		
@D	Matsutani, M.//Hirakawa, H.//Nishikura, M.//Soemphol, W.//Ali, I.A.//Yakushi, T.//Matsushita, K. 	Increased number of Arginine-based salt bridges contributes to the thermotolerance of thermotolerant acetic acid bacteria, Acetobacter tropicalis SKU1100.	Biochem. Biophys. Res. Commun.	2011	409		120-124			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). 		
@D	Matsutani, M.//Kawajiri, E.//Yakushi, T.//Adachi, O.//Matsushita, K. 	Draft Genome Sequence of Dihydroxyacetone-Producing Gluconobacter thailandicus Strain NBRC 3255.	Genome Announcements	2013	1		e00118-13			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. 		
@D	Matsutani, M.//Shirakihara, Y.//Imada, K.//Yakushi, T.//Matsushita, K. 	Draft Genome Sequence of a Thermophilic Member of the Bacillaceae, Anoxybacillus  flavithermus Strain Kn10, Isolated from the Kan-nawa Hot Spring in Japan.	Genome Announcements	2013	1		e00311-13			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. 		
@D	Matsutani, M.//Suzuki, H.//Yakushi, T.//Matsushita, K. 	Draft genome sequence of Gluconobacter thailandicus NBRC 3257.	Standards in Genomic Sciences	2014	9		614-623			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. 		
@D	Matsuura, M.//Saldanha, R.//Ma, H.//Wank, H.//Yang, J.//Mohr, G.//Cavangh, S.//Dunny, G.M.//Belfort, M.//Lambowitz, A.M. 	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.	Genes Dev.	1997	11		2910-2924			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. 		
@D	Matsuura, N.//Ohashi, A.//Tourlousse, D.M.//Sekiguchi, Y. 	Draft Genome Sequence of Thermodesulfovibrio aggregans TGE-P1T, an Obligately Anaerobic, Thermophilic, Sulfate-Reducing Bacterium in the Phylum Nitrospirae.	Genome Announcements	2016	4		e00089-16			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. 		
@D	Matsuura, N.//Ohashi, A.//Tourlousse, D.M.//Sekiguchi, Y. 	Draft Genome Sequence of the Syntrophic Lactate-Degrading Bacterium Tepidanaerobacter syntrophicus JLT.	Genome Announcements	2016	4		e01712-15			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%. 		
@D	Matsuura, N.//Tourlousse, D.M.//Ohashi, A.//Hugenholtz, P.//Sekiguchi, Y. 	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.	Genome Announcements	2015	3		e00975-15			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. 		
@D	Matsuura, N.//Tourlousse, D.M.//Sun, L.//Toyonaga, M.//Kuroda, K.//Ohashi, A.//Cruz, R.//Yamaguchi, T.//Sekiguchi, Y. 	Draft Genome Sequence of Anaerolineae Strain TC1, a Novel Isolate from a Methanogenic Wastewater Treatment System.	Genome Announcements	2015	3		e01104-15			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. 		
@D	Matsuura, S.-I.//Hirano, K.//Zako, T.//Katsura, S.//Nagamune, T.//Mizuno, A. 	Direct observation of sliding of restriction endonuclease EcoRI on a single DNA molecule.	Eur. Biophys. J.	2000	29		255			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. 		
@D	Matsuzaki, S.//Inoue, T.//Tanaka, S. 	Evidence for the existence of a restriction-modification system common to several species of the family Vibronaceae.	FEMS Microbiol. Lett.	1992	94		191-194			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. 		
@D	Matsuzawa, T.//Mori, K.//Kadowaki, T.//Shimada, M.//Tashiro, K.//Kuhara, S.//Inagawa, H.//Soma, G.//Takegawa, K. 	Genome Sequence of Pantoea agglomerans Strain IG1.	J. Bacteriol.	2012	194		1258-1259			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. 		
@D	Mattos-Guaraldi, A.L.//Guimaraes, L.C.//Santos, C.S.//Veras, A.A.//Carneiro, A.R.//Soares, S.C.//Ramos, J.N.//Souza, C.//Vieira, V.V.//Hirata, R. Jr.//Azevedo, V.//Pacheco, L.G.//Silva, A.//Ramos, R.T. 	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.	Genome Announcements	2015	3		e00869-15			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. 		
@D	Maturrano, L.//Aleman, M.//Carhuaricra, D.//Maximiliano, J.//Siuce, J.//Luna, L.//Rosadio, R. 	Draft Genome Sequences of Enterohemorrhagic and Enteropathogenic Escherichia coli Strains Isolated from Alpacas in Peru.	Genome Announcements	2018	6		e01391-17			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. 		
@D	Matveyev, A.V.//Young, K.T.//Meng, A.//Elhai, J. 	DNA methyltransferases of the cyanobacterium Anabaena PCC 7120.	Nucleic Acids Res.	2001	29		1491-1506			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. 		
@D	Matvienko, N.I.//Kramarov, V.M.//Irismetov, A.A. 	Isolation and characterization of a DNA-methylase from Flavobacterium okeanokoites.	Bioorg. Khim.	1985	11		953-956			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. 		
@D	Matvienko, N.I.//Kramarov, V.M.//Pachkunov, D.M. 	Isolation and some properties of the site-specific endonuclease and methylase Bme216I from Bacillus megaterium 216.	Eur. J. Biochem.	1987	165		565-570			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. 		
@D	Matvienko, N.I.//Pachkunov, D.M.//Kramarov, V.M. 	The recognition sequence of site-specific endonuclease BbvII from Bacillus brevis 80.	FEBS Lett.	1984	177		23-26			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. 		
@D	Matvienko, N.N.//Kramarov, V.M.//Ivanov, L.Y.//Matvienko, N.I. 	Bce83I, a restriction endonuclease from Bacillus cereus 83 which recognizes novel nonpalindromic sequence 5'-CTTGAG-3' and is stimulated by S-adenosylmethionine.	Nucleic Acids Res.	1992	20		1803			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. 		
@D	Matvienko, N.N.//Kramarov, V.M.//Zheleznaya, L.A.//Matvienko, N.I. 	New site-specific endonuclease and methylase from Bacillus licheniformis 736.	Biokhimiia	1993	58		1139-1153			*
 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.
 
 		
@D	Matvienko, N.N.//Kramarov, V.M.//Zheleznaya, L.A.//Matvienko, N.I. 	Isolation of site-specific endonuclease and methylase from Bacillus cereus 83.	Biokhimiia	1993	58		1845-1860			
  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.
 
 		
@D	Matvienko, N.N.//Zeleznaja, L.A.//Matvienko, N.I. 	BspLU11I, a novel site specific endonuclease which cleaves 5'-ACATGT-3'.	Nucleic Acids Res.	1993	21		1495					
@D	Matvienko, N.N.//Zheleznaya, L.A.//Chernyshova, E.E.//Buryanov, Y.I.//Matvienko, N.I. 	Peculiarities of gene expression of the EcoRII modification-restriction system.	Biokhimiia	1997	62		1314-1318			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. 		
@D	Matvienko, N.N.//Zheleznaya, L.A.//Zelinskaya, N.V.//Matvienko, N.I. 	Site-specific DNA-methylase M.BspST5I methylates only one strand of the recognized site.	Biokhimiia	1997	62		304-306			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. 		
@D	Matyi, S.A.//Hoyt, P.R.//Ayoubi-Canaan, P.//Hasan, N.A.//Gustafson, J.E. 	Draft Genome Sequence of Strain ATCC 33958, Reported To Be Elizabethkingia miricola.	Genome Announcements	2015	3		e00828-15			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. 		
@D	Matyi, S.A.//Hoyt, P.R.//Hosoyama, A.//Yamazoe, A.//Fujita, N.//Gustafson, J.E. 	Draft Genome Sequences of Elizabethkingia meningoseptica.	Genome Announcements	2013	1		e00444-13			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. 		
@D	Matyi, S.A.//Ramaraj, T.//Sundararajan, A.//Lindquist, I.E.//Devitt, N.P.//Schilkey, F.D.//Lamichhane-Khadka, R.//Hoyt, P.R.//Mudge, J.//Gustafson, J.E. 	Draft Genomes of Heterogeneous Vancomycin-Intermediate Staphylococcus aureus Strain MM66 and MM66 Derivatives with Altered Vancomycin Resistance Levels.	Genome Announcements	2014	2		e00688-14			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. 		
@D	Matz, L.M.//Kamdar, K.Y.//Holder, M.E.//Metcalf, G.A.//Weissenberger, G.M.//Meng, Q.//Vee, V.//Han, Y.//Muzny, D.M.//Gibbs, R.A.//Johnson, C.L.//Revell, P.A.//Petrosino, J.F. 	Challenges of Francisella classification exemplified by an atypical clinical isolate.	Diagn. Microbiol. Infect. Dis.	2018	90		241-247			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. 		
@D	Maus, I.//Wibberg, D.//Stantscheff, R.//Eikmeyer, F.G.//Seffner, A.//Boelter, J.//Szczepanowski, R.//Blom, J.//Jaenicke, S.//Konig, H.//Puhler, A.//Schluter, A. 	Complete Genome Sequence of the Hydrogenotrophic, Methanogenic Archaeon Methanoculleus bourgensis Strain MS2T, Isolated from a Sewage Sludge Digester.	J. Bacteriol.	2012	194		5487-5488			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. 		
@D	Maus, I.//Wibberg, D.//Winkler, A.//Puhler, A.//Schnurer, A.//Schluter, A. 	Complete Genome Sequence of the Methanogen Methanoculleus bourgensis BA1 Isolated from a Biogas Reactor.	Genome Announcements	2016	4		e00568-16			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. 		
@D	Mavian, C.//Lopez-Bueno, A.//Balseiro, A.//Casais, R.//Alcami, A.//Alejo, A. 	The Genome Sequence of the Emerging Common Midwife Toad Virus Identifies an Evolutionary Intermediate within Ranaviruses.	J. Virol.	2012	86		3617-3625			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. 		
@D	Mavian, C.//Lopez-Bueno, A.//Fernandez-Somalo, M.P.//Alcami, A.//Alejo, A. 	Complete genome sequence of European sheatfish virus.	J. Virol.	2012	86		6365-6366			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. 		
@D	Mavrodi, D.V.//Mavrodi, O.V.//McSpadden-Gardener, B.B.//Landa, B.B.//Weller, D.M.//Thomashow, L.S. 	Identification of Differences in Genome Content among phlD-Positive Pseudomonas fluorescens Strains by Using PCR-Based Subtractive Hybridization.	Appl. Environ. Microbiol.	2002	68		5170-5176			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. 		
@D	Mavromatis, K. et al. 	Complete genome sequence of Cryptobacterium curtum type strain (12-3).	Standards in Genomic Sciences	2009	1		93-100			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. 		
@D	Mavromatis, K. et al. 	Complete genome sequence of Alicyclobacillus acidocaldarius type strain (104-IA).	Standards in Genomic Sciences	2010	2		9-18			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. 		
@D	Mavromatis, K. et al. 	Permanent draft genome sequence of the gliding predator Saprospira grandis strain Sa g1 (= HR1).	Standards in Genomic Sciences	2012	6		210-219			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. 		
@D	Mavromatis, K. et al. 	Complete genome sequence of Coraliomargarita akajimensis type strain (04OKA010-24).	Standards in Genomic Sciences	2010	2		290-299			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. 		
@D	Mavromatis, K. et al. 	Complete genome sequence of Vulcanisaeta distributa type strain (IC-017).	Standards in Genomic Sciences	2010	3		117-125			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. 		
@D	Mavromatis, K. et al. 	Complete genome sequence of Spirochaeta smaragdinae type strain (SEBR 4228).	Standards in Genomic Sciences	2010	3		136-144			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. 		
@D	Mavromatis, K. et al. 	Complete genome sequence of Riemerella anatipestifer type strain (ATCC 11845).	Standards in Genomic Sciences	2011	4		144-153			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. 		
@D	Mavromatis, K. et al. 	Complete genome sequence of the moderate thermophile Anaerobaculum mobile type strain (NGA(T)).	Standards in Genomic Sciences	2013	8		47-57			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. 		
@D	Mavromatis, K. et al. 	Complete genome sequence of the bile-resistant pigment-producing anaerobe Alistipes finegoldii type strain (AHN2437(T)).	Standards in Genomic Sciences	2013	8		26-36			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. 		
@D	Mavromatis, K.//Doyle, C.K.//Lykidis, A.//Ivanova, N.//Francino, M.P.//Chain, P.//Shin, M.//Malfatti, S.//Larimer, F.//Copeland, A.//Detter, J.C.//Land, M.//Richardson, P.M.//Yu, X.J.//Walker, D.H.//McBride, J.W.//Kyrpides, N.C. 	The genome of the obligately intracellular bacterium Ehrlichia canis reveals themes of complex membrane structure and immune evasion  strategies.	J. Bacteriol.	2006	188		4015-4023			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). 		
@D	Mavrommatis, K. et al. 	Complete genome sequence of Capnocytophaga ochracea type strain (VPI 2845).	Standards in Genomic Sciences	2009	1		101-109			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. 		
@D	Maxwell, A.//Halford, S.E. 	The SalGI restriction endonuclease.  (Enzyme specificity).	Biochem. J.	1982	203		93-98			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. 		
@D	Maxwell, A.//Halford, S.E. 	The SalGI restriction endonuclease.  (Purification and properties).	Biochem. J.	1982	203		77-84			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. 		
@D	Maxwell, A.//Halford, S.E. 	The mechanism of DNA cleavage by restriction endonuclease SalGI.	Biochem. Soc. Trans.	1981	9		227P			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. 		
@D	Maxwell, A.//Halford, S.E. 	The SalGI restriction endonuclease.  Mechanism of DNA cleavage.	Biochem. J.	1982	203		85-92			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. 		
@D	May, A.C.//Ehrlich, R.L.//Balashov, S.//Ehrlich, G.D.//Shanmugam, M.//Fine, D.H.//Ramasubbu, N.//Mell, J.C.//Cugini, C. 	Complete Genome Sequence of Aggregatibacter actinomycetemcomitans Strain IDH781.	Genome Announcements	2016	4		e01285-16			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. 		
@D	May, A.C.//Ohta, H.//Maeda, H.//Kokeguchi, S.//Cugini, C. 	Draft Genome Sequences of Aggregatibacter actinomycetemcomitans Strains 310a and  310b.	Genome Announcements	2017	5		e01282-17			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. 		
@D	May, B.J.//Zhang, Q.//Li, L.L.//Paustian, M.L.//Whittam, T.S.//Kapur, V. 	Complete genomic sequence of Pasteurella multocida, Pm70.	Proc. Natl. Acad. Sci. U. S. A.	2001	98		3460-3465			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. 		
@D	May, C.E.//Schulman, M.L.//Howell, P.G.//Lourens, C.W.//Gouws, J.//Joone, C.//Monyai, M.S.//le Grange, M.//Bezuidt, O.K.//Harper, C.K.//Guthrie, A.J. 	Draft Genome Sequence of Taylorella equigenitalis Strain ERC_G2224 Isolated from  the Semen of a Lipizzaner Stallion in South Africa.	Genome Announcements	2015	3		e01205-15			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. 		
@D	May, M.A.//Kutish, G.F.//Barbet, A.F.//Michaels, D.L.//Brown, D.R. 	Complete Genome Sequence of Mycoplasma synoviae Strain WVU 1853T.	Genome Announcements	2015	3		e00563-15			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. 		
@D	May, M.S.//Hattman, S. 	Deoxyribonucleic acid-cytosine methylation by host- and plasmid-controlled enzymes.	J. Bacteriol.	1975	122		129-138			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. 		
@D	May, M.S.//Hattman, S. 	Analysis of bacteriophage deoxyribonucleic acid sequences methylated by host- and R-factor-controlled enzymes.	J. Bacteriol.	1975	123		768-770			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'. 		
@D	Mayer, A.//Barany, F. 	DNA photoaffinity crosslinking to TaqI endonuclease by a phosphorothioate-linked aryl azide.	FASEB J.	1992	6		A487			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. 		
@D	Mayer, A.N. 	Defining the contacts between Taq endonuclease and the DNA phosphate backbone.	Diss. Abstr.	1996	57		2359B			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. 		
@D	Mayer, A.N.//Barany, F. 	Interaction of TaqI endonuclease with the phosphate backbone.	J. Biol. Chem.	1994	269		29067-29076			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. 		
@D	Mayer, A.N.//Barany, F. 	Photoaffinity cross-linking of TaqI restriction endonuclease using an aryl azide linked to the phosphate backbone.	Gene	1995	153		1-8			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. 		
@D	Mayer, H. 	Optimization of the EcoRI* activity of EcoRI endonuclease.	FEBS Lett.	1978	90		341-344			None 		
@D	Mayer, H.//Goebel, W. 	Isolierung der Restriktionsendonuclease EcoRI aus einem Antibiotka-Resistenz-freien Stamm von Escherichia coli.	Hoppe Seylers Z. Physiol. Chem.	1975	356		253-254			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. 		
@D	Mayer, H.//Grosschedl, R.//Schutte, H.//Hobom, G. 	ClaI, a new restriction endonuclease from Caryophanon latum L.	Nucleic Acids Res.	1981	9		4833-4845			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. 		
@D	Mayer, H.//Reichenbach, H. 	Restriction Endonucleases: General Survey Procedure and Survey of Gliding Bacteria.	J. Bacteriol.	1978	136		708-713			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. 		
@D	Mayer, M.J.//Narbad, A.//Gasson, M.J. 	Molecular characterization of a Clostridium difficile bacteriophage and its cloned biologically active endolysin.	J. Bacteriol.	2008	190		6734-6740			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. 		
@D	Mayer, M.J.//Payne, J.//Gasson, M.J.//Narbad, A. 	Genomic Sequence and Characterization of the Virulent Bacteriophage {phi}CTP1 from Clostridium tyrobutyricum and Heterologous Expression of Its Endolysin.	Appl. Environ. Microbiol.	2010	76		5415-5422			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. 		
@D	Mayer, W.//Niveleau, A.//Walter, J.//Fundele, R.//Haaf, T. 	Demethylation of the zygotic paternal genome.	Nature	2000	403		501-502			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. 		
@D	Maynard-Smith, M.D.//McKelvie, J.C.//Wood, R.J.//Harmer, J.E.//Ranasinghe, R.T.//Williams, C.L.//Coomber, D.M.//Stares, A.F.//Roach, P.L. 	Direct and continuous fluorescence-based measurements of Pyrococcus horikoshii DNA N-6 adenine methyltransferase activity.	Anal. Biochem.	2011	418		204-212			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. 		
@D	Mayo, B.//Hardisson, C.//Brana, A.F. 	Nucleolytic activities in Lactococcus lactis subsp. lactis NCDO 497.	FEMS Microbiol. Lett.	1991	79		195-198			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. 		
@D	Maze, A. et al. 	Complete genome sequence of the probiotic Lactobacillus casei strain BL23.	J. Bacteriol.	2010	192		2647-2648			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. 		
@D	Mazin, A.L.//Vanyushin, B.F. 	Possible origin and evolution of enzymatic methylation of eukaryotic DNA.  Methylation of cytosine residues in three families of palindromes: RYRY, YYRR, and YYRYRR.	Mol. Biol. (Mosk)	1990	24		16-35			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. 		
@D	Mazuet, C.//Bouchier, C.//Popoff, M.R. 	Draft Genome Sequence of Clostridium botulinum Strain 277-00 Type B2.	Genome Announcements	2015	3		e00211-15			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. 		
@D	Mazur, A.//De Meyer, S.E.//Tian, R.//Wielbo, J.//Zebracki, K.//Seshadri, R.//Reddy, T.//Markowitz, V.//Ivanova, N.N.//Pati, A.//Woyke, T.//Kyrpides, N.C.//Reeve, W. 	High-quality permanent draft genome sequence of Rhizobium leguminosarum bv. viciae strain GB30; an effective microsymbiont of Pisum sativum growing in Poland.	Standards in Genomic Sciences	2015	10		36			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. 		
@D	Mazurek, M.//Sowers, L.C. 	The paradoxical influence of thymine analogues on restriction endonuclease cleavage of oligodeoxynucleotides.	Biochemistry	1996	35		11522-11528			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. 		
@D	Mazzarelli, J.//Scholtissek, S.//McLaughlin, L.W. 	Effects of functional group changes in the EcoRV recognition site on the cleavage reaction catalyzed by the endonuclease.	Biochemistry	1989	28		4616-4622			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. 		
@D	Mbelle, N.M.//Maningi, N.E.//Tshisevhe, V.//Modipane, L.//Amoako, D.G.//Osei, S.J. 	Draft Genome Sequence of a Clinical Enterococcus faecium Sequence Type 18 Strain  from South Africa.	Genome Announcements	2017	5		e01381-17			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. 		
@D	Mbelle, N.M.//Maningi, N.E.//Tshisevhe, V.//Modipane, L.//Amoako, D.G.//Osei, S.J. 	First Report of a Whole-Genome Shotgun Sequence of a Clinical Enterococcus faecalis Sequence Type 6 Strain from South Africa.	Genome Announcements	2017	5		e01382-17			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. 		
@D	McCallum, C.M. 	TILLING for Arabidopsis chromomethylase function.	Ph.D. Thesis, University of Washington, Seattle, USA	2005			1-66			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. 		
@D	McCallum, C.M.//Comai, L.//Greene, E.A.//Henikoff, S. 	Targeted screening for induced mutations.	Nat. Biotechnol.	2000	18		455-459			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. 		
@D	McCann, H.C.//Rikkerink, E.H.//Bertels, F.//Fiers, M.//Lu, A.//Rees-George, J.//Andersen, M.T.//Gleave, A.P.//Haubold, B.//Wohlers, M.W.//Guttman, D.S.//Wang, P.W.//Straub, C.//Vanneste, J.L.//Rainey, P.B.//Templeton, M.D. 	Genomic analysis of the Kiwifruit pathogen Pseudomonas syringae pv. actinidiae provides insight into the origins of an emergent plant disease.	PLoS Pathog.	2013	9		E1003503			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. 		
@D	McCarren, J.//DeLong, E.F. 	Proteorhodopsin photosystem gene clusters exhibit co-evolutionary trends and shared ancestry among diverse marine microbial phyla.	Environ. Microbiol.	2007	9		846-858			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. 		
@D	McCarthy, A.J.//Lindsay, J.A. 	The distribution of plasmids that carry virulence and resistance genes in Staphylococcus aureus is lineage associated.	BMC Microbiol.	2012	12		104			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. 		
@D	McCarthy, C.B.//Romanowski, V. 	Digestion of I-PpoI recognition sites in unfavorable sequence contexts achieved by changing the reaction conditions.	Biochem. Genet.	2006	44		61-67					
@D	McCarthy, K.L.//Jennison, A.//Wailan, A.M.//Paterson, D.L. 	Draft Genome Sequence of an IMP-7-Producing Pseudomonas aeruginosa Bloodstream Infection Isolate from Australia.	Genome Announcements	2017	5		e00596-17			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. 		
@D	McCarthy, K.L.//Jennison, A.V.//Wailan, A.M.//Paterson, D.L. 	Draft Genome Sequences of Two Pseudomonas aeruginosa Bloodstream Infection Isolates Associated with Rapid Patient Death.	Genome Announcements	2017	5		e00597-17			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. 		
@D	McCarthy, S.//Gradnigo, J.//Johnson, T.//Payne, S.//Lipzen, A.//Martin, J.//Schackwitz, W.//Moriyama, E.//Blum, P. 	Complete Genome Sequence of Sulfolobus solfataricus Strain 98/2 and Evolved Derivatives.	Genome Announcements	2015	3		e00549-15			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. 		
@D	McClain, M.S.//Shaffer, C.L.//Israel, D.A.//Peek, R.M. Jr.//Cover, T.L. 	Genome sequence analysis of Helicobacter pylori strains associated with gastric ulceration and gastric cancer.	BMC Genomics	2009	10		3			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. 		
@A	McClarin, J.A.//Frederick, C.A.//Grable, J.//Samudzi, C.T.//Wang, B.-C.//Greene, P.//Boyer, H.W.//Rosenberg, J.M. 		Structural studies on a DNA-EcoRI endonuclease recognition complex.			Sarma, R.H.//Sarma, M.H. 		Biomolecular Sterodynamics				New York	Adenine Press	1986		3		45-68									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. 		
@D	McClarin, J.A.//Frederick, C.A.//Wang, B.C.//Greene, P.//Boyer, H.W.//Grable, J.//Rosenberg, J.M. 	Structure of the DNA-EcoRI endonuclease recognition complex at 3 angstrom resolution.	Science	1986	234		1526-1541			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. 		
@D	McClelland, M. 	Site-specific cleavage of DNA at 8-, 9-, and 10-bp sequences.	Methods Enzymol.	1987	155		22-33			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. 		
@D	McClelland, M. 	Selection against dam methylation sites in the genomes of DNA of enterobacteriophages.	J. Mol. Evol.	1984	21		317-322			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. 		
@D	McClelland, M. 	The effect of sequence specific DNA methylation on restriction endonuclease cleavage.	Nucleic Acids Res.	1981	9		5859-5866			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. 		
@D	McClelland, M. 	Purification and characterization of two new modification methylases: M.ClaI from Caryophanon latum and M.TaqI from Thermus aquaticus YTI.	Nucleic Acids Res.	1981	9		6795-6804			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. 		
@D	McClelland, M. 	The effect of site specific methylation on restriction endonuclease cleavage (update).	Nucleic Acids Res.	1983	11		r169-r173			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. 		
@D	McClelland, M. 	The frequency and distribution of methylatable DNA sequences in leguminous plant protein coding genes.	J. Mol. Evol.	1983	19		346-354			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. 		
@D	McClelland, M. 	Recognition sequences of Type II restriction systems are constrained by the G+C content of host genomes.	Nucleic Acids Res.	1988	16		2283-2294			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. 		
@D	McClelland, M. et al. 	Comparison of genome degradation in Paratyphi A and Typhi, human-restricted serovars of Salmonella enterica that cause typhoid.	Nat. Genet.	2004	36		1268-1274			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). 		
@D	McClelland, M. et al. 	Complete genome sequence of Salmonella enterica serovar typhimurium LT2.	Nature	2001	413		852-856			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. 		
@D	McClelland, M.//Bhagwat, A.S. 	Biased DNA repair.	Nature	1992	355		595-596			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. 		
@D	McClelland, M.//Hanish, J.//Nelson, M.//Patel, Y. 	KGB: a single buffer for all restriction endonucleases.	Nucleic Acids Res.	1988	16		364			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. 		
@D	McClelland, M.//Jones, R.//Patel, Y.//Nelson, M. 	Restriction endonucleases for pulsed field mapping of bacterial genomes.	Nucleic Acids Res.	1987	15		5985-6005			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. 		
@D	McClelland, M.//Kessler, L.G.//Bittner, M. 	Site-specific cleavage of DNA at 8- and 10-base pair sequences.	Proc. Natl. Acad. Sci. U. S. A.	1984	81		983-987			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. 		
@D	McClelland, M.//Nelson, M. 	Effect of site-specific methylation on DNA modification methyltransferases and restriction endonucleases.	Nucleic Acids Res.	1992	20		2145-2157			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. 		
@D	McClelland, M.//Nelson, M. 	The effect of site-specific DNA methylation on restriction endonucleases and DNA modification methyltransferases - a review.	Gene	1988	74		291-304			Review of methylation sensitivity. 		
@D	McClelland, M.//Nelson, M. 	The 5'-GGATCC-3' cleavage specificity of BamHI is increased to 5'-CCGGATCCGG-3' by sequential double methylation with M.HpaII and M.BamHI.	Gene	1988	74		169-176			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. 		
@D	McClelland, M.//Nelson, M. 	The effect of site specific methylation on restriction endonuclease digestion.	Nucleic Acids Res.	1985	13		r201-r207			None 		
@A	McClelland, M.//Nelson, M. 		Enhancement of the apparent cleavage specificities of restriction endonucleases:  applications to megabase mapping of chromosomes.			Chirikjian, J.G. 		Gene Amplif. Anal.					Elsevier North Holland	1987		5		257-282									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. 		
@D	McClelland, M.//Nelson, M.//Cantor, C.R. 	Purification of MboII methylase (GAAGmA) from Moraxella bovis: site specific cleavage of DNA at nine and ten base pair sequences.	Nucleic Acids Res.	1985	13		7171-7182			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. 		
@D	McClelland, M.//Nelson, M.//Raschke, E. 	Effect of site-specific modification on restriction endonucleases and DNA modification methyltransferases.	Nucleic Acids Res.	1994	22		3640-3659			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. 		
@D	McClelland, S.E.//Dryden, D.T.F.//Szczelkun, M.D. 	Continuous assays for DNA translocation using fluorescent triplex dissociation: Application to type I restriction endonucleases.	J. Mol. Biol.	2005	348		895-915			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. 		
@A	McClelland, S.E.//Szczelkun, M.D. 		The type I and III restriction endonucleases: Structural elements in the molecular motors that process DNA.			Pingoud, A. 		Nucleic Acids Mol. Biol.				Berlin Heidelberg	Springer-Verlag	2004		14		111-135									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. 		
@D	McClelland, W.D.//Trachtenberg, A.M.//Brennan, M.A.//MacLea, K.S. 	Draft Genome Sequence of the Marine Bacterium Oceanimonas baumannii ATCC 700832T.	Genome Announcements	2017	5		e01007-17			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. 		
@D	McClure, J.A.//Shideler, S.M.//Zhang, K. 	Complete Genome Sequences of Canadian Epidemic Methicillin-Resistant Staphylococcus aureus Strains CMRSA3 and CMRSA6.	Microbiol. Resour. Announc.	2018	7		e00892-18			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. 		
@D	McClure, J.A.//Zhang, K. 	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.	Genome Announcements	2017	5		e00461-17			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. 		
@D	McClure, J.A.//Zhang, K. 	Complete Genome Sequence of the Methicillin-Resistant Staphylococcus aureus Colonizing Strain M92.	Genome Announcements	2017	5		e00478-17			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. 		
@D	McClure, J.A.//Zhang, K. 	Complete Genome Sequences of Five Representative Staphylococcus aureus ST398 Strains from Five Major Sequence Heterogeneity Groups of a Diverse Isolate  Collection.	Genome Announcements	2017	5		e00473-17			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. 		
@D	McConnell, D.J.//Searcy, D.G.//Sutcliffe, J.G. 	A restriction enzyme ThaI from the thermophilic mycoplasma Thermoplasma acidophilum.	Nucleic Acids Res.	1978	5		1729-1739			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. 		
@D	McConnell, S.A.//Takeuchi, R.//Pellenz, S.//Davis, L.//Maizels, N.//Monnat, R.J. Jr.//Stoddard, B.L. 	Generation of a nicking enzyme that stimulates site-specific gene conversion from the I-AniI LAGLIDADG homing endonuclease.	Proc. Natl. Acad. Sci. U. S. A.	2009	106		5099-5104			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. 		
@D	McCulloch, J.A.//de Oliveira, V.M.//de Almeida, P.A.V.//Perez-Chaparro, P.J.//de Almeida, L.M.//de Vasconcelos, J.M.//de Oliveira, L.F.//da Silva, D.E.//Rogez, H.L.//Cretenet, M.//Mamizuka, E.M.//Nunes, M.R. 	Complete Genome Sequence of Lactococcus lactis Strain AI06, an Endophyte of the Amazonian Acai Palm.	Genome Announcements	2014	2		e01225-14			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. 		
@D	McCulloch, J.A.//Silveira, A.C.//da Costa-Lima-Moraes, A.//Perez-Chaparro, P.J.//Ferreira, S.M.//Almeida, L.M.//d'Azevedo, P.A.//Mamizuka, E.M. 	Complete Genome Sequence of Staphylococcus aureus FCFHV36, a Methicillin-Resistant Strain Heterogeneously Resistant to Vancomycin.	Genome Announcements	2015	3		e00893-15			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. 		
@D	McCully, L.M.//Bitzer, A.S.//Spence, C.A.//Bais, H.P.//Silby, M.W. 	Draft Genome Sequence of Rice Isolate Pseudomonas chlororaphis EA105.	Genome Announcements	2014	2		e01342-14			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. 		
@D	McCusker, M.P.//Hokamp, K.//Buckley, J.F.//Wall, P.G.//Martins, M.//Fanning, S. 	Complete Genome Sequence of Salmonella enterica Serovar Agona Pulsed-Field Type SAGOXB.0066, Cause of a 2008 Pan-European Outbreak.	Genome Announcements	2014	2		e01219-13			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. 		
@D	McDermott, P.F.//Crawford, J.T. 	A plasmid-encoded restriction-modification system in Mycobacterium avium.	Abstr. Gen. Meet. Am. Soc. Microbiol.	1989	89		167			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. 		
@D	McDonald, R.R.//Golding, G.R.//Irvine, J.//Graham, M.R.//Tyler, S.//Mulvey, M.R.//Levett, P.N. 	Draft Genome Sequence of Methicillin-Susceptible Staphylococcus aureus Strain 06BA18369, a Pathogen Associated with Skin and Soft Tissue Infections in Northern  Saskatchewan, Canada.	Genome Announcements	2013	1		e00389-13			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. 		
@D	McDonald, R.R.//Golding, G.R.//Irvine, J.//Graham, M.R.//Tyler, S.//Mulvey, M.R.//Levett, P.N. 	Draft Genome Sequence of Streptococcus pyogenes Strain 06BA18369, a Human Pathogen Associated with Skin and Soft Tissue Infections in Northern Canada.	Genome Announcements	2013	1		e00387-13			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. 		
@D	McDowell, A.//Hunyadkurti, J.//Horvath, B.//Voros, A.//Barnard, E.//Patrick, S.//Nagy, I. 	Draft Genome Sequence of an Antibiotic-Resistant Propionibacterium acnes Strain,  PRP-38, from the Novel Type IC Cluster.	J. Bacteriol.	2012	194		3260-3261			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. 		
@D	McGann, P.//Hang, J.//Clifford, R.J.//Yang, Y.//Kwak, Y.I.//Kuschner, R.A.//Lesho, E.P.//Waterman, P.E. 	Complete Sequence of a Novel 178-Kilobase Plasmid Carrying blaNDM-1 in a Providencia stuartii Strain Isolated in Afghanistan.	Antimicrob. Agents Chemother.	2012	56		1673-1679			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. 		
@D	McGeehan, J.E.//Ball, N.J.//Streeter, S.D.//Thresh, S.J.//Kneale, G.G. 	Recognition of dual symmetry by the controller protein C.Esp1396I based on the structure of the transcriptional activation complex.	Nucleic Acids Res.	2012	40		4158-4167			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. 		
@D	McGeehan, J.E.//Papapanagiotou, I.//Streeter, S.D.//Kneale, G.G. 	Cooperative Binding of the C.AhdI Controller Protein to the C/R Promoter and its Role in Endonuclease Gene Expression.	J. Mol. Biol.	2006	358		523-531			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. 		
@D	McGeehan, J.E.//Streeter, S.//Cooper, J.B.//Mohammed, F.//Fox, G.C.//Kneale, G.G. 	Crystallization and preliminary X-ray analysis of the controller protein C.Ahdl from Aeromonas hydrophilia.	Acta Crystallogr. D Biol. Crystallogr.	2004	60		323-325			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. 		
@D	McGeehan, J.E.//Streeter, S.//Papapanagiotou, I.//Fox, G.C.//Kneale, G.G. 	High-resolution crystal structure of the restriction-modification controller protein C.AhdI from Aeromonas hydrophila.	J. Mol. Biol.	2005	346		689-701			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. 		
@D	McGeehan, J.E.//Streeter, S.D.//Thresh, S.J.//Ball, N.//Ravelli, R.B.//Kneale, G.G. 	Structural analysis of the genetic switch that regulates the expression of restriction-modification genes.	Nucleic Acids Res.	2008	36		4778-4787			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. 		
@D	McGeehan, J.E.//Streeter, S.D.//Thresh, S.J.//Taylor, J.E.//Shevtsov, M.B.//Kneale, G.G. 	Structural Analysis of a Novel Class of R-M Controller Proteins: C.Csp231I from Citrobacter sp. RFL231.	J. Mol. Biol.	2011	409		177-188			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. 		
@D	McGillivary, G.//Tomaras, A.P.//Rhodes, E.R.//Actis, L.A. 	Cloning and sequencing of a genomic island found in the Brazilian purpuric fever clone of Haemophilus influenzae biogroup aegyptius.	Infect. Immun.	2005	73		1927-1938			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. 		
@D	McGrath, K.C.//Thomas-Hall, S.R.//Cheng, C.T.//Leo, L.//Alexa, A.//Schmidt, S.//Schenk, P.M. 	Isolation and analysis of mRNA from environmental microbial communities.	J. Microbiol. Methods	2008	75		172-176			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. 		
@D	McGrath, S.//Seegers, J.F.M.L.//Fitzgerald, G.F.//van Sinderen, D. 	Molecular characterization of a phage-encoded resistance system in Lactococcus lactis.	Appl. Environ. Microbiol.	1999	65		1891-1899			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. 		
@D	McGraw, B.R.//Marinus, M.G. 	Isolation and characterization of Dam+ revertants and suppressor mutations that modify secondary phenotypes of dam-3 strains of Escherichia coli K-12.	Mol. Gen. Genet.	1980	178		309-315			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. 		
@D	McIlroy, S.J.//Lapidus, A.//Thomsen, T.R.//Han, J.//Haynes, M.//Lobos, E.//Huntemann, M.//Pati, A.//Ivanova, N.N.//Markowitz, V.//Verbarg, S.//Woyke, T.//Klenk, H.P.//Kyrpides, N.//Nielsen, P.H. 	High quality draft genome sequence of Meganema perideroedes str. Gr1(T) and a proposal for its reclassification to the family Meganemaceae fam. nov.	Standards in Genomic Sciences	2015	10		23			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. 		
@D	McInerney, M.J.//Rohlin, L.//Mouttaki, H.//Kim, U.//Krupp, R.S.//Rios-Hernandez, L.//Sieber, J.//Struchtemeyer, C.G.//Bhattacharyya, A.//Campbell, J.W.//Gunsalus, R.P. 	The genome of Syntrophus aciditrophicus: Life at the thermodynamic limit of microbial growth.	Proc. Natl. Acad. Sci. U. S. A.	2007	104		7600-7605			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. 		
@D	McKane, M.//Milkman, R. 	Transduction, restriction and recombination patterns in Escherichia coli.	Genetics	1995	139		35-43			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. 		
@D	McKay, L.L.//Bohanon, M.J.//Polzin, K.M.//Rule, P.L.//Baldwin, K.A. 	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.	Appl. Environ. Microbiol.	1989	55		2702-2709			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). 		
@D	McKelvie, J.C.//Richards, M.I.//Harmer, J.E.//Milne, T.S.//Roach, P.L.//Oyston, P.C.F. 	Inhibition of Yersinia pestis DNA adenine methyltransferase in vitro by a stibonic acid compound: identification of a potential novel class of antimicrobial agents.	Br. J. Pharmacol.	2013	168		172-188			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. 		
@D	McKenna, W.G.//Brown, F.L.//Musich, P.R.//Maio, J.J. 	Cleavage of mammalian repetitive deoxyribonucleic acids by a mammalian site-specific endodeoxyribonuclease.	J. Mol. Biol.	1982	154		379-384			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. 		
@D	McKenna, W.G.//Maio, J.J.//Brown, F.L. 	Purification and properties of a mammalian endonuclease showing site-specific cleavage of DNA.	J. Biol. Chem.	1981	256		6435-6443			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. 		
@D	McKenney, P.T.//Ling, L.//Wang, G.//Mane, S.//Pamer, E.G. 	Complete Genome Sequence of Enterococcus faecium ATCC 700221.	Genome Announcements	2016	4		e00386-16			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. 		
@D	McKernan, K.J.//Spangler, J.//Helbert, Y.//Zhang, L.//Tadigotla, V. 	DREAMing of a patent-free human genome for clinical sequencing.	Nat. Biotechnol.	2013	31		884-887			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. 		
@D	McLaughlin, L.W.//Benseler, F.//Graeser, E.//Piel, N.//Scholtissek, S. 	Effects of functional group changes in the EcoRI recognition site on the cleavage reaction catalyzed by the endonuclease.	Biochemistry	1987	26		7238-7245			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. 		
@D	McLaughlin, R.W. et al. 	Draft Genome Sequence of Clostridium mangenotii TR, Isolated from the Fecal Material of a Timber Rattlesnake.	Genome Announcements	2014	2		e01107-13			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. 		
@D	McLean, J.S.//Liu, Q.//Bor, B.//Bedree, J.K.//Cen, L.//Watling, M.//To, T.T.//Bumgarner, R.E.//He, X.//Shi, W. 	Draft Genome Sequence of Actinomyces odontolyticus subsp. actinosynbacter Strain  XH001, the Basibiont of an Oral TM7 Epibiont.	Genome Announcements	2016	4		e01685-15			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). 		
@D	McLean, J.S.//Liu, Q.//Thompson, J.//Edlund, A.//Kelley, S. 	Draft Genome Sequence of 'Candidatus Bacteroides periocalifornicus,' a New Member of the Bacteriodetes Phylum Found within the Oral Microbiome of Periodontitis  Patients.	Genome Announcements	2015	3		e01485-15			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. 		
@D	McLeod, A.//Brede, D.A.//Rud, I.//Axelsson, L. 	Genome Sequence of Lactobacillus sakei subsp. sakei LS25, a Commercial Starter Culture Strain for Fermented Sausage.	Genome Announcements	2013	1		e00475-13			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. 		
@D	McLeod, M.P. et al. 	The complete genome of Rhodococcus sp. RHA1 provides insights into a catabolic powerhouse.	Proc. Natl. Acad. Sci. U. S. A.	2006	103		15582-15587			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. 		
@D	McMahon, S.A.//Roberts, G.A.//Johnson, K.A.//Cooper, L.P.//Liu, H.//White, J.H.//Carter, L.G.//Sanghvi, B.//Oke, M.//Walkinshaw, M.D.//Blakely, G.W.//Naismith, J.H.//Dryden, D.T. 	Extensive DNA mimicry by the ArdA anti-restriction protein and its role in the spread of antibiotic resistance.	Nucleic Acids Res.	2009	37		4887-4897			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. 		
@D	McMillan, K.//Allnutt, T.R.//Fox, E.M. 	Draft Genome Sequences of 15 Staphylococcus aureus Isolates Recovered from Raw Milk and Associated Milk Filters from Victoria, Australia.	Genome Announcements	2017	5		e01463-16			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. 		
@D	McMullen, P.D.//Gillaspy, A.F.//Gipson, J.//Bobo, L.D.//Skiest, D.J.//Freitag, N.E. 	Genome Sequence of Listeria monocytogenes 07PF0776, a Cardiotropic Serovar 4b Strain.	J. Bacteriol.	2012	194		3552			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. 		
@D	McMurdie, P.J.//Behrens, S.F.//Muller, J.A.//Goke, J.//Ritalahti, K.M.//Wagner, R.//Goltsman, E.//Lapidus, A.//Holmes, S.//Loffler, F.E.//Spormann, A.M. 	Localized plasticity in the streamlined genomes of vinyl chloride respiring Dehalococcoides.	PLoS Genet.	2009	5		E1000714			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. 		
@D	McMurrough, T.A.//Dickson, R.J.//Thibert, S.M.F.//Gloor, G.B.//Edgell, D.R. 	Control of catalytic efficiency by a coevolving network of catalytic and noncatalytic residues.	Proc. Natl. Acad. Sci. U. S. A.	2014	111		E2376-E2383			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. 		
@D	McNamara, A.R.//Hurd, P.J.//Smith, A.E.F.//Ford, K.G. 	Characterisation of site-biased DNA methyltransferases: specificity, affinity and subsite relationships.	Nucleic Acids Res.	2002	30		3818-3830			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. 		
@D	McNulty, N.P. et al. 	The impact of a consortium of fermented milk strains on the gut microbiome of gnotobiotic mice and monozygotic twins.	Sci. Transl. Med.	2011	3		106RA106			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. 		
@D	McShan, W.M.//Ferretti, J.J.//Karasawa, T.//Suvorov, A.N.//Lin, S.//Qin, B.//Jia, H.//Kenton, S.//Najar, F.//Wu, H.//Scott, J.//Roe, B.A.//Savic, D.J. 	Genome Sequence of a Nephritogenic and Highly Transformable M49 Strain of Streptococcus pyogenes.	J. Bacteriol.	2008	190		7773-7785			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. 		
@D	McTaggart, T.L.//Benuska, G.//Shapiro, N.//Woyke, T.//Chistoserdova, L. 	Draft genome sequences of five new strains of methylophilaceae isolated from lake washington sediment.	Genome Announcements	2015	3		e01511-14			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. 		
@D	McTaggart, T.L.//Shapiro, N.//Woyke, T.//Chistoserdova, L. 	Draft Genome of Janthinobacterium sp. RA13 Isolated from Lake Washington Sediment.	Genome Announcements	2015	3		e01588-14			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. 		
@D	McTaggart, T.L.//Shapiro, N.//Woyke, T.//Chistoserdova, L. 	Draft genomes of two strains of flavobacterium isolated from lake washington sediment.	Genome Announcements	2015	3		e01597-14			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. 		
@D	McTaggart, T.L.//Shapiro, N.//Woyke, T.//Chistoserdova, L. 	Draft Genome of Pseudomonas sp. Strain 11/12A, Isolated from Lake Washington Sediment.	Genome Announcements	2015	3		e01587-14			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. 		
@D	Mead, D.A. et al. 	Complete Genome Sequence of Paenibacillus strain Y4.12MC10, a Novel Paenibacillus lautus strain Isolated from Obsidian Hot Spring in Yellowstone National Park.	Standards in Genomic Sciences	2012	6		381-400			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. 		
@D	Medema, M.H.//Trefzer, A.//Kovalchuk, A.//van den Berg, M.//Muller, U.//Heijne, W.//Wu, L.//Alam, M.T.//Ronning, C.M.//Nierman, W.C.//Bovenberg, R.A.//Breitling, R.//Takano, E. 	The sequence of a 1.8-mb bacterial linear plasmid reveals a rich evolutionary reservoir of secondary metabolic pathways.	Genome Biol. Evol.	2010	2		212-224			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. 		
@D	Medhi, K.//Mishra, A.//Thakur, I.S. 	Genome Sequence of a Heterotrophic Nitrifier and Aerobic Denitrifier, Paracoccus  denitrificans Strain ISTOD1, Isolated from Wastewater.	Genome Announcements	2018	6		e00210-18			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. 		
@D	Mediannikov, O.//El Karkouri, K.//Diatta, G.//Robert, C.//Fournier, P.E.//Raoult, D. 	Non-contiguous finished genome sequence and description of Bartonella senegalensis sp. nov.	Standards in Genomic Sciences	2013	8		279-289			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. 		
@D	Mediannikov, O.//El Karkouri, K.//Robert, C.//Fournier, P.E.//Raoult, D. 	Non-contiguous finished genome sequence and description of Bartonella florenciae  sp. nov.	Standards in Genomic Sciences	2013	9		185-196			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. 		
@D	Mediannikov, O.//Nguyen, T.T.//Bell-Sakyi, L.//Padmanabhan, R.//Fournier, P.E.//Raoult, D. 	High quality draft genome sequence and description of Occidentia massiliensis gen. nov., sp. nov., a new member of the family Rickettsiaceae.	Standards in Genomic Sciences	2014	9		9			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. 		
@D	Medigue, C. et al. 	Coping with cold: the genome of the versatile marine Antarctica bacterium Pseudoalteromonas haloplanktis TAC125.	Genome Res.	2005	15		1325-1335			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. 		
@D	Medina-Cordoba, L.K.//Chande, A.T.//Rishishwar, L.//Mayer, L.W.//Marino-Ramirez, L.//Valderrama-Aguirre, L.C.//Valderrama-Aguirre, A.//Kostka, J.E.//Jordan, I.K. 	Genome Sequences of 15 Klebsiella sp. Isolates from Sugarcane Fields in Colombia's Cauca Valley.	Genome Announcements	2018	6		e00104-18			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. 		
@D	Medina-Franco, J.L.//Caulfield, T. 	Advances in the computational development of DNA methyltransferase inhibitors.	Drug Discovery Today	2011	16		418-425			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. 		
@D	Medina-Franco, J.L.//Yoo, J. 	Docking of a novel DNA methyltransferase inhibitor identified from high-throughput screening: insights to unveil inhibitors in chemical databases.	Mol. Diversity	2013	17		337-344			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. 		
@D	Medrano, E.G.//Bell, A.A. 	Genome Sequence of Pantoea sp. Strain Sc 1, an Opportunistic Cotton Pathogen.	J. Bacteriol.	2012	194		3019			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. 		
@D	Medrano, E.G.//Bell, A.A. 	Genome Sequence of Pantoea ananatis Strain CFH 7-1, Which Is Associated with a Vector-Borne Cotton Fruit Disease.	Genome Announcements	2015	3		e01029-15			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. 		
@D	Medrano, E.G.//Forray, M.M.//Bell, A.A. 	Complete Genome Sequence of a Klebsiella pneumoniae Strain Isolated from a Known  Cotton Insect Boll Vector.	Genome Announcements	2014	2		e00850-14			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. 		
@D	Medrano-Felix, A.//Estrada-Acosta, M.//Jimenez, M.//Gomez-Gil, B.//Leon-Felix, J.//Amarillas, L.//Chaidez, C. 	Draft Genome Sequence of Salmonella enterica subsp. enterica Serotype Oranienburg Strain S-76, Isolated from an Aquatic Environment.	Genome Announcements	2013	1		e01017-13			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. 		
@D	Medvedeva, E.S.//Siniagina, M.N.//Malanin, S.Y.//Boulygina, E.A.//Malygina, T.Y.//Baranova, N.B.//Mouzykantov, A.A.//Davydova, M.N.//Chernova, O.A.//Chernov, V.M. 	Genome Sequences of Acholeplasma laidlawii Strains Differing in Sensitivity to Ciprofloxacin.	Genome Announcements	2017	5		e01189-17			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. 		
@D	Meehan, R.R.//Ulrich, E.//Bird, A.P. 	Restriction endonuclease NciI is not blocked by CpG methylation.	Nucleic Acids Res.	1993	21		5517-5518			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. 		
@D	Meessen-Pinard, M.//Sekulovic, O.//Fortier, L.C. 	Evidence of in vivo prophage induction during Clostridium difficile infection.	Appl. Environ. Microbiol.	2012	78		7662-7670			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. 		
@D	Mefferd, C.C. et al. 	High-Quality Draft Genomes from Thermus caliditerrae YIM 77777 and T. tengchongensis YIM 77401, Isolates from Tengchong, China.	Genome Announcements	2016	4		e00312-16			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. 		
@D	Megaw, J.//Gilmore, B.F. 	Draft Genome Sequence of Staphylococcus succinus Strain CSM-77, a Moderately Halophilic Bacterium Isolated from a Triassic Salt Mine.	Genome Announcements	2016	4		e00532-16			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. 		
@D	Megias, E.//Dos Reis, J.F.B.//Ribeiro, R.A.//Ollero, F.J.//Megias, M.//Hungria, M. 	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.	Genome Announcements	2018	6		e01547-17			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. 		
@D	Megias, E.//Megias, M.//Ollero, F.J.//Hungria, M. 	Draft Genome Sequence of Pantoea ananatis Strain AMG521, a Rice Plant Growth-Promoting Bacterial Endophyte Isolated from the Guadalquivir Marshes in  Southern Spain.	Genome Announcements	2016	4		e01681-15			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. 		
@D	Megias, E.//Reis, J.F.B.//Ribeiro, R.A.//Megias, M.//Ollero, F.J.//Hungria, M. 	Genome Sequence of Pantoea sp. Strain 1.19, Isolated from Rice Rhizosphere, with  the Capacity To Promote Growth of Legumes and Nonlegumes.	Genome Announcements	2017	5		e00707-17			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. 		
@D	Megias, E.//Reis, J.F.B.//Ribeiro, R.A.//Ollero, F.J.//Megias, M.//Hungria, M. 	Genome Sequence of Pantoea ananatis Strain AMG 501, a Plant Growth-Promoting Bacterium Isolated from Rice Leaves Grown in Paddies of Southern Spain.	Genome Announcements	2017	5		e00848-17			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. 		
@D	Mehari, Y.T.//Arivett, B.A.//Farone, A.L.//Gunderson, J.H.//Farone, M.B. 	Draft Genome Sequences of Two Novel Amoeba-Resistant Intranuclear Bacteria, 'Candidatus Berkiella cookevillensis' and 'Candidatus Berkiella aquae'.	Genome Announcements	2016	4		e01732-15			'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. 		
@D	Mehdizadeh-Gohari, I.//Kropinski, A.M.//Weese, S.J.//Parreira, V.R.//Whitehead, A.E.//Boerlin, P.//Prescott, J.F. 	Plasmid Characterization and Chromosome Analysis of Two netF+ Clostridium perfringens Isolates Associated with Foal and Canine Necrotizing Enteritis.	PLoS ONE	2016	11		E0148344			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. 		
@D	Mehershahi, K.S.//Abraham, S.N.//Chen, S.L. 	Complete Genome Sequence of Uropathogenic Escherichia coli Strain CI5.	Genome Announcements	2015	3		e00558-15			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. 		
@D	Mehershahi, K.S.//Chen, S.L. 	Complete Genome Sequence of the Uropathogenic Escherichia coli Strain NU14.	Genome Announcements	2017	5		e00306-17			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. 		
@D	Mehershahi, K.S.//Hsu, L.Y.//Koh, T.H.//Chen, S.L. 	Complete Genome Sequence of Streptococcus agalactiae Serotype III, Multilocus Sequence Type 283 Strain SG-M1.	Genome Announcements	2015	3		e01188-15			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. 		
@D	Mehling, J.S.//Lavender, H.//Clegg, S. 	A Dam methylation mutant of Klebsiella pneumoniae is partially attenuated.	FEMS Microbiol. Lett.	2007	268		187-193			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. 		
@D	Mehnaz, S.//Bauer, J.S.//Gross, H. 	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.	Genome Announcements	2014	2		e01108-13			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. 		
@D	Mehra, R.S.//Malhotra, V.P.//Rembhotkar, G.W. 	Rapid purification of a restriction endonuclease from Escherichia coli RY13.	Biotechnol. Tech.	1993	7		411-414			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. 		
@D	Mehrabadi, J.F.//Mirzaie, A.//Ahangar, N.//Rahimi, A.//Rokni-Zadeh, H. 	Draft Genome Sequence of Kocuria rhizophila RF, a Radiation-Resistant Soil Isolate.	Genome Announcements	2016	4		e00095-16			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. 		
@D	Mei, Y.//Sun, Y.//He, J.//Wang, Q.//Sun, Y.//Shao, W. 	Genome Sequences of Pseudomonas fragi Strains A22 and B25.	J. Bacteriol.	2012	194		3276-3277			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. 		
@D	Meidler, R.//Morad, I.//Amitsur, M.//Inokuchi, H.//Kaufmann, G. 	Detection of anticodon nuclease residues involved in tRNALys cleavage specificity.	J. Mol. Biol.	1999	287		499-510			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. 		
@D	Meier-Kolthoff, J.P. et al. 	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.	Standards in Genomic Sciences	2014	9		2			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. 		
@D	Meier-Kolthoff, J.P.//Lu, M.//Huntemann, M.//Lucas, S.//Lapidus, A.//Copeland, A.//Pitluck, S.//Goodwin, L.A.//Han, C.//Tapia, R.//Potter, G.//Land, M.//Ivanova, N.//Rohde, M.//Goker, M.//Detter, J.C.//Woyke, T.//Kyrpides, N.C.//Klenk, H.P. 	Genome sequence of the chemoheterotrophic soil bacterium Saccharomonospora cyanea type strain (NA-134(T)).	Standards in Genomic Sciences	2013	9		28-41			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). 		
@D	Meincke, L. et al. 	Complete genome sequence of Polynucleobacter necessarius subsp. asymbioticus type strain (QLW-P1DMWA-1(T)).	Standards in Genomic Sciences	2012	6		74-83			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. 		
@D	Meinersmann, R.J.//Bono, J.L.//Lindsey, R.L.//Genzlinger, L.L.//Loparev, V.N.//Oakley, B.B. 	Genome Sequence of a Urease-Positive Campylobacter lari Strain.	Genome Announcements	2015	3		e01191-15			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. 		
@D	Meinersmann, R.J.//Ladely, S.R.//Bono, J.L.//Plumblee, J.R.//Hall, M.C.//Genzlinger, L.L.//Cook, K.L. 	Complete Genome Sequence of a Colistin Resistance Gene (mcr-1)-Bearing Isolate of Escherichia coli from the United States.	Genome Announcements	2016	4		e01283-16			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. 		
@D	Meinersmann, R.J.//Ladely, S.R.//Plumblee, J.R.//Hall, M.C.//Simpson, S.A.//Ballard, L.L.//Scheffler, B.E.//Genzlinger, L.L.//Cook, K.L. 	Colistin Resistance mcr-1-Gene-Bearing Escherichia coli Strain from the United States.	Genome Announcements	2016	4		e00898-16			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. 		
@D	Meints, G.A.//Drobny, G.P. 	Dynamic impact of methylation at the m. hhai target site: a solid-state deuterium nmr study.	Biochemistry	2001	40		12436-12443			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. 		
@D	Meints, R.H.//Schuster, A.M.//Van Etten, J.L. 	Chlorella Viruses.	Plant Mol. Biol. Rep.	1985	3		180-187			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). 		
@D	Meiron, H.//Nahon, E.//Raveh, D. 	Identification of the heterothallic mutation in HO-endonuclease of S. cerevisiae using HO/ho chimeric genes.	Curr. Genet.	1995	28		367-373			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. 		
@D	Meisel, A.//Bickle, T.A.//Kruger, D.H.//Schroeder, C. 	Type III restriction enzymes need two inversely oriented recognition sites for DNA cleavage.	Nature	1992	355		467-469			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. 		
@D	Meisel, A.//Kruger, D.H.//Bickle, T.A. 	M.EcoP15I methylates the second adenine in its recognition sequence.	Nucleic Acids Res.	1991	19		3997			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. 		
@D	Meisel, A.//Mackeldanz, P.//Bickle, T.A.//Kruger, D.H.//Schroeder, C. 	Type III restriction endonucleases translocate DNA in a reaction driven by recognition site-specific ATP hydrolysis.	EMBO J.	1995	14		2958-2966			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. 		
@D	Meister, G.E. 	Non-associating heterodimeric DNA methyltransferases as a platform for developing designer methyltransferases.	Ph.D. Thesis, Johns Hopkins University, USA	2009						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. 		
@D	Meister, G.E.//Chandrasegaran, S.//Ostermeier, M. 	An engineered split M.Hhal-zinc finger fusion lacks the intended methyltransferase specificity.	Biochem. Biophys. Res. Commun.	2008	377		226-230			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. 		
@D	Meister, G.E.//Chandrasegaran, S.//Ostermeier, M. 	Heterodimeric DNA methyltransferases as a platform for creating designer zinc finger methyltransferases for targeted DNA methylation in cells.	Nucleic Acids Res.	2010	38		1749-1759			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. 		
@D	Meister, G.E.//Chandrasegaran, S.//Ostermeier, M. 	BIOT 149-Heterodimeric DNA methyltransferases.	ACS Abstracts	2008	236		0			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. 		
@D	Meister, J.//MacWilliams, M.//Hubner, P.//Jutte, H.//Skrzypek, E.//Piekarowicz, A.//Bickle, T.A. 	Macroevolution by transposition: drastic modification of DNA recognition by the type I restriction enzyme following Tn5 transposition.	EMBO J.	1993	12		4585-4591			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. 		
@D	Mejean, A.//Mazmouz, R.//Mann, S.//Calteau, A.//Medigue, C.//Ploux, O. 	The genome sequence of the cyanobacterium Oscillatoria sp. PCC 6506 reveals several gene clusters responsible for the biosynthesis of toxins  and secondary metabolites.	J. Bacteriol.	2010	192		5264-5265			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. 		
@D	Melcher, U.//Fletcher, J. 	Inactivation of a Spiroplasma citri DNA modification methylase by a virus-like insertion element suggested by DNA sequence.	J. Plant Pathol.	2000	82		71			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. 		
@D	Melcher, U.//Sha, Y.//Ye, F.//Fletcher, J. 	Mechanisms of Spiroplasma genome variation associated with SpV1-like viral DNA inferred from sequence comparisons.	Microb. Comp. Genomics	1999	4		29-46			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. 		
@D	Mell, J.C.//Sinha, S.//Balashov, S.//Viadas, C.//Grassa, C.J.//Ehrlich, G.D.//Nislow, C.//Redfield, R.J.//Garmendia, J. 	Complete Genome Sequence of Haemophilus influenzae Strain 375 from the Middle Ear of a Pediatric Patient with Otitis Media.	Genome Announcements	2014	2		e01245-14			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. 		
@D	Mellbye, B.L.//Davis, E.W.I.I.//Spieck, E.//Chang, J.H.//Bottomley, P.J.//Sayavedra-Soto, L.A. 	Draft Genome Sequence of Nitrobacter vulgaris Strain Ab1, a Nitrite-Oxidizing Bacterium.	Genome Announcements	2017	5		e00290-17			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. 		
@D	Mellmann, A.//Spindler-Raffel, E.//Bletz, S.//Prax, M.//Bekeredjian-Ding, I. 	Genome Sequences of the First WHO Repository of Platelet Transfusion-Relevant Bacterial Reference Strains.	Genome Announcements	2017	5		e00001-17			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. 		
@D	Melnik, A.I.//Rebentish, B.A.//Bolotin, A.V.//Mendzhul, M.I. 	Two site-specific endonucleases of the Cyanobacterium Nostoc linckia.	Mikrobiol. Zh.	1991	53		24-28			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. 		
@D	Melton, E.D.//Sorokin, D.Y.//Overmars, L.//Chertkov, O.//Clum, A.//Pillay, M.//Ivanova, N.//Shapiro, N.//Kyrpides, N.C.//Woyke, T.//Lapidus, A.L.//Muyzer, G. 	Complete genome sequence of Desulfurivibrio alkaliphilus strain AHT2(T), a haloalkaliphilic sulfidogen from Egyptian hypersaline alkaline lakes.	Standards in Genomic Sciences	2016	11		67			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. 		
@D	Melton, E.D.//Sorokin, D.Y.//Overmars, L.//Lapidus, A.L.//Pillay, M.//Ivanova, N.//Del Rio, T.G.//Kyrpides, N.C.//Woyke, T.//Muyzer, G. 	Draft genome sequence of Dethiobacter alkaliphilus strain AHT1T, a gram-positive  sulfidogenic polyextremophile.	Standards in Genomic Sciences	2017	12		57			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. 		
@D	Mendez-Tenorio, A.//Larios-Serrato, V.//Olguin-Ruiz, G.E.//Sanchez-Vallejo, C.J.//Torres-Lopez, R.C.//Aviles-Jimenez, F.//Camorlinga-Ponce, M.//Torres, J. 	Genome Sequence of a Helicobacter pylori Strain Isolated from a Mexican Patient with Intestinal Gastric Cancer.	Genome Announcements	2014	2		e01214-13			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. 		
@D	Mendoza, L.M.//Saavedra, L.//Raya, R.R. 	Draft Genome Sequence of Oenococcus oeni Strain X2L (CRL1947), Isolated from Red  Wine of Northwest Argentina.	Genome Announcements	2015	3		e01376-14			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. 		
@D	Mendoza-Olazaran, S.//Garcia-Mazcorro, J.F.//Morfin-Otero, R.//Villarreal-Trevino, L.//Camacho-Ortiz, A.//Rodriguez-Noriega, E.//Bocanegra-Ibarias, P.//Maldonado-Garza, H.J.//Dowd, S.E.//Garza-Gonzalez, E. 	Draft genome sequences of two opportunistic pathogenic strains of Staphylococcus  cohnii isolated from human patients.	Standards in Genomic Sciences	2017	12		49			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. 		
@D	Mendzhul, M.I.//Moshinsky, I.D.//Syrchin, S.A. 	Endonuclease activity in cyanobacteria Anabaena variabilis and Plectonema boryanum involving restriction endonuclease and nuclease.	Mikrobiol. Zh.	1999	61		10-14			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. 		
@D	Mendzhul, M.I.//Syrchin, S.A.//Averkiev, A.A.//Rebentish, B.A. 	The way of defense of cyanophage LPP-3 DNA against restriction-modification systems in the cells of the cyanobacterium Plectonema boryanum.	Biopol. Kletka	1993	9		54-61			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. 		
@D	Mendzhul, M.I.//Syrchin, S.A.//Rebentish, B.A.//Averkiev, A.A.//Busakhina, I.V. 	The resistance of the DNA of cyanophage LPP-3 to the action of different restriction endonucleases.	Mikrobiol. Zh.	1993	55		47-53			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. 		
@D	Meneghel, J.//Dugat-Bony, E.//Irlinger, F.//Loux, V.//Vidal, M.//Passot, S.//Beal, C.//Layec, S.//Fonseca, F. 	Draft Genome Sequence of Lactobacillus delbrueckii subsp. bulgaricus CFL1, a Lactic Acid Bacterium Isolated from French Handcrafted Fermented Milk.	Genome Announcements	2016	4		e00052-16			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. 		
@D	Menendez, C.//Bournat, J.C.//Ramirez, J.L. 	Cloning and overexpression of EcoRI methylase.	Interciencia	1989	14		37-40			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. 		
@D	Meng, J.//Sun, X.//Li, S.//Liang, H. 	Draft Genome Sequence of Paenarthrobacter nicotinovorans Hce-1.	Genome Announcements	2017	5		e00727-17			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%. 		
@D	Meng, X.//Bertani, I.//Abbruscato, P.//Piffanelli, P.//Licastro, D.//Wang, C.//Venturi, V. 	Draft Genome Sequence of Rice Endophyte-Associated Isolate Kosakonia oryzae KO348.	Genome Announcements	2015	3		e00594-15			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. 		
@D	Meng, X.//Cai, W.//Schwartz, D.C. 	Inhibition of restriction endonuclease activity by DNA binding fluorochromes.	J. Biomol. Struct. Dyn.	1996	13		945-951			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. 		
@D	Meramveliotaki, C.//Kotsifaki, D.//Androulaki, M.//Hountas, A.//Eliopoulos, E.//Kokkinidis, M. 	Purification, crystallization, x-ray diffraction analysis and phasing of an engineered single-chain PvuII restriction endonuclease.	Acta Crystallogr. F Struct. Biol. Cryst. Commun.	2007	63		836-838			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. 		
@D	Mercante, J.W.//Morrison, S.S.//Desai, H.P.//Raphael, B.H.//Winchell, J.M. 	Genomic Analysis Reveals Novel Diversity among the 1976 Philadelphia Legionnaires' Disease Outbreak Isolates and Additional ST36 Strains.	PLoS ONE	2016	11		E0164074			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. 		
@D	Mercante, J.W.//Morrison, S.S.//Raphael, B.H.//Winchell, J.M. 	Complete Genome Sequences of the Historical Legionella pneumophila Strains OLDA and Pontiac.	Genome Announcements	2016	4		e00866-16			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. 		
@D	Mercier, C.//Lossouarn, J.//Haverkamp, T.//Bienvenu, N.//Godfroy, A.//Cueff-Gauchard, V.//Geslin, C.//Nesbo, C. 	Draft Genome Sequences of Two Marinitoga camini Isolates Producing Bacterioviruses.	Genome Announcements	2016	4		e01261-16			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. 		
@D	Merga, J.Y.//Winstanley, C.//Williams, N.J.//Yee, E.//Miller, W.G. 	Complete Genome Sequence of the Arcobacter butzleri Cattle Isolate 7h1h.	Genome Announcements	2013	1		e00655-13			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. 		
@D	Merhej, V.//Armougom, F.//Robert, C.//Raoult, D. 	Genome Sequence of Lactobacillus ingluviei, a Bacterium Associated with Weight Gain in Animals.	J. Bacteriol.	2012	194		5697			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. 		
@D	Merhej, V.//Croce, O.//Robert, C.//Rolain, J.M.//Raoult, D. 	Genome Sequence of Bartonella rattaustraliani, a Bacterium Isolated from an Australian Rat.	J. Bacteriol.	2012	194		7012			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)). 		
@D	Merhej, V.//Croce, O.//Robert, C.//Rolain, J.M.//Raoult, D. 	Genome Sequence of Bartonella rattimassiliensis, a Bacterium Isolated from European Rattus norvegicus.	J. Bacteriol.	2012	194		7013			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)). 		
@D	Merhej, V.//Pfleiderer, A.//Ramasamy, D.//Lagier, J.C.//Michelle, C.//Raoult, D.//Fournier, P.E. 	Non-contiguous finished genome sequence and description of Clostridium ihumii sp. nov.	Standards in Genomic Sciences	2015	10		63			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. 		
@D	Merino, A.//Gamba, G. 	Biologia molecular en medicina.  II. Enzimas de restriccion.	Rev. Invest. Clin.	1996	48		159-163					
@D	Merino, M.//Alvarez-Fraga, L.//Gomez, M.J.//Aransay, A.M.//Lavin, J.L.//Chaves, F.//Bou, G.//Poza, M. 	Complete Genome Sequence of the Multiresistant Acinetobacter baumannii Strain AbH12O-A2, Isolated during a Large Outbreak in Spain.	Genome Announcements	2014	2		e01182-14			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. 		
@D	Merkiene, E.//Klimasauskas, S. 	Probing a rate-limiting step by mutational perturbation of AdoMet binding in the HhaI methyltransferase.	Nucleic Acids Res.	2005	33		307-315			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. 		
@D	Merkiene, E.//Lukinavicius, G.//Klimasauskas, S. 	Synergy of substrate binding, base flipping and catalytic loop motions in a DNA methyltransferase.	Eur. Biophys. J.	2005	34		617			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. 		
@D	Merkiene, E.//Vilkaitis, G.//Klimasauskas, S. 	Coexistence of single-strand and double-strand DNA cytosine-N4-methyltransferases in the BcnI restriction-modification system.	Biologija	1997	1		5-8			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. 		
@D	Merkiene, E.//Vilkaitis, G.//Klimasauskas, S. 	A pair of single-strand and double-strand DNA cytosine-N4 methyltransferases from Bacillus centrosporus.	Biol. Chem.	1998	379		569-571			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. 		
@D	Merkiene, E.//Weinhold, E.//Klimasauskas, S. 	Kinetics of cofactor binding and catalytic loop movements of HhaI methyltransferase.	Biochem. Soc. Trans.	2000	28		A464			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. 		
@D	Merkl, R.//Fritz, H.J. 	Statistical evidence for a biochemical pathway of natural, sequence-targeted G/C to C/G transversion mutagenesis in Haemophilus influenzae Rd.	Nucleic Acids Res.	1996	24		4146-4151			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. 		
@D	Merkl, R.//Kroeger, M.//Rice, P.//Fritz, H.-J. 	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.	Nucleic Acids Res.	1992	20		1657-1662			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. 		
@D	Merlo, D.J.//Thompson, D.V. 	In vitro sodium bisulfite mutagenesis of restriction endonuclease recognition sites.	Anal. Biochem.	1987	163		79-87			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. 		
@D	Mermelstein, L.D.//Popoutsakis, E.T. 	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.	Appl. Environ. Microbiol.	1993	59		1077-1081			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. 		
@D	Mermelstein, L.D.//Welker, N.E.//Bennett, G.N.//Papoutsakis, E.T. 	Expression of cloned homologous genes in Clostridium acetobutylicum ATCC 824.	Biotechnology	1992	10		190-195			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. 		
@D	Mernagh, D.//Marks, P.//Kneale, G. 	AhdI, a new class of restriction-modification system?	Biochem. Soc. Trans.	1999	27		A126			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. 		
@D	Mernagh, D.R.//Janscak, P.//Firman, K.//Kneale, G.G. 	Protein-protein and protein-DNA interactions in the type I restriction endonuclease R.EcoR124I.	Biol. Chem.	1998	379		497-503			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. 		
@D	Mernagh, D.R.//Kneale, G.G. 	High resolution footprinting of a type I methyltransferase reveals a large structural distortion within the DNA recognition site.	Nucleic Acids Res.	1996	24		4853-4858			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. 		
@D	Mernagh, D.R.//Reynolds, L.A.//Kneale, G.G. 	DNA binding and subunit interactions in the type I methyltransferase M.EcoR124I.	Nucleic Acids Res.	1997	25		987-991			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. 		
@D	Mernagh, D.R.//Taylor, I.A.//Kneale, G.G. 	Interaction of the type I methyltransferase M.EcoR124I with modified DNA substrates: sequence discrimination and base flipping.	Biochem. J.	1998	336		719-725			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. 		
@D	Merritt, J.//Qi, F.X.//Shi, W.Y. 	A unique nine-gene comY operon in Streptococcus mutans.	Microbiology	2005	151		157-166			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. 		
@D	Merten, M.//Brinkrolf, K.//Albersmeier, A.//Kutter, Y.//Ruckert, C.//Tauch, A. 	Complete Genome Sequence and Annotation of Corynebacterium singulare DSM 44357, Isolated from a Human Semen Specimen.	Genome Announcements	2015	3		e00183-15			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. 		
@D	Mertineit, C.//Yoder, J.A.//Taketo, T.//Laird, D.W.//Trasler, J.M.//Bestor, T.H. 	Sex-specific exons control DNA methyltransferase in mammalian germ cells.	Development	1998	125		889-897			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. 		
@D	Mertz, J.E.//Davis, R.W. 	Cleavage of DNA by EcoRI restriction endonuclease generates cohesive ends.	Proc. Natl. Acad. Sci. U. S. A.	1972	69		3370-3374			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. 		
@D	Meselson, M.//Yuan, R. 	DNA restriction enzyme from E. coli.	Nature	1968	217		1110-1114			An endonuclease which degrades foreign DNA has been isolated.  The enzyme requires S-adenosylmethionine, ATP and Mg++. 		
@A	Meselson, M.//Yuan, R. 		DNA-restriction enzyme from E. coli K.			Cantoni, G.I.//Davies, R. 		Procedures in Nucleic Acids Research				New York	Harper and Row	1972		2		889-895									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. 		
@D	Meselson, M.//Yuan, R.//Heywood, J. 	Restriction and modification of DNA.	Annu. Rev. Biochem.	1972	41		447-466			None 		
@D	Meslier, V.//Loux, V.//Renault, P. 	Genome Sequence of Lactococcus raffinolactis Strain 4877, Isolated from Natural Dairy Starter Culture.	J. Bacteriol.	2012	194		6364			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. 		
@D	Meslier, V.//Loux, V.//Renault, P. 	Genome Sequence of Leuconostoc pseudomesenteroides Strain 4882, Isolated from a Dairy Starter Culture.	J. Bacteriol.	2012	194		6637			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. 		
@D	Messer, W.//Noyer-Weidner, M. 	Timing and targeting: the biological functions of Dam methylation in E. coli.	Cell	1988	54		735-737			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. 		
@D	Messick, J.B.//Santos, A.P.//Guimaraes, A.M. 	Complete Genome Sequences of Two Hemotropic Mycoplasmas, Mycoplasma haemofelis Strain Ohio2 and Mycoplasma suis Strain Illinois.	J. Bacteriol.	2011	193		2068-2069			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. 		
@D	Messina, E.//Sorokin, D.Y.//Kublanov, I.V.//Toshchakov, S.//Lopatina, A.//Arcadi, E.//Smedile, F.//La Spada, G.//La Cono, V.//Yakimov, M.M. 	Complete genome sequence of 'Halanaeroarchaeum sulfurireducens' M27-SA2, a sulfur-reducing and acetate-oxidizing haloarchaeon from the deep-sea hypersaline anoxic lake Medee.	Standards in Genomic Sciences	2016	11		35			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. 		
@D	Metcalf, W.W. 	Genetic analysis in the domain Archaea.	Methods Microbiol.	1999	29		277-326			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. 		
@D	Methe, B.A. et al. 	The psychrophilic lifestyle as revealed by the genome sequence of Colwellia psychrerythraea 34H through genomic and proteomic analyses.	Proc. Natl. Acad. Sci. U. S. A.	2005	102		10913-10918			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. 		
@D	Methe, B.A. et al. 	Genome of Geobacter sulfurreducens: metal reduction in subsurface environments.	Science	2003	302		1967-1969			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. 		
@A	Meunier, B.//Tian, G.-L.//Macadre, C.//Slonimski, P.P.//Lazowska, J. 		Group II introns transpose in yeast mitochondria.			Quagliariello, E.//Papa, S.//Palmieri, F.//Saccone, C. 		Structure, function and biogenesis of energy transfer systems.				Amsterdam	Elsevier Scientific Publishing Company	1990		0		169-174									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. 		
@D	Mevada, V.A.//Patel, S.//Pandya, J.V.//Joshi, H.//Patel, R.K. 	Whole Genome sequencing and annotation of halophilic Salinicoccus sp. BAB 3246 isolated from coastal region of Gujarat.	Genomics Data	2017	13		30-34			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. 		
@D	Meyer, J.L.//Dillard, B.A.//Rodgers, J.M.//Ritchie, K.B.//Paul, V.J.//Teplitski, M. 	Draft genome sequence of Halomonas meridiana R1t3 isolated from the surface microbiota of the Caribbean Elkhorn coral Acropora palmata.	Standards in Genomic Sciences	2015	10		75			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. 		
@A	Meyer, P. 		DNA methylation of flower color transgenes in Petunia hybrida.			Russo, V.E.A.//Martienssen, R.A.//Riggs, A.D. 		Epigenetic Mechanisms of Gene Regulation				Cold Spring Harbor	Cold Spring Harbor Laboratory Press	1996		0		305-317									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. 		
@D	Meyer-Cifuentes, I.//Fiedler, S.//Muller, J.A.//Kappelmeyer, U.//Mausezahl, I.//Heipieper, H.J. 	Draft Genome Sequence of Magnetospirillum sp. Strain 15-1, a Denitrifying Toluene Degrader Isolated from a Planted Fixed-Bed Reactor.	Genome Announcements	2017	5		e00764-17			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. 		
@D	Meyerdierks, A.//Kube, M.//Kostadinov, I.//Teeling, H.//Glockner, F.O.//Reinhardt, R.//Amann, R. 	Metagenome and mRNA expression analyses of anaerobic methanotrophic archaea of the ANME-1 group.	Environ. Microbiol.	2010	12		422-439			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. 		
@D	Meyerink, J.H.//Retel, J. 	Topographical analysis of yeast ribosomal DNA by cleavage with restriction endonucleases.  II. The physical map of EcoRI fragments.	Nucleic Acids Res.	1976	3		2697-2707			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. 		
@D	Meyerink, J.H.//Retel, J.//Planta, R.J.//Heidekamp, F. 	Topographical analysis of yeast ribosomal DNA by cleavage with restriction endonucleases.	Mol. Biol. Rep.	1976	2		393-400			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. 		
@D	Meyertons, J.L. 	Actinophages and restriction endonucleases from Micromonospora species (Actinomycetales).	Diss. Abstr.	1988	48		1888			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. 		
@D	Meyertons, J.L. 	Actinophages and restriction endonucleases from Micromonospora species (Actinomycetales).	Ph.D. Thesis, Rutgers University, USA	1987			1-117			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. 		
@D	Meyertons, J.L.//Tilley, B.C.//Lechevalier, M.P.//Lechevalier, H.A. 	Actinophages and restriction enzymes from Micromonospora species (Actinomycetales).	J. Ind. Microbiol.	1987	2		293-303			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. 		
@D	Meygret, A.//Vincent, P.//Moullec, S.//Nacazume, J.//Adnani, Y.//Lavenier, D.//Kayal, S.//Faili, A. 	Genome Sequence of the Uncommon Streptococcus pyogenes M/emm66 Strain STAB13021,  Isolated from Clonal Clustered Cases in French Brittany.	Genome Announcements	2016	4		e00689-16			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. 		
@D	Mhamdi, R.//Ardley, J.//Tian, R.//Seshadri, R.//Reddy, T.B.//Pati, A.//Woyke, T.//Markowitz, V.//Ivanova, N.//Kyrpides, N.//Reeve, W. 	High-quality permanent draft genome sequence of Ensifer meliloti strain 4H41, an  effective salt- and drought-tolerant microsymbiont of Phaseolus vulgaris.	Standards in Genomic Sciences	2015	10		34			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. 		
@D	Mhanni, A.A.//Yoder, J.A.//Dubesky, C.//McGowan, R.A. 	Cloning and sequence analysis of a zebrafish cDNA encoding DNA (cytosine-5)-methyltransferase-1.	Genesis	2001	30		213-219			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. 		
@D	Mi, S.//Alonso, D.//Roberts, R.J. 	Functional analysis of Gln-237 mutants of HhaI methyltransferase.	Nucleic Acids Res.	1995	23		620-627			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. 		
@D	Mi, S.//Roberts, R.J. 	The DNA binding affinity of HhaI methylase is increased by a single amino acid substitution in the catalytic center.	Nucleic Acids Res.	1993	21		2459-2464			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. 		
@D	Mi, S.//Roberts, R.J. 	How M.MspI and M.HpaII decide which base to methylate.	Nucleic Acids Res.	1992	20		4811-4816			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. 		
@D	Mi, S.//Song, J.//Lin, J.//Che, Y.//Zheng, H.//Lin, J. 	Complete genome of Leptospirillum ferriphilum ML-04 provides insight into its physiology and environmental adaptation.	J. Microbiol.	2011	49		890-901			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. 		
@D	Miao, S.//Li, F.//Zhang, M.//Wang, X.//He, J.//Jiang, J. 	Molecular cloning and sequence analysis of Rana tigrina ranavirus (RTV) DNA methyltransferase gene.	Shuichan Xuebao	2002	26		157-160			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. 		
@D	Miao, Y.//Zhou, X.//Xu, Y.//Yu, S. 	Draft Genome Sequence of Gluconobacter oxydans NL71, a Strain That Efficiently Biocatalyzes Xylose to Xylonic Acid at a High Concentration.	Genome Announcements	2015	3		e00615-15			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. 		
@D	Miceli, E.//Presta, L.//Maggini, V.//Fondi, M.//Bosi, E.//Chiellini, C.//Fagorzi, C.//Bogani, P.//Di Pilato, V.//Rossolini, G.M.//Mengoni, A.//Firenzuoli, F.//Perrin, E.//Fani, R. 	New Genome Sequence of an Echinaceapurpurea Endophyte, Arthrobacter sp. Strain EpSL27, Able To Inhibit Human-Opportunistic Pathogens.	Genome Announcements	2017	5		e00565-17			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. 		
@D	Michael, G.B.//Kadlec, K.//Sweeney, M.T.//Brzuszkiewicz, E.//Liesegang, H.//Daniel, R.//Murray, R.W.//Watts, J.L.//Schwarz, S. 	ICEPmu1, an integrative conjugative element (ICE) of Pasteurella multocida: structure and transfer.	J. Antimicrob. Chemother.	2012	67		91-100			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. 		
@D	Michel, F.//Dujon, B. 	Genetic exchanges between bacteriophage T4 and filamentous fungi?	Cell	1986	46		323			Note the sequence similarity between I-TevI and a protein encoded by a class 1 intron in the NADH-dehydrogenase gene of Neurospora crassa. 		
@D	Michiels, J.E.//Van den Bergh, B.//Fauvart, M.//Michiels, J. 	Draft genome sequence of Enterococcus faecium strain LMG 8148.	Standards in Genomic Sciences	2016	11		63			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. 		
@D	Michiels, J.E.//Van den Bergh, B.//Fauvart, M.//Michiels, J. 	Draft genome sequence of Acinetobacter baumannii strain NCTC 13423, a multidrug-resistant clinical isolate.	Standards in Genomic Sciences	2016	11		57			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. 		
@D	Mick, J.M.//Beck, D.J. 	Diamminedichloroplatinum(II) modification of DNA inhibits cutting by restriction endonucleases in a sequence specific manner.	Abstr. Gen. Meet. Am. Soc. Microbiol.	1988	88		164			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. 		
@D	Middleton, D.R.//Lorenz, W.//Avci, F.Y. 	Complete Genome Sequence of the Bacterium Bacillus circulans Jordan Strain 32352.	Genome Announcements	2017	5		e00289-17			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. 		
@A	Middleton, J.H. 		Restriction endonucleases from Haemophilus species: Enzymes for specific fragmentation of DNA.			 		Ph.D. Thesis				Chapel Hill, NC		1973													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. 		
@D	Middleton, J.H.//Edgell, M.H.//Hutchison, C.A. III 	Specific fragments of PhiX174 deoxyribonucleic acid produced by a restriction enzyme from Haemophilus aegyptius, endonuclease Z.	J. Virol.	1972	10		42-50			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. 		
@D	Midha, S.//Ranjan, M.//Sharma, V.//Kumari, A.//Singh, P.K.//Korpole, S.//Patil, P.B. 	Genome Sequence of Pediococcus pentosaceus Strain IE-3.	J. Bacteriol.	2012	194		4468			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. 		
@D	Midha, S.//Ranjan, M.//Sharma, V.//Pinnaka, A.K.//Patil, P.B. 	Genome Sequence of Xanthomonas citri pv. mangiferaeindicae Strain LMG 941.	J. Bacteriol.	2012	194		3031			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. 		
@D	Mierzejewska, K.//Bochtler, M.//Czapinska, H. 	On the role of steric clashes in methylation control of restriction endonuclease  activity.	Nucleic Acids Res.	2015	44		485-495			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. 		
@D	Mierzejewska, K.//Siwek, W.//Czapinska, H.//Kaus-Drobek, M.//Radlinska, M.//Skowronek, K.//Bujnicki, J.M.//Dadlez, M.//Bochtler, M. 	Structural basis of the methylation specificity of R.DpnI.	Nucleic Acids Res.	2014	42		8745-8754			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. 		
@D	Mierzejewska, K.//Siwek, W.//Czapinska, H.//Skowronek, K.//Bujnicki, J.//Bochtler, M. 	Molecular basis of 6-methyladenine recognition by R.DpnI restriction endonuclease.	FEBS J.	2013	280		122-123			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. 		
@D	Mignolet, J.//Fontaine, L.//Kleerebezem, M.//Hols, P. 	Complete Genome Sequence of Streptococcus salivarius HSISS4, a Human Commensal Bacterium Highly Prevalent in the Digestive Tract.	Genome Announcements	2016	4		e01637-15			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. 		
@D	Miki, T.//Okada, N. 	Draft Genome Sequence of Chromobacterium haemolyticum Causing Human Bacteremia Infection in Japan.	Genome Announcements	2014	2		e01047-14			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. 		
@D	Milani, C.//Duranti, S.//Lugli, G.A.//Bottacini, F.//Strati, F.//Arioli, S.//Foroni, E.//Turroni, F.//van Sinderen, D.//Ventura, M. 	Comparative Genomics of Bifidobacterium animalis subsp. lactis Reveals a Strict Monophyletic Bifidobacterial Taxon.	Appl. Environ. Microbiol.	2013	79		4304-4315			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. 		
@D	Milani, C.//Lugli, G.A.//Duranti, S.//Turroni, F.//Bottacini, F.//Mangifesta, M.//Sanchez, B.//Viappiani, A.//Mancabelli, L.//Taminiau, B.//Delcenserie, V.//Barrangou, R.//Margolles, A.//van Sinderen, D.//Ventura, M. 	Genome encyclopaedia of type strains of the genus Bifidobacterium.	Appl. Environ. Microbiol.	2014	80		6290-6302			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. 		
@D	Militello, K.T.//Mandarano, A.H.//Varechtchouk, O.//Simon, R.D. 	Cytosine DNA methylation influences drug resistance in Escherichia coli through increased sugE expression.	FEMS Microbiol. Lett.	2014	350		100-106			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. 		
@D	Militello, K.T.//Simon, R.D.//Qureshi, M.//Maines, R.//VanHorne, M.L.//Hennick, S.M.//Jayakar, S.K.//Pounder, S. 	Dcm-mediated cytosine DNA methylation is conserved in Escherichia coli and influences the expression of ribosomal protein genes.	FASEB J.	2010	24		78-85			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. 		
@D	Militello, K.T.//Simon, R.D.//Qureshi, M.//Maines, R.//VanHorne, M.L.//Hennick, S.M.//Jayakar, S.K.//Pounder, S. 	Conservation of Dcm-mediated cytosine DNA methylation in Escherichia coli.	FEMS Microbiol. Lett.	2012	328		78-85			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. 		
@D	Milkman, R. 	Recombination and population structure in Escherichia coli.	Genetics	1997	146		745-750			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. 		
@D	Milkman, R.//Jaeger, E.//McBride, R.D. 	Molecular evolution of the Escherichia coli chromosome. VI. Two regions of high effective recombination.	Genetics	2003	163		475-483			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. 		
@D	Milkman, R.//Raleigh, E.A.//McKane, M.//Cryderman, D.//Bilodeau, P.//McWeeny, K. 	Molecular evolution of the escherichia coli chromosome. V. Recombination patterns among strains of diverse origin.	Genetics	1999	153		539-554			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. 		
@D	Milla, M.A.//Spears, P.A.//Pearson, R.E.//Walker, G.T. 	Use of the restriction enzyme AvaI and Exo- Bst polymerase in strand displacement amplification.	Biotechniques	1998	24		392-396			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. 		
@D	Millar, J.A.//Beare, P.A.//Moses, A.S.//Martens, C.A.//Heinzen, R.A.//Raghavan, R. 	Whole-Genome Sequence of Coxiella burnetii Nine Mile RSA439 (Phase II, Clone 4),  a Laboratory Workhorse Strain.	Genome Announcements	2017	5		e00471-17			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. 		
@D	Millard, A.//Clokie, M.R.//Shub, D.A.//Mann, N.H. 	Genetic organization of the psbAD region in phages infecting marine Synechococcus strains.	Proc. Natl. Acad. Sci. U. S. A.	2004	101		11007-11012			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. 		
@D	Millard, A.D.//Westblade, L.F.//LiPuma, J.J.//Vavikolanu, K.//Read, T.D.//Pallen, M.J.//Burd, E.M.//Constantinidou, C.I. 	Draft Genome Sequence of the Pandoraea apista LMG 16407 Type Strain.	Genome Announcements	2015	3		e01300-15			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). 		
@D	Millard, J.T.//Beachy, T.M. 	Cytosine methylation enhances mitomycin C cross-linking.	Biochemistry	1993	32		12850-12856			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. 		
@D	Miller, C.A.//Cohen, S.N. 	Phenotypically cryptic EcoRI endonuclease specified by the ColE1 plasmid.	Proc. Natl. Acad. Sci. U. S. A.	1978	75		1265-1269			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. 		
@D	Miller, C.L.//Chen, T.//Chen, P.//Leung, K.P. 	Genome Sequence of Highly Virulent Pseudomonas aeruginosa Strain VA-134, Isolated from a Burn Patient.	Genome Announcements	2016	4		e01662-15			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. 		
@D	Miller, D.A. et al. 	Complete Genome Sequence of the Cellulose-Degrading Bacterium Cellulosilyticum lentocellum.	J. Bacteriol.	2011	193		2357-2358			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. 		
@D	Miller, J.C.//Holmes, M.C.//Wang, J.//Guschin, D.Y.//Lee, Y.L.//Rupniewski, I.//Beausejour, C.M.//Waite, A.J.//Wang, N.S.//Kim, K.A.//Gregory, P.D.//Pabo, C.O.//Rebar, E.J. 	An improved zinc-finger nuclease architecture for highly specific genome editing.	Nat. Biotechnol.	2007	25		778-785			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. 		
@D	Miller, J.F.//Dower, W.J.//Tompkins, L.S. 	High-voltage electroporation of bacteria:  Genetic transformation of Campylobacter jejuni with plasmid DNA.	Proc. Natl. Acad. Sci. U. S. A.	1988	85		856-860			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. 		
@D	Miller, P.A.//Shajani, Z.//Meints, G.A.//Caplow, D.//Goobes, G.//Varani, G.//Drobny, G.P. 	Contrasting Views of the Internal Dynamics of the HhaI Methyltransferase Target DNA Reported by Solution and Solid-State NMR Spectroscopy.	J. Am. Chem. Soc.	2006	128		15970-15971			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? 		
@D	Miller, P.B.//Wakarchuk, W.W.//Warren, R.A.J. 	Alpha-putrescinylthymine and the sensitivity of bacteriophage Phi W-14 DNA to restriction endonucleases.	Nucleic Acids Res.	1985	13		2559-2568			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. 		
@D	Miller, T.R.//Delcher, A.L.//Salzberg, S.L.//Saunders, E.//Detter, J.C.//Halden, R.U. 	Genome Sequence of the Dioxin-Mineralizing Bacterium Sphingomonas wittichii RW1.	J. Bacteriol.	2010	192		6101-6102			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. 		
@D	Miller, W.G. 	Characterization of multiple Campylobacter jejuni type I restriction-modification loci.	Int. J. Med. Microbiol.	2001	291		79			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. 		
@D	Miller, W.G.//Chapman, M.H.//Yee, E.//Revez, J.//Bono, J.L.//Rossi, M. 	Complete Genome Sequence of the Hippuricase-Positive Campylobacter avium Type Strain LMG 24591.	Genome Announcements	2017	5		e01221-17			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. 		
@D	Miller, W.G.//Huynh, S.//Parker, C.T.//Niedermeyer, J.A.//Kathariou, S. 	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.	Genome Announcements	2016	4		e01175-16			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. 		
@D	Miller, W.G.//Keech, A.M.//Pearson, B.M.//Wells, J.M.//Kapitonov, V.V.//Konkel, M.E.//Mandrell, R.E. 	Diversity of Campylobacter type I restriction-modification loci: Induction of hsdS by exogenous DNA.	Abstr. Gen. Meet. Am. Soc. Microbiol.	2004	104		210			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. 		
@D	Miller, W.G.//Pearson, B.M.//Wells, J.M.//Parker, C.T.//Kapitonov, V.V.//Mandrell, R.E. 	Diversity within the Campylobacter jejuni type I restriction - modification loci.	Microbiology	2005	151		337-351			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. 		
@D	Miller, W.G.//Wang, G.//Binnewies, T.T.//Parker, C.T. 	The complete genome sequence and analysis of the human pathogen Campylobacter lari.	Foodborne Pathog. Dis.	2008	5		371-386			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. 		
@D	Miller, W.G.//Yee, E. 	Complete Genome Sequence of Campylobacter gracilis ATCC 33236T.	Genome Announcements	2015	3		e01087-15			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. 		
@D	Miller, W.G.//Yee, E.//Bono, J.L. 	Complete Genome Sequence of the Campylobacter helveticus Type Strain ATCC 51209.	Genome Announcements	2017	5		e00398-17			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). 		
@D	Miller, W.G.//Yee, E.//Chapman, M.H. 	Complete Genome Sequences of Campylobacter hyointestinalis subsp. hyointestinalis Strain LMG 9260 and C. hyointestinalis subsp. lawsonii Strain LMG 15993.	Genome Announcements	2016	4		e00665-16			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. 		
@D	Miller, W.G.//Yee, E.//Chapman, M.H.//Bono, J.L. 	Comparative genomics of all three Campylobacter sputorum biovars and a novel cattle-associated C. sputorum clade.	Genome Biol. Evol.	2017	9		1513-1518			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. 		
@D	Miller, W.G.//Yee, E.//Chapman, M.H.//Smith, T.P.//Bono, J.L.//Huynh, S.//Parker, C.T.//Vandamme, P.//Luong, K.//Korlach, J. 	Comparative genomics of the Campylobacter lari group.	Genome Biol. Evol.	2014	6		3252-3266			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. 		
@D	Miller, W.G.//Yee, E.//Huynh, S.//Chapman, M.H.//Parker, C.T. 	Complete Genome Sequence of Campylobacter iguaniorum Strain RM11343, Isolated from an Alpaca.	Genome Announcements	2016	4		e00646-16			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. 		
@D	Miller, W.G.//Yee, E.//Lopes, B.S.//Chapman, M.H.//Huynh, S.//Bono, J.L.//Parker, C.T.//Forbes, K.J. 	Comparative genomic analysis identifies a Campylobacter clade deficient in selenium metabolism.	Genome Biol. Evol.	2017	9		1843-1858			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. 		
@D	Miller, W.G.//Yee, E.//On, S.L.//Andersen, L.P.//Bono, J.L. 	Complete Genome Sequence of the Campylobacter ureolyticus Clinical Isolate RIGS 9880.	Genome Announcements	2015	3		e01291-15			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. 		
@D	Miller, W.G.//Yee, E.//Revez, J.//Bono, J.L.//Rossi, M. 	Complete Genome Sequence of the Campylobacter cuniculorum Type Strain LMG 24588.	Genome Announcements	2017	5		e00543-17			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). 		
@D	Mills, D.A.//Manias, D.A.//McKay, L.L.//Dunny, G.M. 	Homing of a group II intron from Lactococcus lactis subsp. lactis ML3.	J. Bacteriol.	1997	179		6107-6111			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. 		
@D	Mills, D.A.//McKay, L.L.//Dunny, G.M. 	Splicing of a group II intron involved in the conjugative transfer of pRS01 in Lactococci.	J. Bacteriol.	1996	178		3531-3538			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. 		
@D	Mills, H.J.//Eisen, J.//Sobecky, P.A. 	Insights into the role of cryptic marine plasmids based on sequence analysis.	Abstr. Gen. Meet. Am. Soc. Microbiol.	2003	103		N-147			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. 		
@D	Mills, K.I.//Ramsahoye, B.H. 	Methods in Molecular Biology. DNA methylation protocols.	Methods Mol. Biol.	2002	200		1-7			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. 		
@A	Mills, K.V.//Paulus, H. 		Biochemical mechanisms of intein-mediated protein splicing.			Belfort, M. et al. 		Nucleic Acids Mol. Biol.				Berlin Heidelberg	Springer-Verlag	2005		16		233-255									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. 		
@D	Mills, S.//Griffin, C.//O'Sullivan, O.//Coffey, A.//McAuliffe, O.E.//Meijer, W.C.//Serrano, L.M.//Ross, R.P. 	A new phage on the 'Mozzarella' block: Bacteriophage 5093 shares a low level of homology with other Streptococcus thermophilus phages.	Int. Dairy Journal	2011	21		963-969			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. 		
@D	Mills, S.//McAuliffe, O.E.//Coffey, A.//Fitzgerald, G.F.//Ross, R.P. 	Plasmids of lactococci - genetic accessories or genetic necessities?	FEMS Microbiol. Rev.	2006	30		243-273			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. 		
@D	Milsom, S.E.//Halford, S.E.//Embleton, M.L.//Szczelkun, M.D. 	Analysis of DNA looping interactions by type II restriction enzymes that require two copies of their recognition sites.	J. Mol. Biol.	2001	311		515-527			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. 		
@D	Minami, T.//Ohtsubo, Y.//Anda, M.//Nagata, Y.//Tsuda, M.//Mitsui, H.//Sugawara, M.//Minamisawa, K. 	Complete Genome Sequence of Methylobacterium sp. Strain AMS5, an Isolate from a Soybean Stem.	Genome Announcements	2016	4		e00144-16			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. 		
@D	Minarovits, J. 	MICROBE-INDUCED EPIGENETIC ALTERATIONS IN HOST CELLS: THE COMING ERA OF PATHO-EPIGENETICS OF MICROBIAL INFECTIONS A REVIEW.	Acta Microbiol. Immunol. Hung.	2009	56		1-19			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. 		
@D	Minczuk, M.//Papworth, M.A.//Kolasinska, P.//Murphy, M.P.//Klug, A. 	Sequence-specific modification of mitochondrial DNA using a chimeric zinc finger methylase.	Proc. Natl. Acad. Sci. U. S. A.	2006	103		19689-19694			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. 		
@D	Mindlin, S.//Petrenko, A.//Kurakov, A.//Beletsky, A.//Mardanov, A.//Petrova, M. 	Resistance of Permafrost and Modern Acinetobacter lwoffii Strains to Heavy Metals and Arsenic Revealed by Genome Analysis.	Biomed. Res. Int.	2016	2016		3970831			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. 		
@D	Minegishi, K.//Aikawa, C.//Furukawa, A.//Watanabe, T.//Nakano, T.//Ogura, Y.//Ohtsubo, Y.//Kurokawa, K.//Hayashi, T.//Maruyama, F.//Nakagawa, I.//Eishi, Y. 	Complete Genome Sequence of a Propionibacterium acnes Isolate from a Sarcoidosis  Patient.	Genome Announcements	2013	1		e00016-12			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. 		
@D	Miner, Z. 	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.	Diss. Abstr.	1990	51		588B			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. 		
@D	Miner, Z.//Hattman, S. 	Molecular cloning, sequencing, and mapping of the bacteriophage T2 dam gene.	J. Bacteriol.	1988	170		5177-5184			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. 		
@D	Miner, Z.//Schlagman, S.//Hattman, S. 	Single amino acid changes which alter the sequence specificity of the T4 and T2 (Dam) DNA-adenine methyltransferases.	Gene	1988	74		275-276			Meeting Abstract 		
@D	Miner, Z.//Schlagman, S.//Hattman, S. 	Single amino acid changes which alter the sequence specificity of the T4 (dam) DNA-adenine methyltransferase.	Biochem. Pharmacol.	1988	37		1811-1812			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. 		
@D	Miner, Z.//Schlagman, S.//Hattman, S. 	The dam DNA-methyltransferases of E. coli and its phages T2 and T4.	J. Cell Biochem. Suppl.	1989	13D		199			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. 		
@D	Miner, Z.//Schlagman, S.L.//Hattman, S. 	Single amino acid changes that alter the DNA sequence specificity of the DNA-[N/6-adenine] methyltransferase (Dam) of bacteriophage T4.	Nucleic Acids Res.	1989	17		8149-8157			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. 		
@D	Minion, F.C.//Lefkowitz, E.J.//Madsen, M.L.//Cleary, B.J.//Swartzell, S.M.//Mahairas, G.G. 	The genome sequence of Mycoplasma hyopneumoniae strain 232, the agent of swine mycoplasmosis.	J. Bacteriol.	2004	186		7123-7133			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. 		
@D	Minko, I.//Hattman, S.//Lloyd, R.S.//Kossykh, V. 	Methylation by a mutant T2 DNA [N6-adenine] methyltransferase expands the usage of RecA-assisted endonuclease (RARE) cleavage.	Nucleic Acids Res.	2001	29		1484-1490			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. 		
@D	Minogue, T.D. et al. 	Whole-genome sequences of 24 Brucella strains.	Genome Announcements	2014	2		e00915-14			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. 		
@D	Minogue, T.D.//Daligault, H.A.//Davenport, K.W.//Bishop-Lilly, K.A.//Broomall, S.M.//Bruce, D.C.//Chain, P.S.//Chertkov, O.//Coyne, S.R.//Freitas, T.//Frey, K.G.//Gibbons, H.S.//Jaissle, J.//Redden, C.L.//Rosenzweig, C.N.//Xu, Y.//Johnson, S.L. 	Complete Genome Assembly of Escherichia coli ATCC 25922, a Serotype O6 Reference  Strain.	Genome Announcements	2014	2		e00969-14			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. 		
@D	Minogue, T.D.//Daligault, H.A.//Davenport, K.W.//Bishop-Lilly, K.A.//Broomall, S.M.//Bruce, D.C.//Chain, P.S.//Chertkov, O.//Coyne, S.R.//Freitas, T.//Frey, K.G.//Gibbons, H.S.//Jaissle, J.//Redden, C.L.//Rosenzweig, C.N.//Xu, Y.//Johnson, S.L. 	Complete Genome Assembly of Streptococcus pyogenes ATCC 19615, a Group A beta-Hemolytic Reference Strain.	Genome Announcements	2014	2		e00976-14			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. 		
@D	Minogue, T.D.//Daligault, H.A.//Davenport, K.W.//Bishop-Lilly, K.A.//Bruce, D.C.//Chain, P.S.//Chertkov, O.//Coyne, S.R.//Freitas, T.//Frey, K.G.//Jaissle, J.//Koroleva, G.I.//Ladner, J.T.//Palacios, G.F.//Redden, C.L.//Xu, Y.//Johnson, S.L. 	Complete Genome Assembly of Reference Strain Ochrobactrum anthropi ATCC 49687.	Genome Announcements	2014	2		e00962-14			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. 		
@D	Minogue, T.D.//Daligault, H.A.//Davenport, K.W.//Bishop-Lilly, K.A.//Bruce, D.C.//Chain, P.S.//Chertkov, O.//Coyne, S.R.//Freitas, T.//Frey, K.G.//Jaissle, J.//Koroleva, G.I.//Ladner, J.T.//Palacios, G.F.//Redden, C.L.//Xu, Y.//Johnson, S.L. 	Draft Genome Assembly of Neisseria lactamica Type Strain A7515.	Genome Announcements	2014	2		e00951-14			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. 		
@D	Minogue, T.D.//Daligault, H.E.//Davenport, K.W.//Bishop-Lilly, K.A.//Bruce, D.C.//Chain, P.S.//Coyne, S.R.//Chertkov, O.//Freitas, T.//Frey, K.G.//Jaissle, J.//Koroleva, G.I.//Ladner, J.T.//Palacios, G.F.//Redden, C.L.//Xu, Y.//Johnson, S.L. 	Draft Genome Assemblies of Enterobacter aerogenes CDC 6003-71, Enterobacter cloacae CDC 442-68, and Pantoea agglomerans UA 0804-01.	Genome Announcements	2014	2		e01073-14			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%. 		
@D	Minogue, T.D.//Daligault, H.E.//Davenport, K.W.//Bishop-Lilly, K.A.//Bruce, D.C.//Chain, P.S.//Coyne, S.R.//Chertkov, O.//Freitas, T.//Frey, K.G.//Jaissle, J.//Koroleva, G.I.//Ladner, J.T.//Palacios, G.F.//Redden, C.L.//Xu, Y.//Johnson, S.L. 	Draft Genome Assemblies of Proteus mirabilis ATCC 7002 and Proteus vulgaris ATCC  49132.	Genome Announcements	2014	2		e01064-14			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. 		
@D	Minogue, T.D.//Daligault, H.E.//Davenport, K.W.//Broomall, S.M.//Bruce, D.C.//Chain, P.S.//Coyne, S.R.//Chertkov, O.//Freitas, T.//Gibbons, H.S.//Jaissle, J.//Koroleva, G.I.//Ladner, J.T.//Palacios, G.F.//Rosenzweig, C.N.//Xu, Y.//Johnson, S.L. 	Complete Genome Assembly of Enterococcus faecalis 29212, a Laboratory Reference Strain.	Genome Announcements	2014	2		e00968-14			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). 		
@D	Minogue, T.D.//Daligault, H.E.//Davenport, K.W.//Broomall, S.M.//Bruce, D.C.//Chain, P.S.//Coyne, S.R.//Gibbons, H.S.//Jaissle, J.//Chertkov, O.//Freitas, T.//Rosenzweig, C.N.//Xu, Y.//Johnson, S.L. 	Draft Genome Assembly of Pseudomonas aeruginosa Quality Control Reference Strain  Boston 41501.	Genome Announcements	2014	2		e00960-14			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. 		
@D	Minot, S.//Grunberg, S.//Wu, G.//Lewis, J.//Bushman, F. 	Hypervariable loci in the human gut virome.	Proc. Natl. Acad. Sci. U. S. A.	2012	109		3962-3966			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. 		
@D	Minton, N.//Carter, G.//Herbert, M.//O'Keeffe, T.//Purdy, D.//Elmore, M.//Ostrowski, A.//Pennington, O.//Davis, I. 	The development of Clostridium difficile genetic systems.	Anaerobe	2004	10		75-84			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. 		
@D	Mirajkar, N.S.//Johnson, T.J.//Gebhart, C.J. 	Complete Genome Sequence of Brachyspira hyodysenteriae Type Strain B-78 (ATCC 27164).	Genome Announcements	2016	4		e00840-16			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. 		
@D	Mirajkar, N.S.//Kelley, M.R.//Gebhart, C.J. 	Draft Genome Sequence of Lawsonia intracellularis Strain E40504, Isolated from a  Horse Diagnosed with Equine Proliferative Enteropathy.	Genome Announcements	2017	5		e00330-17			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. 		
@D	Miranda-Rios, J.A.//Ramirez-Trujillo, J.A.//Nova-Franco, B.//Lozano-Aguirre, B.L.F.//Iturriaga, G.//Suarez-Rodriguez, R. 	Draft Genome Sequence of Arthrobacter chlorophenolicus Strain Mor30.16, Isolated  from the Bean Rhizosphere.	Genome Announcements	2015	3		e00360-15			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. 		
@D	Miriagou, V.//Papagiannitsis, C.C.//Kotsakis, S.D.//Loli, A.//Tzelepi, E.//Legakis, N.J.//Tzouvelekis, L.S. 	Sequence of pNL194, a 79.3-Kilobase IncN Plasmid Carrying the blaVIM-1 Metallo-{beta}-Lactamase Gene in Klebsiella pneumoniae.	Antimicrob. Agents Chemother.	2010	54		4497-4502			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. 		
@D	Mironov, K.S.//Sinetova, M.A.//Bolatkhan, K.//Zayadan, B.K.//Ustinova, V.V.//Kupriyanova, E.V.//Skrypnik, A.N.//Gogoleva, N.E.//Gogolev, Y.V.//Los, D.A. 	Draft Genome Sequence of the Thermotolerant Cyanobacterium Desertifilum sp. IPPAS B-1220.	Genome Announcements	2016	4		e01304-16			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. 		
@D	Mironov, K.S.//Sinetova, M.A.//Kupriyanova, E.V.//Ustinova, V.V.//Kozlova, A.Y.//Messineva, E.M.//Gabrielyan, D.A.//Bedbenov, V.S.//Zayadan, B.K.//Los, D.A. 	Draft Genome Sequences of Two Thermotolerant Cyanobacterial Strains Isolated from Hot Springs.	Genome Announcements	2018	6		e01548-17			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. 		
@D	Miroshnichenko, B.A.//Naroditskii, B.S.//Khilko, S.N.//Platonova, N.//Gruber, I.M.//Tikhonenko, T.I. 	Purification of specific endonucleases EcoRI and BglII by affinity chromatography.	Biokhimiia	1982	47		686-694			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. 		
@D	Miroshnikov, K.K. et al. 	Draft Genome Sequence of Methylocapsa palsarum NE2T, an Obligate Methanotroph from Subarctic Soil.	Genome Announcements	2017	5		e00504-17			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. 		
@D	Misaki, W. 	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.	Afr. J. Biotechnol.	2007	6		1750-1756			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. 		
@D	Misaki, W. 	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.	Afr. J. Biotechnol.	2008	7		1791-1796			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. 		
@D	Misaki, W.//Wilson, B.//Henry, K. 	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.	Afr. J. Biotechnol.	2007	6		1225-1232			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. 		
@D	Mise, K.//Miyahara, M. 	Restriction endonucleases: Their characteristics and distribution in pathogenic bacteria.	Eisei Shikenjo Hokoku	1993	111		1-12			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. 		
@A	Mise, K.//Miyahara, M.//Maruyama, T.//Kudoh, Y.//Ohashi, M. 		Usefulness in the epidemiology of food poisoning cases of detection of specific restriction endonucleases in some serotypes of Salmonella and Yersinia.			Pohland, A.E.//Dowell, V.R.//Richard, J.L. 		Microbial Toxins in Foods and Feeds: Cell. Mol. Modes Action				New York	Plenum Press	1990		0		127-129									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. 		
@D	Mise, K.//Nakajima, K. 	Purification of a new restriction endonuclease, StyI, from Escherichia coli carrying the hsd+ miniplasmid.	Gene	1985	33		357-361			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. 		
@D	Mise, K.//Nakajima, K. 	Isolation of restriction enzyme EcoVIII, an isoschizomer of HindIII, produced by Escherichia coli E1585-68.	Gene	1984	30		79-85			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. 		
@D	Mise, K.//Nakajima, K. 	Restriction endonuclease EcoO109 from Escherichia coli H709c with heptanucleotide recognition site 5'-PuG^GNCCPy.	Gene	1985	36		363-367			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. 		
@D	Mise, K.//Nakajima, K.//Terakado, N.//Ishidate, M. 	Production of restriction endonucleases using multicopy Hsd plasmids occurring naturally in pathogenic Escherichia coli and Shigella boydii.	Gene	1986	44		165-169			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. 		
@D	Mishra, A.//Jha, G.//Thakur, I.S. 	Draft Genome Sequence of Zhihengliuella sp. Strain ISTPL4, a Psychrotolerant and  Halotolerant Bacterium Isolated from Pangong Lake, India.	Genome Announcements	2018	6		e01533-17			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. 		
@D	Mishra, A.K.//Edouard, S.//Dangui, N.P.//Lagier, J.C.//Caputo, A.//Blanc-Tailleur, C.//Ravaux, I.//Raoult, D.//Fournier, P.E. 	Non-contiguous finished genome sequence and description of Nosocomiicoccus massiliensis sp. nov.	Standards in Genomic Sciences	2013	9		205-219			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. 		
@D	Mishra, A.K.//Gimenez, G.//Lagier, J.C.//Robert, C.//Raoult, D.//Fournier, P.E. 	Genome sequence and description of Alistipes senegalensis sp. nov.	Standards in Genomic Sciences	2012	6		1-16			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. 		
@D	Mishra, A.K.//Hugon, P.//Lagier, J.C.//Nguyen, T.T.//Couderc, C.//Raoult, D.//Fournier, P.E. 	Non contiguous-finished genome sequence and description of Enorma massiliensis gen. nov., sp. nov., a new member of the Family Coriobacteriaceae.	Standards in Genomic Sciences	2013	8		290-305			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. 		
@D	Mishra, A.K.//Hugon, P.//Lagier, J.C.//Nguyen, T.T.//Robert, C.//Couderc, C.//Raoult, D.//Fournier, P.E. 	Non contiguous-finished genome sequence and description of Peptoniphilus obesi sp. nov.	Standards in Genomic Sciences	2013	7		357-369			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. 		
@D	Mishra, A.K.//Hugon, P.//Robert, C.//Raoult, D.//Fournier, P.E. 	Non contiguous-finished genome sequence and description of Peptoniphilus grossensis sp. nov.	Standards in Genomic Sciences	2012	7		320-330			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. 		
@D	Mishra, A.K.//Lagier, J.C.//Nguyen, T.T.//Raoult, D.//Fournier, P.E. 	Non contiguous-finished genome sequence and description of Peptoniphilus senegalensis sp. nov.	Standards in Genomic Sciences	2013	7		370-381			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. 		
@D	Mishra, A.K.//Lagier, J.C.//Pfleiderer, A.//Nguyen, T.T.//Caputo, A.//Raoult, D.//Fournier, P.E. 	Non-contiguous finished genome sequence and description of Holdemania massiliensis sp. nov.	Standards in Genomic Sciences	2013	9		395-409			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. 		
@D	Mishra, A.K.//Lagier, J.C.//Rivet, R.//Raoult, D.//Fournier, P.E. 	Non-contiguous finished genome sequence and description of Paenibacillus senegalensis sp. nov.	Standards in Genomic Sciences	2012	7		70-81			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. 		
@D	Mishra, A.K.//Lagier, J.C.//Robert, C.//Raoult, D.//Fournier, P.E. 	Non contiguous-finished genome sequence and description of Peptoniphilus timonensis sp. nov.	Standards in Genomic Sciences	2012	7		1-11			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. 		
@D	Mishra, A.K.//Lagier, J.C.//Robert, C.//Raoult, D.//Fournier, P.E. 	Non-contiguous finished genome sequence and description of Clostridium senegalense sp. nov.	Standards in Genomic Sciences	2012	6		386-395			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. 		
@D	Mishra, A.K.//Lagier, J.C.//Robert, C.//Raoult, D.//Fournier, P.E. 	Genome sequence and description of Timonella senegalensis gen. nov., sp. nov., a  new member of the suborder Micrococcinae.	Standards in Genomic Sciences	2013	8		318-335			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. 		
@D	Mishra, A.K.//Pfleiderer, A.//Lagier, J.C.//Robert, C.//Raoult, D.//Fournier, P.E. 	Non-contiguous finished genome sequence and description of Bacillus massilioanorexius sp. nov.	Standards in Genomic Sciences	2013	8		465-479			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. 		
@D	Mishra, M.//Patole, S.//Mohapatra, H. 	Draft Genome Sequences of Nonclinical and Clinical Enterobacter cloacae Isolates  Exhibiting Multiple Antibiotic Resistance and Virulence Factors.	Genome Announcements	2017	5		e01218-17			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. 		
@A	Mishra, N.C. 		Restriction Endonucleases.			none 		Nucleases. Molecular Biology and Applications.				Hoboken, NJ	John Wiley & Sons, Inc.	2002				62-80									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. 		
@D	Mishra, S.R.//Panda, A.N.//Ray, L.//Sahu, N.//Mishra, G.//Jadhao, S.//Suar, M.//Adhya, T.K.//Rastogi, G.//Pattnaik, A.K.//Raina, V. 	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.	Genome Announcements	2016	4		e00342-16			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. 		
@D	Mishra, S.R.//Ray, L.//Panda, A.N.//Sahu, N.//Xess, S.S.//Jadhao, S.//Suar, M.//Adhya, T.K.//Rastogi, G.//Pattnaik, A.K.//Raina, V. 	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.	Genome Announcements	2016	4		e00395-16			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. 		
@D	Misic, A.M.//Cain, C.L.//Morris, D.O.//Rankin, S.C.//Beiting, D.P. 	Complete Genome Sequence and Methylome of Staphylococcus schleiferi, an Important Cause of Skin and Ear Infections in Veterinary Medicine.	Genome Announcements	2015	3		e01011-15			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. 		
@D	Misra, V.K.//Hecht, J.L.//Sharp, K.A.//Friedman, R.A.//Honig, B. 	Salt effects on protein-DNA interactions.  The lambdacI repressor and EcoRI endonuclease.	J. Mol. Biol.	1994	238		264-280			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. 		
@D	Mithoefer, S.//Rheaume, B.A.//MacLea, K.S. 	Draft Whole-Genome Sequence of the Marine Bacterium Idiomarina zobellii KMM 231T.	Genome Announcements	2015	3		e01257-15			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%. 		
@D	Mitra, A.//Higgins, D.W. 	The Chlorella virus adenine methyltransferase gene is a strong promoter in plants.	Plant Mol. Biol.	1994	26		85-93			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. 		
@D	Mitra, A.//Que, Q. 	Ectopic expression of a viral adenine methyltransferase gene in tobacco.	Biochim. Biophys. Acta	1994	1219		244-249			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. 		
@D	Mitrovic, J.//Siewert, C.//Duduk, B.//Hecht, J.//Moelling, K.//Broecker, F.//Beyerlein, P.//Buettner, C.//Bertaccini, A.//Kube, M. 	Generation and Analysis of Draft Sequences of 'Stolbur' Phytoplasma from Multiple Displacement Amplification Templates.	J. Mol. Microbiol. Biotechnol.	2014	24		1-11			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. 		
@D	Mittal, P.//Saxena, R.//Sharma, V.K. 	Draft Genome Sequence of Anoxybacillus mongoliensis Strain MB4, a Sulfur-Utilizing Aerobic Thermophile Isolated from a Hot Spring in Tattapani,  Central India.	Genome Announcements	2017	5		e01709-16			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. 		
@D	Miura, T.//Kusada, H.//Kamagata, Y.//Hanada, S.//Kimura, N. 	Genome Sequence of the Multiple-beta-Lactam-Antibiotic-Resistant Bacterium Acidovorax sp. Strain MR-S7.	Genome Announcements	2013	1		e00412-13			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. 		
@D	Miura, T.//Tsuchikane, K.//Numata, M.//Hashimoto, M.//Hosoyama, A.//Ohji, S.//Yamazoe, A.//Fujita, N. 	Complete Genome Sequence of an Alkane Degrader, Alcanivorax sp. Strain NBRC 101098.	Genome Announcements	2014	2		e00766-14			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. 		
@D	Miura, T.//Uchino, Y.//Tsuchikane, K.//Ohtsubo, Y.//Ohji, S.//Hosoyama, A.//Ito, M.//Takahata, Y.//Yamazoe, A.//Suzuki, K.//Fujita, N. 	Complete Genome Sequences of Sulfurospirillum Strains UCH001 and UCH003 Isolated  from Groundwater in Japan.	Genome Announcements	2015	3		e00236-15			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. 		
@D	Miyada, C.G.//Born, T.L. 	A DNA sequence for the discrimination of Neisseria gonorrhoeae from other Neisseria species.	Mol. Cell. Probes	1991	5		327-335			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. 		
@D	Miyagi, T.//Javorsky, P.//Pristas, P.//Karita, S.//Sakka, K.//Ohmiya, K. 	Partial purification and characterization of RalF40I, a class II restriction endonuclease from Ruminococcus albus F-40, which recognizes and cleaves 5'-/GATC-3'.	FEMS Microbiol. Lett.	1998	164		215-218			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. 		
@D	Miyahara, M.//Fujiwara, R.//Mise, K.//Shimada, T.//Matsushita, S.//Kudoh, Y.//Ishiwata, N.//Tanimura, A. 	Characterization of restriction endonucleases from Vibrio parahaemolyticus.	J. Food. Hyg. Sci. Japan	1994	35		605-609			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. 		
@D	Miyahara, M.//Ishiwata, N.//Yoshida, Y. 	StyD4I restriction-modification system of Salmonella typhi D4: Cloning and sequence analysis.	Biol. Pharm. Bull.	1997	20		201-203			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. 		
@D	Miyahara, M.//Kimizuka, F.//Kita, A.//Matsushita, S.//Kudo, Y.//Shimada, T.//Mise, K. 	Isolation and characterization of restriction endonuclease in Plesiomonas shigelloides and Aeromonas species.	Biol. Pharm. Bull.	1996	19		1506-1507			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. 		
@D	Miyahara, M.//Kudoh, Y.//Mise, K. 	Widespread occurrence of specific restriction endonucleases in Salmonella infantis, Salmonella thompson, and Salmonella blockley isolated from humans in Japan.	Appl. Environ. Microbiol.	1990	56		2248-2250			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. 		
@D	Miyahara, M.//Maruyama, T.//Wake, A.//Mise, K. 	Widespread occurrence of the restriction endonuclease YenI, an isoschizomer of PstI, in Yersinia enterocolitica serotype 08.	Appl. Environ. Microbiol.	1988	54		577-580			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. 		
@D	Miyahara, M.//Mise, K. 	Rapid method for detection of restriction endonuclease-producing strains in enteropathogenic bacteria.	Anal. Chim. Acta	1988	213		273-277			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. 		
@D	Miyahara, M.//Mise, K. 	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.	Gene	1993	129		83-86			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. 		
@D	Miyahara, M.//Mise, K.//Kimizuka, F.//Matsumoto, H.//Terawaki, Y. 	Purification of restriction endonuclease EcoO128I produced by an enteropathogenic Escherichia coli O128Ly3.	Gene	1992	113		135-136			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. 		
@D	Miyahara, M.//Nakajima, K.//Kawanishi, T.//Mise, K. 	SshAI restriction endonuclease from Salmonella shikmonah.	FEMS Microbiol. Lett.	1990	66		245-248			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. 		
@D	Miyahara, M.//Nakajima, K.//Shimada, T.//Mise, K. 	Restriction endonuclease PshAI from Plesiomonas shigelloides with the novel recognition site 5'-GACNN/NNGTC.	Gene	1990	87		119-122			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. 		
@D	Miyahara, M.//Nakamura, A.//Mise, K. 	Characterization of two restriction endonucleases, SenPT14bI and SenPT16I, in standard phage-type strains of Salmonella enteritidis.	Biol. Pharm. Bull.	1997	20		1212-1214			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. 		
@D	Miyahara, M.//Shimada, T.//Kotani, H.//Mise, K. 	Isolation and characterization of new restriction endonucleases from Vibrio parahaemolyticus: VpaK32I enzyme with the class-IIS heptanucleotide specificity, GCTCTTCN1/N4.	Gene	1992	117		103-106			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'. 		
@D	Miyahara, M.//Shimada, T.//Mise, K. 	Characterization of restriction endonucleases from Vibrio cholerae non 01.	J. Food. Hyg. Sci. Japan	1994	35		599-604			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. 		
@D	Miyahara, M.//Shinohara, N.//Mise, K. 	Purification of EcoO44I restriction endonuclease in Escherichia coli O44 isolated from an affected human.	Eisei Shikenjo Hokoku	1996	114		13-15			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. 		
@D	Miyake, M.//Kotani, H.//Asada, Y. 	Isolation and identification of restriction endonuclease, SelI from a cyanobacterium, Synechococcus elongatus.	Nucleic Acids Res.	1992	20		2605			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'. 		
@D	Miyake, T.//Hiraishi, H.//Sammoto, H.//Ono, B.-I. 	Involvement of the VDE homing endonuclease and rapamycin in regulation of the Saccharomyces cerevisiae GSH11 gene encoding the high affinity  glutathione transporter.	J. Biol. Chem.	2003	278		39632-39636			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. 		
@D	Miyamoto, H.//Nakai, W.//Yajima, N.//Fujibayashi, A.//Higuchi, T.//Sato, K.//Matsushiro, A. 	Sequence analysis of Stx2-converting phage VT2-Sa shows a great divergence in early regulation and replication regions.	DNA Res.	1999	6		235-240			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. 		
@D	Miyamoto, K.//Chakrabarti, G.//Morino, Y.//McClane, B.A. 	Organization of the plasmid cpe locus in Clostridium perfringens type A isolates.	Infect. Immun.	2002	70		4261-4272			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. 		
@D	Miyamoto, K.//Fisher, D.J.//Li, J.//Sayeed, S.//Akimoto, S.//McClane, B.A. 	Complete Sequencing and Diversity Analysis of the Enterotoxin-Encoding Plasmids in Clostridium perfringens Type A Non-Food-Borne Human Gastrointestinal Disease Isolates.	J. Bacteriol.	2006	188		1585-1598			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. 		
@D	Miyamoto, K.//Yumine, N.//Mimura, K.//Nagahama, M.//Li, J.//McClane, B.A.//Akimoto, S. 	Identification of Novel Clostridium perfringens Type E Strains That Carry an Iota Toxin Plasmid with a Functional Enterotoxin Gene.	PLoS ONE	2011	6		E20376			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. 		
@D	Miyamoto, S.//Mizutani, R.//Satow, Y.//Kawasaki, M.//Ohya, Y.//Anraku, Y. 	Recognition and cleavage of double-stranded DNA by yeast VMA1-derived endonuclease.	Nucleic Acids Symp. Ser.	1999	42		197-198			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. 		
@D	Miyauchi, T.//Kouzuma, A.//Abe, T.//Watanabe, K. 	Complete Genome Sequence of Acidithiobacillus ferridurans JCM 18981.	Microbiol. Resour. Announc.	2018	7		e01028-18			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. 		
@D	Miyazaki, R.//Sato, Y.//Ito, M.//Ohtsubo, Y.//Nagata, Y.//Tsuda, M. 	Complete nucleotide sequence of an exogenously isolated plasmid, pLB1, involved in .gamma.-hexachlorocyclohexane degradation.	Appl. Environ. Microbiol.	2006	72		6923-6933			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. 		
@D	Miyazono, K.//Furuta, Y.//Watanabe-Matsui, M.//Miyakawa, T.//Ito, T.//Kobayashi, I.//Tanokura, M. 	A sequence-specific DNA glycosylase mediates restriction-modification in Pyrococcus abyssi.	Nat. Commun.	2014	5		3178			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. 		
@D	Miyazono, K.//Watanabe, M.//Kosinski, J.//Ishikawa, K.//Kamo, M.//Sawasaki, T.//Nagata, K.//Bujnicki, J.M.//Endo, Y.//Tanokura, M.//Kobayashi, I. 	Novel protein fold discovered in the PabI family of restriction enzymes.	Nucleic Acids Res.	2007	35		1908-1918			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. 		
@D	Miyoshi-Akiyama, T.//Kuwahara, T.//Tada, T.//Kitao, T.//Kirikae, T. 	Complete Genome Sequence of Highly Multidrug-Resistant Pseudomonas aeruginosa NCGM2.S1, a Representative Strain of a Cluster Endemic to  Japan.	J. Bacteriol.	2011	193		7010			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). 		
@D	Miyoshi-Akiyama, T.//Matsumura, K.//Iwai, H.//Funatogawa, K.//Kirikae, T. 	Complete Annotated Genome Sequence of Mycobacterium tuberculosis Erdman.	J. Bacteriol.	2012	194		2770			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. 		
@D	Miyoshi-Akiyama, T.//Matsumura, K.//Kobayashi, N.//Maeda, S.//Kirikae, T. 	Genome Sequence of Clinical Isolate Mycobacterium tuberculosis NCGM2209.	J. Bacteriol.	2011	193		6792			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. 		
@D	Miyoshi-Akiyama, T.//Satou, K.//Kato, M.//Shiroma, A.//Matsumura, K.//Tamotsu, H.//Iwai, H.//Teruya, K.//Funatogawa, K.//Hirano, T.//Kirikae, T. 	Complete annotated genome sequence of Mycobacterium tuberculosis (Zopf) Lehmann and Neumann (ATCC35812) (Kurono).	Tuberculosis	2014	95		37-39			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. 		
@D	Miyoshi-Akiyama, T.//Takeshita, N.//Ohmagari, N.//Kirikae, T. 	Complete Genome Sequence of Helicobacter cinaedi Type Strain ATCC BAA-847.	J. Bacteriol.	2012	194		5692			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. 		
@D	Miyoshi-Akiyama, T.//Watanabe, S.//Kirikae, T. 	Complete Genome Sequence of Streptococcus pyogenes M1 476, Isolated from a Patient with Streptococcal Toxic Shock Syndrome.	J. Bacteriol.	2012	194		5466			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. 		
@D	Mizumura, H.//Shibata, T.//Morishima, N. 	Association of HSP70 with endonucleases allows the expression of otherwise silent mutations.	FEBS Lett.	2002	522		177-182			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. 		
@D	Mizumura, H.//Shibata, T.//Morishima, N. 	Stable association of 70-kDa heat shock protein induces latent multisite specificity of a unisite-specific endonuclease in yeast mitochondria.	J. Biol. Chem.	1999	274		25682-25690			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. 		
@D	Mizuno, C.M.//Rodriguez-Valera, F.//Garcia-Heredia, I.//Martin-Cuadrado, A.B.//Ghai, R. 	Reconstruction of Novel Cyanobacterial Siphovirus Genomes from Mediterranean Metagenomic Fosmids.	Appl. Environ. Microbiol.	2013	79		688-695			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. 		
@D	Mizuno, C.M.//Rodriguez-Valera, F.//Kimes, N.E.//Ghai, R. 	Expanding the marine virosphere using metagenomics.	PLoS Genet.	2013	9		e1003987			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. 		
@D	Mizuno, H.//Suzuki, T.//Akagawa, M.//Yamasato, K.//Yamada, Y. 	Purification, properties and determination of recognition sequence and cleavage site of restriction endonuclease from Agrobacterium gelatinovorum IAM 12617, a marine bacterium (AgeI).	Agric. Biol. Chem.	1990	54		1797-1802			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. 		
@D	Mizuno, H.//Suzuki, T.//Yamada, Y.//Akagawa, M.//Yamasato, K. 	Purification and properties of restriction endonuclease from Deleya marina IAM 14114, a marine bacterium (DmaI).	Agric. Biol. Chem.	1990	54		2863-2867			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). 		
@D	Mizutani, R.//Anraku, Y.//Satow, Y. 	Protein splicing of yeast VMA1-derived endonuclease via thiazolidine intermediates.	J. Synchrotron Radiat.	2004	11		109-112			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. 		
@D	Mizutani, R.//Nogami, S.//Kawasaki, M.//Ohya, Y.//Anraku, Y.//Satow, Y. 	Protein-splicing reaction via a thiazolidine intermediate: Crystal structure of the VMA1-derived endonuclease bearing the N and C-terminal  propeptides.	J. Mol. Biol.	2002	316		919-929			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. 		
@D	Mizutani, Y.//Tanaka, R. 	Genome Sequence of Arcobacter sp. Strain LA11, Isolated from the Abalone Haliotis discus.	Genome Announcements	2017	5		e00032-17			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. 		
@D	Mizuuchi, K.//Nobbs, T.J.//Halford, S.E.//Adzuma, K.//Qin, J. 	A new method for determining the Stereochemistry of DNA cleavage reactions: Application to the SfiI and HpaII restriction endonucleases and to the MuA transposase.	Biochemistry	1999	38		4640-4648			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. 		
@D	Mo, D.//Wu, L.//Xu, Y.//Ren, J.//Wang, L.//Huang, L.//Wu, Q.-J.//Bao, P.//Xie, M.-H.//Yin, P.//Liu, B.-F.//Liang, Y.//Zhang, Y. 	A maturase that specifically stabilizes and activates its cognate group  I intron at high temperatures.	Biochimie	2011	93		533-541			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. 		
@D	Mo, S.//Kim, B.S.//Yun, S.J.//Lee, J.J.//Yoon, S.H.//Oh, C.H. 	Genome sequencing of Clostridium butyricum DKU-01, isolated from infant feces.	Gut Pathog.	2015	7		8			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. 		
@D	Mo, X.//Pei, J.//Guo, Y.//Lin, L.//Peng, L.//Kou, C.//Fan, D.//Pang, H. 	Genome Sequence of Clostridium acetobutylicum GXAS18-1, a Novel Biobutanol Production Strain.	Genome Announcements	2015	3		e00033-15			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. 		
@D	Mobberley, J.M.//Authement, R.N.//Segall, A.M.//Paul, J.H. 	The temperate marine phage PhiHAP-1 of Halomonas aquamarina possesses a linear plasmid-like prophage genome.	J. Virol.	2008	82		6618-6630			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. 		
@D	Mobberley, J.M.//Romine, M.F.//Cole, J.K.//Maezato, Y.//Lindemann, S.R.//Nelson, W.C. 	Draft Genome Sequence of Cyanobacterium sp. Strain HL-69, Isolated from a Benthic Microbial Mat from a Magnesium Sulfate-Dominated Hypersaline Lake.	Genome Announcements	2018	6		e01583-17			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. 		
@D	Mobius, P.//Holzer, M.//Felder, M.//Nordsiek, G.//Groth, M.//Kohler, H.//Reichwald, K.//Platzer, M.//Marz, M. 	Comprehensive insights in the Mycobacterium avium subsp. paratuberculosis genome using new WGS data of sheep strain JIII-386 from Germany.	Genome Biol. Evol.	2015	7		2585-2601			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. 		
@D	Mobius, P.//Nordsiek, G.//Holzer, M.//Jarek, M.//Marz, M.//Kohler, H. 	Complete Genome Sequence of JII-1961, a Bovine Mycobacterium avium subsp. paratuberculosis Field Isolate from Germany.	Genome Announcements	2017	5		e00870-17			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. 		
@D	Mochizuki, A.//Yahara, K.//Kobayashi, I.//Iwasa, Y. 	Genetic addiction: selfish gene's strategy for symbiosis in the genome.	Genetics	2006	172		1309-1323			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. 		
@D	Modise, T.//Ryder, C.//Mane, S.P.//Bandara, A.B.//Jensen, R.V.//Inzana, T.J. 	Genomic Comparison between a Virulent Type A1 Strain of Francisella tularensis and Its Attenuated O-Antigen Mutant.	J. Bacteriol.	2012	194		2775-2776			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. 		
@D	Modrich, P. 	Studies on sequence recognition by type II restriction and modification enzymes.	CRC Crit. Rev. Biochem.	1982	13		287-323			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. 		
@D	Modrich, P. 	Structures and mechanisms of DNA restriction and modification enzymes.	Q. Rev. Biophys.	1979	12		315-369			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. 		
@A	Modrich, P.//Roberts, R.J. 		Type-II restriction and modification enzymes.			Linn, S.M.//Roberts, R.J. 		Nucleases				Cold Spring Harbor, New York	Cold Spring Harbor Laboratory Press	1982		0		109-154									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. 		
@D	Modrich, P.//Rubin, R.A. 	Role of the 2-amino group of deoxyguanosine in sequence recognition by EcoRI restriction and modifcation enzymes.	J. Biol. Chem.	1977	252		7273-7278			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. 		
@D	Modrich, P.//Zabel, D. 	EcoRI endonuclease.  Physical and catalytic properties of the homogeneous enzyme.	J. Biol. Chem.	1976	251		5866-5874			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. 		
@D	Moencke-Buchner, E.//Mackeldanz, P.//Krueger, D.H.//Reuter, M. 	Overexpression and affinity chromatography purification of the Type III restriction endonuclease EcoP15I for use in transcriptome analysis.	J. Biotechnol.	2004	114		99-106			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. 		
@D	Moffatt, B.A.//Studier, F.W. 	Entry of bacteriophage T7 DNA into the cell and escape from host restriction.	J. Bacteriol.	1988	170		2095-2105			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. 		
@D	Moghadam, M.S.//Albersmeier, A.//Winkler, A.//Cimmino, L.//Rise, K.//Hohmann-Marriott, M.F.//Kalinowski, J.//Ruckert, C.//Wentzel, A.//Lale, R. 	Isolation and genome sequencing of four Arctic marine Psychrobacter strains exhibiting multicopper oxidase activity.	BMC Genomics	2016	17		117			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. 		
@D	Moghaddam, J.A.//Poehlein, A.//Fisch, K.//Alanjary, M.//Daniel, R.//Konig, G.M.//Schaberle, T.F. 	Draft Genome Sequences of the Obligatory Marine Myxobacterial Strains Enhygromyxa salina SWB005 and SWB007.	Genome Announcements	2018	6		e00324-18			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). 		
@D	Mogila, V.A.//Bellaiche, Y.//Perrimon, N. 	Expression of I-SceI in Drosophila to induce DNA double-strand breaks.	Methods Mol. Biol.	1999	113		439-445			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. 		
@D	Moh, T.H.//Lau, N.S.//Furusawa, G.//Amirul, A.A. 	Complete genome sequence of Microbulbifer sp. CCB-MM1, a halophile isolated from  Matang Mangrove Forest, Malaysia.	Standards in Genomic Sciences	2017	12		36			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. 		
@D	Mohamad, N.I.//Tan, W.S.//Chang, C.Y.//Keng, T.K.//Yin, W.F.//Chan, K.G. 	Analysis of Quorum-Sensing Pantoea stewartii Strain M073A through Whole-Genome Sequencing.	Genome Announcements	2015	3		e00022-15			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. 		
@D	Mohamad, N.I.//Yin, W.F.//Chan, K.G. 	Whole-Genome Sequence of Quorum-Sensing Vibrio tubiashii Strain T33.	Genome Announcements	2015	3		e01362-14			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. 		
@D	Mohamed, S.B.//Ali, M.S.//Alamir, F.M.//Alyas, T.B.//Ahmed, A.E.//Seed, A.O.//Omer, R.A. 	First Complete Genome Sequence of Methicillin-Resistant Staphylococcus aureus Strain SO-1977 Isolated from Khartoum, Sudan.	Genome Announcements	2017	5		e00945-17			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. 		
@D	Mohamed-Nor, N.H.//Tan, B.F.//Te, S.H.//Thompson, J.R.//Gin, K.Y. 	Draft Genome Sequence of Cylindrospermopsis sp. Strain CR12 Extracted from the Minimetagenome of a Nonaxenic Unialgal Culture from a Tropical Freshwater Lake.	Genome Announcements	2016	4		e01726-15			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. 		
@D	Mohan, A.//Bhosle, A.//Chandra, N. 	Complete Genome Sequences of an Escherichia coli Laboratory Strain and Trimethoprim-Resistant (TMP32XR) Mutant Strains.	Genome Announcements	2015	3		e01434-15			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. 		
@D	Mohan, A.//Padiadpu, J.//Baloni, P.//Chandra, N. 	Complete Genome Sequences of a Mycobacterium smegmatis Laboratory Strain (MC2 155) and Isoniazid-Resistant (4XR1/R2) Mutant Strains.	Genome Announcements	2015	3		e01520-14			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. 		
@D	Mohan, K.N.//Chaillet, J.R. 	Cell and Molecular Biology of DNA Methyltransferase 1.	Int. Rev. Cell Mol. Biol.	2013	306		1-42			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. 		
@D	Mohn, W.W.//Teather, R.M. 	Partial purification and characterisation of Bfi57I and Bfi89I, restriction endonucleases from different strains of Butyrivibrio fibrisolvens.	Gene	1995	155		131-132			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. 		
@D	Mohr, G.//Smith, D.//Belfort, M.//Lambowitz, A.M. 	Rules for DNA target-site recognition by a lactococcal group II intron enable retargeting of the intron to specific DNA sequences.	Genes Dev.	2000	14		559-573			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. 		
@D	Moine, D.//Kassam, M.//Baert, L.//Tang, Y.//Barretto, C.//Ngom, B.C.//Klijn, A.//Descombes, P. 	Fully Closed Genome Sequences of Five Type Strains of the Genus Cronobacter and One Cronobacter sakazakii Strain.	Genome Announcements	2016	4		e00142-16			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. 		
@D	Moineau, S.//D'Amelio, G.E.//Pandian, S.//Klaenhammer, T.R. 	The susceptibility of evolving dairy bacteriophages to restriction enzymes and lactococcal R/M system.	J. Dairy Sci.	1992	75		114			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. 		
@D	Moineau, S.//Pandian, S.//Klaenhammer, T.R. 	Restriction/modification systems and restriction endonucleases are more effective on lactococcal bacteriophages that have emerged recently in the dairy industry.	Appl. Environ. Microbiol.	1993	59		197-202			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. 		
@D	Moineau, S.//Walker, S.A.//Holler, B.J.//Vedamuthu, E.R.//Vandenbergh, P.A. 	Expression of a Lactococcus lactis phage resistance mechanism by Streptococcus thermophilus.	Appl. Environ. Microbiol.	1995	61		2461-2466			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. 		
@D	Moineau, S.//Walker, S.A.//Vedamuthu, E.R.//Vandenbergh, P.A. 	Cloning and sequencing of LlaII restriction/modification genes from Lactococcus lactis and relatedness of this system to the Streptococcus pneumoniae DpnII system.	Appl. Environ. Microbiol.	1995	61		2193-2202			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. 		
@D	Moissidou, A.//Rina, M.//Bouriotis, V. 	Isolation and identification of restriction BshKI.	Nucleic Acids Res.	1989	17		8884			None 		
@D	Mok, Y.K.//Clark, D.R.//Kam, K.M.//Shaw, P.C. 	Restriction endonuclease from thermophilic bacterial species I.  Isolation and characterization of BsiEI.	Nucleic Acids Res.	1990	18		4954					
@D	Mok, Y.K.//Clark, D.R.//Kam, K.M.//Shaw, P.C. 	Restriction endonuclease from thermophilic bacterial species II. Isolation and characterization of BsiBl.	Nucleic Acids Res.	1990	18		6740			None 		
@D	Mok, Y.K.//Clark, D.R.//Kam, K.M.//Shaw, P.C. 	BsiYI, a novel thermophilic restriction endonuclease that recognizes 5' CCNNNNNNNGG3' and the discovery of a wrongly sequenced site in pACYC177 .	Nucleic Acids Res.	1991	19		2321-2323			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. 		
@D	Mokrishcheva, M.L.//Kertesz-Farkas, A.//Nikitin, D.V. 	New bifunctional restriction-modification enzyme AloI isoschizomer (PcoI): Bioinformatics analysis, purification and activity confirmation.	Gene	2018	660		8-12			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. 		
@D	Mokrishcheva, M.L.//Solonin, A.S.//Nikitin, D.V. 	Fused eco29kIR- and M genes coding for a fully functional hybrid polypeptide as a model of molecular evolution of restriction-modification systems.	BMC Evol. Biol.	2011	11		35			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. 		
@A	Mokrishcheva, M.L.//Solonin, A.S.//Nikitin, D.V. 		Role of gene fusion in evolution of restriction endonucleases.			 		Protein Purification and Analysis				Hong Kong	iConcept Press	2012				163-181									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. 		
@D	Mol, C.D.//Arvai, A.S.//Begley, T.J.//Cunningham, R.P.//Tainer, J.A. 	Structure and activity of a thermostable thymine-DNA glycosylase: Evidence for base twisting to remove mismatched normal DNA bases.	J. Mol. Biol.	2002	315		373-384			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. 		
@D	Molemans, F.//van Emmelo, J.//Fiers, W. 	The sequence specificity of endonucleases CauI and CauII isolated from Chloroflexus aurantiacus.	Gene	1982	18		93-96			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. 		
@D	Molenda, O.//Tang, S.//Edwards, E.A. 	Complete Genome Sequence of Dehalococcoides mccartyi Strain WBC-2, Capable of Anaerobic Reductive Dechlorination of Vinyl Chloride.	Genome Announcements	2016	4		e01375-16			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. 		
@D	Molholt, B.//Fraser, D. 	Host-controlled restriction of T-even bacteriophages:  relation of endonuclease I and T-even-induced nucleases to restriction.	J. Virol.	1968	2		313-319			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. 		
@D	Molina, L.//Bernal, P.//Udaondo, Z.//Segura, A.//Ramos, J.L. 	Complete Genome Sequence of a Pseudomonas putida Clinical Isolate, Strain H8234.	Genome Announcements	2013	1		e00496-13			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. 		
@D	Molina, R.//Marcaida, M.J.//Redondo, P.//Marenchino, M.//Duchateau, P.//D'Abramo, M.//Montoya, G.//Prieto, J. 	Engineering a Nickase on the Homing Endonuclease I-DmoI Scaffold.	J. Biol. Chem.	2015	290		18534-18544			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. 		
@D	Molina, R.//Redondo, P.//Stella, S.//Marenchino, M.//D'Abramo, M.//Gervasio, F.L.//Charles, E.J.//Valton, J.//Grizot, S.//Duchateau, P.//Prieto, J.//Montoya, G. 	Non-specific protein-DNA interactions control I-CreI target binding and cleavage.	Nucleic Acids Res.	2012	40		6936-6945			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. 		
@D	Molina, R.//Stella, S.//Redondo, P.//Gomez, H.//Marcaida, M.J.//Orozco, M.//Prieto, J.//Montoya, G. 	Visualizing phosphodiester-bond hydrolysis by an endonuclease.	Nat. Struct. Mol. Biol.	2015	22		65-72			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. 		
@D	Mollmann, S.//Albersmeier, A.//Ruckert, C.//Tauch, A. 	Complete Genome Sequence of Corynebacterium imitans DSM 44264, Isolated from a Five-Month-Old Boy with Suspected Pharyngeal Diphtheria.	Genome Announcements	2014	2		e01210-14			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. 		
@D	Molloy, P.L.//Symons, R.H. 	Cleavage of DNA.RNA hybrids by Type II restriction enzymes.	Nucleic Acids Res.	1980	8		2939-2946			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. 		
@D	Molloy, P.L.//Watt, F. 	Effect of cytosine methylation on cutting by the restriction enzyme MaeII.	Nucleic Acids Res.	1988	16		2335			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. 		
@D	Molnar, A.//Geck, P.//Orosz, A.//Kulcsar, P.//Nasz, I. 	Purification of a new restriction endonuclese from Streptococcus mutans and identification of its recognition sequence.	Acta Microbiol. Hung.	1991	38		55-60			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. 		
@D	Molnarova, V.//Javorsky, P.//Pristas, P. 	Occurrence of restriction and modification systems in ruminal Selenomonades.	Chemical Papers-Chemicke Zvesti	1998	52		284			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. 		
@D	Molnarova, V.//Pristas, P.//Javorsky, P. 	Prevalence of CTGCAG recognizing restriction and modification systems in ruminal selenomonades.	Anaerobe	1999	5		37-41			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. 		
@D	Molohon, K.J.//Blair, P.M.//Park, S.//Doroghazi, J.R.//Maxson, T.//Hershfield, J.R.//Flatt, K.M.//Schroeder, N.E.//Ha, T.//Mitchell, D.A. 	Plantazolicin is an ultra-narrow spectrum antibiotic that targets the membrane.	ACS Infect Dis	2016	2		207-220			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. 		
@D	Momparler, R.L.//Bovenzi, V. 	DNA methylation and cancer.	J. Cell. Physiol.	2000	183		145-154			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. 		
@D	Momynaliev, K.//Chelysheva, V.//Selezneva, O.//Akopian, T.//Alexeev, D.//Govorun, V. 	Complete Genome Sequences of Helicobacter pylori Rifampin-Resistant Strains.	Genome Announcements	2013	1		e00446-13			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. 		
@D	Momynaliev, K.T.//Rogov, S.I.//Govorun, V.M. 	Nucleotide correspondence between protein-coding sequences of Helicobacter pylori 26695 and J99 strains.	Mol. Biol. (Mosk)	2005	39		945-951			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. 		
@D	Momynaliev, K.T.//Smirnova, O.V.//Kudryavtseva, L.V.//Govorun, V.M. 	Comparative genome analysis of Helicobacter pylori strains.	Mol. Biol. (Mosk)	2003	37		529-536			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. 		
@D	Monastiriakos, S.K.//Doiron, K.M.//Siponen, M.I.//Cupples, C.G. 	Functional interactions between the MutL and Vsr proteins of Escherichia coli are dependent on the N-terminus of Vsr.	DNA Repair	2004	3		639-647			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. 		
@D	Monastyrskaya, G.S.//Fushan, A.A.//Abaev, I.V.//Filyukova, O.B.//Kostina, M.B.//Pecherskih, E.//Sverdlov, E.D. 	Genome-wide comparison reveals great inter- and intraspecies variability in B. pseudomallei and B. mallei pathogens.	Res. Microbiol.	2004	155		781-793			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. 		
@D	Moncke-Buchner, E.//Rothenberg, M.//Reich, S.//Wagenfuhr, K.//Matsumura, H.//Terauchi, R.//Kruger, D.H.//Reuter, M. 	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.	J. Mol. Biol.	2009	387		1309-1319			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. 		
@D	Mondo, S.J. et al. 	Widespread adenine N6-methylation of active genes in fungi.	Nat. Genet.	2017	49		964-968			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. 		
@D	Mondragon, E.//Maher, L.J. III 	RNA aptamer inhibitors of a restriction endonuclease.	Nucleic Acids Res.	2015	43		7544-7555			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. 		
@D	Mondy, S.//Lalouche, O.//Dessaux, Y.//Faure, D. 	Genome Sequence of the Quorum-Quenching Agrobacterium tumefaciens Strain WRT31.	Genome Announcements	2013	1		e00653-13			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. 		
@D	Mondy, S.//Lalouche, O.//Dessaux, Y.//Faure, D. 	Genome Sequence of the Quorum-Sensing-Signal-Producing Nonpathogen Agrobacterium  tumefaciens Strain P4.	Genome Announcements	2013	1		e00798-13			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. 		
@D	Mones, L.//Kulhanek, P.//Florian, J.//Simon, I.//Fuxreiter, M. 	Probing the two-metal ion mechanism in the restriction endonuclease BamHI.	Biochemistry	2007	46		14514-14523			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. 		
@D	Mones, L.//Simon, I.//Fuxreiter, M. 	Metal-binding sites at the active site of restriction endonuclease BamHI can conform to a one-ion mechanism.	Biol. Chem.	2007	388		73-78			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. 		
@D	Mongodin, E.F. et al. 	The genome of Salinibacter ruber: Convergence and gene exchange among hyperhalophilic bacteria and archaea.	Proc. Natl. Acad. Sci. U. S. A.	2005	102		18147-18152			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. 		
@D	Mongodin, E.F.//Hittle, L.L.//Nadendla, S.//Brinkman, C.C.//Xiong, Y.//Bromberg, J.S. 	Complete Genome Sequence of a Strain of Bifidobacterium pseudolongum Isolated from Mouse Feces and Associated with Improved Organ Transplant Outcome.	Genome Announcements	2017	5		e01089-17			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. 		
@D	Mongodin, E.F.//Shapir, N.//Daugherty, S.C.//DeBoy, R.T.//Emerson, J.B.//Shvartsbeyn, A.//Radune, D.//Vamathevan, J.//Riggs, F.//Grinberg, V.//Khouri, H.M.//Wackett, L.P.//Nelson, K.E.//Sadowsky, M.J. 	Secrets of Soil Survival Revealed by the Genome Sequence of Arthrobacter aurescens TC1.	PLoS Genet.	2006	2		e214			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. 		
@D	Moniruzzaman, M.//LeCleir, G.R.//Brown, C.M.//Gobler, C.J.//Bidle, K.D.//Wilson, W.H.//Wilhelm, S.W. 	Genome of brown tide virus (AaV), the little giant of the Megaviridae, elucidates NCLDV genome expansion and host-virus coevolution.	Virology	2014	466-467		60-70			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. 		
@D	Monk, I.R.//Foster, T.J. 	Genetic manipulation of Staphylococci-breaking through the barrier.	Front Cell Infect Microbiol	2012	2		49			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. 		
@D	Monk, I.R.//Shah, I.M.//Xu, M.//Tan, M.W.//Foster, T.J. 	Transforming the Untransformable: Application of Direct Transformation To Manipulate Genetically Staphylococcus aureus and Staphylococcus epidermidis.	MBio	2012	3		e00277			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. 		
@D	Monk, I.R.//Tree, J.J.//Howden, B.P.//Stinear, T.P.//Foster, T.J. 	Complete Bypass of Restriction Systems for Major Staphylococcus aureus Lineages.	MBio	2015	6		e00308-15			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. 		
@D	Monnat, R.J. Jr.//Hackmann, A.F.M.//Cantrell, M.A. 	Generation of highly site-specific DNA double-strand breaks in human cells by the homing endonucleases I-PpoI and I-CreI.	Biochem. Biophys. Res. Commun.	1999	255		88-93			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. 		
@D	Monnerat, M.-P.//Thiaucourt, F.//Nicolet, J.//Frey, J. 	Comparative analysis of the lppA locus in Mycoplasma capricolum subsp. capricolum and Mycoplasma capricolum subsp. capripneumoniae.	Vet. Microbiol.	1999	69		157-172			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. 		
@D	Monnerat, M.P.//Thiaucourt, F.//Poveda, J.B.//Nicolet, J.//Frey, J. 	Genetic and serological analysis of lipoprotein LppA in Mycoplasma mycoides subsp. mycoides LC and Mycoplasma mycoides subsp. capri.	Clin. Diagn. Lab. Immunol.	1999	6		224-230			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. 		
@D	Monnet, C.//Loux, V.//Bento, P.//Gibrat, J.F.//Straub, C.//Bonnarme, P.//Landaud, S.//Irlinger, F. 	Genome Sequence of Corynebacterium casei UCMA 3821, Isolated from a Smear-Ripened Cheese.	J. Bacteriol.	2012	194		738-739			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. 		
@D	Monno, S.//Sugiura, H.//Yamashita, H.//Kato, Y.//Morimitu, K.//Imajoh, M. 	Draft Genome Sequence of Vibrio harveyi Strain GAN1709, Isolated from Diseased Greater Amberjack (Seriola dumerili) Farmed in Japan.	Genome Announcements	2018	6		e00611-18			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%. 		
@D	Monsieurs, P.//Mijnendonckx, K.//Provoost, A.//Venkateswaran, K.//Ott, C.M.//Leys, N.//Van Houdt, R. 	Genome Sequences of Cupriavidus metallidurans Strains NA1, NA4, and NE12, Isolated from Space Equipment.	Genome Announcements	2014	2		e00719-14			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. 		
@D	Monsieurs, P.//Mijnendonckx, K.//Provoost, A.//Venkateswaran, K.//Ott, C.M.//Leys, N.//Van Houdt, R. 	Draft Genome Sequences of Ralstonia pickettii Strains SSH4 and CW2, Isolated from Space Equipment.	Genome Announcements	2014	2		e00887-14			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. 		
@D	Monsieurs, P.//Provoost, A.//Mijnendonckx, K.//Leys, N.//Gaudreau, C.//Van Houdt, R. 	Genome Sequence of Cupriavidus metallidurans Strain H1130, Isolated from an Invasive Human Infection.	Genome Announcements	2013	1		e01051-13			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. 		
@D	Monson, R.E.//Honger, J.//Rawlinson, A.//Salmond, G.P.C. 	Draft Genome Sequences of Enterobacter cloacae Strains CAPREx E7 and CAPREx E2-2.	Genome Announcements	2017	5		e00488-17			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. 		
@D	Monte, D.F.//Fernandes, M.R.//Cerdeira, L.//de Souza, T.A.//Mem, A.//Franco, B.D.G.M.//Landgraf, M.//Lincopan, N. 	Draft Genome Sequences of Colistin-Resistant MCR-1-Producing Escherichia coli ST1850 and ST74 Strains Isolated from Commercial Chicken Meat.	Genome Announcements	2017	5		e00329-17			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. 		
@D	Montecillo, A.D.//Raymundo, A.K.//Papa, I.A.//Aquino, G.M.B.//Rosana, A.R.R. 	Complete Genome Sequence of Rhizobium sp. Strain 11515TR, Isolated from Tomato Rhizosphere in the Philippines.	Microbiol. Resour. Announc.	2018	7		e00903-18			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. 		
@D	Monteilhet, C.//Dziadkowiec, D.//Szczepanek, T.//Lazowska, J. 	Purification and characterization of the DNA cleavage and recognition site of I-ScaI mitochondrial group I intron encoded endonuclease produced in Escherichia coli.	Nucleic Acids Res.	2000	28		1245-1251			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. 		
@D	Monteilhet, C.//Perrin, A.//Thierry, A.//Colleaux, L.//Dujon, B. 	Purification and characterization of the in vitro activity of I-Sce I, a novel and highly specific endonuclease encoded by a group I intron.	Nucleic Acids Res.	1990	18		1407-1413			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. 		
@D	Monteiro-Vitorello, C.B. et al. 	The genome sequence of the gram-positive sugarcane pathogen Leifsonia xyli subsp. xyli.	Mol. Plant Microbe Interact.	2004	17		827-836			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. 		
@D	Monteiro-Vitorello, C.B.//Zerillo, M.M.//Van Sluys, M.A.//Camargo, L.E.//Kitajima, J.P. 	Complete Genome Sequence of Leifsonia xyli subsp. cynodontis Strain DSM46306, a Gram-Positive Bacterial Pathogen of Grasses.	Genome Announcements	2013	1		e00915-13			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. 		
@D	Montenegro, M.A.//Pawlek, B.//Behrens, B.//Trautner, T.A. 	Restriction and modification in Bacillus subtilis:  expression of the cloned methyltransferase gene from B. subtilis phage SPR in E. coli and B. subtilis.	Mol. Gen. Genet.	1983	189		17-20			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. 		
@D	Montes, C.//Altimira, F.//Canchignia, H.//Castro, A.//Sanchez, E.//Miccono, M.//Tapia, E.//Sequeida, A.//Valdes, J.//Tapia, P.//Gonzalez, C.//Prieto, H. 	A draft genome sequence of Pseudomonas veronii R4: a grapevine (Vitis vinifera L.) root-associated strain with high biocontrol potential.	Standards in Genomic Sciences	2016	11		76			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. 		
@D	Montor-Antonio, J.J.//Sachman-Ruiz, B.//Lozano, L.//Del Moral, S. 	Draft Genome Sequence of Bacillus amyloliquefaciens JJC33M, Isolated from Sugarcane Soils in the Papaloapan Region, Mexico.	Genome Announcements	2015	3		e01519-14			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). 		
@D	Moodley, A.//Riley, M.C.//Kania, S.A.//Guardabassi, L. 	Genome Sequence of Staphylococcus pseudintermedius Strain E140, an ST71 European-Associated Methicillin-Resistant Isolate.	Genome Announcements	2013	1		e0020712			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. 		
@D	Moon, B.J.//Kim, S.K.//Kim, N.H.//Kwon, O.S. 	Synthesis and characterization of dodecanucleotides containing the XhoI recognition sequence with a phosphorothioate group at the cleavage site.	Bull. Korean Chem. Soc.	1996	17		1031-1036			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. 		
@D	Moon, B.J.//Vipond, I.B.//Halford, S.E. 	Site-directed mutagenesis studies with restriction endonuclease EcoRV to identify the role of Ile91 in recognition and catalysis.	J. Biochem. Mol. Biol.	1996	29		99-104			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. 		
@D	Moon, B.J.//Vipond, I.B.//Halford, S.E. 	Site-directed mutagenesis of Ile91 of restriction endonuclease EcoRV: Dramatic consequences on the activity and the properties of the enzyme.	J. Biochem. Mol. Biol.	1996	29		17-21			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. 		
@D	Moon, D.C.//Kim, B.Y.//Tamang, M.D.//Nam, H.M.//Jang, G.C.//Jung, S.C.//Lee, H.S.//Park, Y.H.//Lim, S.K. 	Genome Sequence of a Unique t2247-ST692-III Livestock-Associated Methicillin-Resistant Staphylococcus aureus Strain from Chicken Carcass.	Genome Announcements	2016	4		e00026-16			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. 		
@D	Moon, W.J.//Cho, J.-Y.//Chae, Y.K. 	Recombinant expression, purification, and characterization of XorKII: A restriction endonuclease from Xanthomonas oryzae pv. oryzae.	Protein Expr. Purif.	2008	62		230-234			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. 		
@D	Moore, A.M.//Patel, S.//Forsberg, K.J.//Wang, B.//Bentley, G.//Razia, Y.//Qin, X.//Tarr, P.I.//Dantas, G. 	Pediatric fecal microbiota harbor diverse and novel antibiotic resistance genes.	PLoS ONE	2013	8		E78822			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. 		
@D	Moore, G.P.//Moore, A.R. 	The average spacing of restriction enzyme recognition sites in DNA.	J. Theor. Biol.	1982	98		165-169			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. 		
@D	Moore, K.H.//Johnson, P.H.//Chandler, E.W.//Grossman, L.I. 	A restriction endonuclease cleavage map of mouse mitochondrial DNA.	Nucleic Acids Res.	1977	4		1273-1289			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. 		
@D	Moore, S.P.//McAleer, M.A.//Moss, S.H. 	Restriction enzyme cleavage of UV-irradiated DNA:  A comparison of far-UV and mid-UV wavelengths.	Photochem. Photobiol.	1987	45		253-263			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. 		
@D	Morad, I.//Chapman-Shimshoni, D.//Amitsur, M.//Kaufmann, G. 	Functional expression and properties of tRNALys-specific core anticodon nuclease encoded by Escherichia coli prrC.	J. Biol. Chem.	1993	268		26842-26849			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. 		
@D	Moraes, P.H.//Lima, A.R.//Siqueira, A.S.//Dall'Agnol, L.T.//Barauna, A.R.//Aguiar, D.C.//Fuzii, H.T.//Albuquerque, K.C.//de Lima, C.P.//Nunes, M.R.//Vianez-Junior, J.L.//Goncalves, E.C. 	Draft Genome Sequence of Flavihumibacter sp. Strain CACIAM 22H1, a Heterotrophic  Bacterium Associated with Cyanobacteria.	Genome Announcements	2016	4		e00400-16			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. 		
@D	Morais, L.L.//Garza, D.R.//Loureiro, E.C.//Nunes, K.N.//Vellasco, R.S.//da Silva, C.P.//Nunes, M.R.//Thompson, C.C.//Vicente, A.C.//Santos, E.C. 	Complete Genome Sequence of a Sucrose-Nonfermenting Epidemic Strain of Vibrio cholerae O1 from Brazil.	J. Bacteriol.	2012	194		2772			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. 		
@D	Morais-Silva, F.O.//Santos, C.I.//Rodrigues, R.//Pereira, I.A.//Rodrigues-Pousada, C. 	Role of HynAB and Ech, the only two hydrogenases found in the model sulfate reducer Desulfovibrio gigas.	J. Bacteriol.	2013	195		4753			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. 		
@D	Moran, J.C.//Horsburgh, M.J. 	Whole-Genome Sequence of Staphylococcus epidermidis Tu3298.	Genome Announcements	2016	4		e00112-16			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. 		
@D	Moran, J.V.//Mecklenburg, K.L.//Sass, P.//Belcher, S.M.//Mahnke, D.//Lewin, A.//Perlman, P. 	Splicing defective mutants of the COXI gene of yeast mitochondrial DNA: initial definition of the maturase domain of the group II intron AI2.	Nucleic Acids Res.	1994	22		2057-2064			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. 		
@D	Moran, J.V.//Wernette, C.M.//Mecklenburg, K.L.//Butow, R.A.//Perlman, P.S. 	Intron 5a of the COXI gene of yeast mitochondrial DNA is a mobile group I intron.	Nucleic Acids Res.	1992	20		4069-4076			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. 		
@D	Moran, J.V.//Zimmerly, S.//Eskes, R.//Kennell, J.C.//Lambowitz, A.M.//Butow, R.A.//Perlman, P.S. 	Mobile group II introns of yeast mitochrondrial DNA are novel site-specific retroelements.	Mol. Cell. Biol.	1995	15		2828-2838			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. 		
@D	Moran, M.A. et al. 	Genome sequence of Silicibacter pomeroyi reveals adaptations to the marine environment.	Nature	2004	432		910-913			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. 		
@D	Moran, N.A.//Degnan, P.H.//Santos, S.R.//Dunbar, H.E.//Ochman, H. 	The players in a mutualistic symbiosis: Insects, bacteria, viruses, and virulence genes.	Proc. Natl. Acad. Sci. U. S. A.	2005	102		16919-16926			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. 		
@D	Morcrette, H.//Morgan, M.S.//Farbos, A.//O'Neill, P.//Moore, K.//Titball, R.W.//Studholme, D.J. 	Genome Sequence of Staphylococcus aureus Ex1, Isolated from a Patient with Spinal Osteomyelitis.	Genome Announcements	2018	6		e00623-18			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. 		
@D	Mordasini, T.//Curioni, A.//Andreoni, W. 	Why do divalent metal ions either promote or inhibit enzymatic reactions? The case of BamHI restriction endonuclease from combined quantum-classical simulations.	J. Biol. Chem.	2003	278		4381-4384			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. 		
@D	Moreau, H.//Piganeau, G.//Desdevises, Y.//Cooke, R.//Derelle, E.//Grimsley, N. 	Marine prasinovirus genomes show low evolutionary divergence and acquisition of protein metabolism genes by horizontal gene transfer.	J. Virol.	2010	84		12555-12563			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. 		
@D	Moreau, M.R.//Wijetunge, D.S.//Kurundu, H.E.M.//Jayarao, B.M.//Kariyawasam, S. 	Genome Sequences of Two Strains of Salmonella enterica Serovar Enteritidis Isolated from Shell Eggs.	Genome Announcements	2015	3		e00954-15			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. 		
@D	Moreira, A.S.//Germaine, K.J.//Lloyd, A.//Lally, R.D.//Galbally, P.T.//Ryan, D.//Dowling, D.N. 	Draft Genome Sequence of Three Endophyte Strains of Pseudomonas fluorescens Isolated from Miscanthus giganteus.	Genome Announcements	2016	4		e00965-16			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. 		
@D	Moreira, R.F.//Noren, C.J. 	Minimum duplex requirements for restriction enzyme cleavage near the termini of linear DNA fragments.	Biotechniques	1995	19		56-59			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. 		
@D	Moreno, E.//Parks, M.//Pinnell, L.J.//Tallman, J.J.//Turner, J.W. 	Draft Genome Sequence of a Vibrio harveyi Strain Associated with Vibriosis in Pacific White Shrimp (Litopenaeus vannamei).	Genome Announcements	2017	5		e01662-16			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. 		
@D	Moreno, L.Z.//Knobl, T.//Grespan, A.A.//Felizardo, M.R.//Gomes, C.R.//Ferreira, T.S.//Xavier-de-Oliveira, M.G.//Myriantheus, L.//Moreno, A.M. 	Draft Genome Sequence of Bordetella avium Nh1210, an Outbreak Strain of Lockjaw Syndrome.	Genome Announcements	2015	3		e00120-15			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. 		
@D	Moreno, L.Z.//Loureiro, A.P.//Miraglia, F.//Matajira, C.E.//Kremer, F.S.//Eslabao, M.R.//Dellagostin, O.A.//Lilenbaum, W.//Moreno, A.M. 	Draft Genome Sequence of Brazilian Leptospira noguchii Serogroup Panama Strain U73, Isolated from Cattle.	Genome Announcements	2015	3		e01179-15			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. 		
@D	Moreno, L.Z.//Miraglia, F.//de Oliveira, C.H.//Vasconcellos, S.A.//Heinemann, M.B.//Moreno, A.M. 	Draft Genome Sequence of Brazilian Leptospira interrogans Serovar Pomona Strain GR5, Isolated from Apparently Healthy Gilt.	Genome Announcements	2018	6		e00491-18			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. 		
@D	Moreno-Avitia, F.//Lozano, L.//Utrilla, J.//Bolivar, F.//Escalante, A. 	Draft Genome Sequence of Pseudomonas chlororaphis ATCC 9446, a Nonpathogenic Bacterium with Bioremediation and Industrial Potential.	Genome Announcements	2017	5		e00474-17			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. 		
@D	Moreno-Switt, A.I.//Andrus, A.D.//Ranieri, M.L.//Orsi, R.H.//Ivy, R.//den Bakker, H.C.//Martin, N.H.//Wiedmann, M.//Boor, K.J. 	Genomic comparison of sporeforming bacilli isolated from milk.	BMC Genomics	2014	15		26			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. 		
@D	Moreno-Switt, A.I.//Orsi, R.H.//den Bakker, H.C.//Vongkamjan, K.//Altier, C.//Wiedmann, M. 	Genomic characterization provides new insight into Salmonella phage diversity.	BMC Genomics	2013	14		481			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. 		
@D	Moretti, C.//Cortese, C.//Passos-da-Silva, D.//Venturi, V.//Firrao, G.//Buonaurio, R. 	Draft Genome Sequence of Erwinia oleae, a Bacterium Associated with Olive Knots Caused by Pseudomonas savastanoi pv. savastanoi.	Genome Announcements	2014	2		e01308-14			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. 		
@D	Moretti, C.//Cortese, C.//Passos-da-Silva, D.//Venturi, V.//Ramos, C.//Firrao, G.//Buonaurio, R. 	Draft Genome Sequence of Pseudomonas savastanoi pv. savastanoi Strain DAPP-PG 722, Isolated in Italy from an Olive Plant Affected by Knot Disease.	Genome Announcements	2014	2		e00864-14			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. 		
@D	Moretti, C.//Cortese, C.//Passos-da-Silva, D.//Venturi, V.//Torelli, E.//Firrao, G.//Buonaurio, R. 	Draft Genome Sequence of a Hypersensitive Reaction-Inducing Pantoea agglomerans Strain Isolated from Olive Knots Caused by Pseudomonas savastanoi pv. savastanoi.	Genome Announcements	2014	2		e00774-14			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. 		
@D	Morgado, S.M.//Vicente, A.C. 	Beyond the Limits: tRNA Array Units in Mycobacterium Genomes.	Front. Microbiol.	2018	9		1042			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. 		
@D	Morgan, R.//Xiao, J.-P.//Xu, S.-Y. 	Characterization of an extremely thermostable restriction enzyme, PspGI, from a Pyrococcus strain and cloning of the PspGI restriction-modification system in Escherichia coli.	Appl. Environ. Microbiol.	1998	64		3669-3673			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. 		
@D	Morgan, R.D. 	MseI, a unique restriction endonuclease from Micrococcus species which recognizes 5'T^TAA 3'.	Nucleic Acids Res.	1988	16		3104			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. 		
@D	Morgan, R.D. 	Complete Genome Sequence and Methylome Analysis of Bacillus globigii ATCC 49760.	Genome Announcements	2016	4		e00427-16			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. 		
@D	Morgan, R.D. 	Rational engineering of DNA binding and cleavage specificity in a family of Type II restriction endonucleases.	Ph.D. Thesis, Boston University	2009			1-190			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. 		
@D	Morgan, R.D.//Bhatia, T.K.//Lovasco, L.//Davis, T.B. 	MmeI: a minimal Type II restriction-modification system that only modifies one DNA strand for host protection.	Nucleic Acids Res.	2008	36		6558-6570			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. 		
@D	Morgan, R.D.//Calvet, C.//Demeter, M.//Agra, R.//Kong, H.M. 	Characterization of the specific DNA nicking activity of restriction endonuclease N.BstNBI.	Biol. Chem.	2000	381		1123-1125			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. 		
@D	Morgan, R.D.//Camp, R.R.//Wilson, G.G.//Xu, S.-Y. 	Molecular cloning and expression of NlaIII restriction-modification system in E. coli.	Gene	1996	183		215-218			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. 		
@D	Morgan, R.D.//Dalton, M.//Stote, R. 	A unique type II restriction endonuclease from Acinetobacter lwoffi N.	Nucleic Acids Res.	1987	15		7201			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. 		
@D	Morgan, R.D.//Dwinell, E.A.//Bhatia, T.K.//Lang, E.M.//Luyten, Y.A. 	The MmeI family: type II restriction-modification enzymes that employ single-strand modification for host protection.	Nucleic Acids Res.	2009	37		5208-5221			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. 		
@D	Morgan, R.D.//Luyten, Y.A. 	Rational engineering of type II restriction endonuclease DNA binding and cleavage specificity.	Nucleic Acids Res.	2009	37		5222-5233			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. 		
@D	Morgan, R.D.//Luyten, Y.A.//Johnson, S.A.//Clough, E.M.//Clark, T.A.//Roberts, R.J. 	Novel m4C modification in type I restriction-modification systems.	Nucleic Acids Res.	2016	44		9413-9425			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. 		
@D	Morgan, W.F.//Fero, M.L.//Land, M.C.//Winegar, R.A. 	Inducible expression and cytogenic effects of the EcoRI restriction endonuclease in chinese hamster ovary cells.	Mol. Cell. Biol.	1988	8		4204-4211			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. 		
@D	Mori, K.//Kadooka, C.//Masuda, C.//Muto, A.//Okutsu, K.//Yoshizaki, Y.//Takamine, K.//Futagami, T.//Tamaki, H. 	Genome Sequence of Saccharomyces cerevisiae Strain Kagoshima No. 2, Used for Brewing the Japanese Distilled Spirit Shochu.	Genome Announcements	2017	5		e01126-17					
@D	Mori, K.//Yamazoe, A.//Hosoyama, A.//Ohji, S.//Fujita, N.//Ishibashi, J.//Kimura, H.//Suzuki, K. 	Thermotoga profunda sp. nov. and Thermotoga caldifontis sp. nov., anaerobic thermophilic bacteria isolated from terrestrial hot springs.	Int. J. Syst. Evol. Microbiol.	2014	64		2128-2136			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)). 		
@D	Mori, T.//Takahashi, M.//Tanaka, R.//Shibata, T.//Kuroda, K.//Ueda, M.//Takeyama, H. 	Draft Genome Sequence of Falsirhodobacter sp. Strain alg1, an Alginate-Degrading  Bacterium Isolated from Fermented Brown Algae.	Genome Announcements	2014	2		e00826-14			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. 		
@D	Moriel, B.//Cruz, L.M.//Dallagassa, C.B.//Faoro, H.//de Souza, E.M.//Pedrosa, F.O.//Rego, F.G.//Picheth, G.//Fadel-Picheth, C.M. 	Draft Genome Sequence of Aeromonas caviae 8LM, Isolated from Stool Culture of a Child with Diarrhea.	Genome Announcements	2015	3		e00524-15			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. 		
@D	Moriel, D.G. et al. 	Identification of protective and broadly conserved vaccine antigens from the genome of Extraintestinal Pathogenic Escherichia coli (ExPEC).	Proc. Natl. Acad. Sci. U. S. A.	2010	107		9072-9077			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. 		
@D	Morikawa, K.//Shirakawa, M. 	Three-dimensional structural views of damaged-DNA recognition: T4 endonuclease V, E. coli Vsr protein, and human nucleotide excision repair factor XPA.	Mutat. Res.	2000	460		257-275			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. 		
@D	Morishima, N.//Nakagawa, K.-I.//Shibata, T. 	A sequence-specific endonuclease, Endo.SceI, can efficiently induce gene conversion in yeast mitochondria lacking a major exonuclease.	Curr. Genet.	1993	23		537-541			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. 		
@D	Morishima, N.//Nakagawa, K.-I.//Yamamoto, E.//Shibata, T. 	A subunit of yeast site-specific endonuclease SceI is a mitochondrial version of the 70-kDa heat shock protein.	J. Biol. Chem.	1990	265		15189-15197			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. 		
@D	Morishima, N.//Shibata, T. 	SceI: an endonuclease with multiple cutting sites induces homologous genetic recombination.	Seikagaku	1992	64		1420-1431			A review. 		
@D	Morishima, N.//Shibata, T. 	Sequence-specific endonucleases involved in genetic recombination.	Tanpakushitsu Kakusan Koso	1991	36		1716-1720					
@D	Morita, H.//Toh, H.//Fukuda, S.//Horikawa, H.//Oshima, K.//Suzuki, T.//Murakami, M.//Hisamatsu, S.//Kato, Y.//Takizawa, T.//Fukuoka, H.//Yoshimura, T.//Itoh, K.//O'Sullivan, D.J.//McKay, L.L.//Ohno, H.//Kikuchi, J.//Masaoka, T.//Hattori, M. 	Comparative Genome Analysis of Lactobacillus reuteri and Lactobacillus fermentum Reveal a Genomic Island for Reuterin and Cobalamin Production.	DNA Res.	2008	15		151-161			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. 		
@D	Morita, H.//Toh, H.//Nakano, A.//Oshima, K.//Takagi, M.//Suda, W.//Tanabe, S.//Hattori, M. 	Complete Genome Sequence of Bifidobacterium kashiwanohense JCM 15439T, Isolated from Feces from a Healthy Japanese Infant.	Genome Announcements	2015	3		e00255-15			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. 		
@D	Morita, H.//Toh, H.//Oshima, K.//Murakami, M.//Taylor, T.D.//Igimi, S.//Hattori, M. 	Complete genome sequence of probiotic Lactobacillus rhamnosus ATCC 53103.	J. Bacteriol.	2009	191		7630-7631			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. 		
@D	Morita, H.//Toh, H.//Oshima, K.//Nakano, A.//Hano, C.//Yoshida, S.//Bolormaa, T.//Burenjargal, S.//Nguyen, C.T.//Tashiro, K.//Arakawa, K.//Miyamoto, T. 	Draft Genome Sequence of Leuconostoc mesenteroides 213M0, Isolated from Traditional Fermented Mare Milk Airag in Bulgan Aimag, Mongolia.	Genome Announcements	2016	4		e00178-16			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. 		
@D	Morita, H.//Toh, H.//Oshima, K.//Nakano, A.//Hano, C.//Yoshida, S.//Nguyen, T.T.//Wulijideligen, T.K.//Arakawa, K.//Miyamoto, T. 	Draft Genome Sequence of Leuconostoc mesenteroides 406 Isolated from the Traditional Fermented Mare Milk Airag in Tuv Aimag, Mongolia.	Genome Announcements	2016	4		e00166-16			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. 		
@D	Morita, H.//Toh, H.//Oshima, K.//Yoshizaki, M.//Kawanishi, M.//Nakaya, K.//Suzuki, T.//Miyauchi, E.//Ishii, Y.//Tanabe, S.//Murakami, M.//Hattori, M. 	Complete Genome Sequence and Comparative Analysis of the Fish Pathogen Lactococcus garvieae.	PLoS ONE	2011	6		E23184			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. 		
@D	Morita, R.//Ishikawa, H.//Nakagawa, N.//Kuramitsu, S.//Masui, R. 	Crystal structure of a putative DNA methylase TTHA0409 from Thermus thermophilus HB8.	Proteins	2008	73		259-264			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. 		
@D	Moriya, N. et al. 	Complete Genome Sequence of Lactobacillus plantarum Strain LQ80, Selected for Preparation of Fermented Liquid Feed for Pigs.	Genome Announcements	2018	6		e00530-18			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. 		
@D	Moriya, S.//Yanagawa, S.//Aoki, N.//Iwabuchi, M.//Inoue, T.//Ando, T. 	Isolation and characterization of a restriction enzyme BspO4I from an alkalophilic bacterium.	Nucleic Acids Res.	1992	20		3781			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'. 		
@D	Morohoshi, T.//Ikeda, T. 	Complete Genome Sequence of Methylobacterium populi P-1M, Isolated from Pink-Pigmented Household Biofilm.	Genome Announcements	2016	4		e00458-16			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. 		
@D	Morohoshi, T.//Kato, T.//Someya, N.//Ikeda, T. 	Complete Genome Sequence of N-Acylhomoserine Lactone-Producing Pseudomonas sp. Strain StFLB209, Isolated from Potato Phyllosphere.	Genome Announcements	2014	2		e01037-14			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. 		
@D	Morohoshi, T.//Wang, W.Z.//Someya, N.//Ikeda, T. 	Complete Genome Sequence of Chryseobacterium sp. Strain StRB126, an N-Acylhomoserine Lactone-Degrading Bacterium Isolated from Potato Root.	Genome Announcements	2014	2		e00952-14			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. 		
@D	Morohoshi, T.//Wang, W.Z.//Someya, N.//Ikeda, T. 	Genome Sequence of Microbacterium testaceum StLB037, an N-Acylhomoserine Lactone-Degrading Bacterium Isolated from Potato Leaves.	J. Bacteriol.	2011	193		2072-2073			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%. 		
@D	Morozova, N.//Sabantsev, A.//Bogdanova, E.//Fedorova, Y.//Maikova, A.//Vedyaykin, A.//Rodic, A.//Djordjevic, M.//Khodorkovskii, M.//Severinov, K. 	Temporal dynamics of methyltransferase and restriction endonuclease accumulation  in individual cells after introducing a restriction-modification system.	Nucleic Acids Res.	2015	44		790-800			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. 		
@D	Morris, D.W.//Parish, J.H. 	Restriction in Myxococcus virescens.	Arch. Microbiol.	1976	108		227-230			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. 		
@D	Morris, P.//Marinelli, L.J.//Jacobs-Sera, D.//Hendrix, R.W.//Hatfull, G.F. 	Genomic characterization of mycobacteriophage giles: evidence for phage acquisition of host DNA by illegitimate recombination.	J. Bacteriol.	2008	190		2172-2182			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. 		
@D	Morrison, C.K.//Novinscak, A.//Gadkar, V.J.//Joly, D.L.//Filion, M. 	Complete Genome Sequence of Pseudomonas fluorescens LBUM636, a Strain with Biocontrol Capabilities against Late Blight of Potato.	Genome Announcements	2016	4		e00446-16			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. 		
@D	Morrison, E.A.//Garner, S.//Echaubard, P.//Lesbarreres, D.//Kyle, C.J.//Brunetti, C.R. 	Complete genome analysis of a frog virus 3 (FV3) isolate and sequence comparison with isolates of differing levels of virulence.	Virol. J.	2014	11		46			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. 		
@D	Morrison, H.A.//Seligman, L.M. 	Homing endonuclease I-CreI mutants with substitutions at residues 30, 32 and 38 include altered specificity derivatives.	Abstr. Gen. Meet. Am. Soc. Microbiol.	2004	104		313			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. 		
@D	Morrison, M. 	Deoxyribonucleic acid restriction/modification systems and gene transfer strategies in Ruminococcus albus 8 and Ruminococcus flavofaciens FD-1.	Ph.D. Thesis, University of Illinois, USA	1991			1-134			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. 		
@D	Morrison, M.//Mackie, R.I.//White, B.A. 	The restriction endonuclease RflFII, isolated from Ruminococcus flavefaciens FD-1, recognizes the sequence 5'-AGTACT-3', and is inhibited by site-specific adenine methylation.	FEMS Microbiol. Lett.	1994	122		181-185			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. 		
@D	Morrison, M.//Mackie, R.I.//White, B.A. 	Partial characterization of a DNA restriction endonuclease from Ruminococcus flavefaciens FD-1 and its inhibition by site-specific adenine methylation.	Appl. Environ. Microbiol.	1992	58		66-69			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. 		
@D	Morrison, M.//Mackie, R.I.//White, B.A. 	Partial purification and characterization of Ral8I, a class-IIS restriction endonuclease from Ruminococcus albus 8 which recognizes 5'-GGATC .	Gene	1992	111		105-108			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. 		
@D	Morrison, M.//Mackie, R.I.//White, B.A. 	Restriction-modification systems in Ruminococcus and development of a gene transfer system.	Aust. Microbiol.	1992	0		301-303					
@D	Morrison, S.S.//Desai, H.P.//Mercante, J.W.//Lapierre, P.//Raphael, B.H.//Musser, K.//Winchell, J.M. 	Complete Genome Sequences of Three Outbreak-Associated Legionella pneumophila Isolates.	Genome Announcements	2016	4		e00696-16			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. 		
@D	Morrison, S.S.//Kozak-Muiznieks, N.A.//Sammons, S.//Rowe, L.A.//Frace, M.//Winchell, J.M. 	Draft Genome Sequence of Legionella pneumophila D-5864, a Serogroup 6 Strain.	Genome Announcements	2015	3		e01379-14			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. 		
@D	Morrow, J.F.//Berg, P. 	Cleavage of Simian Virus 40 DNA at a unique site by a bacterial restriction enzyme.	Proc. Natl. Acad. Sci. U. S. A.	1972	69		3365-3369			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. 		
@D	Mortusewicz, O.//Schermelleh, L.//Walter, J.//Cardoso, M.C.//Leonhardt, H. 	Recruitment of DNA methyltransferase I to DNA repair sites.	Proc. Natl. Acad. Sci. U. S. A.	2005	102		8905-8909			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. 		
@D	Moser, D.//Kallas, T. 	Characteristics of a restriction endonuclease from the Cyanobacterium Nostoc PCC 7121 and protection of DNA with Eco 47 II methylase.	Abstr. Gen. Meet. Am. Soc. Microbiol.	1991	91		155			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. 		
@D	Moser, D.P.//Zarka, D.//Kallas, T. 	Characterization of a restriction barrier and electrotransformation of the cyanobacterium Nostoc PCC-7121.	Arch. Microbiol.	1993	160		229-237			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. 		
@D	Moses, P.//Horiuchi, K. 	Specific Recombination in Vitro Promoted by the Restriction Endonuclease HgaI.	J. Mol. Biol.	1979	135		517-524			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. 		
@D	Mosier, A.C.//Allen, E.E.//Kim, M.//Ferriera, S.//Francis, C.A. 	Genome Sequence of 'Candidatus Nitrosopumilus salaria' BD31, an Ammonia-Oxidizing Archaeon from the San Francisco Bay Estuary.	J. Bacteriol.	2012	194		2121-2122			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. 		
@D	Mosier, A.C.//Allen, E.E.//Kim, M.//Ferriera, S.//Francis, C.A. 	Genome Sequence of 'Candidatus Nitrosoarchaeum limnia' BG20, a Low-Salinity Ammonia-Oxidizing Archaeon from the San Francisco Bay Estuary.	J. Bacteriol.	2012	194		2119-2120			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. 		
@D	Motamedchaboki, K. 	Characterization of a restriction endonuclease isolated from Bacillus subtilis F2.	Abstr. Gen. Meet. Am. Soc. Microbiol.	2001	101		457			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. 		
@D	Mothupi, B.//Featherston, J.//Gray, V. 	Draft Whole-Genome Sequence and Annotation of Xenorhabdus griffiniae Strain BMMCB Associated with the South African Entomopathogenic Nematode Steinernema khoisanae  Strain BMMCB.	Genome Announcements	2015	3		e00785-15			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. 		
@D	Motoshima, K.//Ishikawa, M.//Hashimoto, Y.//Sugita, K. 	Inhibition of Restriction Enzymes EcoRI, BamHI and HindIII by Phenethylphenylphthalimides Derived from Thalidomide.	Chem. Pharm. Bull. (Tokyo)	2011	59		880-884			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. 		
@D	Motta, E.V.S.//Kwong, W.K.//Moran, N.A. 	Glyphosate perturbs the gut microbiota of honey bees.	Proc. Natl. Acad. Sci. U. S. A.	2018	115		10305-10310			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. 		
@D	Mottawea, W.//Chen, S.//Saleh-Lakha, S.//Belanger, S.//Ogunremi, D. 	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.	Genome Announcements	2017	5		e00258-17			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. 		
@D	Mou, K.T.//Muppirala, U.K.//Severin, A.J.//Clark, T.A.//Boitano, M.//Plummer, P.J. 	A comparative analysis of methylome profiles of Campylobacter jejuni sheep abortion isolate and gastroenteric strains using PacBio data.	Front. Microbiol.	2014	5		782			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. 		
@D	Moulin, L. et al. 	Complete Genome sequence of Burkholderia phymatum STM815(T), a broad host range and efficient nitrogen-fixing symbiont of Mimosa species.	Standards in Genomic Sciences	2014	9		763-774			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). 		
@D	Moulin, L.//Mornico, D.//Melkonian, R.//Klonowska, A. 	Draft Genome Sequence of Rhizobium mesoamericanum STM3625, a Nitrogen-Fixing Symbiont of Mimosa pudica Isolated in French Guiana (South America).	Genome Announcements	2013	1		e00066-12			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. 		
@D	Moure, C.M.//Gimble, F.S.//Quiocho, F.A. 	Crystal structures of I-SceI complexed to nicked DNA substrates: snapshots of intermediates along the DNA cleavage reaction pathway.	Nucleic Acids Res.	2008	36		3287-3296			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. 		
@D	Moure, C.M.//Gimble, F.S.//Quiocho, F.A. 	The crystal structure of the gene targeting homing endonuclease I-SceI reveals the origins of its target site specificity.	J. Mol. Biol.	2003	334		685-695			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. 		
@D	Moure, C.M.//Gimble, F.S.//Quiocho, F.A. 	Crystal structure of the intein homing endonuclease PI-SceI bound to its recognition sequence.	Nat. Struct. Biol.	2002	9		764-770			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. 		
@D	Moure, C.M.//Quiocho, F.A. 	The structure and function of intein-associated homing endonucleases.	Nucleic Acids Mol. Biol.	2005	16		257-271			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. 		
@D	Moxon, E.R.//Rainey, P.B.//Nowak, M.A.//Lenski, R.E. 	Adaptive evolution of highly mutable loci in pathogenic bacteria.	Curr. Biol.	1994	4		24-33			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. 		
@D	Moya-Beltran, A.//Cardenas, J.P.//Covarrubias, P.C.//Issotta, F.//Ossandon, F.J.//Grail, B.M.//Holmes, D.S.//Quatrini, R.//Johnson, D.B. 	Draft Genome Sequence of the Nominated Type Strain of 'Ferrovum myxofaciens,' an  Acidophilic, Iron-Oxidizing Betaproteobacterium.	Genome Announcements	2014	2		e00834-14			'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. 		
@D	Mrazek, J.//Karlin, S. 	Detecting alien genes in bacterial genomes.	Ann. NY Acad. Sci.	1999	870		314-329			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. 		
@D	Mrazek, J.//Piknova, M.//Pristas, P.//Kopecny, J. 	Occurrence of restriction-modification systems in ruminal butyrate-producing bacteria.	Anaerobe	2005	11		280-284			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. 		
@D	Mruk, I.//Blumenthal, R.M. 	Real-time kinetics of restriction-modification gene expression after entry into a new host cell.	Nucleic Acids Res.	2008	36		2581-2593			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. 		
@D	Mruk, I.//Blumenthal, R.M. 	Tuning the relative affinities for activating and repressing operators of a temporally regulated restriction-modification system.	Nucleic Acids Res.	2009	37		983-998			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. 		
@D	Mruk, I.//Cichowicz, M.//Kaczorowski, T. 	Characterization of the LlaCl methyltransferase from Lactococcus lactis subsp cremoris W15 provides new insights into the biology of type II  restriction-modification systems.	Microbiology	2003	149		3331-3341			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. 		
@D	Mruk, I.//Kaczorowski, T. 	A rapid and efficient method for cloning genes of type II restriction-modification systems by use of a killer plasmid.	Appl. Environ. Microbiol.	2007	73		4286-4293			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. 		
@D	Mruk, I.//Kaczorowski, T. 	Genetic organization and molecular analysis of the EcoVIII restriction-modification system of Escherichia coli E1585-68 and its comparison with isospecific homologs.	Appl. Environ. Microbiol.	2003	69		2638-2650			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. 		
@D	Mruk, I.//Kobayashi, I. 	To be or not to be: regulation of restriction-modification systems and other toxin-antitoxin systems.	Nucleic Acids Res.	2013	42		70-86			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. 		
@D	Mruk, I.//Liu, Y.//Ge, L.//Kobayashi, I. 	Antisense RNA associated with biological regulation of a restriction-modification system.	Nucleic Acids Res.	2011	39		5622-5632			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. 		
@D	Mruk, I.//Rajesh, P.//Blumenthal, R.M. 	Regulatory circuit based on autogenous activation-repression: roles of C-boxes and spacer sequences in control of the PvuII  restriction-modification system.	Nucleic Acids Res.	2007	35		6935-6952			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. 		
@D	Mruk, I.//Sektas, M.//Kaczorowski, T. 	Characterization of pEC156, a ColE1-Type Plasmid from Escherichia coli E1585-68 That Carries Genes of the EcoVIII Restriction-Modification System.	Plasmid	2001	46		128-139			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. 		
@D	Mu, D.//Zhao, J.//Wang, Z.//Chen, G.//Du, Z. 	Draft Genome Sequence of Algoriphagus sp. Strain NH1, a Multidrug-Resistant Bacterium Isolated from Coastal Sediments of the Northern Yellow Sea in China.	Genome Announcements	2016	4		e01555-15			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. 		
@D	Muchaamba, F.//Guldimann, C.//Tasara, T.//Mota, M.I.//Braga, V.//Varela, G.//Algorta, G.//Klumpp, J.//Jermini, M.//Stephan, R. 	Full-Genome Sequence of Listeria monocytogenes Strain H34, Isolated from a Newborn with Sepsis in Uruguay.	Genome Announcements	2017	5		e00544-17			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. 		
@D	Muchova, J.//Lacova, B.//Godany, A.//Sevcikova, B. 	High transformable mutants of Streptomyces aureofaciens containing restriction-modification systems.	J. Basic Microbiol.	1991	31		141-147			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. 		
@D	Mucito-Varela, E.//Castillo-Rojas, G.//Cevallos, M.A.//Lozano, L.//Merino, E.//Lopez-Leal, G.//Lopez-Vidal, Y. 	Complete Genome Sequence of Helicobacter pylori Strain 29CaP Isolated from a Mexican Patient with Gastric Cancer.	Genome Announcements	2016	4		e01512-15			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. 		
@D	Mucito-Varela, E.//Castillo-Rojas, G.//Cevallos, M.A.//Lozano, L.//Merino, E.//Lopez-Leal, G.//Lopez-Vidal, Y. 	Complete Genome Sequence of Helicobacter pylori Strain 7C Isolated from a Mexican Patient with Chronic Gastritis.	Genome Announcements	2016	4		e01503-15			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. 		
@D	Mucke, M.//Grelle, G.//Behlke, J.//Kraft, R.//Kruger, D.H.//Reuter, M. 	EcoRII: a restriction enzyme evolving recombination functions?	EMBO J.	2002	21		5262-5268			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. 		
@D	Mucke, M.//Kruger, D.H.//Reuter, M. 	Diversity of Type II restriction endonucleases that require two DNA recognition sites.	Nucleic Acids Res.	2003	31		6079-6084			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. 		
@D	Mucke, M.//Lurz, R.//Mackeldanz, P.//Behlke, J.//Kruger, D.H.//Reuter, M. 	Imaging DNA loops induced by restriction endonuclease EcoRII. A single amino acid substitution uncouples target recognition from cooperative DNA interaction and cleavage.	J. Biol. Chem.	2000	275		30631-30637			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. 		
@D	Mucke, M.//Pingoud, V.//Grelle, G.//Kraft, R.//Kruger, D.H.//Reuter, M. 	Asymmetric photocross-linking pattern of restriction endonuclease EcoRII to the DNA recognition sequence.	J. Biol. Chem.	2002	277		14288-14293			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. 		
@D	Mucke, M.//Reich, S.//Moncke-Buchner, E.//Reuter, M.//Kruger, D.H. 	DNA cleavage by type II restriction-modification enzyme EcoP15I is independent of spacer distance between two head to head oriented recognition sites.	J. Mol. Biol.	2001	312		687-698			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. 		
@D	Muckerman, C.C.//Springhorn, S.S.//Greenberg, B.//Lacks, S.A. 	Transformation of restriction endonuclease phenotype in Streptococcus pneumoniae.	J. Bacteriol.	1982	152		183-190			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. 		
@A	Mueller, J.E.//Bryk, M.//Loizos, N.//Belfort, M. 		Homing endonucleases.			Linn, S.M.//Lloyd, R.S.//Roberts, R.J. 		Nucleases				Cold Spring Harbor	Cold Spring Harbor Laboratory Press	1993		0		111-143									*
 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
 
 		
@D	Mueller, J.E.//Clyman, J.//Huang, Y.-J.//Parker, M.M.//Belfort, M. 	Intron mobility in phage T4 occurs in the context of recombination-dependent DNA replication by way of multiple pathways.	Genes Dev.	1996	10		351-364			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. 		
@D	Mueller, J.E.//Smith, D.//Belfort, M. 	Exon coconversion biases accompanying intron homing: battle of the nucleases.	Genes Dev.	1996	10		2158-2166			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. 		
@D	Mueller, J.E.//Smith, D.//Bryk, M.//Belfort, M. 	Intron-encoded endonuclease I-TevI binds as a monomer to effect sequential cleavage via conformational changes in the td homing site.	EMBO J.	1995	14		5724-5735			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. 		
@D	Muge, G.R.//Veras, A.A.//de Sa, P.H.//Cavalcante, A.L.//Alves, J.T.//Morais, E.//Silva, A.G.//Guimaraes, L.C.//Azevedo, V.//Folador, A.R.//Silva, A.//Ramos, R.T. 	Genome Sequence of Corynebacterium pseudotuberculosis Strain PA02 Isolated from an Ovine Host in the Amazon.	Genome Announcements	2016	4		e00838-16			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. 		
@D	Muhd, S.M.K.//Abdul, R.A.Y.//Saito, J.A.//Hou, S.//Alam, M. 	Complete Genome Sequence of the Thermophilic Bacterium Geobacillus thermoleovorans CCB_US3_UF5.	J. Bacteriol.	2012	194		1239			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. 		
@D	Muir, R.S.//Flores, H.//Zinder, N.D.//Model, P.//Soberon, X.//Heitman, J. 	Temperature-sensitive mutants of the EcoRI endonuclease.	J. Mol. Biol.	1997	274		722-737			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. 		
@D	Mukherjee, A.//Chettri, B.//Langpoklakpam, J.S.//Singh, A.K.//Chattopadhyay, D. 	Draft Genome Sequence of Hydrocarbon-Degrading Staphylococcus saprophyticus Strain CNV2, Isolated from Crude Oil-Contaminated Soil from the Noonmati Oil  Refinery, Guwahati, Assam, India.	Genome Announcements	2016	4		e00370-16			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. 		
@D	Mukherjee, A.//Chettri, B.//Langpoklakpam, J.S.//Singh, A.K.//Chattopadhyay, D. 	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.	Genome Announcements	2016	4		e00367-16			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. 		
@D	Mukherjee, S. et al. 	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.	Standards in Genomic Sciences	2015	10		8			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. 		
@D	Mukherjee, S. et al. 	1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life.	Nat. Biotechnol.	2017	35		676-683			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. 		
@D	Mukherjee, T.//Bose, S.//Sen, U.//Roy, C.//Rameez, M.J.//Ghosh, W.//Mukhopadhyay, S.K. 	Genome Sequence of the Red Pigment-Forming Meiothermus taiwanensis Strain RP Isolated from Paniphala Hot Spring, India.	Genome Announcements	2016	4		e00629-16			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. 		
@D	Mukherjee, U.//Kumar, R.//Mahato, N.K.//Khurana, J.P.//Lal, R. 	Draft Genome Sequence of Sphingobium sp. Strain HDIPO4, an Avid Degrader of Hexachlorocyclohexane.	Genome Announcements	2013	1		e00749-13			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%. 		
@D	Mukherjee, U.//Saxena, A.//Kumari, R.//Singh, P.//Lal, R. 	Draft Genome Sequence of Amycolatopsis mediterranei DSM 40773, a Tangible Antibiotic Producer.	Genome Announcements	2014	2		e00752-14			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%. 		
@D	Mukhopadhyay, A.K.//Kersulyte, D.//Jeong, J.Y.//Datta, S.//Ito, Y.//Chowdhury, A.//Chowdhury, S.//Santra, A.//Bhattacharya, S.K.//Azuma, T.//Nair, G.B.//Berg, D.E. 	Distinctiveness of genotypes of Helicobacter pylori in Calcutta India.	J. Bacteriol.	2000	182		3219-3227			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. 		
@D	Mukhopadhyay, C.//Vandana, K.E.//Chaitanya, T.A.//Shaw, T.//Bhat, H.V.//Chakrabarty, S.//Paul, B.//Mallya, S.//Murali, T.S.//Satyamoorthy, K. 	Genome Sequence of a Burkholderia pseudomallei Clinical Isolate from a Patient with Community-Acquired Pneumonia and Septicemia.	Genome Announcements	2015	3		e00915-15			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. 		
@D	Mukhopadhyay, P.//Roy, K.B. 	Protein engineering of BamHI restriction endonuclease: replacement of Cys54 by Ala enhances catalytic activity.	Protein Eng.	1998	11		931-935			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. 		
@D	Mukhopadhyay, R.//Joaquin, J.//Hogue, R.//Fitzgerald, S.//Jospin, G.//Mars, K.//Eisen, J.A.//Chaturvedi, V. 	Complete Genome Sequence of Dolosigranulum pigrum from a Patient with Interstitial Lung Disease Using Single-Molecule Real-Time Sequencing Technology.	Genome Announcements	2017	5		e00317-17			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. 		
@D	Mukhopadhyay, R.//Joaquin, J.//Hogue, R.//Kilaru, A.//Jospin, G.//Mars, K.//Eisen, J.A.//Chaturvedi, V. 	Complete Genome Sequence of a Paenalcaligenes hominis Strain Isolated from a Paraplegic Patient with Neurogenic Bladder Using Single-Molecule Real-Time  Sequencing Technology.	Genome Announcements	2017	5		e00252-17			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. 		
@D	Mukhopadhyay, S.//Thomason, M.K.//Lentz, S.//Nolan, N.//Willner, K.//Gee, J.E.//Glass, M.B.//Inglis, T.J.//Merritt, A.//Levy, A.//Sozhamannan, S.//Mateczun, A.//Read, T.D. 	High-redundancy draft sequencing of 15 clinical and environmental burkholderia strains.	J. Bacteriol.	2010	192		6313-6314			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. 		
@D	Mukhtar, T.//Afridi, M.S.//McArthur, R.//Van Hamme, J.D.//Rineau, F.//Mahmood, T.//Amna, S.//Zahid, M.//Salam, A.//Khan, M.N.//Ali, F.//Mehmood, S.//Bangash, N.//Chaudhary, H.J. 	Draft Genome Sequence of Bacillus pumilus SCAL1, an Endophytic Heat-Tolerant Plant Growth-Promoting Bacterium.	Genome Announcements	2018	6		e00306-18			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. 		
@D	Mukund, M.A. 	Restriction and modification systems: unrestricted frontiers.	Curr. Sci.	1993	65		509-511			Report on Saxton's River Meeting, July 1993 		
@D	Mulder, C.//Delius, H. 	Specificity of the break produced by restricting endonuclease R in Simian virus 40 DNA, as revealed by partial denaturation mapping.	Proc. Natl. Acad. Sci. U. S. A.	1972	69		3215-3219			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. 		
@D	Mulla, S.I.//Hu, A.//Xu, H.//Yu, C.P. 	Draft Genome Sequence of Triclosan-Degrading Bacterium Sphingomonas sp. Strain YL-JM2C, Isolated from a Wastewater Treatment Plant in China.	Genome Announcements	2015	3		e00603-15			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. 		
@D	Muller, A.//Huptas, C.//Wenning, M.//Schmidt, H.//Weiss, A. 	Draft Genome Sequence of Staphylococcus carnosus subsp. utilis LTH 7013, Isolated from South Tyrolean Ham.	Genome Announcements	2015	3		e00456-15			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. 		
@D	Muller, A.//Klumpp, J.//Schmidt, H.//Weiss, A. 	Complete Genome Sequence of Staphylococcus carnosus LTH 3730.	Genome Announcements	2016	4		e01038-16			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. 		
@D	Muller, D. et al. 	A tale of two oxidation states: bacterial colonization of arsenic-rich environments.	PLoS Genet.	2007	3		e53			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. 		
@D	Muller, E.E.//Pinel, N.//Gillece, J.D.//Schupp, J.M.//Price, L.B.//Engelthaler, D.M.//Levantesi, C.//Tandoi, V.//Luong, K.//Baliga, N.S.//Korlach, J.//Keim, P.S.//Wilmes, P. 	Genome Sequence of 'Candidatus Microthrix parvicella' Bio17-1, a Long-Chain-Fatty-Acid-Accumulating Filamentous Actinobacterium from a Biological    Wastewater Treatment Plant.	J. Bacteriol.	2012	194		6670-6671			'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. 		
@D	Muller, E.E.L.//Narayanasamy, S.//Zeimes, M.//Laczny, C.C.//Lebrun, L.A.//Herold, M.//Hicks, N.D.//Gillece, J.D.//Schupp, J.M.//Keim, P.//Wilmes, P. 	First draft genome sequence of a strain belonging to the Zoogloea genus and its gene expression in situ.	Standards in Genomic Sciences	2017	12		64			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. 		
@D	Muller, H.//Furnkranz, M.//Grube, M.//Berg, G. 	Genome Sequence of Serratia plymuthica Strain S13, an Endophyte with Germination- and Plant-Growth-Promoting Activity from the Flower of Styrian Oil Pumpkin.	Genome Announcements	2013	1		e00594-13			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. 		
@D	Muller, H.//Zachow, C.//Alavi, M.//Tilcher, R.//Krempl, P.M.//Thallinger, G.G.//Berg, G. 	Complete Genome Sequence of the Sugar Beet Endophyte Pseudomonas poae RE*1-1-14,  a Disease-Suppressive Bacterium.	Genome Announcements	2013	1		e0002013			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. 		
@D	Muller, I.//Kube, M.//Reinhardt, R.//Jelkmann, W.//Geider, K. 	The Complete Genome Sequences of three Erwinia amylovora Phages Isolated in North America and a Bacteriophage Induced from an Erwinia tasmaniensis  Strain.	J. Bacteriol.	2010	193		795-796			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. 		
@D	Muller, S.//Willett, J.W.//Bahr, S.M.//Darnell, C.L.//Hummels, K.R.//Dong, C.K.//Vlamakis, H.C.//Kirby, J.R. 	Draft Genome Sequence of Myxococcus xanthus Wild-Type Strain DZ2, a Model Organism for Predation and Development.	Genome Announcements	2013	1		e00217-13			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. 		
@D	Muller, S.//Willett, J.W.//Bahr, S.M.//Scott, J.C.//Wilson, J.M.//Darnell, C.L.//Vlamakis, H.C.//Kirby, J.R. 	Draft Genome of a Type 4 Pilus Defective Myxococcus xanthus Strain, DZF1.	Genome Announcements	2013	1		e00392-13			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. 		
@D	Mulligan, E.A.//Dunn, J.J. 	Cloning, purification and initial characterization of E. coli McrA, a putative 5-methylcytosine-specific nuclease.	Protein Expr. Purif.	2008	62		98-103			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. 		
@D	Mulligan, E.A.//Hatchwell, E.//McCorkle, S.R.//Dunn, J.J. 	Differential binding of Escherichia coli McrA protein to DNA sequences that contain the dinucleotide m5CpG.	Nucleic Acids Res.	2010	38		1997-2005			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. 		
@D	Mullineux, S.T.//Costa, M.//Bassi, G.S.//Michel, F.//Hausner, G. 	A group II intron encodes a functional LAGLIDADG homing endonuclease and self-splices under moderate temperature and ionic conditions.	RNA	2010	16		1818-1831			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. 		
@D	Mullings, R.//Bennett, S.P.//Brown, N.L. 	Investigation of sequence homology in a group of type-II restriction/modification isoschizomers.	Gene	1988	74		245-251			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. 		
@D	Mullings, R.//Evans, L.R.//Brown, N.L. 	Type II restriction endonucleases from Bacillus sphaericus.	FEMS Microbiol. Lett.	1986	37		237-240			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. 		
@D	Mullins, M.A.//Register, K.B.//Bayles, D.O.//Dyer, D.W.//Kuehn, J.S.//Phillips, G.J. 	Genome sequence of Haemophilus parasuis strain 29755.	Standards in Genomic Sciences	2011	5		61-68			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. 		
@D	Mund, C.//Musch, T.//Strodicke, M.//Assmann, B.//Li, E.//Lyko, F. 	Comparative analysis of DNA methylation patterns in transgenic Drosophila overexpressing mouse DNA methyltransferases.	Biochem. J.	2003	378		763-768			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. 		
@D	Mundo, S.L.//Gilardoni, L.R.//Hoffman, F.J.//Lopez, O.J. 	Rapid and Sensitive Method To Identify Mycobacterium avium subsp paratuberculosis in Cow's Milk by DNA Methylase Genotyping.	Appl. Environ. Microbiol.	2013	79		1612-1618			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. 		
@D	Muniesa, M.//Recktenwald, J.//Bielaszewska, M.//Karch, H.//Schmidt, H. 	Characterization of a shiga toxin 2e-converting bacteriophage from an Escherichia coli strain of human origin.	Infect. Immun.	2000	68		4850-4855			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. 		
@D	Munk, A.C. et al. 	Complete genome sequence of Rhodospirillum rubrum type strain (S1).	Standards in Genomic Sciences	2011	4		293-302			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. 		
@D	Munk, A.C. et al. 	Complete genome sequence of Tsukamurella paurometabola type strain (no. 33).	Standards in Genomic Sciences	2011	4		342-351			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. 		
@D	Munk, C. et al. 	Complete genome sequence of Stackebrandtia nassauensis type strain (LLR-40K-21).	Standards in Genomic Sciences	2009	1		234-241			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. 		
@D	Munoz, B.A.//Santillana, G.//Mavrodieva, V.//Liu, Z.//Nakhla, M.//Gabriel, D.W. 	Complete Genome Sequences of Three Xanthomonas citri Strains from Texas.	Genome Announcements	2017	5		e00609-17			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. 		
@D	Munoz, I.G. et al. 	Molecular basis of engineered meganuclease targeting of the endogenous human RAG1 locus.	Nucleic Acids Res.	2011	39		729-743			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. 		
@D	Munoz-Moreno, C.Y.//De La Cruz-Rodriguez, Y.//Vega-Arreguin, J.//Alvarado-Rodriguez, M.//Gomez-Soto, J.M.//Alvarado-Gutierrez, A.//Fraire-Velazquez, S. 	Draft Genome Sequence of Bacillus subtilis 2C-9B, a Strain with Biocontrol Potential against Chili Pepper Root Pathogens and Tolerance to Pb and Zn.	Genome Announcements	2018	6		e01502-17			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. 		
@D	Munson, R.S.//Harrison, A.//Gillaspy, A.//Ray, W.C.//Carson, M.//Armbruster, D.//Gipson, J.//Gipson, M.//Johnson, L.//Lewis, L.//Dyer, D.W.//Bakaletz, L.O. 	Partial analysis of the genomes of two nontypeable Haemophilus influenzae otitis media isolates.	Infect. Immun.	2004	72		3002-3010			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. 		
@D	Muraguchi, Y.//Kushimoto, K.//Ohtsubo, Y.//Suzuki, T.//Dohra, H.//Kimbara, K.//Shintani, M. 	Complete Genome Sequence of Algoriphagus sp. Strain M8-2, Isolated from a Brackish Lake.	Genome Announcements	2016	4		e00347-16			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). 		
@D	Murakami, A.//Yamamoto, Y.//Namba, M.//Iwase, R.//Yamaoka, T. 	Photo-cross-linked oligonucleotide duplex as a decoy-DNA for inhibition of restriction endonuclease activity.	Bioorg. Chem.	2001	29		223-233			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. 		
@D	Murakami, M.//Mizuno, H.//Yamada, Y. 	The restriction endonuclease GinI of Gluconobacter cerinus IFO 3260, an isoschizomer of BamHI, has a monomeric structure.	Agric. Biol. Chem.	1990	54		2747-2749			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. 		
@D	Murakami, M.//Ozawa, O.//Kanematsu, T.//Yamada, Y. 	A new restriction endonuclease from Bacteroides distasonis (BdiI).	Agric. Biol. Chem.	1990	54		275-277			Authors have changed the name to BdiSI to avoid confusion. 		
@D	Murakami, M.//Ozawa, O.//Kanematsu, T.//Yamada, Y. 	Characterization of restriction endonuclease CbiI, an isoschizomer of AsuII, from Clostridium bifermentans strain B-4.	Nucleic Acids Res.	1991	19		3458			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. 		
@D	Murakami, M.//Ozawa, O.//Kanematsu, T.//Yamada, Y. 	Characterization of restriction endonuclease BdiSI, an isoschizomer of SfeI, from Bacteroides distasonis strain S-7.	Agric. Biol. Chem.	1991	55		261-263			This paper describes the purification and properties of the restriction endonuclease BdiSI, an isoschizomer of SfeI (CTRYAG). 		
@D	Murakami, M.//Yamada, Y. 	Purification, properties and recognition sequence and cleavage site determinations of restriction endonuclease from Acetobacter pasteurianus IFO 13753 (ApaLI).	Agric. Biol. Chem.	1990	54		1791-1796			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. 		
@D	Mural, R.J. 	Cleavage by the restriction endonuclease Asp718, an isoschizomer of KpnI, is sensitive to Escherichia coli Dcm methylation.	Nucleic Acids Res.	1987	15		9085			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. 		
@D	Murali, T.S.//Paul, B.//Parikh, H.//Singh, R.P.//Kavitha, S.//Bhat, M.K.//Satyamoorthy, K. 	Genome Sequences of Four Clinical Staphylococcus aureus Strains with Diverse Drug Resistance Profiles Isolated from Diabetic Foot Ulcers.	Genome Announcements	2014	2		e00204-14			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. 		
@D	Murata, T.//Ohnishi, M.//Ara, T.//Kaneko, J.//Han, C.G.//Li, Y.F.//Takashima, K.//Nojima, H.//Nakayama, K.//Kaji, A.//Kamio, Y.//Miki, T.//Mori, H.//Ohtsubo, E.//Terawaki, Y.//Hayashi, T. 	Complete nucleotide sequence of plasmid Rts1: implications for evolution of large plasmid genomes.	J. Bacteriol.	2002	184		3194-3202			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. 		
@D	Murawska, E.//Fiedoruk, K.//Bideshi, D.K.//Swiecicka, I. 	Complete Genome Sequence of Bacillus thuringiensis subsp. thuringiensis Strain IS5056, an Isolate Highly Toxic to Trichoplusia ni.	Genome Announcements	2013	1		e0010813			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. 		
@D	Murchie, A.I.H.//Portugal, J.//Lilley, D.M.J. 	Cleavage of a four-way DNA function by a restriction enzyme spanning the point of strand exchange.	EMBO J.	1991	10		713-718			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. 		
@D	Muro-Pastor, A.M.//Herrero, A.//Flores, E. 	Sequence-specific endonucleases from the cyanobacterium Nostoc sp. ATCC 29132.	FEMS Microbiol. Lett.	1991	77		1-4			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. 		
@D	Murphy, J.//Klumpp, J.//Mahony, J.//O'Connell-Motherway, M.//Nauta, A.//van Sinderen, D. 	Methyltransferases acquired by lactococcal 936-type phage provide protection against restriction endonuclease activity.	BMC Genomics	2014	15		831			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. 		
@D	Murphy, J.//Mahony, J.//Ainsworth, S.//Nauta, A.//van Sinderen, D. 	Bacteriophage Orphan DNA Methyltransferases: Insights from Their Bacterial Origin, Function, and Occurrence.	Appl. Environ. Microbiol.	2013	79		7547			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. 		
@D	Murphy, K.C.//Ritchie, J.M.//Waldor, M.K.//Lobner-Olesen, A.//Marinus, M.G. 	Dam methyltransferase is required for stable lysogeny of the Shiga toxin (Stx2)-encoding bacteriophage 933W of enterohemorrhagic Escherichia coli O157 : H7.	J. Bacteriol.	2008	190		438-441			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. 		
@D	Murphy, M.//Schmid, N.S.//Bickle, T.A. 	Lack of regulation of the modification-dependent restriction enzyme McrBC in Escherichia coli.	J. Bacteriol.	2002	184		1794-1795			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. 		
@D	Murphy, R.A.//Boyd, E.F. 	Three pathogenicity islands of Vibrio cholerae can excise from the chromosome and form circular intermediates.	J. Bacteriol.	2008	190		636-647			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. 		
@D	Murray, I.A.//Clark, T.A.//Morgan, R.D.//Boitano, M.//Anton, B.P.//Luong, K.//Fomenkov, A.//Turner, S.W.//Korlach, J.//Roberts, R.J. 	The methylomes of six bacteria.	Nucleic Acids Res.	2012	40		11450-11462			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. 		
@D	Murray, I.A.//Morgan, R.D.//Luyten, Y.//Fomenkov, A.//Correa, I.R. Jr.//Dai, N.//Allaw, M.B.//Zhang, X.//Cheng, X.//Roberts, R.J. 	The non-specific adenine DNA methyltransferase M.EcoGII.	Nucleic Acids Res.	2018	46		840-848			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. 		
@D	Murray, I.A.//Stickel, S.K.//Roberts, R.J. 	Sequence-specific cleavage of RNA by Type II restriction enzymes.	Nucleic Acids Res.	2010	38		8257-8268			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. 		
@D	Murray, K.//Hughes, S.G.//Brown, J.S.//Bruce, S.A. 	Isolation and characterization of two sequence-specific endonucleases from Anabaena variabilis.	Biochem. J.	1976	159		317-322			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. 		
@D	Murray, K.//Murray, N.E.//Brammar, W.J. 	Restriction enzymes and the cloning of eukaryotic DNA.	FEBS J.	1975	10		193-207			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. 		
@D	Murray, K.//Old, R.W. 	The primary structure of DNA.	Prog. Nucleic Acid Res. Mol. Biol.	1974	14		117-185			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. 		
@D	Murray, N.E. 	Immigration control of DNA in bacteria: self versus non-self.	Microbiology	2002	148		3-20			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. 		
@D	Murray, N.E. 	Type I restriction systems: sophisticated molecular machines.	Microbiol. Mol. Biol. Rev.	2000	64		412-434			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. 		
@D	Murray, N.E. 	The impact of phage lambda: from restriction to recombineering.	Biochem. Soc. Trans.	2006	34		203-207			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. 		
@D	Murray, N.E.//Barcus, V.A.//Campbell, A.J.B.//Dryden, D.T.F.//Kelleher, J.E.//Powell, L.M.//Willcock, D.//Sharp, P.M. 	Type I restriction enzymes of enteric bacteria.	J. Cell Biochem. Suppl.	1993	17C		152			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. 		
@D	Murray, N.E.//Batten, P.L.//Murray, K. 	Restriction of bacteriophage lambda by Escherichia coli K.	J. Mol. Biol.	1973	81		395-407			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. 		
@D	Murray, N.E.//Brammar, W.J. 	The trpE gene of Escherichia coli K contains a recognition sequence for the K-restriction system.	J. Mol. Biol.	1973	77		615-624			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. 		
@D	Murray, N.E.//Daniel, A.S.//Cowan, G.M.//Sharp, P.M. 	Conservation of motifs within the unusually variable polypeptide sequences of type I restriction and modification enzymes.	Mol. Microbiol.	1993	9		133-143			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. 		
@D	Murray, N.E.//de Ritis, P.M.//Foster, L.A. 	DNA targets for the Escherichia coli K restriction system analysed genetically in recombinants between phages Phi80 and lambda.	Mol. Gen. Genet.	1973	120		261-281			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. 		
@D	Murray, N.E.//Gough, J.A.//Suri, B.//Bickle, T.A. 	Structural homologies among type I restriction-modification systems.	EMBO J.	1982	1		535-539			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. 		
@D	Murray, N.E.//Murray, K. 	Manipulation of restriction targets in phage lambda to form receptor chromosomes for DNA fragments.	Nature	1974	251		476-481			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. 		
@D	Murthy, T.//Rolfs, A.//Hu, Y.//Shi, Z.//Raphael, J.//Moreira, D.//Kelley, F.//McCarron, S.//Jepson, D.//Taycher, E.//Zuo, D.//Mohr, S.E.//Fernandez, M.//Brizuela, L.//Labaer, J. 	A Full-Genomic Sequence-Verified Protein-Coding Gene Collection for Francisella tularensis.	PLoS ONE	2007	2		E577			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. 		
@D	Murugan, N.//Malathi, J.//Umashankar, V.//Madhavan, H.N. 	Comparative Genomic Analysis of Multidrug-Resistant Pseudomonas aeruginosa Clinical Isolates VRFPA06 and VRFPA08 with VRFPA07.	Genome Announcements	2014	2		e00140-14			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. 		
@D	Murugapiran, S.K. et al. 	Thermus oshimai JL-2 and T. thermophilus JL-18 genome analysis illuminates pathways for carbon, nitrogen, and sulfur cycling.	Standards in Genomic Sciences	2013	7		449-468			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. 		
@D	Murugapiran, S.K. et al. 	Whole Genome Sequencing of Thermus oshimai JL-2 and Thermus thermophilus JL-18, Incomplete Denitrifiers from the United States Great Basin.	Genome Announcements	2013	1		e00106-12			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. 		
@D	Muscarella, D.E.//Ellison, E.L.//Ruoff, B.M.//Vogt, V.M. 	Characterization of I-Ppo, an intron-encoded endonuclease that mediates homing of a group I intron in the ribosomal DNA of Physarum polycephalum.	Mol. Cell. Biol.	1990	10		3386-3396			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. 		
@D	Muscarella, D.E.//Vogt, V.M. 	A mobile group I intron in the nuclear DNA of Physarum polycephalum.	Cell	1989	56		443-454			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. 		
@D	Mushtaq, M.//Manzoor, S.//Pringle, M.//Rosander, A.//Bongcam-Rudloff, E. 	Draft genome sequence of 'Treponema phagedenis' strain V1, isolated from bovine digital dermatitis.	Standards in Genomic Sciences	2015	10		67			'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'. 		
@D	Mushtaq, R.//Naeem, S.//Sohail, A.//Riazuddin, S. 	BseRI a novel restriction endonuclease from a Bacillus species which recognizes the sequence 5'...GAGGAG...3'.	Nucleic Acids Res.	1993	21		3585			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. 		
@D	Musich, P.R. 	Effects of cytosine methylation on the activity of restriction enzymes.	J. Cell Biol.	1987	105		155a			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. 		
@D	Mussa, H.J.//VanWagoner, T.M.//Morton, D.J.//Seale, T.W.//Whitby, P.W.//Stull, T.L. 	Draft Genome Sequences of Eight Nontypeable Haemophilus influenzae Strains Previously Characterized Using an Electrophoretic Typing Scheme.	Genome Announcements	2015	3		e01374-15			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. 		
@D	Mustapha, M.M.//Li, B.//Pacey, M.P.//Mettus, R.T.//McElheny, C.L.//Marshall, C.W.//Ernst, R.K.//Cooper, V.S.//Doi, Y. 	Phylogenomics of colistin-susceptible and resistant XDR Acinetobacter baumannii.	J. Antimicrob. Chemother.	2018	73		2952-2959			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. 		
@D	Mustapha, M.M.//Marsh, J.W.//Ezeonwuka, C.D.//Pasculle, A.W.//Pacey, M.P.//Querry, A.M.//Muto, C.A.//Harrison, L.H. 	Draft Genome Sequences of Four Hospital-Associated Pseudomonas putida Isolates.	Genome Announcements	2016	4		e01039-16			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. 		
@D	Mutti, M.//Sonnevend, A.//Pal, T.//Junttila, S.//Ekker, H.//Galik, B.//Gyenesei, A.//Nagy, G.//Nagy, E.//Szijarto, V. 	Complete Genome Sequence of Escherichia coli 81009, a Representative of the Sequence Type 131 C1-M27 Clade with a Multidrug-Resistant Phenotype.	Genome Announcements	2018	6		e00056-18			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. 		
@D	Muyyarikkandy, M.S.//Alqahtani, F.H.//Mandoiu, I.//Amalaradjou, M.A. 	Draft Genome Sequence of Lactobacillus paracasei DUP 13076, Which Exhibits Potent Antipathogenic Effects against Salmonella enterica Serovars Enteritidis,  Typhimurium, and Heidelberg.	Genome Announcements	2018	6		e00065-18			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%. 		
@D	Muyyarikkandy, M.S.//Alqahtani, F.H.//Mandoiu, I.//Amalaradjou, M.A. 	Draft Genome Sequence of Lactobacillus rhamnosus NRRL B-442, a Potential Probiotic Strain.	Genome Announcements	2018	6		e00046-18			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. 		
@D	Muyzer, G.//Sorokin, D.Y.//Mavromatis, K.//Lapidus, A.//Clum, A.//Ivanova, N.//Pati, A.//d'Haeseleer, P.//Woyke, T.//Kyrpides, N.C. 	Complete genome sequence of 'Thioalkalivibrio sulfidophilus' HL-EbGr7.	Standards in Genomic Sciences	2011	4		23-35			'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. 		
@D	Muyzer, G.//Sorokin, D.Y.//Mavromatis, K.//Lapidus, A.//Foster, B.//Sun, H.//Ivanova, N.//Pati, A.//D'haeseleer, P.//Woyke, T.//Kyripides, N.C. 	Complete genome sequence of Thioalkalivibrio sp. K90mix.	Standards in Genomic Sciences	2011	5		341-355			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. 		
@D	Myers, G.S. et al. 	Skewed genomic variability in strains of the toxigenic bacterial pathogen, Clostridium perfringens.	Genome Res.	2006	16		1031-1040			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. 		
@D	Nabhan, S.//Bunk, B.//Sproer, C.//Liu, Z.//Bryant, D.A.//Overmann, J. 	Genome Sequence of Prosthecochloris sp. Strain CIB 2401 of the Phylum Chlorobi.	Genome Announcements	2016	4		e01222-16			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. 		
@D	Nacke, H.//Daniel, R.//Poehlein, A. 	Genome Sequence of Creatinine-Fermenting Tissierella creatinophila Strain KRE 4T  (DSM 6911).	Genome Announcements	2017	5		e00051-17			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. 		
@D	Nadeev, A.N.//Chernukhin, V.A.//Sevastyanova, O.O.//Tomilova, Y.E.//Shinkarenko, N.M.//Evdokimov, A.A.//Degtyarev, S.K. 	BstKTI, a new dam-sensitive neoschizomer of restriction endonuclease MboI, which is able to cleave 5 hemimethylated substrate.	Biotekhnologiya	2006	0		5-10			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. 		
@D	Naderer, M.//Brust, J.R.//Knowle, D.//Blumenthal, R.M. 	Mobility of a restriction-modification system revealed by its genetic context in three hosts.	J. Bacteriol.	2002	184		2411-2419			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. 		
@D	Nadig, S.//Velusamy, N.//Lalitha, P.//Kar, S.//Sharma, S.//Arakere, G. 	Staphylococcus aureus eye infections in two Indian hospitals: emergence of ST772 as a major clone.	Clinical Ophthalmology	2012	6		165-173			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. 		
@D	Nadiga, M.//Vaidyanathan, V.V.//Thayumanavan, T. 	Draft Genome Sequence of Aeromonas dhakensis Strain F2S2-1, Isolated from the Skin Surface of an Indian Oil Sardine (Sardinella longiceps).	Genome Announcements	2016	4		e00494-16			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. 		
@D	Nagai, Y.//Nogami, S.//Kumagai-Sano, F.//Ohya, Y. 	Karyopherin-mediated nuclear import of the homing endonuclease VMA1-derived endonuclease is required for self-propagation of the  coding region.	Mol. Cell. Biol.	2003	23		1726-1736			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. 		
@D	Nagamalleswari, E.//Nagaraja, V. 	Draft Genome Sequence of Klebsiella pneumoniae OK8, a Multidrug-Resistant Mouse and Human Pathogen.	Genome Announcements	2017	5		e01018-17			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. 		
@D	Nagamalleswari, E.//Rao, S.//Vasu, K.//Nagaraja, V. 	Restriction endonuclease triggered bacterial apoptosis as a mechanism for long time survival.	Nucleic Acids Res.	2017	45		8423-8434			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. 		
@D	Nagamalleswari, E.//Vasu, K.//Nagaraja, V. 	Ca(2+) binding to the ExDxD motif regulates the DNA cleavage specificity of a promiscuous endonuclease.	Biochemistry	2012	51		8939-8949			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. 		
@D	Nagao, K.//Suzuki, K.//Hamada, S.//Yahara, S.//Yamamura, R.//Uyeda, M. 	1513-DMIa and 1513-DMIb, DNA methyltransferase inhibitors produced by Streptomyces sp. strain no. 1513.	J. Enzym. Inhib.	1998	13		135-146			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). 		
@D	Nagao, K.//Suzuki, K.//Tokunaga, J.//Miyazaki, H.//Katayama, N.//Mitsuyama, R.//Uyeda, M. 	DMI-2 and DMI-3, DNA methyltransferase inhibitors produced by Streptomyces sp. strain no. 560.	J. Enzym. Inhib.	1996	10		115-124			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. 		
@D	Nagao, N.//Hirose, Y.//Misawa, N.//Ohtsubo, Y.//Umekage, S.//Kikuchi, Y. 	Complete Genome Sequence of Rhodovulum sulfidophilum DSM 2351, an Extracellular Nucleic Acid-Producing Bacterium.	Genome Announcements	2015	3		e00388-15			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. 		
@D	Nagaraja, V.//Shepherd, J.C.W.//Bickle, T.A. 	A hybrid recognition sequence in a recombinant restriction enzyme and the evolution of DNA sequence specificity.	Nature	1985	316		371-372			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. 		
@D	Nagaraja, V.//Shepherd, J.C.W.//Pripfl, T.//Bickle, T.A. 	Two Type I restriction enzymes from Salmonella species.  Purification and DNA recognition sequences.	J. Mol. Biol.	1985	182		579-587			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. 		
@D	Nagaraja, V.//Stieger, M.//Nager, C.//Hadi, S.M.//Bickle, T.A. 	The nucleotide sequence recognized by the Escherichia coli D type I restriction and modification enzyme.	Nucleic Acids Res.	1985	13		389-399			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. 		
@A	Nagaraja, V.//Suri, B.//Shepherd, J.C.W.//Bickle, T.A. 		New variations of an old theme:  Type I restriction enzymes and their recognition sequences.			Glass, R.E.//Spizek, J. 		Gene Manipulation and Expression					CroomHelm	1985		0		62-78									None 		
@D	Nagarajan, H.//Butler, J.E.//Klimes, A.//Qiu, Y.//Zengler, K.//Ward, J.//Young, N.D.//Methe, B.A.//Palsson, B.O.//Lovley, D.R.//Barrett, C.L. 	De Novo assembly of the complete genome of an enhanced electricity-producing variant of Geobacter sulfurreducens using only short reads.	PLoS ONE	2010	5		E10922			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. 		
@D	Nagarjuna, D.//Gaind, R.//Dhanda, R.S.//Yadav, M. 	Whole-Genome Shotgun Sequence of Escherichia coli Strain MN067 from India, a Commensal Bacterium with Potent Pathogenic Ability.	Genome Announcements	2017	5		e00054-17			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. 		
@D	Nagashima, S.//Kamimura, A.//Shimizu, T.//Nakamura-Isaki, S.//Aono, E.//Sakamoto, K.//Ichikawa, N.//Nakazawa, H.//Sekine, M.//Yamazaki, S.//Fujita, N.//Shimada, K.//Hanada, S.//Nagashima, K.V. 	Complete Genome Sequence of Phototrophic Betaproteobacterium Rubrivivax gelatinosus IL144.	J. Bacteriol.	2012	194		3541-3542			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). 		
@D	Nagata, Y.//Ohtsubo, Y.//Endo, R.//Ichikawa, N.//Ankai, A.//Oguchi, A.//Fukui, S.//Fujita, N.//Tsuda, M. 	Complete Genome Sequence of the Representative {gamma}-Hexachlorocyclohexane-Degrading Bacterium Sphingobium japonicum  UT26.	J. Bacteriol.	2010	192		5852-5853			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. 		
@D	Nagornykh, M.//Zakharova, M.//Protsenko, A.//Bogdanova, E.//Solonin, A.S.//Severinov, K. 	Regulation of gene expression in restriction-modification system Eco29kI.	Nucleic Acids Res.	2011	39		4653-4663			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. 		
@D	Nagornykh, M.O.//Bogdanova, E.S.//Protsenko, A.S.//Solonin, A.S.//Zakharova, M.V.//Severinov, K.V. 	Regulation of gene expression in a type II restriction-modification system.	Genetika	2008	44		606-615			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. 		
@D	Nagymihaly, M.//Vasarhelyi, B.M.//Barriere, Q.//Chong, T.M.//Balint, B.//Bihari, P.//Hong, K.W.//Horvath, B.//Ibijbijen, J.//Amar, M.//Farkas, A.//Kondorosi, E.//Chan, K.G.//Gruber, V.//Ratet, P.//Mergaert, P.//Kereszt, A. 	The complete genome sequence of Ensifer meliloti strain CCMM B554 (FSM-MA), a highly effective nitrogen-fixing microsymbiont of Medicago truncatula Gaertn.	Standards in Genomic Sciences	2017	12		75			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. 		
@D	Nahar, A.//Baker, A.L.//Bowman, J.P.//Britz, M.L. 	Draft Genome Sequences of Two Lactobacillus casei Strains Isolated from Cheddar Cheese and a Fermented Milk Drink.	Genome Announcements	2017	5		e01235-17			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. 		
@D	Nahar, A.//Baker, A.L.//Charleston, M.A.//Bowman, J.P.//Britz, M.L. 	Draft Genome Sequences of Three Sub-Antarctic Rhodococcus spp., Including Two Novel Psychrophilic Genomospecies.	Genome Announcements	2017	5		e00898-17			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. 		
@D	Nahar, A.//Baker, A.L.//Charleston, M.A.//Bowman, J.P.//Britz, M.L. 	Draft Genome Sequences of Two Novel Sub-Antarctic Williamsia Species.	Genome Announcements	2017	5		e01047-17			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. 		
@D	Nahar, A.//Baker, A.L.//Charleston, M.A.//Britz, M.L. 	Draft Genome Sequence of Subantarctic Rhodococcus sp. Strain 1139.	Genome Announcements	2017	5		e00090-17			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. 		
@D	Nahid, F.//Zahra, R.//Sandegren, L. 	A blaOXA-181-harbouring multi-resistant ST147 Klebsiella pneumoniae isolate from Pakistan that represent an intermediate stage towards pan-drug resistance.	PLoS ONE	2017	12		e0189438			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. 		
@D	Nahon, E.//Raveh, D. 	Targeting a truncated Ho-endonuclease of yeast to novel DNA sites with foreign zinc fingers.	Nucleic Acids Res.	1998	26		1233-1239			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. 		
@D	Naidoo, S.//Featherston, J.//Gray, V.M. 	Draft Whole-Genome Sequence and Annotation of the Entomopathogenic Bacterium Xenorhabdus khoisanae Strain MCB.	Genome Announcements	2015	3		e00872-15			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%. 		
@D	Naidoo, S.//Mothupi, B.//Featherston, J.//Mpangase, P.T.//Gray, V.M. 	Draft Genome Sequence and Assembly of Photorhabdus heterorhabditis Strain VMG, a  Bacterial Symbiont Associated with the Entomopathogenic Nematode Heterorhabditis   zealandica.	Genome Announcements	2015	3		e01279-15			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%. 		
@D	Nair, D.//Memmi, G.//Hernandez, D.//Bard, J.//Beaume, M.//Gill, S.//Francois, P.//Cheung, A.L. 	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.	J. Bacteriol.	2011	193		2332-2335			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. 		
@D	Naito, M.//Hirakawa, H.//Yamashita, A.//Ohara, N.//Shoji, M.//Yukitake, H.//Nakayama, K.//Toh, H.//Yoshimura, F.//Kuhara, S.//Hattori, M.//Hayashi, T.//Nakayama, K. 	Genome sequence determination of Porphyromonas gingivalis strain ATCC 33277 and genomic comparison with strain W83 revealed extensive genome rearrangements in P. gingivalis.	DNA Res.	2008	15		215-225			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). 		
@D	Naito, M.//Ogura, Y.//Itoh, T.//Shoji, M.//Okamoto, M.//Hayashi, T.//Nakayama, K. 	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.	DNA Res.	2015	0		dsv032			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. 		
@D	Naito, T.//Kobayashi, I. 	Cell death programmed by selfish genes -- or, why are there restriction enzymes?	Jikken Igaku	1995	13		1444-1447					
@D	Naito, T.//Kusano, K.//Kobayashi, I. 	Selfish behavior of restriction-modification systems.	Science	1995	267		897-899			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. 		
@D	Naito, Y.//Naito, T.//Kobayashi, I. 	Selfish restriction modification genes: Resistance of a resident R/M plasmid to displacement by an incompatible plasmid mediated by host killing.	Biol. Chem.	1998	379		429-436			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. 		
@D	Najah, S.//Chong, T.M.//Gerbaud, C.//Chan, K.G.//Mellouli, L.//Pernodet, J.L. 	Complete Genome Sequence of Streptomyces sp. TN58, a Producer of Acyl Alpha-l-Rhamnopyranosides.	Genome Announcements	2017	5		e00828-17			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. 		
@D	Najera-Hernandez, S.//Sanchez-Alonso, M.P.//Anastacio-Marcelino, E.//Negrete-Abascal, E.//Vazquez-Cruz, C. 	Draft Genome Sequence of Escherichia coli Strain SN137, a Bacterium with Extracellular Proteolytic Activity on Immunoglobulins and Persistence in Human  Tissue Blood.	Genome Announcements	2018	6		e01455-17			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. 		
@D	Naka, H.//Dias, G.M.//Thompson, C.C.//Dubay, C.//Thompson, F.L.//Crossa, J.H. 	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.	Infect. Immun.	2011	79		2889-2900			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. 		
@D	Nakagawa, K.-I.//Hashikawa, J.-I.//Makino, O.//Ando, T.//Shibata, T. 	Subunit structure of a yeast site-specific endodeoxyribonuclease, endoSceI.  A study using monoclonal antibodies.	Eur. J. Biochem.	1988	171		23			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. 		
@D	Nakagawa, K.-I.//Morishima, N.//Shibata, T. 	An endonuclease with multiple cutting sites, Endo.SceI, initiates genetic recombination at its cutting site in yeast mitochondria.	EMBO J.	1992	11		2707-2715			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. 		
@D	Nakagawa, K.-I.//Morishima, N.//Shibata, T. 	A maturase-like subunit of the sequence-specific endonuclease Endo.SceI from yeast mitochondria.	J. Biol. Chem.	1991	266		1977-1984			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. 		
@D	Nakagawa, S.//Shimamura, S.//Takaki, Y.//Suzuki, Y.//Murakami, S.//Watanabe, T.//Fujiyoshi, S.//Mino, S.//Sawabe, T.//Maeda, T.//Makita, H.//Nemoto, S.//Nishimura, S.//Watanabe, H.//Watsuji, T.//Takai, K. 	Allying with armored snails: the complete genome of gammaproteobacterial endosymbiont.	ISME J.	2014	8		40-51			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. 		
@D	Nakagawa, S.//Takaki, Y.//Shimamura, S.//Reysenbach, A.L.//Takai, K.//Horikoshi, K. 	Deep-sea vent epsilon-proteobacterial genomes provide insights into emergence of pathogens.	Proc. Natl. Acad. Sci. U. S. A.	2007	104		12146-12150			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. 		
@D	Nakagawahara, K.//Mori, M.//Mioka, C. 	Types and uses of restriction enzymes.	Rinsho Kensa	1996	40		826-835			A review (in japanese). 		
@D	Nakahigashi, K.//Kubo, N.//Narita, S.//Shimaoka, T.//Goto, S.//Oshima, T.//Mori, H.//Maeda, M.//Wada, C.//Inokuchi, H. 	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.	Proc. Natl. Acad. Sci. U. S. A.	2002	99		1473-1478			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. 		
@D	Nakai, R.//Fujisawa, T.//Nakamura, Y.//Baba, T.//Nishijima, M.//Karray, F.//Sayadi, S.//Isoda, H.//Naganuma, T.//Niki, H. 	Genome sequence and overview of Oligoflexus tunisiensis Shr3T in the eighth class Oligoflexia of the phylum Proteobacteria.	Standards in Genomic Sciences	2016	11		90			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. 		
@D	Nakai, R.//Fujisawa, T.//Nakamura, Y.//Nishide, H.//Uchiyama, I.//Baba, T.//Toyoda, A.//Fujiyama, A.//Naganuma, T.//Niki, H. 	Complete Genome Sequence of Aurantimicrobium minutum Type Strain KNCT, a Planktonic Ultramicrobacterium Isolated from River Water.	Genome Announcements	2016	4		e00616-16			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. 		
@D	Nakajima, T.//Matsubara, K.//Ueno, H.//Kagawa, S.//Moore, J.E.//Millar, B.C.//Matsuda, M. 	Molecular identification and characterization of type III restriction-modification (R-M) gene cluster in Campylobacter lari.	Ann. Microbiol. (Paris)	2013	63		1629-1637			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. 		
@D	Nakajima, Y.//Yoshizawa, S.//Nakamura, K.//Ogura, Y.//Hayashi, T.//Kogure, K. 	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.	Genome Announcements	2017	5		e00079-17			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. 		
@D	Nakajima, Y.//Yoshizawa, S.//Park, S.//Kumagai, Y.//Wong, S.K.//Ogura, Y.//Hayashi, T.//Kogure, K. 	Draft Genome Sequence of Rubricoccus marinus SG-29T, a Marine Bacterium within the Family Rhodothermaceae, Which Contains Two Different Rhodopsin Genes.	Genome Announcements	2017	5		e00990-17			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. 		
@D	Nakamaye, K.L.//Eckstein, F. 	Inhibition of restriction endonuclease NciI cleavage by phosphorothioate groups and its application to oligonucleotide-directed mutagenesis.	Nucleic Acids Res.	1986	14		9679-9698			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. 		
@D	Nakamura, S.//Ikehata, H.//Ono, T. 	Characteristics of mutations generated through digestion with restriction enzyme and ligation in plasmid DNA.	Environ. Mol. Mutagen.	2001	38		46-54			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. 		
@D	Nakamura, T.//Maeda, Y.//Oka, T.//Tabata, H.//Futai, M.//Kawai, T. 	Atomic force microscope observation of plasmid deoxyribose nucleic acid with restriction enzyme.	J. Vac. Sci. Technol. B	1999	17		288-293			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. 		
@D	Nakamura, Y. et al. 	Complete genome structure of Gloeobacter violaceus PCC 7421, a cyanobacterium that lacks thylakoids.	DNA Res.	2003	10		137-145			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. 		
@D	Nakamura, Y. et al. 	Complete genome structure of the thermophilic cyanobacterium Thermosynechococcus elongatus BP-1 (supplement).	DNA Res.	2002	9		135-148			none 		
@D	Nakamura, Y. et al. 	Complete genome structure of the thermophilic cyanobacterium Thermosynechococcus elongatus BP-1.	DNA Res.	2002	9		123-130			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. 		
@D	Nakanishi, M.//Meirelles, P.//Suzuki, R.//Takatani, N.//Mino, S.//Suda, W.//Oshima, K.//Hattori, M.//Ohkuma, M.//Hosokawa, M.//Miyashita, K.//Thompson, F.L.//Niwa, A.//Sawabe, T.//Sawabe, T. 	Draft Genome Sequences of Marine Flavobacterium Nonlabens Strains NR17, NR24, NR27, NR32, NR33, and Ara13.	Genome Announcements	2014	2		e01165-14			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. 		
@D	Nakanishi, S.//Tazumi, A.//Moore, J.E.//Millar, B.C.//Matsuda, M. 	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.	Br. J. Biomed. Sci.	2010	67		208-215			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. 		
@D	Nakano, K. et al. 	First Complete Genome Sequence of the Skin-Improving Lactobacillus curvatus Strain FBA2, Isolated from Fermented Vegetables, Determined by PacBio  Single-Molecule Real-Time Technology.	Genome Announcements	2016	4		e00884-16			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. 		
@D	Nakano, K.//Minami, M.//Shinzato, M.//Shimoji, M.//Ashimine, N.//Shiroma, A.//Ohki, S.//Nakanishi, T.//Tamotsu, H.//Teruya, K.//Satou, K.//Moriya, N.//Kimoto-Nira, H.//Kobayashi, M.//Hagi, T.//Nomura, M.//Suzuki, C.//Hirano, T. 	Complete Genome Sequence of Lactococcus lactis subsp. lactis G50 with Immunostimulating Activity, Isolated from Napier Grass.	Genome Announcements	2018	6		e00069-18			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. 		
@D	Nakano, K.//Terabayashi, Y.//Shiroma, A.//Shimoji, M.//Tamotsu, H.//Ashimine, N.//Ohki, S.//Shinzato, M.//Teruya, K.//Satou, K.//Hirano, T. 	First Complete Genome Sequence of Pseudomonas aeruginosa (Schroeter 1872) Migula  1900 (DSM 50071T), Determined Using PacBio Single-Molecule Real-Time Technology.	Genome Announcements	2015	3		e00932-15			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. 		
@D	Nakano, K.//Terabayashi, Y.//Shiroma, A.//Shimoji, M.//Tamotsu, H.//Ashimine, N.//Ohki, S.//Shinzato, M.//Teruya, K.//Satou, K.//Hirano, T. 	First Complete Genome Sequence of Clostridium sporogenes DSM 795T, a Nontoxigenic Surrogate for Clostridium botulinum, Determined Using PacBio Single-Molecule  Real-Time Technology.	Genome Announcements	2015	3		e00832-15			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. 		
@D	Nakano, Y.//Steward, N.//Sekine, M.//Kusano, T.//Sano, H. 	A tobacco NtMET1 cDNA encoding a DNA methyltransferase: Molecular characterization and abnormal phenotypes of transgenic tobacco plants.	Plant Cell Physiol.	2000	41		448-457			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. 		
@D	Nakao, K.//Chinen, A.//Nobusato, A.//Fujitani, Y.//Uchiyama, I.//Kobayashi, I. 	Relation between restriction modification genes and genome rearrangements suggested from genome sequence comparison within genus  Neisseria.	Genome Inf. Ser.	2001	12		398-399			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. 		
@D	Nakao, R.//Jongejan, F.//Sugimoto, C. 	Draft Genome Sequences of Three Strains of Ehrlichia ruminantium, a Tick-Borne Pathogen of Ruminants, Isolated from Zimbabwe, The Gambia, and Ghana.	Genome Announcements	2016	4		e00453-16			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. 		
@D	Nakashima, N.//Tamura, T. 	Whole-Genome Sequence of Acetobacter orientalis Strain FAN1, Isolated from Caucasian Yogurt.	Genome Announcements	2018	6		e00201-18			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. 		
@D	Nakatsu, C.H.//Barabote, R.//Thompson, S.//Bruce, D.//Detter, C.//Brettin, T.//Han, C.//Beasley, F.//Chen, W.//Konopka, A.//Xie, G. 	Complete genome sequence of Arthrobacter sp. strain FB24.	Standards in Genomic Sciences	2013	9		106-116			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. 		
@D	Nakayama, H.//Morinaga, Y.//Nomura, N.//Nunoura, T.//Sako, Y.//Uchida, A. 	An archaeal homing endonuclease I-PogI cleaves at the insertion site of the neighboring intron, which has no nested open reading frame.	FEBS Lett.	2003	544		165-170			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. 		
@D	Nakayama, H.//Shimamura, T.//Imagawa, T.//Shirai, N.//Itoh, T.//Sako, Y.//Miyano, M.//Sakuraba, H.//Ohshima, T.//Nomura, N.//Tsuge, H. 	Structure of a hyperthermophilic archaeal homing endonuclease, I-Tsp061I: Contribution of cross-domain polar networks to thermostability.	J. Mol. Biol.	2007	365		362-378			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. 		
@D	Nakayama, K.//Endo, M.//Fujitsuka, M.//Majima, T. 	Monitoring of three distinct structures of restriction enzyme complexes using characteristic fluorescence from site-selectively incorporated solvatochromic probe.	Photochem. Photobiolog.	2007	6		836-841			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. 		
@D	Nakayama, K.//Endo, M.//Majima, T. 	Photochemical regulation of the activity of a restriction enzyme BamHI using an azobenzene moiety incorporated into the dimer interface.	ACS Abstracts	2005	229		U399-U400			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. 		
@D	Nakayama, K.//Endo, M.//Majima, T. 	A hydrophilic azobenzene-bearing amino acid for photochemical control of a restriction enzyme BamHI.	Bioconjugate Chem.	2005	16		1360-1366			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. 		
@D	Nakayama, K.//Yamashita, A.//Kurokawa, K.//Morimoto, T.//Ogawa, M.//Fukuhara, M.//Urakami, H.//Ohnishi, M.//Uchiyama, I.//Ogura, Y.//Ooka, T.//Oshima, K.//Tamura, A.//Hattori, M.//Hayashi, T. 	The Whole-genome Sequencing of the Obligate Intracellular Bacterium Orientia tsutsugamushi Revealed Massive Gene Amplification During  Reductive Genome Evolution.	DNA Res.	2008	15		185-199			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. 		
@D	Nakayama, T.//Inagaki, Y. 	Genomic divergence within non-photosynthetic cyanobacterial endosymbionts in rhopalodiacean diatoms.	Sci. Rep.	2017	7		13075			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. 		
@D	Nakayama, T.//Kamikawa, R.//Tanifuji, G.//Kashiyama, Y.//Ohkouchi, N.//Archibald, J.M.//Inagaki, Y. 	Complete genome of a nonphotosynthetic cyanobacterium in a diatom reveals recent adaptations to an intracellular lifestyle.	Proc. Natl. Acad. Sci. U. S. A.	2014	111		11407-11412			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. 		
@D	Nakayama, Y.//Kobayashi, I. 	Restriction-modification gene complexes as selfish gene entities: roles of a regulatory system in their establishment, maintenance, and apoptotic mutual exclusion.	Proc. Natl. Acad. Sci. U. S. A.	1998	95		6442-6447			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. 		
@D	Nakayashiki, T.//Nishimura, K.//Inokuchi, H. 	Cloning and sequencing of a previously unidentified gene that is involved in the biosynthesis of heme in Escherichia coli.	Gene	1995	153		67-70			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. 		
@D	Nakonieczna, J.//Kaczorowski, T.//Obarska-Kosinska, A.//Bujnicki, J.M. 	Functional Analysis of MmeI from Methanol Utilizer Methylophilus methylotrophus, a Subtype IIC Restriction-Modification Enzyme Related to Type I Enzymes.	Appl. Environ. Microbiol.	2009	75		212-223			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. 		
@D	Nakonieczna, J.//Zmijewski, J.W.//Banecki, B.//Podhajska, A.J. 	Binding of MmeI restriction-modification enzyme to its specific recognition sequence is stimulated by S-adenosyl-L-methionine.	Mol. Biotechnol.	2007	37		127-135			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. 		
@D	Nally, J.E.//Bayles, D.O.//Hurley, D.//Fanning, S.//McMahon, B.J.//Arent, Z. 	Complete Genome Sequence of Leptospira alstonii Serovar Room22 Strain GWTS #1.	Genome Announcements	2016	4		e01230-16			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. 		
@D	Nam, S.H.//Choi, S.H.//Kang, A.//Kim, D.W.//Kim, D.S.//Kim, R.N.//Kim, A.//Park, H.S. 	Genome Sequence of Leuconostoc fallax KCTC 3537.	J. Bacteriol.	2010	193		588-589			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). 		
@D	Nam, S.H.//Choi, S.H.//Kang, A.//Kim, D.W.//Kim, D.S.//Kim, R.N.//Kim, A.//Park, H.S. 	Genome Sequence of Lactobacillus coryniformis subsp. coryniformis KCTC 3167.	J. Bacteriol.	2011	193		1014-1015			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. 		
@D	Nam, S.H.//Choi, S.H.//Kang, A.//Kim, D.W.//Kim, R.N.//Kim, A.//Kim, D.S.//Park, H.S. 	Genome Sequence of Lactobacillus farciminis KCTC 3681.	J. Bacteriol.	2011	193		1790-1791			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. 		
@D	Nam, S.H.//Choi, S.H.//Kang, A.//Kim, D.W.//Kim, R.N.//Kim, A.//Kim, D.S.//Park, H.S. 	Genome Sequence of Lactobacillus animalis KCTC 3501.	J. Bacteriol.	2010	193		1280-1281			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. 		
@D	Nam, S.H.//Choi, S.H.//Kang, A.//Kim, D.W.//Kim, R.N.//Kim, A.//Park, H.S. 	Genome Sequence of Leuconostoc argentinum KCTC 3773.	J. Bacteriol.	2010	192		6490-6491			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). 		
@D	Nam, S.H.//Choi, S.H.//Kang, A.//Kim, D.W.//Kim, R.N.//Kim, D.S.//Kim, A.//Park, H.S. 	Genome Sequence of Lactobacillus suebicus KCTC 3549.	J. Bacteriol.	2011	193		5532-5533			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). 		
@D	Nam, S.H.//Choi, S.H.//Kang, A.//Lee, K.S.//Kim, D.W.//Kim, R.N.//Kim, D.S.//Park, H.S. 	Genome Sequence of Lactobacillus fructivorans KCTC 3543.	J. Bacteriol.	2012	194		2111-2112			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. 		
@D	Nam, S.H.//Kim, A.//Choi, S.H.//Kang, A.//Kim, D.W.//Kim, R.N.//Kim, D.S.//Park, H.S. 	Genome Sequence of Leuconostoc carnosum KCTC 3525.	J. Bacteriol.	2011	193		6100-6101			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. 		
@D	Nam, Y.D.//Chung, W.H.//Seo, M.J.//Lim, S.I. 	Draft Genome Sequence of Staphylococcus vitulinus F1028, a Strain Isolated from a Block of Fermented Soybean.	J. Bacteriol.	2012	194		5961-5962			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. 		
@D	Nam, Y.D.//Chung, W.H.//Seo, M.J.//Lim, S.I.//Yi, S.H. 	Genome Sequence of Staphylococcus lentus F1142, a Strain Isolated from Korean Soybean Paste.	J. Bacteriol.	2012	194		5987			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. 		
@D	Nam, Y.D.//Lee, H.W.//Lee, M.//Yim, K.J.//Kim, K.N.//Roh, S.W.//Kim, D. 	Draft Genome Sequence of Gillisia sp. Strain CBA3202, a Novel Member of the Genus Gillisia, Which Belongs to the Family Flavobacteriaceae.	J. Bacteriol.	2012	194		3739			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. 		
@D	Nam, Y.D.//Seo, M.J.//Lim, S.I.//Lee, S.Y. 	Genome Sequence of Lysinibacillus boronitolerans F1182, Isolated from a Traditional Korean Fermented Soybean Product.	J. Bacteriol.	2012	194		5988			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. 		
@D	Nam, Y.D.//Seo, M.J.//Lim, S.I.//Park, S.L. 	Genome Sequence of Kocuria atrinae C3-8, Isolated from Jeotgal, a Traditional Korean Fermented Seafood.	J. Bacteriol.	2012	194		5996			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%. 		
@D	Nambu, T.//Tsuzukibashi, O.//Uchibori, S.//Mashimo, C. 	Complete Genome Sequence of Rothia mucilaginosa Strain NUM-Rm6536, Isolated from  a Human Oral Cavity.	Genome Announcements	2015	3		e01122-15			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. 		
@D	Nambu, T.//Tsuzukibashi, O.//Uchibori, S.//Yamane, K.//Yamanaka, T.//Maruyama, H.//Wang, P.L.//Mugita, N.//Morioka, H.//Takahashi, K.//Komasa, Y.//Mashimo, C. 	Complete Genome Sequence of Rothia aeria Type Strain JCM 11412, Isolated from Air in the Russian Space Laboratory Mir.	Genome Announcements	2016	4		e01444-16			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. 		
@D	Nambu, T.//Yamane, K.//Maruyama, H.//Mashimo, C.//Yamanaka, T. 	Complete Genome Sequence of Prevotella intermedia Strain 17-2.	Genome Announcements	2015	3		e00951-15			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. 		
@D	Nan, X.//Ng, H.-H.//Johnson, C.A.//Laherty, C.D.//Turner, B.M.//Eisenman, R.N.//Bird, A. 	Transcriptional repression by the methyl-CpG-binding protein MeCP2 involves a histone deacetylase complex.	Nature	1998	393		386-389			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. 		
@D	Nancucheo, I.//Oliveira, R.//Dall'Agnol, H.//Johnson, D.B.//Grail, B.//Holanda, R.//Nunes, G.L.//Cuadros-Orellana, S.//Oliveira, G. 	Draft Genome Sequence of a Novel Acidophilic Iron-Oxidizing Firmicutes Species, 'Acidibacillus ferrooxidans' (SLC66T).	Genome Announcements	2016	4		e00383-16			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. 		
@D	Nandasena, K. et al. 	Complete genome sequence of Mesorhizobium ciceri bv. biserrulae type strain (WSM1271(T)).	Standards in Genomic Sciences	2014	9		462-472			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. 		
@D	Nandi, T. et al. 	Burkholderia pseudomallei sequencing identifies genomic clades with distinct recombination, accessory, and epigenetic profiles.	Genome Res.	2015	25		129-141			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. 		
@D	Nannan, C.//Gillis, A.//Caulier, S.//Mahillon, J. 	Complete Genome Sequence of Bacillus velezensis CN026 Exhibiting Antagonistic Activity against Gram-Negative Foodborne Pathogens.	Genome Announcements	2018	6		e01543-17			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. 		
@D	Naome, A.//Maciejewska, M.//Calusinska, M.//Martinet, L.//Anderssen, S.//Adam, D.//Tenconi, E.//Deflandre, B.//Coppieters, W.//Karim, L.//Hanikenne, M.//Baurain, D.//Delfosse, P.//van Wezel, G.P.//Rigali, S. 	Complete Genome Sequence of Streptomyces lunaelactis MM109(T), Isolated from Cave Moonmilk Deposits.	Genome Announcements	2018	6		e00435-18			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). 		
@D	Naor, A.//Lazary, R.//Barzel, A.//Papke, R.T.//Gophna, U. 	In vivo characterization of the homing endonuclease within the polB gene in the halophilic archaeon Haloferax volcanii.	PLoS ONE	2011	6		e15833			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. 		
@D	Napier, B.A.//Band, V.//Burd, E.M.//Weiss, D.S. 	Colistin heteroresistance in Enterobacter cloacae is associated with cross-resistance to the host antimicrobial lysozyme.	Antimicrob. Agents Chemother.	2014	58		5594-5597			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. 		
@D	Narayan, K.D.//Badhai, J.//Whitman, W.B.//Das, S.K. 	Draft Genome Sequence of Comamonas thiooxydans Strain S23T (DSM 17888T), a Thiosulfate-Oxidizing Bacterium Isolated from a Sulfur Spring in India.	Genome Announcements	2016	4		e00834-16			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. 		
@D	Narayanan, S.//Deshpande, U. 	Whole-Genome Sequences of Four Clinical Isolates of Mycobacterium tuberculosis from Tamil Nadu, South India.	Genome Announcements	2013	1		e00186-13			We report the annotated genome sequences of four clinical isolates of Mycobacterium tuberculosis from Tamil Nadu, India. 		
@D	Nardone, G.//Blakesley, R. 	A new type II restriction enzyme from Haemophilus influenzae.	Fed. Proc.	1981	40		1848			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. 		
@A	Nardone, G.//Chirikjian, J.G. 		The enzymes of the BamHI restriction-modification system.			Chirikjian, J.G. 		Gene Amplif. Anal.					Elsevier North Holland	1987		5		147-184									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. 		
@D	Nardone, G.//Connaughton, J.F.//Kaloss, W.//Chirikjian, J.G. 	Changes in the kinetics of the BamHI restriction/modification enzymes with systematic alterations of the bases flanking the recognition site.	FASEB J.	1990	4		A1794			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. 		
@D	Nardone, G.//George, J.//Chirikjian, J.G. 	Differences in the Kinetic Properties of BamHI Endonuclease and Methylase with Linear DNA Substrates.	J. Biol. Chem.	1986	261		12128-12133			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. 		
@D	Nardone, G.//George, J.//Chirikjian, J.G. 	Sequence-specific BamHI methylase.	J. Biol. Chem.	1984	259		10357-10362			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. 		
@D	Nardone, G.//Wastney, M.//Hensley, P.//Chirikjian, J.G. 	Kinetics of BamHI endonuclease cleavage of form I SV40 DNA.	Fed. Proc.	1986	45		1504			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). 		
@D	Nardone, G.//Wastney, M.E.//Hensley, P. 	DNA structural polymorphism modulates the kinetics of superhelical DNA cleavage by BamHI restriction endonucleases.	J. Biol. Chem.	1990	265		15308-15315			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. 		
@D	Narendra-Kumar, P.//Swapna, T.H.//Sathi, R.K.//Archana, K.//Nageshwar, L.//Nalini, S.//Khan, M.Y.//Hameeda, B. 	Draft Genome Sequence of Bacillus amyloliquefaciens Strain RHNK22, Isolated from  Rhizosphere with Biosurfactant (Surfactin, Iturin, and Fengycin) and Antifungal  Activity.	Genome Announcements	2016	4		e01682-15			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. 		
@D	Narendrakumar, L.//Suryaletha, K.//Reghunathan, D.//Prasannakumar, M.//Thomas, S. 	Insights into the Draft Genome Sequence of a Haitian Variant Vibrio cholerae Strain Isolated from a Clinical Setting in Kerala, South India.	Genome Announcements	2017	5		e00843-17			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. 		
@D	Narihiro, T.//Kusada, H.//Yoneda, Y.//Tamaki, H. 	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.	Genome Announcements	2016	4		e00199-16			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)). 		
@D	Narihiro, T.//Nobu, M.K.//Tamaki, H.//Kamagata, Y.//Liu, W.T. 	Draft Genome Sequence of Syntrophomonas wolfei subsp. methylbutyratica Strain 4J5T (JCM 14075), a Mesophilic Butyrate- and 2-Methylbutyrate-Degrading Syntroph.	Genome Announcements	2016	4		e00047-16			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%. 		
@D	Naroditsky, B.S.//Khilko, S.N.//Loparev, V.N. 	Current methods for the isolation of specific endonucleases.	Vestn. Akad. Med. Nauk SSSR	1981	2		26-28			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. 		
@D	Narsing-Rao, M.P.//Jiao, J.Y.//Liu, L.//Fang, B.Z.//Zhang, X.T.//Chen, W.//Zhao, J.//Xiao, M.//Li, W.J. 	Draft Genome Sequence of MPKL 26, the Type Strain of the Novel Species Sinomonas  mesophila.	Genome Announcements	2017	5		e00247-17			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. 		
@D	Narva, K.E.//Skrdla, M.P.//Wendell, D.L.//Van Etten, J.L. 	Isolation of a DNA methyltransferase gene, M.CviBIII, from Chlorella virus NC-1A.	Abstr. Gen. Meet. Am. Soc. Microbiol.	1987	87		314			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. 		
@D	Narva, K.E.//Van Etten, J.L.//Slatko, B.E.//Benner, J.S. 	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.	Gene	1988	74		253-259			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...]. 		
@D	Narva, K.E.//Wendell, D.L.//Skrdla, M.P.//Van Etten, J.L. 	Molecular cloning and characterization of the gene encoding the DNA methyltransferase, M.CviBIII, from Chlorella virus NC-1A.	Nucleic Acids Res.	1987	15		9807-9823			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. 		
@D	Nascimento, A.L. et al. 	Comparative Genomics of Two Leptospira interrogans Serovars Reveals Novel Insights into Physiology and Pathogenesis.	J. Bacteriol.	2004	186		2164-2172			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. 		
@D	Nasfi, Z.//Poehlein, A.//Harms, H.//Goralski, E.//Fisch, K.M.//Daniel, R.//Konig, G.M.//Schaberle, T.F.//Bachoual, R. 	Draft Genome Sequence of Bacillus sp. Strain M21, Isolated from the Arid Area of  Matmata, Tunisia.	Genome Announcements	2018	6		e00323-18			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. 		
@D	Nash, J.H.//Villegas, A.//Kropinski, A.M.//Aguilar-Valenzuela, R.//Konczy, P.//Mascarenhas, M.//Ziebell, K.//Torres, A.G.//Karmali, M.A.//Coombes, B.K. 	Genome sequence of adherent-invasive Escherichia coli and comparative genomic analysis with other E. coli pathotypes.	BMC Genomics	2010	11		667			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. 		
@D	Nash, J.H.//Young, N.M. 	Draft Whole-Genome Sequence of Morganella morganii Serotype O:1ab.	Genome Announcements	2015	3		e00453-15			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. 		
@D	Nasri, M.//Sayadi, S.//Thomas, D. 	Relaxation of PvuII recognition sequence.	FEBS Lett.	1985	185		101-104			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. 		
@D	Nasri, M.//Thomas, D. 	Alteration of the specificity of PvuII restriction endonuclease.	Nucleic Acids Res.	1987	15		7677-7687			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). 		
@D	Nasri, M.//Thomas, D. 	Increase of the potentialities of restriction endonucleases by specificity relaxation in the presence of organic solvents.	Ann. NY Acad. Sci.	1988	542		255-265			None 		
@D	Nasri, M.//Thomas, D. 	Relaxation of recognition sequence of specific endonuclease HindIII.	Nucleic Acids Res.	1986	14		811-821			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. 		
@D	Nasri, M.//Thomas, D. 	The reactions of SacI, PvuII and EcoRI endonucleases.	Biomed. Biochim. Acta	1986	45		997-1005			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. 		
@D	Nasri, M.//Thomas, D. 	Immobilization of the restriction endonucleases PvuII and HindIII.	Appl. Biochem. Biotechnol.	1987	15		119-130			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. 		
@D	Nasrin, S.//Hossain, M.J.//Liles, M.R. 	Draft Genome Sequence of Bacillus amyloliquefaciens AP183 with Antibacterial Activity against Methicillin-Resistant Staphylococcus aureus.	Genome Announcements	2015	3		e00162-15			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. 		
@D	Nasser, K.//Mustafa, A.S.//Khan, M.W.//Purohit, P.//Al-Obaid, I.//Dhar, R.//Al-Fouzan, W. 	Draft Genome Sequences of Six Multidrug-Resistant Clinical Strains of Acinetobacter baumannii, Isolated at Two Major Hospitals in Kuwait.	Genome Announcements	2018	6		e00264-18			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. 		
@D	Nastri, H.G.//Evans, P.D.//Walker, I.H.//Riggs, P.D. 	Catalytic and DNA binding properties of PvuII restriction endonuclease mutants.	J. Biol. Chem.	1997	272		25761-25767			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. 		
@D	Nath, K. 	Effect of sulfhydryl group inhibitors on restriction endonuclease activities.	Arch. Biochem. Biophys.	1981	212		611-617			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. 		
@A	Nath, K.//Azzolina, B.A. 		Cleavage properties of site-specific restriction endonucleases.			Chirikjian, J.G. 		Gene Amplif. Anal.					Elsevier North Holland	1981		1		113-130									*
   I. Introduction
  II. Site preference by restriction endonucleases
 III. Perturbations in restriction-endonuclease cleavage properties
  IV. Application of manipulated restriction endonuclease cleavage
   V. Summary
 
 		
@D	Nath, K.//Bollon, A.P. 	Generation of discrete yeast DNA fragments by endonuclease RI.	Nature	1975	257		155-157			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. 		
@D	Nathan, D.//Crothers, D.M. 	Bending and flexibility of methylated and unmethylated EcoRI DNA.	J. Mol. Biol.	2002	316		7-17			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. 		
@D	Nathan, P.D.//Brooks, J.E. 	Characterization of clones of the BamHI methyltransferase gene.	Gene	1988	74		35-36			Meeting Abstract 		
@D	Nathan, P.D.//Brooks, J.E. 	Characterization of clones of the BamHI methyltransferase gene.	J. Cell Biochem. Suppl.	1989	13D		212			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. 		
@D	Nathan, P.D.//Brooks, J.E. 	Regulation of the BamHI restriction-modification system.	Abstr. Gen. Meet. Am. Soc. Microbiol.	1989	89		180			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. 		
@D	Nathans, D.//Adler, S.P.//Brockman, W.W.//Danna, K.J.//Lee, T.N.H.//Sack, G.H. Jr. 	Use of restriction endonucleases in analyzing the genome of simian virus 40.	Fed. Proc.	1974	33		1135-1138			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. 		
@D	Nathans, D.//Smith, H.O. 	Restriction endonucleases in the analysis and restructuring of DNA molecules.	Annu. Rev. Biochem.	1975	44		273-293			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. 		
@D	Naughton, S.//Parker, D.//Seemann, T.//Thomas, T.//Turnbull, L.//Rose, B.//Bye, P.//Cordwell, S.//Whitchurch, C.//Manos, J. 	Pseudomonas aeruginosa AES-1 exhibits increased virulence gene expression during chronic infection of cystic fibrosis lung.	PLoS ONE	2011	6		E24526			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. 		
@D	Naumann, T.A.//Tavassoli, A.//Benkovic, S.J. 	Genetic selection of cyclic peptide dam methyltransferase inhibitors.	Chembiochem	2008	9		194-197			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. 		
@D	Naumann, U.//Daxinger, L.//Kanno, T.//Eun, C.//Long, Q.A.//Lorkovic, Z.J.//Matzke, M.//Matzke, A.J.M. 	Genetic Evidence That DNA Methyltransferase DRM2 Has a Direct Catalytic Role in RNA-Directed DNA Methylation in Arabidopsis thaliana.	Genetics	2011	187		977-979			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. 		
@D	Navas, E.//Bohle, H.//Henriquez, P.//Grothusen, H.//Bustamante, F.//Bustos, P.//Mancilla, M. 	Draft Genome Sequence of the Fish Pathogen Yersinia ruckeri Strain 37551, Serotype O1b, Isolated from Diseased, Vaccinated Atlantic Salmon (Salmo salar) in  Chile.	Genome Announcements	2014	2		e00858-14			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. 		
@D	Navas, L.E.//Berretta, M.F.//Ortiz, E.M.//Benintende, G.B.//Amadio, A.F.//Zandomeni, R.O. 	Draft Genome Sequence of Thermus sp. Isolate 2.9, Obtained from a Hot Water Spring Located in Salta, Argentina.	Genome Announcements	2015	3		e01414-14			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. 		
@D	Navas, L.E.//Berretta, M.F.//Ortiz, E.M.//Sauka, D.H.//Benintende, G.B.//Zandomeni, R.O.//Amadio, A.F. 	Draft Genome Sequence of Bacillus thuringiensis INTA Fr7-4.	Genome Announcements	2017	5		e00076-17			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. 		
@D	Naz, S.//Tareb, R.//Bernardeau, M.//Vaisse, M.//Lucchetti-Miganeh, C.//Rechenmann, M.//Vernoux, J.P. 	Genome Sequence of Lactobacillus plantarum Strain UCMA 3037.	Genome Announcements	2013	1		e00251-13			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. 		
@D	Nazarenko, I.A.//Gorbunov, Y.A.//Malysgin, E.G. 	Cleavage of synthetic RNA-DNA hybrids with restriction endonucleases BamHI and Sau3AI.	Bioorg. Khim.	1987	13		928-933			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. 		
@D	Nazari, B.//Forneris, C.C.//Gibson, M.I.//Moon, K.//Schramma, K.R.//Setedsayamdost, M.R. 	Nonomuraea sp. ATCC 55076 harbors the largest actinomycete chromosome to date and the kistamicin biosynthetic gene cluster.	MedChemComm	2017	8		780-788			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. 		
@D	Nazir, R.//Hansen, M.A.//Sorensen, S.//van Elsas, J.D. 	Draft Genome Sequence of the Soil Bacterium Burkholderia terrae Strain BS001, Which Interacts with Fungal Surface Structures.	J. Bacteriol.	2012	194		4480-4481			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. 		
@D	Neave, M.J.//Michell, C.T.//Apprill, A.//Voolstra, C.R. 	Whole-genome sequences of three symbiotic endozoicomonas strains.	Genome Announcements	2014	2		e00802-14			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. 		
@D	Neaves, K.J.//Cooper, L.P.//White, J.H.//Carnally, S.M.//Dryden, D.T.//Edwardson, J.M.//Henderson, R.M. 	Atomic force microscopy of the EcoKI Type I DNA restriction enzyme bound to DNA shows enzyme dimerization and DNA looping.	Nucleic Acids Res.	2009	37		2053-2063			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. 		
@D	Nebendahl, A.//Baumlein, H. 	Analysis of overlapping cDNA clones specific for a putative second DNA methyltransferase-encoding gene in Arabidopsis thaliana.	Gene	1995	157		269-272			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). 		
@D	Nechaeva, A.A.//Kalinina, N.A.//Sukhodolets, V.V. 	Plasmid profiles and stability of industrial strains of lactococci.	Genetika	1995	31		1210-1217			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. 		
@D	Needels, M.C.//Fried, S.R.//Love, R.//Rosenberg, J.M.//Boyer, H.W.//Greene, P.J. 	Determinants of EcoRI endonuclease sequence discrimination.	Proc. Natl. Acad. Sci. U. S. A.	1989	86		3579-3583			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. 		
@D	Needels, M.C.//Reich, N.O.//Boyer, H.W.//Greene, P. 	Cassette mutagenesis of EcoRI endonuclease.	J. Cell Biochem. Suppl.	1987	11C		209			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. 		
@D	Neely, C.//Bou, K.C.//Cervantes, A.//Diaz, R.//Escobar, A.//Ho, K.//Hoefler, S.//Smith, H.H.//Abuyen, K.//Savalia, P.//Nealson, K.H.//Emerson, D.//Tully, B.//Barco, R.A.//Amend, J. 	Genome Sequence of Hydrogenovibrio sp. Strain SC-1, a Chemolithoautotrophic Sulfur and Iron Oxidizer.	Genome Announcements	2018	6		e01581-17			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. 		
@D	Neely, R.K.//Daujotyte, D.//Grazulis, S.//Magennis, S.W.//Dryden, D.T.F.//Klimasauskas, S.//Jones, A.C. 	Time-resolved fluorescence of 2-aminopurine as a probe of base flipping in M.HhaI-DNA complexes.	Nucleic Acids Res.	2005	33		6953-6960			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. 		
@D	Neely, R.K.//Roberts, R.J. 	The BsaHI Restriction-Modification System: Cloning, Sequencing and Analysis of Conserved Motifs.	BMC Mol. Biol.	2008	9		48			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. 		
@D	Neely, R.K.//Tamulaitis, G.//Chen, K.//Kubala, M.//Siksnys, V.//Jones, A.C. 	Time-resolved fluorescence studies of nucleotide flipping by restriction enzymes.	Nucleic Acids Res.	2009	37		6859-6870			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. 		
@D	Neesen, K.//Volckaert, G. 	Construction and shuttling of novel bifunctional vectors for Streptomyces spp. and Escherichia coli.	J. Bacteriol.	1989	171		1569-1573			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. 		
@D	Neff, N.F. 	Protein splicing: selfish genes invade cellular proteins.	Curr. Opin. Cell Biol.	1993	5		971-976			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. 		
@D	Negi, V.//Lata, P.//Sangwan, N.//Kumar-Gupta, S.//Das, S.//Rao, D.L.//Lal, R. 	Draft Genome Sequence of Hexachlorohexane (HCH)-Degrading Sphingobium lucknowense Strain F2T, Isolated from an HCH Dumpsite.	Genome Announcements	2014	2		e00788-14			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%. 		
@D	Negrete-Abascal, E.//Montes-Garcia, F.//Vaca-Pacheco, S.//Leyto-Gil, A.M.//Fragoso-Garcia, E.//Carvente-Garcia, R.//Perez-Agueros, S.//Castelan-Sanchez, H.G.//Garcia-Molina, A.//Villamar, T.E.//Sanchez-Alonso, P.//Vazquez-Cruz, C. 	Genome Sequence of Actinobacillus seminis Strain ATCC 15768, a Reference Strain of Ovine Pathogens That Causes Infections in Reproductive Organs.	Genome Announcements	2018	6		e01453-17			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. 		
@D	Neiger, R.//Thomas, M.//Das, S.//Barnes, M.//Fletcher, B.//Snekvik, K.//Thompson, J.//Scaria, J. 	Draft Genome Sequences of Three Flavobacterium psychrophilum Strains Isolated from Coldwater Disease Outbreaks at Three Production Hatcheries.	Genome Announcements	2016	4		e00035-16			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. 		
@D	Nejedly, K.//Matyasek, R.//Palecek, E. 	Site-specific chemical modification of B-Z junctions in supercoiled DNA as detected by nuclease S1 digestion, inhibition of restriction cleavage and nucleotide sequencing.	J. Biomol. Struct. Dyn.	1988	6		261-273			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. 		
@D	Nekrasov, S.V.//Agafonova, O.V.//Belogurova, N.G.//Delver, E.P.//Belogurov, A.A. 	Plasmid-encoded Antirestriction Protein ArdA Can Discriminate between Type I Methyltransferase and Complete Restriction-Modification System.	J. Mol. Biol.	2007	365		284-297			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. 		
@D	Nell, S.//Estibariz, I.//Krebes, J.//Bunk, B.//Graham, D.Y.//Overmann, J.//Song, Y.//Sproer, C.//Yang, I.//Wex, T.//Korlach, J.//Malfertheiner, P.//Suerbaum, S. 	Genome and Methylome Variation in Helicobacter pylori With a cag Pathogenicity Island During Early Stages of Human Infection.	Gastroenterology	2018	154		612-623.e7			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. 		
@D	Nellemann, L.J.//Aamand, J.L.//Madsen, A.//Josephsen, J. 	Characterization of a non-type II restriction/modification system on plasmid PJW565 from Lactococcus lactis subsp. cremoris W56.	FASEB J.	1997	11		A1035			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. 		
@D	Nelson, B.A.//Ramaiya, P.//Lopez-de-Leon, A.//Kumar, R.//Crinklaw, A.//Jolkovsky, E.//Crane, J.M.//Bergstrom, G.C.//Rey, M.W. 	Complete Genome Sequence for the Fusarium Head Blight Antagonist Bacillus amyloliquefaciens Strain TrigoCor 1448.	Genome Announcements	2014	2		e00219-14			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. 		
@D	Nelson, H.C.M.//Bestor, T.H. 	Base eversion and shuffling by DNA methyltransferases.	Chem. Biol.	1996	3		419-423			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. 		
@D	Nelson, J.M.//Miceli, S.M.//Lechevalier, M.P.//Roberts, R.J. 	FseI, a new type II restriction endonuclease that recognizes the octanucleotide sequence 5' GGCCGGCC 3' .	Nucleic Acids Res.	1990	18		2061-2064			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. 		
@D	Nelson, K.E. et al. 	Complete genome sequence of the oral pathogenic bacterium Porphyromonas gingivalis strain W83.	J. Bacteriol.	2003	185		5591-5601			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. 		
@D	Nelson, K.E. et al. 	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.	Nucleic Acids Res.	2004	32		2386-2395			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. 		
@D	Nelson, K.E. et al. 	Evidence for lateral gene transfer between Archaea and bacteria from genome sequence of Thermotoga maritima.	Nature	1999	399		323-329			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. 		
@D	Nelson, M.//Burbank, D.E.//Van Etten, J.L. 	Chlorella viruses encode multiple DNA methyltransferases.	Biol. Chem.	1998	379		423-428			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. 		
@D	Nelson, M.//Christ, C.//Schildkraut, I. 	Alteration of apparent restriction endonuclease recognition specificities by DNA methylases.	Nucleic Acids Res.	1984	12		5165-5173			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. 		
@D	Nelson, M.//McClelland, M. 	The effect of site-specific methylation on restriction-modification enzymes.	Nucleic Acids Res.	1987	15		r219-r230			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. 		
@D	Nelson, M.//McClelland, M. 	Purification and assay of Type II DNA methylases.	Methods Enzymol.	1987	155		32-41			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. 		
@D	Nelson, M.//McClelland, M. 	Effect of site-specific methylation on DNA modification methyltransferases and restriction endonucleases.	Nucleic Acids Res.	1989	17		r389-r415			Review of the effects of methylation. 		
@D	Nelson, M.//McClelland, M. 	Site-specific methylation: effect on DNA modification methyltransferases and restriction endonucleases.	Nucleic Acids Res.	1991	19		2045-2071			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. 		
@D	Nelson, M.//McClelland, M. 	Chromosome mapping at the megabase level: Guidelines for choosing restriction endonucleases for pulsed field gel mapping.	Promega Notes	1989	18		1-3			A review. 		
@D	Nelson, M.//McClelland, M. 	Use of DNA methyltransferase/endonuclease enzyme combinations for megabase mapping of chromosomes.	Methods Enzymol.	1992	216		279-303			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. 		
@D	Nelson, M.//Raschke, E.//McClelland, M. 	Effect of site-specific methylation on restriction endonucleases and DNA modification methyltransferases.	Nucleic Acids Res.	1993	21		3139-3154			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. 		
@D	Nelson, M.//Schildkraut, I. 	The use of DNA methylases to alter the apparent recognition specificities of restriction endonucleases.	Methods Enzymol.	1987	155		41-48			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. 		
@A	Nelson, M.//Zhang, Y.//Van Etten, J.L. 		DNA methyltransferases and DNA-site-specific endonucleases encoded by chlorella viruses.			Jost, J.P.//Saluz, H.P. 		DNA Methylation: Molecular Biology and Biological Significance				Basel, Switzerland	Birkhauser Verlag	1993		0		186-211									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). 		
@D	Nelson, M.C.//Bomar, L.//Graf, J. 	Complete Genome Sequence of the Novel Leech Symbiont Mucinivorans hirudinis M3T.	Genome Announcements	2015	3		e01530-14			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. 		
@D	Nelson, M.C.//LaPatra, S.E.//Welch, T.J.//Graf, J. 	Complete Genome Sequence of Yersinia ruckeri Strain CSF007-82, Etiologic Agent of Red Mouth Disease in Salmonid Fish.	Genome Announcements	2015	3		e01491-14			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. 		
@D	Nelson, M.C.//Varney, J.S.//Welch, T.J.//Graf, J. 	Draft Genome Sequence of Lactococcus garvieae Strain PAQ102015-99, an Outbreak Strain Isolated from a Commercial Trout Farm in the Northwestern United States.	Genome Announcements	2016	4		e00781-16			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%. 		
@D	Nelson, P.S.//Papas, T.S.//Schweinfest, C.W. 	Restriction endonuclease cleavage of 5-methyl-deoxycytosine hemimethylated DNA at high enzyme-to-substrate ratios.	Nucleic Acids Res.	1993	21		681-686			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. 		
@D	Nelson, R.L.//Castro, M.A.//Katti, M.//Eisen, J.A.//Van Laar, T.A. 	Genome Sequence of a Multidrug-Resistant Strain of Bacillus pumilus, CB01, Isolated from the Feces of an American Crow, Corvus brachyrhynchos.	Genome Announcements	2016	4		e00807-16			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. 		
@D	Nemet, Z.//Albert, E.//Nagy, T.//Olasz, F.//Barta, E.//Kiss, J.//Dan, A.//Banyai, K.//Hermans, K.//Biksi, I. 	Draft Genome Sequence of a Highly Virulent Rabbit Staphylococcus aureus Strain.	Genome Announcements	2015	3		e00461-15			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. 		
@D	Neoh, H.M.//Mohamed-Hussein, Z.A.//Tan, X.E.//Abd-Rahman, B.R.R.M.//Hussin, S.//Mohamad, Z.N.//Jamal, R. 	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.	Genome Announcements	2013	1		e00103-12			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. 		
@D	Nerdal, W.//Hare, D.R.//Reid, B.R. 	Solution structure of the EcoRI DNA sequence: Refinement of NMR-derived distance geometry structures by NOESY spectrum back-calculations.	Biochemistry	1989	28		10008-10021			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. 		
@D	Neri, A.//Fazio, C.//Ciammaruconi, A.//Anselmo, A.//Fortunato, A.//Palozzi, A.//Vacca, P.//Fillo, S.//Lista, F.//Stefanelli, P. 	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.	Genome Announcements	2014	2		e01263-14			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. 		
@D	Neri, F.//Krepelova, A.//Incarnato, D.//Maldotti, M.//Parlato, C.//Galvagni, F.//Matarese, F.//Stunnenberg, H.G.//Oliviero, S. 	Dnmt3L Antagonizes DNA Methylation at Bivalent Promoters and Favors DNA Methylation at Gene Bodies in ESCs.	Cell	2013	155		121-134			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. 		
@D	Nesbo, C.L.//Boucher, Y.//Dlutek, M.//Doolittle, W.F. 	Lateral gene transfer and phylogenetic assignment of environmental fosmid clones.	Environ. Microbiol.	2005	7		2011-2026			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. 		
@D	Nesemann, K.//Braus-Stromeyer, S.A.//Thuermer, A.//Daniel, R.//Braus, G.H. 	Draft Genome Sequence of the Beneficial Rhizobacterium Pseudomonas fluorescens DSM 8569, a Natural Isolate of Oilseed Rape (Brassica napus).	Genome Announcements	2015	3		e00137-15			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. 		
@D	Nesemann, K.//Braus-Stromeyer, S.A.//Thuermer, A.//Daniel, R.//Mavrodi, D.V.//Thomashow, L.S.//Weller, D.M.//Braus, G.H. 	Draft Genome Sequence of the Phenazine-Producing Pseudomonas fluorescens Strain 2-79.	Genome Announcements	2015	3		e00130-15			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. 		
@D	Nesme, J.//Cania, B.//Zadel, U.//Scholer, A.//Plaza, G.A.//Schloter, M. 	Complete Genome Sequences of Two Plant-Associated Pseudomonas putida Isolates with Increased Heavy-Metal Tolerance.	Genome Announcements	2017	5		e01330-17			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. 		
@D	Nesterenko, V.F.//Buryanov, Y.I.//Baev, A.A. 	Isolation and properties of DNA-cytosine-methylase I from Escherichia coli MRE 600.	Biokhimiia	1979	44		130-140			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'. 		
@D	Nesterenko, V.F.//Buryanov, Y.I.//Baev, A.A. 	Determination of DNA-cytosine methylase I (M. Eco MRE600I) in plasmid CoLA.	Dokl. Akad. Nauk.	1980	250		1265-1267			None 		
@D	Nestor, C.//Ruzov, A.//Meehan, R.R.//Dunican, D.S. 	Enzymatic approaches and bisulfite sequencing cannot distinguish between 5-methylcytosine and 5-hydroxymethylcytosine in DNA.	Biotechniques	2010	48		317-319			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. 		
@D	Netesov, S.V.//Grachev, S.A. 	An effective method for isolation of restriction endonucleases.	Bioorg. Khim.	1981	7		790-791			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. 		
@D	Netesova, N.A.//Golikova, L.N.//Ovetchkina, L.G.//Evdokimov, A.A.//Malygin, E.G.//Gololobova, N.S.//Gonchar, D.A.//Degtyarev, S.K. 	Comparative study of the M.BstF5I-1 and M.BstF5I-3 DNA methyltransferases from the Bacillus stearothermophilus F5 restriction-modification system.	Mol. Biol. (Mosk)	2002	36		136-143			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'. 		
@D	Neupane, S. et al. 	Non-contiguous finished genome sequence of plant-growth promoting Serratia proteamaculans S4.	Standards in Genomic Sciences	2013	8		441-449			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. 		
@D	Neupane, S. et al. 	Complete genome sequence of the plant-associated Serratia plymuthica strain AS13.	Standards in Genomic Sciences	2012	7		22-30			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). 		
@D	Neupane, S. et al. 	Complete genome sequence of Serratia plymuthica strain AS12.	Standards in Genomic Sciences	2012	6		165-173			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'. 		
@D	Neupane, S. et al. 	Complete genome sequence of the rapeseed plant-growth promoting Serratia plymuthica strain AS9.	Standards in Genomic Sciences	2012	6		54-62			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). 		
@D	Neurgaonkar, P.S.//Dharne, M.S.//Dastager, S.G. 	Draft Genome Sequence of Arthrobacter enclensis NCIM 5488T for Secondary Metabolism.	Genome Announcements	2016	4		e00497-16			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. 		
@D	Newby, A.E.R.//Lau, E.Y.//Bruice, T.C. 	A theoretical examination of the factors controlling the catalytic efficiency of the DNA-(adenine-N6)-methyltransferase from Thermus aquaticus.	Proc. Natl. Acad. Sci. U. S. A.	2002	99		7922-7927			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. 		
@D	Newman, A.K.//Rubin, R.A.//Kim, S.H.//Modrich, P. 	DNA Sequences of Structural Genes for EcoRI DNA Restriction and Modified Enzymes.	J. Biol. Chem.	1981	256		2131-2139			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. 		
@D	Newman, M.//Lunnen, K.//Wilson, G.//Greci, J.//Schildkraut, I.//Phillips, S.E.V. 	Crystal structure of restriction endonuclease BglI bound to its interrupted DNA recognition sequence.	EMBO J.	1998	17		5466-5476			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. 		
@D	Newman, M.//Strzelecka, T.//Dorner, L.F.//Schildkraut, I.//Aggarwal, A.K. 	Structure of restriction endonuclease BamHI phased at 1.95 A resolution by MAD analysis.	Structure	1994	2		439-452			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. 		
@D	Newman, M.//Strzelecka, T.//Dorner, L.F.//Schildkraut, I.//Aggarwal, A.K. 	Structure of BamHI endonuclease bound to DNA: partial folding and unfolding on DNA binding.	Science	1995	269		656-663			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. 		
@D	Newman, M.//Strzelecka, T.//Dorner, L.F.//Schildkraut, I.//Aggarwal, A.K. 	Structure of restriction endonuclease BamHI and its relationship to EcoRI.	Nature	1994	368		660-664			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. 		
@D	Newman, P.C. 	Investigation of the sequence-specific DNA/protein interactions of the EcoRV restriction enzyme.	Diss. Abstr.	1991	51		3366B			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 		
@D	Newman, P.C.//Nwosu, V.U.//Williams, D.M.//Cosstick, R.//Seela, F.//Connolly, B.A. 	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.	Biochemistry	1990	29		9891-9901			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. 		
@D	Newman, P.C.//Williams, D.M.//Cosstick, R.//Seela, F.//Connolly, B.A. 	Interaction of the EcoRV restriction endonuclease with the deoxyadenosine and thymidine bases in its recognition hexamer d(GATATC).	Biochemistry	1990	29		9902-9910			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. 		
@D	Ng, E.K.O.//Tsang, W.P.//Ng, S.S.M.//Jin, H.C.//Yu, J.//Li, J.J.//Roecken, C.//Ebert, M.P.A.//Kwok, T.T.//Sung, J.J.Y. 	MicroRNA-143 targets DNA methyltransferases 3A in colorectal cancer.	Br. J. Cancer	2009	101		699-706			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 		
@D	Ng, H.F.//Tan, J.L.//Zin, T.//Yap, S.F.//Ngeow, Y.F. 	A mutation in anti-sigma factor MAB_3542c may be responsible for tigecycline resistance in Mycobacterium abscessus.	J. Med. Microbiol.	2018	67		1676-1681			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. 		
@D	Ng, K.P.//Yew, S.M.//Chan, C.L.//Chong, J.//Tang, S.N.//Soo-Hoo, T.S.//Na, S.L.//Hassan, H.//Ngeow, Y.F.//Hoh, C.C.//Lee, K.W.//Yee, W.Y. 	Draft Genome Sequence of the First Isolate of Extensively Drug-Resistant (XDR) Mycobacterium tuberculosis in Malaysia.	Genome Announcements	2013	1		e00056-12			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. 		
@D	Ng, W.V. et al. 	Genome sequence of Halobacterium species NRC-1.	Proc. Natl. Acad. Sci. U. S. A.	2000	97		12176-12181			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. 		
@D	Ng, W.V.//Ciufo, S.A.//Smith, T.M.//Bumgarner, R.E.//Baskin, D.//Faust, J.//Hall, B.//Loretz, C.//Seto, J.//Slagel, J.//Hood, L.//DasSarma, S. 	Snapshot of a large dynamic replicon in a halophilic archaeon: Megaplasmid or minichromosome?	Genome Res.	1998	8		1131-1141			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. 		
@D	Ngeow, Y.F.//Leong, M.L.//Wong, Y.L.//Wong, G.J.//Tan, J.L.//Wee, W.Y.//Ong, C.S.//Pang, Y.K.//Choo, S.W. 	Draft Genome Sequence of Mycobacterium massiliense Strain M159, Showing Phenotypic Resistance to beta-Lactam and Tetracycline Antibiotics.	Genome Announcements	2013	1		e00669-13			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. 		
@D	Ngeow, Y.F.//Wee, W.Y.//Wong, Y.L.//Tan, J.L.//Ongi, C.S.//Ng, K.P.//Choo, S.W. 	Genomic Analysis of Mycobacterium abscessus Strain M139, Which Has an Ambiguous Subspecies Taxonomic Position.	J. Bacteriol.	2012	194		6002-6003			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. 		
@D	Ngeow, Y.F.//Wong, Y.L.//Lokanathan, N.//Wong, G.J.//Ong, C.S.//Ng, K.P.//Choo, S.W. 	Genomic Analysis of Mycobacterium massiliense Strain M115, an Isolate from Human  Sputum.	J. Bacteriol.	2012	194		4786			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. 		
@D	Ngeow, Y.F.//Wong, Y.L.//Tan, J.L.//Arumugam, R.//Wong, G.J.//Ong, C.S.//Ng, K.P.//Choo, S.W. 	Genome Sequence of Mycobacterium massiliense M18, Isolated from a Lymph Node Biopsy Specimen.	J. Bacteriol.	2012	194		4125			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. 		
@D	Ngeow, Y.F.//Wong, Y.L.//Tan, J.L.//Ong, C.S.//Ng, K.P.//Choo, S.W. 	Genome Sequence of Mycobacterium abscessus Strain M152.	J. Bacteriol.	2012	194		6662			Mycobacterium abscessus is an environmental bacterium with increasing clinical relevance. Here, we report the annotated whole-genome sequence of M. abscessus strain M152. 		
@D	Ngom, M.//Oshone, R.//Hurst, S.G. IV//Abebe-Akele, F.//Simpson, S.//Morris, K.//Sy, M.O.//Champion, A.//Thomas, W.K.//Tisa, L.S. 	Permanent Draft Genome Sequence for Frankia sp. Strain CeD, a Nitrogen-Fixing Actinobacterium Isolated from the Root Nodules of Casuarina equistifolia Grown in  Senegal.	Genome Announcements	2016	4		e00265-16			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. 		
@D	Ngugi, D.K.//Stingl, U. 	High-Quality Draft Single-Cell Genome Sequence of the NS5 Marine Group from the Coastal Red Sea.	Genome Announcements	2018	6		e00565-18			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. 		
@D	Ngugi, D.K.//Stingl, U. 	High-Quality Draft Single-Cell Genome Sequence Belonging to the Archaeal Candidate Division SA1, Isolated from Nereus Deep in the Red Sea.	Genome Announcements	2018	6		e00383-18			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. 		
@D	Nguyen, D.T.//Lessor, L.E.//Cahill, J.L.//Rasche, E.S.//Kuty, E.G.F. 	Complete Genome Sequence of Klebsiella pneumoniae Carbapenemase-Producing K. pneumoniae Siphophage Sushi.	Genome Announcements	2015	3		e00994-15			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. 		
@D	Nguyen, L.D.//Cajthamlova, K.//Nguyen, H.T.//Weiser, J.//Holubova, I.//Weiserova, M. 	Identification of the EcoKI and EcoR124I type I restriction-modification enzyme subunits by non-equilibrium pH gradient two-dimensional gel electrophoresis.	Folia Microbiol. (Praha)	2002	47		641-648			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. 		
@D	Nguyen, S.V.//Harhay, D.M.//Bono, J.L.//Smith, T.P.//Fields, P.I.//Dinsmore, B.A.//Santovenia, M.//Kelley, C.M.//Wang, R.//Bosilevac, J.M.//Harhay, G.P. 	Complete and Closed Genome Sequences of 10 Salmonella enterica subsp. enterica Serovar Anatum Isolates from Human and Bovine Sources.	Genome Announcements	2016	4		e00447-16			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. 		
@D	Nguyen, S.V.//Harhay, D.M.//Bono, J.L.//Smith, T.P.//Fields, P.I.//Dinsmore, B.A.//Santovenia, M.//Kelley, C.M.//Wang, R.//Bosilevac, J.M.//Harhay, G.P. 	Complete, Closed Genome Sequences of 10 Salmonella enterica subsp. enterica Serovar Typhimurium Strains Isolated from Human and Bovine Sources.	Genome Announcements	2016	4		e01212-16			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. 		
@D	Nguyen, T.P.//De Mot, R.//Springael, D. 	Draft Genome Sequence of the Carbofuran-Mineralizing Novosphingobium sp. Strain KN65.2.	Genome Announcements	2015	3		e00764-15			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. 		
@D	Nho, S.W.//Hikima, J.I.//Cha, I.S.//Park, S.B.//Jang, H.B.//Del Castillo, C.S.//Kondo, H.//Hirono, I.//Aoki, T.//Jung, T.S. 	Complete genome sequence and immunoproteomic analyses of the fish bacterial pathogen Streptococcus parauberis.	J. Bacteriol.	2011	193		3356-3366			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. 		
@D	Niazi, A.//Manzoor, S.//Bejai, S.//Meijer, J.//Bongcam-Rudloff, E. 	Complete genome sequence of a plant associated bacterium Bacillus amyloliquefaciens subsp. plantarum UCMB5033.	Standards in Genomic Sciences	2014	9		718-725			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. 		
@D	Nicholls, C.//Kump, A.//Ford, S.//Gonser, R.//Cho, K.H. 	Draft Genome Sequence of Streptococcus pyogenes Strain M3KCL.	Genome Announcements	2017	5		e00610-17			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. 		
@D	Nichols, M.//Topaz, N.//Wang, X.//Wang, X.//Boxrud, D. 	Draft Genome Sequences for a Diverse Set of Isolates from 10 Neisseria Species.	Genome Announcements	2018	6		e00409-18			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. 		
@D	Nicholson, A.C.//Bell, M.//Humrighouse, B.W.//McQuiston, J.R. 	Complete Genome Sequences for Two Strains of a Novel Fastidious, Partially Acid-Fast, Gram-Positive Corynebacterineae Bacterium, Derived from Human Clinical  Samples.	Genome Announcements	2015	3		e01462-15			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. 		
@D	Nicholson, A.C.//Humrighouse, B.W.//Graziano, J.C.//Emery, B.//McQuiston, J.R. 	Draft Genome Sequences of Strains Representing Each of the Elizabethkingia Genomospecies Previously Determined by DNA-DNA Hybridization.	Genome Announcements	2016	4		e00045-16			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. 		
@D	Nicholson, A.C.//Whitney, A.M.//Emery, B.D.//Bell, M.E.//Gartin, J.T.//Humrighouse, B.W.//Loparev, V.N.//Batra, D.//Sheth, M.//Rowe, L.A.//Juieng, P.//Knipe, K.//Gulvik, C.//McQuiston, J.R. 	Complete Genome Sequences of Four Strains from the 2015-2016 Elizabethkingia anophelis Outbreak.	Genome Announcements	2016	4		e00563-16			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. 		
@D	Nicholson, A.C.//Whitney, A.M.//Humrighouse, B.//Emery, B.//Loparev, V.//McQuiston, J.R. 	Complete Genome Sequence of Strain H5989 of a Novel Devosia Species.	Genome Announcements	2015	3		e00934-15			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. 		
@D	Nicholson, B.A.//Wannemuehler, Y.M.//Logue, C.M.//Li, G.//Nolan, L.K. 	Complete Genome Sequence of the Neonatal Meningitis-Causing Escherichia coli Strain NMEC O18.	Genome Announcements	2016	4		e01239-16			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. 		
@D	Nicholson, B.A.//Wannemuehler, Y.M.//Logue, C.M.//Li, G.//Nolan, L.K. 	Complete Genome Sequence of the Avian-Pathogenic Escherichia coli Strain APEC O18.	Genome Announcements	2016	4		e01213-16			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. 		
@D	Nicholson, T.L.//Shore, S.M.//Bayles, D.O.//Register, K.B.//Kingsley, R.A. 	Draft Genome Sequence of the Bordetella bronchiseptica Swine Isolate KM22.	Genome Announcements	2014	2		e00670-14			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. 		
@D	Nicholson, W.L.//Davis, C.L.//Shapiro, N.//Huntemann, M.//Clum, A.//Reddy, T.B.//Pillay, M.//Markowitz, V.//Varghese, N.//Pati, A.//Ivanova, N.//Kyrpides, N.//Woyke, T. 	An improved high-quality draft genome sequence of Carnobacterium inhibens subsp.  inhibens strain K1(T).	Standards in Genomic Sciences	2016	11		65			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. 		
@D	Nicholson, W.L.//Leonard, M.T.//Fajardo-Cavazos, P.//Panayotova, N.//Farmerie, W.G.//Triplett, E.W.//Schuerger, A.C. 	Complete Genome Sequence of Serratia liquefaciens Strain ATCC 27592.	Genome Announcements	2013	1		e00548-13			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. 		
@D	Nickoloff, J.A. 	Converting restriction sites by filling in 5' extensions.	Biotechniques	1992	12		512-514			None 		
@D	Nickoloff, J.A.//Chen, E.Y.//Heffron, F. 	A 23-base-pair DNA sequence from the MAT locus stimulates intergenic recombination in yeast.	Proc. Natl. Acad. Sci. U. S. A.	1986	83		7831-7835			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. 		
@D	Nie, H.//Yang, F.//Zhang, X.//Yang, J.//Chen, L.//Wang, J.//Xiong, Z.//Peng, J.//Sun, L.//Dong, J.//Xue, Y.//Xu, X.//Chen, S.//Yao, Z.//Shen, Y.//Jin, Q. 	Complete genome sequence of Shigella flexneri 5b and comparison with Shigella flexneri 2a.	BMC Genomics	2006	7		173			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. 		
@D	Nielsen, H.//Einvik, C.//Lentz, T.E.//Hedegaard, M.M.//Johansen, S.D. 	A conformational switch in the DiGIR1 ribozyme involved in release and folding of the downstream I-DirI mRNA.	RNA	2009	15		958-967			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. 		
@D	Nielsen, H.//Westhof, E.//Johansen, S. 	An mRNA is capped by a 2', 5' lariat catalyzed by a group I-like ribozyme.	Science	2005	309		1584-1587			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. 		
@D	Nielsen, M.//Schreiber, L.//Finster, K.//Schramm, A. 	Draft genome sequence of Bacillus azotoformans MEV2011, a (Co-) denitrifying strain unable to grow with oxygen.	Standards in Genomic Sciences	2014	9		23			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. 		
@D	Nielsen, M.//Schreiber, L.//Finster, K.//Schramm, A. 	Draft genome sequence of Bacillus azotoformans MEV2011, a (Co-) denitrifying strain unable to grow with oxygen.	Standards in Genomic Sciences	2015	10		4			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. 		
@D	Nielsen, P.E.//Egholm, M.//Berg, R.H.//Buchardt, O. 	Sequence-selective recognition of DNA by strand displacement with a Thymine-substituted polyamide.	Science	1991	254		1497-1500			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. 		
@D	Nielsen, P.E.//Egholm, M.//Berg, R.H.//Buchardt, O. 	Sequence specific inhibition of DNA restriction enzyme cleavage by PNA.	Nucleic Acids Res.	1993	21		197-200			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. 		
@D	Nielsen, T.K.//Kot, W.//Sorensen, S.R.//Hansen, L.H. 	Draft Genome Sequence of MCPA-Degrading Sphingomonas sp. Strain ERG5, Isolated from a Groundwater Aquifer in Denmark.	Genome Announcements	2015	3		e01529-14			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. 		
@D	Nielsen, T.K.//Sorensen, S.R.//Hansen, L.H. 	Draft Genome Sequence of Isoproturon-Mineralizing Sphingomonas sp. SRS2, Isolated from an Agricultural Field in the United Kingdom.	Genome Announcements	2015	3		e00569-15			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. 		
@D	Niemi, O.//Laine, P.//Koskinen, P.//Pasanen, M.//Pennanen, V.//Harjunpaa, H.//Nykyri, J.//Holm, L.//Paulin, L.//Auvinen, P.//Palva, E.T.//Pirhonen, M. 	Genome sequence of the model plant pathogen Pectobacterium carotovorum SCC1.	Standards in Genomic Sciences	2017	12		87			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. 		
@D	Nierman, W.C. et al. 	Structural flexibility in the Burkholderia mallei genome.	Proc. Natl. Acad. Sci. U. S. A.	2004	101		14246-14251			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. 		
@D	Nierman, W.C. et al. 	Complete genome sequence of Caulobacter crescentus.	Proc. Natl. Acad. Sci. U. S. A.	2001	98		4136-4141			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. 		
@D	Niharika, N.//Sangwan, N.//Ahmad, S.//Singh, P.//Khurana, J.P.//Lal, R. 	Draft Genome Sequence of Sphingobium chinhatense Strain IP26T, Isolated from a Hexachlorocyclohexane Dumpsite.	Genome Announcements	2013	1		e00680-13			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. 		
@D	Nikiforov, T.T.//Connolly, B.A. 	Oligodeoxynucleotides containing 4-thiothymidine and 6-thiodeoxyguanosine as affinity labels for the Eco RV restriction endonuclease and modification methylase.	Nucleic Acids Res.	1992	20		1209-1214			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. 		
@D	Nikitin, D.//Mokrishcheva, M.//Denjmukhametov, M.//Pertzev, A.//Zakharova, M.//Solonin, A. 	Construction of an overproducing strain, purification, and biochemical characterization of the 6His-Eco29kI restriction endonuclease.	Protein Expr. Purif.	2003	30		26-31			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. 		
@D	Nikitin, D.//Mokrishcheva, M.//Solonin, A. 	6His-Eco29kI methyltransferase methylation site and kinetic mechanism characterization.	Biochim. Biophys. Acta	2007	1774		1014-1019			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. 		
@A	Nikitin, D.V.//Kertesz-Farkas, A.//Solonin, A.S.//Mokrishcheva, M.L. 		Bifunctional prokaryotic DNA-methyltransferases.			Anica Dricu 		Methylation - from DNA, RNa and histones to diseases and treatment				Rijeka, Croatia	InTech	2012		0		71-87									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. 		
@D	Nikitin, D.V.//Mokrishcheva, M.L.//Solonin, A.S. 	Binding of DNA methyltransferase M.Ecl18 to operator-promoter region decreases its methylating activity.	Biokhimiia	2012	77		392-397			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. 		
@D	Nikitin, D.V.//Mokrishcheva, M.L.//Solonin, A.S. 	Binding of DNA methyltransferase M.Ecl18 to operator-promoter region decreases its methylating activity.	Biochemistry	2012	77		307-311			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. 		
@D	Nikitina, A.S.//Kharlampieva, D.D.//Babenko, V.V.//Shirokov, D.A.//Vakhitova, M.T.//Manolov, A.I.//Shkoporov, A.N.//Taraskina, A.E.//Manuvera, V.A.//Lazarev, V.N.//Kostryukova, E.S. 	Complete Genome Sequence of an Enterotoxigenic Bacteroides fragilis Clinical Isolate.	Genome Announcements	2015	3		e00450-15			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. 		
@D	Nikolaichik, Y.//Gorshkov, V.//Gogolev, Y.//Valentovich, L.//Evtushenkov, A. 	Genome Sequence of Pectobacterium atrosepticum Strain 21A.	Genome Announcements	2014	2		e00935-14			We report the annotated genome sequence of the enterobacterial plant pathogen Pectobacterium atrosepticum strain 21A, isolated in Belarus from potato stem with blackleg symptoms. 		
@D	Nikolajewa, S.//Byer, A.//Friedel, M.//Hollunder, J.//Wilhelm, T. 	Common patterns in type II restriction enzyme binding sites.	Nucleic Acids Res.	2005	33		2726-2733			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. 		
@D	Nikolskaya, I.//Lopatina, N.//Suchkov, S.//Kartashova, I.//Debov, S. 	Sequence Specificity of Isolated DNA-Cytosine Methylases from Shigella Sonnei 47 Cells.	Biochem. Int.	1984	9		771-781			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. 		
@D	Nikolskaya, I.//Tediashvili, M.//Lopatina, N.//Chanishvili, T.G.//Debov, S. 	Specificity and functions of guanine methylase of Shigella sonnei DDVI phage.	Biochim. Biophys. Acta	1979	561		232-239			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. 		
@D	Nikolskaya, I.I.//Aleksandrova, S.S.//Lopatina, N.G.//Debov, S.S. 	Fractionation and purification of DNA methylases and specific endonucleases from cells of Escherichia coli SK.	Biokhimiia	1977	42		598-608			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. 		
@D	Nikolskaya, I.I.//Aleksandrova, S.S.//Lopatina, N.G.//Debov, S.S. 	Fractionation and specificity of DNA methylases from the Escherichia coli SK cells.	Mol. Cell. Biochem.	1978	20		17-24			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. 		
@D	Nikolskaya, I.I.//Debov, S.S. 	Molecular and medical aspects of DNA modification.	Vestn. Akad. Med. Nauk SSSR	1987	0		23-29			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. 		
@D	Nikolskaya, I.I.//Karpetz, L.Z.//Kartashova, M.//Lopatina, N.G.//Skripkin, E.A.//Suchkov, S.V.//Uporova, T.M.//Gruber, I.M.//Debov, S.S. 	Enzymes of the new system of the host specificity Sso47II.	Mol. Gen. Mikrobiol. Virusol.	1983	0		5-10			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. 		
@D	Nikolskaya, I.I.//Lopatina, N.G.//Anikeicheva, N.V.//Debov, S.S. 	Determination of the recognition sites of cytosine DNA-methylases from Escherichia coli SK.	Nucleic Acids Res.	1979	7		517-528			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. 		
@D	Nikolskaya, I.I.//Lopatina, N.G.//Chaplygina, N.M.//Debov, S.S. 	The host specificity system in Escherichia coli SK.	Mol. Cell. Biochem.	1976	13		79-87			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. 		
@D	Nikolskaya, I.I.//Lopatina, N.G.//Debov, S.S. 	On heterogeneity of DNA methylases from Escherichia coli SK cells.	Mol. Cell. Biochem.	1981	35		3-10			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. 		
@D	Nikolskaya, I.I.//Lopatina, N.G.//Dedov, S.S. 	Some peculiarities of phage DDVI-specific methylases.	Biokhimiia	1977	42		828-832			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. 		
@D	Nikolskaya, I.I.//Lopatina, N.G.//Lopareva, E.N.//Posypanova, A.M.//Debov, S.S. 	Modifying methylase SsoI from Shigella sonnei 47 cells.	Mol. Gen. Mikrobiol. Virusol.	1988	10		26-30			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. 		
@D	Nikolskaya, I.I.//Lopatina, N.G.//Rekunova, V.N.//Yurkevich, A.M.//Debov, S.S. 	On the effect of S-nucleosyl homocysteines on activity of several DNA methylases.	Vopr. Med. Khim.	1978	24		252-255			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. 		
@D	Nikolskaya, I.I.//Lopatina, N.G.//Sharkova, E.V.//Suchkov, S.V.//Somodi, P.//Foldes, I.//Debov, S.S. 	Sequence specificity of isolated DNA-adenine methylases from Mycobacterium smegmatis (butyricum) and Shigella sonnei 47 cells.	Biochem. Int.	1985	10		405-413			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. 		
@D	Nikolskaya, I.I.//Sharkova, E.V.//Suchkov, S.V.//Karpets, L.Z.//Debov, S.S.//Somodi, P.//Foldes, I. 	Isoelectric focusing of bacterial DNA methylases.	Biochem. Int.	1983	7		605-615			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. 		
@D	Nikolskaya, I.I.//Sharkova, E.V.//Suchkov, S.V.//Lopatina, N.G.//Habar, K.//Somodi, P.//Foldes, I.//Debov, S.S. 	Factors of activation and stabilization of DNA-methylases from Shigella Sonnei 47 and Mycobacterium smegmatis butyricum cells.	Biochem. Int.	1987	15		127-138			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. 		
@D	Nikolskaya, I.I.//Tediashvili, M.G.//Vasileva, M.B.//Chanishvili, T.G.//Debov, S.S. 	System of host specificity and the DNA methylases of Shigellae and their phages.	Vopr. Virusol.	1978	6		724-731			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. 		
@D	Nikolskaya, I.I.//Tediashvili, M.I.//Chanishvili, T.G.//Debov, S.S. 	Investigation of methylation character and DNA methylases specificity in Shigella.	Biokhimiia	1978	43		1228-1232			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. 		
@D	Nikolskaya, I.I.//Uporova, T.M.//Tereshina, E.V.//Gruber, I.M.//Zhdanova, L.G.//Debov, S.S. 	Specificity and properties of DNA methylases in Shigella.	Vestn. Akad. Med. Nauk SSSR	1981	2		16-21			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. 		
@D	Nikolskaya, I.I.//Vanyushin, B.F.//Mardashev, S.R. 	Identification of DNA methylases in cells of Escherichia coli CK.	Biokhimiia	1975	40		1081-1086			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. 		
@D	Nilsson, M.-G.//Skarped, C.//Magnusson, G. 	Structure at restriction endonuclease MboI cleavage sites protected by actinomycin D or distamycin A.	FEBS Lett.	1982	145		360-364			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. 		
@D	Nirwan, N.//Singh, P.//Mishra, G.G.//Johnson, C.M.//Szczelkun, M.D.//Inoue, K.//Vinothkumar, K.R.//Saikrishnan, K. 	Hexameric assembly of the AAA+ protein McrB is necessary for GTPase activity.	Nucleic Acids Res.	2018						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. 		
@D	Nishi, S.//Tsubouchi, T.//Takaki, Y.//Koyanagi, R.//Satoh, N.//Maruyama, T.//Hatada, Y. 	Draft Genome Sequence of Loktanella cinnabarina LL-001T, Isolated from Deep-Sea Floor Sediment.	Genome Announcements	2013	1		e00927-13			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%. 		
@D	Nishibe, C.//Canevari, C.A.B.//Dalla, C.R.//Pinto, B.J.//Varuzza, L.//Cataldi, A.A.//Bernardelli, A.//Bigi, F.//Blanco, F.C.//Zumarraga, M.J.//Almeida, N.F.//Araujo, F.R. 	Draft Genome Sequence of Mycobacterium bovis 04-303, a Highly Virulent Strain from Argentina.	Genome Announcements	2013	1		e00931-13			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. 		
@D	Nishida, H. 	Genome DNA Sequence Variation, Evolution, and Function in Bacteria and Archaea.	Curr. Issues Mol. Biol.	2013	15		19-24			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. 		
@D	Nishigaki, K.//Kaneko, Y.//Wakuda, H.//Husimi, Y.//Tanaka, T. 	Type II restriction endonucleases cleave single-stranded DNAs in general.	Nucleic Acids Res.	1985	13		5747-5759			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. 		
@D	Nishikawa, S.//Ogawa, Y.//Eguchi, M.//Rambukkana, A.//Shimoji, Y. 	Draft Genome Sequences of Lawsonia intracellularis Swine Strains Causing Proliferative Enteropathy in Japan.	Microbiol. Resour. Announc.	2018	7		e01021-18			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. 		
@D	Nishiki, I.//Oinaka, D.//Iwasaki, Y.//Yasuike, M.//Nakamura, Y.//Yoshida, T.//Fujiwara, A.//Nagai, S.//Katoh, M.//Kobayashi, T. 	Complete Genome Sequence of Nonagglutinating Lactococcus garvieae Strain 122061 Isolated from Yellowtail in Japan.	Genome Announcements	2016	4		e00592-16			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. 		
@D	Nishimura, Y.//Tsuboi, M. 	A possible correlation between DNA conformation and the mode of action of restriction enzymes.	J. Biochem. (Tokyo)	1984	96		1807-1811			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. 		
@D	Nishio, Y.//Nakamura, Y.//Kawarabayasi, Y.//Usuda, Y.//Kimura, E.//Sugimoto, S.//Matsui, K.//Yamagishi, A.//Kikuchi, H.//Ikeo, K.//Gojobori, T. 	Comparative complete genome sequence analysis of the amino acid replacements responsible for the thermostability of Corynebacterium efficiens.	Genome Res.	2003	13		1572-1579			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. 		
@D	Nishioka, M.//Fujiwara, S.//Takagi, M.//Imanaka, T. 	Characterization of two intein homing endonucleases encoded in the DNA polymerase gene of Pyrococcus kodakaraensis strain KOD1.	Nucleic Acids Res.	1998	26		4409-4412			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. 		
@D	Nishiyama, R.//Ito, M.//Yamaguchi, Y.//Koizumi, N.//Sano, H. 	Correlation between maternal inheritance of chloroplast genes and a chloroplast-resident DNA methyltransferase in the green alga, Chlamydomonas reinhardtii.	Plant Cell Physiol.	2002	43		s32			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. 		
@D	Nishiyama, R.//Ito, M.//Yamaguchi, Y.//Koizumi, N.//Sano, H. 	A chloroplast-resident DNA methyltransferase is responsible for hypermethylation of chloroplast genes in Chlamydomonas maternal gametes.	Proc. Natl. Acad. Sci. U. S. A.	2002	99		5925-5930			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. 		
@D	Nishiyama, R.//Wada, Y.//Mibu, M.//Yamaguchi, Y.//Shimogawara, K.//Sano, H. 	Role of a nonselective de novo DNA methyltransferase in maternal inheritance of chloroplast genes in the green alga, Chlamydomonas  reinhardtii.	Genetics	2004	168		809-816			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. 		
@D	Nishizawa, A.//Arshad, A.B.//Nishizawa, T.//Asayama, M.//Fujii, K.//Nakano, T.//Harada, K.//Shirai, M. 	Cloning and characterization of a new hetero-gene cluster of nonribosomal peptide synthetase and polyketide synthase from the cyanobacterium Microcystis aeruginosa K-139.	J. Gen. Appl. Microbiol.	2007	53		17-27			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. 		
@D	Nishizawa, T.//Hanami, T.//Hirano, E.//Miura, T.//Watanabe, Y.//Takanezawa, A.//Komatsuzaki, M.//Ohta, H.//Shirai, M.//Asayama, M. 	Isolation and Molecular Characterization of a Multicellular Cyanobacterium, Limnothrix/Pseudanabaena sp Strain ABRG5-3.	Biosci. Biotechnol. Biochem.	2010	74		1827-1835			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. 		
@D	Nishizawa, T.//Miura, T.//Harada, C.//Guo, Y.//Narisawa, K.//Ohta, H.//Takahashi, H.//Shirai, M. 	Complete Genome Sequence of Streptomyces parvulus 2297, Integrating Site-Specifically with Actinophage R4.	Genome Announcements	2016	4		e00875-16			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. 		
@D	Nishizawa, T.//Tago, K.//Oshima, K.//Hattori, M.//Ishii, S.//Otsuka, S.//Senoo, K. 	Complete Genome Sequence of the Denitrifying and N2O-Reducing Bacterium Azoarcus  sp. Strain KH32C.	J. Bacteriol.	2012	194		1255			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. 		
@D	Niu, B.//Kolter, R. 	Complete Genome Sequences of Seven Strains Composing a Model Bacterial Community  of Maize Roots.	Genome Announcements	2017	5		e00997-17			Previously, we assembled a model bacterial community of maize roots. Here, we report the complete genome sequences of the seven strains composing the community. 		
@D	Niu, B.//Rueckert, C.//Blom, J.//Wang, Q.//Borriss, R. 	The Genome of the Plant Growth-Promoting Rhizobacterium Paenibacillus polymyxa M-1 Contains Nine Sites Dedicated to Nonribosomal Synthesis of  Lipopeptides and Polyketides.	J. Bacteriol.	2011	193		5862-5863			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. 		
@D	Niu, Y.//Tenney, K.//Li, H.//Gimble, F.S. 	Engineering Variants of the I-SceI Homing Endonuclease with Strand-specific and Site-specific DNA-nicking Activity.	J. Mol. Biol.	2008	382		188-202			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. 		
@D	Niv, M.Y.//Ripoll, D.R.//Vila, J.A.//Liwo, A.//Vanamee, E.S.//Aggarwal, A.K.//Weinstein, H.//Scheraga, H.A. 	Topology of Type II REases revisited; structural classes and the common conserved core.	Nucleic Acids Res.	2007	35		2227-2237			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. 		
@D	Niv, M.Y.//Skrabanek, L.//Roberts, R.J.//Scheraga, H.A.//Weinstein, H. 	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.	Proteins	2008	71		631-640			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. 		
@D	Niza, B.//Merfa, M.V.//Alencar, V.C.//Menegidio, F.B.//Nunes, L.R.//Machado, M.A.//Takita, M.A.//de Souza, A.A. 	Draft Genome Sequence of 11399, a Transformable Citrus-Pathogenic Strain of Xylella fastidiosa.	Genome Announcements	2016	4		e01124-16			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. 		
@A	Nkenfou, C. 		Cloning and studying of the cleavage flexibility of some type IIs  restriction endonucleases.			 		Ph.D. Thesis, University of Yaounde I, Cameroon				Yaounde		2002				1-226									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. 		
@D	Noar, J.//Makwana, S.T.//Bruno-Barcena, J.M. 	Complete Genome Sequence of Solvent-Tolerant Clostridium beijerinckii Strain SA-1.	Genome Announcements	2014	2		e01310-14			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. 		
@D	Noar, J.D.//Bruno-Barcena, J.M. 	Complete Genome Sequences of Azotobacter vinelandii Wild-Type Strain CA and Tungsten-Tolerant Mutant Strain CA6.	Genome Announcements	2013	1		e00313-13			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. 		
@D	Nobbs, T.F.//Wentzell, L.M.//Szczelkum, M.D.//Halford, S.E. 	SfiI: An unconventional restriction enzyme.	The NEB Transcript	1997	8		10-11			Abrief review of SfiI 		
@D	Nobbs, T.J.//Halford, S.E. 	DNA cleavage at two recognition sites by the SfiI restriction endonuclease: Salt dependence of Cis and Trans interactions between distant DNA sites.	J. Mol. Biol.	1995	252		399-411			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. 		
@D	Nobbs, T.J.//Szczelkun, M.D.//Wentzell, L.M.//Halford, S.E. 	DNA excision by the SfiI restriction endonuclease.	J. Mol. Biol.	1998	281		419-432			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. 		
@D	Nobbs, T.J.//Williams, S.A.//Connolly, B.A.//Halford, S.E. 	Phosphorothioate substrates for the SfiI restriction endonuclease.	Biol. Chem.	1998	379		599-604			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. 		
@D	Nobile, C. 	An improved method for partial restriction digestion of ultraviolet irradiated DNA.	Nucleic Acids Res.	1990	18		4288			None 		
@D	Nobu, M.K.//Narihiro, T.//Tamaki, H.//Qiu, Y.L.//Sekiguchi, Y.//Woyke, T.//Goodwin, L.//Davenport, K.W.//Kamagata, Y.//Liu, W.T. 	Draft Genome Sequence of Syntrophorhabdus aromaticivorans Strain UI, a Mesophilic Aromatic Compound-Degrading Syntroph.	Genome Announcements	2014	2		e01064-13			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%. 		
@D	Nobusato, A.//Uchiyama, I.//Kobayashi, I. 	Diversity of restriction-modification gene homologues in Helicobacter pylori.	Gene	2000	259		89-98			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. 		
@D	Nobusato, A.//Uchiyama, I.//Ohashi, S.//Kobayashi, I. 	Insertion with long target duplication: a mechanism for gene mobility suggested from comparison of two related bacterial genomes.	Gene	2000	259		99-108			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. 		
@D	Noda, M.//Shiraga, M.//Kumagai, T.//Danshiitsoodol, N.//Sugiyama, M. 	Characterization of the SN35N Strain-Specific Exopolysaccharide Encoded in the Whole Circular Genome of a Plant-Derived Lactobacillus plantarum.	Biol. Pharm. Bull.	2018	41		536-545			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. 		
@D	Noda, M.//Sugimoto, S.//Hayashi, I.//Danshiitsoodol, N.//Fukamachi, M.//Sugiyama, M. 	A novel structure of exopolysaccharide produced by a plant-derived lactic acid bacterium Lactobacillus paracasei IJH-SONE68.	J. Biochem. (Tokyo)	2018	164		87-92			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. 		
@D	Noda, S.//Aihara, C.//Yuki, M.//Ohkuma, M. 	Draft Genome Sequence of Lactococcus sp. Strain NtB2 (JCM 32569), Isolated from the Gut of the Higher Termite Nasutitermes takasagoensis.	Genome Announcements	2018	6		e00445-18			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. 		
@D	Noel, A.J.//Wende, W.//Pingoud, A. 	DNA recognition by the homing endonuclease PI-SceI involves a divalent metal ion cofactor-induced conformational change.	J. Biol. Chem.	2004	279		6794-6804			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. 		
@D	Noel, S.J.//Hojberg, O.//Urich, T.//Poulsen, M. 	Draft Genome Sequence of 'Candidatus Methanomethylophilus' sp. 1R26, Enriched from Bovine Rumen, a Methanogenic Archaeon Belonging to the  Methanomassiliicoccales Order.	Genome Announcements	2016	4		e01734-15			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. 		
@D	Nogami, S.//Fukuda, T.//Nagai, Y.//Yabe, S.//Sugiura, M.//Mizutani, R.//Satow, Y.//Anraku, Y.//Ohya, Y. 	Homing at an extragenic locus mediated by VDE (PI-Scel) in  Saccharomyces cerevisiae.	Yeast	2002	19		773-782			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. 		
@D	Noh, Y.//Kim, S.Y.//Lee, Y.S.//Kim, D.W.//Kwon, T.//Hwang, K.J. 	Whole-Genome Sequence of Borrelia garinii Strain 935T Isolated from Ixodes persulcatus in South Korea.	Genome Announcements	2014	2		e01298-14			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. 		
@D	Nolan, M. et al. 	Complete genome sequence of Rhodothermus marinus type strain (R-10).	Standards in Genomic Sciences	2009	1		283-290			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. 		
@D	Nolan, M. et al. 	Complete genome sequence of Streptosporangium roseum type strain (NI 9100).	Standards in Genomic Sciences	2010	2		29-37			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. 		
@D	Nolan, M. et al. 	Complete genome sequence of Streptobacillus moniliformis type strain (9901).	Standards in Genomic Sciences	2009	1		300-307			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. 		
@D	Nolan, M. et al. 	Complete genome sequence of Ferrimonas balearica type strain (PAT).	Standards in Genomic Sciences	2010	3		174-182			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. 		
@D	Noll, L.W.//Worley, J.N.//Yang, X.//Shridhar, P.B.//Bai, J.//Meng, J.//Caragea, D.//Nagaraja, T.G. 	Draft Genome Sequences of Enterohemorrhagic Escherichia coli O103:H2 Strains Isolated from Feces of Feedlot Cattle.	Genome Announcements	2017	5		e00094-17			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. 		
@D	Noll, L.W.//Worley, J.N.//Yang, X.//Shridhar, P.B.//Bai, J.//Meng, J.//Caragea, D.//Nagaraja, T.G. 	Draft Genome Sequences of Enteropathogenic Escherichia coli O103 Strains Isolated from Feces of Feedlot Cattle.	Genome Announcements	2017	5		e00387-17			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. 		
@D	Nolling, J. et al. 	Genome sequencing and comparative analysis of the solvent-producing bacterium Clostridium acetobutylicum.	J. Bacteriol.	2001	183		4823-4838			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. 		
@D	Nolling, J.//de Vos, W.M. 	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.	J. Bacteriol.	1992	174		5719-5726			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. 		
@D	Nolling, J.//de Vos, W.M. 	Identification of the CTAG-recognizing restriction-modification systems MthZI and MthFI from Methanobacterium thermoformicicum and characterization of the plasmid-encoded mthZIM gene.	Nucleic Acids Res.	1992	20		5047-5052			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. 		
@D	Nolling, J.//Groffen, A.//De Vos, W.M. 	PhiF1 and PhiF3, two novel virulent, archaeal phages infecting different thermophilic strains of the genus Methanobacterium.	J. Gen. Microbiol.	1993	139		2511-2516			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. 		
@D	Nolling, J.//Van Eeden, J.M.//Eggen, R.I.L.//de Vos, W.M. 	Modular organization of related Archaeal plasmids encoding different restriction-modification systems in Methanobacterium thermoformicicum.	Nucleic Acids Res.	1992	20		6501-6507			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. 		
@D	Nomura, N.//Morinaga, Y.//Shirai, N.//Sako, Y. 	I-Apel: A novel intron-encoded LAGLIDADG homing endonuclease from the archaeon, Aeropyrum pernix K1.	Nucleic Acids Res.	2005	33		5017			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. 		
@D	Nomura, N.//Nomura, Y.//Sussman, D.//Klein, D.//Stoddard, B.L. 	Recognition of a common rDNA target site in archaea and eukarya by analogous LAGLIDADG and His-Cys box homing endonucleases.	Nucleic Acids Res.	2008	36		6988-6998			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. 		
@D	Nomura, W.//Barbas, C.F. III 	In Vivo Site-Specific DNA Methylation with a Designed Sequence-Enabled DNA Methylase.	J. Am. Chem. Soc.	2007	129		8676-8677			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. 		
@D	Nomura, W.//Masuda, A.//Tamamura, H. 	Development of site-specific DNA methylase for epigenetic regulation of gene expression.	Seikagaku	2010	82		393-397					
@D	Nomura, W.//Tamamura, H.//Barbas, C.F. III 	Site-selective cytosine methylation by a split DNA methylase.	Pept. Sci.	2009	45		491-492			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. 		
@D	Nomura, Y.//Ishino, Y.//Kimizuka, F.//Kato, I. 	A novel Streptomyces restriction endonuclease, Sse1825I, cleaving at 5'-GG/GWCCC-3'.	Gene	1995	157		323-324			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. 		
@D	Nomura, Y.//Kotani, H.//Kita, K.//Sadaoka, A.//Hiraoka, N.//Nakamura, T.//Abe, N.//Izaki, K. 	Purification and properties of a new restriction endonuclease, MxaI, from Myxococcus xanthus F18E.	Agric. Biol. Chem.	1990	54		3011-3012			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. 		
@D	Nonaka, H.//Keresztes, G.//Shinoda, Y.//Ikenaga, Y.//Abe, M.//Naito, K.//Inatomi, K.F.K.//Inui, M.//Yukawa, H. 	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.	J. Bacteriol.	2006	188		2262-2274			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. 		
@D	Noom, M.C.//van den Broek, B.//Wuite, G.J.L. 	Direct observation of the searching mechanism of restriction enzymes using multiple optical traps.	Biophys. J.	2003	84		304a			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. 		
@D	Noor, Y.M.//Samsulrizal, N.H.//Jema'on, N.A.//Low, K.O.//Ramli, A.N.//Alias, N.I.//Damis, S.I.//Fuzi, S.F.//Isa, M.N.//Murad, A.M.//Raih, M.F.//Bakar, F.D.//Najimudin, N.//Mahadi, N.M.//Illias, R.M. 	A comparative genomic analysis of the alkalitolerant soil bacterium Bacillus lehensis G1.	Gene	2014	545		253-261			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. 		
@D	Noorian, P.//Sun, S.//McDougald, D. 	Complete Genome Sequence of Oyster Isolate Vibrio vulnificus Env1.	Genome Announcements	2018	6		e00421-18			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. 		
@D	Nord, D.//Sjoberg, B.M. 	Unconventional GIY-YIG homing endonuclease encoded in group I introns in closely related strains of the Bacillus cereus group.	Nucleic Acids Res.	2008	36		300-310			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. 		
@D	Nord, D.//Torrents, E.//Sjoberg, B.M. 	A Functional Homing Endonuclease in the Bacillus anthracis nrdE Group I Intron.	J. Bacteriol.	2007	189		5293-5301			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. 		
@D	Nordlund, T.M.//Andersson, S.//Nilsson, L.//Rigler, R. 	Structure and dynamics of a fluorescent DNA oligomer containing the EcoRI recognition sequence: fluorescence, molecular dynamics, and NMR studies.	Biochemistry	1989	28		9095-9103			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. 		
@D	Norlander, L.//Davies, J.K.//Hagblom, P.//Normark, S. 	Deoxyribonucleic acid modifications and restriction endonuclease production in Neisseria gonorrhoeae.	J. Bacteriol.	1981	145		788-795			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. ] 		
@D	Norman, A.//Ciofu, O.//Amador, C.I.//Hoiby, N.//Jelsbak, L. 	Genome Sequence of Pseudomonas aeruginosa Strain DK1-NH57388A, a Stable Mucoid Cystic Fibrosis Isolate.	Genome Announcements	2016	4		e00008-16			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. 		
@D	Normand, P.//Gury, J.//Pujic, P.//Chouaia, B.//Crotti, E.//Brusetti, L.//Daffonchio, D.//Vacherie, B.//Barbe, V.//Medigue, C.//Calteau, A.//Ghodhbane-Gtari, F.//Essoussi, I.//Nouioui, I.//Abbassi-Ghozzi, I.//Gtari, M. 	Genome Sequence of Radiation-Resistant Modestobacter marinus Strain BC501, a Representative Actinobacterium That Thrives on Calcareous Stone Surfaces.	J. Bacteriol.	2012	194		4773-4774			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. 		
@D	Norton Hughes, C.A.//Johnson, R.C. 	Identification of a DNA methylase gene homologue in Borrelia burgdorferi.	Abstr. Gen. Meet. Am. Soc. Microbiol.	1994	94		125			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.
 
 		
@D	Nosikov, V.V.//Braga, E.A.//Karlishev, A.V.//Zhuze, A.L.//Polyanovsky, O.L. 	Protection of particular cleavage sites of restriction endonucleases by distamycin A and actinomycin D.	Nucleic Acids Res.	1976	3		2293-2301			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. 		
@D	Nosikov, V.V.//Sain, B. 	Protection of particular endonuclease R.HindIII cleavage sites by distamycin A, propyl-distamycin and netropsin.	Nucleic Acids Res.	1977	4		2263-2273			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. 		
@D	Notani, N.K.//Setlow, J.K. 	Molecular events accompanying the fixation of genetic information in Haemophilus heterospecific transformation.	J. Bacteriol.	1972	112		751-760			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. 		
@D	Noto, J.M.//Chopra, A.//Loh, J.T.//Romero-Gallo, J.//Piazuelo, M.B.//Watson, M.//Leary, S.//Beckett, A.C.//Wilson, K.T.//Cover, T.L.//Mallal, S.//Israel, D.A.//Peek, R.M. 	Pan-genomic analyses identify key Helicobacter pylori pathogenic loci modified by carcinogenic host microenvironments.	Gut	2017	67		1793-1804			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. 		
@D	Noto, M.J.//Kreiswirth, B.N.//Monk, A.B.//Archer, G.L. 	Gene acquisition at the insertion site for SCCmec, the genomic island conferring methicillin resistance in Staphylococcus aureus.	J. Bacteriol.	2008	190		1276-1283			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. 		
@D	Nou, X.//Skinner, B.//Braaten, B.//Blyn, L.//Hirsch, D.//Low, D. 	Regulation of pyelonephritis-associated pili phase-variation in Excherichia coli: binding of the PapI and the Lrp regulatory proteins is controlled by DNA methylation.	Mol. Microbiol.	1993	7		545-553			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. 		
@D	Nouioui, I. et al. 	Draft Genome Sequence of Frankia sp. Strain BMG5.12, a Nitrogen-Fixing Actinobacterium Isolated from Tunisian Soils.	Genome Announcements	2013	1		e00468-13			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. 		
@D	Nouioui, I.//Goker, M.//Carro, L.//Montero-Calasanz, M.D.//Rohde, M.//Woyke, T.//Kyrpides, N.C.//Klenk, H.P. 	High quality draft genome of Nakamurella lactea type strain, a rock actinobacterium, and emended description of Nakamurella lactea.	Standards in Genomic Sciences	2017	12		4			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. 		
@D	Nouioui, I.//Gtari, M.//Goker, M.//Ghodhbane-Gtari, F.//Tisa, L.S.//Fernandez, M.P.//Normand, P.//Huntemann, M.//Clum, A.//Pillay, M.//Varghese, N.//Reddy, T.B.//Ivanova, N.//Woyke, T.//Kyrpides, N.C.//Klenk, H.P. 	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.	Genome Announcements	2016	4		e00437-16			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). 		
@D	Novakova, E.//Hypsa, V.//Nguyen, P.//Husnik, F.//Darby, A.C. 	Genome sequence of Candidatus Arsenophonus lipopteni, the exclusive symbiont of a blood sucking fly Lipoptena cervi (Diptera: Hippoboscidae).	Standards in Genomic Sciences	2016	11		72			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. 		
@D	Novikov, A.D.//Lavrov, K.V.//Kasianov, A.S.//Gerasimova, T.V.//Yanenko, A.S. 	Draft Genome Sequence of Rhodococcus sp. Strain M8, Which Can Degrade a Broad Range of Nitriles.	Genome Announcements	2018	6		e01526-17			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. 		
@D	Novinscak, A.//Gadkar, V.J.//Joly, D.L.//Filion, M. 	Complete Genome Sequence of Pseudomonas brassicacearum LBUM300, a Disease-Suppressive Bacterium with Antagonistic Activity toward Fungal, Oomycete,  and Bacterial Plant Pathogens.	Genome Announcements	2016	4		e01623-15			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. 		
@D	Nowak, A.//Kur, J.//Gospodarek, E.//Bielawski, K. 	Characterization of restriction endonuclease AjoI from Acinetobacter johnsonii.	FEMS Microbiol. Lett.	1994	117		97-102			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. 		
@D	Nowrousian, M.//Stajich, J.E.//Chu, M.//Engh, I.//Espagne, E.//Halliday, K.//Kamerewerd, J.//Kempken, F.//Knab, B.//Kuo, H.C.//Osiewacz, H.D.//Poggeler, S.//Read, N.D.//Seiler, S.//Smith, K.M.//Zickler, D.//Kuck, U.//Freitag, M. 	De novo assembly of a 40 Mb eukaryotic genome from short sequence reads: Sordaria macrospora, a model organism for fungal morphogenesis.	PLoS Genet.	2010	6		E1000891			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. 		
@D	Noy-Malka, C.//Yaari, R.//Itzhaki, R.//Mosquna, A.//Gershovitz, N.A.//Katz, A.//Ohad, N. 	A single CMT methyltransferase homolog is involved in CHG DNA methylation and development of Physcomitrella patens.	Plant Mol. Biol.	2014	84		719-735			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. 		
@D	Noyer-Weidner, M. 	A novel mcrB-based Escherichia coli K-12 vector system and its use in analyzing the genetic determinants for the McrB nuclease.	Gene	1988	74		177-178			Meeting Abstract 		
@D	Noyer-Weidner, M.//Diaz, R.//Reiners, L. 	Cytosine-specific DNA modification interferes with plasmid establishement in Escherichia coli K12:  Involvement of rgl B.	Mol. Gen. Genet.	1986	205		469-475			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. 		
@D	Noyer-Weidner, M.//Jentsch, S.//Kupsch, J.//Bergbauer, M.//Trautner, T.A. 	DNA methyltransferase genes of Bacillus subtilis phages: structural relatedness and gene expression.	Gene	1985	35		143-150			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. 		
@D	Noyer-Weidner, M.//Jentsch, S.//Pawlek, B.//Gunthert, U.//Trautner, T.A. 	Restriction and modification in Bacillus subtilis: DNA methylation potential of the related bacteriophages Z, SPR, SPbeta, Phi3T, and Rho11.	J. Virol.	1983	46		446-453			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. 		
@D	Noyer-Weidner, M.//Pawlek, B.//Jentsch, S.//Gunthert, U.//Trautner, T.A. 	Restriction and modification in Bacillus subtilis: gene coding for a BsuR-specific modification methyltransferase in the temperate bacteriophage Phi3T.	J. Virol.	1981	38		1077-1080			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. 		
@D	Noyer-Weidner, M.//Reiners-Schramm, L. 	Highly efficient positive selection of recombinant plasmids using a novel rglB-based Escherichia coli K-12 vector system.	Gene	1988	66		269-278			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. 		
@A	Noyer-Weidner, M.//Trautner, T.A. 		Methylation of DNA in prokaryotes.			Jost, J.P.//Saluz, H.P. 		DNA Methylation: Molecular Biology and Biological Significance				Basel	Birkhauser Verlag	1993		0		39-108									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. 		
@D	Noyer-Weidner, M.//Walter, J.//Terschuren, P.-A.//Chai, S.//Trautner, T.A. 	M.Phi3TII: a new monospecific DNA (cytosine-C5) methyltransferase with pronounced amino acid sequence similarity to a family of adenine-N6-DNA-methyltransferases.	Nucleic Acids Res.	1994	22		4066-4072			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. 		
@D	Noyer-Weidner, M.//Walter, J.//Terschuren, P.-A.//Chai, S.//Trautner, T.A. 	M.Phi3TII: a new monospecific DNA (cytosine-C5) methyltransferase with pronounced amino acid sequence similarity to a family of adenine-N6-DNA-methyltransferases.	Nucleic Acids Res.	1994	22		5517-5523			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. 		
@D	Ntougias, S.//Lapidus, A.//Copeland, A.//Reddy, T.B.//Pati, A.//Ivanova, N.N.//Markowitz, V.M.//Klenk, H.P.//Woyke, T.//Fasseas, C.//Kyrpides, N.C.//Zervakis, G.I. 	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.	Standards in Genomic Sciences	2015	10		52			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. 		
@D	Ntougias, S.//Lapidus, A.//Han, J.//Mavromatis, K.//Pati, A.//Chen, A.//Klenk, H.P.//Woyke, T.//Fasseas, C.//Kyrpides, N.C.//Zervakis, G.I. 	High quality draft genome sequence of Olivibacter sitiensis type strain (AW-6(T)), a diphenol degrader with genes involved in the catechol pathway.	Standards in Genomic Sciences	2014	9		783-793			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. 		
@D	Nunes, A.//Rocha, R.//Vale, F.F.//Vieira, L.//Sampaio, D.A.//Dias, R.//Gomes, J.P.//Oleastro, M. 	Genome Sequencing of 10 Helicobacter pylori Pediatric Strains from Patients with  Nonulcer Dyspepsia and Peptic Ulcer Disease.	Genome Announcements	2015	3		e01488-14			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. 		
@D	Nunoura, T.//Takaki, Y.//Kakuta, J.//Nishi, S.//Sugahara, J.//Kazama, H.//Chee, G.J.//Hattori, M.//Kanai, A.//Atomi, H.//Takai, K.//Takami, H. 	Insights into the evolution of Archaea and eukaryotic protein modifier systems revealed by the genome of a novel archaeal group.	Nucleic Acids Res.	2011	39		3204-3223			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. 		
@D	Nunvar, J.//Elhottova, D.//Chronakova, A.//Schneider, B.//Licha, I. 	Draft Genome Sequence of Stenotrophomonas maltophilia Strain 5BA-I-2, a Soil Isolate and a Member of a Phylogenetically Basal Lineage.	Genome Announcements	2014	2		e00134-14			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. 		
@D	Nur, I.//Szyf, M.//Razin, A.//Glaser, G.//Rottem, S.//Razin, S. 	Procaryotic and Eucaryotic Traits of DNA Methylation in Spiroplasmas (Mycoplasmas).	J. Bacteriol.	1985	164		19-24			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. 		
@D	Nurjadi, D.//Boutin, S.//Dalpke, A.//Heeg, K.//Zanger, P. 	Draft Genome Sequence of Staphylococcus aureus Strain HD1410, Isolated from a Persistent Nasal Carrier.	Genome Announcements	2018	6		e00411-18			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. 		
@D	Nurminsky, D.I.//Hartl, D.L. 	Design of compact multiple cloning sites.	Biotechniques	1993	15		209-213			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. 		
@D	Nutter, R.L.//Bullas, L.R.//Siapco, B.J.//Pearson, C. 	The role of methylation in host-induced modification of Salmonella bacteriophage P3.	Bacteriol. Proc.	1971	71		196			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%. 		
@D	Nutter, R.L.//Bullas, L.R.//Siapco, B.S.//Pearson, C.A. 	Change in methylation of Salmonella bacteriophage P3 deoxyribonucleic acid with host-controlled modification by Escherichia coli.	J. Virol.	1972	10		560-562			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. 		
@D	Nwaiwu, O.//Moura, A.//Thouvenot, P.//Rees, C.//Leclercq, A.//Lecuit, M. 	Draft Genome Sequences of Listeria monocytogenes, Isolated from Fresh Leaf Vegetables in Owerri City, Nigeria.	Genome Announcements	2017	5		e00354-17			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). 		
@D	Nwankwo, D.//Wilson, G. 	Cloning of two type II methylase genes that recognise asymmetric nucleotide sequences:  FokI and HgaI.	Mol. Gen. Genet.	1987	209		570-574			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. 		
@D	Nwankwo, D.O. 	Cloning of a pair of genes encoding isoschizomeric restriction endonucleases from Bacillus species: the BspEI and BspMII restriction and modification systems.	Gene	1995	157		31-35			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. 		
@D	Nwankwo, D.O.//Lynch, J.J.//Moran, L.S.//Fomenkov, A.//Slatko, B.E. 	The XmnI restriction-modification system: cloning, expression, sequence organization and similarity between the R and M genes.	Gene	1996	173		121-127			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. 		
@D	Nwankwo, D.O.//Maunus, R.E.//Xu, S.-Y. 	Cloning and expression of AatII restriction-modification system.	Gene	1997	185		105-109			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. 		
@D	Nwankwo, D.O.//Moran, L.S.//Slatko, B.E.//Waite-Rees, P.A.//Dorner, L.F.//Benner, J.S.//Wilson, G.G. 	Cloning, analysis and expression of the HindIII R-M-encoding genes.	Gene	1994	150		75-80			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. 		
@D	Nwankwo, D.O.//Wilson, G.G. 	Cloning and expression of the MspI restriction and modification genes.	Gene	1988	64		1-8			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. 		
@D	Nwosu, V.U. 	Overexpression of the wild-type gene coding for Escherichia coli DNA adenine methylase (dam).	Biochem. J.	1992	283		745-750			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. 		
@D	Nwosu, V.U.//Connolly, B.A.//Halford, S.E.//Garnett, J. 	The cloning, purification and characterization of the EcoRV modification methylase.	Nucleic Acids Res.	1988	16		3705-3720			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. 		
@D	Nyarko, E.//Tabata, M.//Watanabe, K. 	Enhanced DNA cleavage by mercury(II) porphyrin at a low concentration of HaeIII restriction enzyme.	Chem. Lett.	2001	0		932-933			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. 		
@D	Nye, T.M.//Schroeder, J.W.//Kearns, D.B.//Simmons, L.A. 	Complete Genome Sequence of Undomesticated Bacillus subtilis Strain NCIB 3610.	Genome Announcements	2017	5		e00364-17			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. 		
@D	Nyengaard, N.//Vogensen, F.K.//Josephsen, J. 	Restriction-modification systems in Lactococcus lactis.	Gene	1995	157		13-18			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. 		
@D	Nyengaard, N.//Vogensen, F.K.//Josephsen, J. 	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'.	Gene	1993	136		371-372			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. 		
@D	Nyengaard, N.R.//Falkenberg-Klok, J.//Josephsen, J. 	Cloning and analysis of the restriction-modification system LlaBI, a bacteriophage resistance system from Lactococcus lactis subsp. cremoris W56.	Appl. Environ. Microbiol.	1996	62		3494-3498			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. 		
@D	Nyyssonen, M.//Tran, H.M.//Karaoz, U.//Weihe, C.//Hadi, M.Z.//Martiny, J.B.//Martiny, A.C.//Brodie, E.L. 	Coupled high-throughput functional screening and next generation sequencing for identification of plant polymer decomposing enzymes in metagenomic libraries.	Front. Microbiol.	2013	4		282			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. 		
@D	O'Brien, K.//Perron, G.G.//Jude, B.A. 	Draft Genome Sequence of a Red-Pigmented Janthinobacterium sp. Native to the Hudson Valley Watershed.	Genome Announcements	2018	6		e01429-17			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. 		
@D	O'Callaghan, A.//Bottacini, F.//O'Connell-Motherway, M.//van Sinderen, D. 	Pangenome analysis of Bifidobacterium longum and site-directed mutagenesis through by-pass of restriction-modification systems.	BMC Genomics	2015	16		832			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. 		
@D	O'Callaghan, A.//Hilliard, A.//Morgan, C.A.//Culligan, E.P.//Leong, D.//DeLappe, N.//Hill, C.//Jordan, K.//Cormican, M.//Gahan, C.G.M. 	Draft Genome Sequences of 25 Listeria monocytogenes Isolates Associated with Human Clinical Listeriosis in Ireland.	Genome Announcements	2017	5		e00184-17			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. 		
@D	O'Connell-Motherway, M. et al. 	Functional genome analysis of Bifidobacterium breve UCC2003 reveals type IVb tight adherence (Tad) pili as an essential and conserved host-colonization factor.	Proc. Natl. Acad. Sci. U. S. A.	2011	108		11217-11222			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. 		
@D	O'Connell-Motherway, M.//O'Driscoll, J.//Fitzgerald, G.F.//van Sinderen, D. 	Overcoming the restriction barrier to plasmid transformation and targeted mutagenesis in Bifidobacterium breve UCC2003.	Micro. Biotech.	2009	2		321-332			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. 		
@D	O'Connell-Motherway, M.//Watson, D.//Bottacini, F.//Clark, T.A.//Roberts, R.J.//Korlach, J.//Garault, P.//Chervaux, C.//van-Hylckama-Vlieg, J.E.//Smokvina, T.//van-Sinderen, D. 	Identification of Restriction-Modification Systems of Bifidobacterium animalis subsp. lactis CNCM I-2494 by SMRT Sequencing and Associated Methylome Analysis.	PLoS ONE	2014	9		e94875			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. 		
@D	O'Connor, B.R.//Perry, B.J.//Yost, C.K. 	Draft Genome Sequence of Rheinheimera sp. KL1, Isolated from a Freshwater Lake in Southern Saskatchewan, Canada.	Genome Announcements	2015	3		e01177-15			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. 		
@D	O'Connor, C.D.//Humphreys, G.O. 	Expression of the EcoRI restriction-modification system and the construction of positive-selection cloning vectors.	Gene	1982	20		219-229			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. 		
@D	O'Connor, C.D.//Metcalf, E.//Wrighton, C.J.//Harris, T.J.R.//Saunders, J.R. 	RsrII - a novel restriction endonuclease with a heptanucleotide recognition site.	Nucleic Acids Res.	1984	12		6701-6708			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. 		
@D	O'Connor, C.D.//Timmis, K.N. 	Highly repressible expression system for cloning genes that specify potentially toxic proteins.	J. Bacteriol.	1987	169		4457-4462			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. 		
@D	O'Connor, C.D.//Walker, J.N.B.//Saunders, J.R. 	RsrII:  a restriction endonuclease with a heptanucleotide recognition sequence.	Methods Enzymol.	1987	155		11-15			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. 		
@D	O'Connor, T.J.//Adepoju, Y.//Boyd, D.//Isberg, R.R. 	Minimization of the Legionella pneumophila genome reveals chromosomal regions involved in host range expansion.	Proc. Natl. Acad. Sci. U. S. A.	2011	108		14733-14740			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. 		
@D	O'Cuiv, P.//Klaassens, E.S.//Smith, W.J.//Mondot, S.//Durkin, A.S.//Harkins, D.M.//Foster, L.//McCorrison, J.//Torralba, M.//Nelson, K.E.//Morrison, M. 	Draft Genome Sequence of Enterococcus faecalis PC1.1, a Candidate Probiotic Strain Isolated from Human Feces.	Genome Announcements	2013	1		e00160-12			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. 		
@D	O'Cuiv, P.//Klaassens, E.S.//Smith, W.J.//Mondot, S.//Durkin, A.S.//Harkins, D.M.//Foster, L.//McCorrison, J.//Torralba, M.//Nelson, K.E.//Morrison, M. 	Draft Genome Sequence of Enterococcus faecium PC4.1, a Clade B Strain Isolated from Human Feces.	Genome Announcements	2014	2		e00022-14			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. 		
@D	O'Dell, K.B.//Woo, H.L.//Utturkar, S.//Klingeman, D.//Brown, S.D.//Hazen, T.C. 	Genome Sequence of Halomonas sp. Strain KO116, an Ionic Liquid-Tolerant Marine Bacterium Isolated from a Lignin-Enriched Seawater Microcosm.	Genome Announcements	2015	3		e00402-15			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. 		
@D	O'Donnell, M.M.//Harris, H.M.//O'Toole, P.W.//Ross, R.P. 	The Genome of the Predominant Equine Lactobacillus Species, Lactobacillus equi, Is Reflective of Its Lifestyle Adaptations to an Herbivorous Host.	Genome Announcements	2014	2		e01155-13			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. 		
@D	O'Driscoll, J.//Fitzgerald, G.F.//van Sinderen, D. 	A dichotomous epigenetic mechanism governs expression of the LlaJI restriction/modification system.	Mol. Microbiol.	2005	57		1532-1544			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. 		
@D	O'Driscoll, J.//Glynn, F.//Cahalane, O.//O'Connell-Motherway, M.//Fitzgerald, G.F.//van Sinderen, D. 	Lactococcal plasmid pNP40 encodes a novel, temperature-sensitive restriction-modification system.	Appl. Environ. Microbiol.	2004	70		5546-5556			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. 		
@D	O'Driscoll, J.//Glynn, F.//Fitzgerald, G.F.//van Sinderen, D. 	Sequence Analysis of the Lactococcal Plasmid pNP40: a Mobile Replicon for Coping with Environmental Hazards.	J. Bacteriol.	2006	188		6629-6639			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. 		
@D	O'Driscoll, J.//Heiter, D.F.//Wilson, G.G.//Fitzgerald, G.F.//Roberts, R.//van Sinderen, D. 	A genetic dissection of the LlaJI restriction cassette reveals insights on a novel bacteriophage resistance system.	BMC Microbiol.	2006	6		40			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. 		
@D	O'Gara, M.//Adams, G.M.//Gong, W.//Kobayashi, R.//Blumenthal, R.M.//Cheng, X. 	Expression, purification, mass spectrometry, crystallization and multiwavelength anomalous diffraction of selenomethionyl PvuII DNA methyltransferase (cytosine-N4-specific).	Eur. J. Biochem.	1997	247		1009-1018			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. 		
@D	O'Gara, M.//Horton, J.R.//Roberts, R.J.//Cheng, X. 	Structures of HhaI methyltransferase complexed with substrates containing mismatches at the target base.	Nat. Struct. Biol.	1998	5		872-877			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. 		
@D	O'Gara, M.//Klimasauskas, S.//Roberts, R.J.//Cheng, X. 	Enzymatic C5-cytosine methylation of DNA: Mechanistic implications of new crystal structures for HhaI methyltransferase-DNA-AdoHcy complexes.	J. Mol. Biol.	1996	261		634-645			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. 		
@D	O'Gara, M.//McCloy, K.//Malone, T.//Cheng, X. 	Structure-based sequence alignment of three AdoMet-dependent DNA methyltransferases.	Gene	1995	157		135-138			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. 		
@D	O'Gara, M.//Roberts, R.J.//Cheng, X. 	A structural basis for the preferential binding of hemimethylated DNA by HhaI DNA methyltransferase.	J. Mol. Biol.	1996	263		597-606			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. 		
@D	O'Gara, M.//Zhang, X.//Roberts, R.J.//Cheng, X. 	Structure of a binary complex of HhaI methyltransferase with S-adenosyl-L-methionine formed in the presence of a short non-specific DNA oligonucleotide.	J. Mol. Biol.	1999	287		201-209			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. 		
@D	O'Hair, J.A.//Li, H.//Thapa, S.//Scholz, M.//Zhou, S. 	Draft Genome Sequences of Three Cellulolytic Bacillus licheniformis Strains Isolated from Imperial Geyser, Amphitheater Springs, and Whiterock Springs inside  Yellowstone National Park.	Genome Announcements	2017	5		e00065-17			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. 		
@D	O'Hair, J.A.//Li, H.//Thapa, S.//Scholz, M.B.//Zhou, S. 	Draft Genome Sequence of Bacillus licheniformis Strain YNP1-TSU Isolated from Whiterock Springs in Yellowstone National Park.	Genome Announcements	2017	5		e01496-16			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. 		
@D	O'Hara-Hanley, K.//Harrison, A.//Soby, S.D. 	Draft Genomic Sequences of Chromobacterium sp. nov. Strains MWU13-2610 and MWU14-2602, Isolated from Wild Cranberry Bogs in Massachusetts.	Genome Announcements	2018	6		e00332-18			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. 		
@D	O'Loughlin, J.L.//Eucker, T.P.//Chavez, J.D.//Samuelson, D.R.//Neal-McKinney, J.//Gourley, C.R.//Bruce, J.E.//Konkel, M.E. 	Analysis of the Campylobacter jejuni genome by SMRT DNA sequencing identifies restriction-modification motifs.	PLoS ONE	2015	10		e0118533			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. 		
@D	O'Loughlin, T.J.//Xu, Q.//Kucera, R.B.//Dorner, L.F.//Sweeney, S.//Schildkraut, I.//Guo, H.-C. 	Crystallization and preliminary X-ray diffraction analysis of MspI restriction endonuclease in complex with its cognate DNA.	Acta Crystallogr. D Biol. Crystallogr.	2000	56		1652-1655			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%. 		
@D	O'Neill, M.//Chen, A.//Murray, N.E. 	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.	Proc. Natl. Acad. Sci. U. S. A.	1997	94		14596-14601			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. 		
@D	O'Neill, M.//Dryden, D.T.F.//Murray, N.E. 	Localization of a protein-DNA interface by random mutagenesis.	EMBO J.	1998	17		7118-7127			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. 		
@D	O'Neill, M.//Powell, L.M.//Murray, N.E. 	Target recognition by EcoKI: the recognition domain is robust and restriction-deficiency commonly results from the proteolytic control of enzyme activity.	J. Mol. Biol.	2001	307		951-963			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. 		
@D	O'Sullivan, D.//Coffey, A.//Fitzgerald, G.F.//Hill, C.//Ross, R.P. 	Design of a phage-insensitive lactococcal dairy starter via sequential transfer of naturally occurring conjugative plasmids.	Appl. Environ. Microbiol.	1998	64		4618-4622			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. 		
@D	O'Sullivan, D.//Ross, R.P.//Twomey, D.P.//Fitzgerald, G.F.//Hill, C.//Coffey, A. 	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.	Appl. Environ. Microbiol.	2001	67		929-937			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. 		
@D	O'Sullivan, D.//Twomey, D.P.//Coffey, A.//Hill, C.//Fitzgerald, G.F.//Ross, R.P. 	Novel type I restriction specificities through domain shuffling of HsdS subunits in lactococcus lactis.	Mol. Microbiol.	2000	36		866-875			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. 		
@D	O'Sullivan, D.J.//Klaenhammer, T.R. 	C.LlaI is a bifunctional regulatory protein of the LlaI restriction modification operon from Lactococcus lactis.	Dev. Biol. Stand.	1995	85		591-595			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. 		
@D	O'Sullivan, D.J.//Klaenhammer, T.R. 	Control of expression of LlaI restriction in Lactococcus lactis.	Mol. Microbiol.	1998	27		1009-1020			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. 		
@D	O'Sullivan, D.J.//Zagula, K.//Klaenhammer, T.R. 	In vivo restriction by LlaI is encoded by three genes, arranged in an operon with llaIM, on the conjugative Lactococcus plasmid pTR2030.	J. Bacteriol.	1995	177		134-143			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. 		
@D	O'Sullivan, O.//O'Callaghan, J.//Sangrador-Vegas, A.//McAuliffe, O.//Slattery, L.//Kaleta, P.//Callanan, M.//Fitzgerald, G.F.//Ross, R.P.//Beresford, T. 	Comparative genomics of lactic acid bacteria reveals a niche-specific gene set.	BMC Microbiol.	2009	9		50			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. 		
@D	O'Sullivan, T.//van Sinderen, D.//Fitzgerald, G. 	Structural and functional analysis of pCI65st, a 6.5 kb plasmid from Streptococcus thermophilus NDI-6.	Microbiology	1999	145		127-134			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. 		
@D	O'Toole, R.F.//Johari, B.M.//Mac, A.M.//Rogers, T.R.//Bower, J.E.//Basu, I.//Freeman, J.T. 	Draft Genome Sequence of the First Isolate of Extensively Drug-Resistant Mycobacterium tuberculosis in New Zealand.	Genome Announcements	2014	2		e00319-14			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. 		
@D	O-Cuiv, P.//Klaassens, E.S.//Durkin, A.S.//Harkins, D.M.//Foster, L.//McCorrison, J.//Torralba, M.//Nelson, K.E.//Morrison, M. 	Draft genome sequence of Bacteroides vulgatus PC510, a strain isolated from human feces.	J. Bacteriol.	2011	193		4025-4026			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. 		
@D	Oakeley, E.J. 	DNA methylation analysis: a review of current methodologies.	Pharmacol. Ther.	1999	84		389-400			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. 		
@D	Oakeley, E.J.//Schmitt, F.//Jost, J.P. 	Quantification of 5-methylcytosine in DNA by the chloroacetaldehyde reaction.	Biotechniques	1999	27		744-746			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. 		
@D	Oakeson, K.F.//Gil, R.//Clayton, A.L.//Dunn, D.M.//von Niederhausern, A.C.//Hamil, C.//Aoyagi, A.//Duval, B.//Baca, A.//Silva, F.J.//Vallier, A.//Jackson, D.G.//Latorre, A.//Weiss, R.B.//Heddi, A.//Moya, A.//Dale, C. 	Genome Degeneration and Adaptation in a Nascent Stage of Symbiosis.	Genome Biol. Evol.	2014	6		76-93			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. 		
@D	Oakeson, K.F.//Miller, A.//Dale, C.//Dearing, D. 	Draft Genome Sequence of an Oxalate-Degrading Strain of Clostridium sporogenes from the Gastrointestinal Tract of the White-Throated Woodrat (Neotoma albigula).	Genome Announcements	2016	4		e00392-16			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. 		
@D	Oakey, H.J.//Cullen, B.R.//Owens, L. 	The complete nucleotide sequence of the Vibrio harveyi bacteriophage VHML.	J. Appl. Microbiol.	2002	93		1089-1098			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. 		
@D	Oana, H.//Tsumoto, K.//Yoshikawa, Y.//Yoshikawa, K. 	Folding transition of large DNA completely inhibits the action of a restriction endonuclease as revealed by single-chain observation.	FEBS Lett.	2002	530		143-146			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. 		
@D	Obarska, A.//Blundell, A.//Feder, M.//Vejsadova, S.//Sisakova, E.//Weiserova, M.//Bujnicki, J.M.//Firman, K. 	Structural model for the multisubunit Type IC restriction-modification DNA methyltransferase M.EcoR124I in complex with DNA.	Nucleic Acids Res.	2006	34		1992-2005			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. 		
@D	Obarska-Kosinska, A.//Taylor, J.E.//Callow, P.//Orlowski, J.//Bujnicki, J.M.//Kneale, G.G. 	HsdR Subunit of the Type I Restriction-Modification Enzyme EcoR124I: Biophysical Characterisation and Structural Modelling.	J. Mol. Biol.	2008	376		438-452			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. 		
@D	Oberto, J.//Gaudin, M.//Cossu, M.//Gorlas, A.//Slesarev, A.//Marguet, E.//Forterre, P. 	Genome Sequence of a Hyperthermophilic Archaeon, Thermococcus nautili 30-1, That  Produces Viral Vesicles.	Genome Announcements	2014	2		e00243-14			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. 		
@D	Obregon, V.//Garcia, P.//Lopez, R.//Garcia, J.L. 	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.	Microb. Drug Resist.	2003	9		7-15			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. 		
@D	Ocampo-Sosa, A.A.//Fernandez-Martinez, M.//Cabot, G.//Pena, C.//Tubau, F.//Oliver, A.//Martinez-Martinez, L. 	Draft Genome Sequence of the Quorum-Sensing and Biofilm-Producing Pseudomonas aeruginosa Strain Pae221, Belonging to the Epidemic High-Risk Clone Sequence Type  274.	Genome Announcements	2015	3		e01343-14			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. 		
@D	Ochiai, H.//Inoue, Y.//Takeya, M.//Sasaki, A.//Kaku, H. 	Genome sequence of Xanthomonas oryzae pv. oryzae suggests contribution of large numbers of effector genes and insertion sequences to its race diversity.	Japan Agricultural Research Quarterly	2005	39		275-287			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. 		
@D	Ochiai, H.//Shibata, H.//Sawa, Y.//Ashida, N. 	Restriction endonucleases from Phormidium lapideum, a strain of filamentous and thermophilic Cyanobacteria.	Bull. Fac. Agr. Shimane Univ.	1989	23		184-191			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. 		
@D	Oda, K.//Marmur, J. 	Purification and properties of deoxyribonucleic acid methylase from Bacillus subtilis.	Biochemistry	1966	5		761-773			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. 		
@D	Oda, M.//Tanaka, S.//Shiota, K. 	DNA methyltransferase 1 is essential for establishment of trophoblast stem cells in culture.	Biol. Reprod.	2001	64		175-176			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. 		
@D	Odom, O.W.//Holloway, S.P.//Deshpande, N.N.//Lee, J.//Herrin, D.L. 	Mobile self-splicing Group I introns from the psbA gene of Chlamydomonas reinhardtii: highly efficient homing of an exogenous intron containing its own promoter.	Mol. Cell. Biol.	2001	21		3472-3481			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. 		
@D	Oehlerking, J.//Kube, M.//Felder, K.M.//Matter, D.//Wittenbrink, M.M.//Schwarzenbach, S.//Kramer, M.M.//Hoelzle, K.//Hoelzle, L.E. 	The complete genome sequence of the hemotrophic Mycoplasma suis_KI3806.	J. Bacteriol.	2011	193		2369-2370			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. 		
@D	Oelgeschlager, T.//Geiger, R.//Ruter, T.//Alves, J.//Fliess, A.//Pingoud, A. 	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.	Gene	1990	89		19-27			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. 		
@D	Ofir, G.//Melamed, S.//Sberro, H.//Mukamel, Z.//Silverman, S.//Yaakov, G.//Doron, S.//Sorek, R. 	DISARM is a widespread bacterial defence system with broad anti-phage activities.	Nature Microbiology	2018	3		90-98			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. 		
@D	Ogasawara, Y.//Torrez-Martinez, N.//Aragon, A.D.//Yackley, B.J.//Weber, J.A.//Sundararajan, A.//Ramaraj, T.//Edwards, J.S.//Melancon, C.E.I.I.I. 	High-Quality Draft Genome Sequence of Actinobacterium Kibdelosporangium sp. MJ126-NF4, Producer of Type II Polyketide Azicemicins, Using Illumina and PacBio   Technologies.	Genome Announcements	2015	3		e00114-15			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. 		
@D	Ogata, H.//Audic, S.//Renesto-Audiffren, P.//Fournier, P.-E.//Barbe, V.//Samson, D.//Roux, V.//Cossart, P.//Weissenbach, J.//Claverie, J.-M.//Raoult, D. 	Mechanisms of evolution in Rickettsia conorii and R. prowazekii.	Science	2001	293		2093-2098			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. 		
@D	Ogata, H.//La Scola, B.//Audic, S.//Renesto, P.//Blanc, G.//Robert, C.//Fournier, P.E.//Claverie, J.M.//Raoult, D. 	Genome sequence of Rickettsia bellii illuminates the role of amoebae in gene exchanges between intracellular pathogens.	PLoS Genet.	2006	2		e76			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. 		
@D	Ogata, H.//Renesto, P.//Audic, S.//Robert, C.//Blanc, G.//Fournier, P.E.//Parinello, H.//Claverie, J.M.//Raoult, D. 	The genome sequence of Rickettsia felis identifies the first putative conjugative plasmid in an obligate intracellular parasite.	PLoS Biology	2005	3		e248			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. 		
@D	Ogawa, S.//Matsuo, K.//Angata, K.//Yanagisawa, K.//Tanaka, Y. 	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.	Curr. Genet.	1997	31		80-88			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. 		
@D	Ogawa, S.//Naito, K.//Angata, K.//Morio, T.//Urushihara, H.//Tanaka, Y. 	A site-specific DNA endonuclease specified by one of two ORFs encoded by a group I intron in Dictyostelium discoideum mitochondrial DNA.	Gene	1997	191		115-121			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. 		
@D	Ogawa, Y.//Ooka, T.//Shi, F.//Ogura, Y.//Nakayama, K.//Hayashi, T.//Shimoji, Y. 	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.	J. Bacteriol.	2011	193		2959-2971			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. 		
@D	Oger, P.//Sokolova, T.G.//Kozhevnikova, D.A.//Chernyh, N.A.//Bartlett, D.H.//Bonch-Osmolovskaya, E.A.//Lebedinsky, A.V. 	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.	J. Bacteriol.	2011	193		7019-7020			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. 		
@D	Oger, P.//Sokolova, T.G.//Kozhevnikova, D.A.//Taranov, E.A.//Vannier, P.//Lee, H.S.//Kwon, K.K.//Kang, S.G.//Lee, J.H.//Bonch-Osmolovskaya, E.A.//Lebedinsky, A.V. 	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.	Genome Announcements	2016	4		e01534-15			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. 		
@D	Oger, P.M. 	Complete Genome Sequences of 11 Type Species from the Thermococcus Genus of Hyperthermophilic and Piezophilic Archaea.	Genome Announcements	2018	6		e00037-18			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. 		
@D	Oger, P.M.//Callac, N.//Oger-Desfeux, C.//Hughes, S.//Gillet, B.//Jebbar, M.//Godfroy, A. 	Complete Genome Sequence of the Hyperthermophilic Piezophilic Archaeon Pyrococcus kukulkanii NCB100 Isolated from the Rebecca's Roost Hydrothermal Vent in the  Guaymas Basin.	Genome Announcements	2017	5		e01667-16			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. 		
@D	Ogg, C.D.//Patel, B.K. 	Draft Genome Sequence of Caloramator australicus strain RC3T a thermoanaerobe from the Great Artesian Basin of Australia.	J. Bacteriol.	2011	193		2664-2665			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. 		
@D	Ogino, H.//Azuma, Y.//Hosoyama, A.//Nakazawa, H.//Matsutani, M.//Hasegawa, A.//Otsuyama, K.//Matsushita, K.//Fujita, N.//Shirai, M. 	Complete Genome Sequence of NBRC 3288, a Unique Cellulose-Nonproducing Strain of Gluconacetobacter xylinus Isolated from Vinegar.	J. Bacteriol.	2011	193		6997-6998			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. 		
@D	Ogunremi, D.//Blais, B.//Huang, H.//Wang, L.//Elmufti, M.//Allain, R.//Hazelwood, J.//Grenier, C.//Amoako, K.//Savic, M.//Fattahi, G.N. 	Draft Genome Sequences of Two Strains of Salmonella enterica Serovar Typhimurium  Displaying Different Virulence in an Experimental Chicken Model.	Genome Announcements	2017	5		e01526-16			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. 		
@D	Ogunremi, D.//Devenish, J.//Amoako, K.//Kelly, H.//Dupras, A.A.//Belanger, S.//Wang, L.R. 	High resolution assembly and characterization of genomes of Canadian isolates of Salmonella Enteritidis.	BMC Genomics	2014	15		713			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. 		
@D	Oguntoyinbo, F.A.//Cho, G.S.//Brinks, E.//Fiedler, G.//Kabisch, J.//Koberg, S.//Bockelmann, W.//Neve, H.//Kang, Y.G.//Yun, D.//Kim, A.R.//Narbad, A.//Franz, C.M. 	Draft Genome Sequence of Lactobacillus plantarum BFE 5092 Isolated from Maasai Fermented Milk.	Genome Announcements	2016	4		e00481-16			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. 		
@D	Oguro, K.//Tamura, K.//Yamane, J.//Shimizu, M.//Yamamoto, T.//Ikawa, T.//Ohnishi, K.//Oshima, S.//Imajoh, M. 	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.	Genome Announcements	2014	2		e00546-14			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. 		
@D	Oguro, K.//Yamane, J.//Yamamoto, T.//Ohnishi, K.//Oshima, S.//Imajoh, M. 	Draft Genome Sequence of Streptococcus parauberis Strain SK-417, Isolated from Diseased Sebastes ventricosus in Kagoshima, Japan.	Genome Announcements	2014	2		e00453-14			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%. 		
@D	Oh, C.//Heo, S.J.//De Zoysa, M.//Affan, A.//Jung, W.K.//Park, H.S.//Lee, Y.//Lee, J.//Yoon, K.T.//Kang, D.H. 	Whole-Genome Sequence of the Xylanase-Producing Mesoflavibacter zeaxanthinifaciens Strain S86.	J. Bacteriol.	2011	193		5557			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. 		
@D	Oh, C.//Kwon, Y.K.//Heo, S.J.//De Zoysa, M.//Affan, A.//Lee, Y.//Lee, J.//Choi, Y.U.//Park, H.S.//Jung, K.H.//Lee, H.Y.//Kang, D.H. 	Complete genome sequence of strain s85, a novel member of the family flavobacteriaceae.	J. Bacteriol.	2011	193		6107			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. 		
@D	Oh, C.//Zoysa, M.D.//Kwon, Y.K.//Heo, S.J.//Affan, A.//Jung, W.K.//Park, H.S.//Lee, J.//Son, S.K.//Yoon, K.T.//Kang, D.H. 	Complete genome sequence of the agarase-producing marine bacterium strain s89, representing a novel species of the genus alteromonas.	J. Bacteriol.	2011	193		5538			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. 		
@D	Oh, H.M.//Giovannoni, S.J.//Ferriera, S.//Johnson, J.//Cho, J.C. 	The Complete Genome Sequence of Erythrobacter litoralis HTCC2594.	J. Bacteriol.	2009	191		2419-2420			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. 		
@D	Oh, H.M.//Giovannoni, S.J.//Lee, K.//Ferriera, S.//Johnson, J.//Cho, J.C. 	Complete Genome Sequence of Robiginitalea biformata HTCC2501.	J. Bacteriol.	2009	191		7144-7145			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. 		
@D	Oh, H.M.//Kang, I.//Ferriera, S.//Giovannoni, S.J.//Cho, J.C. 	Genome Sequence of an Oligotrophic Marine Gammaproteobacterium HTCC2143 Isolated from Oregon Coast.	J. Bacteriol.	2010	192		4530-4531			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. 		
@D	Oh, H.M.//Kang, I.//Lee, K.//Jang, Y.//Lim, S.I.//Cho, J.C. 	Complete Genome Sequence of Strain IMCC9063 Belonging to SAR11 subgroup 3, Isolated from the Arctic Ocean.	J. Bacteriol.	2011	193		3379-3380			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. 		
@D	Oh, H.M.//Kang, I.//Vergin, K.L.//Kang, D.//Rhee, K.H.//Giovannoni, S.J.//Cho, J.C. 	Complete Genome Sequence of Parvularcula bermudensis HTCC2503T, the type species of the order 'Parvularculales' in the Alphaproteobacteria.	J. Bacteriol.	2010	193		305-306			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. 		
@D	Oh, H.M.//Kang, I.//Vergin, K.L.//Lee, K.//Giovannoni, S.J.//Cho, J.C. 	Genome Sequence of Oceanicaulis sp. HTCC2633, Isolated from the Western Sargasso Sea.	J. Bacteriol.	2010	193		317-318			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. 		
@D	Oh, H.M.//Kang, I.//Yang, S.J.//Jang, Y.//Vergin, K.L.//Giovannoni, S.J.//Cho, J.C. 	Complete Genome Sequence of strain HTCC2170, a Novel Member of the Genus Maribacter in the Family Flavobacteriaceae.	J. Bacteriol.	2010	193		303-304			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. 		
@D	Oh, H.M.//Kwon, K.K.//Kang, I.//Kang, S.G.//Lee, J.H.//Kim, S.J.//Cho, J.C. 	Complete genome sequence of 'Candidatus Puniceispirillum marinum' IMCC1322, a representative of the SAR116 clade in the Alphaproteobacteria.	J. Bacteriol.	2010	192		3240-3241			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. 		
@D	Oh, H.M.//Lee, K.//Jang, Y.//Kang, I.//Kim, H.J.//Kang, T.W.//Kim, S.Y.//Cho, J.C. 	Genome Sequence of Strain IMCC9480, a Xanthorhodopsin-bearing Betaproteobacterium Isolated from the Arctic Ocean.	J. Bacteriol.	2011	193		3421			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. 		
@D	Oh, J.D.//Kling-Backhed, H.//Giannakis, M.//Xu, J.//Fulton, R.S.//Fulton, L.A.//Cordum, H.S.//Wang, C.//Elliott, G.//Edwards, J.//Mardis, E.R.//Engstrand, L.G.//Gordon, J.I. 	The complete genome sequence of a chronic atrophic gastritis Helicobacter pylori strain: Evolution during disease progression.	Proc. Natl. Acad. Sci. U. S. A.	2006	103		9999-10004			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. 		
@D	Oh, S.//Zhang, R.//Wu, Q.L.//Liu, W.T. 	Draft Genome Sequence of a Novel SAR11 Clade Species Abundant in a Tibetan Lake.	Genome Announcements	2014	2		e01137-14			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. 		
@D	OHair, J.A.//Li, H.//Thapa, S.//Scholz, M.//Zhou, S. 	Draft Genome Sequence of Bacillus altitudinis YNP4-TSU, Isolated from Yellowstone National Park.	Genome Announcements	2017	5		e00631-17			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. 		
@D	Ohji, S.//Yamazoe, A.//Hosoyama, A.//Tsuchikane, K.//Ezaki, T.//Fujita, N. 	The Complete Genome Sequence of Pseudomonas putida NBRC 14164T Confirms High Intraspecies Variation.	Genome Announcements	2014	2		e00029-14			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. 		
@D	Ohkuma, M.//Yuki, M.//Oshima, K.//Suda, W.//Oshida, Y.//Kitamura, K.//Iida, T.//Hattori, M. 	Draft Genome Sequence of the Alkaliphilic and Xylanolytic Paenibacillus sp. Strain JCM 10914, Isolated from the Gut of a Soil-Feeding Termite.	Genome Announcements	2014	2		e01144-13			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. 		
@D	Ohnishi, N.//Maruyama, F.//Ogawa, H.//Kachi, H.//Yamada, S.//Fujikura, D.//Nakagawa, I.//Hang'ombe, M.B.//Thomas, Y.//Mweene, A.S.//Higashi, H. 	Genome Sequence of a Bacillus anthracis Outbreak Strain from Zambia, 2011.	Genome Announcements	2014	2		e00116-14			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. 		
@D	Ohnishi, Y.//Ishikawa, J.//Hara, H.//Suzuki, H.//Ikenoya, M.//Ikeda, H.//Yamashita, A.//Hattori, M.//Horinouchi, S. 	Genome sequence of the streptomycin-producing microorganism Streptomyces griseus IFO 13350.	J. Bacteriol.	2008	190		4050-4060			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. 		
@D	Ohno, S.//Handa, N.//Watanabe-Matsui, M.//Takahashi, N.//Kobayashi, I. 	Maintenance forced by a restriction-modification system can be modulated by a region in its modification enzyme not essential for methyltransferase activity.	J. Bacteriol.	2008	190		2039-2049			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. 		
@D	Ohsawa, K.//Imai, Y.//Ito, D.//Kohsaka, S. 	Molecular cloning and characterization of annexin V-binding proteins with highly hydrophilic peptide structure.	J. Neurochem.	1996	67		89-97			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. 		
@D	Ohshima, H.//Matsuoka, S.//Asai, K.//Sadaie, Y. 	Molecular organization of intrinsic restriction and modification genes BsuM of Bacillus subtilis Marburg.	J. Bacteriol.	2002	184		381-389			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. 		
@D	Ohta, K.//Keszenman-Pereyra, D.//Nicolas, A.//Shibata, T. 	A novel meiosis-induced site-specific endonuclease activity in yeast mitochondria.	J. Cell Biochem. Suppl.	1993	17C		174			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. 		
@D	Ohta, K.//Nicolas, A.//Keszenman-Pereyra, D.//Shibata, T. 	Endo.SK1: an inducible site-specific endonuclease from yeast mitochondria.	Mol. Gen. Genet.	1996	250		395-404			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. 		
@D	Ohta, Y.//Nishi, S.//Kobayashi, K.//Tsubouchi, T.//Iida, K.//Tanizaki, A.//Kurosawa, K.//Adachi, A.//Nishihara, M.//Sato, R.//Hasegawa, R.//Hatada, Y. 	Draft Genome Sequence of Novosphingobium sp. Strain MBES04, Isolated from Sunken  Wood from Suruga Bay, Japan.	Genome Announcements	2015	3		e01373-14			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%. 		
@D	Ohta, Y.//Shimane, Y.//Nishi, S.//Ichikawa, J.//Kurosawa, K.//Tsubouchi, T.//Ishii, S. 	Complete Genome Sequence of Sphingobium sp. Strain YG1, a Lignin Model Dimer-Metabolizing Bacterium Isolated from Sediment in Kagoshima Bay, Japan.	Genome Announcements	2018	6		e00267-18			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. 		
@D	Ohtani, N.//Sato, M.//Tomita, M.//Itaya, M. 	Restriction on conjugational transfer of pLS20 in Bacillus subtilis 168.	Biosci. Biotechnol. Biochem.	2008	72		2472-2475			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. 		
@D	Ohtani, N.//Tomita, M.//Itaya, M. 	The third plasmid pVV8 from Thermus thermophilus HB8: isolation, characterization, and sequence determination.	Extremophiles	2012	16		237-244			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. 		
@D	Ohtsubo, Y.//Fujita, N.//Nagata, Y.//Tsuda, M.//Iwasaki, T.//Hatta, T. 	Complete Genome Sequence of Ralstonia pickettii DTP0602, a 2,4,6-Trichlorophenol  Degrader.	Genome Announcements	2013	1		e00903-13			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. 		
@D	Ohtsubo, Y.//Kishida, K.//Sato, T.//Tabata, M.//Kawasumi, T.//Ogura, Y.//Hayashi, T.//Tsuda, M.//Nagata, Y. 	Complete Genome Sequence of Pseudomonas sp. Strain TKP, Isolated from a gamma-Hexachlorocyclohexane-Degrading Mixed Culture.	Genome Announcements	2014	2		e01241-13			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. 		
@D	Ohtsubo, Y.//Maruyama, F.//Mitsui, H.//Nagata, Y.//Tsuda, M. 	Complete Genome Sequence of Acidovorax sp. Strain KKS102, a Polychlorinated-Biphenyl Degrader.	J. Bacteriol.	2012	194		6970-6971			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. 		
@D	Ohtsubo, Y.//Moriya, A.//Kato, H.//Ogawa, N.//Nagata, Y.//Tsuda, M. 	Complete Genome Sequence of a Phenanthrene Degrader, Burkholderia sp. HB-1 (NBRC  110738).	Genome Announcements	2015	3		e01283-15			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. 		
@D	Ohtsubo, Y.//Nagata, Y.//Numata, M.//Tsuchikane, K.//Hosoyama, A.//Yamazoe, A.//Tsuda, M.//Fujita, N.//Kawai, F. 	Complete Genome Sequence of Polyvinyl Alcohol-Degrading Strain Sphingopyxis sp. 113P3 (NBRC 111507).	Genome Announcements	2015	3		e01169-15			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. 		
@D	Ohtsubo, Y.//Nagata, Y.//Numata, M.//Tsuchikane, K.//Hosoyama, A.//Yamazoe, A.//Tsuda, M.//Fujita, N.//Kawai, F. 	Complete Genome Sequence of Sphingopyxis macrogoltabida Type Strain NBRC 15033, Originally Isolated as a Polyethylene Glycol Degrader.	Genome Announcements	2015	3		e01401-15			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. 		
@D	Ohtsubo, Y.//Nagata, Y.//Numata, M.//Tsuchikane, K.//Hosoyama, A.//Yamazoe, A.//Tsuda, M.//Fujita, N.//Kawai, F. 	Complete Genome Sequence of a Polypropylene Glycol-Degrading Strain, Microbacterium sp. No. 7.	Genome Announcements	2015	3		e01400-15			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). 		
@D	Ohtsubo, Y.//Nagata, Y.//Numata, M.//Tsuchikane, K.//Hosoyama, A.//Yamazoe, A.//Tsuda, M.//Fujita, N.//Kawai, F. 	Complete Genome Sequence of Polypropylene Glycol- and Polyethylene Glycol-Degrading Sphingopyxis macrogoltabida Strain EY-1.	Genome Announcements	2015	3		e01399-15			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). 		
@D	Ohtsubo, Y.//Nonoyama, S.//Nagata, Y.//Numata, M.//Tsuchikane, K.//Hosoyama, A.//Yamazoe, A.//Tsuda, M.//Fujita, N.//Kawai, F. 	Complete Genome Sequence of Sphingopyxis terrae Strain 203-1 (NBRC 111660), a Polyethylene Glycol Degrader.	Genome Announcements	2016	4		e00530-16			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. 		
@D	Ohtsubo, Y.//Nonoyama, S.//Nagata, Y.//Numata, M.//Tsuchikane, K.//Hosoyama, A.//Yamazoe, A.//Tsuda, M.//Fujita, N.//Kawai, F. 	Complete Genome Sequence of Sphingopyxis macrogoltabida Strain 203N (NBRC 111659), a Polyethylene Glycol Degrader.	Genome Announcements	2016	4		e00529-16			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. 		
@D	Ohtsubo, Y.//Sato, T.//Kishida, K.//Tabata, M.//Ogura, Y.//Hayashi, T.//Tsuda, M.//Nagata, Y. 	Complete Genome Sequence of Pseudomonas aeruginosa MTB-1, Isolated from a Microbial Community Enriched by the Technical Formulation of  Hexachlorocyclohexane.	Genome Announcements	2014	2		e01130-13			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. 		
@D	Ohtsuka, E.//Ishino, Y.//Ibaraki, K.//Ikehara, M. 	Recognition by restriction endonuclease EcoRI of deoxyoctanucleotides containing modified sugar moieties.	Eur. J. Biochem.	1984	139		447-450			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. 		
@D	Ohtsuka, E.//Morisawa, H.//Ikehara, M. 	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.	Chem. Pharm. Bull. (Tokyo)	1982	30		874-880			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. 		
@D	Ohtsuka, K.//Ohnishi, H.//Nozaki, E.//Pais, R.J.//Tortoli, E.//Yonetani, S.//Matsushima, S.//Tateishi, Y.//Matsumoto, S.//Watanabe, T. 	Whole-Genome Sequence of Mycobacterium kyorinense.	Genome Announcements	2014	2		e01062-14			We report here the first draft genome sequence of Mycobacterium kyorinense, which was described in 2009 and exhibits significant pathogenicity to humans. 		
@D	Oinuma, K.I.//Suzuki, M.//Sato, K.//Nakaie, K.//Niki, M.//Takizawa, E.//Niki, M.//Shibayama, K.//Yamada, K.//Kakeya, H.//Kaneko, Y. 	Genome Sequence of an Acinetobacter baumannii Strain Carrying Three Acquired Carbapenemase Genes.	Genome Announcements	2016	4		e01290-16			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. 		
@D	Oishi, K.//Aoi, S.//Ehara, Y.//Otsuka, Y.//Shimamura, K.//Higuchi, Y.//Nomoto, M. 	Inhibition of restriction endonucleases by commercial polysaccharides.	J. Ferment. Bioeng.	1990	69		360-361			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. 		
@D	Ojala, T.//Kuparinen, V.//Koskinen, J.P.//Alatalo, E.//Holm, L.//Auvinen, P.//Edelman, S.//Westerlund-Wikstrom, B.//Korhonen, T.K.//Paulin, L.//Kankainen, M. 	Genome Sequence of Lactobacillus crispatus ST1.	J. Bacteriol.	2010	192		3547-3548			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. 		
@D	Oka, M.//Meacham, A.M.//Hamazaki, T.//Rodic, N.//Chang, L.-J.//Terada, N. 	De novo DNA methyltransferases Dnmt3a and Dnmt3b primarily mediate the cytotoxic effect of 5-aza-2'-deoxycytidine.	Oncogene	2005	24		3091-3099			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. 		
@D	Okada, K.//Na-Ubol, M.//Natakuathung, W.//Roobthaisong, A.//Maruyama, F.//Nakagawa, I.//Chantaroj, S.//Hamada, S. 	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.	PLoS ONE	2014	9		E98120			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. 		
@D	Okada, K.//Natakuathung, W.//Na-Ubol, M.//Roobthaisong, A.//Wongboot, W.//Maruyama, F.//Nakagawa, I.//Chantaroj, S.//Hamada, S. 	Characterization of 3 Megabase-Sized Circular Replicons from Vibrio cholerae.	Emerg. Infect. Dis.	2015	21		1262-1263			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. 		
@D	Okada, K.//Ogura, Y.//Hayashi, T.//Abe, A.//Kuwae, A.//Horiguchi, Y.//Abe, H. 	Complete Genome Sequence of Bordetella bronchiseptica S798, an Isolate from a Pig with Atrophic Rhinitis.	Genome Announcements	2014	2		e00436-14			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. 		
@D	Okada, M. 	Host-controlled restriction and modification of Salmonella typhimurium.	Keio J. Med.	1969	18		81-97			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. 		
@D	Okada, R.//Matsumoto, M.//Zhang, Y.//Isaka, M.//Tatsuno, I.//Hasegawa, T. 	Emergence of type I restriction modification system-negative emm1 type Streptococcus pyogenes clinical isolates in Japan.	APMIS	2014	122		914-921			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. 		
@D	Okai, M.//Watanabe, A.//Ishida, M.//Urano, N. 	Draft Genome Sequence of a Benzo[a]pyrene-Degrading Bacterium, Olleya sp. Strain  ITB9.	Genome Announcements	2015	3		e01328-15			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%. 		
@D	Okamoto, A.//Lee, H.//Yabutani, M.//Yamada, K.//Ohta, M. 	Draft Genome Sequence of a Legionella pneumophila Serogroup 4 Strain Causing Legionellosis.	Genome Announcements	2014	2		e00602-14			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. 		
@D	Okamoto, A.//Tanabe, K.//Saito, I. 	Site-specific discrimination of cytosine and 5-methylcytosine in duplex DNA by peptide nucleic acids.	J. Am. Chem. Soc.	2002	124		10262-10263			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. 		
@D	Okano, K.//Furuta, S.//Ichise, S.//Miyata, N. 	Whole-Genome Sequences of Two Manganese(II)-Oxidizing Bacteria, Bosea sp. Strain  BIWAKO-01 and Alphaproteobacterium Strain U9-1i.	Genome Announcements	2016	4		e01309-16			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. 		
@D	Okano, K.//Miyata, N.//Ozaki, Y. 	Genome Sequence of Microcystis aeruginosa Strain NIES-44.	Genome Announcements	2015	3		e00135-15			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. 		
@D	Okano, K.//Shimizu, K.//Maseda, H.//Kawauchi, Y.//Utsumi, M.//Itayama, T.//Zhang, Z.//Sugiura, N. 	Whole-Genome Sequence of the Microcystin-Degrading Bacterium Sphingopyxis sp. Strain C-1.	Genome Announcements	2015	3		e00838-15			This report describes the whole-genome sequence of an alkalitolerant microcystin-degrading bacterium, Sphingopyxis sp. strain C-1, isolated from a lake in China. 		
@D	Okano, M. 	DNA methyltransferases Dnmt3a and Dnmt3b are essential for de novo methylation in mouse early development.	Jikken Igaku	2000	18		468-471					
@D	Okano, M. 	DNA methylation and DNA methyltransferases in mammals.	Saibo Kogaku	2001	20		381-386					
@D	Okano, M.//Bell, D.W.//Haber, D.A.//Li, E. 	DNA methyltransferases Dnmt3a and Dnmt3b are essential for de novo methylation and mammalian development.	Cell	1999	99		247-257			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. 		
@D	Okano, M.//Li, E. 	Genetic analyses of DNA methyltransferase genes in mouse model system.	J. Nutr.	2002	132		2462S-2465S			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. 		
@D	Okano, M.//Takebayashi, S.//Okumura, K.//Li, E. 	Assignment of cytosine-5 DNA methyltransferases Dnmt3a and Dnmt3b to mouse chromosome bands 12A2-A3 and 2H1 by in situ hybridization.	Cytogenet. Cell Genet.	1999	86		333-334			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. 		
@D	Okano, M.//Xie, S.//Li, E. 	Dnmt2 is not required for de novo and maintenance methylation of viral DNA in embryonic stem cells.	Nucleic Acids Res.	1998	26		2536-2540			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. 		
@D	Okano, M.//Xie, S.//Li, E. 	Cloning and characterization of a family of novel mammalian DNA (cytosine-5) methyltransferases.	Nat. Genet.	1998	19		219-220			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. 		
@D	Okhapkina, S.S.//Netesova, N.A.//Golikova, L.N.//Seregina, E.V.//Sosnovtsev, S.V.//Abdurashitov, M.A.//Degtyarev, S.K. 	Comparison of the homologous SfeI and LlaBI restriction-modification  systems.	Mol. Biol. (Mosk)	2002	36		432-437			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. 		
@D	Okinaka, R.T.//Challacombe, J.//Drees, K.//Birdsell, D.N.//Janke, N.//Naumann, A.//Seymour, M.//Hornstra, H.//Schupp, J.//Sahl, J.//Foster, J.T.//Pearson, T.//Turnbull, P.//Keim, P. 	Genome Sequence of Bacillus anthracis STI, a Sterne-Like Georgian/Soviet Vaccine  Strain.	Genome Announcements	2014	2		e00853-14			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. 		
@D	Okrent, R.A.//Manning, V.A.//Trippe, K.M. 	Draft Genome Sequences of Seven 4-Formylaminooxyvinylglycine Producers Belonging  to the Pseudomonas fluorescens Species Complex.	Genome Announcements	2017	5		e00277-17			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. 		
@D	Okshevsky, M.//Regina, V.R.//Marshall, I.P.//Schreiber, L.//Meyer, R.L. 	Draft Genome Sequence of Bacillus sp. FMQ74, a Dairy-Contaminating Isolate from Raw Milk.	Genome Announcements	2017	5		e01512-16			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. 		
@D	Okstad, O.A.//Hegna, I.//Lindback, T.//Rishovd, A.-L.//Kolsto, A.-B. 	Genome organization is not conserved between Bacillus cereus and Bacillus subtilis.	Microbiology	1999	145		621-631			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. 		
@D	Oktavcovca, B.//Godany, A.//Pristas, P.//Stevcikova, B.//Farkasovska, J. 	Isolation and characterization of the modification methylase M.SauLPI from Streptomyces aureofaciens B-96.	Nucleic Acids Res.	1993	21		4843			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. 		
@D	Okubo, T. et al. 	Complete Genome Sequence of Bradyrhizobium sp. S23321: Insights into Symbiosis Evolution in Soil Oligotrophs.	Microbes Environ.	2012	27		306-315			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. 		
@D	Okubo, T.//Fukushima, S.//Itakura, M.//Oshima, K.//Longtonglang, A.//Teaumroong, N.//Mitsui, H.//Hattori, M.//Hattori, R.//Hattori, T.//Minamisawa, K. 	Soil oligotrophic bacterium Agromonas oligotrophica (Bradyrhizobium oligotrophicum) is a nitrogen-fixing symbiont of Aeschynomene indica as suggested by genome analysis.	Appl. Environ. Microbiol.	2013	79		2542-2551			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. 		
@D	Okuda, Y.//Sasaki, D.//Nogami, S.//Kaneko, Y.//Ohya, Y.//Anraku, Y. 	Occurrence, horizontal transfer and degeneration of VDE intein family in Saccharomycete yeasts.	Yeast	2003	20		563-573			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. 		
@D	Okumura, K.//Arai, R.//Okura, M.//Kirikae, T.//Takamatsu, D.//Osaki, M.//Miyoshi-Akiyama, T. 	Complete Genome Sequence of Melissococcus plutonius ATCC 35311.	J. Bacteriol.	2011	193		4029-4030			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. 		
@D	Okura, M.//Takamatsu, D.//Maruyama, F.//Nozawa, T.//Nakagawa, I.//Osaki, M.//Sekizaki, T.//Gottschalk, M.//Kumagai, Y.//Hamada, S. 	Genetic Analysis of Capsular Polysaccharide Synthesis Gene Clusters from All Serotypes of Streptococcus suis: Potential Mechanisms for the Generation of Capsular Variation.	Appl. Environ. Microbiol.	2013	79		2796-2806			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. 		
@D	Okutani, A.//Osaki, M.//Takamatsu, D.//Kaku, Y.//Inoue, S.//Morikawa, S. 	Draft Genome Sequences of Bacillus anthracis Strains Stored for Several Decades in Japan.	Genome Announcements	2015	3		e00633-15			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. 		
@D	Okutsu, N.//Morohoshi, T.//Ikeda, T. 	Draft Genome Sequence of Alicycliphilus sp. B1, an N-Acylhomoserine Lactone-Producing Bacterium, Isolated from Activated Sludge.	Genome Announcements	2015	3		e00424-15			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. 		
@D	Olano, C.//Cano-Prieto, C.//Losada, A.A.//Bull, A.T.//Goodfellow, M.//Fiedler, H.P.//Mendez, C.//Salas, J.A. 	Draft Genome Sequence of Marine Actinomycete Streptomyces sp. Strain NTK 937, Producer of the Benzoxazole Antibiotic Caboxamycin.	Genome Announcements	2014	2		e00534-14			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. 		
@D	Olasz, F.//Nagy, T.//Szabo, M.//Kiss, J.//Szmolka, A.//Barta, E.//van Tonder, A.//Thomson, N.//Barrow, P.//Nagy, B. 	Genome Sequences of Three Salmonella enterica subsp. enterica Serovar Infantis Strains from Healthy Broiler Chicks in Hungary and in the United Kingdom.	Genome Announcements	2015	3		e01468-14			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. 		
@D	Old, R.//Murray, K.//Roizes, G. 	Recognition Sequence of Restriction Endonuclease III from Hemophilus influenzae.	J. Mol. Biol.	1975	92		331-339			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. 		
@D	Oleastro, M.//Monteiro, L.//Lehours, P.//Megraud, F.//Menard, A. 	Identification of Markers for Helicobacter pylori Strains Isolated from Children with Peptic Ulcer Disease by Suppressive Subtractive Hybridization.	Infect. Immun.	2006	74		4064-4074			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. 		
@D	Olhoft, P.M. 	Cloning and characterization of the 5-methylcytosine methyltransferase gene in maize plants and tissue cultures.	Diss. Abstr.	1999	59		4638			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. 		
@D	Oliveira, D.C.//Wu, S.W.//de Lencastre, H. 	Genetic organization of the downstream region of the mecA element in methicillin-resistant Staphylococcus aureus isolates carrying different polymorphisms of this region.	Antimicrob. Agents Chemother.	2000	44		1906-1910			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. 		
@D	Oliveira, L.C. et al. 	Genome Sequence of Lactococcus lactis subsp. lactis NCDO 2118, a GABA-Producing Strain.	Genome Announcements	2014	2		e00980-14			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. 		
@D	Oliveira, L.M.//Resende, D.M.//Dorneles, E.M.//Horacio, E.C.//Alves, F.L.//Goncalves, L.O.//Tavares, G.S.//Stynen, A.P.//Lage, A.P.//Ruiz, J.C. 	Complete Genome Sequence of Type Strain Campylobacter fetus subsp. fetus ATCC 27374.	Genome Announcements	2016	4		e01344-16			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. 		
@D	Oliveira, M.//Barroco, C.//Mottola, C.//Santos, R.//Lemsaddek, A.//Tavares, L.//Semedo-Lemsaddek, T. 	First report of Corynebacterium pseudotuberculosis from caseous lymphadenitis lesions in Black Alentejano pig (Sus scrofa domesticus).	BMC Vet. Res.	2014	10		218			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. 		
@D	Oliveira, P.H.//Touchon, M.//Rocha, E.P. 	The interplay of restriction-modification systems with mobile genetic elements and their prokaryotic hosts.	Nucleic Acids Res.	2014	42		10618-10631			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. 		
@D	Oliveira, P.H.//Touchon, M.//Rocha, E.P. 	Regulation of genetic flux between bacteria by restriction-modification systems.	Proc. Natl. Acad. Sci. U. S. A.	2016	113		5658-5663			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. 		
@D	Oliynyk, M.//Samborskyy, M.//Lester, J.B.//Mironenko, T.//Scott, N.//Dickens, S.//Haydock, S.F.//Leadlay, P.F. 	Complete genome sequence of the erythromycinproducing bacterium Saccharopolyspora erythraea NRRL23338.	Nat. Biotechnol.	2007	25		447-453			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. 		
@D	Oller, A.R.//Vanden Broek, W.//Conrad, M.//Topal, M.D. 	Ability of DNA and spermidine to affect the activity of restriction endonucleases from several bacterial species.	Biochemistry	1991	30		2543-2549			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. 		
@D	Olmos, A.//Henriquez-Piskulich, P.//Sanchez, C.//Rojas-Herrera, M.//Moreno-Pino, M.//Gomez, M.//Rodriguez, Da.S.R.//Maracaja-Coutinho, V.//Aldea, P.//Trombert, A.N. 	Draft Genome of Chilean Honeybee (Apis mellifera) Gut Strain Lactobacillus kunkeei MP2.	Genome Announcements	2014	2		e01013-14			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. 		
@D	Olonade, I.//van Zyl, L.J.//Trindade, M. 	Draft Genome Sequences of Marine Isolates of Thalassomonas viridans and Thalassomonas actiniarum.	Genome Announcements	2015	3		e00297-15			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. 		
@D	Olsen, D.B.//Kotzorek, G.//Eckstein, F. 	Investigation of the inhibitory role of phosphorothioate internucleotidic linkages on the catalytic activity of the restriction endonuclease EcoRV.	Biochemistry	1990	29		9546-9551			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. 		
@D	Olsen, D.B.//Kotzorek, G.//Sayers, J.R.//Eckstein, F. 	Inhibition of the restriction endonuclease BanII using modified DNA substrates.	J. Biol. Chem.	1990	265		14389-14394			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. 		
@D	Olsen, D.B.//Sayers, J.R.//Kotzorek, G.//Eckstein, F. 	Interaction of restriction endonucleases with phosphorothioate-containing DNA.	Nucleosides and Nucleotides	1991	10		665-667			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. 		
@D	Olsen, R.H.//Thofner, I.C.//Pors, S.E.//Christensen, H.//Bisgaard, M.//Christensen, J.P. 	Draft Genome Sequences of Three Escherichia coli Strains with Different In Vivo Pathogenicities in an Avian (Ascending) Infection Model of the Oviduct.	Genome Announcements	2015	3		e00399-15			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. 		
@D	Olsson, B.E.//Korsakova, E.S.//Anan'ina, L.N.//Pyankova, A.A.//Mavrodi, O.V.//Plotnikova, E.G.//Mavrodi, D.V. 	Draft genome sequences of strains Salinicola socius SMB35T, Salinicola sp. MH3R3-1 and Chromohalobacter sp. SMB17 from the Verkhnekamsk potash mining region  of Russia.	Standards in Genomic Sciences	2017	12		39			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. 		
@D	Olszewski, J.//Wasserman, B.P. 	Effect of glutaraldehyde on the activity of some DNA restriction endonucleases.	Appl. Biochem. Biotechnol.	1986	13		29-35			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. 		
@D	Olvera, C.//Santamaria, R.I.//Bustos, P.//Vallejo, C.//Montor, J.J.//Wacher, C.//Lopez, M.A. 	Draft Genome Sequence of Leuconostoc citreum CW28 Isolated from Pozol, a Pre-Hispanic Fermented Corn Beverage.	Genome Announcements	2017	5		e01283-17			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. 		
@D	Olvera-Garcia, M.//Fontes-Perez, H.//Chavez-Martinez, A.//Ruiz, B.O.//Rodriguez-Almeida, F.A.//Sanchez-Flores, A.//Corral-Luna, A. 	Draft Genome Sequences for Five Strains of Trabulsiella odontotermitis, Isolated  from Heterotermes sp. Termite Gut.	Genome Announcements	2015	3		e01289-15			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. 		
@D	Omar, S.V.//Allam, M.//Joseph, L.//Mtshali, S.//Ismail, N.A.//Ismail, A. 	Draft Genome Sequence of Mycobacterium peregrinum Isolated from an HIV-Positive Patient in South Africa.	Genome Announcements	2017	5		e00759-17			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. 		
@D	Ong, K.S.//Aw, Y.K.//Gan, H.M.//Yule, C.M.//Lee, S.M. 	Draft Genome Sequences of Two Antimicrobial-Producing Burkholderia sp. Strains, MSh1 and MSh2, Isolated from Malaysian Tropical Peat Swamp Forest Soil.	Genome Announcements	2014	2		e01032-14			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. 		
@D	Ong, S.Y.//Pratap, C.B.//Wan, X.//Hou, S.//Abdul, R.A.Y.//Saito, J.A.//Nath, G.//Alam, M. 	Complete Genome Sequence of Salmonella enterica subsp. enterica Serovar Typhi P-stx-12.	J. Bacteriol.	2012	194		2115-2116			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. 		
@D	Ong, S.Y.//Pratap, C.B.//Wan, X.//Hou, S.//Rahman, A.Y.//Saito, J.A.//Nath, G.//Alam, M. 	The Genomic Blueprint of Salmonella enterica subspecies enterica serovar Typhi P-stx-12.	Standards in Genomic Sciences	2013	7		483-496			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. 		
@D	Onkendi, E.M.//Ramesh, A.M.//Kwenda, S.//Naidoo, S.//Moleleki, L. 	Draft Genome Sequence of a Virulent Pectobacterium carotovorum subsp. brasiliense Isolate Causing Soft Rot of Cucumber.	Genome Announcements	2016	4		e01530-15			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. 		
@D	Ono, A.//Matsuo, Y.//Matsuda, A.//Ueda, T. 	Nucleosides and nucleotides. CXIX. Inhibition of DNA-cytosine methylase HhaI by a self-complementary oligonucleotide containing 5-fluorocytosine.	Biol. Pharm. Bull.	1993	16		529-533			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). 		
@D	Ono, A.//Ohtani, Y.//Sato, M.//Ueda, T. 	Oligodeoxynucleotides containing 7-deazaadenine: synthesis and recognition by restriction.	Nucleic Acids Symp. Ser.	1983	12		67-70			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. 		
@D	Ono, A.//Sato, M.//Ohtani, Y.//Ueda, T. 	Synthesis of deoxyoligonucleotides containing 7-deazaadenine: recognition and cleavage by restriction endonuclease BglII and Sau3AI.	Nucleic Acids Res.	1984	12		8939-8949			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. 		
@D	Ono, A.//Ueda, T. 	Synthesis of decadeoxyribonucleotides containing N6-methyladenine, N4-methylcytosine, and 5-methylcytosine: recognition and cleavage by restriction endonucleases (nucleosides and nucleotides part 74).	Nucleic Acids Res.	1987	15		219-232			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. 		
@D	Ono, A.//Ueda, T. 	Minor-groove-modified oligonucleotides: synthesis of decadeoxynucleotides containing hypoxanthine, N2-methylguanine and 3-deazaadenine, and their interactions with restriction endonucleases BglII, Sau3AI, and MboI.	Nucleic Acids Res.	1987	15		3059-3072			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. 		
@D	Onodera, N.T.//Ryu, J.//Durbic, T.//Nislow, C.//Archibald, J.M.//Rohde, J.R. 	Genome Sequence of Shigella flexneri Serotype 5a Strain M90T Sm.	J. Bacteriol.	2012	194		3022			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). 		
@D	Onyango, M.//Wang, Y.//Nickel, O.//Zhao, C.//Zhang, X.//Hartke, A.//Hemberger, J.//Cemic, F. 	First Genome Sequence of Potential Mycotoxin-Degrading Bacterium Devosia nanyangense DDB001.	Genome Announcements	2014	2		e00922-14			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. 		
@D	Ooi, S.K.//Qiu, C.//Bernstein, E.//Li, K.//Jia, D.//Yang, Z.//Erdjument-Bromage, H.//Tempst, P.//Lin, S.P.//Allis, C.D.//Cheng, X.//Bestor, T.H. 	DNMT3L connects unmethylated lysine 4 of histone H3 to de novo methylation of DNA.	Nature	2007	448		714-717			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. 		
@D	Ooka, T.//Ogura, Y.//Katsura, K.//Seto, K.//Kobayashi, H.//Kawano, K.//Tokuoka, E.//Furukawa, M.//Harada, S.//Yoshino, S.//Seto, J.//Ikeda, T.//Yamaguchi, K.//Murase, K.//Gotoh, Y.//Imuta, N.//Nishi, J.//Gomes, T.A.//Beutin, L.//Hayashi, T. 	Defining the genome features of Escherichia albertii, an emerging enteropathogen closely related to Escherichia coli.	Genome Biol. Evol.	2015	7		3170-3179			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. 		
@D	Oosterkamp, M.J. et al. 	Genome sequences of Alicycliphilus denitrificans strains BC and K601T.	J. Bacteriol.	2011	193		5028-5029			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). 		
@D	Ootsuka, M.//Nishizawa, T.//Ohta, H. 	Complete Genome Sequence of the Nonylphenol-Degrading Bacterium Sphingobium cloacae JCM 10874T.	Genome Announcements	2016	4		e01358-16			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. 		
@D	Opazo, A.//Lopes, B.S.//Garcia, P.//Dominguez, Y.M.//Lima, C.//Bello-Toledo, H.//Gonzalez-Rocha, G.//Amyes, S.G. 	Draft Genome Sequence of a Multidrug-Resistant Acinetobacter baumannii Strain from Chile.	Genome Announcements	2015	3		e00687-15			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. 		
@D	Opazo, R.//Gajardo, F.//Ruiz, M.//Romero, J. 	Genome Sequence of a Lactococcus lactis Strain Isolated from Salmonid Intestinal  Microbiota.	Genome Announcements	2016	4		e00881-16			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. 		
@D	Orata, F.D.//Kits, K.D.//Stein, L.Y. 	Complete Genome Sequence of Methylomonas denitrificans Strain FJG1, an Obligate Aerobic Methanotroph That Can Couple Methane Oxidation with Denitrification.	Genome Announcements	2018	6		e00276-18			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. 		
@D	Orata, F.D.//Rosana, A.R.//Xu, Y.//Simkus, D.N.//Bramucci, A.R.//Boucher, Y.//Case, R.J. 	Draft Genome Sequences of Four Bacterial Strains Isolated from a Polymicrobial Culture of Naked (N-Type) Emiliania huxleyi CCMP1516.	Genome Announcements	2016	4		e00674-16			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. 		
@D	Ordinario, D.D.//Burke, A.M.//Long, P.//Jocson, J.-M.//Wang, H.//Dickson, M.N.//Gorodetsky, A.A. 	Sequence Specific Detection of Restriction Enzymes at DNA-Modified Carbon Nanotube Field Effect Transistors.	Anal. Chem.	2014	86		8628-8633			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. 		
@D	Ordogh, L.//Hunyadkurti, J.//Voros, A.//Horvath, B.//Szucs, A.//Urban, E.//Kereszt, A.//Kondorosi, E.//Nagy, I. 	Complete Genome Sequence of Propionibacterium avidum Strain 44067, Isolated from  a Human Skin Abscess.	Genome Announcements	2013	1		e00337-13			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. 		
@D	Ordonez, O.F.//Lanzarotti, E.//Kurth, D.//Gorriti, M.F.//Revale, S.//Cortez, N.//Vazquez, M.P.//Farias, M.E.//Turjanski, A.G. 	Draft Genome Sequence of the Polyextremophilic Exiguobacterium sp. Strain S17, Isolated from Hyperarsenic Lakes in the Argentinian Puna.	Genome Announcements	2013	1		e00480-13			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. 		
@D	Orduna, P.//Cevallos, M.A.//de Leon, S.P.//Arvizu, A.//Hernandez-Gonzalez, I.L.//Mendoza-Hernandez, G.//Lopez-Vidal, Y. 	Genomic and proteomic analyses of Mycobacterium bovis BCG Mexico 1931 reveal a diverse immunogenic repertoire against tuberculosis infection.	BMC Genomics	2011	12		493			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. 		
@D	Ordway, J.M.//Bedell, J.A.//Citek, R.W.//Nunberg, A.N.//Jeddeloh, J.A. 	MethylIMapper: a method for high-throughput, multilocus bisulfite sequence analysis and reporting.	Biotechniques	2005	39		464-468			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. 		
@D	Orekhov, A.V.//Rebentish, B.A.//Debabov, V.G. 	A new site-specific endonuclease from Streptomyces -- SgrII.	Dokl. Akad. Nauk.	1982	263		217-220			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. 		
@D	Orekhov, A.V.//Strokina, I.V.//Foors, A.R. 	Restriction of shuttle Escherichia coli - Streptomyces plasmids in Streptomyces Lividans 66.	Genetika	1989	25		614-625			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. 		
@D	Orellana, P.//Pavon, A.//Cespedes, S.//Salazar, L.//Gutierrez, A.//Castillo, D.//Corsini, G. 	Draft Genome Sequence of Chilean Antarctic Pseudomonas sp. Strain K2I15.	Genome Announcements	2017	5		e00771-17			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. 		
@D	Orlowski, J.//Boniecki, M.//Bujnicki, J.M. 	I-Ssp6803I: the first homing endonuclease from the PD-(D/E)XK superfamily exhibits an unusual mode of DNA recognition.	Bioinformatics	2007	23		527-530			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. 		
@D	Orlowski, J.//Bujnicki, J.M. 	Structural and evolutionary classification of Type II restriction enzymes based on theoretical and experimental analyses.	Nucleic Acids Res.	2008	36		3552-3569			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. 		
@D	Orlowski, J.//Mebrhatu, M.T.//Michiels, C.W.//Bujnicki, J.M.//Aertsen, A. 	Mutational analysis and a structural model of methyl-directed restriction enzyme Mrr.	Biochem. Biophys. Res. Commun.	2008	377		862-866			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. 		
@D	Ormeno-Orrillo, E. et al. 	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.).	BMC Genomics	2012	13		735			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. 		
@D	Ormeno-Orrillo, E.//Aguilar-Cuba, Y.//Zuniga-Davila, D. 	Draft Genome Sequence of Rhizobium sophoriradicis H4, a Nitrogen-Fixing Bacterium Associated with the Leguminous Plant Phaseolus vulgaris on the Coast of Peru.	Genome Announcements	2018	6		e00241-18			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). 		
@D	Ormeno-Orrillo, E.//Rogel, M.A.//Chueire, L.M.//Tiedje, J.M.//Martinez-Romero, E.//Hungria, M. 	Genome Sequences of Burkholderia sp. Strains CCGE1002 and H160, Isolated from Legume Nodules in Mexico and Brazil.	J. Bacteriol.	2012	194		6927			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. 		
@D	Ormeno-Orrillo, E.//Rogel, M.A.//Zuniga-Davila, D.//Martinez-Romero, E. 	Complete Genome Sequence of the Symbiotic Strain Bradyrhizobium icense LMTR 13(T), Isolated from Lima Bean (Phaseolus lunatus) in Peru.	Genome Announcements	2018	6		e00146-18			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. 		
@D	Ormsby, M.J.//Johnson, S.A.//Wall, D.M. 	Draft Genome Sequence of the Commensal Escherichia coli Strain F-18.	Genome Announcements	2016	4		e01416-16			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. 		
@D	Oroguchi, T.//Hashimoto, H.//Shimizu, T.//Sato, M.//Ikeguchi, M. 	Intrinsic Dynamics of Restriction Endonuclease EcoO109I Studied by Molecular Dynamics Simulations and X-Ray Scattering Data Analysis.	Biophys. J.	2009	96		2808-2822			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. 		
@D	Orr, R.J.S.//Rombauts, S.//Van de Peer, Y.//Shalchian-Tabrizi, K. 	Draft Genome Sequences of Two Unclassified Chitinophagaceae Bacteria, IBVUCB1 and IBVUCB2, Isolated from Environmental Samples.	Genome Announcements	2017	5		e00787-17			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. 		
@D	Orr, R.J.S.//Rombauts, S.//Van de Peer, Y.//Shalchian-Tabrizi, K. 	Draft Genome Sequences of Two Unclassified Bacteria, Sphingomonas sp. Strains IBVSS1 and IBVSS2, Isolated from Environmental Samples.	Genome Announcements	2017	5		e00894-17			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. 		
@D	Orr, R.J.S.//Rombauts, S.//Van de Peer, Y.//Shalchian-Tabrizi, K. 	Draft Genome Sequences of Two Unclassified Bacteria, Hydrogenophaga sp. Strains IBVHS1 and IBVHS2, Isolated from Environmental Samples.	Genome Announcements	2017	5		e00884-17			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. 		
@D	Orru, L.//Salvetti, E.//Cattivelli, L.//Lamontanara, A.//Michelotti, V.//Capozzi, V.//Spano, G.//Keller, D.//Cash, H.//Martina, A.//Torriani, S.//Felis, G.E. 	Draft Genome Sequence of Bacillus coagulans GBI-30, 6086, a Widely Used Spore-Forming Probiotic Strain.	Genome Announcements	2014	2		e01080-14			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. 		
@D	Orsini, M.//Cornacchia, A.//Patavino, C.//Torresi, M.//Centorame, P.//Acciari, V.A.//Ruolo, A.//Marcacci, M.//Ancora, M.//Di Domenico, M.//Mangone, I.//Blasi, G.//Duranti, A.//Camma, C.//Pomilio, F.//Migliorati, G. 	Whole-Genome Sequences of Two Listeria monocytogenes Serovar 1/2a Strains Responsible for a Severe Listeriosis Outbreak in Central Italy.	Genome Announcements	2018	6		e00236-18			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. 		
@D	Orsini, M.//Krasteva, I.//Marcacci, M.//Ancora, M.//Ciammaruconi, A.//Gentile, B.//Lista, F.//Pini, A.//Scacchia, M.//Sacchini, F.//Camma, C. 	Whole-Genome Sequencing of Mycoplasma mycoides subsp. mycoides Italian Strain 57/13, the Causative Agent of Contagious Bovine Pleuropneumonia.	Genome Announcements	2015	3		e00197-15			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. 		
@D	Orsini, M.//Mangone, I.//DiPasquale, A.//Perticara, S.//Sacchini, L.//Cito, F.//Iannetti, S.//Marcacci, M.//Ancora, M.//Calistri, P.//Di Giannatale, E.//Camma, C. 	Draft Genome Sequences of 19 Salmonella enterica Serovar Typhimurium [4,5:i:-] Strains Resistant to Nalidixic Acid from a Long-Term Outbreak in Italy.	Genome Announcements	2015	3		e00911-15			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. 		
@D	Ortega, D.B.//Costa, R.A.//Pires, A.S.//Araujo, T.F.//Araujo, J.F.//Kurokawa, A.S.//Magalhaes, B.S.//Reis, A.M.M.//Franco, O.L.//Kruger, R.H.//Pappas, G.J. Jr.//Barreto, C.C. 	Draft Genome Sequence of the Antimicrobial-Producing Strain Paenibacillus elgii AC13.	Genome Announcements	2018	6		e00573-18			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. 		
@D	Ortet, P.//Barakat, M.//Lalaouna, D.//Fochesato, S.//Barbe, V.//Vacherie, B.//Santaella, C.//Heulin, T.//Achouak, W. 	Complete Genome Sequence of a beneficial plant root-associated bacterium Pseudomonas brassicacearum.	J. Bacteriol.	2011	193		3146			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. 		
@D	Ortet, P.//Gallois, N.//Piette, L.//Long, J.//Berthomieu, C.//Armengaud, J.//Barakat, M.//Chapon, V. 	Draft Genome Sequence of Microbacterium oleivorans Strain A9, a Bacterium Isolated from Chernobyl Radionuclide-Contaminated Soil.	Genome Announcements	2017	5		e00092-17			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. 		
@D	Ortiz, E.M.//Berretta, M.F.//Navas, L.E.//Benintende, G.B.//Amadio, A.F.//Zandomeni, R.O. 	Draft Genome Sequence of Geobacillus sp. Isolate T6, a Thermophilic Bacterium Collected from a Thermal Spring in Argentina.	Genome Announcements	2015	3		e00743-15			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. 		
@D	Osama, A.//Gan, H.M.//Teh, C.S.//Yap, K.P.//Thong, K.L. 	Genome Sequence and Comparative Genomics Analysis of a Vibrio cholerae O1 Strain  Isolated from a Cholera Patient in Malaysia.	J. Bacteriol.	2012	194		6933			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. 		
@D	Osborne, A.J.//Jose, B.R.//Perry, J.//Smeele, Z.//Aitken, J.//Gardner, P.P.//Slow, S. 	Complete Genome Sequences of Two Geographically Distinct Legionella micdadei Clinical Isolates.	Genome Announcements	2017	5		e00436-17			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. 		
@D	Osdaghi, E.//Forero, S.N.//Bolot, S.//Fischer-Le, S.M.//Jacques, M.A.//Portier, P.//Carrere, S.//Koebnik, R. 	High-Quality Draft Genome Sequence of Curtobacterium sp. Strain Ferrero.	Genome Announcements	2017	5		e01378-17			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. 		
@D	Osei-Sekyere, J.//Amoako, D.G. 	Genomic and phenotypic characterisation of fluoroquinolone resistance mechanisms in Enterobacteriaceae in Durban, South Africa.	PLoS ONE	2017	12		E0178888			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. 		
@D	Oshiki, M.//Fukushima, T.//Kawano, S.//Nakagawa, J. 	Draft Genome Sequence of Thiohalobacter thiocyanaticus Strain FOKN1, a Neutrophilic Halophile Capable of Thiocyanate Degradation.	Genome Announcements	2017	5		e00799-17			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. 		
@D	Oshiki, M.//Shinyako-Hata, K.//Satoh, H.//Okabe, S. 	Draft Genome Sequence of an Anaerobic Ammonium-Oxidizing Bacterium, 'Candidatus Brocadia sinica'.	Genome Announcements	2015	3		e00267-15			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. 		
@D	Oshima, H.//Asai, K.//Sadaie, Y. 	Restriction and modification system genes of Bacillus subtilis.	Genes Genet. Syst.	2000	75		380			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. 		
@D	Oshima, K.//Hattori, M.//Shimizu, H.//Fukuda, K.//Nemoto, M.//Inagaki, K.//Tamura, T. 	Draft Genome Sequence of Streptomyces incarnatus NRRL8089, which Produces the Nucleoside Antibiotic Sinefungin.	Genome Announcements	2015	3		e00715-15			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. 		
@D	Oshima, K.//Hayashi, J.//Toh, H.//Nakano, A.//Omori, E.//Hattori, Y.//Morita, H.//Honda, K.//Hattori, M. 	Complete Genome Sequence of Scardovia inopinata JCM 12537T, Isolated from Human Dental Caries.	Genome Announcements	2015	3		e00481-15			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. 		
@D	Oshima, K.//Hayashi, J.//Toh, H.//Nakano, A.//Shindo, C.//Komiya, K.//Morita, H.//Honda, K.//Hattori, M. 	Complete Genome Sequence of Parascardovia denticolens JCM 12538T, Isolated from Human Dental Caries.	Genome Announcements	2015	3		e00485-15			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. 		
@D	Oshima, K.//Hisamatsu, S.//Toh, H.//Nakano, A.//Kiuchi, M.//Kuroyanagi, H.//Morita, H.//Hattori, M. 	Complete Genome Sequence of Gardnerella vaginalis Strain JCM 11026T, Isolated from Vaginal Tracts of Women.	Genome Announcements	2015	3		e00286-15			Gardnerella vaginalis strain JCM 11026(T) was isolated from vaginal tracts of women. Here, we report the complete genome sequence of this organism. 		
@D	Oshima, T. et al. 	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).	DNA Res.	1996	3		211-223			none 		
@D	Oshima, T. et al. 	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.	DNA Res.	1996	3		137-155			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. 		
@D	Oshima, T.//Wada, C.//Kawagoe, Y.//Ara, T.//Maeda, M.//Masuda, Y.//Hiraga, S.//Mori, H. 	Genome-wide analysis of deoxyadenosine methyltransferase-mediated control of gene expression in Escherichia coli.	Mol. Microbiol.	2002	45		673-695			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. 		
@D	Oshkin, I.Y.//Miroshnikov, K.K.//Belova, S.E.//Korzhenkov, A.A.//Toshchakov, S.V.//Dedysh, S.N. 	Draft Genome Sequence of Methylovulum psychrotolerans Sph1(T), an Obligate Methanotroph from Low-Temperature Environments.	Genome Announcements	2018	6		e01488-17			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. 		
@D	Oshone, R.//Hurst, S.G. IV//Abebe-Akele, F.//Simpson, S.//Morris, K.//Thomas, W.K.//Tisa, L.S. 	Permanent Draft Genome Sequences for Two Variants of Frankia sp. Strain CpI1, the First Frankia Strain Isolated from Root Nodules of Comptonia peregrina.	Genome Announcements	2016	4		e01588-15			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. 		
@D	Oshone, R.//Ngom, M.//Abebe-Akele, F.//Simpson, S.//Morris, K.//Sy, M.O.//Champion, A.//Thomas, W.K.//Tisa, L.S. 	Permanent Draft Genome Sequence of Frankia sp. Strain Allo2, a Salt-Tolerant Nitrogen-Fixing Actinobacterium Isolated from the Root Nodules of Allocasuarina.	Genome Announcements	2016	4		e00388-16			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. 		
@D	Osieka, V.//Grobbel, M.//Schmoger, S.//Szentiks, C.A.//Irrgang, A.//Kasbohrer, A.//Tenhagen, B.A.//Hammerl, J.A. 	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.	Genome Announcements	2018	6		e00599-18			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. 		
@D	Osipiuk, J.//Walsh, M.A.//Joachimiak, A. 	Crystal structure of MboIIA methyltransferase.	Nucleic Acids Res.	2003	31		5440-5448			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. 		
@D	Oskam, L.//Hillenga, D.J.//Venema, G.//Bron, S. 	The integrated state of the rolling-circle plasmid pTB913 in the composite Bacillus plasmid pTB19.	Mol. Gen. Genet.	1992	233		462-468			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. 		
@D	Osman, W.A.M.//van Berkum, P.//Leon-Barrios, M.//Velazquez, E.//Elia, P.//Tian, R.//Ardley, J.//Gollagher, M.//Seshadri, R.//Reddy, T.B.K.//Ivanova, N.//Woyke, T.//Pati, A.//Markowitz, V.//Baeshen, M.N.//Baeshen, N.N.//Kyrpides, N.//Reeve, W. 	High-quality draft genome sequence of Ensifer meliloti Mlalz-1, a microsymbiont of Medicago laciniata (L.) miller collected in Lanzarote, Canary Islands, Spain.	Standards in Genomic Sciences	2017	12		58			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. 		
@D	Ossandon, F.J.//Cardenas, J.P.//Corbett, M.//Quatrini, R.//Holmes, D.S.//Watkin, E. 	Draft Genome Sequence of the Iron-Oxidizing, Acidophilic, and Halotolerant 'Thiobacillus prosperus' Type Strain DSM 5130.	Genome Announcements	2014	2		e01042-14			'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. 		
@D	Ostendorf, T.//Cherepanov, P.//deVries, J.//Wachernagel, W. 	Characterization of a dam mutant of Serratia marcescens and nucleotide sequence of the dam region.	J. Bacteriol.	1999	181		3880-3885			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. 		
@D	Osterlund, M.//Luthman, H.//Nilsson, S.V.//Magnusson, G. 	Ethidium-bromide-inhibited restriction endonucleases cleave one strand of circular DNA.	Gene	1982	20		121-125			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. 		
@D	Osterman, D.G.//DePillis, G.D.//Wu, J.C.//Matsuda, A.//Santi, D.V. 	5-Fluorocytosine in DNA is a mechanism-based inhibitor of HhaI methylase.	Biochemistry	1988	27		5204-5210			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. 		
@D	Osterman, J.//Marsh, J.//Laine, P.//Zeng, Z.//Alatalo, E.//Sullivan, J.T.//Young, J.P.//Thomas-Oates, J.//Paulin, L.//Lindstrom, K. 	Genome sequencing of two Neorhizobium galegae strains reveals a noeT gene responsible for the unusual acetylation of the nodulation factors.	BMC Genomics	2014	15		500			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. 		
@D	Ostroff, G.R.//Pene, J.J. 	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.	J. Bacteriol.	1983	156		934-936			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. 		
@D	Ostroff, G.R.//Pene, J.J. 	Molecular cloning with bifunctional plasmid vectors in Bacillus subtilis.  II.  Transfer of sequences propagated in Escherichia coli to B. subtilis.	Mol. Gen. Genet.	1984	193		306-311			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. 		
@D	Ostrov, I.//Sela, N.//Freed, M.//Khateb, N.//Kott-Gutkowski, M.//Inbar, D.//Shemesh, M. 	Draft Genome Sequence of Bacillus licheniformis S127, Isolated from a Sheep Udder Clinical Infection.	Genome Announcements	2015	3		e00971-15			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. 		
@D	Osuna, J.//Flores, H.//Soberon, X. 	Combinatorial mutagenesis of three major groove-contacting residues of EcoRI: single and double amino acid replacements retaining methyltransferase-sensitive activities.	Gene	1991	106		7-12			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. 		
@D	Oswald, T.//Hornbostel, G.//Rinas, U.//Anspach, F.B. 	Purification of (His)6EcoRV [recombinant restriction endonuclease EcoRV fused to a (His)6 affinity domain] by metal-chelate affinity chromatography.	Biotechnol. Appl. Biochem.	1997	25		109-115			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. 		
@D	Oswald, T.//Rinas, U. 	Chloramphenicol resistance interferes with purification of histidine-tagged fusion proteins from recombinant Escherichia coli.	Anal. Biochem.	1996	236		357-358			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. 		
@D	Oswald, T.//Wende, W.//Pingoud, A.//Rinas, U. 	Comparison of N-terminal affinity fusion domains: effect on expression level and product heterogeneity of recombinant restriction endonuclease EcoRV.	Appl. Microbiol. Biotechnol.	1994	42		73-77			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. 		
@D	Otani, J.//Nankumo, T.//Arita, K.//Inamoto, S.//Ariyoshi, M.//Shirakawa, M. 	Structural basis for recognition of H3K4 methylation status by the DNA methyltransferase 3A ATRX-DNMT3-DNMT3L domain.	EMBO Rep.	2009	10		1235-1241			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. 		
@D	Ott, B.M.//Beka, L.//Graf, J.//Rio, R.V. 	Draft Genome Sequence of Pedobacter sp. Strain Hv1, an Isolate from Medicinal Leech Mucosal Castings.	Genome Announcements	2015	3		e01469-15			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. 		
@D	Ott, J.//Eckstein, F. 	31P NMR spectral analysis of the dodecamer d(CGCGAATTCGCG).	Biochemistry	1985	24		2530-2535			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]. 		
@D	Ou, H.Y.//He, X.//Shao, Y.//Tai, C.//Rajakumar, K.//Deng, Z. 	dndDB: a database focused on phosphorothioation of the DNA backbone.	PLoS ONE	2009	4		e5132			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/. 		
@D	Oude Essink, B.B.//Berkhout, B. 	The restriction enzyme BanI is inhibited by dcm-methylation of the GGCGCm5C site.	Nucleic Acids Res.	1994	22		108			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. 		
@D	Ouellette, M.//Gogarten, J.P.//Lajoie, J.//Makkay, A.M.//Papke, R.T. 	Characterizing the DNA Methyltransferases of Haloferax volcanii via Bioinformatics, Gene Deletion, and SMRT Sequencing.	Genes (Basel)	2018	9		E129			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. 		
@D	Ouellette, M.//Jackson, L.//Chimileski, S.//Papke, R.T. 	Genome-wide DNA methylation analysis of Haloferax volcanii H26 and identification of DNA methyltransferase related PD-(D/E)XK nuclease family protein HVO_A0006.	Front. Microbiol.	2015	6		251			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. 		
@D	Ouwerkerk, J.P.//Koehorst, J.J.//Schaap, P.J.//Ritari, J.//Paulin, L.//Belzer, C.//de Vos, W.M. 	Complete Genome Sequence of Akkermansia glycaniphila Strain PytT, a Mucin-Degrading Specialist of the Reticulated Python Gut.	Genome Announcements	2017	5		e01098-16			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. 		
@D	Ovechkina, L.G.//Zinoviev, V.V.//Gorbunov, Y.A.//Malygin, E.G. 	The oligomerization of phage T4 DNA-(adenine-N-6)-methyltransferase and its effect on the catalytic characteristics of the enzyme.	Bioorg. Khim.	2000	26		940-943			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. 		
@D	Overballe-Petersen, S.//Roer, L.//Ng, K.//Hansen, F.//Justesen, U.S.//Andersen, L.P.//Stegger, M.//Hammerum, A.M.//Hasman, H. 	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.	Genome Announcements	2018	6		e01542-17			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. 		
@D	Overholt, W.A.//Green, S.J.//Marks, K.P.//Venkatraman, R.//Prakash, O.//Kostka, J.E. 	Draft genome sequences for oil-degrading bacterial strains from beach sands impacted by the deepwater horizon oil spill.	Genome Announcements	2013	1		e01015-13			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. 		
@D	Ozdemir, O. 	The construction of a mammalian transfection vector for expression of cytosine-5 specific DNA methyltransferase gene M.MspI in cultured cells.	Turkish J. Biol.	1998	22		161-170			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. 		
@D	Ozdemir, O.//Hornby, D. 	In vivo DNA methylation of Escherichia coli DH5a and top10F' strains by bacterial cytosine-5 methyltransferase M.MspI.	Turkish J. Biol.	1998	22		143-151			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. 		
@D	Ozer, E.A.//Allen, J.P.//Hauser, A.R. 	Draft Genome Sequence of the Pseudomonas aeruginosa Bloodstream Isolate PABL056.	J. Bacteriol.	2012	194		5999			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. 		
@D	Ozer, E.A.//Fitzpatrick, M.A.//Hauser, A.R. 	Draft Genome Sequence of Acinetobacter baumannii Strain ABBL099, a Multidrug-Resistant Clinical Outbreak Isolate with a Novel Multilocus Sequence  Type.	Genome Announcements	2014	2		e00738-14			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. 		
@D	Ozer, E.A.//Hauser, A.R.//Gerding, D.N.//Espinosa, R.O.//Hecht, D.W.//Kociolek, L.K. 	Complete Genome Sequence of Clostridioides difficile Epidemic Strain DH/NAP11/106/ST-42, Isolated from Stool from a Pediatric Patient with Diarrhea.	Genome Announcements	2017	5		e00923-17			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. 		
@D	Ozer, E.A.//Morris, A.R.//Krapp, F.//Henry, C.S.//Tyo, K.E.//Lathem, W.W.//Hauser, A.R. 	Draft Genome Sequence of a Multidrug-Resistant Klebsiella quasipneumoniae subsp.  similipneumoniae Isolate from a Clinical Source.	Genome Announcements	2016	4		e00422-16			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. 		
@D	Pabo, C.O. 	Specificity by design - The specificity of a homing endonuclease has been altered using computational modeling of the protein-DNA interface.	Nat. Biotechnol.	2006	24		954-955			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. 		
@D	Pace, L.A.//Hemp, J.//Ward, L.M.//Fischer, W.W. 	Draft Genome of Thermanaerothrix daxensis GNS-1, a Thermophilic Facultative Anaerobe from the Chloroflexi Class Anaerolineae.	Genome Announcements	2015	3		e01354-15			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. 		
@D	Pachebat, J.A.//van Keulen, G.//Whitten, M.M.//Girdwood, S.//Del Sol, R.//Dyson, P.J.//Facey, P.D. 	Draft Genome Sequence of Rhodococcus rhodnii Strain LMG5362, a Symbiont of Rhodnius prolixus (Hemiptera, Reduviidae, Triatominae), the Principle Vector of  Trypanosoma cruzi.	Genome Announcements	2013	1		e00329-13			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. 		
@D	Pacheco, L.G.//Castro, T.L.//Carvalho, R.D.//Moraes, P.M.//Dorella, F.A.//Carvalho, N.B.//Slade, S.E.//Scrivens, J.H.//Feelisch, M.//Meyer, R.//Miyoshi, A.//Oliveira, S.C.//Dowson, C.G.//Azevedo, V. 	A Role for Sigma Factor sigma(E) in Corynebacterium pseudotuberculosis Resistance to Nitric Oxide/Peroxide Stress.	Front. Microbiol.	2012	3		126			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. 		
@D	Pacheco-Montealegre, M.//Patino, R.E.//Torres, L.//Jimenez, S.//Rodriguez, J.L.//Caro-Quintero, A. 	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.	Standards in Genomic Sciences	2017	12		89					
@D	Pachkunov, D.M.//Kramarov, B.M.//Dobritsa, A.P.//Matvienko, N.I. 	Site-specific endonuclease BmeI from Bacillus Megaterium 216.	Bioorg. Khim.	1983	9		127-129			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. 		
@D	Pack, S.P.//Doi, A.//Choi, Y.S.//Kodaki, T.//Makino, K. 	Biomolecular response of oxanine in DNA strands to T4 polynucleotide kinase, T4 DNA ligase, and restriction enzymes.	Biochem. Biophys. Res. Commun.	2010	391		118-122			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. 		
@D	Padegimiene, E.//Maneliene, Z.//Petrusyte, M.//Janulaitis, A. 	OliI, a unique restriction endonuclease that recognizes the discontinuous sequence 5'-CACNN/NNGTG-3'.	Nucleic Acids Res.	2001	29		e30			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. 		
@D	Padhy, R.N.//Hottat, F.G.//Coene, M.M.//Hoet, P.P. 	Restriction analysis and quantitative estimation of methylated bases of filamentous and unicellular cyanobacterial DNAs.	J. Bacteriol.	1988	170		1934-1939			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). 		
@D	Padilla, J.C.//Bustos, P.//Castro-Escarpulli, G.//Sanchez-Varela, A.//Palma-Martinez, I.//Arzate-Barbosa, P.//Garcia-Perez, C.A.//Lopez-Lopez, M.J.//Gonzalez, V.//Guo, X. 	Draft Genome Sequence of Aeromonas caviae Strain 429865 INP, Isolated from a Mexican Patient.	Genome Announcements	2015	3		e01240-15			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. 		
@D	Padmanabhan, R.//Dubourg, G.//Lagier, J.C.//Couderc, C.//Michelle, C.//Raoult, D.//Fournier, P.E. 	Genome sequence and description of Corynebacterium ihumii sp. nov.	Standards in Genomic Sciences	2014	9		1128-1143			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. 		
@D	Padmanabhan, R.//Dubourg, G.//Nguyen, T.T.//Couderc, C.//Rossi-Tamisier, M.//Caputo, A.//Raoult, D.//Fournier, P.E. 	Non-contiguous finished genome sequence and description of Collinsella massiliensis sp. nov.	Standards in Genomic Sciences	2014	9		1144-1158			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. 		
@D	Padmanabhan, R.//Lagier, J.C.//Dangui, N.P.//Michelle, C.//Couderc, C.//Raoult, D.//Fournier, P.E. 	Non-contiguous finished genome sequence and description of Megasphaera massiliensis sp. nov.	Standards in Genomic Sciences	2013	8		525-538			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. 		
@D	Padmanabhan, R.//Robert, C.//Fenollar, F.//Raoult, D.//Fournier, P.E. 	Draft Genome Sequence of Necropsobacter rosorum Strain P709T.	Genome Announcements	2014	2		e00913-14			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. 		
@D	Pagani, I. et al. 	Complete genome sequence of Desulfobulbus propionicus type strain (1pr3).	Standards in Genomic Sciences	2011	4		100-110			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. 		
@D	Pagani, I. et al. 	Complete genome sequence of Marivirga tractuosa type strain (H-43).	Standards in Genomic Sciences	2011	4		154-162			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. 		
@D	Pagie, L.//Hogeweg, P. 	Individual- and population-based diversity in restriction-modification systems.	Bull. Math. Biol.	2000	62		759-774			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. 		
@D	Pagnier, I.//Boughalmi, M.//Croce, O.//Robert, C.//Raoult, D.//La Scola, B. 	Genome Sequence of Legionella tunisiensis Strain LegMT, a New Legionella Species  Isolated from Hypersaline Lake Water.	J. Bacteriol.	2012	194		5978			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. 		
@D	Pagnier, I.//Croce, O.//Robert, C.//Raoult, D.//La Scola, B. 	Non-contiguous finished genome sequence and description of Anaerococcus pacaensis sp. nov., a new species of anaerobic bacterium.	Standards in Genomic Sciences	2013	8		548-560			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. 		
@D	Pagnier, I.//Croce, O.//Robert, C.//Raoult, D.//La Scola, B. 	Genome Sequence of Legionella anisa, Isolated from a Respiratory Sample, Using an Amoebal Coculture Procedure.	Genome Announcements	2014	2		e00031-14			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. 		
@D	Pagnier, I.//Croce, O.//Robert, C.//Raoult, D.//La Scola, B. 	Non-contiguous finished genome sequence and description of Anaerococcus provenciensis sp. nov.	Standards in Genomic Sciences	2014	9		1198-1210			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%. 		
@D	Pagnier, I.//Croce, O.//Robert, C.//Raoult, D.//La Scola, B. 	Non-contiguous finished genome sequence and description of Fenollaria massiliensis gen. nov., sp. nov., a new genus of anaerobic bacterium.	Standards in Genomic Sciences	2014	9		704-717			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. 		
@D	Pagnier, I.//Croce, O.//Robert, C.//Raoult, D.//La Scola, B. 	Genome Sequence of Reyranella massiliensis, a Bacterium Associated with Amoebae.	J. Bacteriol.	2012	194		5698			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. 		
@D	Pagnier, I.//Croce, O.//Robert, C.//Raoult, D.//La Scola, B. 	Genome Sequence of Afipia birgiae, a Rare Bacterium Associated with Amoebae.	J. Bacteriol.	2012	194		7018			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. 		
@D	Pagnier, I.//Croce, O.//Robert, C.//Raoult, D.//La Scola, B. 	Genome Sequence of Legionella massiliensis, Isolated from a Cooling Tower Water Sample.	Genome Announcements	2014	2		e01068-14			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. 		
@D	Pai, S.-H.//Chuang, J.-Z.//Kou, M.-C.//Hsu, T.-T. 	Purification of EcoRI endonuclease on heparin sepharose-4B column chromatography.	Proc. Natl. Sci. Counc. Repub. China B	1984	8		41-45			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. 		
@D	Paigen, K.//Weinfeld, H. 	Cooperative infection by host-modified lambda phage.	Virology	1963	19		565-572			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. 		
@D	Paim, T.G.//Pieta, L.//Prichula, J.//Sambrano, G.E.//Soares, R.//Bello, A.D.//Frazzon, J.//d'Azevedo, P.A. 	Draft Genome Sequence of Enterococcus faecalis Strain F165 Isolated from a Urinary Tract Infection.	Genome Announcements	2016	4		e01084-16			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. 		
@D	Paim, T.G.//Pieta, L.//Prichula, J.//Sambrano, G.E.//Soares, R.//Caierao, J.//Frazzon, J.//d'Azevedo, P.A. 	Draft Genome Sequence of Brazilian Escherichia coli Uropathogenic Strain E2.	Genome Announcements	2016	4		e01085-16			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. 		
@D	Paixao, T.A.//Coura, F.M.//Malta, M.C.//Tinoco, H.P.//Pessanha, A.T.//Pereira, F.L.//Leal, C.A.//Heinemann, M.B.//Figueiredo, H.C.//Santos, R.L. 	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.	Genome Announcements	2016	4		e01590-15			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. 		
@D	Pajunen, M.I.//Elizondo, M.R.//Skurnik, M.//Kieleczawa, J.//Molineux, I.J. 	Complete nucleotide sequence and likely recombinatorial origin of bacteriophage T3.	J. Mol. Biol.	2002	319		1115-1132			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. 		
@D	Pak, C.M.//Kim, U.Y.//Ra, S.R. 	Study on recognization and cleavage characteristics of restriction enzyme Bci528I.	Choson Minjujuui Inmin Konghwaguk Kwahagwon Tongbo	2009	98		50-51			We find that restriction enzyme Bci528I isolated Bacillus circulans 528 recognizes pallindromic hexanucleotide sequence. 		
@D	Pak, T.R.//Altman, D.R.//Attie, O.//Sebra, R.//Hamula, C.L.//Lewis, M.//Deikus, G.//Newman, L.C.//Fang, G.//Hand, J.//Patel, G.//Wallach, F.//Schadt, E.E.//Huprikar, S.//van Bakel, H.//Kasarskis, A.//Bashir, A. 	Whole-Genome Sequencing Identifies Emergence of a Quinolone Resistance Mutation in a Case of Stenotrophomonas maltophilia Bacteremia.	Antimicrob. Agents Chemother.	2015	59		7117-7120			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. 		
@D	Pal, K.K.//Dey, R.//Sherathia, D.//Dalsania, T.//Savsani, K.//Patel, I.//Thomas, M.//Ghorai, S.//Vanpariya, S.//Rupapara, R.//Acharya, N.//Rawal, P.//Joshi, P.//Sukhadiya, B.//Mandaliya, M.//Saxena, A.K. 	Draft Genome Sequence of Salinibacillus aidingensis Strain MSP4, an Obligate Halophilic Bacterium Isolated from a Salt Crystallizer of the Rann of Kutch,  India.	Genome Announcements	2013	1		e00253-13			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. 		
@D	Pal, K.K.//Dey, R.//Sherathia, D.//Sukhadiya, B.//Dalsania, T.//Patel, I.//Savsani, K.//Thomas, M.//Vanpariya, S.//Mandaliya, M.//Rupapara, R.//Rawal, P.//Ghorai, S.//Bhayani, S.//Shah, A.//Saxena, A.K. 	Draft Genome Sequence of an Obligate and Moderately Halophilic Bacterium, Thalassobacillus devorans Strain MSP14, the First Draft Genome of the Genus  Thalassobacillus.	Genome Announcements	2013	1		e01103-13			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. 		
@D	Pal, K.K.//Dey, R.//Sherathia, D.//Vanpariya, S.//Patel, I.//Dalsania, T.//Savsani, K.//Sukhadiya, B.//Mandaliya, M.//Thomas, M.//Ghorai, S.//Rupapara, R.//Rawal, P.//Shah, A.//Bhayani, S. 	Draft Genome Sequence of a Moderately Halophilic Bacillus megaterium Strain, MSP20.1, Isolated from a Saltern of the Little Rann of Kutch, India.	Genome Announcements	2014	2		e01134-13			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. 		
@D	Pal, K.K.//Dey, R.//Thomas, M.//Sherathia, D.//Dalsania, T.//Patel, I.//Savsani, K.//Ghorai, S.//Vanpariya, S.//Sukhadiya, B.//Mandaliya, M.//Rupapara, R.//Rawal, P. 	Draft Genome Sequence of the Extremely Halophilic Bacillus sp. Strain SB49, Isolated from a Salt Crystallizer Pond of the Little Rann of Kutch, India.	Genome Announcements	2013	1		e00869-13			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. 		
@D	Pal, K.K.//Dey, R.//Thomas, M.//Sherathia, D.//Dalsania, T.//Patel, I.//Savsani, K.//Ghorai, S.//Vanpariya, S.//Sukhadiya, B.//Mandaliya, M.//Rupapara, R.//Rawal, P.//Saxena, A.K. 	Draft Genome Sequence of Bacillus sp. Strain SB47, an Obligate Extreme Halophile  Isolated from a Salt Pan of the Little Rann of Kutch, India.	Genome Announcements	2013	1		e00816-13			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. 		
@D	Pal, M.//Swarnkar, M.K.//Thakur, R.//Kiran, S.//Chhibber, S.//Singh, A.K.//Gulati, A. 	Complete Genome Sequence of Paenibacillus sp. Strain IHBB 10380 Using PacBio Single-Molecule Real-Time Sequencing Technology.	Genome Announcements	2015	3		e00356-15			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. 		
@D	Pal, S.//Das Banerjee, T.//Roy, A.//Sar, P.//Kazy, S.K. 	Genome Sequence of Hydrocarbon-Degrading Cronobacter sp. Strain DJ34 Isolated from Crude Oil-Containing Sludge from the Duliajan Oil Fields, Assam, India.	Genome Announcements	2015	3		e01321-15			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. 		
@D	Palakawong, Na.A.S.//Hornung, B.//Ravikumar, V.A.//Plugge, W.//Plugge, C.M. 	Draft Genome Sequence of Actinomycessucciniciruminis Strain Am4T, Isolated from Cow Rumen Fluid.	Genome Announcements	2017	5		e01587-16			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. 		
@D	Palakawong, Na.A.S.//Strepis, N.//Pristas, P.//Plugge, C.M. 	Draft Genome Sequence of Actinomyces glycerinitolerans Strain G10T, Isolated from Sheep Rumen Fluid.	Genome Announcements	2017	5		e01589-16			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. 		
@D	Palakawong-Na-Ayudthaya, S.//Marshall, I.P.G.//Schreiber, L.//Plugge, C.M. 	Draft Genome Sequence of Streptococcus caviae Strain Cavy grass 6T, Isolated from Domesticated Guinea Pig Fecal Samples.	Genome Announcements	2017	5		e00080-17			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. 		
@D	Palaniappan, K. et al. 	Genome sequence of the moderately thermophilic sulfur-reducing bacterium Thermanaerovibrio velox type strain (Z-9701(T)) and emended description of the  genus Thermanaerovibrio.	Standards in Genomic Sciences	2013	9		57-70			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. 		
@D	Palau, M.//Boujida, N.//Manresa, A.//Minana-Galbis, D. 	Complete Genome Sequence of Marinobacter flavimaris LMG 23834(T), Which Is Potentially Useful in Bioremediation.	Genome Announcements	2018	6		e00273-18			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. 		
@D	Palecek, E.//Boublikova, P.//Galazka, G.//Klysik, J. 	Inhibition of restriction endonuclease cleavage due to site-specific chemical modification of the B-Z junction in supercoiled DNA.	Gen. Physiol. Biophys.	1987	6		327-341			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. 		
@D	Palenik, B.//Brahamsha, B.//Larimer, F.W.//Land, M.//Hauser, L.//Chain, P.//Lamerdin, J.//Regala, W.//Allen, E.E.//McCarren, J.//Paulsen, I.//Dufresne, A.//Partensky, F.//Webb, E.A.//Waterbury, J. 	The genome of a motile marine Synechococcus.	Nature	2003	424		1037			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. 		
@D	Palenik, B.//Ren, Q.//Dupont, C.L.//Myers, G.S.//Heidelberg, J.F.//Badger, J.H.//Madupu, R.//Nelson, W.C.//Brinkac, L.M.//Dodson, R.J.//Durkin, A.S.//Daugherty, S.C.//Sullivan, S.A.//Khouri, H.//Mohamoud, Y.//Halpin, R.//Paulsen, I.T. 	Genome sequence of Synechococcus CC9311: Insights into adaptation to a coastal environment.	Proc. Natl. Acad. Sci. U. S. A.	2006	103		13555-13559			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. 		
@D	Palevich, N.//Kelly, W.J.//Leahy, S.C.//Altermann, E.//Rakonjac, J.//Attwood, G.T. 	The complete genome sequence of the rumen bacterium Butyrivibrio hungatei MB2003.	Standards in Genomic Sciences	2017	12		72			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. 		
@D	Palkova, L.//Minarik, G.//Soltys, K. 	Draft Genome Sequencing of an Acinetobacter ursingii Isolate from Healthy Human Skin, Carrying Multidrug Resistance Genes.	Genome Announcements	2018	6		e00394-18			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. 		
@D	Palma, L.//Del Valle, E.E.//Frizzo, L.//Berry, C.//Caballero, P. 	Draft Genome Sequence of Photorhabdus luminescens Strain DSPV002N Isolated from Santa Fe, Argentina.	Genome Announcements	2016	4		e00744-16			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. 		
@D	Palma, L.//Munoz, D.//Murillo, J.//Caballero, P. 	Draft Genome Sequence of Bacillus thuringiensis Serovar Tolworthi Strain Na205-3, an Isolate Toxic for Helicoverpa armigera.	Genome Announcements	2014	2		e00187-14			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. 		
@D	Palmer, B.R.//Marinus, M.G. 	The dam and dcm strains of Escherichia coli--a review.	Gene	1994	143		1-12			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. 		
@D	Palmer, K.L.//Carniol, K.//Manson, J.M.//Heiman, D.//Shea, T.//Young, S.//Zeng, Q.//Gevers, D.//Feldgarden, M.//Birren, B.//Gilmore, M.S. 	High-quality draft genome sequences of 28 Enterococcus sp. isolates.	J. Bacteriol.	2010	192		2469-2470			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. 		
@D	Palmer, M.//de Maayer, P.//Poulsen, M.//Steenkamp, E.T.//van Zyl, E.//Coutinho, T.A.//Venter, S.N. 	Draft genome sequences of Pantoea agglomerans and Pantoea vagans isolates associated with termites.	Standards in Genomic Sciences	2016	11		23			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. 		
@D	Palmer, M.E.//Lipsitch, M.//Moxon, E.R.//Bayliss, C.D. 	Broad Conditions Favor the Evolution of Phase-Variable Loci.	MBio	2013	4		e00430-12			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. 		
@D	Palomino, M.M.//Allievi, M.C.//Fina, M.J.//Waehner, P.M.//Prado, A.M.//Sanchez, R.C.//Ruzal, S.M. 	Draft Genome Sequence of the Probiotic Strain Lactobacillus acidophilus ATCC 4356.	Genome Announcements	2015	3		e01421-14			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. 		
@D	Palomino, M.M.//Burguener, G.F.//Campos, J.//Allievi, M.//Fina-Martin, J.//Prado, A.M.//Fernandez, Do.P.D.A.//Ruzal, S.M. 	Draft Genome Sequence of Lactobacillus helveticus ATCC 12046.	Genome Announcements	2018	6		e01595-17			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. 		
@D	Paludo, C.R.//Ruzzini, A.C.//Silva-Junior, E.A.//Pishchany, G.//Currie, C.R.//Nascimento, F.S.//Kolter, R.G.//Clardy, J.//Pupo, M.T. 	Whole-Genome Sequence of Bacillus sp. SDLI1, Isolated from the Social Bee Scaptotrigona depilis.	Genome Announcements	2016	4		e00174-16			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. 		
@D	Pan, L.//Zhou, H.//Li, J.//Huang, B.//Guo, J.//Zhang, X.L.//Gao, L.C.//Xu, C.//Liu, C.T. 	Draft genome sequence of Sphingomonas paucimobilis strain LCT-SP1 isolated from the Shenzhou X spacecraft of China.	Standards in Genomic Sciences	2016	11		18			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. 		
@D	Pan, X.//Lin, L.//Xu, Y.//Yuan, X.//Yao, J.//Yin, W.//Hao, G.//Shen, J. 	Draft Genome Sequence of Aeromonas hydrophila Strain BSK-10 (Serotype O97), Isolated from Carassius carassius with Motile Aeromonad Septicemia in China.	Genome Announcements	2017	5		e00497-17			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. 		
@D	Pan, X.S.//Chen, Z.F. 	A new Type II restriction endonuclease, BsaOI, from Bacillus stearothermophilus.	Chinese Sci. Bull.	1991	36		1231-1232			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. 		
@D	Pan, Y.//Kong, K.F.//Tsang, J.S. 	Complete genome sequence and characterization of the haloacid-degrading Burkholderia caribensis MBA4.	Standards in Genomic Sciences	2015	10		114			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. 		
@D	Pan, Y.//Kong, K.F.//Tsang, J.S. 	Complete Genome Sequence of the Exopolysaccharide-Producing Burkholderia caribensis Type Strain MWAP64.	Genome Announcements	2016	4		e01636-15			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. 		
@D	Pan, Y.//Wang, Y.//Yan, X.//Mazumder, A.//Liang, Y. 	Draft Genome Sequence of Pseudoalteromonas tetraodonis Strain MQS005, a Bacterium with Potential Quorum-Sensing Regulation.	Genome Announcements	2016	4		e00724-16			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%. 		
@D	Pan, Y.//Yang, X.//Duan, J.//Lu, N.//Leung, A.S.//Tran, V.//Hu, Y.//Wu, N.//Liu, D.//Wang, Z.//Yu, X.//Chen, C.//Zhang, Y.//Wan, K.//Liu, J.//Zhu, B. 	Whole-genome sequences of four Mycobacterium bovis BCG vaccine strains.	J. Bacteriol.	2011	193		3152-3153			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. 		
@D	Pan, Y.//Yang, X.//Li, J.//Zhang, R.//Hu, Y.//Zhou, Y.//Wang, J.//Zhu, B. 	The genome sequence of spinosyns-producing bacterium Saccharopolyspora spinosa NRRL 18395.	J. Bacteriol.	2011	193		3150-3151			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. 		
@D	Pan, Y.J.//Lin, T.L.//Lin, Y.T.//Su, P.A.//Chen, C.T.//Hsieh, P.F.//Hsu, C.R.//Chen, C.C.//Hsieh, Y.C.//Wang, J.T. 	Identification of capsular types in carbapenem-resistant Klebsiella pneumoniae strains by wzc sequencing and implications in capsule depolymerase treatment.	Antimicrob. Agents Chemother.	2015	59		1038-1047			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. 		
@D	Panayotatos, N. 	Practical consequences of restriction site symmetry.	Gene	1984	31		291-294			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. 		
@D	Panda, A.//Nagaraj, S.//Zhao, X.//Tettelin, H.//DeTolla, L.J. 	Complete Genome Sequences of Mycobacterium kansasii Strains Isolated from Rhesus  Macaques.	Genome Announcements	2017	5		e00187-17			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. 		
@D	Panda, A.N.//Mishra, S.R.//Ray, L.//Sahu, N.//Acharya, A.//Jadhao, S.//Suar, M.//Adhya, T.K.//Rastogi, G.//Pattnaik, A.K.//Raina, V. 	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.	Genome Announcements	2016	4		e00361-16			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. 		
@D	Panda, P.//Fiers, M.W.//Lu, A.//Armstrong, K.F.//Pitman, A.R. 	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.	Genome Announcements	2015	3		e00874-15			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. 		
@D	Panda, P.//Lu, A.//Armstrong, K.F.//Pitman, A.R. 	Draft Genome Sequence for ICMP 5702, the Type Strain of Pectobacterium carotovorum subsp. carotovorum That Causes Soft Rot Disease on Potato.	Genome Announcements	2015	3		e00875-15			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. 		
@D	Panda, S.//Singh, D.V. 	Whole-Genome Sequences of Staphylococcus haemolyticus Isolated from Infected Eyes and Healthy Conjunctiva in Bhubaneswar, India.	Genome Announcements	2016	4		e00099-16			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. 		
@D	Pandey, A.K.//Cleary, D.W.//Laver, J.R.//Maiden, M.C.J.//Didelot, X.//Gorringe, A.//Read, R.C. 	Neisseria lactamica Y92-1009 complete genome sequence.	Standards in Genomic Sciences	2017	12		41			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%. 		
@D	Pandin, C.//Le Coq, D.//Deschamps, J.//Vedie, R.//Rousseau, T.//Aymerich, S.//Briandet, R. 	Complete genome sequence of Bacillus velezensis QST713: A biocontrol agent that protects Agaricus bisporus crops against the green mould disease.	J. Biotechnol.	2018	278		10-19			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. 		
@D	Pandiyan, A.//Ray, M.K. 	Draft Genome Sequence of the Antarctic Psychrophilic Bacterium Pseudomonas syringae Strain Lz4W.	Genome Announcements	2013	1		e00377-13			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. 		
@D	Panescu, J.//Daly, R.A.//Wrighton, K.C.//Mouser, P.J. 	Draft Genome Sequences of Two Chemosynthetic Arcobacter Strains Isolated from Hydraulically Fractured Wells in Marcellus and Utica Shales.	Genome Announcements	2018	6		e00159-18			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. 		
@D	Panesso, D. et al. 	Methicillin-Susceptible, Vancomycin-Resistant Staphylococcus aureus, Brazil.	Emerg. Infect. Dis.	2015	21		1844-1848			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. 		
@D	Pang, J.//Dong, M.//Li, N.//Zhao, Y.//Liu, B. 	Functional characterization of a rice de novo DNA methyltransferase, OsDRM2, expressed in Escherichia coli and yeast.	Biochem. Biophys. Res. Commun.	2013	432		157-162			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. 		
@D	Pang, M.//Jiang, J.//Xie, X.//Wu, Y.//Dong, Y.//Kwok, A.H.//Zhang, W.//Yao, H.//Lu, C.//Leung, F.C.//Liu, Y. 	Novel insights into the pathogenicity of epidemic Aeromonas hydrophila ST251 clones from comparative genomics.	Sci. Rep.	2015	5		9833			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. 		
@D	Pang, S.//Renvoise, A.//Perret, C.//Guinier, M.//Chelghoum, N.//Brossier, F.//Capton, E.//Jarlier, V.//Sougakoff, W. 	Whole-Genome Sequence of Mycobacterium abscessus Clinical Strain V06705.	Genome Announcements	2013	1		e00690-13			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. 		
@D	Panina, E.M.//Mironov, A.A.//Gelfand, M.S. 	Statistical analysis of complete bacterial genomes: Avoidance of palindromes and restriction-modification systems.	Mol. Biol. (Mosk)	2000	34		246-252			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. 		
@D	Panis, G.//Lambert, C.//Viollier, P.H. 	Complete genome sequence of Caulobacter crescentus bacteriophage phiCbK.	J. Virol.	2012	86		10234-10235			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. 		
@D	Panne, D.//Muller, S.A.//Wirtz, S.//Engel, A.//Bickle, T.A. 	The McrBC restriction endonuclease assembles into a ring structure in the presence of G nucleotides.	EMBO J.	2001	20		3210-3217			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. 		
@D	Panne, D.//Raleigh, E.A.//Bickle, T.A. 	McrBS, a modulator peptide for McrBC activity.	EMBO J.	1998	17		5477-5483			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. 		
@D	Panne, D.//Raleigh, E.A.//Bickle, T.A. 	The McrBC endonuclease translocates DNA in a reaction dependent on GTP hydrolysis.	J. Mol. Biol.	1999	290		49-60			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. 		
@D	Panschin, I. et al. 	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.	Standards in Genomic Sciences	2016	11		37			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. 		
@D	Panthee, S.//Paudel, A.//Hamamoto, H.//Sekimizu, K. 	Draft Genome Sequence of the Vancomycin-Resistant Clinical Isolate Staphylococcus aureus VRS3b.	Genome Announcements	2017	5		e00452-17			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%. 		
@D	Panzenhagen, P.H.N.//Cabral, C.C.//Suffys, P.N.//Aquino, M.H.C.//Franco, R.M.//Pereira, V.L.A.//Rodrigues, D.P.//Conte-Junior, C.A. 	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.	Genome Announcements	2017	5		e00197-17			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. 		
@D	Panzenhagen, P.H.N.//Paul, N.C.//Conte, J.C.A.//Costa, R.G.//Rodrigues, D.P.//Shah, D.H. 	Draft Genome Sequences of 11 Salmonella enterica Serovar Typhimurium Strains Isolated from Human Systemic and Nonsystemic Sites in Brazil.	Genome Announcements	2018	6		e01223-17			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. 		
@D	Paoli, G.C.//Wijey, C.//Nguyen, L.H.//Chen, C.Y.//Yan, X.//Irwin, P.L. 	Complete Genome Sequences of Two Strains of the Meat Spoilage Bacterium Brochothrix thermosphacta Isolated from Ground Chicken.	Genome Announcements	2017	5		e01357-17			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. 		
@D	Papa, C.M.//Springer, N.M.//Muszynski, M.G.//Meeley, R.//Kaeppler, S.M. 	Maize chromomethylase Zea methyltransferase2 is required for CpNpG methyl ation.	Plant Cell	2001	13		1919-1928			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. 		
@D	Papadakos, G.A. 	The effect of active site mutations on the homodimeric behavior of the PvuII restriction endonuclease.	Ph.D. Thesis, University of Missouri	2008			1-233			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. 		
@D	Papadimitriou, K.//Ferreira, S.//Papandreou, N.C.//Mavrogonatou, E.//Supply, P.//Pot, B.//Tsakalidou, E. 	Complete Genome Sequence of the Dairy Isolate Streptococcus macedonicus ACA-DC 198.	J. Bacteriol.	2012	194		1838-1839			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. 		
@D	Papadimitriou, K.//Mavrogonatou, E.//Bolotin, A.//Tsakalidou, E.//Renault, P. 	Whole-Genome Sequence of the Cheese Isolate Streptococcus macedonicus 679.	Genome Announcements	2016	4		e01025-16			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. 		
@D	Papagiannitsis, C.C.//Miriagou, V.//Giakkoupi, P.//Tzouvelekis, L.S.//Vatopoulos, A.C. 	Characterization of pKP1433, a Novel KPC-2-Encoding Plasmid from Klebsiella pneumoniae ST340.	Antimicrob. Agents Chemother.	2013	57		3427-3429			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. 		
@D	Papagiannitsis, C.C.//Tzouvelekis, L.S.//Kotsakis, S.D.//Tzelepi, E.//Miriagou, V. 	Sequence of pR3521, an IncB Plasmid from Escherichia coli Encoding ACC-4, SCO-1, and TEM-1 {beta}-Lactamases.	Antimicrob. Agents Chemother.	2011	55		376-381			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. 		
@D	Papapanagiotou, I.//Streeter, S.D.//Cary, P.D.//Kneale, G.G. 	DNA structural deformations in the interaction of the controller protein C.AhdI with its operator sequence.	Nucleic Acids Res.	2007	35		2643-2650			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. 		
@D	Papke, R.T.//de la Haba, R.R.//Infante-Dominguez, C.//Perez, D.//Sanchez-Porro, C.//Lapierre, P.//Ventosa, A. 	Draft Genome Sequence of the Moderately Halophilic Bacterium Marinobacter lipolyticus Strain SM19.	Genome Announcements	2013	1		e00379-13			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. 		
@D	Pappas, K.M.//Kouvelis, V.N.//Saunders, E.//Brettin, T.S.//Bruce, D.//Detter, C.//Balakireva, M.//Han, C.//Savvakis, G.//Kyrpides, N.C.//Typas, M.A. 	Genome sequence of the ethanol-producing Zymomonas mobilis subsp. mobilis lectotype strain ATCC 10988.	J. Bacteriol.	2011	193		5051-5052			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. 		
@D	Paques, F.//Duchateau, P. 	Meganucleases and DNA double-strand break-induced recombination: Perspectives for gene therapy.	Curr. Gene Ther.	2007	7		49-66			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. 		
@D	Paquin, B.//Laforest, M.-J.//Lang, B.F. 	Interspecific transfer of mitochondrial genes in fungi and creation of a homologous hybrid gene.	Proc. Natl. Acad. Sci. U. S. A.	1994	91		11807-11810			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. 		
@D	Paquin, B.//Lang, B.F. 	The mitochondrial DNA of Allomyces macrogynus: the complete genomic sequence from an ancestral fungus.	J. Mol. Biol.	1996	255		688-701			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. 		
@D	Paquin, B.//O'Kelly, C.J.//Lang, B.F. 	Intron-encoded open reaading frame of the GIY-YIG subclass in a plastid gene.	Curr. Genet.	1995	28		97-99			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. 		
@D	Paradiso, R.//Orsini, M.//Criscuolo, D.//Borrelli, R.//Valvini, O.//Camma, C.//Chiusano, M.L.//Galiero, G.//Borriello, G. 	Complete Genome Sequencing of 10 Brucella abortus Biovar 3 Strains Isolated from  Water Buffalo.	Genome Announcements	2018	6		e00180-18			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. 		
@D	Paradiso, R.//Orsini, M.//Riccardi, M.G.//Cecere, B.//Cerrone, A.//Camma, C.//Chiusano, M.L.//Galiero, G.//Borriello, G. 	Complete Genome Sequencing of Eight Brucella abortus Biovar 1 Strains Isolated from Water Buffalo.	Genome Announcements	2018	6		e00179-18			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. 		
@D	Parajuli, P.//Adamski, M.//Verma, N.K. 	Bacteriophages are the major drivers of Shigella flexneri serotype 1c genome plasticity: a complete genome analysis.	BMC Genomics	2017	18		722			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. 		
@D	Parales, R.E.//Navara, R.//Gettys, R.//Huang, J.J. 	Genome Sequence of Pseudomonas putida Strain ASAD, an Acetylsalicylic Acid-Degrading Bacterium.	Genome Announcements	2017	5		e01169-17			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. 		
@D	Parashar, V.//Capalash, N.//Sharma, P. 	Demonstration of REBASE-assisted restriction mapping to determine the recognition site of unknown restriction endonucleases.	Biochem. Mol. Biol. Educ.	2007	35		337-341			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. 		
@D	Parashar, V.//Capalash, N.//Xu, S.Y.//Sako, Y.//Sharma, P. 	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.	Appl. Microbiol. Biotechnol.	2006	72		917-923			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. 		
@D	Pardo, C.E.//Carr, I.M.//Hoffman, C.J.//Darst, R.P.//Markham, A.F.//Bonthron, D.T.//Kladde, M.P. 	MethylViewer: computational analysis and editing for bisulfite sequencing and methyltransferase accessibility protocol for individual  templates (MAPit) projects.	Nucleic Acids Res.	2011	39		e5			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. 		
@D	Parini, C.//Fortina, M.G. 	Site-specific restriction endonucleases in Bacillus licheniformis.	FEMS Microbiol. Lett.	1995	132		285-289			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. 		
@D	Parise, D.//Parise, M.T.D.//Viana, M.V.C.//Munoz-Bucio, A.V.//Cortes-Perez, Y.A.//Arellano-Reynoso, B.//Diaz-Aparicio, E.//Dorella, F.A.//Pereira, F.L.//Carvalho, A.F.//Figueiredo, H.C.P.//Ghosh, P.//Barh, D.//Gomide, A.C.P.//Azevedo, V.A.C. 	First genome sequencing and comparative analyses of Corynebacterium pseudotuberculosis strains from Mexico.	Standards in Genomic Sciences	2018	13		21			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. 		
@D	Parizzi, L.P.//Grassi, M.C.//Llerena, L.A.//Carazzolle, M.F.//Queiroz, V.L.//Lunardi, I.//Zeidler, A.F.//Teixeira, P.J.//Mieczkowski, P.//Rincones, J.//Pereira, G.A. 	The genome sequence of Propionibacterium acidipropionici provides insights into its biotechnological and industrial potential.	BMC Genomics	2012	13		562			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. 		
@D	Park, B.S.//Han, J.//Shin, D.J.//Jeong, Y.J.//Lee, N. 	Complete Genome Sequence of Actinobacillus pleuropneumoniae Strain KL 16 (Serotype 1).	Genome Announcements	2017	5		e01025-17			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. 		
@D	Park, C.//Shin, H.H.//Kwon, E.Y.//Choi, S.M.//Kim, S.H.//Park, S.H.//Choi, J.H.//Yoo, J.H.//Lee, D.G.//Shin, W.S. 	Two variants of staphylococcal cassette chromosome mec type IVA in community-associated meticillin-resistant Staphylococcus aureus strains in South Korea.	J. Med. Microbiol.	2009	58		1314-1321			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. 		
@D	Park, C.K.//Joshi, H.K.//Agrawal, A.//Ghare, M.I.//Little, E.J.//Dunten, P.W.//Bitinaite, J.//Horton, N.C. 	Domain swapping in allosteric modulation of DNA specificity.	PLoS Biology	2010	8		e1000554			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. 		
@D	Park, D.H.//Thapa, S.P.//Choi, B.S.//Kim, W.S.//Hur, J.H.//Cho, J.M.//Lim, J.S.//Choi, I.Y.//Lim, C.K. 	Complete Genome Sequence of Japanese Erwinia Strain Ejp617, a Bacterial Shoot Blight Pathogen of Pear.	J. Bacteriol.	2010	193		586-587			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. 		
@D	Park, D.S.//Bae, K.S.//Kim, H.//Shin, K.S.//Choi, S.H.//Kim, D.S.//Kim, B.W.//Oh, H.W. 	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.	J. Bacteriol.	2012	194		6648			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. 		
@D	Park, G.S.//Hong, S.J.//Lee, C.H.//Khan, A.R.//Ullah, I.//Jung, B.K.//Choi, J.//Kwak, Y.//Back, C.G.//Jung, H.Y.//Shin, J.H. 	Draft Genome Sequence of Chryseobacterium sp. Strain P1-3, a Keratinolytic Bacterium Isolated from Poultry Waste.	Genome Announcements	2014	2		e01237-14			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. 		
@D	Park, G.S.//Khan, A.R.//Hong, S.J.//Jang, E.K.//Ullah, I.//Jung, B.K.//Choi, J.//Yoo, N.K.//Park, K.J.//Shin, J.H. 	Draft Genome Sequence of Entomopathogenic Bacterium Photorhabdus temperata Strain M1021, Isolated from Nematodes.	Genome Announcements	2013	1		e00747-13			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. 		
@D	Park, H.//Park, B.//Kim, H.J.//Park, W.//Choi, I.G. 	Draft Genome Sequences of Two Ureolytic Bacteria Isolated from Concrete Block Waste.	Genome Announcements	2016	4		e00762-16			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. 		
@D	Park, H.J.//Kim, D. 	Draft Genome Sequence of a Humic Substance-Degrading Paenibacillus sp. Isolated from the Subarctic Grasslands at Low Temperature.	Genome Announcements	2013	1		e00170-12			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. 		
@D	Park, H.J.//Shin, S.C.//Kim, D. 	Draft Genome Sequence of Arctic Marine Bacterium Pseudoalteromonas issachenkonii  PAMC 22718.	J. Bacteriol.	2012	194		4140			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. 		
@D	Park, H.J.//Shin, S.C.//Kim, D. 	Draft genome sequence of a subarctic humic substance-degrading pseudomonad.	Genome Announcements	2013	1		e00070-12			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. 		
@D	Park, I.H.//Baek, J.Y.//Song, J.H.//Ko, K.S.//Kim, K.H. 	Draft Genome Sequences of Clinical Isolates of Serotype 6E Streptococcus pneumoniae from Five Asian Countries.	Genome Announcements	2017	5		e01728-16			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. 		
@D	Park, J.//Zhang, Y.//Buboltz, A.M.//Zhang, X.//Schuster, S.C.//Ahuja, U.//Liu, M.//Miller, J.F.//Sebaihia, M.//Bentley, S.D.//Parkhill, J.//Harvill, E.T. 	Comparative genomics of the classical Bordetella subspecies: the evolution and exchange of virulence-associated diversity amongst closely related pathogens.	BMC Genomics	2012	13		545			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. 		
@D	Park, J.H.//Cho, Y.J.//Chun, J.//Seok, Y.J.//Lee, J.K.//Kim, K.S.//Lee, K.H.//Park, S.J.//Choi, S.H. 	Complete Genome Sequence of Vibrio vulnificus MO6-24/O.	J. Bacteriol.	2011	193		2062-2063			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. 		
@D	Park, J.Y.//Han, S.H.//Lee, J.H.//Han, Y.S.//Lee, Y.S.//Rong, X.//McSpadden, G.B.B.//Park, H.S.//Kim, Y.C. 	Draft Genome Sequence of the Biocontrol Bacterium Pseudomonas putida B001, an Oligotrophic Bacterium That Induces Systemic Resistance to Plant  Diseases.	J. Bacteriol.	2011	193		6795-6796			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. 		
@D	Park, J.Y.//Kim, S.//Kim, S.M.//Cha, S.H.//Lim, S.K.//Kim, J. 	Complete Genome Sequence of Multidrug-Resistant Acinetobacter baumannii Strain 1656-2, Which Forms Sturdy Biofilm.	J. Bacteriol.	2011	193		6393-6394			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. 		
@D	Park, M.A.//Kwon, M.G.//Hwang, J.Y.//Jung, S.H.//Kim, D.W.//Park, J.Y.//Kim, J.S.//Na, Y.J.//Kim, M.Y.//Kim, D.S.//Chae, S.H.//Seo, J.S. 	Genome Sequence of Streptococcus parauberis Strain KCTC11980, Isolated from Diseased Paralichthys olivaceus.	Genome Announcements	2013	1		e00780-13			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%. 		
@D	Park, S.//Ji, Y.//Jung, H.Y.//Park, H.//Kang, J.//Choi, S.H.//Shin, H.//Hyun, C.K.//Kim, K.T.//Holzapfel, W.H. 	Lactobacillus plantarum HAC01 regulates gut microbiota and adipose tissue accumulation in a diet-induced obesity murine model.	Appl. Microbiol. Biotechnol.	2017	101		1605-1614			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. 		
@D	Park, S.-Y.//Lee, H.-J.//Song, J.-M.//Sun, J.//Hwang, H.-J.//Nishi, K.//Kim, J.-S. 	Structural characterization of a modification subunit of a putative type I restriction enzyme from Vibrio vulnificus YJ016.	Acta Crystallogr. D Biol. Crystallogr.	2012	68		1570-1577			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. 		
@D	Park, S.H.//Kim, H.U.//Kim, T.Y.//Park, J.S.//Kim, S.S.//Lee, S.Y. 	Metabolic engineering of Corynebacterium glutamicum for L-arginine production.	Nat. Commun.	2014	5		4618			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. 		
@D	Park, S.J.//Ghai, R.//Martin-Cuadrado, A.B.//Rodriguez-Valera, F.//Jung, M.Y.//Kim, J.G.//Rhee, S.K. 	Draft Genome Sequence of the Sulfur-Oxidizing Bacterium 'Candidatus Sulfurovum sediminum' AR, Which Belongs to the Epsilonproteobacteria.	J. Bacteriol.	2012	194		4128-4129			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%. 		
@D	Park, S.J.//Kim, J.G.//Jung, M.Y.//Kim, S.J.//Cha, I.T.//Ghai, R.//Martin-Cuadrado, A.B.//Rodriguez-Valera, F.//Rhee, S.K. 	Draft Genome Sequence of an Ammonia-Oxidizing Archaeon, 'Candidatus Nitrosopumilus sediminis' AR2, from Svalbard in the Arctic Circle.	J. Bacteriol.	2012	194		6948-6949			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. 		
@D	Park, S.J.//Kim, J.G.//Jung, M.Y.//Kim, S.J.//Cha, I.T.//Kwon, K.//Lee, J.H.//Rhee, S.K. 	Draft Genome Sequence of an Ammonia-Oxidizing Archaeon, 'Candidatus Nitrosopumilus koreensis' AR1, from Marine Sediment.	J. Bacteriol.	2012	194		6940-6941			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. 		
@D	Park, S.K.//Roh, S.W.//Whon, T.W.//Bae, J.W. 	Genome Sequence of Brachybacterium squillarum M-6-3T, Isolated from Salt-Fermented Seafood.	J. Bacteriol.	2011	193		6416-6417			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. 		
@D	Park, S.N.//Cho, E.//Kim, H.S.//Kim, D.S.//Jung, J.//Baek, J.H.//Kyong, L.Y.//Jo, E.//Chang, Y.H.//Hwan, S.J.//Choi, S.H.//Kang, J.//Choi, Y.//Kong, S.W.//Han, S.E.//Park, H.S.//Kim, H.//Kook, J.K. 	Draft Genome Sequence of Fusobacterium nucleatum subsp. animalis ChDC F324, Isolated from a Human Subgingival Plaque in the Republic of Korea.	Genome Announcements	2013	1		e01042-13			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. 		
@D	Park, S.N.//Cho, E.//Kim, H.S.//Kim, D.S.//Jung, J.//Baek, J.H.//Kyong, L.Y.//Jo, E.//Chang, Y.H.//Hwan, S.J.//Choi, S.H.//Kang, J.//Choi, Y.//Park, H.S.//Kim, H.//Kook, J.K. 	Draft Genome Sequence of Fusobacterium nucleatum subsp. nucleatum ChDC F316, Isolated from a Human Peri-implantitis Lesion in the Republic of Korea.	Genome Announcements	2013	1		e01041-13			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. 		
@D	Park, S.N.//Cho, E.//Kim, H.S.//Kim, D.S.//Jung, J.//Baek, J.H.//Kyong, L.Y.//Jo, E.//Chang, Y.H.//Hwan, S.J.//Kim, J.//Choi, S.H.//Kang, J.//Choi, Y.//Park, H.S.//Kim, H.//Kook, J.K. 	Draft Genome Sequence of Fusobacterium nucleatum subsp. vincentii ChDC F8, Isolated from a Human Subgingival Plaque in the Republic of Korea.	Genome Announcements	2013	1		e01040-13			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. 		
@D	Park, S.N.//Cho, E.//Lim, Y.K.//Kim, H.S.//Kim, D.S.//Jung, J.//Baek, J.H.//Jo, E.//Chang, Y.H.//Shin, J.H.//Choi, S.H.//Kang, J.//Choi, Y.//Park, H.S.//Kim, H.//Kook, J.K. 	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.	Genome Announcements	2014	2		e01233-13			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. 		
@D	Park, S.N.//Kong, S.W.//Kim, H.S.//Park, M.S.//Lee, J.W.//Cho, E.//Lim, Y.K.//Choi, M.H.//Chang, Y.H.//Shin, J.H.//Park, H.S.//Choi, S.H.//Kook, J.K. 	Draft Genome Sequence of Fusobacterium nucleatum ChDC F128, Isolated from a Periodontitis Lesion.	J. Bacteriol.	2012	194		6322-6323			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. 		
@D	Park, S.N.//Kong, S.W.//Park, M.S.//Lee, J.W.//Cho, E.//Lim, Y.K.//Choi, M.H.//Kim, H.S.//Chang, Y.H.//Shin, J.H.//Park, H.S.//Choi, S.H.//Kook, J.K. 	Draft Genome Sequence of Fusobacterium nucleatum subsp. fusiforme ATCC 51190T.	J. Bacteriol.	2012	194		5445-5446			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). 		
@D	Park, T.H.//Choi, B.S.//Choi, A.Y.//Choi, I.Y.//Heu, S.//Park, B.S. 	Genome Sequence of Pectobacterium carotovorum subsp. carotovorum Strain PCC21, a  Pathogen Causing Soft Rot in Chinese Cabbage.	J. Bacteriol.	2012	194		6345-6346			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. 		
@D	Park, Y.//Kim, G.-D.//Choi, T.-J. 	Molecular cloning and characterization of the DNA adenine methyltransferase gene in Feldmannia sp virus.	Virus Genes	2007	34		177-183			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. 		
@D	Park, Y.K.//Kang, H.//Yoo, H.//Lee, S.H.//Roh, H.//Kim, H.J.//Ryoo, S. 	Whole-Genome Sequence of Mycobacterium tuberculosis Korean Strain KIT87190.	Genome Announcements	2014	2		e01103-14			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. 		
@D	Park, Y.K.//Lee, K.M.//Lee, W.K.//Cho, M.J.//Lee, H.S.//Cho, Y.G.//Lee, Y.C.//Lee, W.K.//Seong, W.K.//Hwang, K.J. 	Dermabacter jinjuensis sp. nov., a novel species of the genus Dermabacter isolated from a clinical specimen.	Int. J. Syst. Evol. Microbiol.	2016	66		2573-2577			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)). 		
@D	Parker, B.//Marinus, M.G. 	A simple and rapid method to obtain substitution mutations in Escherichia coli:  isolation of a dam deletion/insertion mutation.	Gene	1988	73		531-535			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. 		
@D	Parker, C.T.//Gorski, L.//Huynh, S. 	Complete Genome Sequence of Salmonella enterica subsp. enterica Serovar Thompson  Strain RM6836.	Genome Announcements	2013	1		e00900-13			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. 		
@D	Parker, C.T.//Huynh, S.//Gorski, L.//Cooper, K.K.//Miller, W.G. 	Complete Genome Sequences of Two Outbreak Strains of Salmonella enterica subsp. enterica Serovar Thompson Associated with Cilantro.	Genome Announcements	2015	3		e01365-15			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. 		
@D	Parker, C.T.//Huynh, S.//Heikema, A.P. 	Genomic Sequence of Campylobacter jejuni subsp. jejuni HS:19 Penner Serotype Reference Strain RM3420.	Genome Announcements	2017	5		e01701-16			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. 		
@D	Parker, C.T.//Huynh, S.//Heikema, A.P. 	Complete Genomic Sequence of Campylobacter jejuni subsp. jejuni HS:19 Strain RM1285 Isolated from Packaged Chicken.	Genome Announcements	2016	4		e01100-16			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. 		
@D	Parker, C.T.//Huynh, S.//Heikema, A.P.//Cooper, K.K.//Miller, W.G. 	Complete Genome Sequences of Campylobacter jejuni Strains RM3196 (233.94) and RM3197 (308.95) Isolated from Patients with Guillain-Barre Syndrome.	Genome Announcements	2015	3		e01312-15			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. 		
@D	Parker, D.//Narechania, A.//Sebra, R.//Deikus, G.//Larussa, S.//Ryan, C.//Smith, H.//Prince, A.//Mathema, B.//Ratner, A.J.//Kreiswirth, B.//Planet, P.J. 	Genome Sequence of Bacterial Interference Strain Staphylococcus aureus 502A.	Genome Announcements	2014	2		e00284-14			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. 		
@D	Parker, M.M.//Belisle, M.//Belfort, M. 	Intron homing with limited exon homology. Illegitimate double-strand-break repair in intron acquisition by phage t4.	Genetics	1999	153		1513-1523			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. 		
@D	Parkhill, J. et al. 	The genome sequence of the food-borne pathogen Campylobacter jejuni reveals hypervariable sequences.	Nature	2000	403		665-668			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. 		
@D	Parkhill, J. et al. 	Genome sequence of Yersinia pestis, the causative agent of plague.	Nature	2001	413		523-527			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. 		
@D	Parkhill, J. et al. 	Complete DNA sequence of a serogroup A strain of Neisseria meningitidis Z2491.	Nature	2000	404		502-506			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. 		
@D	Parkhill, J. et al. 	Complete genome sequence of a multiple drug resistant Salmonella enterica serovar Typhi CT18.	Nature	2001	413		848-852			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. 		
@D	Parmeciano, Di.N.G.//Vazquez, S.C.//MacCormack, W.P.//Iriarte, A.//Quiroga, C. 	Draft Genome of Shewanella frigidimarina Ag06-30, a Marine Bacterium Isolated from Potter Peninsula, King George Island, Antarctica.	Genome Announcements	2016	4		e00289-16			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. 		
@D	Parraga, A.//Portugal, J. 	Detection of elsamicin-DNA binding specificity by restriction enzyme cleavage.	FEBS Lett.	1992	300		25-29			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. 		
@D	Parreira, V.R.//Costa, M.//Eikmeyer, F.//Blom, J.//Prescott, J.F. 	Sequence of Two Plasmids from Clostridium perfringens Chicken Necrotic Enteritis Isolates and Comparison with C. perfringens Conjugative Plasmids.	PLoS ONE	2012	7		E49753			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. 		
@D	Parro, V.//Moreno-Paz, M.//Gonzalez-Toril, E. 	Analysis of environmental transcriptomes by DNA microarrays.	Environ. Microbiol.	2007	9		453-464			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.). 		
@D	Parry, D.//Moon, S.A.//Liu, H.H.//Heslop, P.//Connolly, B.A. 	DNA Recognition by the EcoRV Restriction Endonuclease Probed using Base Analogues.	J. Mol. Biol.	2003	331		1005-1016			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. 		
@D	Parsa, Y.L.//Azarbaijani, R.//Sarikhan, S.//Mousavi, H.//Ramezani, M.//Amoozegar, M.A.//Shahzadeh, F.A.//Salekdeh, G.H. 	Complete Genome Sequence of Oceanimonas sp. GK1, a Halotolerant Bacterium from Gavkhouni Wetland in Iran.	J. Bacteriol.	2012	194		2123-2124			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. 		
@D	Parschat, K.//Hauer, B.//Kappl, R.//Kraft, R.//Huttermann, J.//Fetzner, S. 	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.	J. Biol. Chem.	2003	278		27483-27494			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. 		
@D	Parschat, K.//Overhage, J.//Strittmatter, A.W.//Henne, A.//Gottschalk, G.//Fetzner, S. 	Complete Nucleotide Sequence of the 113-Kilobase Linear Catabolic Plasmid pAL1 of Arthrobacter nitroguajacolicus Ru61a and Transcriptional Analysis of Genes Involved in Quinaldine Degradation.	J. Bacteriol.	2007	189		3855-3867			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. 		
@D	Parthasarathy, S.//Azam, S.//Lakshman-Sagar, A.//Narasimha-Rao, V.//Gudla, R.//Parapatla, H.//Yakkala, H.//Ghanta-Vemuri, S.//Siddavattam, D. 	Genome-Guided Insights Reveal Organophosphate-Degrading Brevundimonas diminuta as Sphingopyxis wildii and Define Its Versatile Metabolic Capabilities and Environmental Adaptations.	Genome Biol. Evol.	2017	9		77-81			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. 		
@D	Partridge, S.R.//Ginn, A.N.//Paulsen, I.T.//Iredell, J.R. 	pEl1573 carrying blaIMP-4 from Sydney, Australia, is closely related to other IncL/M plasmids.	Antimicrob. Agents Chemother.	2012	56		6029-6032			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. 		
@D	Partridge, S.R.//Zong, Z.//Iredell, J.R. 	Recombination in IS26 and Tn2 in the Evolution of Multiresistance Regions Carrying blaCTX-M-15 on Conjugative IncF Plasmids from Escherichia coli.	Antimicrob. Agents Chemother.	2011	55		4971-4978			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. 		
@D	Parvataneni, S.//Mijalis, E.M.//Kuty, E.G.F.//Rasche, E.S.//Liu, M.//Gill, J.J. 	Complete Genome Sequence of Citrobacter freundii Myophage Mijalis.	Genome Announcements	2017	5		e00228-17			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. 		
@D	Pascopella, L.//Raupach, B.//Ghori, N.//Monack, D.//Falkow, S.//Small, P.L.C. 	Host restriction phenotypes of Salmonella typhi and Salmonella gallinarum.	Infect. Immun.	1995	63		4329-4335			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. 		
@D	Pascual, J.//Udaondo, Z.//Molina, L.//Segura, A.//Esteve-Nunez, A.//Caballero, A.//Duque, E.//Ramos, J.L.//van Dillewijn, P. 	Draft Genome Sequence of Pseudomonas putida JLR11, a Facultative Anaerobic 2,4,6-Trinitrotoluene Biotransforming Bacterium.	Genome Announcements	2015	3		e00904-15			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. 		
@D	Pashenkov, A.L.//Nikolskaya, I.I.//Nigmatullin, T.G.//Debov, S.S. 	Search for DNA host specificity system in Salmonella typhi.	Zh. Mikrobiol. Epidemiol. Immunobiol.	1985	4		3-6			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. 		
@D	Pashkova, T.M.//Vasilchenko, A.S.//Khlopko, Y.A.//Kochkina, E.E.//Kartashova, O.L.//Sycheva, M.V. 	Genome Sequence of Enterococcus faecium Strain ICIS 96 Demonstrating Intermicrobial Antagonism Associated with Bacteriocin Production.	Genome Announcements	2018	6		e00126-18			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. 		
@D	Passerini, D.//Vuillemin, M.//Laguerre, S.//Amari, M.//Loux, V.//Gabriel, V.//Robert, H.//Morel, S.//Monsan, P.//Gabriel, B.//Fontagne-Faucher, C.//Remaud-Simeon, M.//Moulis, C. 	Complete Genome Sequence of Leuconostoc citreum Strain NRRL B-742.	Genome Announcements	2014	2		e01179-14			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. 		
@D	Passos-da-Silva, D.//Devescovi, G.//Paszkiewicz, K.//Moretti, C.//Buonaurio, R.//Studholme, D.J.//Venturi, V. 	Draft Genome Sequence of Erwinia toletana, a Bacterium Associated with Olive Knots Caused by Pseudomonas savastanoi pv. Savastanoi.	Genome Announcements	2013	1		e00205-13			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. 		
@D	Pasternak, Z.//Pietrokovski, S.//Rotem, O.//Gophna, U.//Lurie-Weinberger, M.N.//Jurkevitch, E. 	By their genes ye shall know them: genomic signatures of predatory bacteria.	ISME J.	2013	7		756-769			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. 		
@D	Patel, B.K. 	Draft Genome Sequence of Fervidicella metallireducens Strain AeBT, an Iron-Reducing Thermoanaerobe from the Great Artesian Basin.	Genome Announcements	2014	2		e00345-14			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. 		
@D	Patel, B.K. 	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.	Genome Announcements	2015	3		e01547-14			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. 		
@D	Patel, B.K.//Te'o, V.S. 	Draft Genome Sequence of Caloramator mitchellensis, a Thermoanaerobe Isolated from the Waters of the Great Artesian Basin.	Genome Announcements	2016	4		e01578-15			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. 		
@D	Patel, D.J. 	A molecular handshake.	Nature	1994	367		688-690			Review of the M.HhaI/DNA crystal structure paper. 		
@D	Patel, H.K.//Passos-da-Silva, D.//Devescovi, G.//Maraite, H.//Paszkiewicz, K.//Studholme, D.J.//Venturi, V. 	Draft Genome Sequence of Pseudomonas fuscovaginae, a Broad-Host-Range Pathogen of Plants.	J. Bacteriol.	2012	194		2765-2766			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. 		
@A	Patel, J.//Firman, K. 		The domain structure of the DNA specificity subunit of type I restriction endonucleases. I. Cloning, mutagenesis and over-production of the EcoR124 DNA methyltransferase.			Balla, E.//Berencsi, G.//Szentirmai, A. 		Proc. Eur. Meet. Genet. Transform.				Andover, UK	Intercept	1993		0		179-187									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). 		
@D	Patel, J.//Taylor, I.//Dutta, C.F.//Kneale, G.//Firman, K. 	High-level expression of the cloned genes encoding the subunits of and intact DNA methyltransferase, M.EcoR124.	Gene	1992	112		21-27			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. 		
@D	Patel, N.//Graslund, A.//Berglund, H.//Nilsson, L.//Rigler, R.//McLaughlin, L.W. 	Interaction of a minor groove binder with a fluorescent DNA oligomer containing the EcoRI recognition sequence.	Nucleosides and Nucleotides	1991	10		547-548			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. 		
@D	Patel, P.A.//Kothari, V.V.//Kothari, C.R.//Faldu, P.R.//Domadia, K.K.//Rawal, C.M.//Bhimani, H.D.//Parmar, N.R.//Nathani, N.M.//Koringa, P.G.//Joshi, C.G.//Kothari, R.K. 	Draft Genome Sequence of Petroleum Hydrocarbon-Degrading Pseudomonas aeruginosa Strain PK6, Isolated from the Saurashtra Region of Gujarat, India.	Genome Announcements	2014	2		e00002-14			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. 		
@D	Patel, P.H.//Suzuki, M.//Adman, E.//Shinkai, A.//Loeb, L.A. 	Prokaryotic DNA polymerase I: evolution, structure, and "base flipping" mechanism for nucleotide selection.	J. Mol. Biol.	2001	308		823-837			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. 		
@D	Patel, P.N.//Lindsey, R.L.//Garcia-Toledo, L.//Rowe, L.A.//Batra, D.//Whitley, S.W.//Drapeau, D.//Stoneburg, D.//Martin, H.//Juieng, P.//Loparev, V.N.//Strockbine, N. 	High-Quality Whole-Genome Sequences for 77 Shiga Toxin-Producing Escherichia coli Strains Generated with PacBio Sequencing.	Genome Announcements	2018	6		e00391-18			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. 		
@D	Patel, S.//Fletcher, B.//Scott, D.C.//Ely, B. 	Genome sequence and phenotypic characterization of Caulobacter segnis.	Curr. Microbiol.	2015	70		355-363			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. 		
@D	Patel, Y.//Nelson, M.//McClelland, M. 	Methylation at overlapping dam (Gm6ATC) sites does not block cleavage by the NruI (TCGCGA) isoschizomer restriction endonucleases AmaI, SalDI and Sbo13I.	Nucleic Acids Res.	1989	17		3613			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. 		
@D	Patel, Y.//Van Cott, E.//Wilson, G.G.//McClelland, M. 	Cleavage at the twelve-base-pair sequence 5'-TCTAGATCTAGA-3' using M.XbaI (TCTAGm6A) methylation and DpnI (Gm6A/TC) cleavage .	Nucleic Acids Res.	1990	18		1603-1607			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. 		
@D	Paterson, J.//Gross, H. 	Draft Genome Sequence and Annotation of the Phytopathogenic Ralstonia pickettii (Previously Burkholderia glumae) Strain ICMP-8657.	Genome Announcements	2018	6		e00128-18			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. 		
@D	Pathak, A.//Green, S.J.//Ogram, A.//Chauhan, A. 	Draft Genome Sequence of Rhodococcus opacus Strain M213 Shows a Diverse Catabolic Potential.	Genome Announcements	2013	1		e00144-12			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. 		
@D	Pathak, A.//Jaswal, R.//Stothard, P.//Brooks, S.//Chauhan, A. 	Draft Genome Sequence of Pseudomonas sp. Strain B1, Isolated from a Contaminated  Sediment.	Genome Announcements	2018	6		e00518-18			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. 		
@D	Pathak, A.//Jaswal, R.//Xu, X.//Chauhan, A. 	Draft Genome Sequence of Serratia sp. Strain S1B, Isolated from Mercury-Contaminated Soil.	Genome Announcements	2018	6		e00534-18			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. 		
@D	Pathania, R.//Ahmad, A.//Srivastava, S. 	Draft Genome Sequence of an Indian Marine Cyanobacterial Strain with Fast Growth  and High Polyglucan Content.	Genome Announcements	2017	5		e01334-17			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. 		
@D	Pati, A. et al. 	Non-contiguous finished genome sequence of the opportunistic oral pathogen Prevotella multisaccharivorax type strain (PPPA20).	Standards in Genomic Sciences	2011	5		41-49			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. 		
@D	Pati, A. et al. 	Complete genome sequence of Saccharomonospora viridis type strain (P101).	Standards in Genomic Sciences	2009	1		141-149			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. 		
@D	Pati, A. et al. 	Complete genome sequence of Sphaerobacter thermophilus type strain (S 6022).	Standards in Genomic Sciences	2010	2		49-56			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. 		
@D	Pati, A. et al. 	Complete genome sequence of Brachyspira murdochii type strain (56-150).	Standards in Genomic Sciences	2010	2		260-269			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. 		
@D	Pati, A. et al. 	Complete genome sequence of Arcobacter nitrofigilis type strain (CI).	Standards in Genomic Sciences	2010	2		300-308			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. 		
@D	Pati, A. et al. 	Complete genome sequence of Bacteroides helcogenes type strain (P 36-108).	Standards in Genomic Sciences	2011	4		45-53			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. 		
@D	Pati, A. et al. 	Complete genome sequence of Oceanithermus profundus type strain (506).	Standards in Genomic Sciences	2011	4		210-220			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. 		
@D	Pati, A. et al. 	Complete genome sequence of Cellulophaga lytica type strain (LIM-21).	Standards in Genomic Sciences	2011	4		221-232			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. 		
@D	Patil, Y.//Muller, N.//Schink, B.//Whitman, W.B.//Huntemann, M.//Clum, A.//Pillay, M.//Palaniappan, K.//Varghese, N.//Mikhailova, N.//Stamatis, D.//Reddy, T.B.//Daum, C.//Shapiro, N.//Ivanova, N.//Kyrpides, N.//Woyke, T.//Junghare, M. 	High-quality-draft genome sequence of the fermenting bacterium Anaerobium acetethylicum type strain GluBS11T (DSM 29698).	Standards in Genomic Sciences	2017	12		24			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. 		
@D	Patole, S.//Mishra, M.//Mohapatra, H. 	Draft Genome Sequences of Clinical and Nonclinical Isolates of Klebsiella spp. Exhibiting Nonheritable Tolerance toward Antimicrobial Compounds.	Genome Announcements	2017	5		e01217-17			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. 		
@D	Patrick, S.//Blakely, G.W.//Houston, S.//Moore, J.//Abratt, V.R.//Bertalan, M.//Cerdeno-Tarraga, A.M.//Quail, M.A.//Corton, N.//Corton, C.//Bignell, A.//Barron, A.//Clark, L.//Bentley, S.D.//Parkhill, J. 	Twenty-eight divergent polysaccharide loci specifying within- and amongst-strain capsule diversity in three strains of Bacteroides fragilis.	Microbiology	2010	156		3255-3269			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. 		
@D	Pattabiraman, V.//Bopp, C.A. 	Draft Whole-Genome Sequences of 10 Serogroup O6 Enterotoxigenic Escherichia coli  Strains.	Genome Announcements	2014	2		e01274-14			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. 		
@D	Pattabiraman, V.//Bopp, C.A. 	Draft Whole-Genome Sequences of Nine Enterotoxigenic Escherichia coli Serogroup O6 Strains.	Genome Announcements	2015	3		e00564-15			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. 		
@D	Patten, C.L.//Jeong, H.//Blakney, A.J.//Wallace, N. 	Draft Genome Sequence of a Diazotrophic, Plant Growth-Promoting Rhizobacterium of the Pseudomonas syringae Complex.	Genome Announcements	2016	4		e01023-16			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. 		
@D	Patterson, N.H.//Pauling, C. 	Evidence for two restriction-modification systems in Halobacterium cutirubrum.	J. Bacteriol.	1985	163		783-784			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. 		
@D	Paul, D.//Austin, F.W.//Arick, T.//Bridges, S.M.//Burgess, S.C.//Dandass, Y.S.//Lawrence, M.L. 	Genome sequence of the solvent-producing bacterium Clostridium carboxidivorans strain P7T.	J. Bacteriol.	2010	192		5554-5555			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. 		
@D	Paul, D.//Bridges, S.//Burgess, S.C.//Dandass, Y.//Lawrence, M.L. 	Genome sequence of the chemolithoautotrophic bacterium Oligotropha carboxidovorans OM5T.	J. Bacteriol.	2008	190		5531-5532			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. 		
@D	Paul, R.//Jinkerson, R.E.//Buss, K.//Steel, J.//Mohr, R.//Hess, W.R.//Chen, M.//Fromme, P. 	Draft Genome Sequence of the Filamentous Cyanobacterium Leptolyngbya sp. Strain Heron Island J, Exhibiting Chromatic Acclimation.	Genome Announcements	2014	2		e01166-13			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. 		
@D	Paulsen, I. et al. 	The Brucella suis genome reveals fundamental similarities between animal and plant pathogens and symbionts.	Proc. Natl. Acad. Sci. U. S. A.	2002	99		13148-13153			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. 		
@D	Paulsen, I.T. et al. 	Role of mobile DNA in the evolution of vancomycin-resistant Enterococcus faecalis.	Science	2003	299		2071-2074			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. 		
@D	Paulsen, I.T. et al. 	Complete genome sequence of the plant commensal Pseudomonas fluorescens Pf-5.	Nat. Biotechnol.	2005	23		873-878			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. 		
@D	Pavan, M.E.//Pavan, E.E.//Lopez, N.I.//Levin, L.//Pettinari, M.J. 	Genome Sequence of the Melanin-Producing Extremophile Aeromonas salmonicida subsp. pectinolytica Strain 34melT.	Genome Announcements	2013	1		e00675-13			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. 		
@D	Pavco, P.A.//Steege, D.A. 	A DNA binding protein acts as a transcriptional roadblock.	J. Cell Biochem. Suppl.	1988	12D		145			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. 		
@D	Pavlopoulou, A.//Kossida, S. 	Plant cytosine-5 DNA methyltransferases: Structure, function, and molecular evolution.	Genomics	2007	90		530-541			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. 		
@D	Pavlopoulou, A.//Kossida, S. 	Phylogenetic analysis of the eukaryotic RNA (cytosine-5)-methyltransferases.	Genomics	2009	93		350-357			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. 		
@D	Pavlov, M.S.//Lira, F.//Martinez, J.L.//Olivares, J.//Marshall, S.H. 	Draft Genome Sequence of Antarctic Pseudomonas sp. Strain KG01 with Full Potential for Biotechnological Applications.	Genome Announcements	2015	3		e00906-15			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. 		
@D	Pavlovic, G.//Burrus, V.//Gintz, B.//Decaris, B.//Guedon, G. 	Evolution of genomic islands by deletion and tandem accretion by site-specific recombination: ICESt1-related elements from Streptococcus thermophilus.	Microbiology	2004	150		759-774			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. 		
@D	Pavlovic, G.//Burrus, V.//Toulmay, A.//Choulet, F.//Decaris, B.//Guedon, G. 	Characterization and evolution of a family of integrative and potentially conjugative or mobilizable elements from Streptococcus  thermophilus.	Lait	2004	84		7-14			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. 		
@D	Pavon, A.//Orellana, P.//Salazar, L.//Cespedes, S.//Muino, L.//Gutierrez, A.//Castillo, D.//Corsini, G. 	Draft Genome Sequence of Bacillus sp. Strain K2I17, Isolated from the Rhizosphere of Deschampsia antarctica Desv.	Genome Announcements	2017	5		e00786-17			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. 		
@D	Pawar, S.P.//Dhotre, D.P.//Shetty, S.A.//Chowdhury, S.P.//Chaudhari, B.L.//Shouche, Y.S. 	Genome Sequence of Janibacter hoylei MTCC8307, Isolated from the Stratospheric Air.	J. Bacteriol.	2012	194		6629-6630			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. 		
@D	Pawitwar, S.S.//Utturkar, S.M.//Brown, S.D.//Yoshinaga, M.//Rosen, B.P. 	Draft Genome Sequence of Burkholderia sp. MR1, a Methylarsenate-Reducing Bacterial Isolate from Florida Golf Course Soil.	Genome Announcements	2015	3		e00608-15			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. 		
@D	Pawlak, S.D.//Radlinska, M.//Chmiel, A.A.//Bujnicki, J.M.//Skowronek, K.J. 	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.	Nucleic Acids Res.	2005	33		661-671			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. 		
@D	Pawlak, S.D.//Skowronek, K.//Radlinska, M.//Bujnicki, J.M. 	Fold-recognition, homology modeling and mutagenesis of restriction enzyme Bsp6I.	FEBS J.	2005	272		95			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. 		
@D	Pazos, A.//Kodaman, N.//Piazuelo, M.B.//Romero-Gallo, J.//Sobota, R.S.//Israel, D.A.//Bravo, L.E.//Morgan, D.R.//Wilson, K.T.//Correa, P.//Peek, R.M. Jr.//Williams, S.M.//Schneider, B.G. 	Draft Genome Sequences of 13 Colombian Helicobacter pylori Strains Isolated from  Pacific Coast and Andean Residents.	Genome Announcements	2017	5		e00113-17			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. 		
@D	Peakman, L.J.//Antognozzi, M.//Bickle, T.A.//Janscak, P.//Szczelkun, M.D. 	S-Adenosyl Methionine Prevents Promiscuous DNA Cleavage by the EcoP1I type III Restriction Enzyme.	J. Mol. Biol.	2003	333		321-335			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. 		
@D	Peakman, L.J.//Szczelkun, M.D. 	DNA communications by Type III restriction endonucleases - confirmation of 1D translocation over 3D looping.	Nucleic Acids Res.	2004	32		4166-4174			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. 		
@D	Peakman, L.J.//Szczelkun, M.D. 	S-Adenosyl homocysteine and DNA ends stimulate promiscuous nuclease activities in the Type III restriction endonuclease EcoPI.	Nucleic Acids Res.	2009	37		3934-3945			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. 		
@D	Pearce, S.L.//Pandey, R.//Dorrian, S.J.//Russell, R.J.//Oakeshott, J.G.//Pandey, G. 	Genome sequence of the newly isolated chemolithoautotrophic Bradyrhizobiaceae strain SG-6C.	J. Bacteriol.	2011	193		5057			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. 		
@D	Pearce, S.L.//Pushiri, H.//Oakeshott, J.G.//Russell, R.J.//Pandey, G. 	Draft Genome Sequence of Ralstonia sp. Strain GA3-3, Isolated from Australian Suburban Soil.	Genome Announcements	2013	1		e00414-13			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. 		
@D	Pearson, B.M.//Gaskin, D.J.//Segers, R.P.//Wells, J.M.//Nuijten, P.J.//Mvan, V.A.H. 	The Complete Genome Sequence of Campylobacter jejuni Strain 81116 (NCTC11828).	J. Bacteriol.	2007	189		8402-8403			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. 		
@D	Pearson, B.M.//Rokney, A.//Crossman, L.C.//Miller, W.G.//Wain, J.//van Vliet, A.H. 	Complete Genome Sequence of the Campylobacter coli Clinical Isolate 15-537360.	Genome Announcements	2013	1		e01056-13			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. 		
@D	Pearson, M.D.//Noller, H.F. 	The Draft Genome of Planococcus donghaensis MPA1U2 Reveals Nonsporulation Pathways Controlled by a Conserved Spo0A Regulon.	J. Bacteriol.	2011	193		6106			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. 		
@D	Pearson, M.M. et al. 	Complete genome sequence of uropathogenic Proteus mirabilis, a master of both adherence and motility.	J. Bacteriol.	2008	190		4027-4037			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. 		
@D	Pech, M.//Streeck, R.E.//Zachau, H.G. 	Patchwork structure of a bovine satellite DNA.	Cell	1979	18		883-893			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. 		
@D	Pechtl, A.//Ruckert, C.//Maus, I.//Koeck, D.E.//Trushina, N.//Kornberger, P.//Schwarz, W.H.//Schluter, A.//Liebl, W.//Zverlov, V.V. 	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.	Genome Announcements	2018	6		e01493-17			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. 		
@D	Pedersen, K.//Bengtsson, A.//Edlund, J.//Rabe, L.//Hazen, T.//Chakraborty, R.//Goodwin, L.//Shapiro, N. 	Complete Genome Sequence of the Subsurface, Mesophilic Sulfate-Reducing Bacterium Desulfovibrio aespoeensis Aspo-2.	Genome Announcements	2014	2		e00509-14			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. 		
@D	Pedersen, T.B.//Kot, W.P.//Hansen, L.H.//Sorensen, S.J.//Broadbent, J.R.//Vogensen, F.K.//Ardo, Y. 	Genome Sequence of Leuconostoc mesenteroides subsp. cremoris Strain T26, Isolated from Mesophilic Undefined Cheese Starter.	Genome Announcements	2014	2		e00485-14			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. 		
@D	Pedersen, T.B.//Kot, W.P.//Hansen, L.H.//Sorensen, S.J.//Broadbent, J.R.//Vogensen, F.K.//Ardo, Y. 	Genome Sequences of Two Leuconostoc pseudomesenteroides Strains Isolated from Danish Dairy Starter Cultures.	Genome Announcements	2014	2		e00484-14			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. 		
@D	Pedulla, M.L. et al. 		Cell	2003	113		171-182			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. 		
@D	Peek, R.M. Jr.//Thompson, S.A.//Atherton, J.C.//Blaser, M.J.//Miller, G.G. 	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.	Gut	1996	39		A71			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. 		
@D	Peet, K.C.//Thompson, J.R. 	Draft Genome Sequences of Supercritical CO2-Tolerant Bacteria Bacillus subterraneus MITOT1 and Bacillus cereus MIT0214.	Genome Announcements	2015	3		e00140-15			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. 		
@D	Pei, D.//Hill-Clemons, C.//Carissimo, G.//Yu, W.//Vernick, K.D.//Xu, J. 	Draft Genome Sequences of Two Strains of Serratia spp. from the Midgut of the Malaria Mosquito Anopheles gambiae.	Genome Announcements	2015	3		e00090-15			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. 		
@D	Pei, D.//Nicholson, A.C.//Jiang, J.//Chen, H.//Whitney, A.M.//Villarma, A.//Bell, M.//Humrighouse, B.//Rowe, L.A.//Sheth, M.//Batra, D.//Juieng, P.//Loparev, V.N.//McQuiston, J.R.//Lan, Y.//Ma, Y.//Xu, J. 	Complete Circularized Genome Sequences of Four Strains of Elizabethkingia anophelis, Including Two Novel Strains Isolated from Wild-Caught Anopheles  sinensis.	Genome Announcements	2017	5		e01359-17			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. 		
@D	Pein, C.-D.//Reuter, M.//Cech, D.//Kruger, D.H. 	Oligonucleotide duplexes containing CC(A/T)GG stimulate cleavage of refractory DNA by restriction endonuclease EcoRII.	FEBS Lett.	1989	245		141-144			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. 		
@D	Pein, C.-D.//Reuter, M.//Meisel, A.//Cech, D.//Kruger, D.H. 	Activation of restriction endonuclease EcoRII does not depend on the cleavage of stimulator DNA.	Nucleic Acids Res.	1991	19		5139-5142			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. 		
@D	Pein, C.D.//Cech, D.//Gromova, E.S.//Orezkaya, T.S.//Shabarova, Z.A.//Kubareva, E.A. 	Interaction of the MvaI restriction enzyme with synthetic DNA fragments.	Nucleic Acids Symp. Ser.	1987	SS18		225-228			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. 		
@D	Pelaez, A.I.//Ribas-Aparicio, R.M.//Gomez, A.//Rodicio, M.R. 	Establishment of a hybrid SalI-HgiDII type II restriction-modification system.	Biol. Chem.	1998	379		583-584			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. 		
@D	Pellenz, S.//Dujon, B.//Schafer, B. 	Target site cleavage by the homing endonuclease I-SpomI from fission yeast mitochondria.	Yeast	2003	20		S47			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. 		
@D	Pellenz, S.//Harington, A.//Dujon, B.//Wolf, K.//Schaefer, B. 	Characterization of the I-SpomI endonuclease from fission yeast: Insights into the evolution of a group I intron-encoded homing  endonuclease.	J. Mol. Evol.	2002	55		302-313			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. 		
@D	Pelletier, E.//Kreimeyer, A.//Bocs, S.//Rouy, Z.//Gyapay, G.//Chouari, R.//Riviere, D.//Ganesan, A.//Daegelen, P.//Sghir, A.//Cohen, G.N.//Medigue, C.//Weissenbach, J.//Le Paslier, D. 	"Candidatus Cloacamonas acidaminovorans": genome sequence reconstruction provides a first glimpse of a new bacterial division.	J. Bacteriol.	2008	190		2572-2579			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. 		
@D	Pelludat, C.//Mirold, S.//Hardt, W.D. 	The SopEPhi Phage Integrates into the ssrA Gene of Salmonella enterica Serovar Typhimurium A36 and Is Closely Related to the Fels-2 Prophage.	J. Bacteriol.	2003	185		5182-5191			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. 		
@D	Pembroke, J.T.//Piterina, A.V. 	A novel ICE in the genome of Shewanella putrefaciens W3-18-1: comparison with the SXT/R391 ICE-like elements.	FEMS Microbiol. Lett.	2006	264		80-88			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. 		
@D	Pena, A.//Busquets, A.//Gomila, M.//Bosch, R.//Nogales, B.//Garcia-Valdes, E.//Lalucat, J.//Bennasar, A. 	Draft Genome of Pseudomonas stutzeri Strain ZoBell (CCUG 16156), a Marine Isolate and Model Organism for Denitrification Studies.	J. Bacteriol.	2012	194		1277-1278			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. 		
@D	Pena, A.//Busquets, A.//Gomila, M.//Mayol, J.//Bosch, R.//Nogales, B.//Garcia-Valdes, E.//Bennasar, A.//Lalucat, J. 	Draft Genome of Pseudomonas stutzeri Strain NF13, a Nitrogen Fixer Isolated from  the Galapagos Rift Hydrothermal Vent.	Genome Announcements	2013	1		e0011313			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. 		
@D	Pena, A.//Busquets, A.//Gomila, M.//Mulet, M.//Gomila, R.M.//Reddy, T.B.//Huntemann, M.//Pati, A.//Ivanova, N.//Markowitz, V.//Garcia-Valdes, E.//Goker, M.//Woyke, T.//Klenk, H.P.//Kyrpides, N.//Lalucat, J. 	High quality draft genome sequences of Pseudomonas fulva DSM 17717(T), Pseudomonas parafulva DSM 17004(T) and Pseudomonas cremoricolorata DSM 17059(T)  type strains.	Standards in Genomic Sciences	2016	11		55			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. 		
@D	Pena-Gonzalez, A.//Marston, C.K.//Rodriguez-R, L.M.//Kolton, C.B.//Garcia-Diaz, J.//Theppote, A.//Frace, M.//Konstantinidis, K.T.//Hoffmaster, A.R. 	Draft Genome Sequence of Bacillus cereus LA2007, a Human-Pathogenic Isolate Harboring Anthrax-Like Plasmids.	Genome Announcements	2017	5		e00181-17			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. 		
@D	Pena-Montenegro, T.D.//Dussan, J. 	Genome sequence and description of the heavy metal tolerant bacterium Lysinibacillus sphaericus strain OT4b.31.	Standards in Genomic Sciences	2013	9		42-56			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. 		
@D	Pena-Montenegro, T.D.//Lozano, L.//Dussan, J. 	Genome sequence and description of the mosquitocidal and heavy metal tolerant strain Lysinibacillus sphaericus CBAM5.	Standards in Genomic Sciences	2015	10		2			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. 		
@D	Peng, J.//Yang, L.//Yang, F.//Yang, J.//Yan, Y.//Nie, H.//Zhang, X.//Xiong, Z.//Jiang, Y.//Cheng, F.//Xu, X.//Chen, S.//Sun, L.//Li, W.//Shen, Y.//Shao, Z.//Liang, X.//Xu, J.//Jin, Q. 	Characterization of ST-4821 complex, a unique Neisseria meningitidis clone.	Genomics	2008	91		78-87			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. 		
@D	Peng, L.//Song, L.//Sun, L.//Cai, Y.//Wang, L.//Yu, B. 	Genome Sequence of Bacillus coagulans P38, an Efficient Polymer-Grade l-Lactate Producer from Cellulosic Substrates.	Genome Announcements	2015	3		e00495-15			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. 		
@D	Peng, Q.//Yi, L.//Peng, Q.//Peng, Y. 	Draft Genome Sequence of the Potassium Feldspar-Solubilizing Bacterium Ensifer adhaerens L18.	Genome Announcements	2017	5		e00199-17			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. 		
@D	Peng, Q.//Yi, L.//Zhou, L.//Peng, Q. 	Draft Genome Sequence of the Vanadium-Leaching Bacterium Pseudomonas chlororaphis Strain L19.	Genome Announcements	2018	6		e00966-17			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. 		
@D	Peng, T.//Pan, S.//Christopher, L.//Sparling, R.//Levin, D.B. 	Draft Genome Sequence of Thermoanaerobacter sp. Strain YS13, a Novel Thermophilic Bacterium.	Genome Announcements	2015	3		e00584-15			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. 		
@D	Peng, X.//Adachi, K.//Chen, C.//Kasai, H.//Kanoh, K.//Shizuri, Y.//Misawa, N. 	Discovery of a marine bacterium producing 4-hydroxybenzoate and its alkyl esters, parabens.	Appl. Environ. Microbiol.	2006	72		5556-5561			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. 		
@D	Peng, Z.//Liang, W.//Liu, W.//Wu, B.//Tang, B.//Tan, C.//Zhou, R.//Chen, H. 	Genomic characterization of Pasteurella multocida HB01, a serotype A bovine isolate from China.	Gene	2016	581		85-93			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. 		
@D	Peng, Z.//Wang, W.//Hu, Y.//Li, F. 	Complete Genome Sequence of Enterococcus hirae R17, a Daptomycin-Resistant Bacterium Isolated from Retail Pork in China.	Genome Announcements	2016	4		e00605-16			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. 		
@D	Penner, M.//Morad, I.//Snyder, L.//Kaufmann, G. 	Phage T4-coded Stp: double-edged effector of coupled DNA and tRNA-restriction systems.	J. Mol. Biol.	1995	249		857-868			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. 		
@D	Penton, P.K.//Tyagi, E.//Humrighouse, B.W.//McQuiston, J.R. 	Complete Genome Sequence of Corynebacterium minutissimum, an Opportunistic Pathogen and the Causative Agent of Erythrasma.	Genome Announcements	2015	3		e00139-15			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. 		
@D	Perea, J.//Desdouets, C.//Schapira, M.//Jacq, C. 	I-SceIII: A novel group I intron-encoded endonuclease from the yeast mitochondria.	Nucleic Acids Res.	1993	21		358			Re-engineered gene with "good" codons and expressed in E. coli. Cleavage site determined. 		
@D	Pereira, J.Q.//Ambrosini, A.//Sant'Anna, F.H.//Tadra-Sfeir, M.//Faoro, H.//Pedrosa, F.O.//Souza, E.M.//Brandelli, A.//Passaglia, L.M. 	Whole-Genome Shotgun Sequence of the Keratinolytic Bacterium Lysobacter sp. A03,  Isolated from the Antarctic Environment.	Genome Announcements	2015	3		e00246-15			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. 		
@D	Pereira, M.F.//Rossi, C.C.//de Carvalho, F.M.//de Almeida, L.G.//Souza, R.C.//de Vasconcelos, A.T.//Bazzolli, D.M. 	Draft Genome Sequences of Six Actinobacillus pleuropneumoniae Serotype 8 Brazilian Clinical Isolates: Insight into New Applications.	Genome Announcements	2015	3		e01585-14			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. 		
@D	Pereira, U.P.//Gouran, H.//Nascimento, R.//Adaskaveg, J.E.//Goulart, L.R.//Dandekar, A.M. 	Complete Genome Sequence of Xanthomonas arboricola pv. juglandis 417, a Copper-Resistant Strain Isolated from Juglans regia L.	Genome Announcements	2015	3		e01126-15			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). 		
@D	Perelman, E.V.//Shtanchaeva, S.M.//Bulk, V.F.//Tarasov, A.P.//Bakh, N.L.//Semina, I.S. 	Use of different media for growing the producers of restricting enzyme XbaI.	Zh. Mikrobiol. Epidemiol. Immunobiol.	1984	12		48-50			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. 		
@D	Perevyazova, T.A.//Rogulin, E.A.//Zheleznaya, L.A.//Matvienko, N.I. 	Cloning and sequencing of the gene of site-specific nickase N.BspD6I.	Biokhimiia	2003	68		1203-1207			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. 		
@D	Perez-de-la-Rosa, D.//Perez-de-la-Rosa, J.J.//Cossio-Bayugar, R.//Miranda-Miranda, E.//Lozano, L.//Bravo-Diaz, M.A.//Rocha-Martinez, M.K.//Sachman-Ruiz, B. 	Complete Genome Sequence of Paenibacillus larvae MEX14, Isolated from Honey Bee Larvae from the Xochimilco Quarter in Mexico City.	Genome Announcements	2015	3		e00968-15			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). 		
@D	Perez-Maya, A.A.//Hinojosa-Robles, R.M.//Barcenas-Walls, J.R.//Rojas-Martinez, A.//Barrera-Saldana, H.A.//Ortiz-Lopez, R. 	Draft Genome Sequence of an Atypical Strain of Streptococcus pneumoniae Serotype  19A Isolated from Cerebrospinal Fluid.	Genome Announcements	2016	4		e00277-16			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. 		
@D	Perez-Maya, A.A.//Hinojosa-Robles, R.M.//Barcenas-Walls, J.R.//Vignau-Cantu, A.//Barrera-Saldana, H.A.//Ortiz-Lopez, R. 	Complete Genome Sequence of Streptococcus pneumoniae Serotype 19A, a Blood Clinical Isolate from Northeast Mexico.	Genome Announcements	2016	4		e00195-16			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%. 		
@D	Perez-Oseguera, A.//Castro-Jaimes, S.//Salgado-Camargo, A.D.//Silva-Sanchez, J.//Garza-Gonzalez, E.//Castillo-Ramirez, S.//Cevallos, M.A. 	Complete Genome Sequence of a blaOXA-58-Producing Acinetobacter baumannii Strain  Isolated from a Mexican Hospital.	Genome Announcements	2017	5		e00949-17			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. 		
@D	Perez-Ramos, A.//Mohedano, M.L.//Puertas, A.//Lamontanara, A.//Orru, L.//Spano, G.//Capozzi, V.//Duenas, M.T.//Lopez, P. 	Draft Genome Sequence of Pediococcus parvulus 2.6, a Probiotic beta-Glucan Producer Strain.	Genome Announcements	2016	4		e01381-16			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. 		
@D	Pericone, C.D.//Bae, D.//Shchepetov, M.//McCool, T.//Weiser, J.N. 	Short-sequence tandem and nontandem DNA repeats and endogenous hydrogen peroxide production contribute to genetic instability of Streptococcus   pneumoniae.	J. Bacteriol.	2002	184		4392-4399			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. 		
@D	Peris-Bondia, F.//Muraille, E.//Van Melderen, L. 	Complete Genome Sequence of the Escherichia coli PMV-1 Strain, a Model Extraintestinal Pathogenic E. coli Strain Used for Host-Pathogen Interaction  Studies.	Genome Announcements	2013	1		e00913-13			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. 		
@D	Perler, F.B. 	Hyperthermophilic inteins.	Methods Enzymol.	2001	334		270-280			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. 		
@D	Perler, F.B. 	InBase, the New England Biolabs Intein Database.	Nucleic Acids Res.	1999	27		346-347			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. 		
@A	Perler, F.B. 		Inteins - A historical perspective.			Belfort, M. 		Nucleic Acids Mol. Biol.				Berlin Heidelberg	Springer-Verlag	2005		16		193-210									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. 		
@D	Perler, F.B.//Comb, D.G.//Jack, W.E.//Moran, L.S.//Qiang, B.//Kucera, R.B.//Benner, J.//Slatko, B.E.//Nwankwo, D.O.//Hempstead, S.K.//Carlow, C.K.S.//Jannasch, H. 	Intervening sequences in an Archaea DNA polymerase gene.	Proc. Natl. Acad. Sci. U. S. A.	1992	89		5577-5581			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. 		
@D	Perler, F.B.//Davis, E.O.//Dean, G.E.//Gimble, F.S.//Jack, W.E.//Neff, N.//Noren, C.J.//Thorner, J.//Belfort, M. 	Protein splicing elements: inteins and exteins--a definition of terms and recommended nomenclature.	Nucleic Acids Res.	1994	22		1125-1127			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. 		
@D	Perlloni, A.//Brown, E.W.//LeClerc, J.E.//Cebula, T.A. 	Phylogenetic evidence for horizontal gene transfer of type I restriction and modification (hsd) genes among highly homogenous Salmonella strains.	Abstr. Gen. Meet. Am. Soc. Microbiol.	2005	105		284			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. 		
@D	Permala, R.R.//Glady-Croue, J.//Watkin, E.L.J.//Ramsay, J.P.//Croue, J.P. 	Complete Genome Sequence of Stenotrophomonas maltophilia AB550, an Environmental  Solar Radiation- and Multidrug-Resistant Strain Isolated in Western Australia.	Microbiol. Resour. Announc.	2018	7		e00914-18			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. 		
@D	Perna, N.T. et al. 	Genome sequence of enterohaemorrhagic Escherichia coli O157:H7.	Nature	2001	409		529-533			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. 		
@D	Pernstich, C.//Halford, S.E. 	Illuminating the reaction pathway of the FokI restriction endonuclease by fluorescence resonance energy transfer.	Nucleic Acids Res.	2012	40		1203-1213			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. 		
@D	Pero, J.//Hannett, N.M.//Talkington, C. 	Restriction cleavage map of SP01 DNA: general location of early, middle, and late genes.	J. Virol.	1979	31		156-171			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. 		
@D	Perona, J.J. 	Type II restriction endonucleases.	Methods	2002	28		353-364			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. 		
@D	Perona, J.J. 	Structural pathways of phosphoryl transfer in type II restriction endonucleases.	ACS Abstracts	2002	223		C-38-C-39			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. 		
@D	Perona, J.J.//Horton, N.C.//Sam, M.D. 	Catalytic mechanism of EcoRV endonuclease derived from crystal structures and transient kinetics.	Transactions ACA	2000	35		9-17			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. 		
@D	Perona, J.J.//Martin, A.M. 	Conformational transitions and structural deformability of EcoRV endonuclease revealed by crystallographic analysis.	J. Mol. Biol.	1997	273		207-225			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. 		
@D	Perotto, S.//Nepote-Fus, P.//Saletta, L.//Bandi, C.//Young, J.P.W. 	A diverse population of introns in the nuclear ribosomal genes of ericoid mycorrhizal fungi includes elements with sequence similarity to endonuclease-coding genes.	Mol. Biol. Evol.	2000	17		44-59			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. 		
@D	Perreten, V.//Chanchaithong, P.//Prapasarakul, N.//Rossano, A.//Blum, S.E.//Elad, D.//Schwendener, S. 	Novel Pseudo-Staphylococcal Cassette Chromosome mec Element ({Psi}SCCmec57395) in Methicillin-Resistant Staphylococcus pseudintermedius CC45.	Antimicrob. Agents Chemother.	2013	57		5509-5515			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. 		
@D	Perrin, A.//Buckle, M.//Dujon, B. 	Asymmetrical recognition and activity of the I-SceI endonuclease on its site and on intron-exon junctions.	EMBO J.	1993	12		2939-2947			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. 		
@D	Perrody, E.//Cirinesi, A.M.//Desplats, C.//Keppel, F.//Schwager, F.//Tranier, S.//Georgopoulos, C.//Genevaux, P. 	A Bacteriophage-Encoded J-Domain Protein Interacts with the DnaK/Hsp70 Chaperone and Stabilizes the Heat-Shock Factor sigma(32) of Escherichia coli.	PLoS Genet.	2012	8		E1003037			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. 		
@D	Perry, B.J.//Bergsveinson, J.//Tambalo, D.D.//Yost, C.K.//Khan, N.H.//Whiting, M. 	Complete Genome Sequence of Delftia acidovorans RAY209, a Plant Growth-Promoting  Rhizobacterium for Canola and Soybean.	Genome Announcements	2017	5		e01224-17			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. 		
@D	Persicke, M.//Albersmeier, A.//Bednarz, H.//Niehaus, K.//Kalinowski, J.//Ruckert, C. 	Genome sequence of the soil bacterium Corynebacterium callunae type strain DSM 20147(T).	Standards in Genomic Sciences	2015	10		5			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. 		
@D	Persinoti, G.F.//Paixao, D.A.A.//Bugg, T.D.H.//Squina, F.M. 	Genome Sequence of Lysinibacillus sphaericus, a Lignin-Degrading Bacterium Isolated from Municipal Solid Waste Soil.	Genome Announcements	2018	6		e00353-18			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. 		
@D	Persson, T. et al. 	Genome Sequence of 'Candidatus Frankia datiscae' Dg1, the Uncultured Microsymbiont from Nitrogen-Fixing Root Nodules of the Dicot Datisca  glomerata.	J. Bacteriol.	2011	193		7017-7018			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. 		
@D	Pertry, I.//Vaclavikova, K.//Depuydt, S.//Galuszka, P.//Spichal, L.//Temmerman, W.//Stes, E.//Schmulling, T.//Kakimoto, T.//Van Montagu, M.C.//Strnad, M.//Holsters, M.//Tarkowski, P.//Vereecke, D. 	Identification of Rhodococcus fascians cytokinins and their modus operandi to reshape the plant.	Proc. Natl. Acad. Sci. U. S. A.	2009	106		929-934			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. 		
@D	Pertsev, A.V.//Denmukhametov, M.M.//Anoshkin, A.G.//Ariskina, E.V.//Berezin, I.A.//Solonin, A.S.//Kuzmin, N.P. 	Restriction endonucleases from various bacterial strains displaying an ice-nucleating activity.	Prikl. Biokhim. Mikrobiol.	2000	36		13-16			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. 		
@D	Pertzev, A.V.//Kravetz, A.N.//Mayorov, S.G.//Zakharova, M.V.//Solonin, A.S. 	Isolation of a strain overproducing endonuclease Eco29kI: Purification and characterization of the homogeneous enzyme.	Biokhimiia	1997	62		858-867			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. 		
@D	Pertzev, A.V.//Ruban, N.M.//Zakharova, M.V.//Beletzkaja, I.V.//Petrov, S.I.//Kravetz, A.N.//Solonin, A.S. 	Eco29kI, a novel plasmid encoded restriction endonuclease from Escherichia coli.	Nucleic Acids Res.	1992	20		1991			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. 		
@D	Pesce, C.//Bolot, S.//Berthelot, E.//Bragard, C.//Cunnac, S.//Fischer-Le, S.M.//Portier, P.//Arlat, M.//Gagnevin, L.//Jacques, M.A.//Noel, L.D.//Carrere, S.//Koebnik, R. 	Draft Genome Sequence of Xanthomonas translucens pv. graminis Pathotype Strain CFBP 2053.	Genome Announcements	2015	3		e01174-15			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. 		
@D	Pesce, C.//Bolot, S.//Cunnac, S.//Portier, P.//Fischer-Le, S.M.//Jacques, M.A.//Gagnevin, L.//Arlat, M.//Noel, L.D.//Carrere, S.//Bragard, C.//Koebnik, R. 	High-Quality Draft Genome Sequence of the Xanthomonas translucens pv. cerealis Pathotype Strain CFBP 2541.	Genome Announcements	2015	3		e01574-14			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. 		
@D	Pester, M. et al. 	Complete Genome Sequences of Desulfosporosinus orientis DSM765T, Desulfosporosinus youngiae DSM17734T, Desulfosporosinus meridiei DSM13257T, and  Desulfosporosinus acidiphilus DSM22704T.	J. Bacteriol.	2012	194		6300-6301			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). 		
@D	Pestova, E.V.//Morrison, D.A. 	Isolation and characterization of three Streptococcus pneumoniae transformation-specific loci by use of a lacZ reporter insertion vector.	J. Bacteriol.	1998	180		2701-2710			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. 		
@D	Petering, H.//Hammerschmidt, S.//Frosch, M.//van Putten, J.P.M.//Ison, C.A.//Robertson, B.D. 	Genes associated with the meningococcal capsule complex are also found in Neisseria gonorrhoeae.	J. Bacteriol.	1996	178		3342-3345			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. 		
@D	Peters, I. 	Changing the sequence specificity of the restriction endonuclease EcoRI.	Ph.D. Thesis, Germany	2003			1-167			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. 		
@D	Peters, W. 	New applications of (S)-adenosyl-L-methionine analogues with protein methyltransferases and click chemistry for sequence specific protein labelling.	Ph.D. Thesis, Germany	2007			1-126					
@D	Petersen, R.//Lomholt, H.B.//Scholz, C.F.//Bruggemann, H. 	Draft Genome Sequences of Two Propionibacterium acnes Strains Isolated from Progressive Macular Hypomelanosis Lesions of Human Skin.	Genome Announcements	2015	3		e01250-15			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. 		
@D	Peterson, K.R.//Mount, D.W. 	Analysis of the genetic requirements for viability of Escherichia coli K-12 DNA adenine methylase (dam) mutants.	J. Bacteriol.	1993	175		7505-7508			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. 		
@D	Peterson, K.R.//Wertman, K.F.//Mount, D.W.//Marinus, M.G. 	Viability of Escherichia coli K-12 DNA adenine methylase (dam) mutants requires increased expression of specific genes in the SOS regulon.	Mol. Gen. Genet.	1985	201		14-19			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. 		
@D	Peterson, R.C. 	Prediction of restriction endonuclease site distribution based on dinucleotide frequency.	Fed. Proc.	1986	45		1850			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. 		
@D	Peterson, R.C. 	Prediction of the frequencies of restriction endonuclease recognition sequences using di- and mononucleotide frequencies.	Biotechniques	1988	6		34-39			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. 		
@D	Peterson, S.N.//Reich, N.O. 	GATC flanking sequences regulate Dam activity: evidence for how Dam specificity may influence pap expression.	J. Mol. Biol.	2005	355		459-472			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. 		
@D	Peterson, S.N.//Reich, N.O. 	Competitive Lrp and Dam assembly at the pap regulatory region: implications for mechanisms of epigenetic regulation.	J. Mol. Biol.	2008	383		92-105			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. 		
@D	Pethick, F.E. et al. 	Complete Genome Sequences of Corynebacterium pseudotuberculosis Strains 3/99-5 and 42/02-A, Isolated from Sheep in Scotland and Australia, Respectively.	J. Bacteriol.	2012	194		4736-4737			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. 		
@D	Pethick, F.E.//Macfadyen, A.C.//Tang, Z.//Sangal, V.//Liu, T.T.//Chu, J.//Kosec, G.//Petkovic, H.//Guo, M.//Kirby, R.//Hoskisson, P.A.//Herron, P.R.//Hunter, I.S. 	Draft Genome Sequence of the Oxytetracycline-Producing Bacterium Streptomyces rimosus ATCC 10970.	Genome Announcements	2013	1		e0006313			We report the draft genome of Streptomyces rimosus (ATCC 10970), a soil isolate that produces oxytetracycline, a commercially important and clinically useful antibiotic. 		
@D	Petranovic, M.//Petranovic, D.//Dohet, C.//Brooks, P.//Radman, M. 	Some restriction endonucleases tolerate single mismatches of the pyrimidine-purine type.	Nucleic Acids Res.	1990	18		2159-2162			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. 		
@D	Petrauskene, O.//Kubareva, E.A.//Gromova, E.S. 	A spectrophotometric method for studying the cleavage of DNA duplexes by restriction endonucleases.	Mol. Biol. (Mosk)	1991	25		1424-1426			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. 		
@D	Petrauskene, O.V.//Babkina, O.V.//Tashlitsky, V.N.//Kazankov, G.M.//Gromova, E.S. 	EcoRII endonuclease has two identical DNA-binding sites and cleaves one of two co-ordinated recognition sites in one catalytic event.	FEBS Lett.	1998	425		29-34			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. 		
@D	Petrauskene, O.V.//Gromova, E.S.//Romanova, E.A.//Volkov, E.M.//Oretskaya, T.S.//Shabarova, Z.A. 	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.	Gene	1995	157		173-176			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. 		
@D	Petrauskene, O.V.//Karpova, E.A.//Gromova, E.S.//Guschlbauer, W. 	Two subunits of EcoRII restriction endonuclease interact with two DNA recognition sites.	Biochem. Biophys. Res. Commun.	1994	198		885-890			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. 		
@D	Petrauskene, O.V.//Krynetskaya, N.F.//Tashlitsky, V.N.//Belkov, V.M.//Kubareva, E.A.//Gromova, E.S.//Guschlbauer, W.//Shabarova, Z.A. 	Use of UV spectroscopy for the study of nucleic acid cleavage by E.coli RNase H and restriction endonucleases.	Biochem. Mol. Biol. Int.	1995	37		1127-1135			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. 		
@D	Petrauskene, O.V.//Kubareva, E.A.//Gromova, E.S.//Pein, C.-D.//Cech, D.//Shabarova, Z.A. 	Synthetic DNA duplexes as a tool in studying the mechanism of EcoRII activation.	Mol. Biol. (Mosk)	1993	27		507-518			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. 		
@D	Petrauskene, O.V.//Kubareva, E.A.//Gromova, E.S.//Shabarova, Z.A. 	Mechanism of the interaction of EcoRII restriction endonuclease with two recognition sites - probing of modified DNA duplexes as activators of the enzyme.	Eur. J. Biochem.	1992	208		617-622			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. 		
@D	Petrauskene, O.V.//Schmidt, S.//Karyagina, A.S.//Nikolskaya, I.I.//Gromova, E.S.//Cech, D. 	The interaction of DNA duplexes containing 2-aminopurine with restriction endonucleases EcoRII and SsoII.	Nucleic Acids Res.	1995	23		2192-2197			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. 		
@D	Petrauskene, O.V.//Tashlitsky, V.N.//Brevnov, M.G.//Bakman, Y.//Gromova, E.S. 	Kinetic modeling of allosteric interaction of EcoRII restriction endonuclease with two DNA sites.	Biokhimiia	1996	61		1257-1269			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. 		
@D	Petrauskene, O.V.//Yakovleva, J.N.//Alekseev, Y.I.//Subach, F.V.//Babkina, O.V.//Gromova, E.S. 	DNA duplexes containing altered sugar residues as probes of EcoRII and MvaI endonuclease interactions with sugar-phosphate backbone.	J. Biomol. Struct. Dyn.	2000	17		857-870			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. 		
@D	Petrauskiene, L.J.//Klimasauskas, S.J.//Butkus, V.V.//Janulaitis, A. 	Synthesis of oligodeoxynucleotides containing N4-methylcytosine.	Bioorg. Khim.	1986	12		1597-1603			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. 		
@D	Petronella, N.//Kenwell, R.//Pagotto, F.//Pightling, A.W. 	Draft Genome Sequences of Two Clostridium botulinum Group II (Nonproteolytic) Type B Strains (DB-2 and KAPB-3).	Genome Announcements	2014	2		e01111-14			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). 		
@D	Petroni, E.A.//Bocca, S.N.//Ielpi, L. 	Sequence-specific DNA modification in Acetobacter xylinum.	Cell. Mol. Biol. (Noisy-le-grand)	1996	42		759-767			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. 		
@D	Petronzio, T.//Schildkraut, I. 	Altered specificity of restriction endonucleases HinfI.	Nucleic Acids Res.	1990	18		3666			None 		
@D	Petrosino, J.F.//Xiang, Q.//Karpathy, S.E.//Jiang, H.//Yerrapragada, S.//Liu, Y.//Gioia, J.//Hemphill, L.//Gonzalez, A.//Raghavan, T.M.//Uzman, A.//Fox, G.E.//Highlander, S.//Reichard, M.//Morton, R.J.//Clinkenbeard, K.D.//Weinstock, G.M. 	Chromosome Rearrangement and Diversification of Francisella tularensis Revealed by the Type B (OSU18) Genome Sequence.	J. Bacteriol.	2006	188		6977-6985			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). 		
@D	Petrosova, H.//Zobanikova, M.//Cejkova, D.//Mikalova, L.//Pospisilova, P.//Strouhal, M.//Chen, L.//Qin, X.//Muzny, D.M.//Weinstock, G.M.//Smajs, D. 	Whole Genome Sequence of Treponema pallidum ssp. pallidum, Strain Mexico A, Suggests Recombination between Yaws and Syphilis Strains.	PLoS Neglected Trop. Dis.	2012	6		E1832			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. 		
@D	Petrossian, T.//Clarke, S. 	Bioinformatic identification of novel methyltransferases.	Epigenomics	2009	1		163-175			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. 		
@D	Petrossian, T.C.//Clarke, S.G. 	Computational methods to identify novel methyltransferases.	BMC Bioinformatics	2009	10		7			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. 		
@D	Petrosyan, V.//Holder, M.//Ajami, N.J.//Petrosino, J.F.//Sahasrabhojane, P.//Thompson, E.J.//Kalia, A.//Shelburne, S.A. 	Complete Genome Sequence of Streptococcus mitis Strain SVGS_061 Isolated from a Neutropenic Patient with Viridans Group Streptococcal Shock Syndrome.	Genome Announcements	2016	4		e00259-16			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. 		
@D	Petrov, N.A.//Gorbunov, Y.A.//Malygin, E.G. 	Interaction of T4 phage DNA-[N6-adenine]-methyltransferase with substrates containing defective recognition sites.	Mol. Biol. (Mosk)	1997	31		973-977			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. 		
@D	Petrov, N.A.//Gorbunov, Y.A.//Naumochkin, A.N.//Malygin, E.G. 	Substrate complexes of DNA-[N6-adenine]-methyltransferases of T-even phages registered by the gel retardation method.	Mol. Biol. (Mosk)	1997	31		966-972			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. 		
@D	Petrov, V.M.//Ratnayaka, S.//Nolan, J.M.//Miller, E.S.//Karam, J.D. 	Genomes of the T4-related bacteriophages as windows on microbial genome evolution.	Virol. J.	2010	7		292			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. 		
@D	Petrovski, S.//Seviour, R.J.//Tillett, D. 	Prevention of Gordonia and Nocardia Stabilized Foam Formation by Using Bacteriophage GTE7.	Appl. Environ. Microbiol.	2011	77		7864-7867			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. 		
@D	Petruska, J.//Horn, D. 	Sequence-specific responses of restriction endonucleases to bromodeoxyuridine substitution in mammalian DNA.	Nucleic Acids Res.	1983	11		2495-2510			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. 		
@D	Petrusyte, M.//Bitinaite, J.//Menkevicius, S.//Klimasauskas, S.//Butkus, V.//Janulaitis, A. 	Restriction endonucleases of a new type.	Gene	1988	74		89-91			Meeting Abstract 		
@D	Petrusyte, M.//Rudokas, K.//Maneliene, Z.//Kiuduliene, E.//Butkus, V.//Janulaitis, A. 	Bsp1407I, a restriction endonuclease from Bacillus stearothermophilus, which recognizes novel palindromic sequence 5'-T^GTACA-3'.	Nucleic Acids Res.	1993	21		2514			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'. 		
@D	Petrusyte, M.P.//Bitinaite, J.B.//Kersulyte, D.R.//Menkevicius, S.J.//Butkus, V.V.//Janulaitis, A. 	New types of restriction endonucleases.	Dokl. Akad. Nauk.	1987	295		1250-1253			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. 		
@D	Petrusyte, M.P.//Janulaitis, A. 	Isolation and some properties of the restriction endonuclease BcnI from Bacillus centrosporus.	Eur. J. Biochem.	1982	121		377-381			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+. 		
@D	Petrusyte, M.P.//Janulaitis, A. 	Specific methylase from Bacillus centrosporus.	Bioorg. Khim.	1981	7		1885-1887			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. 		
@D	Pettengill, E.A.//Hoffmann, M.//Binet, R.//Roberts, R.J.//Payne, J.//Allard, M.//Michelacci, V.//Minelli, F.//Morabito, S. 	Complete Genome Sequence of Enteroinvasive Escherichia coli O96:H19 Associated with a Severe Foodborne Outbreak.	Genome Announcements	2015	3		e00883-15			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. 		
@D	Pettersson, B.M.//Behra, P.R.//Manduva, S.//Das, S.//Dasgupta, S.//Bhattacharya, A.//Kirsebom, L.A. 	Draft Genome Sequence of Saccharopolyspora rectivirgula.	Genome Announcements	2014	2		e01117-13			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%. 		
@D	Petty, N.K.//Bulgin, R.//Crepin, V.F.//Cerdeno-Tarraga, A.M.//Schroeder, G.N.//Quail, M.A.//Lennard, N.//Corton, C.//Barron, A.//Clark, L.//Toribio, A.L.//Parkhill, J.//Dougan, G.//Frankel, G.//Thomson, N.R. 	The Citrobacter rodentium genome sequence reveals convergent evolution with human pathogenic Escherichia coli.	J. Bacteriol.	2010	192		525-538			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. 		
@D	Petzsch, P.//Poehlein, A.//Johnson, D.B.//Daniel, R.//Schlomann, M.//Muhling, M. 	Genome Sequence of the Acidophilic Sulfate-Reducing Peptococcaceae Strain CEB3.	Genome Announcements	2015	3		e00886-15			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. 		
@D	Petzsch, P.//Poehlein, A.//Johnson, D.B.//Daniel, R.//Schlomann, M.//Muhling, M. 	Genome Sequence of the Moderately Acidophilic Sulfate-Reducing Firmicute Desulfosporosinus acididurans (Strain M1T).	Genome Announcements	2015	3		e00881-15			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. 		
@D	Pfaller, S.//Tokarev, V.//Kessler, C.//McLimans, C.//Gomez-Alvarez, V.//Wright, J.//King, D.//Lamendella, R. 	Draft Genome Sequence of Mycobacterium chimaera Type Strain Fl-0169.	Genome Announcements	2017	5		e01620-16			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. 		
@D	Pfeffer, S.//Brown, R.M. Jr. 	Complete Genome Sequence of the Cyanobacterium Anabaena sp. 33047.	Genome Announcements	2016	4		e00809-16			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. 		
@D	Pfeffer, S.//Mehta, K.//Brown, R.M. Jr. 	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.	Genome Announcements	2016	4		e00808-16			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. 		
@D	Pfeffer, S.//Mehta, K.//Brown, R.M. Jr. 	Complete Genome Sequence of Gluconacetobacter hansenii Strain NQ5 (ATCC 53582), an Efficient Producer of Bacterial Cellulose.	Genome Announcements	2016	4		e00785-16			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. 		
@D	Pfeffer, S.//Santos, R.//Ebels, M.//Bordbar, D.//Brown, R.M. Jr. 	Complete Genome Sequence of Komagataeibacter hansenii Strain SC-3B.	Genome Announcements	2017	5		e00169-17			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. 		
@D	Pfeffer, S.//Santos, R.//Ebels, M.//Bordbar, D.//Brown, R.M. Jr. 	Complete Genome Sequence of Komagataeibacter hansenii LMG 23726T.	Genome Announcements	2017	5		e00168-17			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. 		
@D	Pfeffer, S.//Santos, R.//Ebels, M.//Bordbar, D.//Brown, R.M. Jr. 	Complete Genome Sequence of Komagataeibacter hansenii Strain HUM-1.	Genome Announcements	2017	5		e00167-17			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. 		
@D	Pfeffer, S.//Sowa, S.//Brown, R.M. Jr. 	Complete Genome Sequence of a Novel Strain of Cyanobacterium, Anabaena sp. 4-3.	Genome Announcements	2016	4		e00842-16			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. 		
@D	Pfeifer, G.P.//Kohlmaier, L.//Tomassetti, A.//Schleicher, R.//Follmann, H.//Pfohl-Leszkowicz, A.//Dirheimer, G.//Drahovsky, D. 	Polypeptide composition and an immunological analysis of DNA methyltransferases from different species.	Arch. Biochem. Biophys.	1989	268		388-392			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. 		
@D	Pfeiffer, F.//Schuster, S.C.//Broicher, A.//Falb, M.//Palm, P.//Rodewald, K.//Ruepp, A.//Soppa, J.//Tittor, J.//Oesterhelt, D. 	Evolution in the laboratory: The genome of Halobacterium salinarum strain R1 compared to that of strain NRC-1.	Genomics	2008	91		335-346			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. 		
@D	Pfleiderer, A.//Mishra, A.K.//Lagier, J.C.//Robert, C.//Caputo, A.//Raoult, D.//Fournier, P.E. 	Non-contiguous finished genome sequence and description of Alistipes ihumii sp. nov.	Standards in Genomic Sciences	2014	9		1221-1235			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. 		
@D	Pfreundt, U.//Stal, L.J.//Voss, B.//Hess, W.R. 	Dinitrogen fixation in a unicellular chlorophyll d-containing cyanobacterium.	ISME J.	2012	6		1367-1377			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. 		
@D	Phale, P.S.//Paliwal, V.//Raju, S.C.//Modak, A.//Purohit, H.J. 	Genome Sequence of Naphthalene-Degrading Soil Bacterium Pseudomonas putida CSV86.	Genome Announcements	2013	1		e00234-12			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. 		
@D	Phalke, S.//Nickel, O.//Walluscheck, D.//Hortig, F.//Onorati, M.C.//Reuter, G. 	Retrotransposon silencing and telomere integrity in somatic cells of Drosophila depends on the cytosine-5 methyltransferase DNMT2.	Nat. Genet.	2009	41		696-702			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. 		
@D	Pham, T.T.//Jacobs-Sera, D.//Pedulla, M.L.//Hendrix, R.W.//Hatfull, G.F. 	Comparative genomic analysis of mycobacteriophage Tweety: evolutionary insights and construction of compatible site-specific integration vectors for mycobacteria.	Microbiology	2007	153		2711-2723			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. 		
@D	Phelan, J.//de Sessions, P.F.//Tientcheu, L.//Perdigao, J.//Machado, D.//Hasan, R.//Hasan, Z.//Bergval, I.L.//Anthony, R.//McNerney, R.//Antonio, M.//Portugal, I.//Viveiros, M.//Campino, S.//Hibberd, M.L.//Clark, T.G. 	Methylation in Mycobacterium tuberculosis is lineage specific with associated mutations present globally.	Sci. Rep.	2018	8		160			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. 		
@D	Phelippeau, M.//Croce, O.//Robert, C.//Raoult, D.//Drancourt, M. 	Draft Genome Sequence of Mycobacterium lentiflavum CSUR P1491.	Genome Announcements	2015	3		e00817-15			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. 		
@D	Phelippeau, M.//Croce, O.//Robert, C.//Raoult, D.//Drancourt, M. 	Draft Genome Sequence of Mycobacterium europaeum Strain CSUR P1344.	Genome Announcements	2015	3		e00816-15			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. 		
@D	Phelippeau, M.//Robert, C.//Croce, O.//Raoult, D.//Drancourt, M. 	Draft Genome Sequence of Mycobacterium neoaurum Strain DSM 44074T.	Genome Announcements	2014	2		e00699-14			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. 		
@D	Philippe, N.//Legendre, M.//Doutre, G.//Coute, Y.//Poirot, O.//Lescot, M.//Arslan, D.//Seltzer, V.//Bertaux, L.//Bruley, C.//Garin, J.//Claverie, J.M.//Abergel, C. 	Pandoraviruses: amoeba viruses with genomes up to 2.5 Mb reaching that of parasitic eukaryotes.	Science	2013	341		281-286			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. 		
@D	Philippe, N.//Maigre, L.//Santini, S.//Pinet, E.//Claverie, J.M.//Davin-Regli, A.V.//Pages, J.M.//Masi, M. 	In Vivo Evolution of Bacterial Resistance in Two Cases of Enterobacter aerogenes Infections during Treatment with Imipenem.	PLoS ONE	2015	10		E0138828			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. 		
@D	Phillips, K.E.//Schipma, M.J.//Satchell, K.J. 	Draft Genome Sequences of Four Closely Linked Vibrio vulnificus Isolates from the Biotype 1 Environmental Genotype.	Genome Announcements	2015	3		e01317-14			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. 		
@D	Phillips, K.E.//Schipma, M.J.//Satchell, K.J. 	Draft Genome Sequence of Israeli Outbreak-Associated Vibrio vulnificus Biotype 3  Clinical Isolate BAA87.	Genome Announcements	2014	2		e00032-14			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). 		
@D	Phillips, P.L. 	Cloning and characterization of a methyl-dependent restriction endonuclease and a cell cycle regulating DNA methyltransferase from Zymomonas mobilis subspecies mobilis CP4.	Ph.D. Thesis, Univ. of Florida, Gainesville	2005			1-220			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. 		
@D	Phillips, S.E.V. 	Induced flip.	Nat. Struct. Biol.	1994	1		76-77			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. 		
@D	Photolo, M.M.//Mavumengwana, V.//Serepa-Dlamini, M.H.//Tlou, M.G. 	Draft Genome Sequence of Methylobacterium radiotolerans Strain MAMP 4754, a Bacterial Endophyte Isolated from Combretum erythrophyllum in South Africa.	Genome Announcements	2017	5		e00976-17			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%. 		
@D	Phung, L.T.//Silver, S.//Trimble, W.L.//Gilbert, J.A. 	Draft Genome of Halomonas Species Strain GFAJ-1 (ATCC BAA-2256).	J. Bacteriol.	2012	194		1835-1836			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. 		
@D	Phung, L.T.//Trimble, W.L.//Meyer, F.//Gilbert, J.A.//Silver, S. 	Draft Genome Sequence of Alcaligenes faecalis subsp. faecalis NCIB 8687 (CCUG 2071).	J. Bacteriol.	2012	194		5153			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. 		
@D	Picardeau, M. et al. 	Genome sequence of the saprophyte Leptospira biflexa provides insights into the evolution of Leptospira and the pathogenesis of leptospirosis.	PLoS ONE	2008	3		e1607			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. 		
@D	Picchi, S.C.//Vilas-Boas, L.A.//Ceresini, P.C.//de Macedo-Lemos, E.G.//Lemos, M.V. 	Strain variability in the DNA immigration control region (ICR) of Xylella fastidiosa.	Res. Microbiol.	2006	157		254-262			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. 		
@D	Piccinni, F.//Murua, Y.//Ghio, S.//Talia, P.//Rivarola, M.//Campos, E. 	Draft Genome Sequence of Cellulolytic and Xylanolytic Cellulomonas sp. Strain B6  Isolated from Subtropical Forest Soil.	Genome Announcements	2016	4		e00891-16			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. 		
@D	Piechaczyk, M.//Jeanteur, P.//Louarn, J.-M. 	An easy method for the selection of restriction- and modification-deficient mutants of Escherichia coli K-12.	Gene	1980	11		173-175			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. 		
@D	Piechula, S.//Kim, S.C.//Podhajska, A.J. 	PamI and PamII restriction endonucleases from Phormidium ambiguum.	Nucleic Acids Res.	1992	20		619			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. 		
@D	Piechula, S.//Kur, J.//Bielawski, K.//Podhajska, A.J. 	Isolation and identification of the restriction endonuclease PtaI from Phormidium tadzschicicum, an isoschizomer of BspMII.	Nucleic Acids Res.	1992	20		6738			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. 		
@D	Piechula, S.//Kur, J.//Woszczyk, J.//Podhajska, A.J. 	Purification and characterization of two restriction endonucleases isolated from Phormidium inundatum.	Gene	1995	157		315-316			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. 		
@D	Piechula, S.//Piosik, J.//Bielawski, K.//Podhajska, A.J. 	Isolation and characterization of the restriction endonuclease PpeI from Phormidium persicinum.	Mol. Biotechnol.	1996	5		97-99			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. 		
@D	Piechula, S.//Skowron, P.M.//Piatyszek, M.//Podhajska, A.J. 	Isolation and identification of two new Synechococcus-derived restriction endonucleases, SleI and SspAI isoschizomers of EcoRII.	Nucleic Acids Res.	1991	19		2782			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. 		
@D	Piechula, S.//Waleron, K.//Swiatek, W.//Biedrzycka, I.//Podhajska, A.J. 	Mesophilic cyanobacteria producing thermophilic restriction endonucleases.	FEMS Microbiol. Lett.	2001	198		135-140			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. 		
@D	Piekarowicz, A. 	HineI is an isoschizomer of HinfIII restriction endonuclease.	J. Mol. Biol.	1982	157		373-381			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. 		
@D	Piekarowicz, A. 	The influence of methionine deprivation on restriction properties of Haemophilus influenzae Rd and Ra strains.	Acta Microbiol. Pol. A	1974	6		71-74			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. 		
@D	Piekarowicz, A. 	Preferential cleavage by restriction endonuclease HinfIII.	Acta Biochim. Pol.	1984	31		453-464			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. 		
@D	Piekarowicz, A. 	Identification of a new restriction endonuclease R.NciII, from Neisseria cinerea.	Acta Microbiol. Pol.	1994	43		103-105			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. 		
@D	Piekarowicz, A. 	DNA methyltransferases of Neisseria gonorrhoeae.	Acta Microbiol. Pol.	1994	43		269-277			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. 		
@D	Piekarowicz, A.//Baj, J. 	Host specificity of DNA in Haemophilus influenzae:  The physiological and genetical bases of instability of restriction and modification of DNA in strain RD.	Acta Microbiol. Pol. A	1975	8		119-130			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). 		
@D	Piekarowicz, A.//Bickle, T.A.//Shepherd, J.C.W.//Ineichen, K. 	The DNA sequence recognised by the HinfIII restriction endonuclease.	J. Mol. Biol.	1981	146		167-172			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. 		
@D	Piekarowicz, A.//Brzezinski, R. 	Cleavage and methylation of DNA by the restriction endonuclease HinfIII isolated from Haemophilus influenzae Rf.	J. Mol. Biol.	1980	144		415-429			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. 		
@D	Piekarowicz, A.//Brzezinski, R.//Kauc, L. 	Host specificity of DNA in Haemophilus influenzae: DNA restriction enzyme from H. Influenzae Rf232.	Acta Microbiol. Pol.	1976	25		307-312			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. 		
@D	Piekarowicz, A.//Brzezinski, R.//Kauc, L. 	Host Specificity of DNA in Haemophilus influenzae:  The in vivo Action of the Restriction Endonucleases on Phage and Bacterial DNA.	Acta Microbiol. Pol. A	1975	7		51-65			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. 		
@D	Piekarowicz, A.//Bujnicki, J. 	Cloning of the Dam methyltransferase gene from Haemophilus influenzae bacteriophage HP1.	Acta Microbiol. Pol.	1999	48		123-129			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. 		
@D	Piekarowicz, A.//Glover, S.W. 	Host specificity of DNA in Haemophilus influenzae:  the two restriction and modification systems in strain Ra.	Mol. Gen. Genet.	1972	116		11-25			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. 		
@D	Piekarowicz, A.//Goguen, J.D. 	The DNA sequence recognized by the EcoDXXI restriction endonuclease.	Eur. J. Biochem.	1986	154		295-298			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. 		
@D	Piekarowicz, A.//Goguen, J.D.//Skrzypek, E. 	The EcoDXXI restriction and modification system of Escherichia coli ET7.  Purification, subunit structure and properties of the restriction endonuclease.	Eur. J. Biochem.	1985	152		387-393			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. 		
@D	Piekarowicz, A.//Golaszewska, M.//Sunday, A.O.//Siwinska, M.//Stein, D.C. 	The HaeIV restriction modification system of Haemophilus aegyptius is encoded by a single polypeptide.	J. Mol. Biol.	1999	293		1055-1065			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. 		
@D	Piekarowicz, A.//Kalinowska, J. 	Host specificity of DNA in Haemophilus influenzae: Similarity between host-specificity types of Haemophilus influenzae Re and Rf.	J. Gen. Microbiol.	1974	81		405-411			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. 		
@D	Piekarowicz, A.//Kauc, L.//Glover, S.W. 	Host specificity of DNA in Haemophilus influenzae: The restriction and modification systems in strains Rb and Rf.	J. Gen. Microbiol.	1974	81		391-403			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. 		
@D	Piekarowicz, A.//Klyz, A.//Kwiatek, A.//Stein, D.C. 	Analysis of type I restriction modification systems in the Neisseriaceae: Genetic organization and properties of the gene products.	Mol. Microbiol.	2001	41		1199-1210			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. 		
@D	Piekarowicz, A.//Radlinska, M. 	Sensitivity of the restriction endonucleases HaeIII, BsrI, EaeI and CfrI to cytosine N4-methylation.	Acta Microbiol. Pol.	1998	47		405-407			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. 		
@D	Piekarowicz, A.//Radlinska, M.//Wiernicka-Gnas, M. 	DNA methyltransferases of Neisseria gonorrhoeae.	Bull. Acad. Pol. Sci. [Biol]	1996	44		205-210			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. 		
@D	Piekarowicz, A.//Skowronek, K. 	Identification of a new restriction endonuclease R.BcrAI from Bacillus cremoris.	Acta Microbiol. Pol.	1995	44		315-316			Site specific restriction endonuclease R.BcrAI has been purified from Bacillus cremoris.  The enzyme recognizes the sequence 5' CTCTTC 3'. 		
@D	Piekarowicz, A.//Stasiak, A.//Stanczak, J. 	Specific restriction endonucleases from Haemophilus influenzae JC9.	Acta Microbiol. Pol.	1980	29		151-156			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). 		
@D	Piekarowicz, A.//Stein, D.C. 	Purification and characterization of a new DNA methyltransferase from Neisseria gonorrhoeae.	Gene	1995	157		101-102			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. ] 		
@D	Piekarowicz, A.//Weglenska, A. 	Improvement of the strain for the rapid identification of genes encoding restriction and modification enzymes.	Acta Microbiol. Pol.	1994	43		229-231			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. 		
@D	Piekarowicz, A.//Yuan, R.//Stein, D.C. 	Identification of a new restriction endonuclease, R.NgoBI, from Neisseria gonorrhoeae.	Nucleic Acids Res.	1988	16		9868			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. ] 		
@D	Piekarowicz, A.//Yuan, R.//Stein, D.C. 	Purification and characterization of DNA methyltransferases from Neisseria gonorrhoeae.	Nucleic Acids Res.	1988	16		5957-5972			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. ] 		
@D	Piekarowicz, A.//Yuan, R.//Stein, D.C. 	Construction of a temperature-sensitive mutation for the direct identification of plasmids encoding DNA methyltransferases.	Gene	1988	74		233-235			Meeting Abstract 		
@D	Piekarowicz, A.//Yuan, R.//Stein, D.C. 	Neisseria gonorrhoeae M.NgoAI DNA methyltransferase:  physical and catalytic properties of the homogeneous enzyme.	Gene	1988	74		93-97			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. 		
@D	Piekarowicz, A.//Yuan, R.//Stein, D.C. 	Cleavage of DNA by HaeII is inhibited by the presence of 5-methylcytosine at the second cytosine within the recognition sequence.	Nucleic Acids Res.	1989	17		10132			None 		
@D	Piekarowicz, A.//Yuan, R.//Stein, D.C. 	A new method for the rapid identification of genes encoding restriction and modification enzymes.	Nucleic Acids Res.	1991	19		1831-1835			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. 		
@D	Piekarowicz, A.//Yuan, R.//Stein, D.C. 	Isolation of temperature-sensitive McrA and McrB mutations and complementation analysis of the McrBC region of Escherichia coli K-12.	J. Bacteriol.	1991	173		150-155			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. 		
@D	Pieper, U.//Brinkmann, T.//Kruger, T.//Noyer-Weidner, M.//Pingoud, A. 	Characterization of the interaction between the restriction endonuclease McrBC from E. coli and its cofactor GTP.	J. Mol. Biol.	1997	272		190-199			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. 		
@D	Pieper, U.//Groll, D.H.//Wunsch, S.//Gast, F.U.//Speck, C.//Mucke, N.//Pingoud, A. 	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.	Biochemistry	2002	41		5245-5254			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. 		
@D	Pieper, U.//Pingoud, A. 	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.	Biochemistry	2002	41		5236-5244			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. 		
@D	Pieper, U.//Schweitzer, T.//Groll, D.H.//Gast, F.-U.//Pingoud, A. 	The GTP-binding domain of McrB: More than just a variation on common theme?	J. Mol. Biol.	1999	292		547-556			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. 		
@D	Pieper, U.//Schweitzer, T.//Groll, D.H.//Pingoud, A. 	Defining the location and function of domains of McrB by deletion mutagenesis.	Biol. Chem.	1999	380		1225-1230			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. 		
@D	Pierce, J.V.//Bernstein, H.D. 	Genomic Diversity of Enterotoxigenic Strains of Bacteroides fragilis.	PLoS ONE	2016	11		e0158171			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. 		
@D	Pieretti, I.//Bolot, S.//Carrere, S.//Barbe, V.//Cociancich, S.//Rott, P.//Royer, M. 	Draft Genome Sequence of Xanthomonas sacchari Strain LMG 476.	Genome Announcements	2015	3		e00146-15			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. 		
@D	Pieretti, I.//Royer, M.//Barbe, V.//Carrere, S.//Koebnik, R.//Cociancich, S.//Couloux, A.//Darrasse, A.//Gouzy, J.//Jacques, M.A.//Lauber, E.//Manceau, C.//Mangenot, S.//Poussier, S.//Segurens, B.//Szurek, B.//Verdier, V.//Arlat, M.//Rott, P. 	The complete genome sequence of Xanthomonas albilineans provides new insights into the reductive genome evolution of the xylem-limited Xanthomonadaceae.	BMC Genomics	2009	10		616			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. 		
@D	Piet, J.R.//Huis, I.V.R.A.//van Schaik, B.D.//van Kampen, A.H.//Baas, F.//van de Beek, D.//Pannekoek, Y.//van der Ende, A. 	Genome Sequence of Neisseria meningitidis serogroup B strain H44/76.	J. Bacteriol.	2011	193		2371-2372			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. 		
@D	Pieta, L.//Campos, F.S.//Mariot, R.F.//Prichula, J.//de Moura, T.M.//Frazzon, A.P.//Frazzon, J. 	Complete Genome Sequences of Two Listeria monocytogenes Serovars, 1/2a and 4b, Isolated from Dairy Products in Brazil.	Genome Announcements	2015	3		e01494-15			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. 		
@D	Pietila, M.K.//Laurinmaki, P.//Russell, D.A.//Ko, C.C.//Jacobs-Sera, D.//Hendrix, R.W.//Bamford, D.H.//Butcher, S.J. 	Structure of the archaeal head-tailed virus HSTV-1 completes the HK97 fold story.	Proc. Natl. Acad. Sci. U. S. A.	2013	110		10604-10609			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. 		
@D	Pietrokovski, S. 	Modular organization of inteins and C-terminal autocatalytic domains.	Protein Sci.	1998	7		64-71			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. 		
@D	Pietrokovski, S. 	Intein spread and extinction in evolution.	Trends Genet.	2001	17		465-472			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. 		
@D	Pietrokovski, S. 	Conserved sequence features of inteins (protein introns) and their use in identifying new inteins and related proteins.	Protein Sci.	1994	3		2340-2350			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. 		
@D	Pietrokovski, S. 	A new intein in cyanobacteria and its significance for the spread of inteins.	Trends Genet.	1996	12		287-288			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. 		
@D	Pightling, A.W.//Lin, M.//Pagotto, F. 	Draft Genome Sequence of Listeria monocytogenes Strain LI0521 (syn. HPB7171), Isolated in 1983 during an Outbreak in Massachusetts Caused by Contaminated  Cheese.	Genome Announcements	2014	2		e00729-14			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. 		
@D	Pightling, A.W.//Pagotto, F. 	Genome Sequence of Listeria monocytogenes Strain HPB5415, Collected during a 2008 Listeriosis Outbreak in Canada.	Genome Announcements	2015	3		e00637-15			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. 		
@D	Pightling, A.W.//Pagotto, F. 	Draft Genome Sequence of Cronobacter sakazakii Clonal Complex 45 Strain HPB5174,  Isolated from a Powdered Infant Formula Facility in Ireland.	Genome Announcements	2014	2		e00778-14			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. 		
@D	Pightling, A.W.//Rand, H.//Strain, E.//Pagotto, F. 	Genome Sequence of the Listeria monocytogenes Food Isolate HPB913, Collected in Canada in 1993.	Genome Announcements	2016	4		e00911-16			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. 		
@D	Pightling, A.W.//Rand, H.//Strain, E.//Pagotto, F. 	Genome Sequence of Listeria monocytogenes Strain HPB2088 (Serotype 1/2a), an Environmental Isolate Collected in Canada in 1994.	Genome Announcements	2016	4		e00760-16			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. 		
@D	Pignot, M.//Pljevaljcic, G.//Weinhold, E. 	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.	Eur. J. Org. Chem.	2000	2000		549-555			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. 		
@D	Pignot, M.//Siethoff, C.//Linscheid, M.//Weinhold, E. 	Coupling of a nucleoside with DNA by a methyltransferase.	Angew. Chem. Int. Ed. Engl.	1998	37		2888-2891			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). 		
@D	Pikin, S.A. 	On the distinction of the mechanisms of DNA cleavage by restriction enzymes - The I-, II-, and III-type molecular motors.	Crystallogr. Rep.	2008	53		858-867			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. 		
@D	Pikin, S.A. 	On the DNA cleavage by restriction enzymes - molecular motors with polarization properties.	Mol. Cryst. Liq. Cryst.	2009	508		403-413			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. 		
@D	Pikin, S.A. 	Physical aspects of the structure and function of helicases as rotary molecular motors.	Crystallogr. Rep.	2009	54		929-936			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. 		
@D	Piknova, M.//Filova, M.//Javorsky, P.//Pristas, P. 	Different restriction and modification phenotypes in ruminal lactate-utilizing bacteria.	FEMS Microbiol. Lett.	2004	236		91-95			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. 		
@D	Piknova, M.//Filova, M.//Javorsky, P.//Pristas, P. 	A Unique Pair of GATC Specific DNA Methyltransferases in Mitsuokella multiacida.	Mol. Biol. Rep.	2005	32		281-284			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. 		
@D	Piknova, M.//Javorsky, P.//Pristas, P. 	Multiple restriction-modification systems are present in rumen treponemes.	FEMS Microbiol. Lett.	2005	251		99			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. 		
@D	Piknova, M.//Pristas, P.//Javorsky, P. 	GATC-specific restriction-modification systems in ruminal bacteria.	Folia Microbiol. (Praha)	2004	49		191-193			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. 		
@D	Piknova, M.//Pristas, P.//Javorsky, P. 	Some evolutionary aspects of biology of the type II restriction-modification systems.	Biol. Listy	2004	69		15-28			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. 		
@D	Piknova, M.//Pristas, P.//Javorsky, P.//Kasperowic, A.//Michalowski, T. 	GATC-specific restriction and modification systems in treponemes.	Lett. Appl. Microbiol.	2004	38		311-314			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. 		
@D	Pillay, A.//Katz, S.S.//Abrams, A.J.//Ballard, R.C.//Simpson, S.V.//Taleo, F.//Lahra, M.M.//Batra, D.//Rowe, L.//Trees, D.L.//Asiedu, K.//Chen, C.Y. 	Complete Genome Sequences of 11 Haemophilus ducreyi Isolates from Children with Cutaneous Lesions in Vanuatu and Ghana.	Genome Announcements	2016	4		e00459-16			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. 		
@D	Pinarbasi, E.//Elliott, J.//Hornby, D.P. 	Activation of a yeast pseudo DNA methyltransferase by deletion of a single amino acid.	J. Mol. Biol.	1996	257		804-813			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. 		
@D	Pinarbasi, E.//Kan, M.S.//Duran, C.//Ford, G.C.//Hornby, D.P. 	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.	Biol. Chem.	1998	379		591-594			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. 		
@D	Pinarbasi, E.//Pinarbasi, H.//Hornby, D.P. 	Subcloning and expression of a cDNA encoding a Schizosaccharomyces pombe putative C-5 DNA methyltransferase.	Turkish J. Biol.	1996	20		325-331			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. 		
@D	Pinarbasi, H.//Pinarbasi, E.//Hornby, D. 	Recombinant alpha and beta subunits of M.AquI constitute an active DNA methyltransferase.	J. Biochem. Mol. Biol.	2002	35		348-351			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. 		
@D	Pinarbasi, H.//Pinarbasi, E.//Hornby, D.P. 	The small subunit of M.AquI is responsible for sequence-specific DNA recognition and binding in the absence of the catalytic domain.	J. Bacteriol.	2003	185		1284-1288			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. 		
@D	Pinarbasi, H.//Pinarbasi, E.//Hornby, D.P. 	Substitution of the conserved cysteine with glycine (Cys82Gly) of Agmenellum quadruplicatum methylase AquI (M.AquI) is not cytotoxic to  E. coli.	Turkish J. Biol.	2001	25		177-184			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. 		
@D	Pinard, M. 	Multitiered regulation of 5-cytosine DNA methyltransferase expression.	Diss. Abstr.	2000	60		5938			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. 		
@D	Pinard, M.//Szyf, M. 	Regulation of cytosine DNA methyltransferase expression by tumor suppressors.	Mol. Biol. Cell	1996	7		174a			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. 		
@D	Pingoud, A. 	Spermidine increases the accuracy of type II restriction endonucleases.  Suppression of cleavage at degenerate, non-symmetrical sites.	Eur. J. Biochem.	1985	147		105-109			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. 		
@D	Pingoud, A.//Alves, J.//Fliess, A.//Geiger, R.//Rueter, T.//Wolfes, H. 	Site-directed mutagenesis of the EcoRI restriction endonuclease.	Biol. Chem. Hoppe Seyler	1987	368		1093			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+. 		
@D	Pingoud, A.//Alves, J.//Geiger, R. 	Restriction Enzymes.	Methods Mol. Biol.	1993	16		107-200			A review focussing on the practical aspects of the use of these enzymes. 		
@D	Pingoud, A.//Fuxreiter, M.//Pingoud, V.//Wende, W. 	Type II restriction endonucleases: structure and mechanism.	Cell. Mol. Life Sci.	2005	62		685-707			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. 		
@D	Pingoud, A.//Geiger, R.//Alves, J.//Oelgeschlager, T.//Ruter, T. 	Functional sites of the EcoRI restriction endonuclease probed by site directed mutagenesis.	Biol. Chem. Hoppe Seyler	1989	370		943-944			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. 		
@D	Pingoud, A.//Jeltsch, A. 	Structure and function of type II restriction endonucleases.	Nucleic Acids Res.	2001	29		3705-3727			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. 		
@D	Pingoud, A.//Jeltsch, A. 	Recognition and cleavage of DNA by type-II restriction endonucleases.	Eur. J. Biochem.	1997	246		1-22			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. 		
@D	Pingoud, A.//Jeltsch, A.//Lanio, T.//Schulze, C.//Selent, U.//Stahl, F.//Wende, W.//Wenz, C. 	Mechanism of DNA recognition and cleavage by restriction enzymes.	Biol. Chem. Hoppe Seyler	1995	376		S138			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. 		
@D	Pingoud, A.//Jeltsch, A.//Maxwell, A.//Sherratt, D. 	Enzymes that keep DNA under control.	EMBO Rep.	2001	2		271-276			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. 		
@D	Pingoud, A.//Pingoud, V.//Wende, W. 	Homing endonucleases - multifaceted tools for genome engineering.	BIOspektrum	2003	9		592-595					
@D	Pingoud, A.//Silva, G.H. 	Precision genome surgery.	Nat. Biotechnol.	2007	25		743-744			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. 		
@D	Pingoud, A.//Thielking, V.//Selent, U.//Kohler, E.//Liedtke, M.//Wolfes, H.//Pieper, U.//Geiger, R.//Winkler, F.K. 	Identification of functional sites in the EcoRV restriction endonuclease by site-directed mutagenesis.	J. Biomol. Struct. Dyn.	1991	8		A165			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. 		
@D	Pingoud, A.//Urbanke, C.//Alves, J.//Ehbrecht, H.-J.//Zabeau, M.//Gualerzi, C. 	Effect of polyamines and basic proteins on cleavage DNA by restriction endonucleases.	Biochemistry	1984	23		5697-5703			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. 		
@D	Pingoud, A.//Wende, W. 	A sliding restriction enzyme pauses.	Structure	2007	15		391-393			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. 		
@D	Pingoud, A.//Wende, W. 	Generation of Novel Nucleases with Extended Specificity by Rational and Combinatorial Strategies.	Chembiochem	2011	12		1495-1500			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. 		
@D	Pingoud, A.//Wilson, G.G.//Wende, W. 	Type II restriction endonucleases-a historical perspective and more.	Nucleic Acids Res.	2014	42		7489-7527			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. 		
@D	Pingoud, V.//Conzelmann, C.//Kinzebach, S.//Sudina, A.//Metelev, V.//Kubareva, E.//Bujnicki, J.M.//Lurz, R.//Luder, G.//Xu, S.Y.//Pingoud, A. 	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.	J. Mol. Biol.	2003	329		913-929			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. 		
@D	Pingoud, V.//Geyer, H.//Geyer, R.//Kubareva, E.//Bujnicki, J.M.//Pingoud, A. 	Identification of base-specific contacts in protein-DNA complexes by photocrosslinking and mass spectrometry: A case study using the  restriction endonuclease SsoII.	Mol. BioSyst.	2005	1		135-141			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. 		
@D	Pingoud, V.//Grindl, W.//Wende, W.//Thole, H.//Pingoud, A. 	Structural and functional analysis of the homing endonuclease PI-SceI by limited proteolytic cleavage and molecular cloning of partial digestion products.	Biochemistry	1998	37		8233-8243			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. 		
@D	Pingoud, V.//Kubareva, E.//Stengel, G.//Friedhoff, P.//Bujnicki, J.M.//Urbanke, C.//Sudina, A.//Pingoud, A. 	Evolutionary relationship between different subgroups of restriction endonucleases.	J. Biol. Chem.	2002	277		14306-14314			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. 		
@D	Pingoud, V.//Sudina, A.//Geyer, H.//Bujnicki, J.M.//Lurz, R.//Luder, G.//Morgan, R.//Kubareva, E.//Pingoud, A. 	Specificity changes in the evolution of Type II restriction endonucleases - A biochemical and bioinformatic analysis of restriction  enzymes that recognize unrelated sequences.	J. Biol. Chem.	2005	280		4289-4298			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. 		
@D	Pingoud, V.//Thole, H.//Christ, F.//Grindl, W.//Wende, W.//Pingoud, A. 	Photocross-linking of the homing endonuclease PI-SceI to its recognition sequence.	J. Biol. Chem.	1999	274		10235-10243			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. 		
@D	Pingoud, V.//Wende, W.//Friedhoff, P.//Reuter, M.//Alves, J.//Jeltsch, A.//Mones, L.//Fuxreiter, M.//Pingoud, A. 	On the Divalent Metal Ion Dependence of DNA Cleavage by Restriction Endonucleases of the EcoRI Family.	J. Mol. Biol.	2009	393		140-160			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. 		
@D	Pinto, A.J.//Sharp, J.O.//Yoder, M.J.//Almstrand, R. 	Draft Genome Sequences of Two Novel Acidimicrobiaceae Members from an Acid Mine Drainage Biofilm Metagenome.	Genome Announcements	2016	4		e01563-15			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. 		
@D	Pinto, C.//Sousa, S.//Froufe, H.//Egas, C.//Clement, C.//Fontaine, F.//Gomes, A.C. 	Draft genome sequence of Bacillus amyloliquefaciens subsp. plantarum strain Fito_F321, an endophyte microorganism from Vitis vinifera with biocontrol potential.	Standards in Genomic Sciences	2018	13		30			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. 		
@D	Pinto, F.//Tett, A.//Armanini, F.//Asnicar, F.//Boscaini, A.//Pasolli, E.//Zolfo, M.//Donati, C.//Salmaso, N.//Segata, N. 	Draft Genome Sequence of the Planktic Cyanobacterium Tychonema bourrellyi, Isolated from Alpine Lentic Freshwater.	Genome Announcements	2017	5		e01294-17			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. 		
@D	Pinto, F.//Tett, A.//Armanini, F.//Asnicar, F.//Boscaini, A.//Pasolli, E.//Zolfo, M.//Donati, C.//Salmaso, N.//Segata, N. 	Draft Genome Sequences of Novel Pseudomonas, Flavobacterium, and Sediminibacterium Species Strains from a Freshwater Ecosystem.	Genome Announcements	2018	6		e00009-18			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. 		
@D	Pinto, S.B.//Stainton, K.//Harris, S.//Kambris, Z.//Sutton, E.R.//Bonsall, M.B.//Parkhill, J.//Sinkins, S.P. 	Transcriptional Regulation of Culex pipiens Mosquitoes by Wolbachia Influences Cytoplasmic Incompatibility.	PLoS Pathog.	2013	9		E1003647			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. 		
@D	Pintor-Toro, J.A. 	Adenine methylation in zein genes.	Biochem. Biophys. Res. Commun.	1987	147		1082-1087			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. 		
@D	Pique, N.//Aquilini, E.//Alioto, T.//Minana-Galbis, D.//Tomas, J.M. 	Genome Sequence of Plesiomonas shigelloides Strain 302-73 (Serotype O1).	Genome Announcements	2013	1		e00404-13			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. 		
@D	Pires, D.P.//Sillankorva, S.//Kropinski, A.M.//Lu, T.K.//Azeredo, J. 	Complete Genome Sequence of Pseudomonas aeruginosa Phage vB_PaeM_CEB_DP1.	Genome Announcements	2015	3		e00918-15			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. 		
@D	Pirone-Davies, C.//Hoffmann, M.//Roberts, R.J.//Muruvanda, T.//Timme, R.E.//Strain, E.//Luo, Y.//Payne, J.//Luong, K.//Song, Y.//Tsai, Y.C.//Boitano, M.//Clark, T.A.//Korlach, J.//Evans, P.S.//Allard, M.W. 	Genome-Wide Methylation Patterns in Salmonella enterica Subsp. enterica Serovars.	PLoS ONE	2015	10		e0123639			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. 		
@D	Pirrotta, V. 	Two restriction endonucleases from Bacillus globigii.	Nucleic Acids Res.	1976	3		1747-1760			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. 		
@D	Pirrotta, V.//Bickle, T.A. 	General purification schemes for restriction endonucleases.	Methods Enzymol.	1980	65		89-95			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. 		
@D	Pitluck, S. et al. 	Complete genome sequence of Thermosediminibacter oceani type strain (JW/IW-1228P).	Standards in Genomic Sciences	2010	3		108-116			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. 		
@D	Pitluck, S. et al. 	Non-contiguous finished genome sequence of Aminomonas paucivorans type strain (GLU-3).	Standards in Genomic Sciences	2010	3		285-293			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. 		
@D	Pitluck, S. et al. 	Complete genome sequence of Calditerrivibrio nitroreducens type strain (Yu37-1).	Standards in Genomic Sciences	2011	4		54-62			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. 		
@D	Pitsikas, P.//Cupples, C. 	Effects of increasing DCM expression on Vsr repair of site specific and related sequences.	FASEB J.	1997	11		A1369			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. 		
@D	Pitsikas, P.//Cupples, C.G. 	Fate of Dcm cytosine methylase after treatment of Escherichia coli with 5-Azacytidine.	Abstr. Gen. Meet. Am. Soc. Microbiol.	1999	99		334			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. 		
@D	Pitt, M.E.//Elliott, A.G.//Cao, M.D.//Ganesamoorthy, D.//Karaiskos, I.//Giamarellou, H.//Abboud, C.S.//Blaskovich, M.A.//Cooper, M.A.//Coin, L.J. 	Multifactorial chromosomal variants regulate polymyxin resistance in extensively drug-resistant Klebsiella pneumoniae.	Microbial Genomics	2018	0		0			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. 		
@D	Pittard, J. 	Effect of phage-controlled restriction on genetic links in bacterial crosses.	J. Bacteriol.	1964	87		1256-1257			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. 		
@D	Pittet, V.//Abegunde, T.//Marfleet, T.//Haakensen, M.//Morrow, K.//Jayaprakash, T.//Schroeder, K.//Trost, B.//Byrns, S.//Bergsveinson, J.//Kusalik, A.//Ziola, B. 	Complete Genome Sequence of the Beer Spoilage Organism Pediococcus claussenii ATCC BAA-344T.	J. Bacteriol.	2012	194		1271-1272			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. 		
@D	Pittet, V.//Ewen, E.//Bushell, B.R.//Ziola, B. 	Genome Sequence of Lactobacillus rhamnosus ATCC 8530.	J. Bacteriol.	2012	194		726			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. 		
@D	Piya, D.//Vara, L.//Russell, W.K.//Young, R.//Gill, J.J. 	The multicomponent antirestriction system of phage P1 is linked to capsid morphogenesis.	Mol. Microbiol.	2017	105		399-412			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. 		
@D	Planet, P.J. et al. 	Parallel Epidemics of Community-Associated Methicillin-Resistant Staphylococcus aureus USA300 Infection in North and South America.	J. Infect. Dis.	2015	212		1874-1882			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. 		
@D	Planet, P.J.//Rampersaud, R.//Hymes, S.R.//Whittier, S.//Della-Latta, P.A.//Narechania, A.//Daugherty, S.C.//Santana-Cruz, I.//Desalle, R.//Ravel, J.//Ratner, A.J. 	Genome Sequence of the Human Abscess Isolate Streptococcus intermedius BA1.	Genome Announcements	2013	1		e00117-12			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. 		
@D	Platonov, M.E.//Blouin, Y.//Evseeva, V.V.//Afanas'ev, M.V.//Pourcel, C.//Balakhonov, S.V.//Vergnaud, G.//Anisimov, A.P. 	Draft Genome Sequences of Five Yersinia pseudotuberculosis ST19 Isolates and One  Isolate Variant.	Genome Announcements	2013	1		e00122-13			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. 		
@D	Pleska, M.//Qian, L.//Okura, R.//Bergmiller, T.//Wakamoto, Y.//Kussell, E.//Guet, C.C. 	Bacterial Autoimmunity Due to a Restriction-Modification System.	Curr. Biol.	2016	26		404-409			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. 		
@D	Plessis, A.//Perrin, A.//Haber, J.E.//Dujon, B. 	Site-specific recombination determined by I-SceI, a mitochondrial group I intron-encoded endonuclease expressed in the yeast nucleus.	Genetics	1992	130		451-460			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. 		
@D	Pljevaljcic, G.//Pignot, M.//Weinhold, E. 	Design of a new fluorescent cofactor for DNA methyltransferases and sequence-specific labeling of DNA.	J. Am. Chem. Soc.	2003	125		3486-3492			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. 		
@D	Pljevaljcic, G.//Schmidt, F.//Peschlow, A.//Weinhold, E. 	Sequence-specific DNA labeling using methyltransferases.	Methods Mol. Biol.	2004	283		145-161			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. 		
@D	Pljevaljcic, G.//Schmidt, F.//Scheidig, A.J.//Lurz, R.//Weinhold, E. 	Quantitative labeling of long plasmid DNA with nanometer precision.	Chembiochem	2007	8		1516-1519					
@D	Pljevaljcic, G.//Schmidt, F.//Weinhold, E. 	Sequence-specific methyltransferase-induced labeling of DNA (SMILing DNA).	Chembiochem	2004	5		265-269			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. 		
@D	Plugge, C.M.//Henstra, A.M.//Worm, P.//Swarts, D.C.//Paulitsch-Fuchs, A.H.//Scholten, J.C.//Lykidis, A.//Lapidus, A.L.//Goltsman, E.//Kim, E.//McDonald, E.//Rohlin, L.//Crable, B.R.//Gunsalus, R.P.//Stams, A.J.//McInerney, M.J. 	Complete genome sequence of Syntrophobacter fumaroxidans strain (MPOB(T)).	Standards in Genomic Sciences	2012	7		91-106			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. 		
@D	Plumbridge, J. 	The role of dam methylation in controlling gene expression.	Biochimie	1987	69		439-443			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. 		
@D	Plumed-Ferrer, C.//Gazzola, S.//Fontana, C.//Bassi, D.//Cocconcelli, P.S.//von Wright, A. 	Genome Sequence of Lactococcus lactis subsp. cremoris Mast36, a Strain Isolated from Bovine Mastitis.	Genome Announcements	2015	3		e00449-15			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. 		
@D	Plunkett, G. III//Rose, D.J.//Durfee, T.J.//Blattner, F.R. 	Sequence of Shiga toxin 2 phage 933W from Escherichia coli O157:H7: Shiga toxin as a phage late-gene product.	J. Bacteriol.	1999	181		1767-1778			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. 		
@D	Poch, M.T.//Somkuti, G.A. 	Detection of restriction endonuclease activity in Streptococcus thermophilus ST132.	Abstr. Gen. Meet. Am. Soc. Microbiol.	1993	93		330			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. 		
@D	Poch, M.T.//Somkuti, G.A. 	Isolation of SagI, a new HaeIII isoschizomer from Streptococcus agalactiae.	Appl. Microbiol. Biotechnol.	1995	43		282-284			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. 		
@D	Poch, M.T.//Somkuti, G.A. 	Rapid isolation of restriction endonucleases from Streptococci.	Abstr. Gen. Meet. Am. Soc. Microbiol.	1994	94		385			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. 		
@D	Poch, M.T.//Somkuti, G.A. 	Rapid screening of lactic acid bacteria for restriction endonuclease activity.	Biotechnol. Tech.	1993	7		781-784			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. 		
@D	Poch, M.T.//Somkuti, G.A.//Solaiman, D.K.Y. 	Sth132I, a novel class-IIS restriction endonuclease of Streptococcus thermophilus ST132.	Gene	1997	195		201-206			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'. 		
@D	Poddar, A.//Lepcha, R.T.//Whitman, W.B.//Das, S.K. 	Draft Genome Sequence of Tepidiphilus thermophilus Strain JHK30T (JCM 19170T) Isolated from a Terrestrial Hot Spring in India.	Genome Announcements	2016	4		e00832-16			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. 		
@D	Podgorska, B.//Kujawska, G.//Skurzewski, M.//Batsko, O.//Kaczorowski, T. 	A rapid and simple method for detection of type II restriction endonucleases in cells of bacteria with high activity of nonspecific nucleases.	Acta Biochim. Pol.	2012	59		669-672			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. 		
@D	Podhajska, A.J.//Kim, S.C.//Szybalski, W. 	Conferring new specificities on restriction enzymes: cleavage at any predetermined site by combining adapter oligodeoxynucleotide and Class-IIS enzyme.	Methods Enzymol.	1992	216		303-309					
@D	Podhajska, A.J.//Szybalski, W. 	Conversion of the FokI endonuclease to a universal restriction enzyme:  cleavage of phage M13mp7 DNA at predetermined sites.	Gene	1985	40		175-182			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. 		
@D	Poehlein, A.//Alghaithi, H.S.//Chandran, L.//Chibani, C.M.//Davydova, E.//Dhamotharan, K.//Ge, W.//Gutierrez-Gutierrez, D.A.//Jagirdar, A.//Khonsari, B.//Nair, K.P.//Daniel, R. 	First Insights into the Genome of the Amino Acid-Metabolizing Bacterium Clostridium litorale DSM 5388.	Genome Announcements	2014	2		e00754-14			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). 		
@D	Poehlein, A.//Anbalagan, A.//Nagel, A.//Daniel, R. 	First Insight into the Genome Sequence of Clostridium thermobutyricum DSM 4928, a Butyrate-Producing Moderate Thermophile.	Genome Announcements	2017	5		e00367-17			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. 		
@D	Poehlein, A.//Andreesen, J.R.//Daniel, R. 	Complete Genome Sequence of Amino Acid-Utilizing Eubacterium acidaminophilum al-2 (DSM 3953).	Genome Announcements	2014	2		e00573-14			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. 		
@D	Poehlein, A.//Bandera, A.//Horne, D.//Maier, J.//Pawlowicz, D.//Siebert, V.//Daniel, R. 	First Insights into the Genome of the N-Methylhydantoin-Degrading Clostridium sp. Strain FS41 (DSM 6877).	Genome Announcements	2015	3		e00394-15			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. 		
@D	Poehlein, A.//Bengelsdorf, F.R.//Esser, C.//Schiel-Bengelsdorf, B.//Daniel, R.//Durre, P. 	Complete Genome Sequence of the Type Strain of the Acetogenic Bacterium Moorella  thermoacetica DSM 521T.	Genome Announcements	2015	3		e01159-15			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). 		
@D	Poehlein, A.//Bengelsdorf, F.R.//Schiel-Bengelsdorf, B.//Daniel, R.//Durre, P. 	Genome Sequence of the Acetogenic Bacterium Acetobacterium wieringae DSM 1911T.	Genome Announcements	2016	4		e01430-16			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. 		
@D	Poehlein, A.//Bengelsdorf, F.R.//Schiel-Bengelsdorf, B.//Daniel, R.//Durre, P. 	Draft Genome Sequence of Purine-Degrading Gottschalkia purinilyticum (Formerly Clostridium purinilyticum) WA1 (DSM 1384).	Genome Announcements	2015	3		e01088-15			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). 		
@D	Poehlein, A.//Bengelsdorf, F.R.//Schiel-Bengelsdorf, B.//Gottschalk, G.//Daniel, R.//Durre, P. 	Complete Genome Sequence of Rnf- and Cytochrome-Containing Autotrophic Acetogen Clostridium aceticum DSM 1496.	Genome Announcements	2015	3		e00786-15			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). 		
@D	Poehlein, A.//Berg, A.//Welsing, G.//Daniel, R. 	First Insights into the Genome Sequence of the Alkaliphilic Thermotolerant Bacterium Clostridium thermoalcaliphilum JW/YL23-2T.	Genome Announcements	2017	5		e00368-17			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. 		
@D	Poehlein, A.//Boer, T.//Steensen, K.//Daniel, R. 	Draft Genome Sequence of the Hydrogenogenic Carboxydotroph Moorella stamsii DSM 26271.	Genome Announcements	2018	6		e00345-18			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. 		
@D	Poehlein, A.//Bolz, S.//Fischer, B.//Daniel, R. 	First Insight into the Genome Sequence of Clostridium vincentii DSM 10228, Isolated from Sediment of the McMurdo Ice Shelf, Antarctica.	Genome Announcements	2018	6		e00334-18			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. 		
@D	Poehlein, A.//Bremekamp, R.//Lutz, V.T.//Schulz, L.M.//Daniel, R. 	Draft Genome Sequence of the Butanoic Acid-Producing Bacterium Clostridium luticellarii DSM 29923, Used for Strong Aromatic Chinese Liquor Production.	Genome Announcements	2018	6		e00377-18			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. 		
@D	Poehlein, A.//Daniel, R.//Simeonova, D.D. 	Draft Genome Sequence of Desulfotignum phosphitoxidans DSM 13687 Strain FiPS-3.	Genome Announcements	2013	1		e00227-13			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. 		
@D	Poehlein, A.//Daniel, R.//Simeonova, D.D. 	Genome sequence of Pedobacter glucosidilyticus DD6b, isolated from zooplankton Daphnia magna.	Standards in Genomic Sciences	2015	10		100			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. 		
@D	Poehlein, A.//Daniel, R.//Thurmer, A.//Bollinger, A.//Thies, S.//Katzke, N.//Jaeger, K.E. 	First Insights into the Genome Sequence of Pseudomonas oleovorans DSM 1045.<jour_book>Genome Announc.		2017	5		e00774-17			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. 		
@D	Poehlein, A.//Deutzmann, J.S.//Daniel, R.//Simeonova, D.D. 	Draft Genome Sequence of the Methanotrophic Gammaproteobacterium Methyloglobulus  morosus DSM 22980 Strain KoM1.	Genome Announcements	2013	1		e01078-13			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. 		
@D	Poehlein, A.//Freese, H.//Daniel, R.//Simeonova, D.D. 	Genome sequence of Shinella sp. strain DD12, isolated from homogenized guts of starved Daphnia magna.	Standards in Genomic Sciences	2016	11		14			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. 		
@D	Poehlein, A.//Freese, H.M.//Daniel, R.//Simeonova, D.D. 	Draft Genome Sequence of Serratia sp. Strain DD3, Isolated from the Guts of Daphnia magna.	Genome Announcements	2014	2		e00903-14			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. 		
@D	Poehlein, A.//Friedrich, I.//Kruger, L.//Daniel, R. 	First Insights into the Genome of the Moderately Thermophilic Bacterium Clostridium tepidiprofundi SG 508T.	Genome Announcements	2016	4		e00379-16			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). 		
@D	Poehlein, A.//Funkner, K.//Schuler, M.A.//Daniel, R. 	First Insights into the Genome Sequence of the Cellulolytic Bacterium Clostridium hungatei DSM 14427.	Genome Announcements	2017	5		e00363-17			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. 		
@D	Poehlein, A.//Galperin, M.Y.//Andreesen, J.R.//Daniel, R. 	Genome Sequence of Uric Acid-Fermenting Eubacterium angustum DSM 1989T (MK-1).	Genome Announcements	2017	5		e01439-16			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. 		
@D	Poehlein, A.//Gippert, A.L.//Bierenbroodspot, M.J.//Daniel, R. 	First Insights into the Genome Sequence of Clostridium oryzae DSM 28571, Isolated from the Soil of a Japanese Rice Field.	Genome Announcements	2017	5		e00539-17			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. 		
@D	Poehlein, A.//Gottschalk, G.//Daniel, R. 	First Insights into the Genome of the Gram-Negative, Endospore-Forming Organism Sporomusa ovata Strain H1 DSM 2662.	Genome Announcements	2013	1		e00734-13			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. 		
@D	Poehlein, A.//Grosse-Honebrink, A.//Zhang, Y.//Minton, N.P.//Daniel, R. 	Complete Genome Sequence of the Nitrogen-Fixing and Solvent-Producing Clostridium pasteurianum DSM 525.	Genome Announcements	2015	3		e01591-14			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. 		
@D	Poehlein, A.//Hartwich, K.//Krabben, P.//Ehrenreich, A.//Liebl, W.//Durre, P.//Gottschalk, G.//Daniel, R. 	Complete Genome Sequence of the Solvent Producer Clostridium saccharobutylicum NCP262 (DSM 13864).	Genome Announcements	2013	1		e00997-13			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. 		
@D	Poehlein, A.//Hettwer, E.//Mohnike, L.//Daniel, R. 	First Insights into the Genome Sequence of Clostridium thermopalmarium DSM 5974,  a Butyrate-Producing Bacterium Isolated from Palm Wine.	Genome Announcements	2018	6		e00338-18			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. 		
@D	Poehlein, A.//Heym, D.//Quitzke, V.//Fersch, J.//Daniel, R.//Rother, M. 	Complete Genome Sequence of the Methanococcus maripaludis Type Strain JJ (DSM 2067), a Model for Selenoprotein Synthesis in Archaea.	Genome Announcements	2018	6		e00237-18			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. 		
@D	Poehlein, A.//Hoche, N.//Mehr, A.//Daniel, R. 	First Insights into the Genome of the Cr(VI)-Reducing Bacterium Clostridium chromiireducens DSM 23318.	Genome Announcements	2017	5		e00420-17			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. 		
@D	Poehlein, A.//Hollensteiner, J.//Granzow, S.//Wemheuer, B.//Vidal, S.//Wemheuer, F. 	First Insights into the Draft Genome Sequence of the Endophyte Paenibacillus amylolyticus Strain GM1FR, Isolated from Festuca rubra L.	Genome Announcements	2018	6		e01516-17			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. 		
@D	Poehlein, A.//Keyl, A.//Milsch, J.C.//Daniel, R. 	Draft Genome Sequence of the Thermophilic Acetogen Moorella humiferrea DSM 23265.	Genome Announcements	2018	6		e00357-18			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. 		
@D	Poehlein, A.//Krabben, P.//Durre, P.//Daniel, R. 	Complete Genome Sequence of the Solvent Producer Clostridium saccharoperbutylacetonicum Strain DSM 14923.	Genome Announcements	2014	2		e01056-14			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. 		
@D	Poehlein, A.//Kusian, B.//Friedrich, B.//Daniel, R.//Bowien, B. 	Complete genome sequence of the type strain Cupriavidus necator N-1.	J. Bacteriol.	2011	193		5017			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. 		
@D	Poehlein, A.//Montoya, S.J.D.//Bengelsdorf, F.R.//Schiel-Bengelsdorf, B.//Daniel, R.//Durre, P. 	Draft Genome Sequence of Purine-Degrading Clostridium cylindrosporum HC-1 (DSM 605).	Genome Announcements	2015	3		e00917-15			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). 		
@D	Poehlein, A.//Mucek, K.//Enders, M.//Pankok, F.//Daniel, R. 	First Insights into the Genome Sequence of the Halophilic Archaeon Halalkalicoccus paucihalophilus (DSM 24557).	Genome Announcements	2016	4		e00382-16			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. 		
@D	Poehlein, A.//Najdenski, H.//Simeonova, D.D. 	Draft Genome Sequence of Klebsiella pneumoniae subsp. pneumoniae ATCC 9621.	Genome Announcements	2017	5		e01718-16			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. 		
@D	Poehlein, A.//Najdenski, H.//Simeonova, D.D. 	Draft Genome Sequence of Flavobacterium succinicans Strain DD5b.	Genome Announcements	2017	5		e01492-16			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. 		
@D	Poehlein, A.//Neubauer, H.//Niemeyer, P.//Daniel, R. 	First Insight into the Genome Sequence of Clostridium liquoris DSM 100320, a Butyrate- and Ethanol-Producing Bacterium.	Genome Announcements	2018	6		e00376-18			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. 		
@D	Poehlein, A.//Riegel, K.//Konig, S.M.//Leimbach, A.//Daniel, R.//Durre, P. 	Genome sequence of Clostridium sporogenes DSM 795(T), an amino acid-degrading, nontoxic surrogate of neurotoxin-producing Clostridium botulinum.	Standards in Genomic Sciences	2015	10		40			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. 		
@D	Poehlein, A.//Schilling, T.//Bhaskar, S.N.U.//Daniel, R. 	First Insights into the Draft Genome of Clostridium colicanis DSM 13634, Isolated from Canine Feces.	Genome Announcements	2016	4		e00385-16			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. 		
@D	Poehlein, A.//Schlien, K.//Chowdhury, N.P.//Gottschalk, G.//Buckel, W.//Daniel, R. 	Complete Genome Sequence of the Amino Acid-Fermenting Clostridium propionicum X2  (DSM 1682).	Genome Announcements	2016	4		e00294-16			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. 		
@D	Poehlein, A.//Seedorf, H. 	Draft Genome Sequences of Methanobrevibacter curvatus DSM11111, Methanobrevibacter cuticularis DSM11139, Methanobrevibacter filiformis DSM11501,   and Methanobrevibacter oralis DSM7256.	Genome Announcements	2016	4		e00617-16			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. 		
@D	Poehlein, A.//Wubbeler, J.H.//Daniel, R.//Steinbuchel, A. 	Draft Genome Sequences of Sphingomonas mucosissima DSM 17494 and Sphingomonas dokdonensis DSM 21029.	Genome Announcements	2017	5		e00889-17			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. 		
@D	Poehlein, A.//Zverlov, V.V.//Daniel, R.//Schwarz, W.H.//Liebl, W. 	Complete Genome Sequence of Clostridium stercorarium subsp. stercorarium Strain DSM 8532, a Thermophilic Degrader of Plant Cell Wall Fibers.	Genome Announcements	2013	1		e0007313			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. 		
@D	Pogge von Strandmann, R.//Stadtler, R.//Walter, T.//Frey, B.//Kaluza, K.//Hengstenberg, W.//Schmitz, G. 	BpuAI, a novel BbsI and BbvII isoschizomer from Bacillus pumilus recognizing 5'-GAAGAC-3'.	Nucleic Acids Res.	1992	20		4664			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. 		
@D	Pogolotti, A.L.//Ono, A.//Subramaniam, R.//Santi, D.V. 	On the mechanism of DNA-adenine methylase.	J. Biol. Chem.	1988	263		7461-7464			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. 		
@D	Pohl, F.M.//Thomae, R.//Karst, A. 	Temperature dependence of the activity of DNA-modifying enzymes: endonucleases and DNA ligase.	Eur. J. Biochem.	1982	123		141-152			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. 		
@D	Pohlner, M.//Marshall, I.//Schreiber, L.//Cypionka, H.//Engelen, B. 	Draft Genome Sequence of Pseudoruegeria sp. SK021, a Representative of the Marine Roseobacter Group, Isolated from North Sea Sediment.	Genome Announcements	2017	5		e00541-17			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. 		
@D	Poirier, S.//Coeuret, G.//Champomier-Verges, M.C.//Chaillou, S. 	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.	Genome Announcements	2018	6		e00479-18			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. 		
@D	Poland, B.W.//Xu, M.Q.//Quiocho, F.A. 	Structural Insights into the Protein Splicing Mechanism of PI-SceI.	J. Biol. Chem.	2000	275		16408-16413			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. 		
@D	Pold, G.//Conlon, E.M.//Huntemann, M.//Pillay, M.//Mikhailova, N.//Stamatis, D.//Reddy, T.B.K.//Daum, C.//Shapiro, N.//Kyrpides, N.//Woyke, T.//DeAngelis, K.M. 	Genome Sequence of Verrucomicrobium sp. Strain GAS474, a Novel Bacterium Isolated from Soil.	Genome Announcements	2018	6		e01451-17			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. 		
@D	Pold, G.//Huntemann, M.//Pillay, M.//Mikhailova, N.//Stamatis, D.//Reddy, T.B.K.//Daum, C.//Shapiro, N.//Kyrpides, N.//Woyke, T.//DeAngelis, K.M. 	Draft Genome Sequences of Three Strains of a Novel Rhizobiales Species Isolated from Forest Soil.	Genome Announcements	2018	6		e01452-17			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. 		
@D	Poli, A.//Nicolaus, B.//Chan, K.G.//Kahar, U.M.//Chan, C.S.//Goh, K.M. 	Genome Sequence of Anoxybacillus thermarum AF/04T, Isolated from the Euganean Hot Springs in Abano Terme, Italy.	Genome Announcements	2015	3		e00490-15			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. 		
@D	Polishchuk, L.V.//Lukyanchuk, V.V.//Matselyuch, B.P. 	Site-specific endonucleases of Streptomycetes.	Actinomycetes	2000	10		13-15			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. 		
@D	Polisky, B.//Greene, P.//Garfin, D.E.//McCarthy, B.J.//Goodman, H.M.//Boyer, H.W. 	Specificity of substrate recognition by the EcoRI restriction endonuclease.	Proc. Natl. Acad. Sci. U. S. A.	1975	72		3310-3314			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. 		
@D	Polisson, C. 	MscI, a type II restriction endonuclease from Micrococcus species which recognizes 5' TGGCCA 3' .	Nucleic Acids Res.	1989	17		5858			None 		
@D	Polisson, C.//Morgan, R.D. 	AseI, a restriction endonuclease from Aquaspirillum serpens which recognizes 5'ATTAAT3'.	Nucleic Acids Res.	1988	16		10365			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). 		
@D	Polisson, C.//Morgan, R.D. 	BsrI, a unique restriction endonuclease from Bacillus stearothermophilus which recognizes 5'ACTGG3'.	Nucleic Acids Res.	1988	16		5205			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. 		
@D	Polisson, C.//Morgan, R.D. 	AciI, a unique restriction endonuclease from Arthrobacter citreus which recognizes 5' CCGC3'.	Nucleic Acids Res.	1990	18		5911			None 		
@D	Polisson, C.//Morgan, R.D. 	DrdI, a unique restriction endonuclease from Deinococcus radiodurans which recognizes 5'GACN6GTC3'.	Nucleic Acids Res.	1989	17		3316			None 		
@D	Polisson, C.//Morgan, R.D. 	EarI, a restriction endonuclease from Enterobacter aerogenes which recognizes 5'CTCTTC3'.	Nucleic Acids Res.	1988	16		9872			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'. 		
@D	Polisson, C.//Robinson, D. 	ApoI, a unique restriction endonuclease from Arthrobacter protophormiae which recognizes 5' RAATTY-3'.	Nucleic Acids Res.	1992	20		2888			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. 		
@D	Pollak, A.J.//Reich, N.O. 	Proximal Recognition Sites Facilitate Intrasite Hopping by DNA Adenine Methyltransferase MECHANISTIC EXPLORATION OF EPIGENETIC GENE REGULATION.	J. Biol. Chem.	2012	287		22873-22881			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. 		
@D	Pollo, S.M.//Charchuk, R.//Nesbo, C.L. 	Draft Genome Sequences of Kosmotoga sp. Strain DU53 and Kosmotoga arenicorallina  S304.	Genome Announcements	2016	4		e00570-16			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. 		
@D	Polosina, Y.Y.//Mui, J.//Pitsikas, P.//Cupples, C.G. 	The Escherichia coli Mismatch Repair Protein MutL Recruits the Vsr and MutH Endonucleases in Response to DNA Damage.	J. Bacteriol.	2009	191		4041-4043			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. 		
@D	Poltaraus, A.B.//Sokolova, D.S.//Grouzdev, D.S.//Ivanov, T.M.//Malakho, S.G.//Korshunova, A.V.//Rozanov, A.S.//Tourova, T.P.//Nazina, T.N. 	Draft Genome Sequence of Aeribacillus pallidus Strain 8m3, a Thermophilic Hydrocarbon-Oxidizing Bacterium Isolated from the Dagang Oil Field (China).	Genome Announcements	2016	4		e00500-16			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. 		
@D	Poltaraus, A.B.//Sokolova, D.S.//Grouzdev, D.S.//Ivanov, T.M.//Malakho, S.G.//Korshunova, A.V.//Tourova, T.P.//Nazina, T.N. 	Draft Genome Sequence of Geobacillus subterraneus Strain K, a Hydrocarbon-Oxidizing Thermophilic Bacterium Isolated from a Petroleum Reservoir   in Kazakhstan.	Genome Announcements	2016	4		e00782-16			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. 		
@D	Polter, S.J.//Caraballo, A.A.//Lee, Y.P.//Eng, W.W.//Gan, H.M.//Wheatley, M.S.//Savka, M.A.//Thomas, B.N.//Hudson, A.O. 	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.	Genome Announcements	2015	3		e00847-15			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. 		
@D	Poly, F.//Read, T.//Tribble, D.R.//Baqar, S.//Lorenzo, M.//Guerry, P. 	Genome sequence of a clinical isolate of Campylobacter jejuni from Thailand.	Infect. Immun.	2007	75		3425-3433			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. 		
@D	Poly, F.//Read, T.D.//Chen, Y.H.//Monteiro, M.A.//Serichantalergs, O.//Pootong, P.//Bodhidatta, L.//Mason, C.J.//Rockabrand, D.//Baqar, S.//Porter, C.K.//Tribble, D.//Darsley, M.//Guerry, P. 	Characterization of two Campylobacter jejuni strains for use in volunteer experimental-infection studies.	Infect. Immun.	2008	76		5655-5667			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. 		
@D	Poly, F.//Threadgill, D.//Stintzi, A. 	Genomic diversity in Campylobacter jejuni: Identification of C-jejuni 81-176-specific genes.	J. Clin. Microbiol.	2005	43		2330-2338			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. 		
@D	Poly, F.//Threadgill, D.//Stintzi, A. 	Identification of Campylobacter jejuni ATCC 43431-specific genes by whole microbial genome comparisons.	J. Bacteriol.	2004	186		4781-4795			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. 		
@D	Polyachenko, V.M.//Melnikova, V.A.//Gruber, I.M.//Smirnova, G.A.//Raskin, B.M. 	Development of a culture medium for bacteria of the genus Haemophilus, producing restriction endonucleases.	Zh. Mikrobiol. Epidemiol. Immunobiol.	1989	3		3-8			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. 		
@D	Polyanovsky, O.L.//Nosikov, V.V.//Zhuze, A.L.//Braga, E.A.//Karlyshev, A.V. 	Regulation of restriction endonuclease activity with antibiotics.	Adv. Enzyme Regul.	1979	17		307-321			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. 		
@D	Ponger, L.//Li, W.H. 	Evolutionary diversification of DNA methyltransferases in eukaryotic Genomes.	Mol. Biol. Evol.	2005	22		1119-1128			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. 		
@D	Ponnudurai, R.//Sayavedra, L.//Kleiner, M.//Heiden, S.E.//Thurmer, A.//Felbeck, H.//Schluter, R.//Sievert, S.M.//Daniel, R.//Schweder, T.//Markert, S. 	Genome sequence of the sulfur-oxidizing Bathymodiolus thermophilus gill endosymbiont.	Standards in Genomic Sciences	2017	12		50			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. 		
@D	Pope, W.H. et al. 	Expanding the diversity of mycobacteriophages: insights into genome architecture and evolution.	PLoS ONE	2011	6		E16329			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. 		
@D	Pope, W.H. et al. 	Genome Sequences of Gordonia terrae Phages Benczkowski14 and Katyusha.	Genome Announcements	2016	4		e00578-16			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. 		
@D	Popin, R.V.//Rigonato, J.//Abreu, V.A.//Andreote, A.P.//Silveira, S.B.//Odebrecht, C.//Fiore, M.F. 	Draft Genome Assembly of the Bloom-Forming Cyanobacterium Nodularia spumigena Strain CENA596 in Shrimp Production Ponds.	Genome Announcements	2016	4		e00466-16			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. 		
@D	Popovski, B. 	The location of genes coding the specific modification and restriction system in the recombinant E. coli strain tF.	Vet. Med. Nauki	1987	24		9-12			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. 		
@D	Popovski, B. 	Structure and mechanisms of action of restrictional endonucleases.	Vet. Med. Nauki	1986	23		13-17			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. 		
@D	Popovski, B. 	Phenotypic characteristics of a new modificational and restriction system in Escherichia coli.	Vet. Med. Nauki	1987	24		19-24			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. 		
@D	Poratti, G.W.//Yaakop, A.S.//Chan, C.S.//Urbieta, M.S.//Chan, K.G.//Ee, R.//Tan-Guan-Sheng, A.//Goh, K.M.//Donati, E.R. 	Draft Genome Sequence of the Sulfate-Reducing Bacterium Desulfotomaculum copahuensis Strain CINDEFI1 Isolated from the Geothermal Copahue System, Neuquen, Argentina.	Genome Announcements	2016	4		e00870-16			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. 		
@D	Porcellato, D.//Frantzen, C.//Rangberg, A.//Umu, O.C.//Gabrielsen, C.//Nes, I.F.//Amdam, G.V.//Diep, D.B. 	Draft Genome Sequence of Lactobacillus kunkeei AR114 Isolated from Honey Bee Gut.	Genome Announcements	2015	3		e00144-15			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. 		
@D	Porcellato, D.//Ostlie, H.M.//Skeie, S.B. 	Draft Genome Sequence of Enterococcus hirae Strain INF E1 Isolated from Cultured  Milk.	Genome Announcements	2014	2		e00498-14			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. 		
@D	Pore, S.D.//Arora, P.//Dhakephalkar, P.K. 	Draft Genome Sequence of Geobacillus sp. Strain FW23, Isolated from a Formation Water Sample.	Genome Announcements	2014	2		e00352-14			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. 		
@D	Poret-Peterson, A.T.//Bhatnagar, S.//McClean, A.E.//Kluepfel, D.A. 	Draft Genome Sequence of Agrobacterium tumefaciens Biovar 1 Strain 186, Isolated  from Walnut.	Genome Announcements	2017	5		e01232-17			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. 		
@D	Port, G.C.//Paluscio, E.//Caparon, M.G. 	Complete Genome Sequence of emm Type 14 Streptococcus pyogenes Strain HSC5.	Genome Announcements	2013	1		e00612-13			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. 		
@D	Port, G.C.//Paluscio, E.//Caparon, M.G. 	Complete Genome Sequences of emm6 Streptococcus pyogenes JRS4 and Parental Strain D471.	Genome Announcements	2015	3		e00725-15			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. 		
@D	Porter, S.L.//Wilkinson, D.A.//Byles, E.D.//Wadhams, G.H.//Taylor, S.//Saunders, N.J.//Armitage, J.P. 	Genome Sequence of Rhodobacter sphaeroides strain WS8N.	J. Bacteriol.	2011	193		4027-4028			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. 		
@D	Portillo, F.G.D.//Pucciarelli, M.G.//Casadesus, J. 	DNA adenine methylase mutants of Salmonella typhimurium show defects in protein secretion, cell invasion, and M cell cytotoxicity.	Proc. Natl. Acad. Sci. U. S. A.	1999	96		11578-11583			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. 		
@D	Portmann, A.C.//Fournier, C.//Gimonet, J.//Ngom-Bru, C.//Barretto, C.//Baert, L. 	A Validation Approach of an End-to-End Whole Genome Sequencing Workflow for Source Tracking of Listeria monocytogenes and Salmonella enterica.	Front. Microbiol.	2018	9		446			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. 		
@D	Posey, K.L.//Gimble, F.S. 	Insertion of a reversible redox switch into a rare-cutting DNA endonuclease.	Biochemistry	2002	41		2184-2190			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. 		
@D	Posey, K.L.//Koufopanou, V.//Burt, A.//Gimble, F.S. 	Evolution of divergent DNA recognition specificities in VDE homing endonucleases from two yeast species.	Nucleic Acids Res.	2004	32		3947-3956			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. 		
@D	Posfai, G.//Baldauf, F.//Erdei, S.//Posfai, J.//Venetianer, P.//Kiss, A. 	Structure of the gene coding for the sequence-specific DNA-methyltransferase of the B. subtilis phage SPR.	Nucleic Acids Res.	1984	12		9039-9049			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. 		
@D	Posfai, G.//Kim, S.C.//Szilak, L.//Kovacs, A.//Venetianer, P. 	Complementation by detached parts of GGCC-specific DNA methyltransferases.	Nucleic Acids Res.	1991	19		4843-4847			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. 		
@D	Posfai, G.//Kiss, A.//Erdei, S.//Posfai, J.//Venetianer, P. 	Structure of the Bacillus sphaericus R modification methylase gene.	J. Mol. Biol.	1983	170		597-610			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. 		
@D	Posfai, G.//Kiss, A.//Venetianer, P. 	Overproduction of the Bacillus sphaericus R modification methylase in Escherichia coli and its purification to homogeneity.	Gene	1986	50		63-67			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. 		
@D	Posfai, G.//Szybalski, W. 	Increasing the FokI cleavage specificity from 5 to 7 base pairs by two-step methylation.	Nucleic Acids Res.	1988	16		6245			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. 		
@D	Posfai, G.//Szybalski, W. 	A simple method for locating methylated bases in DNA, as applied to detect asymmetric methylation by M.FokIA.	Gene	1988	69		147-151			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. 		
@D	Posfai, G.//Szybalski, W. 	A simple method for locating methylated bases in DNA using class-IIS restriction enzymes.	Gene	1988	74		179-181			Meeting Abstract 		
@D	Posfai, J.//Bhagwat, A.S.//Posfai, G.//Roberts, R.J. 	Predictive motifs derived from cytosine methyltransferases.	Nucleic Acids Res.	1989	17		2421-2435			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. 		
@D	Posfai, J.//Bhagwat, A.S.//Roberts, R.J. 	Sequence motifs specific for cytosine methyltransferases.	Gene	1988	74		261-265			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. 		
@D	Posfai, J.//Roberts, R.J. 	Predictive motifs of cytosine methylases.	J. Cell Biochem. Suppl.	1989	13D		213			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. 		
@D	Potnis, N.//Krasileva, K.//Chow, V.//Almeida, N.F.//Patil, P.B.//Ryan, R.P.//Sharlach, M.//Behlau, F.//Dow, J.M.//Momol, M.//White, F.F.//Preston, J.F.//Vinatzer, B.A.//Koebnik, R.//Setubal, J.C.//Norman, D.J.//Staskawicz, B.J.//Jones, J.B. 	Comparative genomics reveals diversity among xanthomonads infecting tomato and pepper.	BMC Genomics	2011	12		146			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. 		
@D	Potshangbam, M.//Sahoo, D.//Verma, P.//Verma, S.//Kalita, M.C.//Indira, D.S. 	Draft Genome Sequence of Bacillus altitudinis Lc5, a Biocontrol and Plant Growth-Promoting Endophyte Strain Isolated from Indigenous Black Rice of Manipur.	Genome Announcements	2018	6		e00601-18			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. 		
@D	Potter, A.A.//Loutit, J.S. 	Exonuclease activity from Pseudomonas aeruginosa which is missing in phenotypically restrictionless mutants.	J. Bacteriol.	1982	151		1204-1209			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. 		
@D	Potter, B.V.L.//Eckstein, F. 	Cleavage of phosphorothioate-substituted DNA by restriction endonucleases.	J. Biol. Chem.	1984	259		14243-14248			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. 		
@D	Potter, R.F.//D'Souza, A.W.//Wallace, M.A.//Shupe, A.//Patel, S.//Gul, D.//Kwon, J.H.//Andleeb, S.//Burnham, C.A.//Dantas, G. 	Draft Genome Sequence of the blaOXA-436- and blaNDM-1-Harboring Shewanella putrefaciens SA70 Isolate.	Genome Announcements	2017	5		e00644-17			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. 		
@D	Potter, S.S.//Bott, K.F.//Newbold, J.E. 	Two-dimensional restriction analysis of the Bacillus subtilis genome: gene purification and ribosomal ribonucleic acid gene organization.	J. Bacteriol.	1977	129		492-500			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. 		
@D	Pouillot, F.//Fayolle, C.//Carniel, E. 	A putative DNA adenine methyltransferase is involved in Yersinia pseudo tuberculosis pathogenicity.	Microbiology	2007	153		2426-2434			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. 		
@D	Poulter, R.//Taiaroa, G.//Sumpter, N.//Stockwell, P.//Butler, M. 	Complete Genome Sequence of the Kiwifruit Pathogen Pseudomonas syringae pv. actinidiae Biovar 5, Originating from Japan.	Genome Announcements	2017	5		e01409-17			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. 		
@D	Poulter, R.T.M.//Goodwin, T.J.D.//Butler, M.I. 	The nuclear-encoded inteins of fungi.	Fungal Genet. Biol.	2007	44		153-179			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. 		
@D	Povilionis, P.I.//Lubys, A.A.//Janulaitis, A. 	Cloning of the restriction-modification genes of Bacillus centrosporus in Escherichia coli.	Genetika	1988	24		210-215			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. 		
@D	Povilionis, P.I.//Lubys, A.A.//Vaisvila, R.I.//Kulakauskas, S.T.//Janulaitis, A. 	Investigation of methyl-cytosine specific restriction in Escherichia coli K-12.	Genetika	1989	25		753-755			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. 		
@D	Powell, I.B.//Davidson, B.E. 	Resistance to in vitro restriction of DNA from lactic streptococcal bacteriophage c6A.	Appl. Environ. Microbiol.	1986	51		1358-1360			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. 		
@D	Powell, L.M.//Connolly, B.A.//Dryden, D.T.F. 	The DNA binding characteristics of the trimeric EcoKI methyltransferase and its partially assembled dimeric form determined by fluorescence polarization and DNA footprint.	J. Mol. Biol.	1998	283		947-961			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. 		
@D	Powell, L.M.//Dryden, D.T.F.//Murray, N.E. 	Sequence-specific DNA binding by EcoKI, a type IA DNA restriction enzyme.	J. Mol. Biol.	1998	283		963-976			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. 		
@D	Powell, L.M.//Dryden, D.T.F.//Willcock, D.F.//Pain, R.H.//Murray, N.E. 	DNA recognition by the EcoK methyltransferase. The influence of DNA methylation and the cofactor S-adenosyl-L-methionine.	J. Mol. Biol.	1993	234		60-71			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. 		
@D	Powell, L.M.//Lejeune, E.//Hussain, F.S.//Cronshaw, A.D.//Kelly, S.M.//Price, N.C.//Dryden, D.T. 	Assembly of EcoKI DNA methyltransferase requires the C-terminal region of the HsdM modification subunit.	Biophys. Chem.	2003	103		129-137			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. 		
@D	Powell, L.M.//Murray, N.E. 	S-adenosyl methionine alters the DNA contacts of the EcoKI methyltransferase.	Nucleic Acids Res.	1995	23		967-974			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. 		
@D	Powell, R.J.//Bachvaroff, T.R.//Hill, R.T. 	Draft Genome Sequence of the Alga-Aggregating Bacterium Bacillus sp. Strain RP1137.	Genome Announcements	2014	2		e00973-13			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. 		
@D	Power, K.A.//Yan, Q.//Fox, E.M.//Cooney, S.//Fanning, S. 	Genome Sequence of Cronobacter sakazakii SP291, a Persistent Thermotolerant Isolate Derived from a Factory Producing Powdered Infant Formula.	Genome Announcements	2013	1		e0008213			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. 		
@D	Power, S.E.//Harris, H.M.//Bottacini, F.//Ross, R.P.//O'Toole, P.W.//Fitzgerald, G.F. 	Draft Genome Sequence of Lactobacillus crispatus EM-LC1, an Isolate with Antimicrobial Activity Cultured from an Elderly Subject.	Genome Announcements	2013	1		e01070-13			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. 		
@D	Powers, J.G.//Weigman, V.J.//Shu, J.//Pufky, J.M.//Cox, D.//Hurban, P. 	Efficient and accurate whole genome assembly and methylome profiling of E. coli.	BMC Genomics	2013	14		675			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. 		
@D	Powney, R.//Smits, T.H.//Sawbridge, T.//Frey, B.//Blom, J.//Frey, J.E.//Plummer, K.M.//Beer, S.V.//Luck, J.//Duffy, B.//Rodoni, B. 	Genome Sequence of an Erwinia amylovora Strain with Restricted Pathogenicity to Rubus Plants.	J. Bacteriol.	2010	193		785-786			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. 		
@D	Pozidis, C.//Vlatakis, G.//Bouriotis, V. 	Sequence-specific DNA affinity chromatography: Application of a group specific adsorbent for the isolation of restriction endonucleases.	Prog. Biotechnol.	1994	9		543-546			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. 		
@D	Pozidis, C.//Vlatakis, G.//Bouriotis, V. 	Sequence-specific DNA affinity chromatography: application of a group-specific adsorbent for the isolation of restriction endonucleases.	J. Chromatogr.	1993	630		151-157			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. 		
@D	Prabhakara, S.//Khedkar, S.//Loganathan, R.M.//Chandana, S.//Gowda, M.//Arakere, G.//Seshasayee, A.S. 	Draft Genome Sequence of Staphylococcus aureus 118 (ST772), a Major Disease Clone from India.	J. Bacteriol.	2012	194		3727-3728			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. 		
@D	Prabhakaran, D.M.//Chowdhury, G.//Pazhani, G.P.//Ramamurthy, T.//Thomas, S. 	Draft Genome Sequence of an Environmental trh+ Vibrio parahaemolyticus K23 Strain Isolated from Kerala, India.	Genome Announcements	2016	4		e00282-16			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. 		
@D	Prabhakaran, M.//Couger, M.B.//Jackson, C.A.//Weirick, T.//Fathepure, B.Z. 	Genome Sequences of the Lignin-Degrading Pseudomonas sp. Strain YS-1p and Rhizobium sp. Strain YS-1r Isolated from Decaying Wood.	Genome Announcements	2015	3		e00019-15			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. 		
@D	Pradeep, B.E.//Mahalingam, N.//Manivannan, B.//Padmanabhan, K.//Nilawe, P.//Gurung, G.//Chhabra, A.//Nagaraja, V. 	Draft Genome Sequence of Elizabethkingia meningoseptica, Isolated from a Postoperative Endophthalmitis Patient.	Genome Announcements	2014	2		e01335-14			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. 		
@D	Pradel, N.//Ji, B.//Gimenez, G.//Talla, E.//Lenoble, P.//Garel, M.//Tamburini, C.//Fourquet, P.//Lebrun, R.//Bertin, P.//Denis, Y.//Pophillat, M.//Barbe, V.//Ollivier, B.//Dolla, A. 	The First Genomic and Proteomic Characterization of a Deep-Sea Sulfate Reducer: Insights into the Piezophilic Lifestyle of Desulfovibrio piezophilus.	PLoS ONE	2013	8		E55130			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. 		
@D	Pradhan, S.//Adams, R.L.P. 	DNA methylation in plants: involvement of two different methyltransferases.	Biochem. Soc. Trans.	1994	22		297S			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. 		
@D	Pradhan, S.//Adams, R.L.P. 	Distinct CG and CNG DNA methyltransferases in Pisum sativum.	Plant J.	1995	7		471-481			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. 		
@D	Pradhan, S.//Bacolla, A.//Wells, R.D.//Roberts, R.J. 	Recombinant human DNA (cytosine-5) methyltransferase.	J. Biol. Chem.	1999	274		33002-33010			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. 		
@D	Pradhan, S.//Cummings, M.//Roberts, R.J.//Adams, R.L.P. 	Isolation, characterization and baculovirus-mediated expression of cDNA encoding cytosine DNA methyltransferase from Pisum sativum.	Nucleic Acids Res.	1998	26		1214-1222			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. 		
@D	Pradhan, S.//Esteve, P.O. 	Allosteric activator domain of maintenance human DNA (cytosine-5) methyltransferase and its role in methylation spreading.	Biochemistry	2003	42		5321-5332			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. 		
@D	Pradhan, S.//Esteve, P.O. 	Mammalian DNA (cytosine-5) methyltransferases and their expression.	Clin. Immunol.	2003	109		6-16			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. 		
@D	Pradhan, S.//Houlston, C.//Cummings, M.//Adams, R.L.P. 	CG and CNG methyltransferases in plants.	Gene	1995	157		289-291			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. 		
@D	Pradhan, S.//Kim, G.D. 	The retinoblastoma gene product interacts with maintenance human DNA (cytosine-5) methyltransferase and modulates its activity.	EMBO J.	2002	21		779-788			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. 		
@D	Pradhan, S.//Roberts, R.J. 	Hybrid mouse-prokaryotic DNA (cytosine-5) methyltransferases retain the specificity of the parental C-terminal domain.	EMBO J.	2000	19		2103-2114			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. 		
@D	Pradhan, S.//Talbot, D.//Sha, M.//Benner, J.//Hornstra, L.//Li, E.//Jaenisch, R.//Roberts, R.J. 	Baculovirus-mediated expression and characterization of the full-length murine DNA methyltransferase.	Nucleic Acids Res.	1997	25		4666-4673			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. 		
@D	Pragasam, A.K.//Yesurajan, F.//Doss, C.G.P.//George, B.//Devanga, R.N.K.//Walia, K.//Veeraraghavan, B. 	Draft Genome Sequence of Extremely Drug-Resistant Pseudomonas aeruginosa (ST357)  Strain CMC_VB_PA_B22862 Isolated from a Community-Acquired Bloodstream Infection.	Genome Announcements	2016	4		e01092-16			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. 		
@D	Prajapati, J.B.//Khedkar, C.D.//Chitra, J.//Suja, S.//Mishra, V.//Sreeja, V.//Patel, R.K.//Ahir, V.B.//Bhatt, V.D.//Sajnani, M.R.//Jakhesara, S.J.//Koringa, P.G.//Joshi, C.G. 	Whole-Genome Shotgun Sequencing of Lactobacillus rhamnosus MTCC 5462, a Strain with Probiotic Potential.	J. Bacteriol.	2012	194		1264-1265			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). 		
@D	Prajapati, J.B.//Khedkar, C.D.//Chitra, J.//Suja, S.//Mishra, V.//Sreeja, V.//Patel, R.K.//Ahir, V.B.//Bhatt, V.D.//Sajnani, M.R.//Jakhesara, S.J.//Koringa, P.G.//Joshi, C.G. 	Whole-Genome Shotgun Sequencing of an Indian-Origin Lactobacillus helveticus Strain, MTCC 5463, with Probiotic Potential.	J. Bacteriol.	2011	193		4282-4283			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. 		
@D	Prakash, A.//Chung, S.//Ryu, J.-I. 	Study of the expression of hsd genes of E. coli K-12 after conjugal transfer.	Abstr. Gen. Meet. Am. Soc. Microbiol.	1991	91		165			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. 		
@D	Prakash, A.//Valinluck, B.//Ryu, J.-I. 	Genomic hsd-Mu(lac) operon fusion mutants of Escherichia coli K-12.	Gene	1991	99		9-14			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. 		
@D	Prakash, O.//Muduli, S.//Kumar, R.//Kumari, C.//Nimonkar, Y.//Shouche, Y.S.//Sharma, R. 	Description of Auricoccucs indicus gen. nov., sp. nov., isolated from skin of human ear.	Int. J. Syst. Evol. Microbiol.	2017	67		1212-1218			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. 		
@D	Prakash, T.//Oshima, K.//Morita, H.//Fukuda, S.//Imaoka, A.//Kumar, N.//Sharma, V.K.//Kim, S.-W.//Takahashi, M.//Saitou, N.//Taylor, T.D.//Ohno, H.//Umesaki, Y.//Hattori, M. 	Complete Genome Sequences of Rat and Mouse Segmented Filamentous Bacteria, a Potent Inducer of Th17 Cell Differentiation.	Cell Host Microbe	2011	10		273-284			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. 		
@D	Prakash-Cheng, A.//Chung, S.S.//Ryu, J.-I. 	The expression and regulation of hsdK genes after conjugative transfer.	Mol. Gen. Genet.	1993	241		491-496			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. 		
@D	Prakash-Cheng, A.//Ryu, J. 	Delayed expression of in vivo restriction activity following conjugal transfer of Escherichia coli hsdk (restriction-modification) genes.	J. Bacteriol.	1993	175		4905-4906			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. 		
@D	Pramono, A.K.//Kuwahara, H.//Itoh, T.//Toyoda, A.//Yamada, A.//Hongoh, Y. 	Discovery and Complete Genome Sequence of a Bacteriophage from an Obligate Intracellular Symbiont of a Cellulolytic Protist in the Termite Gut.	Microbes Environ.	2017	32		112-117			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. 		
@D	Prangishvili, D.A.//Chinchaladze, D.Z.//Chelidze, M.G. 	Thermostability of nucleic acid and restriction endonuclease template synthesis enzymes from extremely thermophilic archebacteria.	Biotekhnologiya	1987	3		440-446			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. 		
@D	Prangishvili, D.A.//Vashakidze, R.P.//Chelidze, M.G.//Chinchaladze, D.Z.//Tsalkalamanidze, N.V. 	Isolation and properties of a restriction endonuclease SuaI from the thermoacidophilic archaebacterium Sulfolobus acidocaldarius.	Biokhimiia	1987	52		1043-1050			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. 		
@D	Prangishvili, D.A.//Vashakidze, R.P.//Chelidze, M.G.//Gabriadze, I.Y. 	A restriction endonuclease SuaI from the thermoacidophilic archaebacterium Sulfolobus acidocaldarius.	FEBS Lett.	1985	192		57-60			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. 		
@D	Prasad, B.J.//Sabnis, K.//Deobagkar, D.D.//Deobagkar, D.N. 	Deinococcus radiodurans strain R1 contains N6-methyladenine in its genome.	Biochem. Biophys. Res. Commun.	2005	335		412-416			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. 		
@D	Prasanna, L.//Moharana, T.R.//Sheikh, N.//Arravapalli, V.R.//Kumaraswamy, T.//Eijsink, V.G.H.//Nalam, M.R. 	Draft Genome Sequence of Entomopathogenic Brevibacillus laterosporus Strain Lak 1210, an Alkaliphilic Chitin Degrader.	Genome Announcements	2017	5		e01251-17			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%. 		
@D	Prasannan, C.B. 	Modulation of restriction enzyme PvuII activity by metal ion cofactors.	Ph.D. Thesis, University of Missouri	2009						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. 		
@D	Premkrishnan, B.N.V. et al. 	Complete Genome Sequence of Staphylococcus haemolyticus Type Strain SGAir0252.	Genome Announcements	2018	6		e00229-18			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. 		
@D	Prere, M.F.//Fayet, O. 	DNA methylase activities in a Neisseria gonorrhoeae extract.	FEMS Microbiol. Lett.	1986	33		37-41			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. 		
@D	Prere, M.F.//Fayet, O. 	Susceptibility of Neisseria Gonorrhoeae DNA to Cleavage by Restriction Endonuclease KpnI.	Ann. Inst. Pasteur Microbiol.	1985	136A		329-338			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. 		
@D	Prere, M.F.//Fayet, O. 	DNA modification in Neisseria gonorrhoeae: Resistance of DNA of 19 strains to cleavage by restriction enzymes.	Ann. Inst. Pasteur Microbiol.	1985	136A		323-328			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. 		
@D	Presta, L.//Bosi, E.//Fondi, M.//Maida, I.//Perrin, E.//Miceli, E.//Maggini, V.//Bogani, P.//Firenzuoli, F.//Di Pilato, V.//Rossolini, G.M.//Mengoni, A.//Fani, R. 	Draft Genome Sequence of Pseudomonas sp. EpS/L25, Isolated from the Medicinal Plant Echinacea purpurea and Able To Synthesize Antimicrobial Compounds.	Genome Announcements	2016	4		e00346-16			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. 		
@D	Presta, L.//Inzucchi, I.//Bosi, E.//Fondi, M.//Perrin, E.//Maida, I.//Miceli, E.//Tutino, M.L.//Lo, G.A.//de Pascale, D.//Fani, R. 	Draft Genome Sequences of the Antimicrobial Producers Pseudomonas sp. TAA207 and  Pseudomonas sp. TAD18 Isolated from Antarctic Sediments.	Genome Announcements	2016	4		e00728-16			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. 		
@D	Presta, L.//Inzucchi, I.//Bosi, E.//Fondi, M.//Perrin, E.//Miceli, E.//Tutino, M.L.//Lo, G.A.//de Pascale, D.//Fani, R. 	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.	Genome Announcements	2016	4		e00410-16			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. 		
@D	Price, C.//Bickle, T.A. 	A possible role for DNA restriction in bacterial evolution.	Microbiol. Sci.	1986	3		296-299			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. 		
@D	Price, C.//Bickle, T.A. 	Evolution of DNA sequence specificity in type I restriction enzymes.	Biochem. Soc. Trans.	1988	16		942-943			None 		
@D	Price, C.//Gubler, M.//Braguglia, D.//Meister, J.//Tyndall, C.//Piekarowicz, A.//Bickle, T.A. 	Evolution of DNA sequence specificity in type 1C restriction and modification systems.	J. Cell Biochem. Suppl.	1993	17C		151			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. 		
@D	Price, C.//Lingner, J.//Bickle, T.A.//Firman, K.//Glover, S.W. 	Basis for changes in DNA recognition by the EcoR124 and EcoR124/3 Type I DNA restriction and modification enzymes.	J. Mol. Biol.	1989	205		115-125			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. 		
@D	Price, C.//Pripfl, T.//Bickle, T.A. 	EcoR124 and EcoR124/3:  the first members of a new family of type I restriction and modification systems.	Eur. J. Biochem.	1987	167		111-115			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. 		
@D	Price, C.//Shepherd, J.C.W.//Bickle, T.A. 	DNA recognition by a new family of type I restriction enzymes:  a unique relationship between two different DNA specificities.	EMBO J.	1987	6		1493-1497			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. 		
@D	Price, E.P.//Smith, M.L.//Paxinos, E.E.//Tallon, L.J.//Sadzewicz, L.//Sengamalay, N.//Baird, R.W.//Currie, B.J.//Sarovich, D.S. 	Whole-Genome Sequences of Burkholderia pseudomallei Isolates Exhibiting Decreased Meropenem Susceptibility.	Genome Announcements	2017	5		e00053-17			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. 		
@D	Price, M.N. et al. 	Mutant phenotypes for thousands of bacterial genes of unknown function.	Nature	2018	557		503-509			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. 		
@D	Price, T.K.//Mehrtash, A.//Kalesinskas, L.//Malki, K.//Hilt, E.E.//Putonti, C.//Wolfe, A.J. 	Genome sequences and annotation of two urinary isolates of E. coli.	Standards in Genomic Sciences	2016	11		79			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. 		
@D	Price, T.K.//Shaheen, M.//Kalesinskas, L.//Malki, K.//Hilt, E.E.//Putonti, C.//Wolfe, A.J. 	Draft Genome Sequence of a Urinary Isolate of Lactobacillus crispatus.	Genome Announcements	2016	4		e01278-16			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. 		
@D	Price, V.J.//Huo, W.//Sharifi, A.//Palmer, K.L. 	CRISPR-Cas and Restriction-Modification Act Additively against Conjugative Antibiotic Resistance Plasmid Transfer in Enterococcus faecalis.		2016	1		e00064-16			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. 		
@D	Prichodko, E.A.//Rechnukova, N.I.//Degtyarev, S.K. 	Determination of substrate specificity of restriction endonuclease Tru9I.	Sib. Biol. J.	1991	1		57-59			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. 		
@D	Prichodko, G.G.//Degtyarev, S.K.//Rechkunova, N.I.//Sosnovsev, S.V.//Tchigikov, V.E. 	General method for determining the sites of DNA cleavage by restriction endonucleases.	Biotekhnologiya	1990	1		12-16			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. 		
@D	Prichodko, G.G.//Petrov, N.A.//Chizhikov, V.E.//Degtyarev, S.K. 	A modified method for determining the sites of DNA cleavage by restriction endonucleases.	Biotekhnologiya	1988	4		618-620			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. 		
@D	Prichodko, G.G.//Petrov, N.A.//Repin, V.E.//Degtyarev, S.K. 	Establishing the substrate specificity of restriction endonuclease Bsu15I.	Izv. Sib. Otd. Akad. Nauk SSSR	1988	14		108-109			The recognition sequence and cleavage point of restriction endonuclease Bsu15I has been determined as 5'AT^CGAT. 		
@D	Prichodko, G.G.//Rechnukova, N.I.//Repin, V.E.//Degtyarev, S.K. 	Determination of substrate specificity of restriction endonuclease Acc65I.	Sib. Biol. J.	1991	1		59-60			The recognition sequence and cleavage point of restriction endonuclease Acc65I have been determined as 5'G^GTACC. 		
@D	Prichula, J.//Campos, F.S.//Pereira, R.I.//Cardoso, L.A.//Wachholz, G.R.//Pieta, L.//Mariot, R.F.//de Moura, T.M.//Tavares, M.//d'Azevedo, P.A.//Frazzon, J.//Frazzon, A.P. 	Complete Genome Sequence of Enterococcus faecalis Strain P8-1 Isolated from Wild  Magellanic Penguin (Spheniscus magellanicus) Feces on the South Coast of Brazil.	Genome Announcements	2016	4		e01531-15			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. 		
@D	Pride, D.T.//Blaser, M.J. 	Identification of horizontally acquired genetic elements in Helicobacter pylori and other prokaryotes using oligonucleotide difference analysis.	Genome Lett.	2002	1		2-15			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. 		
@D	Pridgeon, J.W.//Zhang, D.//Zhang, L. 	Complete Genome Sequence of a Moderately Virulent Aeromonas hydrophila Strain, pc104A, Isolated from Soil of a Catfish Pond in West Alabama.	Genome Announcements	2014	2		e00554-14			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. 		
@D	Pridgeon, J.W.//Zhang, D.//Zhang, L. 	Complete Genome Sequence of a Virulent Strain, Streptococcus iniae ISET0901, Isolated from Diseased Tilapia.	Genome Announcements	2014	2		e00553-14			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. 		
@D	Pridgeon, J.W.//Zhang, D.//Zhang, L. 	Complete Genome Sequence of the Attenuated Novobiocin-Resistant Streptococcus iniae Vaccine Strain ISNO.	Genome Announcements	2014	2		e00510-14			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. 		
@D	Pridgeon, J.W.//Zhang, D.//Zhang, L. 	Complete Genome Sequence of the Highly Virulent Aeromonas hydrophila AL09-71 Isolated from Diseased Channel Catfish in West Alabama.	Genome Announcements	2014	2		e00450-14			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. 		
@D	Pridmore, R.D.//Berger, B.//Desiere, F.//Vilanova, D.//Barretto, C.//Pittet, A.-C.//Zwahlen, M.-C.//Rouvet, M.//Altermann, E.//Barrangou, R.//Mollet, B.//Mercenier, A.//Klaenhammer, T.//Arigoni, F.//Schell, M.A. 	The genome sequence of the probiotic intestinal bacterium Lactobacillus johnsonii NCC 533.	Proc. Natl. Acad. Sci. U. S. A.	2004	101		2512-2517			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. 		
@D	Prieto, J.//Epinat, J.C.//Redondo, P.//Ramos, E.//Padro, D.//Cedrone, F.//Montoya, G.//Paques, F.//Blanco, F.J. 	Generation and analysis of mesophilic variants of the thermostable archaeal I-DmoI homing endonuclease.	J. Biol. Chem.	2008	283		4364-4374			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. 		
@D	Prieto, J.//Molina, R.//Montoya, G. 	Molecular scissors for in situ cellular repair.	Crit. Rev. Biochem. Mol. Biol.	2012	47		207-221			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. 		
@D	Prieto, J.//Redondo, P.//Merino, N.//Villate, M.//Montoya, G.//Blanco, F.J.//Molina, R. 	Structure of the I-SceI nuclease complexed with its dsDNA target and three catalytic metal ions.	Acta Crystallogr. F Struct. Biol. Cryst. Commun.	2016	72		473-479			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. 		
@D	Prieto, J.//Redondo, P.//Padro, D.//Arnould, S.//Epinat, J.C.//Paques, F.//Blanco, F.J.//Montoya, G. 	The C-terminal loop of the homing endonuclease I-CreI is essential for site recognition, DNA binding and cleavage1.	Nucleic Acids Res.	2007	35		3262-3271			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. 		
@D	Pristas, P.//Fliegerova, K.//Javorsky, P. 	Two restriction endonucleases in Selenomonas ruminantium subsp. lactilytica.	Lett. Appl. Microbiol.	1998	27		83-85			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'. 		
@D	Pristas, P.//Godany, A.//Sevcikova, B.//Oktavcova, B.//Farkasovska, J. 	Characterization of restriction endonuclease activities in tetracycline producing strains of Streptomyces aureofaciens.	Nucleic Acids Res.	1992	20		4364			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). 		
@A	Pristas, P.//Javorsky, P. 		Restriction-modification systems in ruminal bacteria: occurrence and some evolutionary implications.			Chesson, A.//Stewart, C.S.//Flint, J.H. 		Reprod. Nutr. Dev.					Elsevier	1997		37		74-75									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. 		
@D	Pristas, P.//Molnarova, V.//Javorsky, P. 	Diversity of restriction and modification phenotypes in local population of rumen bacterium Selenomonas ruminantium.	Biologia (Bratisl)	2002	57		777-782			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. 		
@D	Pristas, P.//Molnarova, V.//Javorsky, P. 	Restriction and modification systems of ruminal bacteria.	Folia Microbiol. (Praha)	2001	46		71-72			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). 		
@D	Pristas, P.//Molnarova, V.//Javorsky, P. 	Detection of N6-methyladenine in GATC sequences of Selenomonas ruminantium.	J. Basic Microbiol.	1998	38		283-287			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. 		
@D	Pristas, P.//Piknova, M. 	Underrepresentation of short palindromes in Selenomonas ruminantium DNA: evidence for horizontal gene transfer of restriction and  modification systems?	Can. J. Microbiol.	2005	51		315-318			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. 		
@D	Pristas, P.//Vanat, I.//Godany, A.//Javorsky, P. 	Restriction endonucleases from Selenomonas ruminantium which recognize and cleave 5'-AT/TAAT-3'.	Arch. Microbiol.	1994	161		439-441			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. 		
@D	Pristas, P.//Vanat, I.//Javorsky, P. 	Isolation and characterization of a new restriction endonuclease, Sru30DI, from Selenomonas ruminantium.	Gene	1995	158		139-140			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. 		
@D	Pristas, P.//Vanat, I.//Javorsky, P. 	Variability of endonucleolytic activity indicates high genetic diversity within the natural population of Selenomonas ruminantium.	Folia Microbiol. (Praha)	1997	42		121-124			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. 		
@D	Pritchard, L.//Humphris, S.//Baeyen, S.//Maes, M.//Van Vaerenbergh, J.//Elphinstone, J.//Saddler, G.//Toth, I. 	Draft Genome Sequences of Four Dickeya dianthicola and Four Dickeya solani Strains.	Genome Announcements	2013	1		e00087-12			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. 		
@D	Pritchard, L.//Humphris, S.//Saddler, G.S.//Elphinstone, J.G.//Pirhonen, M.//Toth, I.K. 	Draft Genome Sequences of 17 Isolates of the Plant Pathogenic Bacterium Dickeya.	Genome Announcements	2013	1		e00978-13			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. 		
@D	Privman, E. 	Bioinformatic Identification of Homing Endonucleases and Their Target Sites.	Methods Mol. Biol.	2014	1123		27-35			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. 		
@D	Probst, M.//Aeschimann, W.//Chau, T.T.//Langenegger, S.M.//Stocker, A.//Haner, R. 	Structural insight into DNA-assembled oligochromophores: crystallographic analysis of pyrene- and phenanthrene-modified DNA in complex with BpuJI  endonuclease.	Nucleic Acids Res.	2016	44		7079-7089			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. 		
@D	Prochazka, B.//Indra, A.//Hasenberger, P.//Blaschitz, M.//Wagner, L.//Wewalka, G.//Sorschag, S.//Schmid, D.//Ruppitsch, W. 	Draft Genome Sequence of Legionella jamestowniensis Isolated from a Patient with  Chronic Respiratory Disease.	Genome Announcements	2016	4		e01007-16			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. 		
@D	Proenca, D.N.//Espirito, S.C.//Grass, G.//Morais, P.V. 	Draft Genome Sequence of Serratia sp. Strain M24T3, Isolated from Pinewood Disease Nematode Bursaphelenchus xylophilus.	J. Bacteriol.	2012	194		3764			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. 		
@D	Proenca, D.N.//Espirito, S.C.//Grass, G.//Morais, P.V. 	Draft Genome Sequence of Pseudomonas sp. Strain M47T1, Carried by Bursaphelenchus xylophilus Isolated from Pinus pinaster.	J. Bacteriol.	2012	194		4789-4790			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. 		
@D	Proenca, D.N.//Whitman, W.B.//Shapiro, N.//Woyke, T.//Kyrpides, N.C.//Morais, P.V. 	Draft genome sequence of the cellulolytic endophyte Chitinophaga costaii A37T2T.	Standards in Genomic Sciences	2017	12		53			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. 		
@D	Proffitt, J.H.//Davie, J.R.//Swinton, D.//Hattman, S. 	5-methylcytosine is not detectable in Saccharomyces cerevisiae.	Mol. Cell. Biol.	1984	4		985-988			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. 		
@D	Protozanova, E.//Demidov, V.V.//Nielsen, P.E.//Frank-Kamenetskii, M.D. 	Pseudocomplementary PNAs as selective modifiers of protein activity on duplex DNA: the case of type IIs restriction enzymes.	Nucleic Acids Res.	2003	31		3929-3935			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. 		
@D	Protozanova, E.//Demidov, V.V.//Soldatenkov, V.//Chasovskikh, S.//Frank-Kamenetskii, M.D. 	Tailoring the activity of restriction endonuclease PleI by PNA-induced DNA looping.	EMBO Rep.	2002	3		956-961			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. 		
@D	Protsenko, A.//Zakharova, M.//Nagornykh, M.//Solonin, A.//Severinov, K. 	Transcription regulation of restriction-modification system Ecl18kI.	Nucleic Acids Res.	2009	37		5322-5330			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. 		
@D	Proust, L.//Loux, V.//Martin, V.//Magnabosco, C.//Pedersen, M.//Monnet, V.//Juillard, V. 	Complete Genome Sequence of the Industrial Fast-Acidifying Strain Streptococcus thermophilus N4L.	Microbiol. Resour. Announc.	2018	7		e01029-18			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. 		
@D	Proux, C.//Van Sinderen, D.//Suarez, J.//Garcia, P.//Ladero, V.//Fitzgerald, G.F.//Desiere, F.//Brussow, H. 	The dilemma of phage taxonomy illustrated by comparative genomics of sfi21-like siphoviridae in lactic acid bacteria.	J. Bacteriol.	2002	184		6026-6036			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. 		
@D	Prozorov, A.A.//Belova, T.S.//Surikov, N.N. 	Transformation and transduction of Bacillus subtilis strains with the BsuR restriction-modification system by means of modified and unmodified DNA of pUB110 plasmid.	Mol. Gen. Genet.	1980	180		135-138			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. 		
@D	Pryshliak, M.//Hammerl, J.A.//Reetz, J.//Strauch, E.//Hertwig, S. 	Vibrio vulnificus Phage PV94 Is Closely Related to Temperate Phages of V. cholerae and Other Vibrio Species.	PLoS ONE	2014	9		E94707			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. 		
@D	Ptashne, M. 	Replication and host modification of DNA transferred during bacterial mating.	J. Mol. Biol.	1965	11		829-838			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. 		
@D	Pu, A.T.//Radany, E.H. 	Regulated expression of restriction endonuclease activity in mammalian cells.	J. Cell. Biochem.	1995	S21		327			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. 		
@D	Pucciarelli, M.G.//Prieto, A.I.//Casadesus, J.//Portillo, F.G.D. 	Envelope instability in DNA adenine methylase mutants of Salmonella  enterica.	Microbiology	2002	148		1171-1182			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. 		
@D	Puchkova, L.I.//Kalmykova, G.V.//Burtseva, L.I.//Repin, V.E. 	Entomapathogenic bacteria Bacillus thuringiensis as producers of restriction endonucleases.	Prikl. Biokhim. Mikrobiol.	2002	38		140-144			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. 		
@D	Puchkova, L.I.//Krivopalova, G.N.//Andreeva, I.S.//Selina, A.V.//Serov, G.D.//Rechkunova, N.I.//Degtyarev, S.K. 	Streptomyces fradiae is the producer of the restriction endonuclease Sfr274I.	Izv. Sib. Otd. Akad. Nauk SSSR	1990	1		32-34			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). 		
@D	Puchkova, L.I.//Ushakova, T.A.//Mikhailova, V.K.//Serov, G.D.//Krivopalova, G.N.//Repin, V.E. 	Testing and isolation of high-purity restriction endonucleases.	Prikl. Biokhim. Mikrobiol.	2002	38		20-24			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. 		
@D	Puchta, H.//Dujon, B.//Hohn, B. 	Homologous recombination in plant cells in enhanced by in vivo induction of double strand breaks into DNA by a site-specific endonuclease.	Nucleic Acids Res.	1993	21		5034-5040			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. 		
@D	Puente-Sanchez, F.//Gonzalez-Silva, C.//Parro, V.//Tamames, J.//Azua-Bustos, A. 	Draft Genome Sequence of the Extremely Desiccation-Tolerant Cyanobacterium Gloeocapsopsis sp. Strain AAB1.	Genome Announcements	2018	6		e00216-18			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. 		
@D	Puente-Sanchez, F.//Pieper, D.H.//Arce-Rodriguez, A. 	Draft Genome Sequence of the Deep-Subsurface Actinobacterium Tessaracoccus lapidicaptus IPBSL-7T.	Genome Announcements	2016	4		e01078-16			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. 		
@D	Puertas, A.I.//Capozzi, V.//Llamas, M.G.//Lopez, P.//Lamontanara, A.//Orru, L.//Russo, P.//Spano, G.//Duenas, M.T. 	Draft Genome Sequence of Lactobacillus collinoides CUPV237, an Exopolysaccharide  and Riboflavin Producer Isolated from Cider.	Genome Announcements	2016	4		e00506-16			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. 		
@D	Pues, H.//Bleimling, N.//Holz, B.//Wolcke, J.//Weinhold, E. 	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.	Biochemistry	1999	38		1426-1434			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. 		
@D	Pugatsch, T.//Weber, H. 	A thermostable, sequence-specific restriction endonuclease from Bacillus stearothermophilus: BstPI.	Nucleic Acids Res.	1979	7		1429-1444			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. 		
@D	Puglisi, E.//Mattarelli, P.//Modesto, M.//Bonetti, A.//Spiezio, C.//Sandri, C.//Morelli, L. 	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.	Genome Announcements	2018	6		e01449-17			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. 		
@D	Puiu, D.//Salzberg, S.L. 	Re-assembly of the genome of Francisella tularensis subsp. holarctica OSU18.	PLoS ONE	2008	3		E3427			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. 		
@D	Pujic, P.//Bolotin, A.//Fournier, P.//Sorokin, A.//Lapidus, A.//Richau, K.H.//Briolay, J.//Mebarki, F.//Normand, P.//Sellstedt, A. 	Genome Sequence of the Atypical Symbiotic Frankia R43 Strain, a Nitrogen-Fixing and Hydrogen-Producing Actinobacterium.	Genome Announcements	2015	3		e01387-15			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. 		
@D	Pukall, R. et al. 	Complete genome sequence of Slackia heliotrinireducens type strain (RHS 1).	Standards in Genomic Sciences	2009	1		234-241			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. 		
@D	Pukall, R. et al. 	Complete genome sequence of Jonesia denitrificans type strain (Prevot 55134).	Standards in Genomic Sciences	2009	1		262-269			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. 		
@D	Pukall, R. et al. 	Complete genome sequence of Kribbella flavida type strain (IFO 14399).	Standards in Genomic Sciences	2010	2		186-193			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. 		
@D	Pukall, R. et al. 	Complete genome sequence of Conexibacter woesei type strain (ID131577).	Standards in Genomic Sciences	2010	2		212-219			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. 		
@D	Pukall, R. et al. 	Complete genome sequence of Deinococcus maricopensis type strain (LB-34).	Standards in Genomic Sciences	2011	4		163-172			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. 		
@D	Pukkila, P.J.//Peterson, J.//Herman, G.//Modrich, P.//Meselson, M. 	Effects of high levels of DNA adenine methylation on methyl-directed mismatch repair in Escherichia coli.	Genetics	1983	104		571-582			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. 		
@D	Pullan, S.T.//Chandra, G.//Bibb, M.J.//Merrick, M. 	Genome-wide analysis of the role of GlnR in Streptomyces venezuelae provides new insights into global nitrogen regulation in actinomycetes.	BMC Genomics	2011	12		175			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. 		
@D	Pullan, S.T.//Miles, R.W.//Lewandowski, K.//Vipond, R. 	Closed genome sequence using hybrid Nanopore/Illumina assembly of a Bacillus anthracis isolate from an animal-skin-drum-associated anthrax case in the UK.	Microbiol. Resour. Announc.	2018	7		e00802-18			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. 		
@D	Pullinger, G.D.//Bevir, T.//Lax, A.J. 	The Pasteurella multocida toxin is encoded within a lysogenic bacteriophage.	Mol. Microbiol.	2004	51		255-269			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. 		
@D	Pullinger, G.D.//Dziva, F.//Charleston, B.//Wallis, T.S.//Stevens, M.P. 	Identification of Salmonella enterica serovar Dublin-specific sequences by subtractive hybridization and analysis of their role in intestinal colonization and systemic translocation in cattle.	Infect. Immun.	2008	76		5310-5321			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. 		
@D	Puopolo, G.//Sonego, P.//Engelen, K.//Pertot, I. 	Draft Genome Sequence of Lysobacter capsici AZ78, a Bacterium Antagonistic to Plant-Pathogenic Oomycetes.	Genome Announcements	2014	2		e00325-14			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. 		
@D	Pupo, E.//Perez, E.//Trujillo, L.E.//Miranda, F.//Gonzalez, E.//Brito, J. 	Validation of radioactive methods in the quality control of DNA restriction enzymes.	Biotecnol. Apl.	1996	13		197-200			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. 		
@D	Puranik, R.//Quan, G.//Werner, J.//Zhou, R.//Xu, Z. 	A pipeline for completing bacterial genomes using in silico and wet lab approaches.	BMC Genomics	2015	16		S7			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. 		
@D	Puranik, S.//Talkal, R.//Qureshi, A.//Khardenavis, A.//Kapley, A.//Purohit, H.J. 	Genome Sequence of the Pigment-Producing Bacterium Pseudogulbenkiania ferrooxidans, Isolated from Loktak Lake.	Genome Announcements	2013	1		e01115-13			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. 		
@D	Purdy, D.//O'Keeffe, T.A.//Elmore, M.//Herbert, M.//McLeod, A.//Bokori-Brown, M.//Ostrowski, A.//Minton, N.P. 	Conjugative transfer of clostridial shuttle vectors from Escherichia coli to Clostridium difficile through circumvention of the restriction  barrier.	Mol. Microbiol.	2002	46		439-452			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. 		
@D	Purdy, M.M.//Holz-Schietinger, C.//Reich, N.O. 	Identification of a second DNA binding site in human DNA methyltransferase 3A by substrate inhibition and domain deletion.	Arch. Biochem. Biophys.	2010	498		13-22			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. 		
@D	Purdy, M.M.//Reich, N.O. 	Modulation of mammalian DNA methyltransferase activity by RNA.	ACS Abstracts	2006	232		244			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. 		
@D	Purdy, M.M.//Reich, N.O. 	DNA binding by HhaI DNA methyltransferase domain interface mutants.	FASEB J.	2006	20		A901			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. 		
@D	Purdy, M.M.//Reich, N.O. 	DNA binding and hemimethylation preference of HhaI DNA methyltransferase domain interface mutants.	ACS Abstracts	2005	230		U626			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. 		
@D	Purmal, A.A.//Shabarova, Z.A.//Gumport, R.I. 	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.	Nucleic Acids Res.	1992	20		3713-3719			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. 		
@D	Purmal, A.A.//Vinogradova, M.N.//Elov, A.A.//Gromova, E.S.//Drutsa, V.L. 	Interaction of EcoRII restriction and modification enzymes with DNA duplexes containing pyrophosphate bonds.	Dokl. Akad. Nauk.	1984	276		992-995					
@D	Purswani, J.//Guisado, I.M.//Gonzalez-Lopez, J.//Pozo, C. 	Draft Genome Sequence of Paenibacillus etheri sp. nov. SH7T, a Methyl Tert-Butyl  Ether Degrader.	Genome Announcements	2016	4		e01696-15			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. 		
@D	Purvis, I.J.//Moseley, B.E.B. 	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.	Nucleic Acids Res.	1983	11		5467-5474			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. 		
@D	Pushiri, H.//Pearce, S.L.//Oakeshott, J.G.//Russell, R.J.//Pandey, G. 	Draft Genome Sequence of Pandoraea sp. Strain SD6-2, Isolated from Lindane-Contaminated Australian Soil.	Genome Announcements	2013	1		e00415-13			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. 		
@D	Putonti, C.//Cudone, E.//Kalesinskas, L.//Engelbrecht, K.C.//Koenig, D.W.//Wolfe, A.J. 	Draft Genome Sequence of Micrococcus luteus (Schroeter) Cohn (ATCC 12698).	Genome Announcements	2017	5		e00576-17			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%. 		
@D	Putonti, C.//Kalesinskas, L.//Cudone, E.//Engelbrecht, K.C.//Koenig, D.W.//Wolfe, A.J. 	Draft Genome Sequence of Enterococcus faecalis ATCC BAA-2128.	Genome Announcements	2017	5		e00575-17			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. 		
@D	Putonti, C.//Kalesinskas, L.//Cudone, E.//Engelbrecht, K.C.//Koenig, D.W.//Wolfe, A.J. 	Draft Genome Sequences of Two ATCC Staphylococcus aureus subsp. aureus Strains.	Genome Announcements	2017	5		e00618-17			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. 		
@D	Putonti, C.//Kalesinskas, L.//Cudone, E.//Engelbrecht, K.C.//Koenig, D.W.//Wolfe, A.J. 	Draft Genome Sequence of Staphylococcus epidermidis (Winslow and Winslow) Evans (ATCC 14990).	Genome Announcements	2017	5		e00619-17			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. 		
@D	Putonti, C.//Polley, N.//Castignetti, D. 	Draft Genome Sequence of an Active Heterotrophic Nitrifier-Denitrifier, Cupriavidus pauculus UM1.	Genome Announcements	2018	6		e00028-18			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. 		
@D	Puvvada, M.S.//Hartley, J.A.//Jenkins, T.C.//Thurston, D.E. 	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.	Nucleic Acids Res.	1993	21		3671-3675			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. 		
@D	Pylro, V.S.//Dias, A.C.F.//Andreote, F.D.//Morais, D.K.//Varani, A.M.//Andreote, C.C.F.//Bernardo, E.R.A.//Zucchi, T. 	Closed Genome Sequence of Phytopathogen Biocontrol Agent Bacillus velezensis Strain AGVL-005, Isolated from Soybean.	Genome Announcements	2018	6		e00057-18			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. 		
@D	Pyne, M.E.//Moo-Young, M.//Chung, D.A.//Chou, C.P. 	Expansion of the genetic toolkit for metabolic engineering of Clostridium pasteurianum: chromosomal gene disruption of the endogenous CpaAI restriction  enzyme.	Biotechnol. Biofuels.	2014	7		163			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. 		
@D	Pyne, M.E.//Moo-Young, M.//Chung, D.A.//Chou, C.P. 	Development of an electrotransformation protocol for genetic manipulation of Clostridium pasteurianum.	Biotechnol. Biofuels.	2013	6		50			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. 		
@D	Pyne, M.E.//Utturkar, S.//Brown, S.D.//Moo-Young, M.//Chung, D.A.//Chou, C.P. 	Improved Draft Genome Sequence of Clostridium pasteurianum Strain ATCC 6013 (DSM  525) Using a Hybrid Next-Generation Sequencing Approach.	Genome Announcements	2014	2		e00790-14			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. 		
@D	Qi, G.R.//Wong, P.//Cedergren, R. 	Restriction of single-stranded M13 DNA using synthetic oligonucleotides:  the structural requirement of restriction enzymes.	Biochem. Cell Biol.	1987	65		50-55			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. 		
@D	Qi, J.//Guo, A.//Cui, P.//Chen, Y.//Mustafa, R.//Ba, X.//Hu, C.//Bai, Z.//Chen, X.//Shi, L.//Chen, H. 	Comparative Geno-Plasticity Analysis of Mycoplasma bovis HB0801 (Chinese Isolate).	PLoS ONE	2012	7		E38239			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. 		
@D	Qi, M.//Nelson, K.E.//Daugherty, S.C.//Nelson, W.C.//Hance, I.R.//Morrison, M.//Forsberg, C.W. 	Novel molecular features of the fibrolytic intestinal bacterium Fibrobacter intestinalis not shared with Fibrobacter succinogenes as  determined by suppressive subtractive hybridization.	J. Bacteriol.	2005	187		3739-3751			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. 		
@D	Qi, M.//Wang, D.//Bradley, C.A.//Zhao, Y. 	Genome Sequence Analyses of Pseudomonas savastanoi pv. glycinea and Subtractive Hybridization-Based Comparative Genomics with Nine Pseudomonads.	PLoS ONE	2011	6		E16451			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. 		
@D	Qi, Y.//D'Alessandro, J.M.//Blodgett, J.A.V. 	Draft Genome Sequence of Streptomyces sp. Strain JV178, a Producer of Clifednamide-Type Polycyclic Tetramate Macrolactams.	Genome Announcements	2018	6		e01401-17			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. 		
@D	Qian, L.//Kussell, E. 	Evolutionary Dynamics of Restriction Site Avoidance.	Phys. Rev. Lett.	2012	108		158105			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. 		
@D	Qian, Y.//Matsumoto, H.//Li, W.//Zhu, G.//Hashidoko, Y.//Hu, Y.//Wang, M. 	Genome Sequence of Burkholderia plantarii ZJ171, a Tropolone-Producing Bacterial  Pathogen Responsible for Rice Seedling Blight.	Genome Announcements	2016	4		e01318-16			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. 		
@D	Qian, Y.//Xi, Y.//Cheng, B.//Zhu, S. 	Genome-wide identification and expression profiling of DNA methyltransferase gene family in maize.	Plant Cell	2014	33		1661-1672			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. 		
@D	Qiang, B.-Q.//McClelland, M.//Poddar, S.//Spokauskas, A.//Nelson, M. 	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 .	Gene	1990	88		101-105			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. 		
@D	Qiang, B.-Q.//Schildkraut, I. 	A type II restriction endonuclease with an eight nucleotide specificity from Streptomyces fimbriatus.	Nucleic Acids Res.	1984	12		4507-4515			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. 		
@D	Qiang, B.-Q.//Schildkraut, I. 	Two unique restriction endonucleases from Neisseria lactamica.	Nucleic Acids Res.	1986	14		1991-1999			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. 		
@D	Qiang, B.-Q.//Schildkraut, I. 	NotI and SfiI:  restriction endonucleases with octanucleotide recognition sequences.	Methods Enzymol.	1987	155		15-21			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. 		
@D	Qiao, J.//Chen, L.//Li, Y.//Wang, J.//Zhang, W.//Chen, S. 	Whole-Genome Sequence of Nocardiopsis alba Strain ATCC BAA-2165, Associated with  Honeybees.	J. Bacteriol.	2012	194		6358-6359			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. 		
@D	Qiao, J.//Liu, Y.//Liang, X.//Hu, Y.//Du, Y. 	Draft Genome Sequence of Root-Colonizing Bacterium Bacillus sp. Strain PTS-394.	Genome Announcements	2014	2		e00038-14			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. 		
@D	Qin, N.//Ding, W.//Yao, J.//Su, K.//Wu, L.//Li, L. 	Genome Sequence of Staphylococcus capitis QN1, Which Causes Infective Endocarditis.	J. Bacteriol.	2012	194		4469-4470			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%. 		
@D	Qin, N.//Zheng, B.//Yang, F.//Chen, Y.//Guo, J.//Hu, X.//Li, L. 	Genome Sequence of Aerococcus viridans LL1.	J. Bacteriol.	2012	194		4143			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%. 		
@D	Qin, Q.L.//Li, Y.//Zhang, Y.J.//Zhou, Z.M.//Zhang, W.X.//Chen, X.L.//Zhang, X.Y.//Zhou, B.C.//Wang, L.//Zhang, Y.Z. 	Comparative genomics reveals a deep-sea sediment-adapted life style of Pseudoalteromonas sp. SM9913.	ISME J.	2011	5		274-284			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. 		
@D	Qin, Q.L.//Xie, B.B.//Shu, Y.L.//Rong, J.C.//Zhao, D.L.//Zhang, X.Y.//Chen, X.L.//Zhou, B.C.//Zhang, Y.Z. 	Genome Sequence of Proteorhodopsin-Containing Sea Ice Bacterium Glaciecola punicea ACAM 611T.	J. Bacteriol.	2012	194		3267			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. 		
@D	Qin, Q.L.//Zhang, X.Y.//Wang, X.M.//Liu, G.M.//Chen, X.L.//Xie, B.B.//Dang, H.Y.//Zhou, B.C.//Yu, J.//Zhang, Y.Z. 	The complete genome of Zunongwangia profunda SM-A87 reveals its adaptation to the deep-sea environment and ecological role in sedimentary organic nitrogen degradation.	BMC Genomics	2010	11		247			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. 		
@D	Qin, S.//Zhang, H.//Li, F.//Zhu, B.//Zheng, H. 	Draft Genome Sequence of Marine Streptomyces sp. Strain W007, Which Produces Angucyclinone Antibiotics with a Benz[a]anthracene Skeleton.	J. Bacteriol.	2012	194		1628-1629			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. 		
@D	Qin, T.//Cui, Y.//Cen, Z.//Liang, T.//Ren, H.//Yang, X.//Zhao, X.//Liu, Z.//Xu, L.//Li, D.//Song, Y.//Yang, R.//Shao, Z.//Song, Y. 	Draft Genome Sequences of Two Legionella dumoffii Strains, TEX-KL and NY-23.	J. Bacteriol.	2012	194		1251-1252			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. 		
@D	Qin, W.//Yung, L.Y.L. 	Efficient manipulation of nanoparticle-bound DNA by restriction endonuclease.	ACS Abstracts	2005	230		U1077					
@D	Qin, W.H.//Leonhardt, H.//Spada, F. 	Usp7 and Uhrf1 Control Ubiquitination and Stability of the Maintenance DNA Methyltransferase Dnmt1.	J. Cell. Biochem.	2011	112		439-444			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. 		
@D	Qin, W.J.//Yung, L.Y.L. 	Efficient manipulation of nanoparticle-bound DNA via restriction endonuclease.	Biomacromolecules	2006	7		3047-3051			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. 		
@D	Qin, X.//Evans, J.D.//Aronstein, K.A.//Murray, K.D.//Weinstock, G.M. 	Genome sequences of the honey bee pathogens Paenibacillus larvae and Ascosphaera apis.	Insect Mol. Biol.	2006	15		715-718			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. 		
@D	Qin, Y.//Hasman, H.//Aarestrup, F.M.//Alwathnani, H.A.//Rensing, C. 	Genome Sequences of Three Highly Copper-Resistant Salmonella enterica subsp. I Serovar Typhimurium Strains Isolated from Pigs in Denmark.	Genome Announcements	2014	2		e01334-14			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. 		
@D	Qin, Y.//Wang, D.//Brandt, K.K.//Rensing, C. 	Two draft genome sequences of Pseudomonas jessenii strains isolated from a copper contaminated site in Denmark.	Standards in Genomic Sciences	2016	11		86			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. 		
@D	Qin, Z.//Deng, Z.//Zhou, Q.//Chen, H. 	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.	I Chuan Hsueh Pao	1993	20		180-184			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. 		
@D	Qin, Z.//Peng, K.//Zhou, X.//Lliang, R.//Zhou, Q.//Chen, H.//Hopwood, D.A.//Kieser, T.//Deng, Z. 	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.	J. Bacteriol.	1994	176		2090-2095			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. 		
@D	Qiu, C.//Sawada, K.//Zhang, X.//Cheng, X. 	The PWWP domain of mammalian DNA methyltransferase Dnmt3b defines a new family of DNA-binding folds.	Nat. Struct. Biol.	2002	9		217-224			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. 		
@D	Qiu, D.//Eisinger, V.M.//Head, N.E.//Pier, G.B.//Yu, H.D. 	ClpXP proteases positively regulate alginate overexpression and mucoid conversion in Pseudomonas aeruginosa.	Microbiology	2008	154		2119-2130			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. 		
@D	Qiu, D.//Wei, H.//Tu, Q.//Yang, Y.//Xie, M.//Chen, J.//Pinkerton, M.H.//Liang, Y.//He, Z.//Zhou, J. 	Combined Genomics and Experimental Analyses of Respiratory Characteristics of Shewanella putrefaciens W3-18-1.	Appl. Environ. Microbiol.	2013	79		5250-5257			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. 		
@D	Qiu, J.//Ren, J. 	Database management system for recognition sequences and sequences assembly of restriction endonuclease and methylase.	Zhongguo Yaoke Daxue Xuebao	1989	20		185-187			None 		
@D	Qiu, T.//Zuo, Z.//Gao, J.//Gao, M.//Han, M.//Sun, L.//Zhang, L.//Wang, X. 	Diaphorobacter polyhydroxybutyrativorans sp. nov., a novel poly(3-hydroxybutyrate-co-3-hydroxyvalerate)-degrading bacterium isolated from biofilms.	Int. J. Syst. Evol. Microbiol.	2015	65		2913-2918			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)). 		
@D	Qiu, X.//Han, R.//Yan, X.//Liu, M.//Cao, L.//Yoshiga, T.//Kondo, E. 	Identification and Characterization of a Novel Gene Involved in the trans-Specific Nematicidal Activity of Photorhabdus luminescens LN2.	Appl. Environ. Microbiol.	2009	75		4221-4223			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. 		
@D	Qiu, X.//Zhan, Z.B.//Yan, X.//Han, R. 	Draft Genome Sequence and Annotation of the Entomopathogenic Bacterium Photorhabdus luminescens LN2, Which Shows Nematicidal Activity against  Heterorhabditis bacteriophora H06 Nematodes.	Genome Announcements	2014	2		e01268-14			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. 		
@D	Qiu, Y.L.//Tourlousse, D.M.//Matsuura, N.//Ohashi, A.//Sekiguchi, Y. 	Draft Genome Sequence of Terrimicrobium sacchariphilum NM-5T, a Facultative Anaerobic Soil Bacterium of the Class Spartobacteria.	Genome Announcements	2017	5		e00666-17			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. 		
@D	Qiu, Y.L.//Tourlousse, D.M.//Matsuura, N.//Ohashi, A.//Sekiguchi, Y. 	Draft Genome Sequence of Paludibacter jiangxiensis NM7T, a Propionate-Producing Fermentative Bacterium.	Genome Announcements	2017	5		e00667-17			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. 		
@D	Qu, G.//Kaushal, P.S.//Wang, J.//Shigematsu, H.//Piazza, C.L.//Agrawal, R.K.//Belfort, M.//Wang, H.W. 	Structure of a group II intron in complex with its reverse transcriptase.	Nat. Struct. Mol. Biol.	2016	23		549-557			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. 		
@D	Qu, J.//Miao, L.L.//Liu, Y.//Liu, Z.P. 	Complete Genome Sequence of Rhodococcus sp. Strain IcdP1 Shows Diverse Catabolic  Potential.	Genome Announcements	2015	3		e00711-15			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. 		
@D	Qu, Y.//Liu, Z.//Shen, W.//Li, S.//Tang, H.//Xu, P. 	Genome Sequence of an Indigoid-Producing Strain, Pseudomonas sp. PI1.	Genome Announcements	2015	3		e00622-15			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. 		
@D	Qu, Y.//Zhang, X.//Yu, H.//Tang, H.//Shen, E.//Zhou, H.//Ma, Q.//Cao, X.//Zhou, J.//Xu, P. 	Genome Sequence of Sphingomonas xenophaga QYY, an Anthraquinone-Degrading Strain.	Genome Announcements	2013	1		e00031-12			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. 		
@D	Quada, J.C.//Izbicka, E.//Rashidi, H.H. 	Dual flipping and novel motifs of DNA methyltransferase.	Proc. Amer. Assoc. Cancer Res.	2000	41		79			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. 		
@D	Quandt, E.M.//Summers, R.M.//Subramanian, M.V.//Barrick, J.E. 	Draft Genome Sequence of the Bacterium Pseudomonas putida CBB5, Which Can Utilize Caffeine as a Sole Carbon and Nitrogen Source.	Genome Announcements	2015	3		e00640-15			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. 		
@D	Quatrini, R.//Escudero, L.V.//Moya-Beltran, A.//Galleguillos, P.A.//Issotta, F.//Acosta, M.//Cardenas, J.P.//Nunez, H.//Salinas, K.//Holmes, D.S.//Demergasso, C. 	Draft genome sequence of Acidithiobacillus thiooxidans CLST isolated from the acidic hypersaline Gorbea salt flat in northern Chile.	Standards in Genomic Sciences	2017	12		84			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. 		
@D	Que, Q.//Zhang, Y.//Nelson, M.//Ropp, S.//Burbank, D.E.//Van Etten, J.L. 	Chlorella virus SC-1A encodes at least five functional and one nonfunctional DNA methyltransferases.	Gene	1997	190		237-244			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. 		
@D	Quesada, J.M.//Aguilar, I.//de la Torre, J.//Wittich, R.M.//van Dillewijn, P. 	Draft Genome Sequences of Isolates from Sediments of the River Elbe That Are Highly Tolerant to Diclofenac.	Microbiol. Resour. Announc.	2018	7		e00849-18			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. 		
@D	Quick, J.//Constantinidou, C.//Pallen, M.J.//Oppenheim, B.//Loman, N.J. 	Draft Genome Sequence of Elizabethkingia meningoseptica Isolated from a Traumatic Wound.	Genome Announcements	2014	2		e00355-14			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. 		
@D	Quinones, B.//Yambao, J.C.//Lee, B.G. 	Draft Genome Sequences of Escherichia coli O113:H21 Strains Recovered from a Major Produce Production Region in California.	Genome Announcements	2017	5		e01203-17			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. 		
@D	Quint, A.//Cedar, H. 	In vitro methylation of DNA with HpaII methylase.	Nucleic Acids Res.	1981	9		633-646			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. 		
@D	Quirk, S.M.//Bell-Pedersen, D.//Belfort, M. 	Intron mobility in the T-even phages:  high frequency inheritance of group I introns promoted by intron open reading frames.	Cell	1989	56		455-465			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. 		
@D	Quiroz-Castaneda, R.E.//Martinez-Ocampo, F.//Dantan-Gonzalez, E. 	Draft Genome Sequence of Mycoplasma wenyonii, a Second Hemotropic Mycoplasma Species Identified in Mexican Bovine Cattle.	Microbiol. Resour. Announc.	2018	7		e00875-18			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. 		
@D	Qureshi, A.//Itankar, Y.//Ojha, R.//Mandal, M.//Khardenavis, A.//Kapley, A.//Purohit, H.J. 	Genome Sequence of Lactobacillus plantarum EGD-AQ4, Isolated from Fermented Product of Northeast India.	Genome Announcements	2014	2		e01122-13			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. 		
@D	Ra, S.R.//Ri, D.C. 	Isolation-purification of a new restriction endonuclease, CglI and its optimum reaction condition.	Choson Minjujuui Inmin Konghwaguk Kwahagwon Tongbo	2000	0		36-38			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. 		
@D	Raaijmakers, H.//Toro, I.//Birkenbihl, R.//Kemper, B.//Suck, D. 	Conformational flexibility in T4 endonuclease VII revealed by crystallography: implications for substrate binding and cleavage.	J. Mol. Biol.	2001	308		311-323			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. 		
@D	Rabinkova, E.V.//Torosyan, M.V.//Fradkin, G.E. 	Restriction alleviation of phage lambda in Escherichia coli K-12 cells after gamma-irradiation.	Radiobiologiia	1987	27		563-564			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). 		
@D	Rabsch, W.//Helm, R.A.//Eisenstark, A. 	Diversity of phage types among archived cultures of the demerec collection of Salmonella enterica serovar Typhimurium strains.	Appl. Environ. Microbiol.	2004	70		664-669			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. 		
@D	Rabus, R.//Kube, M.//Heider, J.//Beck, A.//Heitmann, K.//Widdel, F.//Reinhardt, R. 	The genome sequence of an anaerobic aromatic-degrading denitrifying bacterium, strain EbN1.	Arch. Microbiol.	2005	183		27-36			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/. 		
@D	Rabus, R.//Ruepp, A.//Frickey, T.//Rattei, T.//Fartmann, B.//Stark, M.//Bauer, M.//Zibat, A.//Lombardot, T.//Becker, I.//Amann, J.//Gellner, K.//Teeling, H.//Leuschner, W.D.//Glockner, F.O.//Lupas, A.N.//Amann, R.//Klenk, H.P. 	The genome of Desulfotalea psychrophila, a sulfate-reducing bacterium from permanently cold Arctic sediments.	Environ. Microbiol.	2004	6		887-902			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. 		
@D	Rachinger, M.//Volland, S.//Meinhardt, F.//Daniel, R.//Liesegang, H. 	First Insights into the Completely Annotated Genome Sequence of Bacillus licheniformis Strain 9945A.	Genome Announcements	2013	1		e00525-13			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. 		
@D	Rachkevych, N.//Sybirna, K.//Boyko, S.//Boretsky, Y.//Sibirny, A. 	Improving the efficiency of plasmid transformation in Shewanella oneidensis MR-1 by removing ClaI restriction site.	J. Microbiol. Methods	2014	99		35-37			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. 		
@D	Radford, D.R.//Leon-Velarde, C.G.//Chen, S.//Hamidi, O.A.M.//Balamurugan, S. 	Draft Genome Sequences of Two Novel Salmonella enterica subsp. enterica Strains Isolated from Low-Moisture Foods with Applications in Food Safety Research.	Genome Announcements	2018	6		e00183-18			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. 		
@D	Radlinska, M.//Bujnicki, J.M. 	Cloning of enterohemorrhagic Escherichia coli Phage VT-2 Dam methyltransferase.	Acta Microbiol. Pol.	2001	50		161-167			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. 		
@D	Radlinska, M.//Bujnicki, J.M. 	Site-directed mutagenesis defines the catalytic aspartate in the active site of the atypical DNA: m4C methyltransferase M.NgoMXV.	Acta Microbiol. Pol.	2001	50		97-105			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. 		
@D	Radlinska, M.//Bujnicki, J.M.//Piekarowicz, A. 	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.	Proteins	1999	37		717-728			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. 		
@D	Radlinska, M.//Kondrzycka-Dada, A.//Piekarowicz, A.//Bujnicki, J.M. 	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.	Proteins	2005	58		263-270			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. 		
@D	Radlinska, M.//Piekarowicz, A. 	Cloning and characterization of the gene encoding a new DNA methyltransferase from Neisseria gonorrhoeae.	Biol. Chem.	1998	379		1391-1395			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. 		
@D	Radlinska, M.//Piekarowicz, A.//Galimand, M.//Bujnicki, J.M. 	Cloning and preliminary characterization of a GATC-specific beta(2)-class DNA:m(6)A methyltransferase encoded by transposon Tn1549  from Enterococcus spp.	Pol. J. Microbiol.	2005	54		249-252			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. 		
@D	Radlinska, M.//Skowronek, K. 	Novel procedure for the detection of 5-methylcytosine.	Acta Microbiol. Pol.	1998	47		327-334			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. 		
@D	Radnedge, L.//Pinney, R.J. 	Ultraviolet light induction of lambda from dcm host strains alleviates EcoRII restriction of phage.	FEMS Microbiol. Lett.	1991	121-125		121-126			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. 		
@D	Raftis, E.J.//Forde, B.M.//Claesson, M.J.//O'Toole, P.W. 	Unusual genome complexity in Lactobacillus salivarius JCM1046.	BMC Genomics	2014	15		771			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. 		
@D	Raghavendra, N.K.//Bheemanaik, S.//Rao, D.N. 	Mechanistic insights into type III restriction enzymes.	Front. Biosci.	2012	17		1094-1107			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. 		
@D	Raghavendra, N.K.//Rao, D.N. 	Exogenous AdoMet and its analogue sinefungin differentially influence DNA cleavage by R.EcoP15I-Usefulness in SAGE.	Biochem. Biophys. Res. Commun.	2005	334		803-811			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. 		
@D	Raghavendra, N.K.//Rao, D.N. 	Functional cooperation between exonucleases and endonucleases - basis for the evolution of restriction enzymes.	Nucleic Acids Res.	2003	31		1888-1896			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. 		
@D	Raghavendra, N.K.//Rao, D.N. 	Unidirectional translocation from recognition site and a necessary interaction with DNA end for cleavage by Type III restriction enzyme.	Nucleic Acids Res.	2004	32		5703-5711			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. 		
@D	Raghupathi, P.K.//Herschend, J.//Roder, H.L.//Sorensen, S.J.//Burmolle, M. 	Genome Sequence of Psychrobacter cibarius Strain W1.	Genome Announcements	2016	4		e00078-16			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. 		
@D	Raghupathi, P.K.//Herschend, J.//Roder, H.L.//Sorensen, S.J.//Burmolle, M. 	Draft Genome Assembly of Two Pseudoclavibacter helvolus Strains, G8 and W3, Isolated from Slaughterhouse Environments.	Genome Announcements	2016	4		e00077-16			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. 		
@D	Raghupathi, P.K.//Herschend, J.//Roder, H.L.//Sorensen, S.J.//Burmolle, M. 	Genome Sequence of Kocuria varians G6 Isolated from a Slaughterhouse in Denmark.	Genome Announcements	2016	4		e00076-16			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. 		
@D	Rahman, A.//Nahar, N.//Jass, J.//Olsson, B.//Mandal, A. 	Complete Genome Sequence of Lysinibacillus sphaericus B1-CDA, a Bacterium That Accumulates Arsenic.	Genome Announcements	2016	4		e00999-15			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. 		
@D	Rahman, A.//Nahar, N.//Olsson, B.//Mandal, A. 	Complete Genome Sequence of Enterobacter cloacae B2-DHA, a Chromium-Resistant Bacterium.	Genome Announcements	2016	4		e00483-16			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. 		
@D	Rahman, M.//Nguyen, S.V.//McCullor, K.A.//King, C.J.//Jorgensen, J.H.//McShan, W.M. 	Complete Genome Sequence of Streptococcus anginosus J4211, a Clinical Isolate.	Genome Announcements	2015	3		e01440-15			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. 		
@D	Rahman, M.A.//Mullany, P.//Roberts, A.P. 	Draft Genome Sequence of Eggerthia catenaformis Strain MAR1 Isolated from Saliva  of Healthy Humans.	Genome Announcements	2017	5		e00638-17			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. 		
@D	Rai, K. 	Roles of DNA and histone methyltransferases during zebrafish development.	Ph.D. Thesis, Univ. of Utah	2006			1-160			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. 		
@D	Rai, R.//Swanson, E.//Sarkar, I.//Lama, D.//Abebe-Aleke, F.//Simpson, S.//Morris, K.//Thomas, W.K.//Kar, P.//Gtari, M.//Sen, A.//Tisa, L.S. 	Permanent Draft Genome Sequence of the French Bean Symbiont Rhizobium sp. Strain  RSm-3 Isolated from the Eastern Himalayan Region of India.	Genome Announcements	2017	5		e00175-17			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. 		
@D	Raiol, T.//De-Souza, M.T.//Oliveira, J.V.//Silva, H.S.//Orem, J.C.//Cavalcante, D.A.//Almeida, N.F.//Telles, G.P.//Setubal, J.C.//Brigido, M.M.//Torres, F.A.//Stadler, P.S.//Walter, M.E.//Moraes, L.M. 	Draft Genome Sequence of FT9, a Novel Bacillus cereus Strain Isolated from a Brazilian Thermal Spring.	Genome Announcements	2014	2		e01027-14			A Bacillus cereus strain, FT9, isolated from a hot spring in the midwest region of Brazil, had its entire genome sequenced. 		
@D	Raiol, T.//Ribeiro, G.M.//Maranhao, A.Q.//Bocca, A.L.//Silva-Pereira, I.//Junqueira-Kipnis, A.P.//Brigido, M.M.//Kipnis, A. 	Complete Genome Sequence of Mycobacterium massiliense.	J. Bacteriol.	2012	194		5455			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. 		
@D	Raizis, A.M.//Schmitt, F.//Jost, J.-P. 	A bisulfite method of 5-methylcytosine mapping that minimizes template degradation.	Anal. Biochem.	1995	226		161-166			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. 		
@D	Raja, M.C.//Dharmalingam, K. 	Heat shock-induced relaxation of restriction enzyme specificity in Escherichia coli.	J. Genetics	1991	70		91-101			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. 		
@D	Rajagopal, K. 	Draft Genome Sequence of Enterococcus raffinosus Strain CFTRI 2200, Isolated from Infant Fecal Material.	Genome Announcements	2013	1		e00932-13			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. 		
@D	Rajanna, C.//Revazishvili, T.//Rashid, M.H.//Chubinidze, S.//Bakanidze, L.//Tsanava, S.//Imnadze, P.//Bishop-Lilly, K.A.//Sozhamannan, S.//Gibbons, H.S.//Morris, J.G.//Sulakvelidze, A. 	Characterization of pPCP1 Plasmids in Yersinia pestis Strains Isolated from the Former Soviet Union.	Int. J. Microbiol.	2010	2010		760-819			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. 		
@D	Rajeshwari, K.//Uppal, B.//Singh, R.//Malakar, A.K.//Chikara, S.K. 	Draft Genome of Escherichia coli O146 Isolate from Maulana Azad Medical College,  New Delhi, India.	Genome Announcements	2015	3		e01515-14			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. 		
@D	Rajkumari, J.//Singha, L.P.//Pandey, P. 	Draft Genome Sequence of Klebsiella pneumoniae AWD5.	Genome Announcements	2017	5		e01531-16			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. 		
@D	Rajoo, S.//Jeon, W.//Park, K.//Yoo, S.//Yoon, I.//Lee, H.//Ahn, J. 	Complete Genome Sequence of Streptococcus iniae YSFST01-82, Isolated from Olive Flounder in Jeju, South Korea.	Genome Announcements	2015	3		e00319-15			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. 		
@D	Rajski, S.R.//Kumar, S.//Roberts, R.J.//Barton, J.K. 	Protein-modulated DNA electron transfer.	J. Am. Chem. Soc.	1999	121		5615-5616			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. 		
@D	Raleigh, E.//Dila, D.//Sutherland, E.//Kelleher, J.//Moran, L.//Slatko, B.//Briggs, P. 	McrBC, a novel multisubunit GTP-dependent restriction endonuclease.	J. Cell Biochem. Suppl.	1993	17C		152			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. 		
@D	Raleigh, E.A. 	Organization and function of the mcrBC genes of Escherichia coli K-12.	Mol. Microbiol.	1992	6		1079-1086			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. 		
@D	Raleigh, E.A. 	Restriction and modification in vivo by Escherichia coli K12.	Methods Enzymol.	1987	152		130-141			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. 		
@D	Raleigh, E.A.//Benner, J.//Bloom, F.//Braymer, H.D.//DeCruz, E.//Dharmalingam, K.//Heitman, J.//Noyer-Weidner, M.//Piekarowicz, A.//Kretz, P.L.//Short, J.M.//Woodcock, D. 	Nomenclature relating to restriction of modified DNA in Escherichia coli.	J. Bacteriol.	1991	173		2707-2709			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. 		
@A	Raleigh, E.A.//Brooks, J.E. 		Restriction modification systems: where they are and what they do.			De Bruijn, F.J.//Lupski, J.R.//Weinstock, G.M. 		Bacterial Genomes				New York	Chapman & Hall	1998				78-92									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. 		
@D	Raleigh, E.A.//Murray, N.E.//Revel, H.//Blumenthal, R.M.//Westaway, D.//Reith, A.D.//Rigby, P.W.J.//Elhai, J.//Hanahan, D. 	McrA and McrB restriction phenotypes of some E. coli strains and implications for gene cloning.	Nucleic Acids Res.	1988	15		1563-1575			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. 		
@D	Raleigh, E.A.//Sutherland, E.//Dila, D.//Briggs, P.//Kelleher, J.//Coe, L.//Slatko, B.//Moran, L. 	Molecular analysis of McrBC, a GTP-dependent restriction endonuclease from E. coli K-12.	J. Cell Biochem. Suppl.	1992	16B		21			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. 		
@D	Raleigh, E.A.//Trimarchi, R.//Revel, H. 	Genetic and physical mapping of the mcrA (rglA) and mcrB (rglB) loci of Escherichia coli K-12.	Genetics	1989	122		279-296			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. 		
@D	Raleigh, E.A.//Wilson, G. 	Escherichia coli K-12 restricts DNA containing 5-methylcytosine.	Proc. Natl. Acad. Sci. U. S. A.	1986	83		9070-9074			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. 		
@D	Ralph, D.//Que, Q.//Van Etten, J.L.//McClelland, M. 	Leptospira genomes are modified at 5'-GTAC.	J. Bacteriol.	1993	175		3913-3915			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. 		
@D	Ralston, D.J.//Baer, B.S. 	A new property of phage group II Staphylococcus aureus strains:  Host restriction of phage K14.	J. Gen. Microbiol.	1964	36		1-16			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. 		
@D	Ralston, D.J.//Kruger, A.P. 	Phage multiplication on two hosts, isolation and activity of variants of Staphylococcus phage P1.	Proc. Soc. Exp. Biol. Med.	1952	80		217-220			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. 		
@D	Ramaiah, A.//Dasch, G.A. 	Genome Sequence of Coxiella-Like Endosymbiont Strain CLE-RmD, a Bacterial Agent in the Cattle Tick (Rhipicephalus microplus) Deutsch Strain.	Genome Announcements	2018	6		e00003-18			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. 		
@D	Ramakrishna, J.//Mathee, K.//Plaut, A.G.//Wright, A. 	Restriction enzyme systems of Helicobacter pylori.	Gastroenterology	1995	108		A200			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. 		
@D	Ramalingam, R.//Prasad, R.//Shivapriya, R.//Dharmalingam, K. 	Molecular cloning and sequencing of mcrA locus and identification of McrA protein in Escherichia coli.	J. Biosci.	1992	17		217-232			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. 		
@D	Ramalingam, S.//Kandavelou, K.//Rajenderan, R.//Chandrasegaran, S. 	Creating Designed Zinc-Finger Nucleases with Minimal Cytotoxicity.	J. Mol. Biol.	2011	405		630-641			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. 		
@D	Raman, G.//Sakthivel, N.//Park, S. 	Draft Genome Sequence of a Novel Nicotine-Degrading Bacterium, Pseudomonas plecoglossicida TND35.	Genome Announcements	2015	3		e01162-14			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. 		
@D	Ramanathan, S.P.//van Aelst, K.//Sears, A.//Peakman, L.J.//Diffin, F.M.//Szczelkun, M.D.//Seidel, R. 	Type III restriction enzymes communicate in 1D without looping between their target sites.	Proc. Natl. Acad. Sci. U. S. A.	2009	106		1748-1753			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. 		
@D	Ramanujam, R.//Heaster, J.//Huang, C.//Jolly, J.//Koelbl, J.//Lively, C.//Ogutu, E.//Ting, E.//Treml, S.//Aldous, B.//Hatley, R.//Mathias, S.//Franks, F.//Burdick, B. 	Ambient temperature-stable molecular biology reagents.	Biotechniques	1993	14		470-474			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. 		
@D	Ramaraj, T.//Matyi, S.A.//Sundararajan, A.//Lindquist, I.E.//Devitt, N.P.//Schilkey, F.D.//Lamichhane-Khadka, R.//Hoyt, P.R.//Mudge, J.//Gustafson, J.E. 	Draft Genome Sequences of Vancomycin-Susceptible Staphylococcus aureus Related to Heterogeneous Vancomycin-Intermediate S. aureus.	Genome Announcements	2014	2		e01033-14			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. 		
@D	Ramaraj, T.//Sundararajan, A.//Schilkey, F.D.//Delvecchio, V.G.//Donlon, M.//Ziemer, C.//Mudge, J. 	Improved Hybrid Genome Assemblies of Two Strains of Bacteroides xylanisolvens, SD_CC_1b and SD_CC_2a, Obtained Using Illumina and 454 Sequencing Technologies.	Genome Announcements	2014	2		e00237-14			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. 		
@D	Ramasamy, D.//Dubourg, G.//Robert, C.//Caputo, A.//Papazian, L.//Raoult, D.//Fournier, P.E. 	Non contiguous-finished genome sequence and description of Enorma timonensis sp.  nov.	Standards in Genomic Sciences	2014	9		970-986			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. 		
@D	Ramasamy, D.//Kokcha, S.//Lagier, J.C.//Nguyen, T.T.//Raoult, D.//Fournier, P.E. 	Genome sequence and description of Aeromicrobium massiliense sp. nov.	Standards in Genomic Sciences	2012	7		246-257			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. 		
@D	Ramasamy, D.//Lagier, J.C.//Gorlas, A.//Raoult, D.//Fournier, P.E. 	Non contiguous-finished genome sequence and description of Bacillus massiliosenegalensis sp. nov.	Standards in Genomic Sciences	2013	8		264-278			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. 		
@D	Ramasamy, D.//Lagier, J.C.//Nguyen, T.T.//Raoult, D.//Fournier, P.E. 	Non contiguous-finished genome sequence and description of Dielma fastidiosa gen. nov., sp. nov., a new member of the Family Erysipelotrichaceae.	Standards in Genomic Sciences	2013	8		336-351			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. 		
@D	Ramasamy, D.//Lagier, J.C.//Rossi-Tamisier, M.//Pfleiderer, A.//Michelle, C.//Couderc, C.//Raoult, D.//Fournier, P.E. 	Genome sequence and description of Bacteroides timonensis sp. nov.	Standards in Genomic Sciences	2014	9		1181-1197			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. 		
@D	Ramasubban, G.//Lakshmipathy, D.//Vetrivel, U.//Kulandai, L.T.//Madhavan, H.N.//Sridhar, R.//Meenakshi, N. 	Whole-Genome Sequencing of Streptomycin-Resistant Mycobacterium tuberculosis Isolate VRFCWCF MRTB 180 Reveals Novel and Potential Mutations for Resistance.	Genome Announcements	2014	2		e00919-14			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. 		
@D	Ramazzotti, M.//Cimaglia, F.//Gallo, A.//Ranaldi, F.//Surico, G.//Mita, G.//Bleve, G.//Marchi, G. 	Insights on a founder effect: the case of Xylella fastidiosa in the Salento area of Apulia, Italy.	Phytopathol. Mediterr.	2018	0		0			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. 		
@D	Rambach, A. 	Purification and properties of the SstI endonuclease.	Methods Enzymol.	1980	65		170-173			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. 		
@D	Ramchandani, S.//Bhattacharya, S.K.//Cervoni, N.//Szyf, M. 	DNA methylation is a reversible biological signal.	Proc. Natl. Acad. Sci. U. S. A.	1999	96		6107-6112			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. 		
@D	Ramchandani, S.//Bigey, P.//Szyf, M. 	Genomic structure of the human DNA methyltransferase gene.	Biol. Chem.	1998	379		535-540			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. 		
@D	Ramchandani, S.//MacLeod, A.R.//Pinard, M.//von Hofe, E.//Szyf, M. 	Inhibition of tumorigenesis by a cytosine-DNA, methyltransferase, antisense oligodeoxynucleotide.	Proc. Natl. Acad. Sci. U. S. A.	1997	94		684-689			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. 		
@D	Ramchandani, S.//Szyf, M. 	A novel RNA element mediates the cell cycle dependent posttranscriptional regulation of DNA methyltransferase.	Mol. Biol. Cell	1996	7		302a			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. 		
@D	Ramchandani, S.K.//Rouleau, J.//Szyf, M. 	Cloning of the human DNA methyltransferase gene.	Am. J. Hum. Genet.	1994	55		A137			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. 		
@D	Ramesh, R.//Gaitonde, S.//Achari, G.//Asolkar, T.//Singh, N.P.//Carrere, S.//Genin, S.//Peeters, N. 	Genome Sequencing of Ralstonia solanacearum Biovar 3, Phylotype I, Strains Rs-09-161 and Rs-10-244, Isolated from Eggplant and Chili in India.	Genome Announcements	2014	2		e00323-14			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. 		
@D	Ramijan, K.//van Wezel, G.P.//Claessen, D. 	Genome Sequence of the Filamentous Actinomycete Kitasatospora viridifaciens.	Genome Announcements	2017	5		e01560-16			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. 		
@D	Ramirez, M.S.//Adams, M.D.//Bonomo, R.A.//Centron, D.//Tolmasky, M.E. 	Genomic Analysis of Acinetobacter baumannii A118 by Comparison of Optical Maps: Identification of Structures Related to its Susceptibility Phenotype.	Antimicrob. Agents Chemother.	2011	55		1520-1526			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. 		
@D	Ramirez, M.S.//Xie, G.//Johnson, S.//Davenport, K.//van Duin, D.//Perez, F.//Bonomo, R.A.//Chain, P.//Tolmasky, M.E. 	Genome Sequences of Two Carbapenemase-Resistant Klebsiella pneumoniae ST258 Isolates.	Genome Announcements	2014	2		e00558-14			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. 		
@D	Ramirez-Diaz, M.I.//Diaz-Magana, A.//Meza-Carmen, V.//Johnstone, L.//Cervantes, C.//Rensing, C. 	Nucleotide sequence of Pseudomonas aeruginosa conjugative plasmid pUM505 containing virulence and heavy-metal resistance genes.	Plasmid	2011	66		7-18			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. 		
@D	Ramirez-Paredes, J.G.//Larsson, P.//Wehner, S.//Bekaert, M.//Ohrman, C.//Metselaar, M.//Thompson, K.D.//Richards, R.H.//Penman, D.J.//Adams, A. 	Draft Genome Sequence of Francisella noatunensis subsp. orientalis STIR-GUS-F2f7, a Highly Virulent Strain Recovered from Diseased Red Nile Tilapia Farmed in  Europe.	Genome Announcements	2017	5		e01555-16			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. 		
@D	Ramos, R.T. et al. 	Genome Sequence of the Corynebacterium pseudotuberculosis Cp316 Strain, Isolated  from the Abscess of a Californian Horse.	J. Bacteriol.	2012	194		6620-6621			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. 		
@D	Ramos-Garcia, A.A.//Shankar, V.//Saski, C.A.//Hsiang, T.//Freedman, D.L. 	Draft Genome Sequence of the 1,4-Dioxane-Degrading Bacterium Pseudonocardia dioxanivorans BERK-1.	Genome Announcements	2018	6		e00207-18			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. 		
@D	Ramos-Silva, P.//Brito, P.H.//Serrano, M.//Henriques, A.O.//Pereira-Leal, J.B. 	Rethinking the Niche of Upper-Atmosphere Bacteria: Draft Genome Sequences of Bacillus aryabhattai C765 and Bacillus aerophilus C772, Isolated from Rice  Fields.	Genome Announcements	2015	3		e00094-15			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. 		
@D	Ramsahoye, B.H.//Biniszkiewicz, D.//Lyko, F.//Clark, V.//Bird, A.P.//Jaenisch, R. 	Non-CpG methylation is prevalent in embryonic stem cells and may be mediated by DNA methyltransferase 3a.	Proc. Natl. Acad. Sci. U. S. A.	2000	97		5237-5242			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. 		
@D	Ramsahoye, B.H.//Burnett, A.K.//Taylor, C. 	Restriction endonuclease isoschizomers ItaI, BsoFI and Fsp4HI are characterized by differences in their sensitivities to CpG methylation.	Nucleic Acids Res.	1997	25		3196-3198			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. 		
@D	Ramsay, B.D. et al. 	High-Quality Draft Genome Sequence of Desulfovibrio carbinoliphilus FW-101-2B, an Organic Acid-Oxidizing Sulfate-Reducing Bacterium Isolated from  Uranium(VI)-Contaminated Groundwater.	Genome Announcements	2015	3		e00092-15			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. 		
@D	Ramsden, J.J.//Dreier, J. 	Kinetics of the interaction between DNA and the type IC restriction enzyme EcoR124II.	Biochemistry	1996	35		3746-3753			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. 		
@D	Rand, A.C.//Jain, M.//Eizenga, J.M.//Musselman-Brown, A.//Olsen, H.E.//Akeson, M.//Paten, B. 	Mapping DNA methylation with high-throughput nanopore sequencing.	Nat. Methods	2017	14		411-413			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. 		
@D	Rand, K.N.//Young, G.P.//Ho, T.//Molloy, P.L. 	Sensitive and selective amplification of methylated DNA sequences using helper-dependent chain reaction in combination with a methylation-dependent restriction enzymes.	Nucleic Acids Res.	2013	41		e15			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. 		
@D	Rangel, W.M.//Thijs, S.//Moreira, F.M.//Weyens, N.//Vangronsveld, J.//Van Hamme, J.D.//Bottos, E.M.//Rineau, F. 	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.	Genome Announcements	2016	4		e00050-16			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. 		
@D	Ranjan, V.K.//Saha, T.//Mukherjee, S.//Chakraborty, R. 	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.	Genome Announcements	2018	6		e01443-17			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. 		
@D	Ransom-Jones, E.//McDonald, J.E. 	Draft Genome Sequence of Clostridium sp. Strain W14A Isolated from a Cellulose-Degrading Biofilm in a Landfill Leachate Microcosm.	Genome Announcements	2016	4		e00985-16			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. 		
@D	Ranson, H.J.//LaPorte, J.//Spinard, E.//Chistoserdov, A.Y.//Gomez-Chiarri, M.//Nelson, D.R.//Rowley, D.C. 	Draft Genome Sequence of the Putative Marine Pathogen Aquimarina sp. Strain I32.4.	Genome Announcements	2018	6		e00313-18			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. 		
@D	Ranson, H.J.//LaPorte, J.//Spinard, E.//Gomez-Chiarri, M.//Nelson, D.R.//Rowley, D.C. 	Draft Genome Sequence of Loktanella maritima Strain YPC211, a Commensal Bacterium of the American Lobster (Homarus americanus).	Genome Announcements	2018	6		e00314-18			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. 		
@D	Rao, B.S.//Buckler-White, A. 	Direct visualization of site-specific and strand-specific DNA methylation patterns in automated DNA sequencing data.	Nucleic Acids Res.	1998	26		2505-2507			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. 		
@D	Rao, C.//Guyard, C.//Pelaz, C.//Wasserscheid, J.//Bondy-Denomy, J.//Dewar, K.//Ensminger, A.W. 	Active and Adaptive Legionella CRISPR-Cas reveals a recurrent challenge to the pathogen.	Cell. Microbiol.	2016	18		1319-1338			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. 		
@D	Rao, D.N.//Dryden, D.T.//Bheemanaik, S. 	Type III restriction-modification enzymes: a historical perspective.	Nucleic Acids Res.	2014	42		45-55			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. 		
@D	Rao, D.N.//Eberle, H.//Bickle, T.A. 	Characterization of mutations of the bacteriophage P1 mod gene encoding the recognition subunit of the EcoPI restriction and modification system.	J. Bacteriol.	1989	171		2347-2352			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. 		
@D	Rao, D.N.//Page, M.G.P.//Bickle, T.A. 	Cloning, over-expression and the catalytic properties of the EcoP15 modification methylase from Escherichia coli.	J. Mol. Biol.	1989	209		599-606			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. 		
@D	Rao, D.N.//Saha, S.//Krishnamurthy, V. 	ATP-dependent restriction enzymes.	Prog. Nucleic Acid Res. Mol. Biol.	2000	64		1-63			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. 		
@D	Rao, M.//Suvarna, K.//Srinivasan, M.C.//Vasanti, D. 	Development of Chainia as a host for xlanase gene cloning: evidence for occurrence of a restriction-modification system.	Biotechnol. Lett.	1996	18		327-332			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-). 		
@D	Rao, Q.//Wang, S.//Su, Y.L.//Bing, X.L.//Liu, S.S.//Wang, X.W. 	Draft Genome Sequence of 'Candidatus Hamiltonella defensa,' an Endosymbiont of the Whitefly Bemisia tabaci.	J. Bacteriol.	2012	194		3558			'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. 		
@D	Rao, Q.//Wang, S.//Zhu, D.T.//Wang, X.W.//Liu, S.S. 	Draft Genome Sequence of Rickettsia sp. Strain MEAM1, Isolated from the Whitefly  Bemisia tabaci.	J. Bacteriol.	2012	194		4741-4742			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. 		
@D	Rao, S.B.//Gupta, V.K.//Kumar, M.//Hegde, N.R.//Splitter, G.A.//Reddanna, P.//Radhakrishnan, G.K. 	Draft Genome Sequence of the Field Isolate Brucella melitensis Strain Bm IND1 from India.	Genome Announcements	2014	2		e00497-14			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. 		
@D	Rapa, R.A.//Islam, A.//Monahan, L.G.//Mutreja, A.//Thomson, N.//Charles, I.G.//Stokes, H.W.//Labbate, M. 	A genomic island integrated into recA of Vibrio cholerae contains a divergent recA and provides multi-pathway protection from DNA damage.	Environ. Microbiol.	2015	17		1090-1102			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. 		
@D	Raphael, B.H.//Kozak-Muiznieks, N.A.//Morrison, S.S.//Mercante, J.W.//Winchell, J.M. 	Complete Genome Sequences of Legionella pneumophila subsp. fraseri Strains Detroit-1 and Dallas 1E.	Genome Announcements	2017	5		e01525-16			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. 		
@D	Rappert, S.//Song, L.//Sabra, W.//Wang, W.//Zeng, A.P. 	Draft Genome Sequence of Type Strain Clostridium pasteurianum DSM 525 (ATCC 6013), a Promising Producer of Chemicals and Fuels.	Genome Announcements	2013	1		e00232-12			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. 		
@D	Raschke, E. 	Comprehensive restriction enzyme lists to update to any DNA sequence computer program.	Genet. Anal. Tech. Appl.	1993	10		49-60			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. 		
@D	Rashid, S.R.//Clokie, M.R.//Millard, A.D. 	Draft Genome Sequences of Three Novel Clostridium Isolates from Northern Iraq.	Genome Announcements	2016	4		e00033-16			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. 		
@D	Rashmi, B.S.//Gayathri, D. 	Draft Genome Sequence of the Gluten-Hydrolyzing Bacterium Bacillus subtilis GS 188, Isolated from Wheat Sourdough.	Genome Announcements	2017	5		e00952-17			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. 		
@D	Rasko, D.A. et al. 	Origins of the E. coli strain causing an outbreak of hemolytic-uremic syndrome in Germany.	N. Engl. J. Med.	2011	365		709-717			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. 		
@D	Rasko, D.A.//Ravel, J.//Okstad, O.A.//Helgason, E.//Cer, R.Z.//Jiang, L.//Shores, K.A.//Fouts, D.E.//Tourasse, N.J.//Angiuoli, S.V.//Kolonay, J.//Nelson, W.C.//Kolsto, A.-B.//Fraser, C.M.//Read, T.D. 	The genome sequence of Bacillus cereus ATCC 10987 reveals metabolic adaptations and a large plasmid related to Bacillus anthracis pXO1.	Nucleic Acids Res.	2004	32		977-988			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. 		
@D	Rasko, T.//Der, A.//Klement, E.//Slaska-Kiss, K.//Posfai, E.//Medzihradszky, K.F.//Marshak, D.R.//Roberts, R.J.//Kiss, A. 	BspRI restriction endonuclease: cloning, expression in Escherichia coli and sequential cleavage mechanism.	Nucleic Acids Res.	2010	38		7155-7166			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. 		
@D	Rasko, T.//Finta, C.//Kiss, A. 	DNA bending induced by DNA (cytosine-5) methyltransferases.	Nucleic Acids Res.	2000	28		3083-3091			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. 		
@D	Rasmussen, L.H.//Dargis, R.//Christensen, J.J.//Skovgaard, O.//Nielsen, X.C. 	Draft Genome Sequence of Type Strain Streptococcus gordonii ATCC 10558.	Genome Announcements	2016	4		e01745-15			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. 		
@D	Rasmussen, L.J.//Lobner-Olesen, A.//Marinus, M.G. 	Growth-rate-dependent transcription initiation from the dam P2 promoter.	Gene	1995	157		213-215			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. 		
@D	Rasmussen, L.J.//Marinus, M.G.//Lcbner-Olesen, A. 	Regulation of expression of the dam methyltransferase gene (dam) from Escherichi coli.	J. Cell Biochem. Suppl.	1993	17E		303			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. 		
@D	Rasmussen, L.J.//Marinus, M.G.//Lobner-Olesen, A. 	Novel growth rate control of dam gene expression in Escherichia coli.	Mol. Microbiol.	1994	12		631-638			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. 		
@A	Rasmussen, L.J.//Samson, L.//Marinus, M.G. 		Dam-directed DNA mismatch repair.			Nickloff, J.A. and Hoekstra//M.F. 		DNA Damage and Repair				Totowa, NJ	Humana Press, Inc.	1998		1		205-228									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. 		
@D	Rastorguev, S.M.//Zavilgelskii, G.B.//Suzuki, K.//Sakka, K. 	Alleviation of type I restriction in Escherichia coli K12 in the presence of the arsR gene from pKW301 of Acidiphilium multivorum AIU 301.	Mol. Biol. (Mosk)	2001	35		79-82			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. 		
@D	Rastorguev, S.M.//Zavilgelsky, G.B. 	Role of "antirestriction" motif in functional activity of antirestriction protein ArdA pKM101 (IncN).	Genetika	2003	39		286-292			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. 		
@D	Rastorguev, S.M.//Zavilgelsky, G.B.//Tchurikov, N.A. 	IncI1 plasmid R64 encodes the ArsR protein that alleviates type I restriction.	FEBS Lett.	1998	426		21-23			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. 		
@D	Rathert, P.//Rasko, T.//Roth, M.//Slaska-Kiss, K.//Pingoud, A.//Kiss, A.//Jeltsch, A. 	Reversible inactivation of the CG specific Sssl DNA (cytosine-C5)-methyltransferase with a photocleavable protecting group.	Chembiochem	2007	8		202-207			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. 		
@D	Raven, N.D.H.//Kelly, C.D.//Carter, N.D.//Eastlake, P.//Brown, C.//Williams, R.A.D. 	A new restriction endonuclease, TspEI, from the genus Thermus that generates cohesive termini compatible with those of EcoRI.	Gene	1993	131		83-86			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. 		
@D	Raven, N.D.H.//Williams, R.A.D.//Smith, K.E.//Kelly, C.D.//Carter, N.D. 	Tsp45I, a new thermostable site-specific endonuclease that cleaves the recognition sequence 5'-GTSAC-3'.	Nucleic Acids Res.	1993	21		4397			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'. 		
@D	Ravetch, J.V.//Horiuchi, K.//Zinder, N.D. 	Nucleotide sequence of the recognition site for the restriction-modification enzyme of Escherichia coli B.	Proc. Natl. Acad. Sci. U. S. A.	1978	75		2266-2270			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. 		
@D	Ravi, R.S.//Sozhamannan, S.//Dharmalingam, K. 	Transposon mutagenesis and genetic mapping of the rglA and rglB loci of Escherichia coli.	Mol. Gen. Genet.	1985	198		390-392			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. 		
@D	Ravin, N.V.//Mardanov, A.V.//Beletsky, A.V.//Kublanov, I.V.//Kolganova, T.V.//Lebedinsky, A.V.//Chernyh, N.A.//Bonch-Osmolovskaya, E.A.//Skryabin, K.G. 	Complete genome sequence of the anaerobic, protein-degrading hyperthermophilic crenarchaeon Desulfurococcus kamchatkensis.	J. Bacteriol.	2009	191		2371-2379			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. 		
@D	Ravin, V.//Raisanen, L.//Alatossava, T. 	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.	J. Bacteriol.	2002	184		2455-2459			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. 		
@D	Ravin, V.//Ravin, N.//Casjens, S.//Ford, M.E.//Hatfull, G.F.//Herdrix, R.W. 	Genomic sequence and analysis of the atypical temperate bacteriophage N15.	J. Mol. Biol.	2000	299		53-73			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. 		
@D	Ravindran, A.//Jalan, N.//Yuan, J.S.//Wang, N.//Gross, D.C. 	Comparative genomics of Pseudomonas syringae pv. syringae strains B301D and HS191 and insights into intrapathovar traits associated with plant pathogenesis.	Microbiologyopen	2015	4		553-573			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. 		
@D	Rawal, C.M.//Raval, V.H.//Bhimani, H.D.//Bhensdadia, D.V.//Kothari, C.R.//Patel, A.B.//Bhatt, V.D.//Parmar, N.R.//Sajnani, M.R.//Koringa, P.G.//Joshi, C.G.//Kothari, R.K.//Singh, S.P. 	Whole-Genome Shotgun Sequencing of the Extremophile Alkalibacillus haloalkaliphilus C-5, of Indian Origin.	J. Bacteriol.	2012	194		4775			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. 		
@D	Rawat, S.R.//Mannisto, M.K.//Starovoytov, V.//Goodwin, L.//Nolan, M.//Hauser, L.//Land, M.//Davenport, K.W.//Woyke, T.//Haggblom, M.M. 	Complete genome sequence of Terriglobus saanensis type strain SP1PR4(T), an Acidobacteria from tundra soil.	Standards in Genomic Sciences	2012	7		59-69			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. 		
@D	Rawat, S.R.//Mannisto, M.K.//Starovoytov, V.//Goodwin, L.//Nolan, M.//Hauser, L.//Land, M.//Davenport, K.W.//Woyke, T.//Haggblom, M.M. 	Complete genome sequence of Granulicella tundricola type strain MP5ACTX9(T), an Acidobacteria from tundra soil.	Standards in Genomic Sciences	2014	9		449-461			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. 		
@D	Rawat, S.R.//Mannisto, M.K.//Starovoytov, V.//Goodwin, L.//Nolan, M.//Hauser, L.J.//Land, M.//Davenport, K.W.//Woyke, T.//Haggblom, M.M. 	Complete genome sequence of Granulicella mallensis type strain MP5ACTX8(T), an acidobacterium from tundra soil.	Standards in Genomic Sciences	2013	9		71-82			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. 		
@D	Ray, J.//Waters, R.J.//Skerker, J.M.//Kuehl, J.V.//Price, M.N.//Huang, J.//Chakraborty, R.//Arkin, A.P.//Deutschbauer, A. 	Complete Genome Sequence of Cupriavidus basilensis 4G11, Isolated from the Oak Ridge Field Research Center Site.	Genome Announcements	2015	3		e00322-15			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%. 		
@D	Raychaudhuri, S.//Saha, A.//Ghoshal, T.//Thakur, A.R. 	Draft Genome Sequence of Ammonia-Producing Aeromonas sp. MDS8 Strain MCC2167 from Sludge of a Dairy Effluent Treatment Plant.	Genome Announcements	2013	1		e00710-13			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. 		
@D	Raygoza-Garay, J.A.//Hughes, G.L.//Koundal, V.//Rasgon, J.L.//Mwangi, M.M. 	Genome Sequence of Elizabethkingia anophelis Strain EaAs1, Isolated from the Asian Malaria Mosquito Anopheles stephensi.	Genome Announcements	2016	4		e00084-16			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. 		
@D	Rayyan, A.A.//Meyer, T.E.//Kyndt, J.A. 	Draft Genome Sequence and Brief History of Rhodovulum sp. Strain BSW8.	Microbiol. Resour. Announc.	2018	7		e00983-18			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. 		
@A	Razin, A. 		Methylated bases in the single-stranded DNA phages.			Denhardt, D.T.//Dressler, D.//D.S. Ray. 		The Single-Stranded DNA Phages				New York	Cold Spring Harbor Laboratory Press	1978		0		165-175									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. 		
@A	Razin, A. 		DNA methylases.			Setlow, J.K. 		Genet. Eng. (N Y)				New York	Plenum Press	1989		11		1-11									A review. 		
@D	Razin, A.//Friedman, J. 	DNA methylation and its possible biological roles.	Prog. Nucleic Acid Res. Mol. Biol.	1981	25		33-52			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. 		
@D	Razin, A.//Goren, D.//Friedman, J. 	Studies on the biological role of DNA methylation:  inhibition of methylation and maturation of the bacteriophage PhiX174 by nicotinamide.	Nucleic Acids Res.	1975	2		1967-1974			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. 		
@D	Razin, A.//Razin, S. 	Methylated bases in mycoplasmal DNA.	Nucleic Acids Res.	1980	8		1383-1390			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. 		
@D	Razin, A.//Riggs, D. 	DNA methylation and gene function.	Science	1980	210		604-610			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. 		
@D	Razin, A.//Sedat, J. 	Analysis of 5-methylcytosine in DNA.	Anal. Biochem.	1977	77		370-377			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. 		
@D	Razin, A.//Urieli, S.//Pollack, Y.//Gruenbaum, Y.//Glaser, G. 	Studies on the biological role of DNA methylation; IV.  Mode of methylation of DNA in E. coli cells.	Nucleic Acids Res.	1980	8		1783-1792			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. 		
@D	Read, T.D. et al. 	Genome sequences of Chlamydia trachomatis MoPn and Chlamydia pneumoniae AR39.	Nucleic Acids Res.	2000	28		1397-1406			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. 		
@D	Read, T.D. et al. 	Genome sequence of Chlamydophila caviae (Chlamydia psittaci GPIC): examining the role of niche-specific genes in the evolution of the   Chlamydiaceae.	Nucleic Acids Res.	2003	31		2134-2147			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. 		
@D	Read, T.D. et al. 	The genome sequence of Bacillus anthracis Ames and comparison to closely related bacteria.	Nature	2003	423		81-86			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. 		
@D	Read, T.D.//Salzberg, S.L.//Pop, M.//Shumway, M.//Umayam, L.//Jiang, L.//Holtzapple, E.//Busch, J.D.//Smith, K.L.//Schupp, J.M.//Solomon, D.//Keim, P.//Fraser, C.M. 	Comparative genome sequencing for discovery of novel polymorphisms in Bacillus anthracis.	Science	2002	296		2028-2033			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. 		
@D	Read, T.D.//Thomas, A.T.//Wilkins, B.M. 	Evasion of type I and type II DNA restriction systems by IncI1 plasmid Collb-P9 during transfer by bacterial conjugation.	Mol. Microbiol.	1992	6		1933-1941			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. 		
@D	Reale, A.//Lindsay, H.//Saluz, H.P.//Pradhan, S.//Adams, R.L.P.//Jost, J.-P.//Strom, R. 	DNA binding and methyl transfer catalysed by mouse DNA methyltransferase.	Biochem. J.	1995	312		855-861			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. 		
@D	Reaston, J.//Duyvesteyn, M.G.C.//de Waard, A. 	Nostoc PCC7524, a cyanobacterium which contains five sequence-specific deoxyribonucleases.	Gene	1982	20		103-110			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. 		
@D	Rebentish, B.A.//Bolotin, A.P.//Grachova, I.M.//Ren, L.S.//Uyan, J.M. 	A new site-specific endodeoxyribonuclease FmuI from the strain Flavobacterium multivorum.	Biotekhnologiya	1994	3		15-16			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. 		
@D	Rech, G.//Vilaplana, C.//Velasco, J.//Pluvinet, R.//Santin, S.//Prat, C.//Julian, E.//Alcaide, F.//Comas, I.//Sumoy, L.//Cardona, P.J. 	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.	Genome Announcements	2015	3		e01485-14			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. 		
@D	Rechkunova, N.I.//Lokhov, S.G.//Gorbunov, Y.A.//Zinovev, V.V.//Buryanov, Y.I.//Malygin, E.G. 	Stability of the secondary structure of the oligonucleotide substrates.  The effect of Ecodam DNA-methylase.	Biopol. Kletka	1989	5		43-49			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. 		
@D	Rechkunova, N.I.//Ovetchkina, L.G.//Jashina, L.N.//Vtorushina, I.A.//Gorbunov, J.A.//Zinoviev, V.V.//Malygin, E.G. 	Effects of oligonucleotide structure on the kinetic values of the interaction with BamHI endonuclease.	Mol. Biol. (Mosk)	1988	22		217-223			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. 		
@D	Rechkunova, N.I.//Zinovev, V.V.//Malygin, E.G.//Gorbunov, Y.A.//Popov, S.G.//Nesterenko, V.F.//Buryanov, Y.I. 	Dimerization of Ecodam-methylase induced by the oligonucleotide substrate.	Biopol. Kletka	1987	3		152-154			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. 		
@D	Reckmann, B.//Krauss, G. 	The cleavage of single-stranded DNA by the isoschizomeric restriction endonuclease HhaI and CfoI.	Biochim. Biophys. Acta	1987	908		90-96			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. 		
@D	Recktenwald, J.//Schmidt, H. 	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.	Infect. Immun.	2002	70		1896-1908			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. 		
@D	Redaschi, N.//Bickle, T.A. 	Posttranscriptional regulation of EcoP1I and EcoP15I restriction activity.	J. Mol. Biol.	1996	257		790-803			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. 		
@A	Redaschi, N.//Bickle, T.A. 		DNA restriction and modification systems.			F.C. Neidhardt 		Escherichia coli and Salmonella: Cellular and Molecular Biology				Washington, DC	ASM Press	1996		1		773-781									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. 		
@D	Reddy, G.S.//Ara, S.//Singh, A.//Kumar, P.A.//Shivaji, S. 	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.	Genome Announcements	2013	1		e00918-13			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. 		
@D	Reddy, G.S.//Sreenivas, A.//Shivaji, S. 	Draft Genome Sequence of Cryobacterium roopkundensis Strain RuGl7, Isolated from  a Soil Sample in the Vicinity of Roopkund Lake, Himalayas, India.	Genome Announcements	2014	2		e01206-14			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. 		
@D	Reddy, Y.V.//Rao, D.N. 	Binding of EcoP15I DNA methyltransferase to DNA reveals a large structural distortion within the recognition sequence.	J. Mol. Biol.	2000	298		597-610			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. 		
@D	Reddy, Y.V.R.//Rao, D.N. 	Probing the role of cysteine residues in the EcoP15I DNA methyltransferase.	J. Biol. Chem.	1998	273		23866-23876			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. 		
@D	Redenbach, M.//Ikeda, K.//Yamasaki, M.//Kinashi, H. 	Cloning and physical mapping of the EcoRI fragments of the giant linear plasmid SCP1.	J. Bacteriol.	1998	180		2796-2799			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. 		
@D	Redenbach, M.//Kieser, H.M.//Denapaite, D.//Eichner, A.//Cullum, J.//Kinashi, H.//Hopwood, D.A. 	A set of ordered cosmids and a detailed genetic and physical map for the 8 Mb Streptomyces coelicolor A3(2) chromosome.	Mol. Microbiol.	1996	21		77-96			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. 		
@D	Redondo, P.//Merino, N.//Villate, M.//Blanco, F.J.//Montoya, G.//Molina, R. 	Crystallization and preliminary X-ray diffraction analysis of the homing endonuclease I-CvuI from Chlorella vulgaris in complex with its target DNA.	Acta Crystallogr. F Struct. Biol. Cryst. Commun.	2014	70		256-259			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. 		
@D	Redondo, P.//Prieto, J.//Munoz, I.G.//Alibes, A.//Stricher, F.//Serrano, L.//Cabaniols, J.P.//Daboussi, F.//Arnould, S.//Perez, C.//Duchateau, P.//Paques, F.//Blanco, F.J.//Montoya, G. 	Molecular basis of xeroderma pigmentosum group C DNA recognition by engineered meganucleases.	Nature	2008	456		107-111			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. 		
@D	Redondo, P.//Prieto, J.//Ramos, E.//Blanco, F.J.//Montoya, G. 	Crystallization and preliminary x-ray diffraction analysis on the homing endonuclease I-Dmo-I in complex with its target DNA.	Acta Crystallogr. F Struct. Biol. Cryst. Commun.	2007	63		1017-1020			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). 		
@D	Redondo-Nieto, M. et al. 	Genome Sequence of the Biocontrol Strain Pseudomonas fluorescens F113.	J. Bacteriol.	2012	194		1273-1274			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. 		
@D	Redzuan, R.A.//Bakar, N.A.//Rozano, L.//Badrun, R.//Amin, N.M.//Raih, M.F.M. 	Draft Genome Sequence of Erwinia mallotivora BT-MARDI, Causative Agent of Papaya  Dieback Disease.	Genome Announcements	2014	2		e00375-14			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. 		
@D	Reeben, M.//Prydz, H. 	An improved method for detection of 5-methylcytosine by PCR-based genomic sequencing.	Biotechniques	1994	16		416-417					
@D	Rees, P.A.//Nwankwo, D.O.//Wilson, G.G.//Benner, J.S. 	Cloning, purification and characterization of the HincII and HindII methyltransferases from Haemophilus influenzae.	Gene	1988	74		37			Meeting Abstract 		
@D	Reeve, J.N.//Amann, E.//Tailor, R.//Gunthert, U.//Scholz, K.//Trautner, T.A. 	Unusual behaviour of SPO1 DNA with respect to restriction and modification enzymes recognizing the sequence 5'-G-G-C-C.	Mol. Gen. Genet.	1980	178		229-231			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. 		
@D	Reeve, W. et al. 	Complete genome sequence of Mesorhizobium australicum type strain (WSM2073(T)).	Standards in Genomic Sciences	2013	9		410-419			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. 		
@D	Reeve, W. et al. 	Genome sequence of the Lebeckia ambigua-nodulating 'Burkholderia sprentiae' strain WSM5005(T.).	Standards in Genomic Sciences	2013	9		385-394			'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. 		
@D	Reeve, W. et al. 	Complete genome sequence of Mesorhizobium opportunistum type strain WSM2075(T.).	Standards in Genomic Sciences	2013	9		294-303			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. 		
@D	Reeve, W. et al. 	Genome sequence of the Trifolium rueppellianum -nodulating Rhizobium leguminosarum bv. trifolii strain WSM2012.	Standards in Genomic Sciences	2013	9		283-293			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. 		
@D	Reeve, W. et al. 	Genome sequence of the lupin-nodulating Bradyrhizobium sp. strain WSM1417.	Standards in Genomic Sciences	2013	9		273-282			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. 		
@D	Reeve, W. et al. 	Genome sequence of the South American clover-nodulating Rhizobium leguminosarum bv. trifolii strain WSM597.	Standards in Genomic Sciences	2013	9		264-272			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. 		
@D	Reeve, W. et al. 	Genome sequence of the Ornithopus/Lupinus-nodulating Bradyrhizobium sp. strain WSM471.	Standards in Genomic Sciences	2013	9		254-263			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. 		
@D	Reeve, W. et al. 	Genome sequence of the clover-nodulating Rhizobium leguminosarum bv. trifolii strain TA1.	Standards in Genomic Sciences	2013	9		243-253			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. 		
@D	Reeve, W. et al. 	Complete genome sequence of Rhizobium leguminosarum bv trifolii strain WSM2304, an effective microsymbiont of the South American clover Trifolium polymorphum.	Standards in Genomic Sciences	2010	2		66-76			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. 		
@D	Reeve, W. et al. 	Complete genome sequence of the Medicago microsymbiont Ensifer (Sinorhizobium) medicae strain WSM419.	Standards in Genomic Sciences	2010	2		77-86			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. 		
@D	Reeve, W. et al. 	Genome sequence of the Listia angolensis microsymbiont Microvirga lotononidis strain WSM3557(T.).	Standards in Genomic Sciences	2014	9		540-550			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. 		
@D	Reeve, W. et al. 	Complete genome sequence of Rhizobium leguminosarum bv. trifolii strain WSM1325,  an effective microsymbiont of annual Mediterranean clovers.	Standards in Genomic Sciences	2010	2		347-356			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. 		
@D	Reeve, W.//Ballard, R.//Drew, E.//Tian, R.//Brau, L.//Goodwin, L.//Huntemann, M.//Han, J.//Tatiparthi, R.//Chen, A.//Mavrommatis, K.//Markowitz, V.//Palaniappan, K.//Ivanova, N.//Pati, A.//Woyke, T.//Kyrpides, N. 	Genome sequence of the Medicago-nodulating Ensifer meliloti commercial inoculant  strain RRI128.	Standards in Genomic Sciences	2014	9		602-613			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. 		
@D	Reeve, W.//Ballard, R.//Howieson, J.//Drew, E.//Tian, R.//Brau, L.//Munk, C.//Davenport, K.//Chain, P.//Goodwin, L.//Pagani, I.//Huntemann, M.//Mavrommatis, K.//Pati, A.//Markowitz, V.//Ivanova, N.//Woyke, T.//Kyrpides, N. 	Genome sequence of Ensifer medicae strain WSM1115; an acid-tolerant Medicago-nodulating microsymbiont from Samothraki, Greece.	Standards in Genomic Sciences	2014	9		514-526			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. 		
@D	Reeve, W.//Drew, E.//Ballard, R.//Melino, V.//Tian, R.//De Meyer, S.//Brau, L.//Ninawi, M.//Daligault, H.//Davenport, K.//Erkkila, T.//Goodwin, L.//Gu, W.//Munk, C.//Teshima, H.//Xu, Y.//Chain, P.//Kyrpides, N. 	Genome sequence of the clover-nodulating Rhizobium leguminosarum bv. trifolii strain SRDI943.	Standards in Genomic Sciences	2013	9		232-242			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. 		
@D	Reeve, W.//Drew, E.//Ballard, R.//Melino, V.//Tian, R.//De Meyer, S.//Brau, L.//Ninawi, M.//Teshima, H.//Goodwin, L.//Chain, P.//Liolios, K.//Pati, A.//Mavromatis, K.//Ivanova, N.//Markowitz, V.//Woyke, T.//Kyrpides, N. 	Genome sequence of the clover-nodulating Rhizobium leguminosarum bv. trifolii strain SRDI565.	Standards in Genomic Sciences	2013	9		220-231			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. 		
@D	Reeve, W.//Parker, M.//Tian, R.//Goodwin, L.//Teshima, H.//Tapia, R.//Han, C.//Han, J.//Liolios, K.//Huntemann, M.//Pati, A.//Woyke, T.//Mavromatis, K.//Markowitz, V.//Ivanova, N.//Kyrpides, N. 	Genome sequence of Microvirga lupini strain LUT6(T), a novel Lupinus alphaproteobacterial microsymbiont from Texas.	Standards in Genomic Sciences	2014	9		1159-1167			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. 		
@D	Reeve, W.//Sullivan, J.//Ronson, C.//Tian, R.//Brau, L.//Davenport, K.//Goodwin, L.//Chain, P.//Woyke, T.//Lobos, E.//Huntemann, M.//Pati, A.//Mavromatis, K.//Markowitz, V.//Ivanova, N.//Kyrpides, N. 	Genome sequence of the Lotus corniculatus microsymbiont Mesorhizobium loti strain R88B.	Standards in Genomic Sciences	2014	9		3			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. 		
@D	Reeve, W.//Sullivan, J.//Ronson, C.//Tian, R.//Munk, C.//Han, C.//Reddy, T.B.//Seshadri, R.//Woyke, T.//Pati, A.//Markowitz, V.//Ivanova, N.//Kyrpides, N. 	High-Quality draft genome sequence of the Lotus spp. microsymbiont Mesorhizobium  loti strain CJ3Sym.	Standards in Genomic Sciences	2015	10		54			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. 		
@D	Reeve, W.//Tian, R.//Brau, L.//Goodwin, L.//Munk, C.//Detter, C.//Tapia, R.//Han, C.//Liolios, K.//Huntemann, M.//Pati, A.//Woyke, T.//Mavrommatis, K.//Markowitz, V.//Ivanova, N.//Kyrpides, N.//Willems, A. 	Genome sequence of Ensifer arboris strain LMG 14919(T); a microsymbiont of the legume Prosopis chilensis growing in Kosti, Sudan.	Standards in Genomic Sciences	2014	9		473-483			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. 		
@D	Reeve, W.//van Berkum, P.//Ardley, J.//Tian, R.//Gollagher, M.//Marinova, D.//Elia, P.//Reddy, T.B.//Pillay, M.//Varghese, N.//Seshadri, R.//Ivanova, N.//Woyke, T.//Baeshen, M.N.//Baeshen, N.A.//Kyrpides, N. 	High-quality permanent draft genome sequence of the Bradyrhizobium elkanii type strain USDA 76T, isolated from Glycine max (L.) Merr.	Standards in Genomic Sciences	2017	12		26			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. 		
@D	Reeves, P.R.//Liu, B.//Zhou, Z.//Li, D.//Guo, D.//Ren, Y.//Clabots, C.//Lan, R.//Johnson, J.R.//Wang, L. 	Rates of Mutation and Host Transmission for an Escherichia coli Clone over 3 Years.	PLoS ONE	2011	6		E26907			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. 		
@D	Regar, R.K.//Gaur, V.K.//Mishra, G.//Jadhao, S.//Kamthan, M.//Manickam, N. 	Draft Genome Sequence of Alcaligenes faecalis Strain IITR89, an Indole-Oxidizing  Bacterium.	Genome Announcements	2016	4		e00067-16			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. 		
@D	Regar, R.K.//Gaur, V.K.//Mishra, G.//Jadhao, S.//Kamthan, M.//Manickam, N. 	Draft Genome Sequence of Acinetobacter baumannii IITR88, a Bacterium Degrading Indoles and Other Aromatic Compounds.	Genome Announcements	2016	4		e00065-16			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. 		
@D	Regenbogen, B.//Willmann, M.//Steglich, M.//Bunk, B.//Nubel, U.//Peter, S.//Neher, R.A. 	Rapid and Consistent Evolution of Colistin Resistance in Extensively Drug-Resistant Pseudomonas aeruginosa during Morbidostat Culture.	Antimicrob. Agents Chemother.	2017	61		e00043-17			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. 		
@D	Register, K.B.//Ivanov, Y.V.//Harvill, E.T.//Brinkac, L.//Kim, M.//Losada, L. 	Draft Genome Sequences of Six Bordetella hinzii Isolates Acquired from Avian and  Mammalian Hosts.	Genome Announcements	2015	3		e00081-15			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. 		
@D	Register, K.B.//Ivanov, Y.V.//Jacobs, N.//Meyer, J.A.//Goodfield, L.L.//Muse, S.J.//Smallridge, W.E.//Brinkac, L.//Kim, M.//Sanka, R.//Harvill, E.T.//Losada, L. 	Draft Genome Sequences of 53 Genetically Distinct Isolates of Bordetella bronchiseptica Representing 11 Terrestrial and Aquatic Hosts.	Genome Announcements	2015	3		e00152-15			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. 		
@D	Regmi, S.M.//Chaiprasert, A.//Coker, O.O.//Disratthakit, A.//Prammananan, T.//Suriyaphol, P.//Yik-Ying, T.//Twee, H.O. 	Draft Genome Sequence of an Extensively Drug-Resistant Mycobacterium tuberculosis Manu-Ancestor Spoligo-International Type 523 Isolate from Thailand.	Genome Announcements	2015	3		e01589-14			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. 		
@D	Rego, R.O.M.//Bestor, A.//Rosa, P.A. 	Defining the plasmid-encoded restriction-modification systems of the Lyme disease spirochete Borrelia burgdorferi.	J. Bacteriol.	2010	193		1161-1171			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. 		
@D	Rehman, M.A.//Carrillo, C.//Malouin, F.//Diarra, M.S. 	Draft Whole-Genome Sequences of Multidrug-Resistant Escherichia coli O157:H7 Strains Isolated from Feedlot Cattle Treated with Growth-Promoting Agents.	Genome Announcements	2017	5		e00284-17			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. 		
@D	Rehman, M.A.//Labbe, G.//Ziebell, K.//Johnson, R.P.//Nash, J.H. 	Complete Genome and Plasmid Sequences of Three Canadian Strains of Salmonella enterica subsp. enterica Serovar Enteritidis Belonging to Phage Types 8, 13, and  13a.	Genome Announcements	2015	3		e01017-15			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. 		
@D	Rehman, M.A.//Ziebell, K.//Nash, J.H.//Kropinski, A.M.//Ross, A.//Al-Lami, M.//Boerlin, P.//Chui, L.//Devenish, J.//Bekal, S.//Graham, M.//Amoako, K.K.//Johnson, R.P. 	Complete Genome Sequences of 16 Canadian Strains of Salmonella enterica subsp. enterica Serovar Enteritidis.	Genome Announcements	2014	2		e00330-14			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. 		
@D	Rehman, M.A.//Ziebell, K.//Nash, J.H.//Kropinski, A.M.//Zong, Z.//Nafziger, E.//Boerlin, P.//Chui, L.//Devenish, J.//Bekal, S.//Graham, M.//Johnson, R.P. 	High-Quality Draft Whole-Genome Sequences of 162 Salmonella enterica subsp. enterica Serovar Enteritidis Strains Isolated from Diverse Sources in Canada.	Genome Announcements	2014	2		e00348-14			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. 		
@D	Rehvathy, V.//Tan, M.H.//Gunaletchumy, S.P.//Teh, X.//Wang, S.//Baybayan, P.//Singh, S.//Ashby, M.//Kaakoush, N.O.//Mitchell, H.M.//Croft, L.J.//Goh, K.L.//Loke, M.F.//Vadivelu, J. 	Multiple Genome Sequences of Helicobacter pylori Strains of Diverse Disease and Antibiotic Resistance Backgrounds from Malaysia.	Genome Announcements	2013	1		e00687-13			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. 		
@D	Reich, N.O.//Danzitz, M.J. 	High resolution mapping of the DNA-protein interface in the EcoRI DNA methylase system.	ACS Abstracts	1987	194		63			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. 		
@D	Reich, N.O.//Danzitz, M.J. 	EcoRI DNA methyltransferase-DNA interactions.	Biochemistry	1992	31		1937-1945			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. 		
@D	Reich, N.O.//Danzitz, M.J. 	Non-additivity of sequence-specific enzyme-DNA interactions in the EcoRI DNA methyltransferase.	Nucleic Acids Res.	1991	19		6587-6594			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. 		
@D	Reich, N.O.//Danzitz, M.J.//Osti, F. 	Mechanisms of substrate discrimination in the EcoRI DNA methylase.	FASEB J.	1990	4		A1793			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. 		
@D	Reich, N.O.//DiMichele, L. 	Functional analysis of cysteines in the EcoRI DNA methylase.	ACS Abstracts	1987	194		64			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). 		
@D	Reich, N.O.//Everett, E.A. 	Identification of peptides involved in S-Adenosylmethionine binding in the EcoRI DNA methylase.	J. Biol. Chem.	1990	265		8929-8934			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. 		
@D	Reich, N.O.//Maegley, K.A.//Shoemaker, D.D.//Everett, E. 	Structural and functional analysis of EcoRI DNA methyltransferase by proteolysis.	Biochemistry	1991	30		2940-2946			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. 		
@D	Reich, N.O.//Mashhoon, N. 	Presteady state kinetics of an S-adenosylmethionine-dependent enzyme.	J. Biol. Chem.	1993	268		9191-9193			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. 		
@D	Reich, N.O.//Mashhoon, N. 	Inhibition of EcoRI DNA methylase with cofactor analogs.	J. Biol. Chem.	1990	265		8966-8970			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. 		
@D	Reich, N.O.//Mashhoon, N. 	Kinetic mechanism of the EcoRI DNA methyltransferase.	Biochemistry	1991	30		2933-2939			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. 		
@D	Reich, N.O.//Mashhoon, N.//Everett, E.//Danzitz, M. 	Structure-function analysis of enzyme-DNA interactions in the EcoRI DNA methylase.	J. Cell Biochem. Suppl.	1989	13D		213			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. 		
@D	Reich, N.O.//Olsen, C.//Osti, F.//Murphy, J. 	In vitro specificity of EcoRI DNA methyltransferase.	J. Biol. Chem.	1992	267		15802-15807			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. 		
@D	Reich, N.O.//Olsen, C.//Osti, F.//Murphy, J.//Smith, D.//Crowder, S. 	In vitro and in vivo specificity analysis of the EcoRI DNA methyltransferase.	ACS Abstracts	1992	203		113-BIOL			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. 		
@D	Reich, N.O.//Olsen, C.//Osti, F.//Murphy, J.//Smith, D.//Crowder, S. 	In vitro and in vivo specificity analysis of the EcoRI DNA methyltransferase.	FASEB J.	1992	6		A217			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. 		
@D	Reich, N.O.//Olsen, C.//Osti, F.//Murphy, J.//Smith, D.//Crowder, S. 	In vitro and in vivo specificity analysis of the EcoRI DNA methyltransferase.	Biochemistry	1992	31		2208			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. 		
@D	Reich, N.O.//Olsen, C.//Osti, F.//Murphy, J.//Smith, D.//Crowder, S. 	In vitro and in vivo specificity analysis of the EcoRI DNA methyltransferase.	Biophys. J.	1992	61		A217			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. 		
@D	Reich, N.O.//Svedruzic, Z.//Flynn, J.//Aubol, B. 	The enzymology of epigenetics: Mechanism and inhibition of mammalian DNA cytosine methyltransferase.	Proc. Amer. Assoc. Cancer Res.	2000	41		346-347			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. 		
@D	Reich, S. 	Reaction mechanism of type III restriction endonuclease EcoP151 and possible application in molecular diagnostics.	Ph.D. Thesis, Germany	2003			1-100			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. 		
@D	Reich, S.//Gossl, D.//Reuter, M.//Rabe, J.P.//Kruger, D.H. 	Scanning force microscopy of DNA translocation by the type III restriction enzyme EcoP15I.	J. Mol. Biol.	2004	341		337-343			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. 		
@D	Reich, S.//Mucke, M.//Moncke-Buchner, E.//Reuter, M.//Kruger, D.H. 	DNA cleavage by the restriction endonuclease EcoP15I.	Biochem. Soc. Trans.	2000	28		A331			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. 		
@D	Reichley, S.R.//Waldbieser, G.C.//Lawrence, M.L.//Griffin, M.J. 	Complete Genome Sequence of Edwardsiella hoshinae ATCC 35051.	Genome Announcements	2017	5		e01605-16			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. 		
@D	Reichley, S.R.//Waldbieser, G.C.//Lawrence, M.L.//Griffin, M.J. 	Complete Genome Sequence of an Edwardsiella piscicida-Like Species, Recovered from Tilapia in the United States.	Genome Announcements	2015	3		e01004-15			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. 		
@D	Reichley, S.R.//Waldbieser, G.C.//Soto, E.//Lawrence, M.L.//Griffin, M.J. 	Complete Genome Sequence of Edwardsiella ictaluri Isolate RUSVM-1 Recovered from  Nile Tilapia (Oreochromis niloticus) in the Western Hemisphere.	Genome Announcements	2017	5		e00390-17			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. 		
@D	Reichley, S.R.//Waldbieser, G.C.//Tekedar, H.C.//Lawrence, M.L.//Griffin, M.J. 	Complete Genome Sequence of Edwardsiella tarda Isolate FL95-01, Recovered from Channel Catfish.	Genome Announcements	2015	3		e00682-15			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). 		
@D	Reichley, S.R.//Waldbieser, G.C.//Tekedar, H.C.//Lawrence, M.L.//Griffin, M.J. 	Complete Genome Sequence of Edwardsiella piscicida Isolate S11-285 Recovered from Channel Catfish (Ictalurus punctatus) in Mississippi, USA.	Genome Announcements	2016	4		e01259-16			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. 		
@D	Reichley, S.R.//Waldbieser, G.C.//Ucko, M.//Colorni, A.//Dubytska, L.//Thune, R.L.//Lawrence, M.L.//Griffin, M.J. 	Complete Genome Sequence of an Edwardsiella piscicida-Like Species Isolated from  Diseased Grouper in Israel.	Genome Announcements	2015	3		e00829-15			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. 		
@D	Reid, S.L.//Parry, D.//Liu, H.-H.//Connolly, B.A. 	Binding and recognition of GATATC target sequences by the EcoRV restriction endonuclease: A study using fluorescent oligonucleotides and fluorescence polarization.	Biochemistry	2001	40		2484-2494			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. 		
@D	Reik, W.//Allen, N.D. 	Imprinting with and without methylation.	Curr. Biol.	1994	4		145-147			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. 		
@D	Reik, W.//Kelsey, G.//Walter, J. 	Dissecting de novo methylation.	Nat. Genet.	1999	23		380-382			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. 		
@D	Reik, W.//Walter, J. 	Imprinting mechanisms in mammals.	Current Opinion in Genetics	1998	8		154-164			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. 		
@D	Reimundo, P.//Rivas, A.J.//Osorio, C.R.//Mendez, J.//Perez-Pascual, D.//Navais, R.//Gomez, E.//Sotelo, M.//Lemos, M.L.//Guijarro, J.A. 	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.	Microbiology	2011	157		2106-2119			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. 		
@D	Rein, T.//DePamphilis, M.L.//Zorbas, H. 	Identifying 5-methylcytosine and related modifications in DNA genomes.	Nucleic Acids Res.	1998	26		2255-2264			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. 		
@D	Reinecke, S.N.//Morgan, R.D. 	BfaI, a new MaeI isoschizomer from Bacteroides fragilis, recognizes the sequence 5' C^TAG 3'.	Nucleic Acids Res.	1991	19		1152			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. 		
@D	Reiner, J.E.//Lapp, C.J.//Bunk, B.//Sproer, C.//Overmann, J.//Gescher, J. 	Complete Genome Sequence of Kyrpidia sp. Strain EA-1, a Thermophilic Knallgas Bacterium, Isolated from the Azores.	Genome Announcements	2018	6		e01505-17			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%. 		
@D	Reinhard, B.M.//Sheikholeslami, S.//Mastroianni, A.//Alivisatos, A.P.//Liphardt, J. 	Use of plasmon coupling to reveal the dynamics of DNA bending and cleavage by single EcoRV restriction enzymes.	Proc. Natl. Acad. Sci. U. S. A.	2007	104		2667-2672			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. 		
@D	Reinhardt, M.//Hammerl, J.A.//Hertwig, S. 	Complete Genome Sequences of 10 Yersinia pseudotuberculosis Isolates Recovered from Wild Boars in Germany.	Genome Announcements	2018	6		e00266-18			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. 		
@D	Reinisch, K.M. 	The crystal structure of HaeIII methylase covalently complexed to DNA: An extrahelical cytosine and rearranged base pairing.	Diss. Abstr.	1996	56		3746B			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. 		
@D	Reinisch, K.M.//Chen, L.//Verdine, G.L.//Lipscomb, W.N. 	Crystallization and preliminary crystallographic anlaysis of a DNA (cytosine-5)-methyltransferase from Haemophilus aegyptius bound covalently to DNA.	J. Mol. Biol.	1994	238		626-629			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. 		
@D	Reinisch, K.M.//Chen, L.//Verdine, G.L.//Lipscomb, W.N. 	The crystal structure of HaeIII methyltransferase covalently complexed to DNA: an extrahelical cytosine and rearranged base pairing.	Cell	1995	82		143-153			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. 		
@D	Reis, A.C.//Kroll, K.//Gomila, M.//Kolvenbach, B.A.//Corvini, P.F.X.//Nunes, O.C. 	Complete Genome Sequence of Achromobacter denitrificans PR1.	Genome Announcements	2017	5		e00762-17			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. 		
@D	Reisenauer, A.//Kahng, L.S.//McCollum, S.//Shapiro, L. 	Bacterial DNA Methylation: a Cell Cycle Regulator?	J. Bacteriol.	1999	181		5135-5139			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. 		
@D	Reisenauer, A.//Shapiro, L. 	DNA methylation affects the cell cycle transcription of the CtrA global regulator in Caulobacter.	EMBO J.	2002	21		4969-4977			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. 		
@D	Reiser, J.//Yuan, R. 	Purification and properties of the P15 specific restriction endonuclease from Escherichia coli.	J. Biol. Chem.	1977	252		451-456			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. 		
@D	Reiser, J.//Yuan, R. 	A new cleavage assay for restriction endonucleases.	Experientia	1975	31		745			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). 		
@D	Reith, M.//Munholland, J. 	Complete nucleotide sequence of the Porphyra purpurea chloroplast genome.	Plant Mol. Biol. Rep.	1995	13		333-335			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. 		
@D	Reither, S.//Li, F.//Gowher, H.//Jeltsch, A. 	Catalytic mechanism of DNA-(cytosine-C5)-methyltransferases revisited: covalent intermediate formation is not essential for methyl group transfer by the murine Dnmt3a enzyme.	J. Mol. Biol.	2003	329		675-684			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. 		
@D	Remenant, B.//Babujee, L.//Lajus, A.//Medigue, C.//Prior, P.//Allen, C. 	Sequencing of K60, Type Strain of the Major Plant Pathogen Ralstonia solanacearum.	J. Bacteriol.	2012	194		2742-2743			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. 		
@D	Remenant, B.//Borges, F.//Cailliez-Grimal, C.//Revol-Junelles, A.M.//Marche, L.//Lajus, A.//Medigue, C.//Pilet, M.F.//Prevost, H.//Zagorec, M. 	Draft Genome Sequence of Carnobacterium divergens V41, a Bacteriocin-Producing Strain.	Genome Announcements	2016	4		e01109-16			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. 		
@D	Remenant, B.//Coupat-Goutaland, B.//Guidot, A.//Cellier, G.//Wicker, E.//Allen, C.//Fegan, M.//Pruvost, O.//Elbaz, M.//Calteau, A.//Salvignol, G.//Mornico, D.//Mangenot, S.//Barbe, V.//Medigue, C.//Prior, P. 	Genomes of three tomato pathogens within the Ralstonia solanacearum species complex reveal significant evolutionary divergence.	BMC Genomics	2010	11		379			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. 		
@D	Remenant, B.//de Cambiaire, J.C.//Cellier, G.//Jacobs, J.M.//Mangenot, S.//Barbe, V.//Lajus, A.//Vallenet, D.//Medigue, C.//Fegan, M.//Allen, C.//Prior, P. 	Phylotype IV strains of Ralstonia solanacearum, R. syzygii and the blood disease bacterium form a single genomic species despite their divergent life-styles.	PLoS ONE	2011	6		e24356					
@D	Remus-Emsermann, M.N.//Kim, E.B.//Marco, M.L.//Tecon, R.//Leveau, J.H. 	Draft Genome Sequence of the Phyllosphere Model Bacterium Pantoea agglomerans 299R.	Genome Announcements	2013	1		e00036-13			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. 		
@D	Remus-Emsermann, M.N.//Schmid, M.//Gekenidis, M.T.//Pelludat, C.//Frey, J.E.//Ahrens, C.H.//Drissner, D. 	Complete genome sequence of Pseudomonas citronellolis P3B5, a candidate for microbial phyllo-remediation of hydrocarbon-contaminated sites.	Standards in Genomic Sciences	2016	11		75			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. 		
@D	Ren, L.//Shi, Y.//Jia, Y.//Yan, Y. 	Genome Sequence of Arthrobacter sp. YC-RL1, an Aromatic Compound-Degrading Bacterium.	Genome Announcements	2015	3		e00749-15			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. 		
@D	Ren, L.S.//Oreshkin, E.N.//Grachyov, Y.P. 	Biosynthesis of restriction endonuclease SalGI and optimal conditions of its purification.	Prikl. Biokhim. Mikrobiol.	1986	22		736-741			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. 		
@D	Ren, S.-X. et al. 	Unique physiological and pathogenic features of Leptospira interrogans revealed by whole-genome sequencing.	Nature	2003	422		888			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. 		
@D	Ren, W.//Liu, G.//Yin, J.//Chen, S.//Li, T.//Kong, X.//Peng, Y.//Yin, Y.//Hardwidge, P.R. 	Draft Genome Sequence of Enterotoxigenic Escherichia coli Strain W25K.	Genome Announcements	2014	2		e00593-14			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. 		
@D	Ren, Y.//Ren, Y.//Zhou, Z.//Guo, X.//Li, Y.//Feng, L.//Wang, L. 	Complete genome sequence of Enterobacter cloacae subsp. cloacae type strain ATCC 13047.	J. Bacteriol.	2010	192		2463-2464			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. 		
@D	Renbaum, P.//Abrahamove, D.//Fainsod, A.//Wilson, G.G.//Rottem, S.//Razin, A. 	Cloning, characterization, and expression in Escherichia coli of the gene coding for the CpG DNA methylase from Spiroplasma sp. strain MQ1(M.SssI) .	Nucleic Acids Res.	1990	18		1145-1152			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. 		
@D	Renbaum, P.//Razin, A. 	Footprint analysis of M.SssI and M.HhaI methyltransferases reveals extensive interactions with the substrate DNA backbone.	J. Mol. Biol.	1995	248		19-26			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. 		
@D	Renbaum, P.//Razin, A. 	Mode of action of the Spiroplasma CpG methylase M.SssI.	FEBS Lett.	1992	313		243-247			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. 		
@D	Renbaum, P.//Razin, A. 	Interaction of M.SssI and M.HhaI with single-base mismatched oligodeoxynucleotide duplexes.	Gene	1995	157		177-179			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. 		
@D	Rendulic, S.//Jagtap, P.//Rosinus, A.//Eppinger, M.//Baar, C.//Lanz, C.//Keller, H.//Lambert, C.//Evans, K.J.//Goesmann, A.//Meyer, F.//Sockett, R.E.//Schuster, S.C. 	A predator unmasked: life cycle of Bdellovibrio bacteriovorus from a genomic perspective.	Science	2004	303		689-692			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. 		
@D	Rensing, S.A. et al. 	The Physcomitrella genome reveals evolutionary insights into the conquest of land by plants.	Science	2008	319		64-69			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. 		
@D	Renvoise, A.//Pang, S.//Bernard, C.//Brossier, F.//Veziris, N.//Capton, E.//Jarlier, V.//Sougakoff, W. 	First Whole-Genome Sequence of a Clinical Isolate of Multidrug-Resistant Mycobacterium bovis BCG.	Genome Announcements	2014	2		e00611-14			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. 		
@D	Renye, J.A. Jr.//Needleman, D.S.//Somkuti, G.A.//Steinberg, D.H. 	Complete Genome Sequence of Streptococcus thermophilus Strain B59671, Which Naturally Produces the Broad-Spectrum Bacteriocin Thermophilin 110.	Genome Announcements	2017	5		e01213-17			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%. 		
@D	Repik, A.V. 	Structural and functional organization of the genes of the EcoRII restriction-modification system.	Ph.D. Thesis, Russian Academy of Sciences	1994			1-22					
@D	Repin, V.E.//Andreeva, I.S.//Kileva, E.V.//Shevchenko, A.V.//Abdurashitov, M.A.//Repin, M.V.//Degtyarev, S.K. 	MspR91, a new isoschizomer of ScrFI restriction endonuclease from Micrococcus species.	Prikl. Biokhim. Mikrobiol.	1997	33		284-286			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'. 		
@D	Repin, V.E.//Babkin, I.V.//Tereshchenko, T.A. 	Bse118I, an isoschizomer of the Cfr10I restriction endonuclease from Bacillus coagulans.	Bioorg. Khim.	1993	19		406-409			The recognition sequence and cleavage point for Bse118I restriction endonuclease have been determined as (5') R^CCGGY. 		
@D	Repin, V.E.//Burtseva, L.I.//Burlak, V.A.//Trusova, S.I. 	Search of restriction endonuclease producers with required specificity.	Mol. Gen. Mikrobiol. Virusol.	1991	11		20-22			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. 		
@D	Repin, V.E.//Chizhikov, V.E.//Tereshchenko, T.A.//Lebedev, L.R. 	Bco116I, An isoschizomer of Ksp632I from Bacillus coagulans.	Bioorg. Khim.	1993	4		410-413			The recognition sequence and cleavage point of restriction endonuclease Bco116I have been determined as (5') CTCTTC (1/4). 		
@D	Repin, V.E.//Degtyarev, S.K. 	Comparison of express-methods used for the detection of restriction endonucleases in microorganisms.	Prikl. Biokhim. Mikrobiol.	1992	28		152-155			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. 		
@D	Repin, V.E.//Lebedev, L.R.//Andreeva, I.S.//Puchkova, L.I.//Zernov, Y.P.//Serov, G.D.//Tereshchenko, T.A.//Aphinogenova, G.N.//Pustoshilova, N.M. 	The producers of restriction endonucleases from natural microbe isolates and the development on this basis of enzyme production technologies.	Biotekhnologiya	1998	0		18-27			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. 		
@D	Repin, V.E.//Lebedev, L.R.//Puchkova, L.//Serov, G.D.//Tereschenko, T.//Chizikov, V.E.//Andreeva, I. 	New restriction endonucleases from thermophilic soil bacteria.	Gene	1995	157		321-322			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. 		
@D	Repin, V.E.//Polshina, S.V.//Bozhko, N.A.//Degtyarev, S.K. 	The cultivation of Bacillus species 21, producer of restriction endonuclease Bse21I.	Izv. Sib. Otd. Akad. Nauk SSSR	1989	15		108-111			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. 		
@D	Repin, V.E.//Prichodko, E.A.//Degtyarev, S.K. 	Search of soil microorganisms for production of restriction endonucleases.	Izv. Sib. Otd. Akad. Nauk SSSR	1988	14		110-113			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. 		
@D	Repin, V.E.//Puchkova, L.I.//Ananko, G.G.//Reshetnikov, O.V.//Kurilovich, S.A. 	HpyNI is the first restriction endonuclease isolated from Helicobacter pylori.	Gut	1999	45		A6			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. 		
@D	Repin, V.E.//Puchkova, L.I.//Rodicheva, E.K.//Vydryakova, G.A. 	Luminescent bacteria as producers of specific restriction endonucleases.	Microbiology	1995	64		751-755			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. 		
@D	Repin, V.E.//Puchkova, L.I.//Rodicheva, E.K.//Vydryakova, G.A. 	Restriction endonucleases from symbiotic luminous bacteria.	Prikl. Biokhim. Mikrobiol.	1997	33		152-155			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. 		
@D	Repin, V.E.//Rechkunova, N.I.//Degtyarev, S.K.//Hachaturyan, A.A.//Afrikyan, E.K. 	Aerobic spore-forming bacteria as producers of restriction endonucleases.	Biol. J. Armenia	1989	42		969-972			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. 		
@D	Repin, V.E.//Serov, G.D.//Puchkova, L.I.//Tereshenko, T.A.//Lebedev, L.R.//Chigikov, V.E. 	New restriction endonucleases from thermophilic bacteria of the genus Bacillus.	Bioorg. Khim.	1993	19		583-585			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. 		
@D	Repin, V.E.//Shelkunov, S.N. 	Occurrence and function of restriction endonucleases (A Review).	Usp. Sovrem. Biol.	1990	110		34-47			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. 		
@A	Repin, V.E.//Shilyayeva, O.H. 		Screening microorganisms isolated from air for restriction endonuclease producers.			Klevenskaya, I.L. 		Microbiological investigations in Western Siberia				Novosibirsk	Nauka Siberian Division	1989		0		14-17									None 		
@D	Resch, G.//Kulik, E.M.//Dietrich, F.S.//Meyer, E. 	Complete genomic nucleotide sequence of the temperate bacteriophage Aaphi23 of Actinobacillus actinomycetemcomitans.	J. Bacteriol.	2004	186		5523-5528			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. 		
@D	Retamales, J.//Segovia, C.//Alvarado, R.//Nunez, P.//Santander, J. 	Draft Genome Sequence of Xanthomonas arboricola pv. juglandis J303, Isolated from Infected Walnut Trees in Southern Chile.	Genome Announcements	2017	5		e01085-17			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. 		
@D	Retamales, J.//Vasquez, I.//Santos, L.//Segovia, C.//Ayala, M.//Alvarado, R.//Nunez, P.//Santander, J. 	Complete Genome Sequences of Lytic Bacteriophages of Xanthomonas arboricola pv. juglandis.	Genome Announcements	2016	4		e00336-16			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. 		
@D	Reuss, D.R.//Schuldes, J.//Daniel, R.//Altenbuchner, J. 	Complete Genome Sequence of Bacillus subtilis subsp. subtilis Strain 3NA.	Genome Announcements	2015	3		e00084-15			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. 		
@D	Reuss, D.R.//Thurmer, A.//Daniel, R.//Quax, W.J.//Stulke, J. 	Complete Genome Sequence of Bacillus subtilis subsp. subtilis Strain 6.	Genome Announcements	2016	4		e00759-16			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. 		
@D	Reuter, M.//Kruger, D.H.//Scholz, D.//Rosenthal, H.A. 	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.	Z. Allg. Mikrobiol.	1980	20		345-354			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. 		
@D	Reuter, M.//Kupper, D.//Meisel, A.//Schroeder, C.//Kruger, D.H. 	Cooperative binding properties of restriction endonuclease EcoRII with DNA recognition sites.	J. Biol. Chem.	1998	273		8294-8300			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. 		
@D	Reuter, M.//Kupper, D.//Pein, C.D.//Petrusyte, M.//Siksnys, V.//Frey, B.//Kruger, D.H. 	Use of specific oligonucleotide duplexes to stimulate cleavage of refractory DNA sites by restriction endonucleases.	Anal. Biochem.	1993	209		232-237			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. 		
@A	Reuter, M.//Muecke, M.//Krueger, D.H. 		Structure and function of Type IIE restriction endonucleases or: From a plasmid that restricts phage replication to a new molecular DNA recognition mechanism.			Pingoud, A. 		Nucleic Acids Mol. Biol.				Berlin Heidelberg	Springer-Verlag	2004		14		261-295									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. 		
@D	Reuter, M.//Pein, C.-D.//Butkus, V.//Kruger, D.H. 	An improved method for the detection of Dcm methylation in DNA molecules.	Gene	1990	95		161-162			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. 		
@D	Reuter, M.//Schneider-Mergener, J.//Kupper, D.//Meisel, A.//Mackeldanz, P.//Kruger, D.H.//Schroeder, C. 	Regions of endonuclease EcoRII involved in DNA target recognition identified by membrane-bound peptide repertoires.	J. Biol. Chem.	1999	274		5213-5221			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. 		
@D	Reuter, V.M.//Bogdarina, I.G.//Kruger, D.H. 	Evidence for a specific inhibitor protein of DNA methyltransferases.	Biol. Rundsch.	1986	24		323-325			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. 		
@D	Reva, O.M.//Lukyanchuk, V.V.//Polishchuk, L.V. 	Bsu5044I - Isoschisomer of endonuclease restriction AsuI.	Mikrobiol. Zh.	2002	64		57-59			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. 		
@D	Revel, H.R. 	Restriction of nonglucosylated T-even bacteriophage: properties of permissive mutants of Escherichia coli B and K12.	Virology	1967	31		688-701			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. 		
@A	Revel, H.R. 		DNA Modification:  Glucosylation.			Mathews, C.K.//Kutter, E.M.//Mosig, G.//Berget, P. 		Bacteriophage T4				Washington, DC	Amer. Soc. Microbiol.	1983		0		156-165									None 		
@D	Revel, H.R.//Georgopoulos, C.P. 	Restriction of nonglucosylated T-even bacteriophages by prophage P1.	Virology	1969	39		1-17			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. 		
@D	Revel, H.R.//Hattman, S.M. 	Mutants of T2gt with altered DNA methylase activity:  relation to restriction by prophage P1.	Virology	1971	45		484-495			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. 		
@D	Revel, H.R.//Luria, S.E. 	DNA-glucosylation in T-even phage:  Genetic determination and role in phage-host interaction.	Annu. Rev. Genet.	1970	4		177-192			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. 		
@D	Revez, J.//Schott, T.//Rossi, M.//Hanninen, M.L. 	Complete Genome Sequence of a Variant of Campylobacter jejuni NCTC 11168.	J. Bacteriol.	2012	194		6298-6299			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. 		
@D	Rexer, B.U.//Jarsch, M.//Sagmeister, C.//Gluck, B.//Berger, G.//Kessler, C. 	AsnI:  a novel class II restriction endonuclease from Arthrobacter sp., strain N-CM, recognizing 5'-AT/TAAT-3'.	FEBS Lett.	1988	235		241-246			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. 		
@D	Rey, A.//Silva-Quintero, L.//Dussan, J. 	Complete Genome Sequence of the Larvicidal Bacterium Lysinibacillus sphaericus Strain OT4b.25.	Genome Announcements	2016	4		e00257-16			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. 		
@D	Rey, M.W. et al. 	Complete genome sequence of the industrial bacterium Bacillus licheniformis and comparisons with closely related Bacillus species.	Genome Biology	2004	5		R77			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. 		
@D	Reyna-Flores, F.//Barrios-Camacho, H.//Dantan-Gonzalez, E.//Ramirez-Trujillo, J.A.//Lozano, A.B.L.F.//Rodriguez-Medina, N.//Garza-Ramos, U.//Suarez-Rodriguez, R. 	Draft Genome Sequences of Endophytic Isolates of Klebsiella variicola and Klebsiella pneumoniae Obtained from the Same Sugarcane Plant.	Genome Announcements	2018	6		e00147-18			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. 		
@D	Reysenbach, A.-L.//Flores, G.E. 	Electron microscopy encounters with unusual thermophiles helps direct genomic analysis of Aciduliprofundum boonei.	Geobiology	2008	6		331-336			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. 		
@D	Reysenbach, A.L.//Donaho, J.A.//Hinsch, T.M.//Kelley, J.F.//Kouba, K.//Podar, M.//Stott, M.B. 	Draft Genome Sequence of a Novel Thermofilum sp. Strain from a New Zealand Hot Spring Enrichment Culture.	Genome Announcements	2018	6		e00005-18			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. 		
@D	Reysenbach, A.L.//Donaho, J.A.//Kelley, J.F.//St. John//E.//Turner, C.//Podar, M.//Stott, M.B. 	Draft Genome Sequence of a Dictyoglomus sp. from an Enrichment Culture of a New Zealand Geothermal Spring.	Genome Announcements	2018	6		e00150-18			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. 		
@D	Reysenbach, A.L.//Hamamura, N.//Podar, M.//Griffiths, E.//Ferreira, S.//Hochstein, R.//Heidelberg, J.//Johnson, J.//Mead, D.//Pohorille, A.//Sarmiento, M.//Schweighofer, K.//Seshadri, R.//Voytek, M.A. 	Complete and draft genome sequences of six members of the Aquificales.	J. Bacteriol.	2009	191		1992-1993			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. 		
@D	Reznicek, O.//Facey, S.J.//Hauer, B. 	Draft Genome Sequence of a Papaverine-Degrading, Gram-positive Arthrobacter sp.,  Isolated from Soil Near Hohenheim, Germany.	Genome Announcements	2015	3		e00422-15			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. 		
@D	Reznicek, O.//Luesken, F.//Facey, S.J.//Hauer, B. 	Draft Genome Sequence of Phenylobacterium immobile Strain E (DSM 1986), Isolated  from Uncontaminated Soil in Ecuador.	Genome Announcements	2015	3		e00420-15			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). 		
@D	Rezulak, M.//Borsuk, I.//Mruk, I. 	Natural C-independent expression of restriction endonuclease in a C protein-associated restriction-modification system.	Nucleic Acids Res.	2015	44		2646-2660			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. 		
@D	Rezvani, M.//Mendoza, M.//Koci, M.D.//Daron, C.//Levy, J.//Hassan, H.M. 	Draft Genome Sequences of Lactobacillus animalis Strain P38 and Lactobacillus reuteri Strain P43 Isolated from Chicken Cecum.	Genome Announcements	2016	4		e01229-16			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. 		
@D	Rezvani, M.//Mendoza, M.//Koci, M.D.//Daron, C.//Levy, J.//Hassan, H.M. 	Draft Genome Sequence of Lactobacillus crispatus C25 Isolated from Chicken Cecum.	Genome Announcements	2016	4		e01223-16			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. 		
@D	Rheaume, B.A.//Mithoefer, S.//MacLea, K.S. 	Genome Sequence of the Deep-Sea Bacterium Idiomarina abyssalis KMM 227T.	Genome Announcements	2015	3		e01256-15			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. 		
@D	Rhee, I.//Bachman, K.E.//Park, B.H.//Jair, K.-W.//Yen, R.-W.C.//Schuebel, K.E.//Cui, H.//Feinberg, A.P.//Lengauer, C.//Kinzler, K.W.//Baylin, S.B.//Vogelstein, B. 	DNMT1 and DNMT3b cooperate to silence genes in human cancer cells.	Nature	2002	416		552-556			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. 		
@D	Rhee, I.//Jair, K.W.//Yen, R.W.//Lengauer, C.//Herman, J.G.//Kinzler, K.W.//Vogelstein, B.//Baylin, S.B.//Schuebel, K.E. 	CpG methylation is maintained in human cancer cells lacking DNMT1.	Nature	2000	404		1003-1007			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. 		
@D	Rhee, J.I.//Bode, J.//Diaz-Ricci, J.C.//Poock, D.//Weigel, B.//Kretzmer, G.//Schugerl, K. 	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.	J. Biotechnol.	1997	55		69-83			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. 		
@D	Rhee, J.I.//Schuegerl, K. 	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.	Bioprocess Eng.	1998	19		261-267			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. 		
@D	Rhee, M.S.//Moritz, B.E.//Xie, G.//Glavina-del-Rio, T.//Dalin, E.//Tice, H.//Bruce, D.//Goodwin, L.//Chertkov, O.//Brettin, T.//Han, C.//Detter, C.//Pitluck, S.//Land, M.L.//Patel, M.//Ou, M.//Harbrucker, R.//Ingram, L.O.//Shanmugam, K.T. 	Complete genome sequence of a thermotolerant sporogenic lactic acid bacterium, Bacillus coagulans strain 36D1.	Standards in Genomic Sciences	2011	5		331-340			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. 		
@D	Ri, S.//Ra, S.R. 	Determination of cleavage sites of restriction endonuclease FmuI to plasmid pUB110 DNA.	Choson Minjujuui Inmin Konghwaguk Kwahagwon Tongbo	2002	0		50-53			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. 		
@D	Riazuddin, S.//Athar, A.//Sohail, A.//Ahmed, Z. 	Molecular mechanism of host controlled restriction and modification in Haemophilus influenzae 1.  Isolation of a restriction positive mutant.	Pak. J. Zool.	1987	19		393-405			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. 		
@D	Riazuddin, S.//Sohail, A.//Maqbool, T.//Khan, E.//Mushtaq, R. 	Presence of new TypeII specificity restriction enzymes in local bacteria.	Pak. J. Sci. Ind. Res.	1987	30		819-824			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. 		
@D	Ribeiro, F.J.//Przybylski, D.//Yin, S.//Sharpe, T.//Gnerre, S.//Abouelleil, A.//Berlin, A.M.//Montmayeur, A.//Shea, T.P.//Walker, B.J.//Young, S.K.//Russ, C.//Nusbaum, C.//Maccallum, I.//Jaffe, D.B. 	Finished bacterial genomes from shotgun sequence data.	Genome Res.	2012	22		2270-2277			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. 		
@D	Ribeiro, R.A.//Delamuta, J.R.//Gomes, D.F.//Souza, R.C.//Chueire, L.M.//Hungria, M. 	Genome Sequence of Rhizobium ecuadorense Strain CNPSo 671T, an Indigenous N2-Fixing Symbiont of the Ecuadorian Common Bean (Phaseolus vulgaris L.) Genetic  Pool.	Genome Announcements	2015	3		e01058-15			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. 		
@D	Ribeiro, R.A.//Helene, L.C.F.//Delamuta, J.R.M.//Hungria, M. 	Genome Sequence of Bradyrhizobium mercantei Strain SEMIA 6399T, Isolated from Nodules of Deguelia costata in Brazil.	Genome Announcements	2017	5		e00943-17			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. 		
@D	Ricaboni, D.//Mailhe, M.//Labas, N.//Vitton, V.//Raoult, D.//Million, M. 	Draft Genome Sequence of Blautia faecis Strain Marseille-P328, Isolated from the  Human Ascending Colon.	Genome Announcements	2016	4		e01383-16			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. 		
@D	Riccelli, P.V.//Vallone, P.M.//Kashin, I.//Faldasz, B.D.//Lane, M.J.//Benight, A.S. 	Thermodynamic, spectroscopic, and equilibrium binding studies of DNA sequence context effects in six 22-base pair deoxyoligonucleotides.	Biochemistry	1999	38		11197-11208			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. 		
@D	Riccelli, P.V.//Vallone, P.M.//Lane, M.J.//Benight, A.S. 	Investigations of DNA context effects: influences of flanking sequence stability on site specific binding of BamHI restriction enzyme to duplex DNA oligomers.	J. Biophys.	1997	72		A95			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. 		
@D	Ricci, G.//Ferrario, C.//Borgo, F.//Eraclio, G.//Fortina, M.G. 	Genome Sequences of Two Lactococcus garvieae Strains Isolated from Meat.	Genome Announcements	2013	1		e00018-12			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. 		
@D	Ricci, G.//Ferrario, C.//Borgo, F.//Rollando, A.//Fortina, M.G. 	Genome Sequences of Lactococcus garvieae TB25, Isolated from Italian Cheese, and  Lactococcus garvieae LG9, Isolated from Italian Rainbow Trout.	J. Bacteriol.	2012	194		1249-1250			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. 		
@D	Riccobono, E.//Di Pilato, V.//Della, M.N.//Meini, S.//Ciraolo, F.//Torricelli, F.//Rossolini, G.M. 	Draft Genome Sequence of Clostridium difficile Belonging to Ribotype 018 and Sequence Type 17.	Genome Announcements	2016	4		e00907-16			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. 		
@D	Rice, M.C. et al. 	Complete genome of Nitrosospira briensis C-128, an ammonia-oxidizing bacterium from agricultural soil.	Standards in Genomic Sciences	2016	11		46			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. 		
@D	Rice, M.C. et al. 	Complete Genome Sequence of Nitrosomonas cryotolerans ATCC 49181, a Phylogenetically Distinct Ammonia-Oxidizing Bacterium Isolated from Arctic  Waters.	Genome Announcements	2017	5		e00011-17			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. 		
@D	Rice, M.R.//Blumenthal, R.M. 	Recognition of native DNA methylation by the PvuII restriction endonuclease.	Nucleic Acids Res.	2000	28		3143-3150			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. 		
@D	Rice, M.R.//Calvin-Koons, M.D.//Blumenthal, R.M. 	The PvuII (CAGCTG) endonuclease binds to and cleaves CAG5mCTG sites.	FASEB J.	1995	9		A1400			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. 		
@D	Rice, M.R.//Koons, M.D.//Blumenthal, R.M. 	Substrate recognition by the PvuII endonuclease: binding and cleavage of CAG5mCTG sites.	Nucleic Acids Res.	1999	27		1032-1038			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. 		
@D	Richard, D.//Boyer, C.//Lefeuvre, P.//Canteros, B.I.//Beni-Madhu, S.//Portier, P.//Pruvost, O. 	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.	Genome Announcements	2017	5		e01693-16			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. 		
@D	Richard, D.//Boyer, C.//Lefeuvre, P.//Pruvost, O. 	Complete Genome Sequence of a Copper-Resistant Bacterium from the Citrus Phyllosphere, Stenotrophomonas sp. Strain LM091, Obtained Using Long-Read  Technology.	Genome Announcements	2016	4		e01327-16			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. 		
@D	Richard, D.//Boyer, C.//Verniere, C.//Canteros, B.I.//Lefeuvre, P.//Pruvost, O. 	Complete Genome Sequences of Six Copper-Resistant Xanthomonas citri pv. citri Strains Causing Asiatic Citrus Canker, Obtained Using Long-Read Technology.	Genome Announcements	2017	5		e00010-17			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. 		
@D	Richards, D.F.//Linnett, P.E.//Oultram, J.D.//Young, M. 	Restriction endonucleases in Clostridium pasteurianum ATCC 6013 and Clostridium thermohydrosulfuricum DSM568.	J. Gen. Microbiol.	1988	134		3151-3157			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. 		
@D	Richards, G.P.//Bono, J.L.//Watson, M.A.//Needleman, D.S. 	Complete Genome Sequence for the Shellfish Pathogen Vibrio coralliilyticus RE98 Isolated from a Shellfish Hatchery.	Genome Announcements	2014	2		e01253-14			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). 		
@D	Richards, G.P.//Needleman, D.S.//Watson, M.A. 	Complete Genome Sequence of Pseudoalteromonas piscicida Strain DE2-B, a Bacterium with Broad Inhibitory Activity toward Human and Fish Pathogens.	Genome Announcements	2017	5		e00752-17			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. 		
@D	Richards, G.P.//Needleman, D.S.//Watson, M.A.//Bono, J.L. 	Complete Genome Sequence of the Larval Shellfish Pathogen Vibrio tubiashii Type Strain ATCC 19109.	Genome Announcements	2014	2		e01252-14			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). 		
@D	Richards, V.P.//Lang, P.//Pavinski-Bitar, P.D.//Lefebure, T.//Schukken, Y.H.//Zadoks, R.N.//Stanhope, M.J. 	Comparative genomics and the role of lateral gene transfer in the evolution of bovine adapted Streptococcus agalactiae.	Infect. Genet. Evol.	2011	11		1263-1275			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. 		
@D	Richardson, B.//Yung, R. 	Role of DNA methylation in the regulation of cell function.	J. Lab. Clin. Med.	1999	134		333-340			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. 		
@A	Richardson, C.//Elliott, B.//Jasin, M. 		Chromosomal double strand breaks induced in mammalian cells by expression of I-SceI endonuclease.			Henderson, D.S. 		Methods Mol. Biol.				Totowa	Humana Press, Inc.	1999		113		453-463									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. 		
@D	Richardson, E.J.//Limaye, B.//Inamdar, H.//Datta, A.//Manjari, K.S.//Pullinger, G.D.//Thomson, N.R.//Joshi, R.R.//Watson, M.//Stevens, M.P. 	Genome sequences of Salmonella enterica serovar Typhimurium, Choleraesuis, Dublin and Gallinarum strains of highly defined virulence in  food-producing animals.	J. Bacteriol.	2011	193		3162-3163			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. 		
@D	Richardson, F.C.//Richardson, K.K. 	Alterations in DNA-restriction enzyme interactions by O4-alkyldeoxythymidines.	Mol. Carcinog.	1991	4		162-168			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. 		
@D	Richardson, F.C.//Richardson, K.K.//Kroin, J.S.//Hertel, L.W. 	Synthesis and restriction enzyme analysis of oligodeoxyribonucleotides containing the anti-cancer drug 2', 2'-difluoro-2'-deoxycytidine.	Nucleic Acids Res.	1992	20		1763-1768			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. 		
@D	Richter, M.//Kube, M.//Bazylinski, D.A.//Lombardot, T.//Glockner, F.O.//Reinhardt, R.//Schuler, D. 	Comparative genome analysis of four magnetotactic bacteria reveals a complex set of group-specific genes implicated in magnetosome biomineralization and function.	J. Bacteriol.	2007	189		4899-4910			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. 		
@D	Ricker, N.//Shen, S.Y.//Goordial, J.//Jin, S.//Fulthorpe, R.R. 	PacBio SMRT assembly of a complex multi-replicon genome reveals chlorocatechol degradative operon in a region of genome plasticity.	Gene	2016	586		239-247			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. 		
@D	Ricks, N.J.//Carroll, C.//Walters, A.//Newell, P.D.//Chaston, J.M. 	Genome Sequence of Weissella cibaria DmW_103, Isolated from Wild Drosophila.	Genome Announcements	2017	5		e00512-17			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. 		
@D	Riddihough, G. 	No limits on restriction.	Nature	1994	370		78			The structure of the endonuclease R.PvuII in the absence and presence of its recognition site indicates how the interaction with DNA might proceed. 		
@D	Ridl, J.//Suman, J.//Fraraccio, S.//Hradilova, M.//Strejcek, M.//Cajthaml, T.//Zubrova, A.//Macek, T.//Strnad, H.//Uhlik, O. 	Complete genome sequence of Pseudomonas alcaliphila JAB1 (=DSM 26533), a versatile degrader of organic pollutants.	Standards in Genomic Sciences	2018	13		3			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. 		
@D	Riedel, T. et al. 	Genome sequence of the Leisingera aquimarina type strain (DSM 24565(T)), a member of the marine Roseobacter clade rich in extrachromosomal elements.	Standards in Genomic Sciences	2013	8		389-402			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). 		
@D	Riedel, T. et al. 	Genome sequence of the orange-pigmented seawater bacterium Owenweeksia hongkongensis type strain (UST20020801(T)).	Standards in Genomic Sciences	2012	7		120-130			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. 		
@D	Riedel, T. et al. 	Genome sequence of the Antarctic rhodopsins-containing flavobacterium Gillisia limnaea type strain (R-8282(T)).	Standards in Genomic Sciences	2012	7		107-119			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. 		
@D	Riedel, T.//Bunk, B.//Thurmer, A.//Sproer, C.//Brzuszkiewicz, E.//Abt, B.//Gronow, S.//Liesegang, H.//Daniel, R.//Overmann, J. 	Genome Resequencing of the Virulent and Multidrug-Resistant Reference Strain Clostridium difficile 630.	Genome Announcements	2015	3		e00276-15			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. 		
@D	Riedel, T.//Bunk, B.//Wittmann, J.//Thurmer, A.//Sproer, C.//Gronow, S.//Liesegang, H.//Daniel, R.//Overmann, J. 	Complete Genome Sequence of the Clostridium difficile Type Strain DSM 1296T.	Genome Announcements	2015	3		e01186-15			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. 		
@D	Riedel, T.//Fiebig, A.//Goker, M.//Klenk, H.P. 	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.	Standards in Genomic Sciences	2014	9		840-854			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). 		
@D	Riedel, T.//Fiebig, A.//Han, J.//Huntemann, M.//Spring, S.//Petersen, J.//Ivanova, N.N.//Markowitz, V.//Woyke, T.//Goker, M.//Kyrpides, N.C.//Klenk, H.P. 	Genome sequence of the Wenxinia marina type strain (DSM 24838(T)), a representative of the Roseobacter group isolated from oilfield sediments.	Standards in Genomic Sciences	2014	9		855-865			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). 		
@D	Riedel, T.//Fiebig, A.//Petersen, J.//Gronow, S.//Kyrpides, N.C.//Goker, M.//Klenk, H.P. 	Genome sequence of the Litoreibacter arenae type strain (DSM 19593(T)), a member  of the Roseobacter clade isolated from sea sand.	Standards in Genomic Sciences	2013	9		117-127			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). 		
@D	Riedel, T.//Spring, S.//Fiebig, A.//Petersen, J.//Goker, M.//Klenk, H.P. 	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.	Standards in Genomic Sciences	2014	9		902-913			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). 		
@D	Riedel, T.//Spring, S.//Fiebig, A.//Petersen, J.//Kyrpides, N.C.//Goker, M.//Klenk, H.P. 	Genome sequence of the exopolysaccharide-producing Salipiger mucosus type strain  (DSM 16094(T)), a moderately halophilic member of the Roseobacter clade.	Standards in Genomic Sciences	2014	9		1333-1345			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). 		
@D	Riedel, T.//Spring, S.//Fiebig, A.//Scheuner, C.//Petersen, J.//Goker, M.//Klenk, H.P. 	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.	Standards in Genomic Sciences	2015	10		17			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. 		
@D	Riedel, T.//Wetzel, D.//Hofmann, J.D.//Plorin, S.P.//Dannheim, H.//Berges, M.//Zimmermann, O.//Bunk, B.//Schober, I.//Sproer, C.//Liesegang, H.//Jahn, D.//Overmann, J.//Gross, U.//Neumann-Schaal, M. 	High metabolic versatility of different toxigenic and non-toxigenic Clostridioides difficile isolates.	Int. J. Med. Microbiol.	2017	307		311-320			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. 		
@D	Rieger, A.//Nassal, M. 	Restriction endonuclease AlwNI is blocked by overlapping Dcm methylation.	Nucleic Acids Res.	1993	21		4148			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). 		
@D	Rieger, M.//Denapaite, D.//Bruckner, R.//Maurer, P.//Hakenbeck, R. 	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.	Genome Announcements	2017	5		e00401-17			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. 		
@D	Rifat, D.//Wright, N.T.//Varney, K.M.//Weber, D.J.//Black, L.W. 	Restriction Endonuclease Inhibitor IPI* of Bacteriophage T4: A Novel Structure for a Dedicated Target.	J. Mol. Biol.	2008	375		720-734			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. 		
@D	Riggs, A.D. 	X chromosome inactivation, differentiation, and DNA methylation revisited, with a tribute to Susumu Ohno.	Cytogenet. Genome Res.	2002	99		17-24			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. 		
@D	Rigonato, J.//Alvarenga, D.O.//Branco, L.H.//Varani, A.M.//Brandini, F.P.//Fiore, M.F. 	Draft genome sequence of a novel culturable marine chroococcalean cyanobacterium  from the South atlantic ocean.	Genome Announcements	2015	3		e00384-15			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. 		
@D	Rihova, J.//Novakova, E.//Husnik, F.//Hypsa, V. 	Legionella becoming a mutualist: adaptive processes shaping the genome of symbiont in the louse Polyplax serrata.	Genome Biol. Evol.	2017	9		2946-2957			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. 		
@D	Riipinen, K.A.//Forsman, P.//Alatossava, T. 	The genomes and comparative genomics of Lactobacillus delbrueckii phages.	Arch. Virol.	2011	156		1217-1233			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. 		
@D	Riley, A.B.//Kim, D.//Hansen, A.K. 	Genome Sequence of 'Candidatus Carsonella ruddii' Strain BC, a Nutritional Endosymbiont of Bactericera cockerelli.	Genome Announcements	2017	5		e00236-17			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%. 		
@D	Riley, M.C.//Perreten, V.//Bemis, D.A.//Kania, S.A. 	Complete Genome Sequences of Three Important Methicillin-Resistant Clinical Isolates of Staphylococcus pseudintermedius.	Genome Announcements	2016	4		e01194-16			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. 		
@D	Rimbara, E.//Matsui, M.//Mori, S.//Suzuki, S.//Suzuki, M.//Kim, H.//Sekizuka, T.//Kuroda, M.//Shibayama, K. 	Draft Genome Sequence of Helicobacter fennelliae Strain MRY12-0050, Isolated from a Bacteremia Patient.	Genome Announcements	2013	1		e00512-13			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. 		
@D	Rimseliene, R.//Janulaitis, A. 	Mutational analysis of two putative catalytic motifs of the Type IV restriction endonuclease Eco57I.	J. Biol. Chem.	2001	276		10492-10497			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. 		
@D	Rimseliene, R.//Janulaitis, A. 	Saturation mutagenesis of Thr862, the amino acid essential for substrate specificity of Eco57I restriction endonuclease.	Biologija	2005	1		11-14			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. 		
@D	Rimseliene, R.//Maneliene, Z.//Lubys, A.//Janulaitis, A. 	Engineering of restriction endonucleases: using methylation activity of the bifunctional endonuclease Eco571 to select the mutant with a novel sequence specificity.	J. Mol. Biol.	2003	327		383-391			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. 		
@D	Rimseliene, R.//Timinskas, A. 	Site-directed mutagenesis of type IV restriction endonuclease Eco57I.	Biologija	1997	1		31-33			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. 		
@D	Rimseliene, R.//Vaisvila, R. 	Cloning the PaeI restriction-modification system in Escherichia coli.	Biologija	1998	2		77-78			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. 		
@D	Rimseliene, R.//Vaisvila, R.//Janulaitis, A. 	The eco72IC gene specifies a trans-acting factor which influences expression of both DNA methyltransferase and endonuclease from the Eco72I restriction-modification system.	Gene	1995	157		217-219			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. 		
@D	Rina, M.//Bouriotis, V. 	Cloning, purification and characterization of the BseCI DNA methyltransferase from Bacillus stearothermophilus.	Gene	1993	133		91-94			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. 		
@D	Rina, M.//Bouriotis, V. 	Isolation and identification of restriction endonuclease BsiSI.	Nucleic Acids Res.	1990	18		1654			None 		
@D	Rina, M.//Caufrier, F.//Markaki, M.//Mavromatis, K.//Kokkinidis, M.//Bouriotis, V. 	Cloning and characterization of the gene encoding PspPI methyltransferase from the Antarctic psychrotroph Psychrobacter sp. strain TA137.	Gene	1997	197		353-360			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. 		
@D	Rina, M.//Clark, D.//Bouriotis, V. 	Isolation and identification of restriction endonuclease BsiKI.	Nucleic Acids Res.	1990	18		1655			None 		
@D	Rina, M.//Dialektakis, D.//Clark, D.//Pagomenou, M.//Bouriotis, V. 	Isolation and identification of restriction endonuclease BseCl.	Nucleic Acids Res.	1992	20		1807			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. 		
@D	Rina, M.//Karagouni, A.//Pagomenou, M.//Bouriotis, V. 	Isolation and identification of restriction endonuclease SgrBI.	Nucleic Acids Res.	1991	19		6342			SgrBI, an isoschizomer of SacII has been purified from Streptomyces griseus. SgrBI recognises the palindromic sequence 5'...CCGCGG...3' generating 3'-protruding GC-dinucleotides. 		
@D	Rina, M.//Karagouni, A.//Pagomenou, M.//Tsigos, I.//Bouriotis, V. 	Isolation and identification of restriction endonuclease SseAI.	Nucleic Acids Res.	1991	19		6341			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. 		
@D	Rina, M.//Markaki, M.//Bouriotis, V. 	Sequence of the cloned bseCIM gene: M.BseCI reveals high homology to M.BanIII.	Gene	1994	150		71-73			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. 		
@D	Rina, M.//Stratidakis, I.//Bouriotis, V. 	Isolation and identification of restriction endonuclease BssAI.	Nucleic Acids Res.	1990	18		6161			None 		
@D	Rina, M.//Tsigos, I.//Karagouni, A.//Pagomenou, M.//Bouriotis, V. 	Isolation and identification of restriction endonuclease BseBI.	Nucleic Acids Res.	1991	19		4776			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. 		
@D	Rina, M.//Tzanodaskalaki, M.//Karagouni, A.//Pagomenou, M.//Bouriotis, V. 	Isolation and identification of restriction endonuclease SseBI.	Nucleic Acids Res.	1992	20		1808			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. 		
@D	Rina, M.//Tzanodaskalaki, M.//Karagouni, A.//Pagomenou, M.//Bouriotis, V. 	Isolation and identification of restriction endonuclease MspCI.	Nucleic Acids Res.	1992	20		1806			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. 		
@A	Rine, J.//Barnes, G. 		Entry of a procaryotic endonuclease into the nucleus of Saccharomyces cerevisiae.			Hicks, J. 		Yeast Cell Biology				NY	Alan R. Liss, Inc.	1986		0		395-413									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. 		
@D	Ring, N.//Abrahams, J.//Jain, M.//Olsen, H.//Preston, A.//Bagby, S. 	Resolving the complex Bordetella pertussis genome using barcoded nanopore sequencing.	bioRxiv	2018	381640		0			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. 		
@D	Ringquist, S.//Smith, C.L. 	The Escherichia coli chromosome contains specific, unmethylated dam and dcm sites.	Proc. Natl. Acad. Sci. U. S. A.	1992	89		4539-4543			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. 		
@D	Rinke, C. et al. 	Insights into the phylogeny and coding potential of microbial dark matter.	Nature	2013	499		431-437			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. 		
@D	Rinkel, L.J.//van der Marel, G.A.//van Boom, J.H.//Altona, C. 	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.	Eur. J. Biochem.	1987	163		275-286			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. 		
@D	Rischer, M.//Klassen, J.L.//Wolf, T.//Guo, H.//Shelest, E.//Clardy, J.//Beemelmanns, C. 	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.	Genome Announcements	2016	4		e00003-16			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. 		
@D	Risser, R.//Hopkins, N.//Davis, R.W.//Delius, H.//Mulder, C. 	Action of Escherichia coli P1 restriction endonuclease on Simian Virus 40 DNA.	J. Mol. Biol.	1974	89		517-544			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. 		
@D	Ritchie, L.//Podger, D.M.//Hall, R.M. 	A mutation in the DNA adenine methylase gene (dam) of Salmonella typhimurium decreases susceptibility to 9-aminoacridine-induced frameshift mutagenesis.	Mutat. Res.	1988	194		131-141			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. 		
@D	Ritchie, L.J.//Hall, R.M.//Podger, D.M. 	Mutant of Salmonella typhimurium LT2 deficient in DNA adenine methylation.	J. Bacteriol.	1986	167		420-422			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. 		
@D	Ritchot, N.//Roy, P.H. 	DNA methylation in Neisseria gonorrhoeae and other Neisseriae.	Gene	1990	86		103-106			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. ] 		
@D	Rival, A.//Jaligot, E.//Beule, T.//Finnegan, E.J. 	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.	J. Exp. Bot.	2008	59		3271-3281			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. 		
@D	Rivera, D.//Revale, S.//Molina, R.//Gualpa, J.//Puente, M.//Maroniche, G.//Paris, G.//Baker, D.//Clavijo, B.//McLay, K.//Spaepen, S.//Perticari, A.//Vazquez, M.//Wisniewski-Dye, F.//Watkins, C.//Martinez-Abarca, F.//Vanderleyden, J.//Cassan, F. 	Complete Genome Sequence of the Model Rhizosphere Strain Azospirillum brasilense  Az39, Successfully Applied in Agriculture.	Genome Announcements	2014	2		e00683-14			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. 		
@D	Riveros-Mckay, F.//Campos, I.//Giles-Gomez, M.//Bolivar, F.//Escalante, A. 	Draft Genome Sequence of Leuconostoc mesenteroides P45 Isolated from Pulque, a Traditional Mexican Alcoholic Fermented Beverage.	Genome Announcements	2014	2		e01130-14			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. 		
@D	Rivers, A.R.//Smith, C.B.//Moran, M.A. 	An Updated genome annotation for the model marine bacterium Ruegeria pomeroyi DSS-3.	Standards in Genomic Sciences	2014	9		11			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. 		
@D	Roa, M.B.//Liles, V.R.//Torres, B.C.//Klinzing, D.C.//Lagamayo, E.//Navoa-Ng, J.//Daroy, M.L.G. 	Draft Whole-Genome Assemblies of Drug-Resistant Clinical Isolates of Klebsiella pneumoniae from the Philippines.	Genome Announcements	2017	5		e00475-17			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. 		
@D	Robbins, J.B.//Smith, D.//Belfort, M. 	Redox-Responsive Zinc Finger Fidelity Switch in Homing Endonuclease and  Intron Promiscuity in Oxidative Stress.	Curr. Biol.	2011	21		243-248			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]. 		
@D	Robbins, J.B.//Stapleton, M.//Stanger, M.J.//Smith, D.//Dansereau, J.T.//Derbyshire, V.//Belfort, M. 	Homing endonuclease I-TevIII: dimerization as a means to a double-strand break.	Nucleic Acids Res.	2007	35		1589-1600			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. 		
@D	Robene, I.//Bolot, S.//Pruvost, O.//Arlat, M.//Noel, L.D.//Carrere, S.//Jacques, M.A.//Koebnik, R.//Gagnevin, L. 	High-Quality Draft Genome Sequences of Two Xanthomonas Pathotype Strains Infecting Aroid Plants.	Genome Announcements	2016	4		e00902-16			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. 		
@D	Roberts, C.H.//Shaw, H.A.//Ferguson, N.//Holland, M.//Wren, B.W.//Stabler, R.A. 	Draft Genome Sequence of Robinsoniella peoriensis 6600698, a Confounder of Clostridium difficile Diagnosis.	Genome Announcements	2016	4		e01275-16			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. 		
@D	Roberts, D.//Hoopes, B.C.//McClure, W.R.//Kleckner, N. 	IS10 transposition is regulated by DNA adenine methylation.	Cell	1985	43		117-130			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. 		
@D	Roberts, G.A.//Chen, K.//Bower, E.K.M.//Madrzak, J.//Woods, A.//Barker, A.M.//Cooper, L.P.//White, J.H.//Blakely, G.W.//Manfield, I.//Dryden, D.T.F. 	Mutations of the domain forming the dimeric interface of the ArdA protein affect dimerization and antimodification activity but not antirestriction activity.	FEBS J.	2013	280		4903-4914			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) 		
@D	Roberts, G.A.//Chen, K.//Cooper, L.P.//White, J.H.//Blakely, G.W.//Dryden, D.T. 	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.	Nucleic Acids Res.	2012	40		10916-10924			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. 		
@D	Roberts, G.A.//Cooper, L.P.//White, J.H.//Su, T.J.//Zipprich, J.T.//Geary, P.//Kennedy, C.//Dryden, D.T. 	An investigation of the structural requirements for ATP hydrolysis and DNA cleavage by the EcoKI Type I DNA restriction and modification enzyme.	Nucleic Acids Res.	2011	39		7667-7676			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. 		
@D	Roberts, G.A.//Houston, P.J.//White, J.H.//Chen, K.//Stephanou, A.S.//Cooper, L.P.//Dryden, D.T.//Lindsay, J.A. 	Impact of target site distribution for Type I restriction enzymes on the evolution of methicillin-resistant Staphylococcus aureus (MRSA) populations.	Nucleic Acids Res.	2013	41		7472-7484			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. 		
@D	Roberts, G.A.//Stephanou, A.S.//Kanwar, N.//Dawson, A.//Cooper, L.P.//Chen, K.//Nutley, M.//Cooper, A.//Blakely, G.W.//Dryden, D.T. 	Exploring the DNA mimicry of the Ocr protein of phage T7.	Nucleic Acids Res.	2012	40		8129-8143			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. 		
@D	Roberts, M.D.//Martin, N.L.//Kropinski, A.M. 	The genome and proteome of coliphage T1.	Virology	2004	318		245-266			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. 		
@D	Roberts, R.J. 	How restriction enzymes became the workhorses of molecular biology.	Proc. Natl. Acad. Sci. U. S. A.	2005	102		5905-5908			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. 		
@D	Roberts, R.J. 	An amazing distortion in DNA induced by a methyltransferase.	Biosci. Rep.	1994	14		103-117			republication of the Nobel lecture 		
@D	Roberts, R.J. 	An amazing distortion in DNA induced by a methyltransferase (Nobel lecture).	Angew. Chem. Int. Ed. Engl.	1994	33		1222-1228					
@D	Roberts, R.J. 	Analysis of Restriction Modification systems from whole genome sequences.	Abstracts AAAS Ann. Mtg.	2000	166		A37			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. 		
@D	Roberts, R.J. 	Directory of restriction endonucleases.	Methods Enzymol.	1980	65		1-15			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. 		
@D	Roberts, R.J. 	Directory of restriction endonucleases.	Methods Enzymol.	1979	68		27-41			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. 		
@D	Roberts, R.J. 	Restriction endonucleases:  a new role in vivo?	Nature	1978	271		502			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. 		
@D	Roberts, R.J. 	The Nobel Prizewinners 1978: Medicine.	Nature	1978	275		689-690			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. 		
@D	Roberts, R.J. 	Restriction and modification enzymes and their recognition sequences.	Nucleic Acids Res.	1982	10		r117-r144			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. 		
@D	Roberts, R.J. 	Hans Krebs Lecture Bacterial methylomes.	FEBS J.	2013	280		0			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. 		
@D	Roberts, R.J. 	Restriction and modification enzymes and their recognition sequences.	Nucleic Acids Res.	1980	8		r63-r80			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. 		
@D	Roberts, R.J. 	Restriction enzymes and their isoschizomers.	Nucleic Acids Res.	1990	18		2331-2365			A review 		
@D	Roberts, R.J. 	Restriction and modification enzymes and their recognition sequences.	Nucleic Acids Res.	1984	12		r167-r204			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. 		
@D	Roberts, R.J. 	Restriction and modification enzymes and their recognition sequences.	Gene	1980	8		329-343			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. 		
@D	Roberts, R.J. 	Restriction and modification enzymes and their recognition sequences.	Nucleic Acids Res.	1981	9		r75-r96			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. . 		
@D	Roberts, R.J. 	Restriction and modification enzymes and their recognition sequences.	Gene	1978	4		183-193			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. 		
@D	Roberts, R.J. 	Restriction enzymes and their isoschizomers.	Nucleic Acids Res.	1987	15		r189-r217			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. 		
@D	Roberts, R.J. 	Restriction enzymes and their isoschizomers.	Nucleic Acids Res.	1989	17		r347-r387			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). 		
@D	Roberts, R.J. 	Restriction and modification enzymes and their recognition sequences.	Nucleic Acids Res.	1983	11		r135-r167			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. 		
@D	Roberts, R.J. 	Restriction and modification enzymes and their recognition sequences.	Nucleic Acids Res.	1985	13		r165-r200			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. 		
@D	Roberts, R.J. 	Restriction enzymes and their isoschizomers.	Nucleic Acids Res.	1988	16		r271-r313			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. 		
@D	Roberts, R.J. 	Restriction endonucleases.	CRC Crit. Rev. Biochem.	1976	4		123-164			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. 		
@A	Roberts, R.J. 		Restriction endonucleases, DNA sequencing, and computers.			Brown, D.D. 		Developmental Biology Using Purified Genes					Academic Press, Inc.	1981		0		621-634									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. 		
@A	Roberts, R.J. 		Restriction and modification enzymes and their recognition sequence.			Chirikjian, J.G. 		Gene Amplif. Anal.					Elsevier	1987		5		1-49									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. 		
@A	Roberts, R.J. 		Restriction and modification enzymes and their recognition sequences.			 		Life Illuminated				Cold Spring Harbor, NY	Cold Spring Harbor Laboratory Press	2008		0		215-216											
@A	Roberts, R.J. 		Restriction enzymes.			Hoelzel, A.R. 		Molecular Genetic Analysis of Populations: A Practical Approach				Oxford	IRL Press	1998				379-397									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). 		
@A	Roberts, R.J. 		Restriction enzymes.			Hames, B.D.//Higgins, S.J. 		Nucleic Acid Hybridisation: A Practical Approach				Oxford, Washington DC	IRL Press	1985		0		203-210									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). 		
@A	Roberts, R.J. 		Restriction enzymes.			Hoelzel, A.R. 		Molecular Genetic Analysis of Populations: A Practical Approach				NY	Oxford University Press	1992		0		281-296									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). 		
@A	Roberts, R.J. 		Restriction endonucleases.			Schlessinger, D. 		Microbiology-1982				Washington	American Society for Microbiology	1978		0		5-9									None 		
@A	Roberts, R.J. 		Restriction endonucleases, DNA sequencing and computers.			Khan, A.M.//Riazuddin, S.//Qadir, A.//Qazi, M.N. 		In Physics and Contemporary Needs				New York	Plenum Press	1984		6		305-316									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. 		
@A	Roberts, R.J. 		Restriction endonucleases.			Linn, S.M.//Roberts, R.J. 		Nucleases				New York	Cold Spring Harbor Laboratory Press	1982		0		311-340									None 		
@A	Roberts, R.J. 		The role of restriction endonucleases in genetic engineering.			Beers, R.F.Jr.//Barrett, E.G. 		In: Recombinant Molecules: Impact on Science Society				New York	Raven Press	1977		0		21-32									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. 		
@A	Roberts, R.J. 		Restriction and modification enzymes and their recognition sequences.			Fasman, G.D. 		In Handbook of Biochemistry and Molecular Biology				Ohio	CRC Press	1976		0		532-534									None 		
@A	Roberts, R.J. 		Restriction and modification enzymes and their recognition sequences.			Bukhari, A.I.//Shapiro, J.A.//Adhya, S.L. 		DNA Insertion Elements, Plasmids, and Episomes.				New York	Cold Spring Harbor Laboratory Press	1977		0		757-768									None 		
@D	Roberts, R.J. et al. 	A nomenclature for restriction enzymes, DNA methyltransferases, homing endonucleases and their genes.	Nucleic Acids Res.	2003	31		1805-1812			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. 		
@A	Roberts, R.J. et al. 		A nomenclature for restriction enzymes, DNA methyltransferases, homing endonucleases, and their genes.			Pingoud, A. 		Nucleic Acids Mol. Biol.				Berlin Heidelberg	Springer-Verlag	2004		14		1-18									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. 		
@D	Roberts, R.J.//Breitmeyer, J.B.//Tabachnik, N.F.//Myers, P.A. 	A second specific endonuclease from Haemophilus aegyptius.	J. Mol. Biol.	1975	91		121-123			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. 		
@D	Roberts, R.J.//Cheng, X. 	Base flipping.	Annu. Rev. Biochem.	1998	67		181-198			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. 		
@A	Roberts, R.J.//Halford, S.E. 		Type II restriction enzymes.			Linn, S.M.//Lloyd, R.S.//Roberts, R.J. 		Nucleases				Cold Spring Harbor	Cold Spring Harbor Laboratory Press	1993		0		35-88									
     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
 
 		
@D	Roberts, R.J.//Macelis, D. 	Restriction enzymes and their isoschizomers.	Nucleic Acids Res.	1992	20		2167-2180			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. 		
@D	Roberts, R.J.//Macelis, D. 	REBASE-restriction enzymes and methylases.	Nucleic Acids Res.	1993	21		3125-3137			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. 		
@D	Roberts, R.J.//Macelis, D. 	REBASE - restriction enzymes and methylases.	Nucleic Acids Res.	1994	22		3628-3639			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. 		
@D	Roberts, R.J.//Macelis, D. 	REBASE--restriction enzymes and methylases.	Nucleic Acids Res.	1996	24		223-235			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. 		
@D	Roberts, R.J.//Macelis, D. 	REBASE - restriction enzymes and methylases.	Nucleic Acids Res.	1998	26		338-350			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. 		
@D	Roberts, R.J.//Macelis, D. 	REBASE-restriction enzymes and methylases.	Nucleic Acids Res.	2001	29		268-269			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). 		
@D	Roberts, R.J.//Macelis, D. 	REBASE - restriction enzymes and methylases.	Nucleic Acids Res.	2000	28		306-307			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). 		
@D	Roberts, R.J.//Macelis, D. 	Restriction enzymes and their isoschizomers.	Nucleic Acids Res.	1991	19		2077-2109			A review of all known restriction enzymes and a description of the REBASE database. 		
@D	Roberts, R.J.//Macelis, D. 	REBASE-restriction enzymes and methylases.	Nucleic Acids Res.	1997	25		248-262			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. 		
@D	Roberts, R.J.//Macelis, D. 	REBASE-restriction enzymes and methylases.	Nucleic Acids Res.	1999	27		312-313			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. 		
@A	Roberts, R.J.//Macelis, D. 		The restriction enzymes.			Linn, S.M.//Lloyd, R.S.//Roberts, R.J. 		Nucleases				Cold Spring Harbor	Cold Spring Harbor Laboratory Press	1993		0		439-444											
@D	Roberts, R.J.//Myers, P.A.//Morrison, A.//Murray, K. 	A specific endonuclease from Haemophilus haemolyticus.	J. Mol. Biol.	1976	103		199-208			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. 		
@D	Roberts, R.J.//Myers, P.A.//Morrison, A.//Murray, K. 	A specific endonuclease from Arthrobacter luteus.	J. Mol. Biol.	1976	102		157-165			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. 		
@D	Roberts, R.J.//Vincze, T.//Posfai, J.//Macelis, D. 	REBASE--a database for DNA restriction and modification: enzymes, genes and genomes.	Nucleic Acids Res.	2010	38		D234-D236			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. 		
@D	Roberts, R.J.//Vincze, T.//Posfai, J.//Macelis, D. 	REBASE - Restriction enzymes and DNA methyltransferases.	Nucleic Acids Res.	2005	33		D230-D232			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. 		
@D	Roberts, R.J.//Vincze, T.//Posfai, J.//Macelis, D. 	REBASE--enzymes and genes for DNA restriction and modification.	Nucleic Acids Res.	2007	35		D269-D270			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. 		
@D	Roberts, R.J.//Vincze, T.//Posfai, J.//Macelis, D. 	REBASE-a database for DNA restriction and modification: enzymes, genes and genomes.	Nucleic Acids Res.	2015	43		D298-D299			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. 		
@D	Roberts, R.J.//Vincze, T.//Posfai, J.//Macelis, D. 	REBASE: restriction enzymes and methyltransferases.	Nucleic Acids Res.	2003	31		418-420			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. 		
@D	Roberts, R.J.//Wilson, G.A.//Young, F.E. 	Recognition sequence of specific endonuclease BamHI from Bacillus amyloliquefaciens H.	Nature	1977	265		82-84			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. 		
@D	Robertson, A.K.//Geiman, T.M.//Sankpal, U.T.//Hager, G.L.//Robertson, K.D. 	Effects of chromatin structure on the enzymatic and DNA binding functions of DNA methyltransferases DNMT1 and Dnmt3a in vitro.	Biochem. Biophys. Res. Commun.	2004	322		110-118			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. 		
@D	Robertson, G.T.//Reisenauer, A.//Wright, R.//Jensen, R.B.//Jensen, A.//Shapiro, L.//Roop, R.M. 	The Brucella abortus CcrM DNA methyltransferase is essential for viability, and its overexpression attenuates intracellular replication in murine macrophages.	J. Bacteriol.	2000	182		3482-3489			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. 		
@D	Robertson, J.//Lin, J.//Levett, P.N.//Nadon, C.//Nash, J.//Berry, C. 	Complete Genome Sequence of an Escherichia coli O121:H19 Strain from an Outbreak  in Canada Associated with Flour.	Genome Announcements	2018	6		e01561-17			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. 		
@D	Robertson, J.//Yoshida, C.//Gurnik, S.//Nash, J.H.E. 	Completed Genome Sequences of Strains from 36 Serotypes of Salmonella.	Genome Announcements	2018	6		e01472-17			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. 		
@D	Robertson, K. 	DNA methyltransferase function and regulation.	J. Nutr.	2003	133		3845S			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. 		
@D	Robertson, K.D. 	DNA methylation, methyltransferases, and cancer.	Oncogene	2001	20		3139-3155			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. 		
@D	Robertson, K.D.//Ait-Si-Ali, S.//Yokochi, T.//Wade, P.A.//Jones, P.L.//Wolffe, A.P. 	DNMT1 forms a complex with Rb, E2F1 and HDAC1 and represses transcription from E2F-responsive promoters.	Nat. Genet.	2000	25		338-342			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. 		
@D	Robertson, K.D.//Jones, P.A. 	DNA methylation: past, present and future directions.	Carcinogenesis	2000	21		461-467			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. 		
@D	Robertson, K.D.//Keyomarsi, K.//Gonzales, F.A.//Velicescu, M.//Jones, P.A. 	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.	Nucleic Acids Res.	2000	28		2108-2113			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. 		
@D	Robertson, K.D.//Uzvolgyi, E.//Liang, G.//Talmadge, C.//Sumegi, J.//Gonzales, F.A.//Jones, P.A. 	The human DNA methyltransferases 1, 3a and 3b: coordinate mRNA expression in normal tissues and overexpression in tumors.	Nucleic Acids Res.	1999	27		2291-2298			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. 		
@D	Robertson, K.D.//Wolffe, A.P. 	DNA methylation in health and disease.	Genetics	2000	1		11-19			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. 		
@D	Robinson, C.R.//Sligar, S.G. 	Mediation of molecular recognition in protein-DNA complexes by bound water: a mechanism for "star activity" of restriction endonucleases.	Biophys. J.	1994	66		A34			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. 		
@D	Robinson, C.R.//Sligar, S.G. 	Changes in solvation during DNA binding and cleavage are critical to altered specificity of the EcoRI endonuclease.	Proc. Natl. Acad. Sci. U. S. A.	1998	95		2186-2191			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. 		
@D	Robinson, C.R.//Sligar, S.G. 	Mediation of molecular recognition in protein-DNA complexes by bound water: a mechanism for "star activity" of restriction endonucleases.	J. Cell Biochem. Suppl.	1994	18C		138			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. 		
@D	Robinson, C.R.//Sligar, S.G. 	Molecular recognition mediated by bound water. A mechanism for star activity of the restriction endonuclease EcoRI.	J. Mol. Biol.	1993	234		302-306			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. 		
@D	Robinson, C.R.//Sligar, S.G. 	Hydrostatic pressure reverses osmotic pressure effects on the specificity of EcoRI-DNA interactions.	Biochemistry	1994	33		3787-3793			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. 		
@D	Robinson, C.R.//Sligar, S.G. 	Heterogeneity in molecular recognition by restriction endonucleases: Osmotic and hydrostatic pressure effects on BamHI, PvuII, and EcoRV specificity.	Proc. Natl. Acad. Sci. U. S. A.	1995	92		3444-3448			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. 		
@A	Robinson, D.//Walsh, P.R.//Bonventre, J.A. 		Restriction endonucleases.			Gerstein, A.S. 		Molecular biology problem solver.				New York	Wiley-Liss, Inc.	2001				225-266									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. 		
@D	Robinson, L.S.//Perry, J.//Lek, S.//Wollam, A.//Sodergren, E.//Weinstock, G.//Lewis, W.G.//Lewis, A.L. 	Genome Sequences of 15 Gardnerella vaginalis Strains Isolated from the Vaginas of Women with and without Bacterial Vaginosis.	Genome Announcements	2016	4		e00879-16			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. 		
@D	Robinson, V.L.//Oyston, P.C.//Titball, R.W. 	A dam mutant of Yersinia pestis is attenuated and induces protection against plague.	FEMS Microbiol. Lett.	2005	252		251-256			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. 		
@D	Robson, R.L.//Jones, R.//Robson, R.M.//Schwartz, A.//Richardson, T.H. 	Azotobacter Genomes: The Genome of Azotobacter chroococcum NCIMB 8003 (ATCC 4412).	PLoS ONE	2015	10		E0127997			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. 		
@D	Rocap, G. et al. 	Genome divergence in two Prochlorococcus ecotypes reflects oceanic niche differentiation.	Nature	2003	424		1042-1047			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. 		
@D	Rocha, E.P.//Danchin, A.//Viari, A. 	Evolutionary role of restriction/modification systems as revealed by comparative genome analysis.	Genome Res.	2001	11		946-958			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. 		
@D	Rocha, E.P.C.//Blanchard, A. 	Genomic repeats, genome plasticity and the dynamics of Mycoplasma evolution.	Nucleic Acids Res.	2002	30		2031-2042			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. 		
@D	Rocha, T.S.//Bertolotti, L.//Catania, S.//Pourquier, P.//Rosati, S. 	Genome Sequence of a Mycoplasma meleagridis Field Strain.	Genome Announcements	2016	4		e00017-16			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. 		
@D	Rochaix, J.D.//Rahire, M.//Michel, F. 	The chloroplast ribosomal intron of Chlamydomonas reinhardii codes for a polypeptide related to mitochondrial maturases.	Nucleic Acids Res.	1985	13		975-984			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. 		
@D	Rochat, T.//Barbier, P.//Nicolas, P.//Loux, V.//Perez-Pascual, D.//Guijarro, J.A.//Bernardet, J.F.//Duchaud, E. 	Complete Genome Sequence of Flavobacteriumpsychrophilum Strain OSU THCO2-90, Used for Functional Genetic Analysis.	Genome Announcements	2017	5		e01665-16			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. 		
@D	Rochefort, A.//Boukthir, S.//Moullec, S.//Meygret, A.//Adnani, Y.//Lavenier, D.//Faili, A.//Kayal, S. 	Full Sequencing and Genomic Analysis of Three emm75 Group A Streptococcus Strains Recovered in the Course of an Epidemiological Shift in French Brittany.	Genome Announcements	2017	5		e00957-17			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. 		
@D	Rochepeau, P.//Selinger, L.B.//Hynes, M.F. 	Transposon-like structure of a new plasmid-encoded restriction-modification system in Rhizobium leguminosarum VF39SM.	Mol. Gen. Genet.	1997	256		387-396			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. 		
@D	Rockah-Shmuel, L.//Tawfik, D.S. 	Evolutionary transitions to new DNA methyltransferases through target site expansion and shrinkage.	Nucleic Acids Res.	2012	40		11627-11637			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. 		
@D	Rockah-Shmuel, L.//Toth-Petroczy, A.//Tawfik, D.S. 	Systematic Mapping of Protein Mutational Space by Prolonged Drift Reveals the Deleterious Effects of Seemingly Neutral Mutations.	PLOS Comp. Biol.	2015	11		e1004421			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. 		
@D	Roddy, E.S.//Price, M.//Ewing, A.G. 	Continuous monitoring of a restriction enzyme digest of DNA on a microchip with automated capillary sample introduction.	Anal. Chem.	2003	75		3704-3711			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. 		
@D	Rodicio, M.R.//Alvarez, M.A.//Chater, K.F. 	Isolation and genetic structure of IS112, an insertion sequence responsible for the inactivation of the SalI restriction-modification system of Streptomyces albus G.	Mol. Gen. Genet.	1991	225		142-147			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. 		
@D	Rodicio, M.R.//Chater, K.F. 	Cloning and expression of the SalI restriction-modification genes of Streptomyces albus G.	Mol. Gen. Genet.	1988	213		346-353			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. 		
@D	Rodicio, M.R.//Chater, K.F. 	The SalI (SalGI) restriction-modification system of Streptomyces albus G.	Gene	1988	74		39-42			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. 		
@D	Rodicio, M.R.//Quinton-Jager, T.//Moran, L.S.//Slatko, B.E.//Wilson, G.G. 	Organization and sequence of the SalI restriction-modification system.	Gene	1994	151		167-172			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. 		
@D	Rodrigues, C.//Kapil, A.//Sharma, A.//Devanga, R.N.K.//Inbanathan, F.Y.//Veeraraghavan, B.//Kang, G. 	Whole-Genome Shotgun Sequencing of Cephalosporin-Resistant Salmonella enterica Serovar Typhi.	Genome Announcements	2017	5		e01639-16			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. 		
@D	Rodrigues, E.M.//Pylro, V.S.//Dobbler, P.T.//Victoria, F.//Roesch, L.F.//Totola, M.R. 	Draft Genome of Rhodococcus rhodochrous TRN7, Isolated from the Coast of Trindade Island, Brazil.	Genome Announcements	2016	4		e01707-15			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. 		
@D	Rodrigues, G.N.//Lago-Leston, A.//Costa, R.//Keller-Costa, T. 	Draft Genome Sequence of Labrenzia sp. Strain EL143, a Coral-Associated Alphaproteobacterium with Versatile Symbiotic Living Capability and Strong  Halogen Degradation Potential.	Genome Announcements	2018	6		e00132-18			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. 		
@D	Rodriguez, A.//Lleonart, R.//Martinez, A.S.//Ryes, G.//Gonzalez, E.//Brito, J.E. 	Cloning and expression of genes coding for Haemophilus influenzae Rf restriction and modification enzymes.  Purification of the recombinant endonuclease.	Biotecnol. Apl.	1995	12		156-159			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. 		
@D	Rodriguez, J.G.//Pino, C.//Tauch, A.//Murcia, M.I. 	Complete Genome Sequence of the Clinical Beijing-Like Strain Mycobacterium tuberculosis 323 Using the PacBio Real-Time Sequencing Platform.	Genome Announcements	2015	3		e00371-15			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. 		
@D	Rodriguez, R.J. 	Polyphosphate present in DNA preparations from Filamentous fungal species of Colletotrichum inhibits restriction endonucleases and other enzymes.	Anal. Biochem.	1993	209		291-297			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. 		
@D	Rodriguez-Osorio, N.//Wang, H.F.//Rupinski, J.//Bridges, S.M.//Memili, E. 	Comparative functional genomics of mammalian DNA methyltransferases.	Reprod. Biomed. Online	2010	20		243-255			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. 		
@D	Rodriguez-Palenzuela, P. et al. 	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.	Environ. Microbiol.	2010	12		1604-1620			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. 		
@D	Roer, L.//Aarestrup, F.M.//Hasman, H. 	EcoKI Type I Restriction-Modification System in Escherichia coli Affect, but is Not an Absolute Barrier for, Conjugation.	J. Bacteriol.	2014	197		337-342			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. 		
@D	Roer, L.//Hendriksen, R.S.//Leekitcharoenphon, P.//Lukjancenko, O.//Kaas, R.S.//Hasman, H.//Aarestrup, F.M. 	Is the Evolution of Salmonella enterica subsp. enterica Linked to Restriction-Modification Systems?	mSystems	2016	1		e00009-16			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. 		
@D	Rogel-Hernandez, M.A.//Guerrero, G.//Rincon-Molina, C.I.//Ruiz-Valdiviezo, V.M.//Cisneros-Perez, C.//Castanon-Gonzalez, J.H.//Lopez-Lopez, A.//Martinez-Romero, E.//Rincon-Rosales, R. 	Genome Sequence of Acinetobacter lactucae OTEC-02, Isolated from Hydrocarbon-Contaminated Soil.	Genome Announcements	2017	5		e00400-17			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. 		
@D	Rogulin, E.A.//Perevyazova, T.A.//Zheleznaya, L.A.//Matvienko, N.I. 	Plasmid pRARE as a vector for cloning to construct a superproducer of the site-specific nickase N.BspD6I.	Biokhimiia	2004	69		1123-1127			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. 		
@D	Roh, H.//Ko, H.J.//Kim, D.//Choi, D.G.//Park, S.//Kim, S.//Chang, I.S.//Choi, I.G. 	Complete Genome Sequencing of A Carbon Monooxide Utilizing Acetogen, Eubacterium limosum KIST612.	J. Bacteriol.	2010	193		307-308			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. 		
@D	Roh, H.//Uguru, G.C.//Ko, H.J.//Kim, S.//Kim, B.Y.//Goodfellow, M.//Bull, A.T.//Kim, K.H.//Bibb, M.J.//Choi, I.G.//Stach, J.E. 	Genome Sequence of the Abyssomicin- and Proximicin-Producing Marine Actinomycete Verrucosispora maris AB-18-032.	J. Bacteriol.	2011	193		3391-3392			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. 		
@D	Roh, H.//Yun, E.J.//Lee, S.//Ko, H.J.//Kim, S.//Kim, B.Y.//Song, H.//Lim, K.I.//Kim, K.H.//Choi, I.G. 	Genome Sequence of Vibrio sp. Strain EJY3, an Agarolytic Marine Bacterium Metabolizing 3,6-Anhydro-L-Galactose as a Sole Carbon Source.	J. Bacteriol.	2012	194		2773-2774			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. 		
@D	Roh, S.W.//Nam, Y.D.//Nam, S.H.//Choi, S.H.//Park, H.S.//Bae, J.W. 	Complete Genome Sequence of Halalkalicoccus jeotgali B3T, an Extremely Halophilic Archaeon.	J. Bacteriol.	2010	192		4528-4529			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. 		
@D	Rohit, A.//Kumar, B.K.//Deekshit, V.K.//Rai, P.//Kumar, R.V.//Jayaprakash, J.//Madhushankara, B.//Karunasagar, I.//Karunasagar, I. 	Draft Genome Sequence of Campylobacter fetus MMM01, Isolated from a Chronic Kidney Disease Patient with Sepsis.	Genome Announcements	2015	3		e01055-15			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. 		
@D	Rohmer, L.//Brittnacher, M.//Svensson, K.//Buckley, D.//Haugen, E.//Zhou, Y.//Chang, J.//Levy, R.//Hayden, H.//Forsman, M.//Olson, M.//Johansson, A.//Kaul, R.//Miller, S.I. 	Potential source of Francisella tularensis live vaccine strain attenuation determined by genome comparison.	Infect. Immun.	2006	74		6895-6906			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. 		
@D	Roizes, G.//Charlieu, J.-P.//Marcais, B.//Bellis, M. 	Use of the DNA fragments generated by a restriction enzyme (Bcg I) for the construction of overlapping clone libraries.	DNA Seq.	1991	2		65-67			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. 		
@D	Roizes, G.//Nardeux, P.C.//Monier, R. 	A new specific endonuclease from Anabaena variabilis.	FEBS Lett.	1979	104		39-44			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. 		
@D	Roizes, G.//Pages, M.//Lecou, C.//Patillon, M.//Kovoor, A. 	A new site-specific endonuclease showing phenotypical crypticity in a tumorigenic strain of Agrobacterium tumefaciens.	Gene	1979	6		43-50			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. 		
@D	Roizes, G.//Patillon, M.//Kovoor, A. 	A restriction endonuclease from Agrobacterium tumefaciens.	FEBS Lett.	1977	82		69-70			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. 		
@D	Rojas, J.D.//Starcevic, A.//Baranasic, D.//Ferreira-Torres, M.A.//Contreras, C.A.//Garrido, L.M.//Araujo, W.L.//de Souza, R.F.//Zucko, J.//Hranueli, D.//Long, P.F.//Cullum, J.//Padilla, G. 	Genome Sequence of Streptomyces olindensis DAUFPE 5622, Producer of the Antitumoral Anthracycline Cosmomycin D.	Genome Announcements	2014	2		e00541-14			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. 		
@D	Rojas, R.//Miranda, C.D.//Romero, J.//Asenjo, F.//Valderrama, K.//Segovia, C.//Ugalde, J.A.//Santander, J. 	Genome Sequence of Vibrio VPAP30, Isolated from an Episode of Massive Mortality of Reared Larvae of the Scallop Argopecten purpuratus.	Genome Announcements	2015	3		e00745-15			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. 		
@D	Rojas, T.C.//Maluta, R.P.//Parizzi, L.P.//Koenigkan, L.V.//Yang, J.//Yu, J.//Pereira, G.A.//Dias-da-Silveira, W. 	Genome Sequences of Avian Pathogenic Escherichia coli Strains Isolated from Brazilian Commercial Poultry.	Genome Announcements	2013	1		e0011013			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. 		
@D	Rojas, T.C.//Parizzi, L.P.//Tiba, M.R.//Chen, L.//Pereira, G.A.//Sangal, V.//Yang, J.//Yu, J.//Dias-da-Silveira, W. 	Draft Genome of a Brazilian Avian-Pathogenic Escherichia coli Strain and In Silico Characterization of Virulence-Related Genes.	J. Bacteriol.	2012	194		3023			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. 		
@D	Rojas-Rojas, F.U. et al. 	Draft genome of Paraburkholderia caballeronis TNe-841(T), a free-living, nitrogen-fixing, tomato plant-associated bacterium.	Standards in Genomic Sciences	2017	12		80			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. 		
@D	Rojas-Rojas, F.U.//Huntemann, M.//Clum, A.//Pillay, M.//Palaniappan, K.//Varghese, N.//Mikhailova, N.//Stamatis, D.//Reddy, T.B.//Markowitz, V.//Ivanova, N.//Kyrpides, N.//Woyke, T.//Shapiro, N.//Ibarra, J.A.//Estrada-de, L.S.P. 	Draft Genome Sequence of Heavy Metal-Resistant Cupriavidus alkaliphilus ASC-732T, Isolated from Agave Rhizosphere in the Northeast of Mexico.	Genome Announcements	2016	4		e01013-16			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%. 		
@D	Rolain, J.M.//Vayssier-Taussat, M.//Gimenez, G.//Robert, C.//Fournier, P.E.//Raoult, D. 	Genome Sequence of Bartonella birtlesii, a Bacterium Isolated from Small Rodents  of the Genus Apodemus.	J. Bacteriol.	2012	194		4779			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)). 		
@D	Romanenko, E.B.//Pushkareva, M.Y.//Alessenko, A.V.//Vanyushin, B.F. 	Effects of Sphingomyelin and its enzymatic hydrolysis products on heterologous methylation of calf thymus DNA by cytosine-DNA methyltransferase EcoRII.	Biokhimiia	1991	56		295-300			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. 		
@D	Romanenkov, A.S.//Kisil, O.V.//Zatsepin, T.S.//Yamskova, O.V.//Karyagina, A.S.//Metelev, V.G.//Oretskaya, T.S.//Kubareva, E.A. 	DNA-methyltransferase SsoII as a bifunctional protein: Features of the interaction with the promoter region of SsoII restriction-modification genes.	Biokhimiia	2006	71		1341-1349			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. 		
@D	Romano, A.//Bellio, A.//Macori, G.//Cotter, P.D.//Bianchi, D.M.//Gallina, S.//Decastelli, L. 	Whole-Genome Shotgun Sequence of Salmonella bongori, First Isolated in Northwestern Italy.	Genome Announcements	2017	5		e00560-17			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%. 		
@D	Romano, A.//Trip, H.//Campbell-Sills, H.//Bouchez, O.//Sherman, D.//Lolkema, J.S.//Lucas, P.M. 	Genome Sequence of Lactobacillus saerimneri 30a (Formerly Lactobacillus sp. Strain 30a), a Reference Lactic Acid Bacterium Strain Producing Biogenic Amines.	Genome Announcements	2013	1		e00097-12			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. 		
@D	Romanovskaya, V.A.//Alexeyev, M.F.//Gunkovskaya, N.V.//Stolyar, S.M.//Shatohina, E.S.//Malashenko, Y.R. 	Screening for restriction endonucleases in methane-oxidizing bacteria.	Mikrobiol. Zh.	1992	54		32-39			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. 		
@D	Romao, F.T.//Hernandes, R.T.//Ooka, T.//Hayashi, T.//Sperandio, V.//Gomes, T.A.T. 	Complete Genome Sequence of Escherichia albertii Strain 1551-2, a Potential Extracellular and Intracellular Pathogen.	Genome Announcements	2018	6		e00075-18			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. 		
@D	Romero, D.A.//Klaenhammer, T.R. 	Abortive phage infection and restriction/modification activities directed by pTR2030 determinants are enhanced by recombination with conjugal elements in lactococci.	J. Gen. Microbiol.	1990	136		1817-1824			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. 		
@D	Romine, M.F.//Stillwell, L.C.//Wong, K.-K.//Thurston, S.J.//Sisk, E.C.//Sensen, C.//Gaasterland, T.//Fredrickson, J.K.//Saffer, J.D. 	Complete sequence of a 184-kilobase catabolic plasmid from Sphingomonas aromaticivorans F199.	J. Bacteriol.	1999	181		1585-1602			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. 		
@D	Ronca, S.//Frossard, A.//Guerrero, L.D.//Makhalanyane, T.P.//Aislabie, J.M.//Cowan, D.A. 	Draft Genome Sequence of Sphingomonas sp. Strain Ant20, Isolated from Oil-Contaminated Soil on Ross Island, Antarctica.	Genome Announcements	2015	3		e01309-14			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. 		
@D	Ronco, T.//Stegger, M.//Andersen, P.S.//Pedersen, K.//Li, L.//Thofner, I.C.//Olsen, R.H. 	Draft Genome Sequences of Two Avian Pathogenic Escherichia coli Strains of Clinical Importance, E44 and E51.	Genome Announcements	2016	4		e00768-16			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. 		
@D	Ronco, T.//Stegger, M.//Pedersen, K. 	Draft Genome Sequence of a Sequence Type 398 Methicillin-Resistant Staphylococcus aureus Isolate from a Danish Dairy Cow with Mastitis.	Genome Announcements	2017	5		e00492-17			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. 		
@D	Rondelet, G.//Dal Maso, T.//Willems, L.//Wouters, J. 	Structural basis for recognition of histone H3K36me3 nucleosome by human de novo  DNA methyltransferases 3A and 3B.	J. Struct. Biol.	2016	194		357-367			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. 		
@D	Rondelet, G.//Fleury, L.//Faux, C.//Masson, V.//Dubois, J.//Arimondo, P.B.//Willems, L.//Wouters, J. 	Inhibition studies of DNA methyltransferases by maleimide derivatives of RG108 as non-nucleoside inhibitors.	Future Med Chem	2017	9		1465-1481			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]. 		
@D	Rong, X.//Baysal, G.F.//Meulia, T.//McSpadden, G.B.B. 	Draft Genome Sequences of the Pseudomonas fluorescens Biocontrol Strains Wayne1R and Wood1R.	J. Bacteriol.	2012	194		724-725			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. 		
@D	Rong, X.//Gurel, F.B.//Meulia, T.//McSpadden, G.B.B. 	Draft Genome Sequences of the Biocontrol Bacterium Mitsuaria sp. Strain H24L5A.	J. Bacteriol.	2012	194		734-735			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. 		
@D	Ronholm, J.//Petronella, N.//Kenwell, R.//Banerjee, S. 	Draft Whole-Genome Sequences of 14 Vibrio parahaemolyticus Clinical Isolates with an Ambiguous K Serogroup.	Genome Announcements	2015	3		e00217-15			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. 		
@D	Ronholm, J.//Petronella, N.//Tamber, S. 	Draft Genome Sequences of Two Salmonella enterica Strains Isolated from Sprouted  Chia and Flax Seed Powders.	Genome Announcements	2016	4		e00963-16			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. 		
@D	Ronholm, J.//Petronella, N.//Tamber, S. 	Draft Genome Sequences of 11 Salmonella enterica Strains with Variable Levels of  Barotolerance.	Genome Announcements	2016	4		e00952-16			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. 		
@D	Ronka, J.//Hjorleifsdottir, S.//Tenkanen, T.//Pitkanen, K.//Mattila, P.//Kristjansson, J.K. 	RmaI, a type II restriction endonuclease from Rhodothermus marinus which recognizes 5' CTAG 3'.	Nucleic Acids Res.	1991	19		2789			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'. 		
@D	Ronneseth, A.//Castillo, D.//D'Alvise, P.//Tonnesen, O.//Haugland, G.//Grotkjaer, T.//Engell-Sorensen, K.//Norremark, L.//Bergh, O.//Wergeland, H.I.//Gram, L. 	Comparative assessment of Vibrio virulence in marine fish larvae.	J. Fish Dis.	2017	40		1373-1385			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. 		
@D	Rooney, E.A. et al. 	Draft Genome Sequence of the Cellulolytic and Xylanolytic Thermophile Clostridium clariflavum Strain 4-2a.	Genome Announcements	2015	3		e00797-15			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. 		
@D	Roquigny, R.//Arseneault, T.//Gadkar, V.J.//Novinscak, A.//Joly, D.L.//Filion, M. 	Complete Genome Sequence of Biocontrol Strain Pseudomonas fluorescens LBUM223.	Genome Announcements	2015	3		e00443-15			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. 		
@D	Rosa, B.A.//Hallsworth-Pepin, K.//Martin, J.//Wollam, A.//Mitreva, M. 	Genome Sequence of Christensenella minuta DSM 22607T.	Genome Announcements	2017	5		e01451-16			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. 		
@D	Rosamond, J.//Endlich, B.//Linn, S. 	Electron microscopic studies of the mechanism of action of the restriction endonuclease of Escherichia coli B.	J. Mol. Biol.	1979	129		619-635			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. 		
@D	Rosana, A.R.//Orata, F.D.//Xu, Y.//Simkus, D.N.//Bramucci, A.R.//Boucher, Y.//Case, R.J. 	Draft Genome Sequences of Seven Bacterial Strains Isolated from a Polymicrobial Culture of Coccolith-Bearing (C-Type) Emiliania huxleyi M217.	Genome Announcements	2016	4		e00673-16			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. 		
@D	Rosas-Morales, J.P.//Perez-Mancilla, X.//Lopez-Kleine, L.//Montoya, C.D.//Riano-Pachon, D.M. 	Draft genome sequences of clostridium strains native to Colombia with the potential to produce solvents.	Genome Announcements	2015	3		e00486-15			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. 		
@D	Rosati, O.//Srivastava, T.K.//Katti, S.B.//Alves, J. 	Importance of phosphate contacts for sequence recognition by EcoRI restriction enzyme.	Biochem. Biophys. Res. Commun.	2002	295		198-205			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. 		
@D	Rose, T.M.//Schultz, E.R.//Henikoff, J.G.//Pietrokovski, S.//McCallum, C.M.//Henikoff, S. 	Consensus-degenerate hybrid oligonucleotide primers for amplification of distantly related sequences.	Nucleic Acids Res.	1998	26		1628-1635			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. 		
@D	Rosen, L.E.//Morrison, H.A.//Masri, S.//Brown, M.J.//Springstubb, B.//Sussman, D.//Stoddard, B.L.//Seligman, L.M. 	Homing endonuclease I-CreI derivatives with novel DNA target specificities - mutant homing enzyme via mutagenesis for DNA cleavage and gene therapy.	Nucleic Acids Res.	2006	34		4791-4800			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. 		
@D	Rosenberg, A.H.//Simon, M.N.//Studier, F.W.//Roberts, R.J. 	Survey and mapping of restriction endonuclease cleavage sites in bacteriophage T7 DNA.	J. Mol. Biol.	1979	135		907-915			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. 		
@A	Rosenberg, J.//Wang, B.//Frederick, C.//Reich, N.//Greene, P.//Grable, J.//McClarin, J. 		Development of a Protein Design Strategy for EcoRI Endonuclease.			Oxender, D.//Fox, C.F. 		Protein Eng.					A.R. Liss Inc.	1987		0		237-250									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. 		
@D	Rosenberg, J.M. 	Structure and function of restriction endonucleases.	Curr. Opin. Struct. Biol.	1991	1		104-113			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. 		
@A	Rosenberg, J.M.//Boyer, H.W.//Greene, P. 		The structure and function of the EcoRI restriction endonuclease.			Chirikjian, J.G. 		Gene Amplif. Anal.					Elsevier North Holland	1981		1		131-164									*
   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
 
 		
@D	Rosenberg, J.M.//Dickerson, R.E.//Greene, P.J.//Boyer, H.W. 	Preliminary X-ray diffraction analysis of crystalline EcoRI endonuclease.	J. Mol. Biol.	1978	122		241-245			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. 		
@D	Rosenberg, J.M.//Greene, P. 	EcoRI* specificity and hydrogen bonding.	DNA	1982	1		117-124			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. 		
@D	Rosenberg, J.M.//McClarin, J.//Grable, J.//Frederick, C.//Samudzi, C.//Jen-Jacobson, L. 	Structure of DNA-EcoRI endonuclease complex at 3 angstroms resolution.	J. Cell Biochem. Suppl.	1985	9B		101			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. 		
@A	Rosenberg, J.M.//McClarin, J.A.//Frederick, C.A.//Grable, J.//Boyer, H.W.//Greene, P.J. 		Structure and function of the EcoRI restriction endonuclease.			Chirikjian, J.G. 		Gene Amplif. Anal.					Elsevier North Holland	1987		5		119-145									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. 		
@A	Rosenberg, J.M.//McClarin, J.A.//Frederick, C.A.//Wang, B.-C.//Boyer, H.W.//Grable, J.//Greene, P. 		The structure and function of EcoRI endonuclease.			Burnett, R.M.//Vogle, H.J. 		Biological Organization: Macromolecular Interactions at High Resolution.					Academic Press	1987		0		11-43									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. 		
@D	Rosenberg, J.M.//McClarin, J.A.//Frederick, C.A.//Wang, B.-C.//Boyer, H.W.//Greene, P. 	The 3 angstrom structure of a DNA-EcoRI endonuclease recognition complex.	Chem. Scr.	1986	26B		147-157			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. 		
@D	Rosenberg, J.M.//McClarin, J.A.//Frederick, C.A.//Wang, B.-C.//Grable, J.//Boyer, H.W.//Greene, P. 	Structure and recognition mechanism of EcoRI endonuclease.	Trends Biochem. Sci.	1987	12		395-398			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. 		
@A	Rosenberg, J.M.//McClarin, J.A.//Frederick, C.A.//Wang, B.-C.//Grable, J.//Boyer, H.W.//Greene, P. 		Structure of the DNA-EcoRI endonuclease recognition complex.			Ehrenberg, A. 		Structure, Dynamics and Function of Biomolecules				New York	Springer-Verlag	1987		0		255-259									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. 		
@D	Rosenberg, S.M. 	EcoK restriction during in vitro packaging of coliphage lambda DNA.	Gene	1985	39		313-315			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. 		
@D	Rosenstein, R.//Nerz, C.//Biswas, L.//Resch, A.//Raddatz, G.//Schuster, S.C.//Gotz, F. 	Genome analysis of the meat starter culture bacterium Staphylococcus carnosus TM300.	Appl. Environ. Microbiol.	2009	75		811-822			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. 		
@D	Rosenthal, A.Z.//Matson, E.G.//Eldar, A.//Leadbetter, J.R. 	RNA-seq reveals cooperative metabolic interactions between two termite-gut spirochete species in co-culture.	ISME J.	2011	5		1133-1142			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. 		
@D	Rosewarne, C.P.//Cheung, J.L.//Smith, W.J.//Evans, P.N.//Tomkins, N.W.//Denman, S.E.//O'Cuiv, P.//Morrison, M. 	Draft Genome Sequence of Treponema sp. Strain JC4, a Novel Spirochete Isolated from the Bovine Rumen.	J. Bacteriol.	2012	194		4130			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. 		
@D	Rosewarne, C.P.//Greenfield, P.//Li, D.//Tran-Dinh, N.//Bradbury, M.I.//Midgley, D.J.//Hendry, P. 	Draft Genome Sequence of Clostridium sp. Maddingley, Isolated from Coal-Seam Gas  Formation Water.	Genome Announcements	2013	1		e00081-12			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. 		
@D	Rosewarne, C.P.//Greenfield, P.//Li, D.//Tran-Dinh, N.//Midgley, D.J.//Hendry, P. 	Draft Genome Sequence of Methanobacterium sp. Maddingley, Reconstructed from Metagenomic Sequencing of a Methanogenic Microbial Consortium Enriched from  Coal-Seam Gas Formation Water.	Genome Announcements	2013	1		e00082-12			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. 		
@D	Rosinski-Chupin, I.//Sauvage, E.//Mairey, B.//Mangenot, S.//Ma, L.//Da Cunha, V.//Rusniok, C.//Bouchier, C.//Barbe, V.//Glaser, P. 	Reductive evolution in Streptococcus agalactiae and the emergence of a host adapted lineage.	BMC Genomics	2013	14		252			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. 		
@D	Roske, K.//Calcutt, M.J.//Wise, K.S. 	The Mycoplasma fermentans prophage phiMFV1: genome organization, mobility and variable expression of an encoded surface protein.	Mol. Microbiol.	2004	52		1703-1720			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. 		
@D	Roslan, N.N.//Sabri, S.//Oslan, S.N.//Baharum, S.N.//Leow, T.C. 	Complete Genome Sequence of Photobacterium sp. Strain J15, Isolated from Seawater of Southwestern Johor, Malaysia.	Genome Announcements	2016	4		e00739-16			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. 		
@D	Roslan, N.S.//Jabeen, S.//Mat, I.N.//Omar, A.R.//Bejo, M.H.//Ideris, A. 	Whole-Genome Sequence of Salmonella enterica subsp. enterica Serovar Typhimurium  Strain UPM 260, Isolated from a Broiler Chicken in Perak, Malaysia.	Genome Announcements	2017	5		e01272-17			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. 		
@D	Rosner, J.L. 	Modification-deficient mutants of bacteriophage Pl.  I. Restriction by Pl cryptic lysogens.	Virology	1973	52		213-222			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. 		
@D	Ross, D.E.//Gulliver, D. 	Metagenome-Assembled Genome Sequence of Pseudomonas stutzeri Strain CO183 Isolated from a Coalbed Methane Well.	Genome Announcements	2016	4		e01237-16			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. 		
@D	Ross, D.E.//Gulliver, D. 	Reconstruction of a Nearly Complete Pseudomonas Draft Genome Sequence from a Coalbed Methane-Produced Water Metagenome.	Genome Announcements	2016	4		e01024-16			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. 		
@D	Ross, D.E.//Marshall, C.W.//May, H.D.//Norman, R.S. 	Metagenome-Assembled Genome Sequences of Acetobacterium sp. Strain MES1 and Desulfovibrio sp. Strain MES5 from a Cathode-Associated Acetogenic Microbial  Community.	Genome Announcements	2017	5		e00938-17			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. 		
@D	Ross, D.E.//Marshall, C.W.//May, H.D.//Norman, R.S. 	Draft Genome Sequence of Sulfurospirillum sp. Strain MES, Reconstructed from the  Metagenome of a Microbial Electrosynthesis System.	Genome Announcements	2015	3		e01336-14			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. 		
@D	Ross, D.W. 	Restriction enzymes.	Arch. Pathol. Lab. Med.	1990	114		906			None 		
@D	Ross, T.K.//Achberger, E.C.//Braymer, H.D. 	Characterization of the Escherichia coli modified cytosine restriction (mcrB) gene.	Gene	1987	61		277-289			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. 		
@D	Ross, T.K.//Achberger, E.C.//Braymer, H.D. 	Nucleotide sequence of the McrB region of Escherichia coli K-12 and evidence for two independent translational initiation sites at the mcrB locus.	J. Bacteriol.	1989	171		1974-1981			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. 		
@D	Ross, T.K.//Achberger, E.C.//Braymer, H.D. 	Identification of a second polypeptide required for McrB restriction of 5-methylcytosine-containing DNA in Escherichia coli K12.	Mol. Gen. Genet.	1989	216		402-407			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. 		
@D	Ross, T.K.//Braymer, H.D. 	Localization of a genetic region involved in McrB restriction by Escherichia coli K-12.	J. Bacteriol.	1987	169		1757-1759			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. 		
@D	Rossi, S.//Buera, M.P.//Moreno, S.//Chirife, J. 	Stabilization of the restriction enzyme EcoRI dried with Trehalose and other selected glass-forming solutes.	Biotechnol. Prog.	1997	13		609-616			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. 		
@D	Rossino, R.//Gosalvez, J.//Mezzanotte, R. 	The effects of enzyme inactivation and incubation buffer on digestion in situ with restriction endonucleases.	Biotech. Histochem.	1998	73		325-328			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. 		
@D	Roszczyk, E.//Goodgal, S. 	Methylase Activities from Haemophilus influenzae that protect Haemophilus parainfluenzae Transforming Deoxyribonucleic Acid from Inactivation by Haemophilus influenzae Endonuclease R.	J. Bacteriol.	1975	123		287-293			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. 		
@D	Roth, M.//Helm-Kruse, S.//Friedrich, T.//Jeltsch, A. 	Functional roles of conserved amino acid residues in DNA methyltransferases investigated by site-directed mutagenesis of the EcoRV adenine-M6-methyltransferase.	J. Biol. Chem.	1998	273		17333-17342			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. 		
@D	Roth, M.//Jeltsch, A. 	Biotin-Avidin microplate assay for the quantitative analysis of enzymatic methylation of DNA by DNA methyltransferases.	Biol. Chem.	2000	381		269-272			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. 		
@D	Roth, M.//Jeltsch, A. 	Changing the target base specificity of the EcoRV DNA methyltransferase by rational de novo protein-design.	Nucleic Acids Res.	2001	29		3137-3144			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. 		
@D	Rothen, J.//Schindler, T.//Pothier, J.F.//Younan, M.//Certa, U.//Daubenberger, C.//Pfluger, V.//Jores, J. 	Draft Genome Sequences of Seven Streptococcus agalactiae Strains Isolated from Camelus dromedarius at the Horn of Africa.	Genome Announcements	2017	5		e00525-17			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. 		
@D	Rothrock, M.J. Jr.//Fan, P.//Jeong, K.C.//Kim, S.A.//Ricke, S.C.//Park, S.H. 	Complete Genome Sequence of Listeria monocytogenes Strain MR310, Isolated from a  Pastured-Flock Poultry Farm System.	Genome Announcements	2018	6		e00171-18			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. 		
@D	Rotman, E.//Kouzminova, E.//Plunkett, G. III//Kuzminov, A. 	Genome of Enterobacteriophage Lula/phi80 and Insights into Its Ability To Spread in the Laboratory Environment.	J. Bacteriol.	2012	194		6802-6817			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. 		
@D	Rotta, C.//Poehlein, A.//Schwarz, K.//McClure, P.//Daniel, R.//Minton, N.P. 	Closed Genome Sequence of Clostridium pasteurianum ATCC 6013.	Genome Announcements	2015	3		e01596-14			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. 		
@D	Rouet, P.//Smih, F.//Jasin, M. 	Introduction of double-strand breaks into the genome of mouse cells by expression of a rare-cutting endonuclease.	Mol. Cell. Biol.	1994	14		8096-8106			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. 		
@D	Rouet, P.//Smith, F.//Jasin, M. 	Expression of a site-specific endonuclease stimulates homologous recombination in mammalian cells.	Proc. Natl. Acad. Sci. U. S. A.	1994	91		6064-6068			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. 		
@D	Rouleau, J.//MacLeod, A.R.//Szyf, M. 	Regulation of the DNA methyltransferase by the Ras-AP-1 signaling pathway.	J. Biol. Chem.	1995	270		1595-1601			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. 		
@D	Rouleau, J.//Szyf, M. 	Regulation of the mouse DNA methyltransferase by signal transduction pathways.	Mol. Biol. Cell	1992	3		A25			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. 		
@D	Rouleau, J.//Tanigawa, G.//Szyf, M. 	The mouse DNA methyltransferase 5'-region .	J. Biol. Chem.	1992	267		7368-7377			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. 		
@D	Rouli, L.//Robert, C.//Raoult, D.//Yagupsky, P. 	Kingella kingae KK247, an Atypical Pulsed-Field Gel Electrophoresis Clone A Strain.	Genome Announcements	2014	2		e01228-14			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. 		
@D	Rouli, L.//Rolain, J.M.//El Filali, A.//Robert, C.//Raoult, D. 	Genome Sequence of Coxiella burnetii 109, a Doxycycline-Resistant Clinical Isolate.	J. Bacteriol.	2012	194		6939			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. 		
@D	Roulland-Dussoix, D.//Boyer, H.W. 	The Escherichia coli B restriction endonuclease.	Biochim. Biophys. Acta	1969	195		219-229			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. 		
@D	Roulland-Dussoix, D.//Boyer, H.W. 	B Restriction endonuclease of Escherichia coli.	Bacteriol. Proc.	1969	69		46			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. 		
@A	Roulland-Dussoix, D.//Yoshimori, R.//Greene, P.//Betlach, M.//Goodman, H.M.//Boyer, H.W. 		R Factor-Controlled Restriction and Modification of Deoxyribonucleic Acid.			Schlesinger, D. 		Microbiology-1974				Washington, D.C.	American Society for Microbiology	1975		0		187-198									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. 		
@D	Rountree, M.R.//Bachman, K.E.//Baylin, S.B. 	DNMT1 binds HDAC2 and a new co-repressor, DMAP1, to form a complex at replication foci.	Nat. Genet.	2000	25		269-277			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. 		
@D	Rountree, P.M. 	Variations in a related series of staphylococcal bacteriophages.	J. Gen. Microbiol.	1956	15		266-279			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. 		
@A	Roustan-Espinosa, I.//Guerrero, D.//Flores, E.//Huete-Perez, J. 		Restriction enzymes in native bacteria of Nicaragua.			 		Revista Univ. Centroamer.					Revista de la Universidad Centroamericana	2000		52		10-18									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. 		
@D	Rout, S.P.//Rai, A.//Humphreys, P.N. 	Draft Genome Sequence of Alkaliphilic Exiguobacterium sp. Strain HUD, Isolated from a Polymicrobial Consortia.	Genome Announcements	2015	3		e01451-14			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. 		
@D	Roux, V.//El Karkouri, K.//Lagier, J.C.//Robert, C.//Raoult, D. 	Non-contiguous finished genome sequence and description of Kurthia massiliensis sp. nov.	Standards in Genomic Sciences	2012	7		221-232			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. 		
@D	Roux, V.//Lagier, J.C.//Gorlas, A.//Robert, C.//Raoult, D. 	Non-contiguous finished genome sequence and description of Kurthia senegalensis sp. nov.	Standards in Genomic Sciences	2014	9		1321-1332			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. 		
@D	Roux, V.//Million, M.//Robert, C.//Magne, A.//Raoult, D. 	Non-contiguous finished genome sequence and description of Oceanobacillus massiliensis sp. nov.	Standards in Genomic Sciences	2013	9		370-384			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. 		
@D	Roux, V.//Robert, C.//Gimenez, G.//Gharbi, R.//Raoult, D. 	Draft Genome Sequence of Actinomyces massiliensis Strain 4401292T.	J. Bacteriol.	2012	194		5121			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. 		
@D	Roux, V.//Robert, C.//Gimenez, G.//Raoult, D. 	Draft Genome Sequence of Brevibacterium massiliense Strain 541308T.	J. Bacteriol.	2012	194		5151-5152			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. 		
@D	Roux, V.//Robert, C.//Gimenez, G.//Raoult, D. 	Draft Genome Sequence of Staphylococcus massiliensis Strain 5402776T.	J. Bacteriol.	2012	194		6984-6985			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. 		
@D	Roux, V.//Robert, C.//Raoult, D. 	Non-contiguous finished genome sequence of Phocaeicola abscessus type strain 7401987(T.).	Standards in Genomic Sciences	2013	9		351-358			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. 		
@D	Roux, V.//Robert, C.//Raoult, D. 	Non-contiguous finished genome sequence of Prevotella timonensis type strain 4401737(T.).	Standards in Genomic Sciences	2014	9		1346-1353			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. 		
@D	Roux, V.//Robert, C.//Raoult, D. 	Non-contiguous finished genome sequence of Corynebacterium timonense type strain  5401744(T.).	Standards in Genomic Sciences	2014	9		948-955			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. 		
@D	Rowland, G.C.//Lim, P.P.//Glass, R.E. 	'Stop-codon-specific' restriction endonucleases: their use in mapping and gene manipulation.	Gene	1992	116		21-26			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. 		
@D	Roy, A.C.//Wilson, G.G.//Edgell, D.R. 	Perpetuating the homing endonuclease life cycle: identification of mutations that modulate and change I-TevI cleavage preference.	Nucleic Acids Res.	2016	44		7350-7359			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. 		
@D	Roy, A.S.//Baruah, R.//Gogoi, D.//Borah, M.//Singh, A.K.//Deka, B.H.P. 	Draft Genome Sequence of Pseudomonas aeruginosa Strain N002, Isolated from Crude  Oil-Contaminated Soil from Geleky, Assam, India.	Genome Announcements	2013	1		e00104-12			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. 		
@D	Roy, K.B.//Vrushank, D. 	Bam HI cleaves the self complementary dodecamer d-CGCGGAGCCGCG, before the two G's and possibly binds in the DNA major groove.	Biochem. Mol. Biol. Int.	1995	36		759-770			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. 		
@D	Roy, K.B.//Vrushank, D.//Jayaram, B. 	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.	Anal. Biochem.	1994	220		160-164			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. 		
@D	Roy, P.H.//Smith, H.O. 	DNA methylases of Hemophilus influenzae Rd.  II. Partial recognition site base sequences.	J. Mol. Biol.	1973	81		445-459			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. 		
@D	Roy, P.H.//Smith, H.O. 	DNA methylases of Hemophilus influenzae Rd I.  Purification and properties.	J. Mol. Biol.	1973	81		427-444			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. 		
@D	Roy, P.H.//Tetu, S.G.//Larouche, A.//Elbourne, L.//Tremblay, S.//Ren, Q.//Dodson, R.//Harkins, D.//Shay, R.//Watkins, K.//Mahamoud, Y.//Paulsen, I.T. 	Complete genome sequence of the multiresistant taxonomic outlier Pseudomonas aeruginosa PA7.	PLoS ONE	2010	5		e8842			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. 		
@D	Roycroft, E.//Mac, A.M.//O'Toole, R.F.//Fitzgibbon, M.//Rogers, T.R. 	Draft Genome Sequence of the First Isolate of Extensively Drug-Resistant Mycobacterium tuberculosis in Ireland.	Genome Announcements	2014	2		e01002-14			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. 		
@D	Rozanov, A.S.//Bryanskaya, A.V.//Kotenko, A.V.//Malup, T.K.//Peltek, S.E. 	Draft Genome Sequence of Anoxybacillus flavithermus Strain 25, Isolated from the  Garga Hot Spring in the Barguzin Valley, Baikal Region, Russian Federation.	Genome Announcements	2014	2		e01258-14			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. 		
@D	Rozanov, A.S.//Bryanskaya, A.V.//Malup, T.K.//Kotenko, A.V.//Peltek, S.E. 	Draft genome sequence of a halorubrum h3 strain isolated from the burlinskoye salt lake (altai krai, Russia).	Genome Announcements	2015	3		e00566-15			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. 		
@D	Rozanov, A.S.//Korzhuk, A.V.//Shipova, A.A.//Bryanskaya, A.V.//Peltek, S.E. 	Draft Genome Sequence of Bacillus altitudinis Strain KU-skv2(2), Isolated from a  Microbial Mat on an Anthropogenic Pipe from Caldera Uzon (Kamchatka, Russia).	Genome Announcements	2018	6		e01572-17			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. 		
@D	Rozanov, A.S.//Logacheva, M.D.//Peltek, S.E. 	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.	Genome Announcements	2014	2		e01205-14			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). 		
@D	Rozanov, A.S.//Shipova, A.A.//Bryanskaya, A.V.//Tekutieva, L.A.//Son, O.M.//Peltek, S.E. 	Draft Genome Sequence of Bacillus altitudinis Strain KL4, Isolated from Bottom Sediments in Lake Krotovaya Lyaga (Novosibirsk Region, Russia).	Genome Announcements	2018	6		e01494-17			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. 		
@D	Ruan, H.//Lunnen, K.D.//Pelletier, J.J.//Xu, S.-Y. 	Overexpression of BsoBI restriction endonuclease in E. coli, purification of the recombinant BsoBI, and identification of catalytic residues of BsoBI by random mutagenesis.	Gene	1997	188		35-39			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. 		
@D	Ruan, H.//Lunnen, K.D.//Scott, M.E.//Moran, L.S.//Slatko, B.E.//Pelletier, J.J.//Hess, E.J.//Benner, J.//Wilson, G.G.//Xu, S.-Y. 	Cloning and sequence comparison of AvaI and BsoBI restriction-modification systems.	Mol. Gen. Genet.	1996	252		695-699			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. 		
@D	Ruan, L.//Xu, X. 	Sequence analysis and characterizations of two novel plasmids isolated from Thermus sp. 4C.	Plasmid	2007	58		84-87			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. 		
@D	Ruan, Z.//Wang, Y.//Song, J.//Zhai, Y.//Zhang, C.//Chen, C.//Li, Y.//Zhao, B.//Zhao, B. 	Draft Genome Sequence of Kurthia huakuii LAM0618T, an Organic-Pollutant-Degrading Strain Isolated from Biogas Slurry.	Genome Announcements	2014	2		e01158-13			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. 		
@D	Ruben, G.//Spielman, P.//Tu, C.-P.D.//Jay, E.//Siegel, B.//Wu, R. 	Relaxed circular SV40 DNA as cleavage intermediate of two restriction endonucleases.	Nucleic Acids Res.	1977	4		1803-1813			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. 		
@D	Rubin, R.A.//Modrich, P. 	Substrate dependence of the mechanism of EcoRI endonuclease.	Nucleic Acids Res.	1978	5		2991-2997			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. 		
@D	Rubin, R.A.//Modrich, P. 	EcoRI methylase physical and catalytic properties of the homogeneous enzyme.	J. Biol. Chem.	1977	252		7265-7272			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. 		
@D	Rubin, R.A.//Modrich, P. 	Purification and properties of EcoRI endonuclease.	Methods Enzymol.	1980	65		96-104			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. 		
@D	Rubin, R.A.//Modrich, P.//Vanaman, T.C. 	Partial NH2- and C00H-Terminal Sequence Analyses of EcoRI DNA Restriction and Modification Enzymes.	J. Biol. Chem.	1981	256		2140-2142			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. 		
@D	Ruby, E.G.//Urbanowski, M.//Campbell, J.//Dunn, A.//Faini, M.//Gunsalus, R.//Lostroh, P.//Lupp, C.//McCann, J.//Millikan, D.//Schaefer, A.//Stabb, E.//Stevens, A.//Visick, K.//Whistler, C.//Greenberg, E.P. 	Complete genome sequence of Vibrio fischeri: A symbiotic bacterium with pathogenic congeners.	Proc. Natl. Acad. Sci. U. S. A.	2005	102		3004-3009			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. 		
@D	Ruckert, C.//Albersmeier, A.//Al-Dilaimi, A.//Bednarz, H.//Niehaus, K.//Szczepanowski, R.//Kalinowski, J. 	Genome sequence of the squalene-degrading bacterium Corynebacterium terpenotabidum type strain Y-11(T) (= DSM 44721(T)).	Standards in Genomic Sciences	2014	9		505-513			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. 		
@D	Ruckert, C.//Albersmeier, A.//Al-Dilaimi, A.//Niehaus, K.//Szczepanowski, R.//Kalinowski, J. 	Genome sequence of the halotolerant bacterium Corynebacterium halotolerans type strain YIM 70093(T) (= DSM 44683(T)).	Standards in Genomic Sciences	2012	7		284-293			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. 		
@D	Ruckert, C.//Albersmeier, A.//Winkler, A.//Tauch, A. 	Complete Genome Sequence of Corynebacterium camporealensis DSM 44610, Isolated from the Milk of a Manchega Sheep with Subclinical Mastitis.	Genome Announcements	2015	3		e00572-15			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. 		
@D	Ruckert, C.//Albersmeier, A.//Winkler, A.//Tauch, A. 	Complete Genome Sequence of Corynebacterium kutscheri DSM 20755, a Corynebacterial Type Strain with Remarkably Low G+C Content of Chromosomal DNA.	Genome Announcements	2015	3		e00571-15			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. 		
@D	Ruckert, C.//Eimer, J.//Winkler, A.//Tauch, A. 	Complete Genome Sequence of the Type Strain Corynebacterium epidermidicanis DSM 45586, Isolated from the Skin of a Dog Suffering from Pruritus.	Genome Announcements	2015	3		e00959-15			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. 		
@D	Ruckert, C.//Eimer, J.//Winkler, A.//Tauch, A. 	Complete Genome Sequence of the Type Strain Corynebacterium mustelae DSM 45274, Isolated from Various Tissues of a Male Ferret with Lethal Sepsis.	Genome Announcements	2015	3		e01012-15			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. 		
@D	Ruckert, C.//Kalinowski, J.//Heide, L.//Apel, A.K. 	Draft Genome Sequence of Streptomyces roseochromogenes subsp. oscitans DS 12.976, Producer of the Aminocoumarin Antibiotic Clorobiocin.	Genome Announcements	2014	2		e01147-13			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. 		
@D	Ruckert, C.//Kriete, M.//Jaenicke, S.//Winkler, A.//Tauch, A. 	Complete Genome Sequence of the Type Strain Corynebacterium testudinoris DSM 44614, Recovered from Necrotic Lesions in the Mouth of a Tortoise.	Genome Announcements	2015	3		e00784-15			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. 		
@D	Ruckert, C.//Kriete, M.//Jaenicke, S.//Winkler, A.//Tauch, A. 	Virulence Factor Genes Detected in the Complete Genome Sequence of Corynebacterium uterequi DSM 45634, Isolated from the Uterus of a Maiden Mare.	Genome Announcements	2015	3		e00783-15			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. 		
@D	Ruckert, C.//Licht, K.//Kalinowski, J.//Espirito, S.C.//Antwerpen, M.//Hanczaruk, M.//Reischl, U.//Holzmann, T.//Gessner, A.//Tiemann, C.//Grass, G. 	Draft Genome Sequence of Bacillus anthracis UR-1, Isolated from a German Heroin User.	J. Bacteriol.	2012	194		5997-5998			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. 		
@D	Rueckert, C.//Blom, J.//Chen, X.H.//Reva, O.//Borriss, R. 	Genome sequence of B. amyloliquefaciens type strain DSM7T reveals differences to plant-associated B. amyloliquefaciens FZB42.	J. Biotechnol.	2011	155		78-85			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. 		
@D	Ruepp, A.//Graml, W.//Santos-Martinez, M.-L.//Koretke, K.K.//Volker, C.//Mewes, H.W.//Frishman, D.//Stocker, S.//Lupas, A.N.//Baumeister, W. 	The genome sequence of the thermoacidophilic scavenger Thermoplasma acidophilum.	Nature	2000	407		508-513			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. 		
@D	Ruffing, A.M.//Castro-Melchor, M.//Hu, W.S.//Chen, R.R. 	Genome Sequence of the Curdlan-Producing Agrobacterium sp. Strain ATCC 31749.	J. Bacteriol.	2011	193		4294-4295			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. 		
@D	Ruh, M.//Briand, M.//Bonneau, S.//Jacques, M.A.//Chen, N.W.G. 	Xanthomonas adaptation to common bean is associated with horizontal transfers of genes encoding TAL effectors.	BMC Genomics	2017	18		670			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. 		
@D	Ruh, M.//Briand, M.//Bonneau, S.//Jacques, M.A.//Chen, N.W.G. 	First Complete Genome Sequences of Xanthomonas citri pv. vignicola Strains CFBP7111, CFBP7112, and CFBP7113 Obtained Using Long-Read Technology.	Genome Announcements	2017	5		e00813-17			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. 		
@D	Ruinelli, M.//Blom, J.//Pothier, J.F. 	Complete Genome Sequence of Pseudomonas viridiflava CFBP 1590, Isolated from Diseased Cherry in France.	Genome Announcements	2017	5		e00662-17			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. 		
@D	Ruiz, O.N.//Brown, L.M.//Striebich, R.C.//Mueller, S.S.//Gunasekera, T.S. 	Draft Genome Sequence of Pseudomonas frederiksbergensis SI8, a Psychrotrophic Aromatic-Degrading Bacterium.	Genome Announcements	2015	3		e00811-15			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. 		
@D	Ruiz, S.M.//Letourneau, S.//Cupples, C.G. 	Isolation and characterization of an Escherichia coli strain with a high frequency of C-to-T mutations at 5-methylcytosines.	J. Bacteriol.	1993	175		4985-4989			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. 		
@D	Ruiz-Herrera, J.//Ruiz-Medrano, R.//Dominguez, A. 	Selective inhibition of cytosine-DNA methylases by polyamines.	FEBS Lett.	1995	357		192-196			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. 		
@D	Ruiz-Valdiviezo, V.M.//Rogel-Hernandez, M.A.//Guerrero, G.//Rincon-Molina, C.I.//Garcia-Perez, L.G.//Gutierrez-Miceli, F.A.//Villalobos-Maldonado, J.J.//Lopez-Lopez, A.//Martinez-Romero, E.//Rincon-Rosales, R. 	Complete Genome Sequence of a Novel Nonnodulating Rhizobium Species Isolated from Agave americana L. Rhizosphere.	Genome Announcements	2017	5		e01280-17			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. 		
@D	Rume, F.I.//Antwerpen, M.//Braun, P.//Biswas, P.K.//Yasmin, M.//Grass, G.//Ahsan, C.R.//Hanczaruk, M. 	Genome Sequence of Bacillus anthracis Strain Tangail-1 from Bangladesh.	Genome Announcements	2016	4		e00748-16			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. 		
@D	Rump, L.V.//Strain, E.A.//Cao, G.//Allard, M.W.//Fischer, M.//Brown, E.W.//Gonzalez-Escalona, N. 	Draft Genome Sequences of Six Escherichia coli Isolates from the Stepwise Model of Emergence of Escherichia coli O157:H7.	J. Bacteriol.	2011	193		2058-2059			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(+)). 		
@D	Ruoff, B.//Johansen, S.//Vogt, V.M. 	Characterization of the self-splicing products of a mobile intron from the nuclear rDNA of Physarum polycephalum.	Nucleic Acids Res.	1992	20		5899-5906			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. 		
@D	Ruppe, E.//Olearo, F.//Pires, D.//Baud, D.//Renzi, G.//Cherkaoui, A.//Goldenberger, D.//Huttner, A.//Francois, P.//Harbarth, S.//Schrenzel, J. 	Clonal or not clonal? Investigating hospital outbreaks of KPC-producing Klebsiella pneumoniae with whole-genome sequencing.	Clin. Microbiol. Infect.	2017	23		470475			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. 		
@D	Rusch, D.B. et al. 	The Sorcerer II Global Ocean Sampling Expedition: Northwest Atlantic through Eastern Tropical Pacific.	PLoS Biology	2007	5		e77			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. 		
@D	Rusch, D.B.//Lombardo, M.J.//Yee-Greenbaum, J.//Novotny, M.//Brinkac, L.M.//Lasken, R.S.//Dupont, C.L. 	Draft Genome Sequence of a Single Cell of SAR86 Clade Subgroup IIIa.	Genome Announcements	2013	1		e00030-12			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. 		
@D	Rusch, D.B.//Rowe-Magnus, D.A. 	Complete Genome Sequence of the Pathogenic Vibrio vulnificus Type Strain ATCC 27562.	Genome Announcements	2017	5		e00907-17			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. 		
@D	Ruscher, K.//Reuter, M.//Kupper, D.//Trendelenburg, G.//Dirnagl, U.//Meisel, A. 	A fluorescence based non-radioactive electrophoretic mobility shift assay.	J. Biotechnol.	2000	78		163-170			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. 		
@D	Rusconi, B.//Chen, Y.//Koenig, S.S.//El-Helow, E.R.//Eppinger, M. 	Genome Sequence of Bacillus thuringiensis Strain Btm27, an Egyptian Isolate Highly Toxic to Cotton Leafworm.	Genome Announcements	2015	3		e00446-15			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. 		
@A	Rushizky, G.W. 		Purification of the sequence-specific endonuclease PalI.			Chirikjian, J.G. 		Gene Amplif. Anal.					Elsevier North Holland	1981		1		239-242									*
   I. Growth of cells
  II. Purification of PalI
 III. Physical and chemical properties of the enzyme
  IV. Purification of other enzymes
 
 		
@D	Rusinov, I.//Ershova, A.//Karyagina, A.//Spirin, S.//Alexeevski, A. 	Lifespan of restriction-modification systems critically affects avoidance of their recognition sites in host genomes.	BMC Genomics	2015	16		1084			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. 		
@D	Rusling, D.A.//Laurens, N.//Pernstich, C.//Wuite, G.J.//Halford, S.E. 	DNA looping by FokI: the impact of synapse geometry on loop topology at varied site orientations.	Nucleic Acids Res.	2012	40		4977-4987			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. 		
@D	Rusmintratip, V.//Riggs, A.D.//Sowers, L.C. 	Examination of the DNA substrate selectivity of DNA cytosine methyltransferases using mass tagging.	Nucleic Acids Res.	2000	28		3594-3599			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. 		
@D	Rusniok, C.//Couve, E.//Da Cunha, V.//El Gana, R.//Zidane, N.//Bouchier, C.//Poyart, C.//Leclercq, R.//Trieu-Cuot, P.//Glaser, P. 	Genome Sequence of Streptococcus gallolyticus: Insights into Its Adaptation to the Bovine Rumen and Its Ability To Cause Endocarditis.	J. Bacteriol.	2010	192		2266-2276			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. 		
@D	Russell, D.A.//Bowman, C.A.//Hatfull, G.F. 	Genome Sequence of Salmonella enterica subsp. enterica Strain Durban.	Genome Announcements	2014	2		e00399-14			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. 		
@D	Russell, D.A.//Guerrero, B.C.A.//Garlena, R.A.//Hatfull, G.F. 	Complete Genome Sequence of Gordonia terrae 3612.	Genome Announcements	2016	4		e01058-16			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. 		
@D	Russell, D.A.//Hatfull, G.F. 	Complete Genome Sequence of Arthrobacter sp. ATCC 21022, a Host for Bacteriophage Discovery.	Genome Announcements	2016	4		e00168-16			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. 		
@D	Russell, D.F.//Betts, D.H. 	Alternative splicing and expression analysis of bovine DNA methyltransferase 1.	Dev. Dyn.	2008	237		1051-1059			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. 		
@D	Russell, D.W.//Hirata, R.K. 	The detection of extremely rare DNA modifications.	J. Biol. Chem.	1989	264		10787-10794			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. 		
@D	Russell, D.W.//Zinder, N.D. 	Hemimethylation prevents DNA replication in E. coli.	Cell	1987	50		1071-1079			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. 		
@D	Russo, T.A.//Gill, S.R. 	Draft Genome Sequence of the Hypervirulent Klebsiella pneumoniae Strain hvKP1, Isolated in Buffalo, New York.	Genome Announcements	2013	1		e0006513			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. 		
@D	Rusu, V.//Dorobat-Baron, O.//Cosman, M.//Lazaroae, D. 	Restriction and modification of typing phages by an R factor in S. typhi.	Zentralbl. Bakteriol. [Orig. A]	1976	234		491-501			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. 		
@D	Rutebuka, O.B. 	Molecular studies of restriction genes in enteric bacteria.	Diss. Abstr.	1997	57		4210			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. 		
@D	Rutebuka, O.B.//Lee, N.S.//Ryu, J. 	DNA sequence analysis of the KpnAI restriction gene of Klebsiella pneumoniae M5a1.	Abstr. Gen. Meet. Am. Soc. Microbiol.	1995	95		522			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. 		
@D	Rutkauskas, D.//Petkelyte, M.//Naujalis, P.//Sasnauskas, G.//Tamulaitis, G.//Zaremba, M.//Siksnys, V. 	Restriction Enzyme Ecl18kI-Induced DNA Looping Dynamics by Single-Molecule FRET.	J. Phys. Chem. B	2014	118		8575-8582			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. 		
@D	Rutkowska, S.M.//Skowron, P.M.//Bielawski, K.//Podhajska, A.J. 	SacNI, an isoschizomer of BanII isolated from Streptomyces achromogenes recognizes the 5'-GRGCY/C sequence.	Gene	1995	157		319-320			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). 		
@D	Rutkowska, S.M.//Skowron, P.M.//Podhajska, A.J. 	Purification and characterization of the restriction endonuclease AvcI from Actinomyces cristalomycini.	Gene	1995	157		317-318			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. 		
@D	Rutter, J.M. 	Recent Advances in Microbial Genetics.	Br. Vet. J.	1975	131		284-289			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. 		
@D	Ryan, K.A.//Lo, Y.C. 	Characterization of a CACAG pentanucleotide repeat in Pasteurella haemolytica and its possible role in modulation of a novel type III restriction-modification system.	Nucleic Acids Res.	1999	27		1505-1511			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. 		
@D	Ryan, P.M.//Guinane, C.M.//London, L.E.//Kelleher, P.R.//Fitzgerald, G.F.//Caplice, N.M.//Ross, R.P.//Stanton, C. 	Genome Sequence of the Heteropolysaccharide-Producing Strain Lactobacillus mucosae DPC 6426.	Genome Announcements	2015	3		e01350-14			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. 		
@D	Ryazanova, A.//Migur, A.//Norkin, M.//Timofeyeva, N.//Fedorova, O.//Kubareva, E. 	DNA methyltransferase SsoII: a balance between DNA methylation and transcription repression.	FEBS J.	2013	280		127			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. 		
@A	Ryazanova, A.Y.//Abrosimova, L.A.//Oretskaya, T.S.//Kubareva, E.A. 		Diverse domains of (cytosine-5)-DNA methyltransferases: Structural and functional characterization.			Anica Dricu 		Methylation - from DNA, RNa and histones to diseases and treatment				Rijeka, Croatia	InTech	2012		0		29-69									(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. 		
@D	Ryazanova, A.Y.//Kubareva, E.A.//Grman, I.//Lavrova, N.V.//Ryazanova, E.M.//Oretskaya, T.S.//Hianik, T. 	The study of the interaction of (cytosine-5)-DNA methyltransferase SsoII with DNA by acoustic method.	Analyst	2011	136		1227-1233			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. 		
@D	Ryazanova, A.Y.//Molochkov, N.V.//Abrosimova, L.A.//Alexeevsky, A.V.//Karyagina, A.S.//Protsenko, A.S.//Friedhoff, P.//Oretskaya, T.S.//Kubareva, E.A. 	Secondary structure of SsoII-like (Cytosine-5)-DNA methyltransferases N-terminal region determined by Circular dichroism spectroscopy.	Mol. Biol. (Mosk)	2010	44		911-921			(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. 		
@D	Ryazanova, A.Y.//Winkler, I.//Friedhoff, P.//Viryasov, M.B.//Oretskaya, T.S.//Kubareval, E.A. 	Crosslinking of (cytosine-5)-DNA methyltransferase SsoII and its complexes with specific DNA duplexes provides an insight into their structures.	Nucleosides Nucleotides Nucleic Acids	2011	30		632-650			(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. 		
@D	Rybakova, D.//Wetzlinger, U.//Muller, H.//Berg, G. 	Complete Genome Sequence of Paenibacillus polymyxa Strain Sb3-1, a Soilborne Bacterium with Antagonistic Activity toward Plant Pathogens.	Genome Announcements	2015	3		e00052-15			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. 		
@D	Rye, P.T. 	Biochemical characterization of the Escherichia coli very short patch repair pathway and its coordination with methyltransferase repair of  O6-methylguanine.	Ph.D. Thesis, MIT, USA	2006			1-273			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. 		
@D	Ryu, C.J.//Lee, C.H.//Yoo, O.J. 	A new restriction endonuclease, Bsp1894I, from Bacillus sphaericus 1894.	Korean Biochem. J.	1989	22		444-447			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. 		
@D	Ryu, J. 	Establishment of the KpnAI R-M system of Klebsiella pneumoniae requires prior host modification.	Abstr. Gen. Meet. Am. Soc. Microbiol.	1998	0		288			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. 		
@D	Ryu, J. 	The restriction enzyme KpnAI of Klebsiella pneumoniae is a new member of the type ID family.	Abstr. Gen. Meet. Am. Soc. Microbiol.	1997	97		285			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. 		
@D	Ryu, J.//Rowsell, E. 	Quick identification of Type I restriction enzyme isoschizomers using newly developed pTypeI and reference plasmids.	Nucleic Acids Res.	2008	36		e81			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). 		
@D	Ryu, J.-I.//Rajadas, P.T.//Bullas, L.R. 	Complementation and hybridization evidence for additional families of Type I DNA restriction and modification genes in Salmonella serotypes.	J. Bacteriol.	1988	170		5785-5788			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. 		
@D	Saad, J.//Levasseur, A.//Drancourt, M. 	Draft Genome Sequence of Mycobacterium parafortuitum Strain P7335.	Microbiol. Resour. Announc.	2018	7		e00950-18			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. 		
@D	Saavedra, C.//Gonzalez, E.//Vasquez, C. 	Studies on the heterologous expression of BstVI restriction endonuclease in Escherichia coli.	Biochem. Mol. Biol. Int.	1998	44		391-397			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. 		
@D	Saavedra, C.//Vasquez, C.//Encinas, M.V. 	Structural studies of the BstVI restriction-modification proteins by fluorescence spectroscopy.	Eur. J. Biochem.	1999	263		65-70			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. 		
@D	Saavedra, L.//Hebert, E.M.//Albarracin, L.//Salva, S.//Alvarez, S.//Kitazawa, H.//Villena, J. 	Draft Genome Sequence of Lactobacillus plantarum CRL1506, an Immunomodulatory Strain Isolated from Goat Milk.	Genome Announcements	2016	4		e00108-16			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. 		
@D	Saavedra, S.Y.//Prada-Cardozo, D.//Rincon, V.//Perez-Cardona, H.//Hidalgo, A.M.//Gonzalez, M.N.//Reguero, M.T.//Valenzuela-de-Silva, E.M.//Mantilla, J.R.//Falquet, L.//Barreto-Hernandez, E.//Duarte, C. 	Whole-Genome Sequence of a Colombian Acinetobacter baumannii Strain, a Coproducer of OXA-72 and OXA-255-Like Carbapenemases.	Genome Announcements	2017	5		e01558-16			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. 		
@D	Sabat, A.J.//Hermelijn, S.M.//Akkerboom, V.//Juliana, A.//Degener, J.E.//Grundmann, H.//Friedrich, A.W. 	Complete-genome sequencing elucidates outbreak dynamics of CA-MRSA USA300 (ST8-spa t008) in an academic hospital of Paramaribo, Republic of Suriname.	Sci. Rep.	2017	7		41050			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. 		
@D	Sabat, A.J.//Kock, R.//Akkerboom, V.//Hendrix, R.//Skov, R.L.//Becker, K.//Friedrich, A.W. 	Novel Organization of the Arginine Catabolic Mobile Element and Staphylococcal Cassette Chromosome mec Composite Island and Its Horizontal Transfer between Distinct Staphylococcus aureus Genotypes.	Antimicrob. Agents Chemother.	2013	57		5774-5777			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. 		
@D	Sabat, A.J.//Pournaras, S.//Akkerboom, V.//Tsakris, A.//Grundmann, H.//Friedrich, A.W. 	Whole-genome analysis of an oxacillin-susceptible CC80 mecA-positive Staphylococcus aureus clinical isolate: insights into the mechanisms of cryptic methicillin resistance.	J. Antimicrob. Chemother.	2015	70		2956-2964			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. 		
@D	Sabehi, G.//Beja, O.//Suzuki, M.T.//Preston, C.M.//DeLong, E.F. 	Different SAR86 subgroups harbour divergent proteorhodopsins.	Environ. Microbiol.	2004	6		903-910			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. 		
@D	Sabelnikov, A.G.//Greenberg, B.//Lacks, S.A. 	An extended -10 promoter alone directs transcription of the DpnII operon of Streptococcus pneumoniae.	J. Mol. Biol.	1995	250		144-155			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. 		
@D	Sabharwal, A.//Liao, Y.C.//Lin, H.H.//Haase, E.M.//Scannapieco, F.A. 	Draft genome sequences of 18 oral streptococcus strains that encode amylase-binding proteins.	Genome Announcements	2015	3		e00510-15			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. 		
@D	Sabirova, J.S.//Xavier, B.B.//Coppens, J.//Zarkotou, O.//Lammens, C.//Janssens, L.//Burggrave, R.//Wagner, T.//Goossens, H.//Malhotra-Kumar, S. 	Whole-genome typing and characterization of blaVIM19-harbouring ST383 Klebsiella pneumoniae by PFGE, whole-genome mapping and WGS.	J. Antimicrob. Chemother.	2016	71		1501-1509			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. 		
@D	Sabirova, J.S.//Xavier, B.B.//Hernalsteens, J.P.//De Greve, H.//Ieven, M.//Goossens, H.//Malhotra-Kumar, S. 	Complete Genome Sequences of Two Prolific Biofilm-Forming Staphylococcus aureus Isolates Belonging to USA300 and EMRSA-15 Clonal Lineages.	Genome Announcements	2014	2		e00610-14			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. 		
@D	Sacher, J.C.//Yee, E.//Szymanski, C.M.//Miller, W.G. 	Complete Genome Sequences of Three Campylobacter jejuni Phage-Propagating Strains.	Genome Announcements	2018	6		e00514-18			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. 		
@D	Sacher, J.C.//Yee, E.//Szymanski, C.M.//Miller, W.G. 	Complete Genome Sequence of Campylobacter jejuni Strain 12567, a Livestock-Associated Clade Representative.	Genome Announcements	2018	6		e00513-18			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. 		
@D	Sack, G.H. Jr.//Nathans, D. 	Studies of SV40 DNA. IV.  Cleavage of SV40 DNA by restriction endonuclease from Hemophilus parainfluenzae.	Virology	1973	51		517-520			None 		
@D	Sadri, R.//Hornsby, P.J. 	Rapid analysis of DNA methylation using new restriction enzyme sites created by bisulfite modification.	Nucleic Acids Res.	1996	24		5058-5059			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. 		
@D	Sadykov, M.//Asami, Y.//Niki, H.//Handa, N.//Itaya, M.//Tanokura, M.//Kobayashi, I. 	Multiplication of a restriction-modification gene complex.	Mol. Microbiol.	2003	48		417-427			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. 		
@D	Sadykov, M.//Handa, N.//Asami, Y.//Tanokura, M.//Itaya, M.//Kobayashi, I. 	Selfish maintenance and amplification of BamHI restriction modification gene complex on Bacillus subtilis chromosome.	Mutat. Res.	2001	483		S159			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. 		
@D	Saelens, J.W.//Lau-Bonilla, D.//Moller, A.//Xet-Mull, A.M.//Medina, N.//Guzman, B.//Calderon, M.//Herrera, R.//Stout, J.E.//Arathoon, E.//Samayoa, B.//Tobin, D.M. 	Annotated Genome Sequences of 16 Lineage 4 Mycobacterium tuberculosis Strains from Guatemala.	Genome Announcements	2018	6		e00024-18			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. 		
@D	Saenz, H.L.//Engel, P.//Stoeckli, M.C.//Lanz, C.//Raddatz, G.//Vayssier-Taussat, M.//Birtles, R.//Schuster, S.C.//Dehio, C. 	Genomic analysis of Bartonella identifies type IV secretion systems as host adaptability factors.	Nat. Genet.	2007	39		1469-1476			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. 		
@D	Saffarian, A.//Mulet, C.//Naito, T.//Bouchier, C.//Tichit, M.//Ma, L.//Grompone, G.//Sansonetti, P.J.//Pedron, T. 	Draft Genome Sequences of Acinetobacter parvus CM11, Acinetobacter radioresistens CM38, and Stenotrophomonas maltophilia BR12, Isolated from Murine Proximal Colonic Tissue.	Genome Announcements	2015	3		e01089-15			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. 		
@D	Saffarian, A.//Mulet, C.//Tournebize, R.//Naito, T.//Sansonetti, P.J.//Pedron, T. 	Complete Genome Sequence of Delftia tsuruhatensis CM13 Isolated from Murine Proximal Colonic Tissue.	Genome Announcements	2016	4		e01398-16			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. 		
@D	Sagarkar, S.//Bhardwaj, P.//Yadav, T.C.//Qureshi, A.//Khardenavis, A.//Purohit, H.J.//Kapley, A. 	Draft genome sequence of atrazine-utilizing bacteria isolated from Indian agricultural soil.	Genome Announcements	2014	2		e01149-13			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. 		
@D	Sagawa, H.//Ohshima, A.//Kato, I. 	Sse8387I, a useful eight base cutter for mammalian genome analysis (influence of methylation on the activity of Sse8387I).	Nucleic Acids Res.	1995	23		2367-2370			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. 		
@D	Sagawa, H.//Takagi, M.//Nomura, Y.//Inagaki, K.//Tano, T.//Kishimato, N.//Kotani, H.//Nakajima, K. 	Isolation and identification of restriction endonuclease Aor51HI from Acidiphilium organovorum 51H.	Nucleic Acids Res.	1992	20		365			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. 		
@D	Sager, R.//Kitchin, R. 	Selective Silencing of eukaryotic DNA.	Science	1975	189		426-433			A molecular basis is proposed for programmed inactivation or loss of eukaryotic DNA. 		
@D	Sager, R.//Lane, D. 	Molecular basis of maternal inheritance.	Proc. Natl. Acad. Sci. U. S. A.	1972	69		2410-2413			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. 		
@D	Saghatelyan, A.//Poghosyan, L.//Panosyan, H.//Birkeland, N.K. 	Draft Genome Sequence of Thermus scotoductus Strain K1, Isolated from a Geothermal Spring in Karvachar, Nagorno Karabakh.	Genome Announcements	2015	3		e01346-15			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. 		
@D	Sagitov, V.R.//Aleksandrov, A.A. 	Selectivity of DNA methylase BspRI.	Dokl. Akad. Nauk.	1988	298		1266-1268			None 		
@D	Sagredo-Beltran, J.//De La Cruz-Rodriguez, Y.//Alvarado-Rodriguez, M.//Vega-Arreguin, J.//Rodriguez-Guerra, R.//Alvarado-Gutierrez, A.//Fraire-Velazquez, S. 	Genome Sequence of Bacillus halotolerans Strain MS50-18A with Antifungal Activity against Phytopathogens, Isolated from Saline Soil in San Luis Potosi, Mexico.	Genome Announcements	2018	6		e00135-18			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. 		
@D	Saguez, C.//Lecellier, G.//Koll, F. 	Intronic GIY-YIUG endonuclease gene in the mitochondrial genome of Podospora curvicolla: evidence for mobility.	Nucleic Acids Res.	2000	28		1299-1306			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. 		
@D	Saha, S. et al. 	Genome Sequences of Mycobacteriophages Findley, Hurricane, and TBond007.	Genome Announcements	2017	5		e01123-17			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. 		
@D	Saha, S.//Ahmad, I.//Reddy, Y.V.R.//Krishnamurthy, V.//Rao, D.N. 	Functional analysis of conserved motifs in type III restriction-modification enzymes.	Biol. Chem.	1998	379		511-517			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. 		
@D	Saha, S.//Rao, D.N. 	ATP hydrolysis is required for DNA cleavage by EcoPI restriction enzyme.	J. Mol. Biol.	1995	247		559-567			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. 		
@D	Saha, S.//Rao, D.N. 	Mutations in the Res subunit of the EcoPI restriction enzyme that affect ATP-dependent reactions.	J. Mol. Biol.	1997	269		342-354			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. 		
@D	Sahl, J.W.//Mayo, M.//Price, E.P.//Sarovich, D.S.//Kaestli, M.//Pearson, T.//Williamson, C.H.D.//Nottingham, R.//Sheridan, K.//Wagner, D.M.//Currie, B.J.//Keim, P. 	Complete Genome Sequence of the Environmental Burkholderia pseudomallei Sequence  Type 131 Isolate MSHR1435, Associated with a Chronic Melioidosis Infection.	Genome Announcements	2018	6		e00072-18			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. 		
@D	Sahl, J.W.//Stone, J.K.//Gelhaus, H.C.//Warren, R.L.//Cruttwell, C.J.//Funnell, S.G.//Keim, P.//Tuanyok, A. 	Genome Sequence of Burkholderia pseudomallei NCTC 13392.	Genome Announcements	2013	1		e00183-13			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. 		
@D	Sahni, R.D.//Amalanathan, R.//Devanga, R.N.K.//Mathai, J.//Veeraraghavan, B.//Biswas, I. 	Complete Genome Sequence of Serratia marcescens U36365, a Green Pigment-Producing Strain Isolated from a Patient with Urinary Tract Infection.	Genome Announcements	2016	4		e00837-16			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. 		
@D	Saikawa, Y.//Kubota, T.//Maeda, S.//Otani, Y.//Kumai, K.//Kitajima, M. 	Inhibition of DNA methyltransferase by antisense oligodeoxynucleotide modifies cell characteristics in gastric cancer cell lines.	Oncol. Rep.	2004	12		527-531			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. 		
@D	Saile, N.//Schwarz, L.//Eissenberger, K.//Klumpp, J.//Fricke, F.W.//Schmidt, H. 	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.	Int. J. Med. Microbiol.	2018	308		459-468			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. 		
@D	Saile, N.//Voigt, A.//Kessler, S.//Stressler, T.//Klumpp, J.//Fischer, L.//Schmidt, H. 	In Silico and Functional Analysis of Prophage-Encoded 5-N-Acetyl-9-O-Acetyl Neuraminic Acid Esterases of E. coli O157:H7 Strain EDL933.	Appl. Environ. Microbiol.	2016	82		5940-5950			(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. 		
@D	Sain, B.//Murray, N.E. 	The hsd (host specificity) genes of E. coli K12.	Mol. Gen. Genet.	1980	180		35-46			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. 		
@D	Sainz, F.//Mas, A.//Torija, M.J. 	Draft Genome Sequence of Acetobacter malorum CECT 7742, a Strain Isolated from Strawberry Vinegar.	Genome Announcements	2016	4		e00620-16			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. 		
@D	Sainz, F.//Mas, A.//Torija, M.J. 	Draft Genome Sequences of Gluconobacter cerinus CECT 9110 and Gluconobacter japonicus CECT 8443, Acetic Acid Bacteria Isolated from Grape Must.	Genome Announcements	2016	4		e00621-16			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. 		
@D	Sait, M.//Aitchison, K.//Wheelhouse, N.//Wilson, K.//Lainson, F.A.//Longbottom, D.//Smith, D.G. 	Genome Sequence of Lawsonia intracellularis Strain N343, Isolated from a Sow with Hemorrhagic Proliferative Enteropathy.	Genome Announcements	2013	1		e00027-13			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. 		
@D	Saito, H.//Shibata, T.//Ando, T. 	Mapping of genes determining nonpermissiveness and host-specific restriction to bacteriophages in Bacillus subtilis Marburg.	Mol. Gen. Genet.	1979	170		117-122			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. 		
@D	Saito, M.//Hirasawa, M.//Kuwahara, N.//Okada, T.//Umezawa, K.//Kobayashi, T.//Okamoto, M.//Naito, M.//Hirasawa, M.//Takada, K. 	Complete Genome Sequence of Aggregatibacter actinomycetemcomitans Serotype g Strain NUM4039 (JCM 30399).	Genome Announcements	2016	4		e00158-16			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%. 		
@D	Sakaguchi, Y.//Hayashi, T.//Kurokawa, K.//Nakayama, K.//Oshima, K.//Fujinaga, Y.//Ohnishi, M.//Ohtsubo, E.//Hattori, M.//Oguma, K. 	The genome sequence of Clostridium botulinum type C neurotoxin-converting phage and the molecular mechanisms of unstable lysogeny.	Proc. Natl. Acad. Sci. U. S. A.	2005	102		17472-17477			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. 		
@D	Sakaguchi, Y.//Hosomi, K.//Uchiyama, J.//Ogura, Y.//Umeda, K.//Sakaguchi, M.//Kohda, T.//Mukamoto, M.//Misawa, N.//Matsuzaki, S.//Hayashi, T.//Kozaki, S. 	Draft Genome Sequence of Clostridium botulinum Type B Strain Osaka05, Isolated from an Infant Patient with Botulism in Japan.	Genome Announcements	2014	2		e01010-13			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. 		
@D	Sakai-Kawada, F.E.//Yakym, C.J.//Helmkampf, M.//Hagiwara, K.//Ip, C.G.//Antonio, B.J.//Armstrong, E.//Ulloa, W.J.//Awaya, J.D. 	Draft Genome Sequence of Marine Sponge Symbiont Pseudoalteromonas luteoviolacea IPB1, Isolated from Hilo, Hawaii.	Genome Announcements	2016	4		e01002-16			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. 		
@D	Sakamoto, M.//Ikeyama, N.//Yuki, M.//Ohkuma, M. 	Draft Genome Sequence of Lawsonibacter asaccharolyticus JCM 32166(T), a Butyrate-Producing Bacterium, Isolated from Human Feces.	Genome Announcements	2018	6		e00563-18			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. 		
@D	Sakamoto, M.//Ikeyama, N.//Yuki, M.//Ohkuma, M. 	Draft Genome Sequence of Faecalimonas umbilicata JCM 30896(T), an Acetate-Producing Bacterium Isolated from Human Feces.	Microbiol. Resour. Announc.	2018	7		e01091-18			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. 		
@D	Sakamoto, M.//Lapidus, A.L.//Han, J.//Trong, S.//Haynes, M.//Reddy, T.B.//Mikhailova, N.//Huntemann, M.//Pati, A.//Ivanova, N.N.//Pukall, R.//Markowitz, V.M.//Woyke, T.//Klenk, H.P.//Kyrpides, N.C.//Ohkuma, M. 	High quality draft genome sequence of Bacteroides barnesiae type strain BL2(T) (DSM 18169(T)) from chicken caecum.	Standards in Genomic Sciences	2015	10		48			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. 		
@D	Sakamoto, M.//Oshima, K.//Suda, W.//Kitamura, K.//Iida, T.//Hattori, M.//Ohkuma, M. 	Draft Genome Sequences of Three Strains of Bacteroides pyogenes Isolated from a Cat and Swine.	Genome Announcements	2014	2		e01242-13			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. 		
@D	Sakamoto, M.//Tanaka, N.//Shiwa, Y.//Yoshikawa, H.//Ohkuma, M. 	Draft Genome Sequences of Porphyromonas crevioricanis JCM 15906T and Porphyromonas cansulci JCM 13913T Isolated from a Canine Oral Cavity.	Genome Announcements	2013	1		e00483-13			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. 		
@D	Sakata, T.//Kanesaki, Y.//Yoshikawa, H.//Tsurumaru, H.//Yamakawa, T. 	Draft Genome Sequence of Bradyrhizobium japonicum Is-1, Which Is Incompatible with Rj2 Genotype Soybeans.	Genome Announcements	2015	3		e01219-15			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. 		
@D	Sakihara, K.//Maeda, J.//Tashiro, K.//Fujino, Y.//Kuhara, S.//Ohshima, T.//Ogata, S.//Doi, K. 	Draft Genome Sequence of Thiostrepton-Producing Streptomyces azureus ATCC 14921.	Genome Announcements	2015	3		e01183-15			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%. 		
@D	Sakoula, D.//Nowka, B.//Spieck, E.//Daims, H.//Lucker, S. 	The draft genome sequence of 'Nitrospira lenta' strain BS10, a nitrite oxidizing  bacterium isolated from activated sludge.	Standards in Genomic Sciences	2018	13		32			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. 		
@D	Salah, Z.B.//Rout, S.P.//Humphreys, P.N. 	Draft Whole-Genome Sequence of the Alkaliphilic Alishewanella aestuarii Strain HH-ZS, Isolated from Historical Lime Kiln Waste-Contaminated Soil.	Genome Announcements	2016	4		e01447-16			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. 		
@D	Salaj-Smic, E.//Donjerkovic, D.//Trgovcevic, Z. 	In vivo modulation of the EcoK restriction endonuclease.	Periodicum Biologorum	1994	96		357-358			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. 		
@D	Salaj-Smic, E.//Marsic, N.//Trgovcevic, Z.//Lloyd, R.G. 	Modulation of EcoKI restriction in vivo: Role of the lambda gam protein and plasmid metabolism.	J. Bacteriol.	1997	179		1852-1856			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. 		
@D	Salama, N.//Guillemin, K.//McDaniel, T.K.//Sherlock, G.//Tompkins, L.//Falkow, S. 	A whole-genome microarray reveals genetic diversity among Helicobacter pylori strains.	Proc. Natl. Acad. Sci. U. S. A.	2000	97		14668-14673			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. 		
@D	Salama, N.R.//Gonzalez-Valencia, G.//Deatherage, B.//Aviles-Jimenez, F.//Atherton, J.C.//Graham, D.Y.//Torres, J. 	Genetic analysis of Helicobacter pylori strain populations colonizing the stomach at different times postinfection.	J. Bacteriol.	2007	189		3834-3845			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. 		
@D	Salanoubat, M. et al. 	Genome sequence of the plant pathogen Ralstonia solanacearum.	Nature	2002	415		497-502			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. 		
@D	Salauen, L.//Linz, B.//Suerbaum, S.//Saunders, N.J. 	The diversity within an expanded and redefined repertoire of phase-variable genes in Helicobacter pylori.	Microbiology	2004	150		817-830			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. 		
@D	Salazar, J.K.//Gonsalves, L.J.//Schill, K.M.//Sanchez, L.M.//Anderson, N.//Keller, S.E. 	Complete Genome Sequence of Listeria monocytogenes DFPST0073, Isolated from Imported Mexican Soft Cheese.	Genome Announcements	2018	6		e00496-18			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. 		
@D	Saldana-Ahuactzi, Z.//Cruz-Cordova, A.//Rodea, G.E.//Porta, H.//Navarro-Ocana, A.//Eslava-Campos, C.//Cevallos, M.A.//Xicohtencatl-Cortes, J. 	Genome Sequence of Enterotoxigenic Escherichia coli Strain FMU073332.	Genome Announcements	2017	5		e01600-16			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. 		
@D	Saldanha, R.//Chen, B.//Wank, H.//Matsuura, M.//Edwards, J.//Lambowitz, A.M. 	RNA and protein catalysis in group II intron splicing and mobility reactions using purified components.	Biochemistry	1999	38		9069-9083			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. 		
@D	Sales, A.I.L.//Milanez, G.P.//Nascimento, L.C.//do Carmo, C.P.//da Costa, F.L.P.//Pereira, G.A.G.//Martinez, R.//Brocchi, M. 	Draft Genome Sequences of Three Salmonella enterica Serovar 4,[5],12:i:- Strains  and One S. enterica Serovar Typhimurium Strain, Isolated in Brazil.	Genome Announcements	2018	6		e00488-18			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. 		
@D	Sales, C.M.//Mahendra, S.//Grostern, A.//Parales, R.E.//Goodwin, L.//Woyke, T.//Nolan, M.//Lapidus, A.//Chertkov, O.//Ovchinnikova, G.//Szcyrba, A.//Alvarez-Cohen, L. 	Genome sequence of 1,4-dioxane degrading Pseudonocardia dioxanivorans strain CB1190.	J. Bacteriol.	2011	193		4549-4550			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. 		
@D	Salgado-Morales, R.//Rivera-Gomez, N.//Lozano-Aguirre, B.L.F.//Hernandez-Mendoza, A.//Dantan-Gonzalez, E. 	Draft Genome Sequence of a Pseudomonas aeruginosa NA04 Bacterium Isolated from an Entomopathogenic Nematode.	Genome Announcements	2017	5		e00746-17			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%. 		
@D	Salgado-Morales, R.//Rivera-Gomez, N.//Martinez-Ocampo, F.//Lozano-Aguirre, B.L.F.//Hernandez-Mendoza, A.//Dantan-Gonzalez, E. 	Draft Genome Sequence of Photorhabdus luminescens HIM3 Isolated from an Entomopathogenic Nematode in Agricultural Soils.	Genome Announcements	2017	5		e00745-17			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. 		
@D	Salipante, S.J.//Roach, D.J.//Kitzman, J.O.//Snyder, M.W.//Stackhouse, B.//Butler-Wu, S.M.//Lee, C.//Cookson, B.T.//Shendure, J. 	Large-scale genomic sequencing of extraintestinal pathogenic Escherichia coli strains.	Genome Res.	2014	25		119-128			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. 		
@D	Salka, I.//Srivastava, A.//Allgaier, M.//Grossart, H.P. 	The Draft Genome Sequence of Sphingomonas sp. Strain FukuSWIS1, Obtained from Acidic Lake Grosse Fuchskuhle, Indicates Photoheterotrophy and a Potential for  Humic Matter Degradation.	Genome Announcements	2014	2		e01183-14			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. 		
@D	Salman, V.//Berben, T.//Bowers, R.M.//Woyke, T.//Teske, A.//Angert, E.R. 	Insights into the single cell draft genome of 'Candidatus Achromatium palustre'.	Standards in Genomic Sciences	2016	11		28			'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. 		
@D	Salmon-Divon, M.//Banai, M.//Bardenstein, S.//Blum, S.E.//Kornspan, D. 	Complete Genome Sequence of the Live Attenuated Vaccine Strain Brucella melitensis Rev.1.	Genome Announcements	2018	6		e00175-18			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. 		
@D	Salva-Serra, F.//Jakobsson, H.E.//Busquets, A.//Gomila, M.//Jaen-Luchoro, D.//Segui, C.//Aliaga-Lozano, F.//Garcia-Valdes, E.//Lalucat, J.//Moore, E.R.//Bennasar-Figueras, A. 	Genome Sequences of Two Naphthalene-Degrading Strains of Pseudomonas balearica, Isolated from Polluted Marine Sediment and from an Oil Refinery Site.	Genome Announcements	2017	5		e00116-17			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. 		
@D	Salva-Serra, F.//Jakobsson, H.E.//Thorell, K.//Gonzales-Siles, L.//Hallback, E.T.//Jaen-Luchoro, D.//Boulund, F.//Sikora, P.//Karlsson, R.//Svensson, L.//Bennasar, A.//Engstrand, L.//Kristiansson, E.//Moore, E.R. 	Draft Genome Sequence of Streptococcus gordonii Type Strain CCUG 33482T.	Genome Announcements	2016	4		e00175-16			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. 		
@D	Salwan, R.//Swarnkar, M.K.//Singh, A.K.//Kasana, R.C. 	First draft genome sequence of a member of the genus planomicrobium, isolated from the chandra river, India.	Genome Announcements	2014	2		e01259-13			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%. 		
@D	Salzberg, S.L. et al. 	Genome sequence and rapid evolution of the rice pathogen Xanthomonas oryzae pv. oryzae PXO99A.	BMC Genomics	2008	9		204			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. 		
@D	Sam, K.K.//Lau, N.S.//Furusawa, G.//Amirul, A.A. 	Draft Genome Sequence of Halophilic Hahella sp. Strain CCB-MM4, Isolated from Matang Mangrove Forest in Perak, Malaysia.	Genome Announcements	2017	5		e01147-17			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. 		
@D	Sam, M.D.//Horton, N.C.//Nissan, T.A.//Perona, J.J. 	Catalytic efficiency and sequence selectivity of a restriction endonuclease modulated by a distal manganese ion binding site.	J. Mol. Biol.	2001	306		851-861			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. 		
@D	Sam, M.D.//Perona, J.J. 	Mn2+-dependent catalysis by restriction enzymes: Pre-steady-state analysis of EcoRV endonuclease reveals burst kinetics and the origins of reduced activity.	J. Am. Chem. Soc.	1999	121		1444-1447			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. 		
@D	Sam, M.D.//Perona, J.J. 	Catalytic roles of divalent metal ions in phosphoryl transfer by EcoRV endonuclease.	Biochemistry	1999	38		6576-6586			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. 		
@D	Samad, A.//Trognitz, F.//Antonielli, L.//Compant, S.//Sessitsch, A. 	High-Quality Draft Genome Sequence of an Endophytic Pseudomonas viridiflava Strain with Herbicidal Properties against Its Host, the Weed Lepidium draba L.	Genome Announcements	2016	4		e01170-16			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. 		
@D	Sambles, C.M.//White, D.A. 	Genome Sequence of Rhodococcus sp. Strain PML026, a Trehalolipid Biosurfactant Producer and Biodegrader of Oil and Alkanes.	Genome Announcements	2015	3		e00433-15			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. 		
@D	Samko, O.T.//Kalugin, A.A.//Eldarov, M.A.//Karpychev, I.V.//Anikeitcheva, N.V.//Khoroshutina, E.B.//Skryabin, K.G.//Librik, G.I.//Sokolov, N.N. 	Isolation, purification and characterization of new site-specific endonucleases BciBI and BciBII produced by Bacillus circulans.	Bioorg. Khim.	1994	20		1327-1333			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. 		
@D	Sampaio, J.L.//Ribeiro, V.B.//Campos, J.C.//Rozales, F.P.//Magagnin, C.M.//Falci, D.R.//da Silva, R.C.//Dalarosa, M.G.//Luz, D.I.//Vieira, F.J.//Antochevis, L.C.//Barth, A.L.//Zavascki, A.P. 	Detection of OXA-370, an OXA-48-Related Class D beta-Lactamase, in Enterobacter hormaechei from Brazil.	Antimicrob. Agents Chemother.	2014	58		3566-3567			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. 		
@D	Sampath, J.//Vijayakumar, M.N. 	A DNA cytosine methyltransferase-like gene in Streptococcal conjugative transposon, Tn5252.	Abstr. Gen. Meet. Am. Soc. Microbiol.	1995	95		511			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. 		
@D	Sampath, J.//Vijayakumar, M.N. 	Identification of a DNA cytosine methyltransferase gene in conjugative transposon Tn5252.	Plasmid	1998	39		63-76			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. 		
@D	Samrakandi, M.M.//Cirillo, S.L.G.//Ridenour, D.A.//Bermudez, L.E.//Cirillo, J.D. 	Genetic and phenotypic differences between Legionella pneumophila strains.	J. Clin. Microbiol.	2002	40		1352-1362			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. 		
@D	Samson, J.E.//Belanger, M.//Moineau, S. 	Effect of the abortive infection mechanism and type III toxin/antitoxin system AbiQ on the lytic cycle of Lactococcus lactis phages.	J. Bacteriol.	2013	195		3947-3956			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. 		
@D	Samson, J.E.//Magadan, A.H.//Sabri, M.//Moineau, S. 	Revenge of the phages: defeating bacterial defences.	Nat. Rev. Microbiol.	2013	11		675-687			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. 		
@D	Samson, J.E.//Moineau, S. 	Characterization of Lactococcus lactis phage 949 and comparison with other lactococcal phages.	Appl. Environ. Microbiol.	2010	76		6843-6852			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. 		
@D	Samuel, B.S.//Hansen, E.E.//Manchester, J.K.//Coutinho, P.M.//Henrissat, B.//Fulton, R.//Latreille, P.//Kim, K.//Wilson, R.K.//Gordon, J.I. 	Genomic and metabolic adaptations of Methanobrevibacter smithii to the human gut.	Proc. Natl. Acad. Sci. U. S. A.	2007	104		10643-10648			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. 		
@D	Samuelson, J.C.//Morgan, R.D.//Benner, J.S.//Claus, T.E.//Packard, S.L.//Xu, S.Y. 	Engineering a rare-cutting restriction enzyme: genetic screening and selection of NotI variants.	Nucleic Acids Res.	2006	34		796-805			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. 		
@D	Samuelson, J.C.//Xu, S.-Y. 	Directed evolution of restriction endonuclease BstYI to achieve increased substrate specificity.	J. Mol. Biol.	2002	319		673-683			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. 		
@D	Samuelson, J.C.//Zhu, Z.//Xu, S.-y. 	The isolation of strand-specific nicking endonucleases from a randomized SapI expression library.	Nucleic Acids Res.	2004	32		3661-3671			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. 		
@D	San Martin-Uriz, P.//Gomez, M.J.//Arcas, A.//Bargiela, R.//Amils, R. 	Draft Genome Sequence of the Electricigen Acidiphilium sp. Strain PM (DSM 24941).	J. Bacteriol.	2011	193		5585-5586			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. 		
@D	Sanabria, L.//Lagrave, L.//Nishibe, C.//Ribas, A.C.A.//Zumarraga, M.J.//Almeida, N.F.//Araujo, F.R. 	Draft Genome Sequences of Two Mycobacterium bovis Strains Isolated from Beef Cattle in Paraguay.	Genome Announcements	2017	5		e00616-17			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. 		
@D	Sanchez, D.O.//Zandomeni, R.O.//Cravero, S.//Verdun, R.E.//Pierrou, E.//Faccio, P.//Diaz, G.//Lanzavecchia, S.//Aguero, F.//Frasch, A.C.C.//Andersson, S.G.E.//Rosetti, O.L.//Grau, O.//Ugalde, R.A. 	Gene discovery through genomic sequencing of Brucella abortus.	Infect. Immun.	2001	69		865-868			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. 		
@D	Sanchez, J.//Barbes, C.//Hernandez, A.//de los Reyes-Gavilan, C.G.//Hardisson, C. 	Restriction-modification systems in Streptomyces antibioticus.	Can. J. Microbiol.	1985	31		942-946			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. 		
@D	Sanchez-Canizares, C.//Jorrin, B.//Duran, D.//Nadendla, S.//Albareda, M.//Rubio-Sanz, L.//Lanza, M.//Gonzalez-Guerrero, M.//Prieto, R.//Brito, B.//Giglio, M.//Rey, L.//Ruiz-Argueso, T.//Palacios, J.M.//Imperial, J. 	Genomic Diversity in the Endosymbiotic Bacterium Rhizobium leguminosarum.	Genes (Basel)	2018	9		E60			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. 		
@D	Sanchez-Castro, I.//Bakkali, M.//Merroun, M.L. 	Draft Genome Sequence of Stenotrophomonas bentonitica BII-R7T, a Selenite-Reducing Bacterium Isolated from Spanish Bentonites.	Genome Announcements	2017	5		e00719-17			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. 		
@D	Sanchez-Leon, M.//Fashae, K.//Kastanis, G.//Allard, M. 	Draft Genome Sequences of 23 Salmonella enterica Strains Isolated from Cattle in  Ibadan, Nigeria, Representing 21 Salmonella Serovars.	Genome Announcements	2017	5		e01128-17			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. 		
@D	Sanchez-Porro, C.//de la Haba, R.R.//Cruz-Hernandez, N.//Gonzalez, J.M.//Reyes-Guirao, C.//Navarro-Sampedro, L.//Carballo, M.//Ventosa, A. 	Draft Genome of the Marine Gammaproteobacterium Halomonas titanicae.	Genome Announcements	2013	1		e0008313			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. 		
@D	Sanchez-Romero, M.A.//Cota, I.//Casadesus, J. 	DNA methylation in bacteria: from the methyl group to the methylome.	Curr. Opin. Microbiol.	2015	25		9-16			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. 		
@D	Sanchez-Vizuete, P.//Tanaka, K.//Bridier, A.//Shirae, Y.//Yoshida, K.//Bouchez, T.//Aymerich, S.//Briandet, R.//Le Coq, D. 	Genome Sequences of Two Nondomesticated Bacillus subtilis Strains Able To Form Thick Biofilms on Submerged Surfaces.	Genome Announcements	2014	2		e00946-14			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. 		
@D	Sandal, I.//Seleem, M.N.//Elswaifi, S.F.//Sriranganathan, N.//Inzana, T.J. 	Construction of a high-efficiency shuttle vector for Histophilus somni.	J. Microbiol. Methods	2008	74		106-109			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. 		
@D	Sandegren, L.//Linkevicius, M.//Lytsy, B.//Melhus, A.//Andersson, D.I. 	Transfer of an Escherichia coli ST131 multiresistance cassette has created a Klebsiella pneumoniae-specific plasmid associated with a major nosocomial outbreak.	J. Antimicrob. Chemother.	2012	67		74-83			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. 		
@D	Sandegren, L.//Nord, D.//Sjoberg, B.M. 	SegH and Hef: two novel homing endonucleases whose genes replace the mobC and mobE genes in several T4-related phages.	Nucleic Acids Res.	2005	33		6203-6213			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. 		
@D	Sandegren, L.//Sjoberg, B.M. 	Distribution, sequence homology, and homing of group I introns among T-even-like bacteriophages: evidence for recent transfer of old introns.	J. Biol. Chem.	2004	279		22218-22227			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. 		
@D	Sanders, K.L.//Catto, L.E.//Bellamy, S.R.//Halford, S.E. 	Targeting individual subunits of the FokI restriction endonuclease to specific DNA strands.	Nucleic Acids Res.	2009	37		2105-2115			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. 		
@D	Sanders, M.E. 	Phage resistance in lactic acid bacteria.	Biochimie	1988	70		411-422			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. 		
@D	Sanders, M.E.//Klaenhammer, T.R. 	Evidence for plasmid linkage of restriction and modification in Streptococcus cremoris KH.	Appl. Environ. Microbiol.	1981	42		944-950			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. 		
@D	Sanders, M.E.//Klaenhammer, T.R. 	Phage resistance in a phage-insensitive strain of Streptococcus lactis:  temperature-dependent phage development and host-controlled phage replication.	Appl. Environ. Microbiol.	1984	47		979-985			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. 		
@D	Sanders, M.E.//Klaenhammer, T.R. 	Restriction and modification in group N streptococci: Effect of heat on development of modified lytic bacteriophage.	Appl. Environ. Microbiol.	1980	40		500-506			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. 		
@D	Sanders, M.E.//Klaenhammer, T.R. 	Characterization of phage-sensitive mutants from a phage-insensitive strain of Streptococcus lactis: Evidence for a plasmid determinant that prevents phage adsorption.	Appl. Environ. Microbiol.	1983	46		1125-1133			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. 		
@D	Sanders, M.E.//Shultz, J.W. 	Cloning of phage resistance genes from Lactococcus lactis ssp. cremoris KH.	J. Dairy Sci.	1990	73		2044-2053			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. 		
@D	Sandner-Miranda, L.//Vinuesa, P.//Soberon-Chavez, G.//Morales-Espinosa, R. 	Complete Genome Sequence of Serratia marcescens SmUNAM836, a Nonpigmented Multidrug-Resistant Strain Isolated from a Mexican Patient with Obstructive  Pulmonary Disease.	Genome Announcements	2016	4		e01417-15			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. 		
@D	Sandoval, N.R.//Venkataramanan, K.P.//Groth, T.S.//Papoutsakis, E.T. 	Whole-genome sequence of an evolved Clostridium pasteurianum strain reveals Spo0A deficiency responsible for increased butanol production and superior growth.	Biotechnol. Biofuels.	2015	8		227			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. 		
@D	Sands, T.W.//Petras, M.L.//Van Wijngaarden, J. 	A computer program to assist in the choice of restriction endonucleases for use in DNA analysis.	Int. J. Biomed. Comput.	1990	26		39-52			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. 		
@D	Sangal, V.//Blom, J.//Sutcliffe, I.C.//von Hunolstein, C.//Burkovski, A.//Hoskisson, P.A. 	Adherence and invasive properties of Corynebacterium diphtheriae strains correlates with the predicted membrane-associated and secreted proteome.	BMC Genomics	2015	16		765			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. 		
@D	Sangal, V.//Burkovski, A.//Hunt, A.C.//Edwards, B.//Blom, J.//Hoskisson, P.A. 	A lack of genetic basis for biovar differentiation in clinically important Corynebacterium diphtheriae from whole genome sequencing.	Infect. Genet. Evol.	2014	21		54-57			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. 		
@D	Sangal, V.//Tucker, N.P.//Burkovski, A.//Hoskisson, P.A. 	Draft Genome Sequence of Corynebacterium diphtheriae Biovar Intermedius NCTC 5011.	J. Bacteriol.	2012	194		4738			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. 		
@D	Sangal, V.//Tucker, N.P.//Burkovski, A.//Hoskisson, P.A. 	The Draft Genome Sequence of Corynebacterium diphtheriae bv. mitis NCTC 3529 Reveals Significant Diversity between the Primary Disease-Causing Biovars.	J. Bacteriol.	2012	194		3269			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. 		
@D	Sanjar, F. et al. 	Genome Sequence of Escherichia coli O157:H7 Strain 2886-75, Associated with the First Reported Case of Human Infection in the United States.	Genome Announcements	2014	2		e01120-13			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. 		
@D	Sanjar, F.//Karna, S.L.//Chen, T.//Chen, P.//Abercrombie, J.J.//Leung, K.P. 	Whole-Genome Sequence of Multidrug-Resistant Pseudomonas aeruginosa Strain BAMCPA07-48, Isolated from a Combat Injury Wound.	Genome Announcements	2016	4		e00547-16			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. 		
@D	Sanko, T.J.//Kraemer, A.S.//Niemann, N.//Gupta, A.K.//Flett, B.C.//Mienie, C.//Bezuidenhout, C.C. 	Draft Genome Assemblages of 10 Xanthomonas vasicola pv. zeae Strains, Pathogens Causing Leaf Streak Disease of Maize in South Africa.	Genome Announcements	2018	6		e00532-18			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. 		
@D	Sankpal, U.T.//Rao, D.N. 	Mutational analysis of conserved residues in HhaI DNA methyltransferase.	Nucleic Acids Res.	2002	30		2628-2638			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. 		
@D	Sankpal, U.T.//Rao, D.N. 	Structure, function, and mechanism of HhaI DNA methyltransferases.	Crit. Rev. Biochem. Mol. Biol.	2002	37		167-197			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. 		
@D	Sannazzaro, A.I.//Torres, T.G.A.//Caballero, M.//Dip, D.//Pistorio, M.//Estrella, M.J. 	Genome Sequence of the Symbiotic Type Strain Mesorhizobium helmanticense CSLC115N Isolated from Lotus corniculatus Nodules.	Genome Announcements	2018	6		e00412-18			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. 		
@D	Sannino, D.//Angert, E.R. 	Genomic insights into the thiamin metabolism of Paenibacillus thiaminolyticus NRRL B-4156 and P. apiarius NRRL B-23460.	Standards in Genomic Sciences	2017	12		59			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. 		
@D	Sano, H.//Sager, R. 	Deoxyribonucleic acid methyltransferase from the eukaryote, Chlamydomonas reinhardi.	Eur. J. Biochem.	1980	105		471-480			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. 		
@D	Sano, K.I.//Anraku, A. 	Draft Genome Sequence of Brevibacillusreuszeri Strain NIT02, Isolated from a Laundered Rental Cloth Hot Towel.	Genome Announcements	2018	6		e01353-17			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. 		
@D	Sansom, C.E.//Biro, J.C.//Benyo, B.//Benyo, Z. 	Codes in the codons: codon-amino acid complementarity revealed in the structures of restriction enzyme - DNA complexes.	FEBS J.	2005	272		100			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. 		
@D	Santagati, M.//Iannelli, F.//Cascone, C.//Campanile, F.//Oggioni, M.R.//Stefani, S.//Pozzi, G. 	The novel conjugative transposon tn1207.3 carries the macrolide efflux gene mef(A) in Streptococcus pyogenes.	Microb. Drug Resist.	2003	9		243-247			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. 		
@D	Santamaria, R.I.//Bustos, P.//Perez-Carrascal, O.M.//Miranda-Sanchez, F.//Vinuesa, P.//Martinez-Flores, I.//Juarez, S.//Lozano, L.//Martinez-Romero, E.//Cevallos, M.A.//Romero, D.//Davila, G.//Ormeno-Orrillo, E.//Gonzalez, V. 	Complete Genome Sequences of Eight Rhizobium Symbionts Associated with Common Bean (Phaseolus vulgaris).	Genome Announcements	2017	5		e00645-17			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. 		
@D	SantAnna, B.M.//Marbach, P.P.//Rojas-Herrera, M.//De Souza, J.T.//Roque, M.R.//Queiroz, A.T. 	High-Quality Draft Genome Sequence of Bacillus amyloliquefaciens Strain 629, an Endophyte from Theobroma cacao.	Genome Announcements	2015	3		e01325-15			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. 		
@D	Santhoshkumar, P.//Sharma, K.K. 	Analysis of alpha-crystallin chaperone function using restriction enzymes and citrate synthase.	Mol. Vis.	2001	7		172-177			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. 		
@D	Santi, D.V.//Garrett, C.E.//Barr, P.J. 	On the mechanism of inhibition of DNA-cytosine methyltransferases by cytosine analogs.	Cell	1983	33		9-10			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). 		
@D	Santi, D.V.//Norment, A.//Garrett, C.E. 	Covalent bond formation between a DNA-cytosine methyltransferase and DNA containing 5-azacytosine.	Proc. Natl. Acad. Sci. U. S. A.	1984	81		6993-6997			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. 		
@D	Santini, S.//Jeudi, S.//Bartoli, J.//Poirot, O.//Lescot-David, M.//Barbe, V.//Wommack, E.K.//Abergel, C.//Brussaard, C.//Claverie, J.-M. 	The genome of Phaeocystis globosa virus PgV-16T highlights the common ancestry of the largest known DNA viruses infecting eukaryotes.	Proc. Natl. Acad. Sci. U. S. A.	2013	110		10800-10805			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. 		
@D	Santopolo, L.//Marchi, E.//Decorosi, F.//Galardini, M.//Brilli, M.//Giovannetti, L.//Viti, C. 	Draft Genome Sequence of Chromate-Resistant and Biofilm-Producing Strain Pseudomonas alcaliphila 34.	Genome Announcements	2013	1		e00125-12			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. 		
@D	Santoro, A.E.//Dupont, C.L.//Richter, R.A.//Craig, M.T.//Carini, P.//McIlvin, M.R.//Yang, Y.//Orsi, W.//Moran, D.//Saito, M. 	Genomic and proteomic characterization of Candidatus Nitrosopelagicus brevis: an ammonia-oxidizing archaeon from the open ocean.	Proc. Natl. Acad. Sci. U. S. A.	2015	112		1173-1178			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. 		
@D	Santos, A.P.//Guimaraes, A.M.S.//do Nascimento, N.C.//SanMiguel, P.J.//Martin, S.W.//Messick, J.B. 	Genome of Mycoplasma haemofelis, unraveling its strategies for survival and persistence.	Vet. Res.	2011	42		102			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. 		
@D	Santos, F.//Yarza, P.//Parro, V.//Briones, C.//Anton, J. 	The metavirome of a hypersaline environment.	Environ. Microbiol.	2010	12		2965-2976			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. 		
@D	Santos, O.C.//Duarte, A.F.//Albano, R.M.//Bastos, M.C. 	Draft Genome Sequence of the Aureocin A53-Producing Strain Staphylococcus aureus  A53.	Genome Announcements	2016	4		e00858-16			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. 		
@D	Santos, S.N.//Gacesa, R.//Taketani, R.G.//Long, P.F.//Melo, I.S. 	Genome Sequence of Streptomyces caatingaensis CMAA 1322, a New Abiotic Stress-Tolerant Actinomycete Isolated from Dried Lake Bed Sediment in the Brazilian Caatinga Biome.	Genome Announcements	2015	3		e01020-15			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. 		
@D	Santos, S.N.//Kavamura, V.N.//Taketani, R.G.//Vasconcellos, R.L.//Zucchi, T.D.//Melo, I.S. 	Draft Genome Sequence of Bacillus sp. Strain CMAA 1185, a Cellullolytic Bacterium Isolated from Stain House Lake, Antarctic Peninsula.	Genome Announcements	2015	3		e00436-15			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. 		
@D	Santos, T.//Cruz, A.//Caetano, T.//Covas, C.//Mendo, S. 	Draft Genome Sequence of Pedobacter sp. Strain NL19, a Producer of Potent Antibacterial Compounds.	Genome Announcements	2015	3		e00184-15			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. 		
@D	Santos-Garcia, D.//Farnier, P.A.//Beitia, F.//Zchori-Fein, E.//Vavre, F.//Mouton, L.//Moya, A.//Latorre, A.//Silva, F.J. 	Complete Genome Sequence of 'Candidatus Portiera aleyrodidarum' BT-QVLC, an Obligate Symbiont That Supplies Amino Acids and Carotenoids to Bemisia tabaci.	J. Bacteriol.	2012	194		6654-6655			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. 		
@D	Santourlidis, S.//Schulz, W.A. 	The cytotoxic effect of DNA methyltransferase I over-expression is mediated by the N-terminal.	Biochem. Soc. Trans.	2000	28		A182			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. 		
@D	Sanudo, A.I.//Olivares, M.M.//Banuelos, O. 	Draft Genome Sequence of Lactobacillus reuteri CECT8605.	Genome Announcements	2017	5		e00297-17			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. 		
@D	Sapienza, P.//Kurpiewski, M.//Jen-Jacobson, L. 	Thermodynamic and kinetic basis of promiscuity in mutant EcoRI endonucleases.	Biophys. J.	2003	84		367a			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. 		
@D	Sapienza, P.J.//Dela-Torre, C.A.//McCoy, W.H.//Jana, S.V.//Jen-Jacobson, L. 	Thermodynamic and kinetic basis for the relaxed DNA sequence specificity of "promiscuous" mutant EcoRI endonucleases.	J. Mol. Biol.	2005	348		307-324			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. 		
@D	Sapienza, P.J.//Rosenberg, J.M.//Jen-Jacobson, L. 	Structural and Thermodynamic Basis for Enhanced DNA Binding by a Promiscuous Mutant EcoRI Endonuclease.	Structure	2007	15		1368-1382			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. 		
@D	Sapp, A.//Huguet-Tapia, J.C.//Sanchez-Lamas, M.//Antelo, G.T.//Primo, E.D.//Rinaldi, J.//Klinke, S.//Goldbaum, F.A.//Bonomi, H.R.//Christner, B.C.//Otero, L.H. 	Draft Genome Sequence of Methylobacterium sp. Strain V23, Isolated from Accretion Ice of the Antarctic Subglacial Lake Vostok.	Genome Announcements	2018	6		e00145-18			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. 		
@D	Sapranauskas, R. 	Investigation of type IIS restriction endonuclease BfiI domain organization by using a new random gene dissection approach.	Ph.D. Thesis, Vilnius University	2008			1-42			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. 		
@D	Sapranauskas, R.//Lubys, A. 	Random gene dissection: a tool for the investigation of protein structural organization.	Biotechniques	2005	39		395-402			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. 		
@D	Sapranauskas, R.//Sasnauskas, G.//Lagunavicius, A.//Vilkaitis, G.//Lubys, A.//Siksnys, V. 	Novel subtype of type IIs restriction enzymes. BfiI endonuclease exhibits similarities to the EDTA-resistant nuclease Nuc of Salmonella typhimurium.	J. Biol. Chem.	2000	275		30878-30885			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. 		
@D	Saranathan, R.//Tomar, A.//Sudhakar, P.//Arunkumar, K.P.//Prashanth, K. 	Draft Genome Sequence of a Multidrug-Resistant Acinetobacter baumannii PKAB07 Clinical Strain from India Belonging to Sequence Type 195.	Genome Announcements	2014	2		e00184-14			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. 		
@D	Saravanan, M.//Bujnicki, J.M.//Cymerman, I.A.//Rao, D.N.//Nagaraja, V. 	Type II restriction endonuclease R.KpnI is a member of the HNH nuclease superfamily.	Nucleic Acids Res.	2004	32		6129-6135			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. 		
@D	Saravanan, M.//Elango, K.//Chandrashekaran, S.//Anand, N.//Nagaraja, V. 	A new type II restriction endonuclease, OfoI from nonheterocystous cynobacterium Oscillatoria foreaui.	Curr. Sci.	2003	85		188-190			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. 		
@D	Saravanan, M.//Vasu, K.//Ghosh, S.//Nagaraja, V. 	Dual role for Zn2+ in maintaining structural integrity and inducing DNA sequence specificity in a promiscuous endonuclease.	J. Biol. Chem.	2007	282		32320-32326			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. 		
@D	Saravanan, M.//Vasu, K.//Kanakaraj, R.//Rao, D.N.//Nagaraja, V. 	R.KpnI, an HNH superfamily REase, exhibits differential discrimination at non-canonical sequences in the presence of Ca2+ and Mg2+.	Nucleic Acids Res.	2007	35		2777-2786			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. 		
@D	Saravanan, M.//Vasu, K.//Nagaraja, V. 	Evolution of sequence specificity in a restriction endonuclease by a point mutation.	Proc. Natl. Acad. Sci. U. S. A.	2008	105		10344-10347			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. 		
@D	Sargueil, B.//Delahodde, A.//Hatat, D.//Tian, G.L.//Lazowska, J.//Jacq, C. 	A new specific DNA endonuclease activity in yeast mitochondria.	Mol. Gen. Genet.	1991	225		340-341			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. 		
@D	Sargueil, B.//Hatat, D.//Delahodde, A.//Jacq, C. 	In vivo and in vitro analyses of an intron-encoded DNA endonuclease from yeast mitochondria.  Recognition site by site-directed mutagenesis.	Nucleic Acids Res.	1990	18		5659-5665			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. 		
@D	Saridaki, A.//Sapountzis, P.//Harris, H.L.//Batista, P.D.//Biliske, J.A.//Pavlikaki, H.//Oehler, S.//Savakis, C.//Braig, H.R.//Bourtzis, K. 	Wolbachia Prophage DNA Adenine Methyltransferase Genes in Different Drosophila-Wolbachia Associations.	PLoS ONE	2011	6		e19708			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. 		
@D	Sarikhan, S.//Azarbaijani, R.//Yeganeh, L.P.//Fazeli, A.S.//Amoozegar, M.A.//Salekdeh, G.H. 	Draft Genome Sequence of Nesterenkonia sp. Strain F, Isolated From Aran-Bidgol Salt Lake in Iran.	J. Bacteriol.	2011	193		5580			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. 		
@D	Sarker, M.S.A.//Rahman, M.T.//Mahmud, M.M.//Tagliamonte, M.S.//Chowdhury, S.M.Z.H.//Islam, M.R.//Rahman, M.B.//El Zowalaty, M.E.//Nazir, K.H.M.N.H. 	First Genome Sequence of Pasteurella multocida Type B Strain BAUTB2, a Major Pathogen Responsible for Mortality of Bovines in Bangladesh.	Microbiol. Resour. Announc.	2018	7		e00901-18			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). 		
@D	Sarma, M.H.//Dhingra, M.M.//Gupta, G.//Sarma, R.H. 	Conformational Microheterogeniety in a DNA Double Helix:  Structure of Restriction Endonuclease BamHI Recognition Site.	Biochem. Biophys. Res. Commun.	1985	131		269-276			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. 		
@D	Sarnacki, S.H.//Marolda, C.L.//Noto, L.M.//Giacomodonato, M.N.//Valvano, M.A.//Cerquetti, M.C. 	Dam methylation controls O-antigen chain length in Salmonella enterica serovar enteritidis by regulating the expression of Wzz protein.	J. Bacteriol.	2009	191		6694-6700			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. 		
@D	Sarrade-Loucheur, A.//Xu, S.Y.//Chan, S.H. 	The Role of the Methyltransferase Domain of Bifunctional Restriction Enzyme RM.BpuSI in Cleavage Activity.	PLoS ONE	2013	8		e80967			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. 		
@D	Sarver, J.//Stone, K.//Townsend, J.//Sapienza, P.//Jen-Jacobson, L.//Saxena, S. 	In the Arms of EcoRI - probing the Binding Specificity of the Restriction Endonuclease Using Electron Spin Resonance.	Biophys. J.	2011	100		144a-145a			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. 		
@D	Sasaki, H.//Ishikawa, H.//Asano, R.//Ueshiba, H.//Matsumoto, T.//Boot, R.//Kawamoto, E. 	Draft Genome Sequence of the Rodent Opportunistic Pathogen Pasteurella pneumotropica ATCC 35149T.	Genome Announcements	2014	2		e00771-14			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. 		
@D	Sasaki, J.//Murakami, M.//Yamada, Y. 	Purification, properties and recognition sequence of site-specific restriction endonuclease from Gluconobacter cerinus IFO 3285.	Agric. Biol. Chem.	1985	49		3017-3022			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. 		
@D	Sasaki, J.//Yamada, Y. 	Purification, properties and recognition sequence of site-specific restriction endonuclease from Acetobacter liquefaciens AJ 2881.	Agric. Biol. Chem.	1984	48		3027-3034			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). 		
@D	Sasaki, M.//Akahira, A.//Oshiman, K.//Tsuchido, T.//Matsumura, Y. 	Purification of cytochrome P450 and ferredoxin, involved in bisphenol A degradation, from Sphingomonas sp. strain AO1.	Appl. Environ. Microbiol.	2005	71		8024-8030			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. 		
@D	Sasaki, T.//Tsubakishita, S.//Kuwahara-Arai, K.//Matsuo, M.//Lu, Y.J.//Tanaka, Y.//Hiramatsu, K. 	Complete Genome Sequence of Methicillin-Resistant Staphylococcus schleiferi Strain TSCC54 of Canine Origin.	Genome Announcements	2015	3		e01268-15			We report a complete genome sequence of the methicillin-resistant Staphylococcus  schleiferi strain TSCC54, isolated from the skin of a dog in Tokyo, Japan. 		
@D	Sasaki, Y.//Ishikawa, J.//Yamashita, A.//Oshima, K.//Kenri, T.//Furuya, K.//Yoshino, C.//Horino, A.//Shiba, T.//Sasaki, T.//Hattori, M. 	The complete genomic sequence of Mycoplasma penetrans, an intracellular bacterial pathogen in humans.	Nucleic Acids Res.	2002	30		5293-5300			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. 		
@D	Sasnauskas, G.//Connolly, B.A.//Halford, S.E.//Siksnys, V. 	Site-specific DNA transesterification catalyzed by a restriction enzyme.	Proc. Natl. Acad. Sci. U. S. A.	2007	104		2115-2120			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. 		
@D	Sasnauskas, G.//Connolly, B.A.//Halford, S.E.//Siksnys, V. 	Template-directed addition of nucleosides to DNA by the BfiI restriction enzyme.	Nucleic Acids Res.	2008	36		3969-3977			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. 		
@D	Sasnauskas, G.//Halford, S.E.//Siksnys, V. 	How the BfiI restriction enzyme uses one active site to cut two DNA strands.	Proc. Natl. Acad. Sci. U. S. A.	2003	100		6410-6415			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. 		
@D	Sasnauskas, G.//Jeltsch, A.//Pingoud, A.//Siksnys, V. 	Plasmid DNA cleavage by MunI restriction enzyme: Single-turnover and steady-state kinetic analysis.	Biochemistry	1999	38		4028-4036			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. 		
@D	Sasnauskas, G.//Kostiuk, G.//Tamulaitis, G.//Siksnys, V. 	Target site cleavage by the monomeric restriction enzyme BcnI requires translocation to a random DNA sequence and a switch in enzyme orientation.	Nucleic Acids Res.	2011	39		8844-8856			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. 		
@D	Sasnauskas, G.//Tamulaitiene, G.//Tamulaitis, G.//Calyseva, J.//Laime, M.//Rimseliene, R.//Lubys, A.//Siksnys, V. 	UbaLAI is a monomeric Type IIE restriction enzyme.	Nucleic Acids Res.	2017	45		9583-9594			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. 		
@D	Sasnauskas, G.//Zagorskaite, E.//Kauneckaite, K.//Tamulaitiene, G.//Siksnys, V. 	Structure-guided sequence specificity engineering of the modification-dependent restriction endonuclease LpnPI.	Nucleic Acids Res.	2015	43		6144-6155			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. 		
@D	Sasnauskas, G.//Zakrys, L.//Zaremba, M.//Cosstick, R.//Gaynor, J.W.//Halford, S.E.//Siksnys, V. 	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.	Nucleic Acids Res.	2010	38		2399-2410			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. 		
@D	Sass, P.//Berscheid, A.//Jansen, A.//Oedenkoven, M.//Szekat, C.//Strittmatter, A.//Gottschalk, G.//Bierbaum, G. 	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.	J. Bacteriol.	2012	194		2107-2108			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. 		
@D	Sassera, D.//Gaiarsa, S.//Scaltriti, E.//Morganti, M.//Bandi, C.//Casadei, G.//Pongolini, S. 	Draft Genome Sequence of Salmonella enterica subsp. enterica Serovar Manhattan Strain 111113, from an Outbreak of Human Infections in Northern Italy.	Genome Announcements	2013	1		e00632-13			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%. 		
@D	Sassera, D.//Leardini, I.//Villa, L.//Comandatore, F.//Carta, C.//Almeida, A.//do Ceu, S.M.//Gaiarsa, S.//Marone, P.//Pozio, E.//Caccio, S.M. 	Draft Genome Sequence of Stenotrophomonas maltophilia Strain EPM1, Found in Association with a Culture of the Human Parasite Giardia duodenalis.	Genome Announcements	2013	1		e00182-13			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%. 		
@D	Sassera, D.//Lo, N.//Epis, S.//D'Auria, G.//Montagna, M.//Comandatore, F.//Horner, D.//Pereto, J.//Luciano, A.M.//Franciosi, F.//Ferri, E.//Crotti, E.//Bazzocchi, C.//Daffonchio, D.//Sacchi, L.//Moya, A.//Latorre, A.//Bandi, C. 	Phylogenomic evidence for the presence of a flagellum and cbb3 oxidase in the free-living mitochondrial ancestor.	Mol. Biol. Evol.	2011	28		3285-3296			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. 		
@D	Sassi, M.//Croce, O.//Robert, C.//Raoult, D.//Drancourt, M. 	Draft Genome Sequence of Mycobacterium triplex DSM 44626.	Genome Announcements	2014	2		e00499-14			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. 		
@D	Sassi, M.//Felden, B.//Augagneur, Y. 	Draft Genome Sequence of Staphylococcus aureus subsp. aureus Strain HG003, an NCTC8325 Derivative.	Genome Announcements	2014	2		e00855-14			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. 		
@D	Sassi, M.//Robert, C.//Raoult, D.//Drancourt, M. 	Noncontiguous Genome Sequence of Mycobacterium septicum Strain DSM 44393T.	Genome Announcements	2013	1		e00574-13			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. 		
@D	Sassi, M.//Robert, C.//Raoult, D.//Drancourt, M. 	Non-contiguous genome sequence of Mycobacterium simiae strain DSM 44165(T.).	Standards in Genomic Sciences	2013	8		306-317			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. 		
@D	Sassi, M.//Sharma, D.//Brinsmade, S.R.//Felden, B.//Augagneur, Y. 	Genome Sequence of the Clinical Isolate Staphylococcus aureus subsp. aureus Strain UAMS-1.	Genome Announcements	2015	3		e01584-14			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. 		
@D	Sastre, D.E.//Santos, L.P.//Kagohara, E.//Andrade, L.H. 	Draft Whole-Genome Sequence of Psychrotrophic Arthrobacter sp. Strain 7749, Isolated from Antarctic Marine Sediments with Applications in Enantioselective  Alcohol Oxidation.	Genome Announcements	2017	5		e01197-17			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. 		
@D	Sater, M.R.//Lamelas, A.//Wang, G.//Clark, T.A.//Roltgen, K.//Mane, S.//Korlach, J.//Pluschke, G.//Schmid, C.D. 	DNA Methylation Assessed by SMRT Sequencing Is Linked to Mutations in Neisseria meningitidis Isolates.	PLoS ONE	2015	10		e0144612			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. 		
@D	Sato'o, Y.//Hisatsune, J.//Hirakawa, H.//Ono, H.K.//Omoe, K.//Sugai, M. 	Complete Sequence of a Staphylococcus aureus Clonal Complex 81 Strain, the Dominant Lineage in Food Poisoning Outbreaks in Japan.	Genome Announcements	2017	5		e00853-17			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. 		
@D	Sato, H.//Suzuki, T.//Yamada, Y. 	Purification of restriction endonuclease from Acetobacter aceti IFO 3281 (AatII) and its properties.	Agric. Biol. Chem.	1990	54		3319-3325			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. 		
@D	Sato, H.//Yamada, Y. 	The restriction endonuclease AatI from Acetobacter aceti IFO 3281, an isoschizomer of StuI, has a dimeric structure.	J. Gen. Appl. Microbiol.	1990	36		273-277			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. 		
@D	Sato, S.//Hutchison, C.A. III//Harris, J.I. 	A thermostable sequence-specific endonuclease from Thermus aquaticus.	Proc. Natl. Acad. Sci. U. S. A.	1977	74		542-546			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'. 		
@D	Sato, S.//Nakazawa, K.//Shinomiya, T. 	A DNA methylase from Thermus thermophilus HB8.	J. Biochem. (Tokyo)	1980	88		737-747			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. 		
@D	Sato, S.//Shinomiya, T. 	An isoschizomer of TaqI from Thermus thermophilus HB8.	J. Biochem. (Tokyo)	1978	84		1319-1321			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. 		
@D	Sato, S.//Umemura, M.//Koike, H.//Habe, H. 	Draft Genome Sequence of Gluconobacter frateurii NBRC 103465, a Glyceric Acid-Producing Strain.	Genome Announcements	2013	1		e00369-13			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. 		
@D	Sato, T.//Ohkoshi, Y.//Wada, T.//Fukushima, Y.//Murabayashi, H.//Takakuwa, Y.//Nishiyama, K.//Shiraishi, T.//Nakajima, C.//Suzuki, Y.//Yokota, S.I. 	Complete Genome Sequence of Multidrug-Resistant Streptococcus pneumoniae Serotype 19F Isolated from an Invasive Infection in Sapporo, Japan.	Genome Announcements	2017	5		e01239-17			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. 		
@D	Sato, T.//Shimizu, T.//Watarai, M.//Kobayashi, M.//Kano, S.//Hamabata, T.//Takeda, Y.//Yamasaki, S. 	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.	J. Bacteriol.	2003	185		3966-3971			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. 		
@D	Sato, Y.//Koike, H.//Kondo, S.//Hori, T.//Kanno, M.//Kimura, N.//Morita, T.//Kirimura, K.//Habe, H. 	Draft Genome Sequence of Burkholderia stabilis LA20W, a Trehalose Producer That Uses Levulinic Acid as a Substrate.	Genome Announcements	2016	4		e00795-16			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. 		
@D	Satoh, K.//Arai, H.//Sanzen, T.//Kawaguchi, Y.//Hayashi, H.//Yokobori, S.I.//Yamagishi, A.//Oono, Y.//Narumi, I. 	Draft Genome Sequence of the Radioresistant Bacterium Deinococcus aerius TR0125,  Isolated from the High Atmosphere above Japan.	Genome Announcements	2018	6		e00080-18			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. 		
@D	Satoh, K.//Onodera, T.//Omoso, K.//Takeda-Yano, K.//Katayama, T.//Oono, Y.//Narumi, I. 	Draft Genome Sequence of the Radioresistant Bacterium Deinococcus grandis, Isolated from Freshwater Fish in Japan.	Genome Announcements	2016	4		e01631-15			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. 		
@D	Satou, K.//Shimoji, M.//Tamotsu, H.//Juan, A.//Ashimine, N.//Shinzato, M.//Toma, C.//Nohara, T.//Shiroma, A.//Nakano, K.//Teruya, K.//Terabayashi, Y.//Ohki, S.//Koizumi, N.//Okano, S.//Suzuki, T.//Hirano, T. 	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-.	Genome Announcements	2015	3		e00882-15			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. 		
@D	Satou, K.//Shiroma, A.//Teruya, K.//Shimoji, M.//Nakano, K.//Juan, A.//Tamotsu, H.//Terabayashi, Y.//Aoyama, M.//Teruya, M.//Suzuki, R.//Matsuda, M.//Sekine, A.//Kinjo, N.//Kinjo, F.//Yamaoka, Y.//Hirano, T. 	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.	Genome Announcements	2014	2		e00286-14			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. 		
@D	Saunders, E. et al. 	Complete genome sequence of Eggerthella lenta type strain (IPP VPI 0255).	Standards in Genomic Sciences	2009	1		174-182			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. 		
@D	Saunders, E. et al. 	Complete genome sequence of Haloterrigena turkmenica type strain (4k).	Standards in Genomic Sciences	2010	2		107-116			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. 		
@D	Saunders, N.//Snyder, L. 	The minimal mobile element.	Microbiology	2002	148		3756-3760			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. 		
@D	Saunders, N.J.//Jeffries, A.C.//Peden, P.F.//Hood, D.W.//Tettelin, H.//Rappuoli, R.//Moxon, E.R. 	Repeat-associated phase variable genes in the complete genome sequence of Neisseria meningitidis strain MC58.	Mol. Microbiol.	2000	37		207-215			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. 		
@D	Saunders, N.J.//Peden, J.F.//Hood, D.W.//Moxon, E.R. 	Simple sequence repeats in the Helicobacter pylori genome.	Mol. Microbiol.	1998	27		1091-1098			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. 		
@D	Saves, I.//Eleaume, H.//Dietrich, J.//Masson, J.-M. 	The Thy Pol-2 intein of Thermococcus hydrothermalis is an isoschizomer of PI-TliI and PI-TfuII endonucleases.	Nucleic Acids Res.	2000	28		4391-4396			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. 		
@D	Saves, I.//Morlot, C.//Thion, L.//Rolland, J.-L.//Dietrich, J.//Masson, J.-M. 	Investigating the endonuclease activity of four Pyrococcus abyssi inteins.	Nucleic Acids Res.	2002	30		4158-4165			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. 		
@D	Saves, I.//Ozanne, V.//Dietrich, J.//Masson, J.M. 	Inteins of Thermococcus fumicolans DNA Polymerase Are Endonucleases with Distinct Enzymatic Behaviors.	J. Biol. Chem.	2000	275		2335-2341			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. 		
@D	Saves, I.//Westrelin, F.//Daffe, M.//Masson, J.-M. 	Identification of the first eubacterial endonuclease coded by an intein allele in the pps1 gene of mycobacteria.	Nucleic Acids Res.	2001	29		4310-4318			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. 		
@D	Savin, C.//Frangeul, L.//Ma, L.//Bouchier, C.//Moszer, I.//Carniel, E. 	Draft Genome Sequence of a Clinical Strain of Yersinia enterocolitica (IP10393) of Bioserotype 4/O:3 from France.	Genome Announcements	2013	1		e00150-12			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. 		
@D	Saw, J.H.//Yuryev, A.//Kanbe, M.//Hou, S.//Young, A.G.//Aizawa, S.//Alam, M. 	Complete genome sequencing and analysis of Saprospira grandis str. Lewin, a predatory marine bacterium.	Standards in Genomic Sciences	2012	6		84-93			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. 		
@D	Saw, J.H.W.//Schatz, M.//Brown, M.V.//Kunkel, D.D.//Foster, J.S.//Shick, H.//Christensen, S.//Hou, S.//Wan, X.//Donachie, S.P. 	Cultivation and Complete Genome Sequencing of Gloeobacter kilaueensis sp. nov., from a Lava Cave in Kilauea Caldera, Hawai'i.	PLoS ONE	2013	8		e76376			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. 		
@D	Sawaya, M.R.//Zhu, Z.//Mersha, F.//Chan, S.-h.//Dabur, R.//Xu, S.-y.//Balendiran, G.K. 	Crystal structure of the restriction-modification system control element C.BclI and mapping of its binding site.	Structure	2005	13		1837-1847			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. 		
@D	Saxena, A.//Kumari, R.//Mukherjee, U.//Singh, P.//Lal, R. 	Draft Genome Sequence of the Rifamycin Producer Amycolatopsis rifamycinica DSM 46095.	Genome Announcements	2014	2		e00662-14			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. 		
@D	Saxena, A.//Nayyar, N.//Sangwan, N.//Kumari, R.//Khurana, J.P.//Lal, R. 	Genome Sequence of Novosphingobium lindaniclasticum LE124T, Isolated from a Hexachlorocyclohexane Dumpsite.	Genome Announcements	2013	1		e00715-13			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. 		
@D	Saxena, D.//Caufield, P.W.//Li, Y.//Brown, S.//Song, J.//Norman, R. 	Genetic Classification of Severe Early Childhood Caries Using Subtracted DNA Fragments from Streptococcus mutans.	J. Clin. Microbiol.	2008	46		2868-2873			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. 		
@D	Saxena, R.//Chaudhary, N.//Dhakan, D.B.//Sharma, V.K. 	Draft Genome Sequence of Gulbenkiania mobilis Strain MB1, a Sulfur-Metabolizing Thermophile Isolated from a Hot Spring in Central India.	Genome Announcements	2015	3		e01295-15			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. 		
@D	Sayed, M.//Sayed, W.F.//Hatti-Kaul, R.//Pyo, S.H. 	Complete Genome Sequence of Mycobacterium sp. MS1601, a Bacterium Performing Selective Oxidation of Polyols.	Genome Announcements	2017	5		e00156-17			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. 		
@D	Sayers, J.R.//Olsen, D.B.//Eckstein, F. 	Inhibition of restriction endonuclease hydrolysis by phosphorothioate-containing DNA.	Nucleic Acids Res.	1989	17		9495			None 		
@D	Sayers, J.R.//Schmidt, W.//Wendeler, A.//Eckstein, F. 	Strand specific cleavage of phosphorothioate-containing DNA by reaction with restriction endonucleases in the presence of ethidium bromide.	Nucleic Acids Res.	1988	16		803-813			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. 		
@D	Scales, B.S.//Erb-Downward, J.R.//Falkowski, N.R.//LiPuma, J.J.//Huffnagle, G.B. 	Genome Sequences of 12 Pseudomonas lundensis Strains Isolated from the Lungs of Humans.	Genome Announcements	2018	6		e01461-17			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. 		
@D	Scales, B.S.//Erb-Downward, J.R.//Huffnagle, I.M.//LiPuma, J.J.//Huffnagle, G.B. 	Draft Genome Sequences of Seven Pseudomonas fluorescens Subclade III Strains Isolated from Cystic Fibrosis Patients.	Genome Announcements	2015	3		e01285-14			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. 		
@D	Scales, B.S.//Erb-Downward, J.R.//LiPuma, J.J.//Huffnagle, G.B. 	Draft Genome Sequences of Five Pseudomonas fluorescens Subclade I and II Strains, Isolated from Human Respiratory Samples.	Genome Announcements	2015	3		e00837-15			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. 		
@D	Scalley-Kim, M.//McConnell-Smith, A.//Stoddard, B.L. 	Coevolution of a Homing Endonuclease and Its Host Target Sequence.	J. Mol. Biol.	2007	372		1305-1319			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. 		
@D	Scarpelis, G.//Moissidou, A.//Rina, M.//Bouriotis, V. 	Isolation and identification of restriction endonuclease BshGI.	Nucleic Acids Res.	1989	17		8883			None 		
@D	Scavetta, R.D.//Thomas, C.B.//Walsh, M.A.//Szegedi, S.//Joachimiak, A.//Gumport, R.I.//Churchill, M.E.A. 	Structure of RsrI methyltransferase, a member of the N6-adenine beta class of DNA methyltransferases.	Nucleic Acids Res.	2000	28		3950-3961			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. 		
@D	Schaefer, B.//Wilde, B.//Massardo, D.R.//Manna, F.//Del Giudice, L.//Wolf, K. 	A mitochondrial group-I intron in fission yeast encodes a maturase and is mobile in crosses.	Curr. Genet.	1994	25		336-341			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. 		
@D	Schaeffer, C.J.//Huang, B.//Tsai, M.-D. 	A new class IIS zinc finger restriction enzyme with specificity for SP1 binding sites.	FASEB J.	1996	10		A1241			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. 		
@D	Schaefler, S. 	Staphylococcus epidermidis BV:  Antibiotic resistance patterns, physiological characteristics, and bacteriophage susceptibility.	Appl. Microbiol.	1971	22		693-699			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. 		
@D	Schafer, A.//Schwarzer, A.//Kalinowski, J.//Puhler, A. 	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.	J. Bacteriol.	1994	176		7309-7319			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. 		
@D	Schafer, A.//Tauch, A.//Droste, N.//Puhler, A.//Kalinowski, J. 	The Corynebacterium glutamicum cglIM gene encoding a 5-cytosine methyltransferase enzyme confers a specific DNA methylation pattern in an McrBC-deficient Escherichia coli strain.	Gene	1997	203		95-101			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. 		
@D	Schafer, B.//Kaulich, K.//Wolf, K. 	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.	Gene	1998	214		101-112			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. 		
@D	Schafers, C.//Blank, S.//Wiebusch, S.//Elleuche, S.//Antranikian, G. 	Complete genome sequence of Thermus brockianus GE-1 reveals key enzymes of xylan/xylose metabolism.	Standards in Genomic Sciences	2017	12		22			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. 		
@D	Schaffert, L.//Albersmeier, A.//Bednarz, H.//Niehaus, K.//Kalinowski, J.//Ruckert, C. 	Genome sequence of the marine bacterium Corynebacterium maris type strain Coryn-1(T) (= DSM 45190(T)).	Standards in Genomic Sciences	2013	8		516-524			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. 		
@D	Schaffert, L.//Albersmeier, A.//Winkler, A.//Kalinowski, J.//Zotchev, S.B.//Ruckert, C. 	Complete genome sequence of the actinomycete Actinoalloteichus hymeniacidonis type strain HPA 177T isolated from a marine sponge.	Standards in Genomic Sciences	2016	11		91			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. 		
@D	Schapira, M.//Desdouets, C.//Jacq, C.//Perea, J. 	I-SceIII an intron-encoded DNA endonuclease from yeast mitochondria. Asymmetrical DNA binding properties and cleavage reaction.	Nucleic Acids Res.	1993	21		3683-3689			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. 		
@D	Scharnagl, M.//Richter, S.//Hagemann, M. 	The cyanobacterium Synechocystis sp. strain PCC 6803 expresses a DNA methyltransferase specific for the recognition sequence of the restriction endonuclease PvuI.	J. Bacteriol.	1998	180		4116-4122			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. 		
@D	Scheidt, G.//Graessmann, A.//Weber, H. 	Cloning of the methyltransferase gene from Arabidopsis thaliana.	Biol. Chem. Hoppe Seyler	1991	372		742-743			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. 		
@D	Scheidt, G.//Weber, H.//Graessmann, M.//Graessmann, A. 	Are there two DNA methyltransferase gene families in plant cells?  A new potential methyltransferase gene isolated from an Arabidopsis thaliana genomic library.	Nucleic Acids Res.	1994	22		953-958			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. 		
@D	Scheinbart, L.S.//Johnson, M.A.//Gross, L.A.//Edelstein, S.R.//Richardson, B.C. 	Procainamide inhibits DNA methyltransferase in a human T cell line.	J. Rheumatol.	1991	18		530-534			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. 		
@D	Schell, J. 	The mechanism of restriction of bacteriophage lambda in Escherichia coli strains: Demonstration of an in vivo requirement for S-adenosylmethionine.	Virology	1969	39		66-73			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. 		
@D	Schell, J.//Glover, S.W. 	The effect of heat on host-controlled restriction of phage lambda in Escherichia coli K(P1).	J. Gen. Microbiol.	1966	45		61-72			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. 		
@D	Schell, J.//Glover, S.W. 	The effect of various physiological conditions on host-controlled restriction in Escherichia coli K (P1).	Genet. Res.	1966	7		273-276			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. 		
@D	Schell, J.//Glover, S.W. 	On the localization of a factor responsible for host-controlled restriction in Escherichia coli K(P1).	Genet. Res.	1966	7		277-279			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. 		
@D	Schell, J.//Glover, S.W.//Stacey, K.A.//Broda, P.M.A.//Symonds, N. 	The restriction of phage T3 by certain strains of Escherichia coli.	Genet. Res.	1963	4		483-484			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. 		
@D	Schell, M.A.//Karmirantzou, M.//Snel, B.//Vilanova, D.//Berger, B.//Pessi, G.//Zwahlen, M.C.//Desiere, F.//Bork, P.//Delley, M.//Prodmore, R.D.//Arigoni, F. 	The genome sequence of Bifidobacterium longum reflects its adaptation to the human gastrointestinal tract.	Proc. Natl. Acad. Sci. U. S. A.	2002	99		14422-14427			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. 		
@D	Schenk, J.A.//Heymann, S.//Micheel, B. 	The accessibility of thiophosphorylated groups in DNA fragments to the enzymatic activity of ligases and restriction endonuclease BbsI.	Biochem. Mol. Biol. Int.	1995	36		1037-1043			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. 		
@D	Schermelleh, L.//Haemmer, A.//Spada, F.//Rosing, N.//Meilinger, D.//Rothbauer, U.//Cristina, C.M.//Leonhardt, H. 	Dynamics of Dnmt1 interaction with the replication machinery and its role in postreplicative maintenance of DNA methylation.	Nucleic Acids Res.	2007	35		4301-4312			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. 		
@D	Schermelleh, L.//Spada, F.//Easwaran, H.P.//Zolghadr, K.//Margot, J.B.//Cardoso, M.C.//Leonhardt, H. 	Trapped in action: direct visualization of DNA methyltransferase activity in living cells.	Nat. Methods	2005	2		751-756			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. 		
@D	Scherr, M.//Reed, M.//Huang, C.F.//Riggs, A.D.//Rossi, J.J. 	Oligonucleotide scanning of native mRNAs in extracts predicts intracellular ribozyme efficiency: ribozyme-mediated reduction of the murine DNA methyltransferase.	Mol. Ther.	2000	2		26-38			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. 		
@D	Scherzer, E.//Auer, B.//Schweiger, M. 	Identification, purification and characterization of Escherichia coli virus T1 DNA methyltransferase.	J. Biol. Chem.	1987	262		15225-15231			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. 		
@D	Scheuner, C. et al. 	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.	Standards in Genomic Sciences	2014	9		10			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. 		
@A	Scheuring-Vanamee, E.//Viadiu, H.//Lukacs, C.M.//Aggarwal, A.K. 		Two of a kind: BamHI and BglII.			Pingoud, A. 		Nucleic Acids Mol. Biol.				Berlin Heidelberg	Springer-Verlag	2004		14		215-236									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. 		
@D	Schicklberger, M.//Shapiro, N.//Loque, D.//Woyke, T.//Chakraborty, R. 	Draft Genome Sequence of Raoultella terrigena R1Gly, a Diazotrophic Endophyte.	Genome Announcements	2015	3		e00607-15			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. 		
@D	Schierling, B.//Dannemann, N.//Gabsalilow, L.//Wende, W.//Cathomen, T.//Pingoud, A. 	A novel zinc-finger nuclease platform with a sequence-specific cleavage module.	Nucleic Acids Res.	2012	40		2623-2638			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. 		
@D	Schierling, B.//Noel, A.J.//Thi, L.H.//Wende, W.//Pingoud, A. 	Development of a 'photoswitchable' restriction endonuclease.	FEBS J.	2009	276		291			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. 		
@D	Schierling, B.//Noel, A.J.//Wende, W.//Hien, L.T.//Volkov, E.//Kubareva, E.//Oretskaya, T.//Kokkinidis, M.//Rompp, A.//Spengler, B.//Pingoud, A. 	Controlling the enzymatic activity of a restriction enzyme by light.	Proc. Natl. Acad. Sci. U. S. A.	2010	107		1361-1366			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). 		
@D	Schierling, B.//Wende, W.//Pingoud, A. 	Redesigning the single-chain variant of the restriction endonuclease PvuII by circular permutation.	FEBS Lett.	2012	586		1736-1741			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. 		
@D	Schiestl, R.H.//Petes, T.D. 	Integration of DNA fragments by illegitimate recombination in Saccharomyces cerevisiae.	Proc. Natl. Acad. Sci. U. S. A.	1991	88		7585-7589			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. 		
@D	Schijffelen, M.J.//Boel, C.H.//van Strijp, J.A.//Fluit, A.C. 	Whole genome analysis of a livestock-associated methicillin-resistant Staphylococcus aureus ST398 isolate from a case of human endocarditis.	BMC Genomics	2010	11		376			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 		
@A	Schildkraut, I. 		Screening for and characterizing restriction endonucleases.			Setlow J.K.//Hollaender, A. 		Genet. Eng. (N Y)				New York	Plenum Press	1984		6		117-140									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). 		
@D	Schildkraut, I.//Banner, C.D.B.//Rhodes, C.S.//Parekh, S. 	The cleavage site for the restriction endonuclease EcoRV is 5'-GAT^ATC-3'.	Gene	1984	27		327-329			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). 		
@D	Schildkraut, I.//Lynch, J.//Morgan, R. 	The cleavage site for the restriction endonucleases BanI and HgiCI is 5' ...G^GPyPuCC ...3'.	Nucleic Acids Res.	1987	15		5492			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. 		
@D	Schink, A.K.//Kadlec, K.//Schwarz, S. 	Detection of qnr genes among Escherichia coli isolates of animal origin and complete sequence of the conjugative qnrB19-carrying plasmid pQNR2078.	J. Antimicrob. Chemother.	2012	67		1099-1102			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. 		
@D	Schinzel, R.//Burger, K.J. 	A site-specific endonuclease activity in Halobacterium halobium.	FEMS Microbiol. Lett.	1986	37		325-329			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. 		
@D	Schirawski, J.//van Sinderen, D.//Fitzgerald, G. 	Bacteriophage resistance in Streptococcus thermophilus.	Abstr. Gen. Meet. Am. Soc. Microbiol.	2001	101		476			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. 		
@D	Schirrmacher, E.//Beck, C.//Brueckner, B.//Schmitges, F.//Siedlecki, P.//Bartenstein, P.//Lyko, F.//Schirrmacher, R. 	Synthesis and in vitro evaluation of biotinylated RG108: a high affinity compound for studying binding interactions with human DNA  methyltransferases.	Bioconjugate Chem.	2006	17		261-266			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. 		
@D	Schirwitz, K.//Lundin, A.//Skoglund, A.//Krabbe, M.//Engstrand, L.//Enroth, C. 	Cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of HP1352, a putative DNA methyltransferase  in Helicobacter pylori.	Acta Crystallogr. D Biol. Crystallogr.	2003	59		719-720			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. 		
@D	Schlagman, S.//Hattman, S. 	Mutants of the N-3 R-Factor conditionally defective in hspII modification and deoxyribonucleic acid-cytosine methylase activity.	J. Bacteriol.	1974	120		234-239			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). 		
@D	Schlagman, S.//Hattman, S.//May, M.S.//Berger, L. 	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).	J. Bacteriol.	1976	126		990-996			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. 		
@D	Schlagman, S.L.//Hattman, S. 	The bacteriophage T2 and T4 DNA-[N6-adenine] methyltransferase (Dam) sequence specificities are not identical.	Nucleic Acids Res.	1989	17		9101-9112			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. 		
@D	Schlagman, S.L.//Hattman, S. 	Molecular cloning of a functional dam+ gene coding for phage T4 DNA adenine methylase.	Gene	1983	22		139-156			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. 		
@D	Schlagman, S.L.//Hattman, S.//Marinus, M.G. 	Direct role of the Escherichia coli Dam DNA methyltransferase in methylation-directed mismatch repair.	J. Bacteriol.	1986	165		896-900			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. 		
@D	Schlagman, S.L.//Miner, Z.//Feher, Z.//Hattman, S. 	The DNA [adenine-N6]methyltransferase (Dam) of bacteriophage T4.	Gene	1988	73		517-530			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. 		
@D	Schleheck, D.//Weiss, M.//Pitluck, S.//Bruce, D.//Land, M.L.//Han, S.//Saunders, E.//Tapia, R.//Detter, C.//Brettin, T.//Han, J.//Woyke, T.//Goodwin, L.//Pennacchio, L.//Nolan, M.//Cook, A.M.//Kjelleberg, S.//Thomas, T. 	Complete genome sequence of Parvibaculum lavamentivorans type strain (DS-1(T)).	Standards in Genomic Sciences	2011	5		298-310			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. 		
@D	Schleif, R. 	Assaying of organisms for the presence of restriction endonucleases.	Methods Enzymol.	1980	65		19-23			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. 		
@D	Schleper, C. 	Metagenomic analysis of ammonia oxidizing archaea affiliated with the soil group.	Front. Microbiol.	2012	3		208			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. 		
@D	Schleper, C.//DeLong, E.F.//Preston, C.M.//Feldman, R.A.//Wu, K.-Y.//Swanson, R.V. 	Genomic analysis reveals chromosomal variation in natural populations of the uncultured psychrophilic archaeon Cenarchaeum symbiosum.	J. Bacteriol.	1998	180		5003-5009			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. 		
@D	Schlesinger, D.J.//Shoemaker, N.B.//Salyers, A.A. 	Possible Origins of CTnBST, a Conjugative Transposon Found Recently in a Human Colonic Bacteroides Strain.	Appl. Environ. Microbiol.	2007	73		4226-4233			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. 		
@D	Schlickenrieder, M. 	Structure, localization/regulation and interaction-partners of the Dam-Methyltransferase of Escherichia coli.	Ph.D. Thesis, Germany	2006			1-161					
@D	Schluckebier, G.//Kozak, M.//Bleimling, N.//Weinhold, E.//Saenger, W. 	Differential binding of S-adenosylmethionine, S-adenosylhomocysteine and sinefungin to the adenine-specific DNA methyltransferase M.TaqI.	J. Mol. Biol.	1997	265		56-67			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. 		
@D	Schluckebier, G.//Labahn, J.//Granzin, J.//Saenger, W. 	Structure and function of the adenine specific DNA methyltransferase M.TaqI.	J. Biomol. Struct. Dyn.	1995	12		A206			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. 		
@D	Schluckebier, G.//Labahn, J.//Granzin, J.//Saenger, W. 	M.TaqI: Possible catalysis via cation-pi interactions in N-specific DNA methyltransferases.	Biol. Chem.	1998	379		389-400			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. 		
@D	Schluckebier, G.//Labahn, J.//Granzin, J.//Schildkraut, I.//Saenger, W. 	A model for DNA binding and enzyme action derived from crystallographic studies of the TaqI N6-adenine-methyltransferase.	Gene	1995	157		131-134			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. 		
@D	Schluckebier, G.//O'Gara, M.//Saenger, W.//Cheng, X. 	Universal catalytic domain structure of AdoMet-dependent methyltransferases.	J. Mol. Biol.	1995	247		16-20			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. 		
@D	Schluter, A.//Heuer, H.//Szczepanowski, R.//Poler, S.M.//Schneiker, S.//Puhler, A.//Top, E.M. 	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.	Plasmid	2005	54		135-148			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. 		
@D	Schmeisser, C. et al. 	Rhizobium sp. NGR234 possesses a remarkable number of secretion systems.	Appl. Environ. Microbiol.	2009	75		4035-4045			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 		
@D	Schmid, E.N.//von Recklinghausen, G.//Ansorg, R. 	Bacteriophages in Helicobacter (Campylobacter) pylori.	J. Med. Microbiol.	1990	32		101-104			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. 		
@D	Schmid, J.//Huptas, C.//Wenning, M. 	Draft Genome Sequence of the Xanthan Producer Xanthomonas campestris LMG 8031.	Genome Announcements	2016	4		e01069-16			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%. 		
@D	Schmid, J.//Koenig, S.//Pick, A.//Steffler, F.//Yoshida, S.//Miyamoto, K.//Sieber, V. 	Draft Genome Sequence of Kozakia baliensis SR-745, the First Sequenced Kozakia Strain from the Family Acetobacteraceae.	Genome Announcements	2014	2		e00594-14			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. 		
@D	Schmid, K.//Thomm, M.//Laminet, A.//Laue, F.G.//Kessler, C.//Stetter, K.O.//Schmitt, R. 	Three new restriction endonucleases MaeI, MaeII and MaeIII from Methanococcus aeolicus.	Nucleic Acids Res.	1984	12		2619-2628			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. 		
@D	Schmidt, A.//Reinert, H.//Venner, H.//Bieber, J. 	Studies on the substrate specificity of the DNA methylase activity from Escherichia coli K-12.	Z. Allg. Mikrobiol.	1979	19		489-495			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. 		
@D	Schmidt, F.H.-G.//Hueben, M.//Gider, B.//Renault, F.//Teulade-Fichou, M.-P.//Weinhold, E. 	Sequence-specific methyltransferase-induced labelling (SMILing) of plasmid DNA for studying cell transfection.	Bioorg. Med. Chem.	2008	16		40-48			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. 		
@D	Schmidt, I.//Riedel, T.//Schober, I.//Bunk, B.//Sproer, C.//Bierbrodt, A.//Lehnherr, H.//Wittmann, J. 	Genome Sequence of Escherichia coli E28, a Multidrug-Resistant Strain Isolated from a Chicken Carcass, and Its Spontaneously Inducible Prophage.	Genome Announcements	2017	5		e00348-17			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. 		
@D	Schmidt, S.//Cech, D.//Fritz, H.-J. 	Enzyme - substrate investigation of dcm methylase.	Biol. Chem. Hoppe Seyler	1991	372		748			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. 		
@D	Schmitz-Esser, S.//Gram, L.//Wagner, M. 	Complete Genome Sequence of the Persistent Listeria monocytogenes Strain R479a.	Genome Announcements	2015	3		e00150-15			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. 		
@D	Schmutte, C.//Jones, P.A. 	Involvement of DNA methylation in human carcinogenesis.	Biol. Chem.	1998	379		377-388			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. 		
@D	Schmutz, J. et al. 	Genome sequence of the palaeopolyploid soybean.	Nature	2010	463		178-183			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. 		
@D	Schnegg, B.//Hofschneider, P.H. 	Mutant of PhiX174 accessible to host-controlled modification.	J. Virol.	1969	3		541-542			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. 		
@D	Schneider-Scherzer, E.//Auer, B.//de Groot, E.J.//Schweiger, M. 	Primary structure of a DNA (N6-Adenine)-methyltransferase from Escherichia coli virus T1.	J. Biol. Chem.	1990	265		6086-6091			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. 		
@D	Schneider-Scherzer, E.//Auer, B.//Schweiger, M. 	Identification, purification, characterization and sequencing of DNA-methyltransferase from E. coli virus T1.	Biol. Chem. Hoppe Seyler	1988	369		910			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. 		
@D	Schneiker, S. et al. 	Complete genome sequence of the myxobacterium Sorangium cellulosum.	Nat. Biotechnol.	2007	25		1281-1289			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. 		
@D	Schneiker-Bekel, S.//Wibberg, D.//Bekel, T.//Blom, J.//Linke, B.//Neuweger, H.//Stiens, M.//Vorholter, F.J.//Weidner, S.//Goesmann, A.//Puhler, A.//Schluter, A. 	The complete genome sequence of the dominant Sinorhizobium meliloti field isolate SM11 extends the S. meliloti pan-genome.	J. Biotechnol.	2011	155		20-33			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. 		
@D	Schnetz, K.//Rak, B. 	Cleavage by EcoO109I and DraII is inhibited by overlapping dcm methylation.	Nucleic Acids Res.	1988	16		1623			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. 		
@D	Schniete, J.K.//Salih, T.S.//Algora-Gallardo, L.//Santos, T.//Filgueira-Martinez, S.//Herron, P.R. 	Draft Genome Sequence of Streptomyces phaeoluteigriseus DSM41896.	Genome Announcements	2017	5		e00371-17			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. 		
@D	Schoen, C.//Weber-Lehmann, J.//Blom, J.//Joseph, B.//Goesmann, A.//Strittmatter, A.//Frosch, M. 	Whole-Genome Sequence of the Transformable Neisseria meningitidis Serogroup A Strain WUE2594.	J. Bacteriol.	2011	193		2064-2065			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. 		
@D	Schoenfeld, T. 	A Practical Guide to DNA Methylation.	Promega Notes	1993	42		22-27			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). 		
@D	Schoenfeld, T. 	Bca77I: A restriction enzyme from Bacillus caldolyticus cleaving the novel hexanucleotide (A/T)^CCGG(A/T) .	FASEB J.	1992	6		A77			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. 		
@D	Schoenfeld, T. 	Bca77I: A restriction enzyme from Bacillus caldolyticus cleaving the novel hexanucleotide (A/T)^CCGG(A/T) .	Biophys. J.	1992	61		A77			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. 		
@D	Schoenfeld, T.//Fiandt, M.//Schink, M. 	Bst71I: an isoschizomer of the type-IIS restriction enzyme, BbvI, recognizing the GCAGC(8/12) site.	Gene	1992	111		141-142			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. 		
@D	Schoenfeld, T.//King, K.B.//Schink, M. 	Bca771: a new type-II restriction endonuclease from Bacillus caldolyticus cutting at the (A/T)^CCGG(A/T) site.	Gene	1992	117		99-101			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. 		
@D	Schoenfeld, T.//Mead, D.A.//Fiandt, M. 	Purification and characterization of an isoschizomer of AsuII from Clostridium sporogenes.	Nucleic Acids Res.	1989	17		4417			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. 		
@D	Schoenfeld, T.W.//Murugapiran, S.//Dodsworth, J.A.//Floyd, S.//Lodes, M.//Mead, D.A.//Hedlund, B.P. 	Lateral gene transfer of Family A DNA polymerases between thermophilic viruses, Aquificae, and Apicomplexa.	Mol. Biol. Evol.	2013	30		1653-1664			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. 		
@D	Schoettler, S.//Christ, F.//Pingoud, V.//Wende, W.//Pingoud, A. 	Identification of the catalytic centres of the homing endonuclease PI-SceI by site-directed mutagenesis.	Biochem. Soc. Trans.	2000	28		A332			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. 		
@D	Schoettler, S.//Wende, W.//Pingoud, V.//Pingoud, A. 	Identification of Asp218 and Asp326 as the principal Mg2+ binding ligands of the homing endonuclease PI-SceI.	Biochemistry	2000	39		15895-15900			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. 		
@D	Schofield, B.J.//Skarshewski, A.//Lachner, N.//Ouwerkerk, D.//Klieve, A.V.//Dart, P.//Hugenholtz, P. 	Near complete genome sequence of the animal feed probiotic, Bacillus amyloliquefaciens H57.	Standards in Genomic Sciences	2016	11		60			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. 		
@D	Scholl, D.//Merril, C. 	The genome of bacteriophage K1F, a T7-like phage that has acquired the ability to replicate on K1 strains of Escherichia coli.	J. Bacteriol.	2005	187		8499-8503			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. 		
@D	Scholl, D.R.//Patterson, R.B. Jr.//Jollick, J.D. 	Modification of EcoRI restriction sites by Cauloacter vibrioides.	Gene	1982	17		163-166			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. 		
@D	Scholtissek, S.//Pingoud, A.//Maass, G.//Zabeau, M. 	Polypeptide sequences involved in the cleavage of DNA by the restriction endonuclease EcoRI.	J. Biol. Chem.	1986	261		2228-2234			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. 		
@D	Schoner, B.//Kelly, S.//Smith, H.O. 	The nucleotide sequence of the HhaII restriction and modification genes from Haemophilus haemolyticus.	Gene	1983	24		227-236			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. 		
@D	Schopf, S.//Ullrich, S.R.//Heine, T.//Schlomann, M. 	Draft Genome of the Heterotrophic Iron-Oxidizing Bacterium 'Acidibacillus ferroxidans' Huett2, Isolated from a Mine Drainage Ditch in Freiberg, Germany.	Genome Announcements	2017	5		e00323-17			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. 		
@D	Schork, S.//Schluter, A.//Blom, J.//Schneiker-Bekel, S.//Puhler, A.//Goesmann, A.//Frosch, M.//Schoen, C. 	Genome Sequence of a Neisseria meningitidis Capsule Null Locus Strain from the Clonal Complex of Sequence Type 198.	J. Bacteriol.	2012	194		5144-5145			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. 		
@D	Schott, T.//Rossi, M.//Hanninen, M.L. 	Genome sequence of Helicobacter bizzozeronii strain CIII-1, an isolate from human gastric mucosa.	J. Bacteriol.	2011	193		4565-4566			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. 		
@D	Schottler, S.//Wenz, C.//Lanio, T.//Jeltsch, A.//Pingoud, A. 	Protein engineering of the restriction endonuclease EcoRV: structure-guided design of enzyme variants that recognize the base pairs flanking the recognition site.	Eur. J. Biochem.	1998	258		184-191			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. 		
@D	Schouler, C.//Clier, F.//Luisa, A.//Lerayer, L.//Ehrlich, S.D.//Chopin, M.-C. 	A type IC restriction-modification system in Lactococcus lactis.	J. Bacteriol.	1998	180		407-411			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. 		
@D	Schouler, C.//Gautier, M.//Ehrlich, S.D.//Chopin, M.-C. 	Combinational variation of restriction modification specificities in Lactococcus lactis.	Mol. Microbiol.	1998	28		169-178			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. 		
@D	Schreier, H.J.//Schott, E.J. 	Draft Genome Sequence of the Oyster Larval Probiotic Bacterium Vibrio sp. Strain  OY15.	Genome Announcements	2014	2		e01006-14			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. 		
@D	Schreier, H.J.//Schott, E.J. 	Draft Genome Sequence of the Shellfish Bacterial Pathogen Vibrio sp. Strain B183.	Genome Announcements	2014	2		e00914-14			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. 		
@D	Schroder, J.//Braun, B.//Liere, K.//Szewzyk, U. 	Draft Genome Sequence of Rheinheimera sp. Strain SA_1 Isolated from Iron Backwash Sludge in Germany.	Genome Announcements	2016	4		e00853-16			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. 		
@D	Schroder, J.//Glaub, A.//Schneider, J.//Trost, E.//Tauch, A. 	Draft Genome Sequence of Corynebacterium bovis DSM 20582, Which Causes Clinical Mastitis in Dairy Cows.	J. Bacteriol.	2012	194		4437			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. 		
@D	Schroder, J.//Maus, I.//Meyer, K.//Wordemann, S.//Blom, J.//Jaenicke, S.//Schneider, J.//Trost, E.//Tauch, A. 	Complete genome sequence, lifestyle, and multi-drug resistance of the human pathogen Corynebacterium resistens DSM 45100 isolated from blood samples of a leukemia patient.	BMC Genomics	2012	13		141			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. 		
@D	Schroeder, C.//Jurkschat, H.//Meisel, A.//Reich, J.G.//Kruger, D. 	Unusual occurrence of EcoP1 and EcoP15 recognition sites and counterselection of type II methylation and restriction sequences in bacteriophage T7 DNA.	Gene	1986	45		77-86			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. 		
@D	Schroeder, C.//Reuter, M.//Kruger, D.H. 	DNA methylation of T3 virus ocr+ and ocr- strains in Escherichia coli cells harbouring the EcoK DNA host specificity system.	Biomed. Biochim. Acta	1984	43		K1-K5			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. 		
@D	Schroeder, D.C.//Park, Y.//Yoon, H.M.//Lee, Y.S.//Kang, S.W.//Meints, R.H.//Ivey, R.G.//Choi, T.J. 	Genomic analysis of the smallest giant virus--Feldmannia sp. virus 158.	Virology	2009	384		223-232			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. 		
@D	Schroeder, J.W.//Simmons, L.A. 	Complete Genome Sequence of Bacillus subtilis Strain PY79.	Genome Announcements	2013	1		e01085-13			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. 		
@D	Schroeder, S.G. 	Structure-function studies of lima bean trypsin inhibitor and EcoRII methyltransferase.	Diss. Abstr.	2000	61		3052-B			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. 		
@D	Schroeder, S.G.//Samudzi, C.T. 	Structural studies of EcoRII methylase: exploring similarities among methylases.	Protein Eng.	1997	10		1385-1393			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. 		
@D	Schubert, H.L.//Blumenthal, R.M.//Cheng, X. 	Protein Methyltransferases: Their Distribution Among the Five Structural Classes of AdoMet-Dependent Methyltransferases.	Enzymes	2006	24		3-28			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 		
@D	Schubert, H.L.//Blumenthal, R.M.//Cheng, X. 	Many paths to methyltransfer: a chronicle of convergence.	Trends Biochem. Sci.	2003	28		329-335			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. 		
@D	Schubert, H.L.//Phillips, J.D.//Hill, C.P. 	Structures along the catalytic pathway of PrmC/HemK, an N(5)-glutamine AdoMet-dependent methyltransferase.	Biochemistry	2003	42		5592-5599			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. 		
@D	Schuch, R.//Pelzek, A.J.//Fazzini, M.M.//Nelson, D.C.//Fischetti, V.A. 	Complete Genome Sequence of Bacillus cereus Sensu Lato Bacteriophage Bcp1.	Genome Announcements	2014	2		e00334-14			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. 		
@A	Schugerl, K. 		Comparison of different reactor designs and performances.			Ladisch, M.R.//Bose, A. 		Proc. Ninth Int. Biotech. Symp. Expo.				Washington, DC	American Chemical Society	1992		0		232-235									*
 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.
 
 		
@D	Schuldes, J.//Rodriguez, O.M.//Schmeisser, C.//Krishnan, H.B.//Daniel, R.//Streit, W.R. 	Complete Genome Sequence of the Broad-Host-Range Strain Sinorhizobium fredii USDA257.	J. Bacteriol.	2012	194		4483			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. 		
@D	Schuler, W.//Bunikis, I.//Weber-Lehman, J.//Comstedt, P.//Kutschan-Bunikis, S.//Stanek, G.//Huber, J.//Meinke, A.//Bergstrom, S.//Lundberg, U. 	Complete Genome Sequence of Borrelia afzelii K78 and Comparative Genome Analysis.	PLoS ONE	2015	10		E0120548			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. 		
@D	Schultz, J.//de Souza, Y.A.P.//Mansur, M.C.P.P.R.//Vermelho, A.B.//da Mota, F.F.//Rosado, A.S. 	Draft Genome Sequence of Microbacterium sp. Strain LEMMJ01, Isolated from Antarctic Ornithogenic Soil.	Genome Announcements	2017	5		e00672-17			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. 		
@D	Schultz, P.G. 	The interplay between chemistry and biology in the design of enzymatic catalysts.	Science	1988	240		426-433			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. 		
@D	Schultz, P.G.//Dervan, P.B. 	Sequence-specific double-strand cleavage of DNA by penta-N-methylpyrrolecarboxamide-EDTA.Fe(II).	Proc. Natl. Acad. Sci. U. S. A.	1983	80		6834-6837			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". 		
@D	Schultz-Johansen, M.//Glaring, M.A.//Bech, P.K.//Stougaard, P. 	Draft Genome Sequence of a Novel Marine Bacterium, Paraglaciecola sp. Strain S66, with Hydrolytic Activity against Seaweed Polysaccharides.	Genome Announcements	2016	4		e00304-16			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. 		
@D	Schulze, C.//Jeltsch, A.//Franke, I.//Urbanke, C.//Pingoud, A. 	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.	EMBO J.	1998	17		6757-6766			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. 		
@D	Schumann, J.//Walter, J.//Willert, J.//Wild, C.//Koch, D.//Trautner, T.A. 	M.BssHII, a multispecific cytosine-C5-DNA-methyltransferase with unusual target recognizing properties.	J. Mol. Biol.	1996	257		949-959			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. 		
@D	Schumann, J.//Willert, J.//Wild, C.//Waler, J.//Trautner, T.A. 	M.BssHII: a new multispecific C5-DNA-methyltransferase.	Gene	1995	157		103-104			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. 		
@D	Schuster, A.K.//Szewzyk, U. 	Draft Genome Sequence of Rheinheimera sp. F8, a Biofilm-Forming Strain Which Produces Large Amounts of Extracellular DNA.	Genome Announcements	2016	4		e00082-16			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. 		
@D	Schuster, A.M.//Burbank, D.E.//Meister, B.//Skrdla, M.P.//Meints, R.H.//Hattman, S.//Swinton, D.//Van Etten, J.L. 	Characterization of viruses infecting a eukaryotic chlorella-like green alga.	Virology	1986	150		170-177			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. 		
@D	Schutzer, S.E.//Fraser-Liggett, C.M.//Casjens, S.R.//Qiu, W.G.//Dunn, J.J.//Mongodin, E.F.//Luft, B.J. 	Whole-Genome Sequences of Thirteen Isolates of Borrelia burgdorferi.	J. Bacteriol.	2011	193		1018-1020			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. 		
@D	Schutzer, S.E.//Fraser-Liggett, C.M.//Qiu, W.G.//Kraiczy, P.//Mongodin, E.F.//Dunn, J.J.//Luft, B.J.//Casjens, S.R. 	Whole-Genome Sequences of Borrelia bissettii, Borrelia valaisiana, and Borrelia spielmanii.	J. Bacteriol.	2012	194		545-546			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. 		
@D	Schuyler, J.A.//Chadwick, S.G.//Mordechai, E.//Adelson, M.E.//Gygax, S.E.//Hilbert, D.W. 	Draft Genome Sequence of a Metronidazole-Resistant Gardnerella vaginalis Isolate.	Genome Announcements	2015	3		e00992-15			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. 		
@D	Schuyler, J.A.//Mordechai, E.//Adelson, M.E.//Gygax, S.E.//Hilbert, D.W. 	Draft Genome Sequence of a Metronidazole-Resistant Derivative of Gardnerella vaginalis Strain ATCC 14019.	Genome Announcements	2015	3		e01345-15			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. 		
@D	Schuyler, J.A.//Mordechai, E.//Adelson, M.E.//Gygax, S.E.//Hilbert, D.W. 	Draft Genome Sequence of a Metronidazole-Susceptible Atopobium vaginae Isolate.	Genome Announcements	2015	3		e00991-15			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. 		
@D	Schwabe, G.//Posseckert, G.//Klingmuller, W. 	Restriction endonucleases in Azospirillum.	Gene	1985	39		113-116			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. 		
@D	Schwartz, E.//Henne, A.//Cramm, R.//Eitinger, T.//Friedrich, B.//Gottschalk, G. 	Complete nucleotide sequence of pHG1: a Ralstonia eutropha H16 megaplasmid encoding key enzymes of H(2)-based ithoautotrophy and anaerobiosis.	J. Mol. Biol.	2003	332		369-383			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. 		
@D	Schwarz, F.W.//Toth, J.//van Aelst, K.//Cui, G.//Clausing, S.//Szczelkun, M.D.//Seidel, R. 	The helicase-like domains of type III restriction enzymes trigger long-range diffusion along DNA.	Science	2013	340		353-356			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. 		
@D	Schwarz, F.W.//Toth, J.//van Aelst, K.//Cui, G.//Szczelkun, M.D.//Seidel, R. 	Type III Restriction Enzymes Use 1D Diffusion to Communicate the Relative Orientation of their Distant Target Sites.	Biophys. J.	2011	100		191			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. 		
@D	Schwarz, F.W.//van Aelst, K.//Toth, J.//Seidel, R.//Szczelkun, M.D. 	DNA cleavage site selection by Type III restriction enzymes provides evidence for head-on protein collisions following 1D bidirectional motion.	Nucleic Acids Res.	2011	39		8042-8051			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. 		
@D	Schwarzhans, J.P.//Wibberg, D.//Winkler, A.//Kalinowski, J.//Friehs, K. 	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.	Genome Announcements	2017	5		e00933-17			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. 		
@D	Schweikart, K.M.//Ribeiro, E.//Larcom, L.L. 	Analysis of the inhibition of restriction endonuclease cleavage by UV damage.	Photochem. Photobiol.	1987	45		76s			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. 		
@D	Schwendener, S.//Cotting, K.//Perreten, V. 	Novel methicillin resistance gene mecD in clinical Macrococcus caseolyticus strains from bovine and canine sources.	Sci. Rep.	2017	7		43797			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. 		
@D	Schwibbert, K.//Marin-Sanguino, A.//Bagyan, I.//Heidrich, G.//Lentzen, G.//Seitz, H.//Rampp, M.//Schuster, S.C.//Klenk, H.-P.//Pfeiffer, F.//Oesterhelt, D.//Kunte, H.J. 	A blueprint of ectoine metabolism from the genome of the Industrial producer Halomonas elongata DSM 2581(T).	Environ. Microbiol.	2011	13		1973-1994			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. 		
@D	Schwinghamer, E.A. 	Host-controlled modification of Rhizobium bacteriophage.	Aust. J. Biol. Sci.	1964	18		333-343			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. 		
@D	Schwudke, D.//Ergin, A.//Michael, K.//Volkmar, S.//Appel, B.//Knabner, D.//Konietzny, A.//Strauch, E. 	Broad-host-range Yersinia phage PY100: genome sequence, proteome analysis of virions, and DNA packaging strategy.	J. Bacteriol.	2008	190		332-342			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. 		
@D	Schyns, G.//Serra, C.R.//Lapointe, T.//Pereira-Leal, J.B.//Potot, S.//Fickers, P.//Perkins, J.B.//Wyss, M.//Henriques, A.O. 	Genome of a Gut Strain of Bacillus subtilis.	Genome Announcements	2013	1		e00184-12			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. 		
@D	Sclair, M.//Edgell, M.H.//Hutchison, C.A. 	Mapping of new Escherichia coli K and 15 restriction sites on specific fragments of bacteriophage PhiX174 DNA.	J. Virol.	1973	11		378-385			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. 		
@D	Scott, A.//Song, J.//Ewing, R.//Wang, Z. 	Regulation of protein stability of DNA methyltransferase 1 by post-translational modifications.	Acta Biochim. Biophys. Sin.	2014	46		199-203			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. 		
@D	Scott, K.M. et al. 	The Genome of Deep-Sea Vent Chemolithoautotroph Thiomicrospira crunogena XCL-2.	PLoS Biology	2006	4		e383			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. 		
@D	Sczesnak, A.//Segata, N.//Qin, X.//Gevers, D.//Petrosino, J.F.//Huttenhower, C.//Littman, D.R.//Ivanov, I.I. 	The genome of th17 cell-inducing segmented filamentous bacteria reveals extensive auxotrophy and adaptations to the intestinal environment.	Cell Host Microbe	2011	10		260-272			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. 		
@D	Sears, A.//Peakman, L.J.//Wilson, G.G.//Szczelkun, M.D. 	Characterization of the Type III restriction endonuclease PstII from Providencia stuartii.	Nucleic Acids Res.	2005	33		4775-4787			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. 		
@D	Sears, A.//Szczelkun, M.D. 	Subunit assembly modulates the activities of the Type III restriction-modification enzyme PstII in vitro.	Nucleic Acids Res.	2005	33		4788-4796			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. 		
@D	Sears, L.E.//Zhou, B.//Aliotta, J.M.//Morgan, R.D.//Kong, H. 	BaeI, another unusual BcgI-like restriction endonuclease.	Nucleic Acids Res.	1996	24		3590-3592			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. 		
@D	Sebaihia, M. et al. 	The multidrug-resistant human pathogen Clostridium difficile has a highly mobile, mosaic genome.	Nat. Genet.	2006	38		779-786			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. 		
@D	Sebaihia, M. et al. 	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.	J. Bacteriol.	2006	188		6002-6015			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. 		
@D	Sebaihia, M. et al. 	Genome sequence of a proteolytic (Group I) Clostridium botulinum strain Hall A and comparative analysis of the clostridial genomes.	Genome Res.	2007	17		1082-1092			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. 		
@D	Sebaihia, M.//Bocsanczy, A.M.//Biehl, B.S.//Quail, M.A.//Perna, N.T.//Glasner, J.D.//Declerck, G.A.//Cartinhour, S.//Schneider, D.J.//Bentley, S.D.//Parkhill, J.//Beer, S.V. 	Complete Genome Sequence Of The Plant Pathogen Erwinia amylovora Strain ATCC 49946.	J. Bacteriol.	2010	192		2020-2021			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. 		
@D	Sebastiani, H.//Jager, H. 	Bacteriophages of Streptococcus-salivarius ssp thermophilus: Characterization of hereditary relationships and determination of virus-host interaction.	Milchwissenschaft	1992	48		25-29			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. 		
@D	Sechler, J.M.G.//Clouse, K.A.//Strebel, K.//Weih, K.A.//Rosenberg, A.S. 	Effect of restriction endonucleases on HIV infection.	J. Cell Biochem. Suppl.	1993	17D		76			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. 		
@D	See-Too, W.S.//Ee, R.//Lim, Y.L.//Convey, P.//Pearce, D.A.//Mohidin, T.B.M.//Yin, W.F.//Chan, K.G. 	Complete genome of Arthrobacter alpinus strain R3.8, bioremediation potential unraveled with genomic analysis.	Standards in Genomic Sciences	2017	12		52			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. 		
@D	Seeber, S.//Kessler, C.//Gotz, F. 	Cloning, expression and characterization of the Sau3AI restriction and modification genes in Staphylococcus carnosus TM300.	Gene	1990	94		37-43			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. 		
@D	Seed, K.D.//Bodi, K.L.//Kropinski, A.M.//Ackermann, H.W.//Calderwood, S.B.//Qadri, F.//Camilli, A. 	Evidence of a Dominant Lineage of Vibrio cholerae-Specific Lytic Bacteriophages Shed by Cholera Patients over a 10-Year Period in Dhaka, Bangladesh.	MBio	2011	2		e00334-10			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. 		
@D	Seed, K.D.//Dennis, J.J. 	Isolation and characterization of bacteriophages of the Burkholderia cepacia complex.	FEMS Microbiol. Lett.	2005	251		273-280			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. 		
@D	Seedorf, H.//Fricke, W.F.//Veith, B.//Bruggemann, H.//Liesegang, H.//Strittmatter, A.//Miethke, M.//Buckel, W.//Hinderberger, J.//Li, F.//Hagemeier, C.//Thauer, R.K.//Gottschalk, G. 	The genome of Clostridium kluyveri, a strict anaerobe with unique metabolic features.	Proc. Natl. Acad. Sci. U. S. A.	2008	105		2128-2133			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. 		
@D	Seegers, J.F.M.L.//van Sinderen, D.//Fitzgerald, G.F. 	Molecular characterization of the lactococcal plasmid pCIS3: natural stacking of specificity subunits of a type I restriction/modification system in a single lactococcal strain.	Microbiology	2000	146		435-443			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. 		
@D	Seela, F.//Driller, H. 	Palindromic oligonucleotides containing 7-deaza-2'-deoxyguanosine: solid-phase synthesis of d[(p)GG*AATTCC] octamers and recognition by the endodeoxyribonuclease EcoRI.	Nucleic Acids Res.	1986	14		2319-2332			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. 		
@D	Seela, F.//Kehne, A. 	Palindromic  octa-  and  dodecanucleotides containing 2'-deoxytubercidin: synthesis,  hairpin formation, and recognition by the endodeoxyribonuclease EcoRI.	Biochemistry	1987	26		2232-2238			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. 		
@D	Seela, F.//Roling, A. 	7-Deazapurine containing DNA: efficiency of c7GdTP, c7AdTP and c7IdTP incorporation during PCR-amplification and protection from endodeoxyribonuclease hydrolysis.	Nucleic Acids Res.	1992	20		55-61			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. 		
@D	Seeman, N.C.//Rosenberg, J.M.//Rich, A. 	Sequence-specific recognition of double helical nucleic acids by proteins.	Proc. Natl. Acad. Sci. U. S. A.	1976	73		804-808			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. 		
@D	Seemann, T.//Bulach, D.M.//Carter, G.//Albert, M.J. 	Draft Genome Sequences of Two Strains of a Newly Described Species, Sphingobacterium cellulitidis.	Genome Announcements	2017	5		e00956-17			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. 		
@D	Seersholm, F.V.//Fischer, A.//Heller, M.//Jores, J.//Sachse, K.//Mourier, T.//Hansen, A.J. 	Draft Genome Sequence of the First Human Isolate of the Ruminant Pathogen Mycoplasma capricolum subsp. capricolum.	Genome Announcements	2015	3		e00583-15			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. 		
@D	Segata, N.//Ballarini, A.//Jousson, O. 	Genome Sequence of Pseudomonas aeruginosa PA45, a Highly Virulent Strain Isolated from a Patient with Bloodstream Infection.	Genome Announcements	2013	1		e00289-13			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. 		
@D	Segura, A.//Auffret, P.//Klopp, C.//Bertin, Y.//Forano, E. 	Draft genome sequence and characterization of commensal Escherichia coli strain BG1 isolated from bovine gastro-intestinal tract.	Standards in Genomic Sciences	2017	12		61			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. 		
@D	Seib, K.L.//Jen, F.E.//Tan, A.//Scott, A.L.//Kumar, R.//Power, P.M.//Chen, L.T.//Wu, H.J.//Wang, A.H.//Hill, D.M.//Luyten, Y.A.//Morgan, R.D.//Roberts, R.J.//Maiden, M.C.//Boitano, M.//Clark, T.A.//Korlach, J.//Rao, D.N.//Jennings, M.P. 	Specificity of the ModA11, ModA12 and ModD1 epigenetic regulator N6-adenine DNA methyltransferases of Neisseria meningitidis.	Nucleic Acids Res.	2015	43		4150-4162			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. 		
@D	Seib, K.L.//Peak, I.R.//Jennings, M.P. 	Phase variable restriction-modification systems in Moraxella catarrhalis.	FEMS Immunol. Med. Microbiol.	2002	32		159-165			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. 		
@D	Seib, K.L.//Pigozzi, E.//Muzzi, A.//Gawthorne, J.A.//Delany, I.//Jennings, M.P.//Rappuoli, R. 	A novel epigenetic regulator associated with the hypervirulent Neisseria meningitidis clonal complex 41/44.	FASEB J.	2011	25		3622-3633			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. 		
@D	Seidel, R.//Bloom, J.G.//Dekker, C.//Szczelkun, M.D. 	Motor step size and ATP coupling efficiency of the dsDNA translocase EcoR124I.	EMBO J.	2008	27		1388-1398			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. 		
@D	Seidel, R.//Szczelkun, M.D. 	Switching roles for a helicase.	Cell Cycle	2013	12		3125-3126			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. 		
@D	Seidel, R.//van der Scheer, C.//van Noort, J.//Firman, K.//Dekker, C. 	Translocation of type I restriction endonuclease EcoR124I along DNA measured with magnetic tweezers.	Biophys. J.	2004	86		316a			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. 		
@D	Seidel, R.//van Noort, J.//van der Scheer, C.//Bloom, J.G.P.//Dekker, N.H.//Dutta, C.F.//Blundell, A.//Robinson, T.//Firman, K.//Dekker, C. 	Real-time observation of DNA translocation by the type I restriction modification enzyme EcoR124I.	Nat. Struct. Mol. Biol.	2004	11		838-843			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. 		
@D	Seipke, R.F.//Crossman, L.//Drou, N.//Heavens, D.//Bibb, M.J.//Caccamo, M.//Hutchings, M.I. 	Draft Genome Sequence of Streptomyces Strain S4, a Symbiont of the Leaf-Cutting Ant Acromyrmex octospinosus.	J. Bacteriol.	2011	193		4270-4271			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. 		
@D	Sekiguchi, H.//Komiya, K.//Kiga, D.//Yamamura, M. 	A design and feasibility study of reactions comprising DNA molecular machine that walks autonomously by using a restriction enzyme.	Nat. Comput.	2008	7		303-315			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. 		
@D	Sekine, M.//Tanikawa, S.//Omata, S.//Saito, M.//Fujisawa, T.//Tsukatani, N.//Tajima, T.//Sekigawa, T.//Kosugi, H.//Matsuo, Y.//Nishiko, R.//Imamura, K.//Ito, M.//Narita, H.//Tago, S.//Fujita, N.//Harayama, S. 	Sequence analysis of three plasmids harboured in Rhodococcus erythropolis strain PR4.	Environ. Microbiol.	2006	8		334-346			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. 		
@D	Sekizaki, T.//Osaki, M.//Takamatsu, D.//Shimoji, Y. 	Distribution of the SsuDAT1I restriction-modification system among different serotypes of Streptococcus suis.	J. Bacteriol.	2001	183		5436-5440			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. 		
@D	Sekizaki, T.//Otani, Y.//Osaki, M.//Takamatsu, D.//Shimoji, Y. 	Evidence for horizontal transfer of SsuDAT1I restriction-modification genes to the Streptococcus suis genome.	J. Bacteriol.	2001	183		500-511			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. 		
@D	Sekizaki, T.//Takamatsu, D.//Osaki, M.//Shimoji, Y. 	Different foreign genes incidentally integrated into the same locus of the Streptococcus suis genome.	J. Bacteriol.	2005	187		872-883			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. 		
@D	Sekizuka, T.//Kai, M.//Nakanaga, K.//Nakata, N.//Kazumi, Y.//Maeda, S.//Makino, M.//Hoshino, Y.//Kuroda, M. 	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.	PLoS ONE	2014	9		e114848			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. 		
@D	Sekizuka, T.//Kawanishi, M.//Ohnishi, M.//Shima, A.//Kato, K.//Yamashita, A.//Matsui, M.//Suzuki, S.//Kuroda, M. 	Elucidation of quantitative structural diversity of remarkable rearrangement regions, shufflons, in IncI2 plasmids.	Sci. Rep.	2017	7		928			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. 		
@D	Sekizuka, T.//Lee, K.//Kuroda, M.//Kusumoto, M.//Iwata, T.//Uchida, I.//Tanaka, K.//Tamamura, Y.//Akiba, M. 	Whole-Genome Sequence of CMY-2 beta-Lactamase-Producing Salmonella enterica Serovar Typhimurium Strain L-3553.	Genome Announcements	2014	2		e00711-14			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. 		
@D	Sekizuka, T.//Matsui, M.//Yamane, K.//Takeuchi, F.//Ohnishi, M.//Hishinuma, A.//Arakawa, Y.//Kuroda, M. 	Complete sequencing of the blaNDM-1-positive IncA/C plasmid from Escherichia coli ST38 isolate suggests a possible origin from plant pathogens.	PLoS ONE	2011	6		e25334			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. 		
@D	Sekizuka, T.//Yamamoto, A.//Komiya, T.//Kenri, T.//Takeuchi, F.//Shibayama, K.//Takahashi, M.//Kuroda, M.//Iwaki, M. 	Corynebacterium ulcerans 0102 carries the gene encoding diphtheria toxin on a prophage different from the C. diphtheriae NCTC 13129 prophage.	BMC Microbiol.	2012	12		72			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. 		
@D	Sektas, M.//Kaczorowski, T.//Podhajska, A.J. 	Purification and properties of the MboII, a class-IIS restriction endonuclease.	Nucleic Acids Res.	1992	20		433-438			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. 		
@D	Sektas, M.//Kaczorowski, T.//Podhajska, A.J. 	Interaction of the MboII restriction endonuclease with DNA.	Gene	1995	157		181-185			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. 		
@D	Sela, D.A.//Chapman, J.//Adeuya, A.//Kim, J.H.//Chen, F.//Whitehead, T.R.//Lapidus, A.//Rokhsar, D.S.//Lebrilla, C.B.//German, J.B.//Price, N.P.//Richardson, P.M.//Mills, D.A. 	The genome sequence of Bifidobacterium longum subsp. infantis reveals adaptations for milk utilization within the infant microbiome.	Proc. Natl. Acad. Sci. U. S. A.	2008	105		18964-18969			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. 		
@D	Selent, U.//Pingoud, A. 	Altering the substrate specificity of the restriction endonuclease EcoRV.	Biol. Chem. Hoppe Seyler	1995	376		S152			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. 		
@D	Selent, U.//Ruter, T.//Kohler, E.//Liedtke, M.//Thielking, V.//Alves, J.//Oelgeschlager, T.//Wolfes, H.//Peters, F.//Pingoud, A. 	A site-directed mutagenesis study to identify amino acid residues involved in the catalytic function of the restriction endonuclease EcoRV.	Biochemistry	1992	31		4808-4815			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. 		
@D	Seligman, L.M.//Chisholm, K.M.//Chevalier, B.S.//Chadsey, M.S.//Edwards, S.T.//Savage, J.H.//Veillet, A.L. 	Mutations altering the cleavage specificity of a homing endonuclease.	Nucleic Acids Res.	2002	30		3870-3879			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. 		
@D	Selker, E.U.//Cambareri, E.B.//Garrett, P.W.//Haack, K.R.//Jensen, B.C.//Shabtach, E. 	DNA methylation and control of genome organization in Neurospora crassa.	Gene	1988	74		109-111			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. 		
@D	Selker, E.U.//Freitag, M.//Kothe, G.O.//Margolin, B.S.//Rountree, M.R.//Allis, C.D.//Tamaru, H. 	Induction and maintenance of nonsymmetrical DNA methylation in Neurospora.	Proc. Natl. Acad. Sci. U. S. A.	2002	99		16485-16490			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. 		
@D	Selker, E.U.//Fritz, D.Y.//Singer, M.J. 	Dense nonsymmetrical DNA methylation resulting from repeat-induced point mutation in Neurospora.	Science	1993	262		1724-1728			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. 		
@D	Selker, E.U.//Tountas, N.A.//Cross, S.H.//Margolin, B.S.//Murphy, J.G.//Bird, A.P.//Freitag, M. 	The methylated component of the Neurospora crassa genome.	Nature	2003	422		893-897			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. 		
@D	Sellem, C.H.//Belcour, L. 	Intron open reading frames as mobile elements and evolution of a group I intron.	Mol. Biol. Evol.	1997	14		518-526			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. 		
@D	Sellmann, E.//Knoblich, I.-M.//Kaluza, K.//Frey, B.//Schmitz, G.G.//Westermann, P. 	Bsp423I, a novel isoschizomer of BbvI from Bacillus recognizing 5'-GCAGC-3'.	Nucleic Acids Res.	1992	20		2377			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'. 		
@D	Selvakumar, K.S.//Shanmugasundaram, S. 	Studies on DNA modification in Oscillatoria sp. MKU 178.	Curr. Sci.	1993	64		49-50			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. 		
@D	Selvaraj, S.//Kono, H.//Sarai, A. 	Specificity of Protein-DNA Recognition Revealed by Structure-based Potentials: Symmetric/Asymmetric and Cognate/Non-cognate Binding.	J. Mol. Biol.	2002	322		907			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. 		
@D	Semenova, E.//Minakhin, L.//Bogdanova, E.//Nagornykh, M.//Vasilov, A.//Heyduk, T.//Solonin, A.//Zakharova, M.//Severinov, K. 	Transcription regulation of the EcoRV restriction-modification system.	Nucleic Acids Res.	2005	33		6942-6951			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. 		
@D	Semmler, T.//Eichhorn, I.//Bethe, A.//Bauerfeind, R.//Pickard, D.//Kingsley, R.A.//Dougan, G.//Wieler, L.H. 	Genome Sequence of Porcine Escherichia coli Strain IMT8073, an Atypical Enteropathogenic E. coli Strain Isolated from a Piglet with Diarrhea.	Genome Announcements	2013	1		e00573-13			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. 		
@D	Sen, A. et al. 	Draft Genome Sequence of Frankia sp. Strain QA3, a Nitrogen-Fixing Actinobacterium Isolated from the Root Nodule of Alnus nitida.	Genome Announcements	2013	1		e0010313			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. 		
@D	Sen, D.//Brown, C.J.//Top, E.M.//Sullivan, J. 	Inferring the Evolutionary History of IncP-1 Plasmids Despite Incongruence among Backbone Gene Trees.	Mol. Biol. Evol.	2012	30		154-166			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. 		
@D	Sen, D.//Chandrababunaidu, M.M.//Singh, D.//Sanghi, N.//Ghorai, A.//Mishra, G.P.//Madduluri, M.//Adhikary, S.P.//Tripathy, S. 	Draft Genome Sequence of the Terrestrial Cyanobacterium Scytonema millei VB511283, Isolated from Eastern India.	Genome Announcements	2015	3		e00009-15			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. 		
@D	Sen, D.//Van der Auwera, G.A.//Rogers, L.M.//Thomas, C.M.//Brown, C.J.//Top, E.M. 	Broad-Host-Range Plasmids from Agricultural Soils Have IncP-1 Backbones with Diverse Accessory Genes.	Appl. Environ. Microbiol.	2011	77		7975-7983			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. 		
@D	Sen, S.//Nilsson, L. 	Free energy calculations and molecular dynamics simulations of wild-type and variants of the DNA-EcoRI complex.	Biophys. J.	1999	77		1801-1810			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. 		
@D	Sen, S.//Nilsson, L. 	Structure, interaction, dynamics and solvent effects on the DNA-EcoRI complex in aqueous solution from molecular dynamics simulation.	Biophys. J.	1999	77		1782-1800			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. 		
@D	Sen, U.//Mukherjee, T.//Bose, S.//Roy, C.//Rameez, M.J.//Ghosh, W.//Mukhopadhyay, S.K. 	Genome Sequence of the Arsenic-Resistant Haladaptatus sp. Strain R4 Isolated from Ramnagar, West Bengal, India.	Genome Announcements	2016	4		e01017-16			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. 		
@D	Senejani, A.G.//Gogarten, J.P. 	Structural stability and endonuclease activity of a PI-SceI GFP-fusion protein.	Int. J. Biol. Sci.	2007	3		205-211			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. 		
@D	Senesac, J.H.//Allen, J.R. 	Oligonucleotide activation of the type IIe restriction enzyme NaeI for digestion of refractory sites.	Biotechniques	1995	19		990-993			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. 		
@D	Senesac, J.H.//Romanin, J.K. 	Application of oligonucleotide activation to restriction endonuclease NarI.	Biotechniques	1997	22		1166-1168			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. 		
@D	Sengupta, S.//Pramanik, A.//Basak, P.//Bhattacharyya, M. 	Draft Genome Sequence of Bioactive Strain Streptomyces sp. SMS_SU21, Isolated from Soil Sediment of the Sundarbans Mangrove Ecosystem.	Genome Announcements	2018	6		e00614-18			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. 		
@D	Seni, J.//Mshana, S.E.//Msigwa, F.//Matee, M.//Mazigo, H.//Parkhill, J.//Holmes, M.A.//Paterson, G.K. 	Draft Genome Sequence of a Multiresistant Bovine Isolate of Staphylococcus lentus from Tanzania.	Genome Announcements	2016	4		e01345-16			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%. 		
@D	Sentausa, E.//Abdad, M.Y.//Robert, C.//Stenos, J.//Raoult, D.//Fournier, P.E. 	Genome Sequence of Rickettsia gravesii, Isolated from Western Australian Ticks.	Genome Announcements	2013	1		e00975-13			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. 		
@D	Sentausa, E.//El Karkouri, K.//Michelle, C.//Caputo, A.//Raoult, D.//Fournier, P.E. 	Genome Sequence of Rickettsia tamurae, a Recently Detected Human Pathogen in Japan.	Genome Announcements	2014	2		e00838-14			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. 		
@D	Sentausa, E.//El Karkouri, K.//Michelle, C.//Raoult, D.//Fournier, P.E. 	Draft Genome Sequence of Rickettsia aeschlimannii, Associated with Hyalomma marginatum Ticks.	Genome Announcements	2014	2		e00666-14			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. 		
@D	Sentausa, E.//El Karkouri, K.//Nguyen, T.T.//Caputo, A.//Raoult, D.//Fournier, P.E. 	Genome Sequence of Rickettsia hoogstraalii, a Geographically Widely Distributed Tick-Associated Bacterium.	Genome Announcements	2014	2		e01171-14			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. 		
@D	Sentausa, E.//El Karkouri, K.//Robert, C.//Raoult, D.//Fournier, P.E. 	Genome Sequence of Rickettsia conorii subsp. caspia, the Agent of Astrakhan Fever.	J. Bacteriol.	2012	194		4763-4764			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. 		
@D	Sentausa, E.//El Karkouri, K.//Robert, C.//Raoult, D.//Fournier, P.E. 	Genome Sequence of Rickettsia conorii subsp. indica, the Agent of Indian Tick Typhus.	J. Bacteriol.	2012	194		3288-3289			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). 		
@D	Sentausa, E.//El Karkouri, K.//Robert, C.//Raoult, D.//Fournier, P.E. 	Genome Sequence of Rickettsia conorii subsp. israelensis, the Agent of Israeli Spotted Fever.	J. Bacteriol.	2012	194		5130-5131			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. 		
@D	Sentausa, E.//El Karkouri, K.//Robert, C.//Raoult, D.//Fournier, P.E. 	Sequence and Annotation of Rickettsia sibirica sibirica Genome.	J. Bacteriol.	2012	194		2377			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. 		
@D	Sentausa, E.//El Karkouri, K.//Robert, C.//Raoult, D.//Fournier, P.E. 	Genome Sequence of 'Rickettsia sibirica subsp. mongolitimonae'.	J. Bacteriol.	2012	194		2389-2390			'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. 		
@D	Sentis, C.//Santos, J.//Fernandez-Piqueras, J. 	In situ methylation of insect chromosomes with methylase HpaII.	Chromosoma	1989	98		105-108			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. 		
@D	Seo, J.H.//Cho, Y.D. 	Studies on the role of arginyl residue in EcoRI methylase.	Korean Biochem. J.	1992	25		54-59			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. 		
@D	Seo, J.H.//Cho, Y.D. 	Studies on the role of cysteinyl residue in EcoRI methylase.	Korean Biochem. J.	1991	24		193-199			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. 		
@D	Seo, Y.S.//Lim, J.Y.//Choi, B.S.//Kim, H.//Goo, E.//Lee, B.//Lim, J.S.//Choi, I.Y.//Moon, J.S.//Kim, J.//Hwang, I. 	Complete Genome Sequence of Burkholderia gladioli BSR3.	J. Bacteriol.	2011	193		3149			We report the complete genome sequence of Burkholderia gladioli BSR3 isolated from a diseased rice sheath in Korea. 		
@D	Seo, Y.S.//Lim, J.Y.//Park, J.//Kim, S.//Lee, H.H.//Cheong, H.//Kim, S.M.//Moon, J.S.//Hwang, I. 	Comparative genome analysis of rice-pathogenic Burkholderia provides insight into capacity to adapt to different environments and hosts.	BMC Genomics	2015	16		349			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. 		
@D	Seoane, A.//Sangari, F.J.//Lobo, J.M. 	Complete nucleotide sequence of the fosfomycin resistance transposon Tn2921.	Int. J. Antimicrob. Agents	2010	35		413-414			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. 		
@D	Seong, H.J.//Park, H.J.//Hong, E.//Lee, S.C.//Sul, W.J.//Han, S.W. 	Methylome Analysis of Two Xanthomonas spp. Using Single-Molecule Real-Time Sequencing.	Plant Pathol. J.	2016	32		500-507			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. 		
@D	Seraphin, B.//Faye, G.//Hatat, D.//Jacq, C. 	The yeast mitochondrial intron aI5a: associated endonuclease activity and in vivo mobility.	Gene	1992	113		1-8			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. 		
@D	Seraphin, B.//Simon, M.//Faye, G. 	A mitochondrial reading frame which may code for a maturase-like protein in Saccharomyces cerevisiae.	Nucleic Acids Res.	1985	13		3005-3014			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. 		
@D	Serepa, M.H.//Gray, V.M. 	Draft Whole-Genome Sequence of Serratia marcescens Strain MCB, Associated with Oscheius sp. MCB (Nematoda: Rhabditidae) Isolated from South Africa.	Genome Announcements	2014	2		e00911-14			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%. 		
@D	Serfiotis-Mitsa, D.//Herbert, A.P.//Roberts, G.A.//Soares, D.C.//White, J.H.//Blakely, G.W.//Uhrin, D.//Dryden, D.T. 	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.	Nucleic Acids Res.	2010	38		1723-1737			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. 		
@D	Serfiotis-Mitsa, D.//Roberts, G.A.//Cooper, L.P.//White, J.H.//Nutley, M.//Cooper, A.//Blakely, G.W.//Dryden, D.T. 	The Orf18 Gene Product from Conjugative Transposon Tn916 Is an ArdA Antirestriction Protein that Inhibits Type I DNA Restriction-Modification  Systems.	J. Mol. Biol.	2008	383		970-981			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. 		
@D	Sergeev, V.N.//Chalov, S.E.//Drutsa, V.L.//Gromova, E.S. 	A study of the Asp110-Glu112 region of EcoRII restriction endonuclease by site-directed mutagenesis.	Biochemistry	2000	65		1006-1010			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. 		
@D	Seribelli, A.A.//Frazao, M.R.//Gonzales, J.C.//Cao, G.//Leon, M.S.//Kich, J.D.//Allard, M.W.//Falcao, J.P. 	Draft Genome Sequences of 20 Salmonella enterica subsp. enterica Serovar Typhimurium Strains Isolated from Swine in Santa Catarina, Brazil.	Genome Announcements	2018	6		e00232-18			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. 		
@D	Serrano, A.E.//Escudero, L.V.//Tebes-Cayo, C.//Acosta, M.//Encalada, O.//Fernandez-Moroso, S.//Demergasso, C. 	First draft genome sequence of a strain from the genus Fusibacter isolated from Salar de Ascotan in Northern Chile.	Standards in Genomic Sciences	2017	12		43			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. 		
@D	Serrano, W.//Tarazona, U.I.//Olaechea, R.M.//Friedrich, M.W. 	Draft Genome Sequence of Vibrio sp. Strain V1B Isolated from the Gut Microflora of the Scallop Argopecten purpuratus.	Genome Announcements	2017	5		e01130-17			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. 		
@D	Serrano, W.//Tarazona, U.I.//Olaechea, R.M.//Friedrich, M.W. 	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).	Genome Announcements	2018	6		e00419-18			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. 		
@D	Serva, S.//Klimasauskas, S.//Weinhold, E. 	Fluorescence studies of the DNA base flipping induced by a cytosine-5 methyltransferase.	Biologija	1997	1		9-12			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. 		
@D	Serva, S.//Velyvis, R.//Lazareviciute, L.//Klimasauskas, S. 	High-level expression of MvaI DNA methyltransferase.	Biologija	1996	0		48-50			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. 		
@D	Serva, S.//Weinhold, E.//Klimasauskas, S. 	Stopped-flow fluorescence studies of DNA base flipping by HhaI methyltransferase.	Biochem. Soc. Trans.	2000	2000		A468			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. 		
@D	Serva, S.//Weinhold, E.//Roberts, R.J.//Klimasauskas, S. 	Chemical display of thymine residues flipped out by DNA methyltransferases.	Nucleic Acids Res.	1998	26		3473-3479			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. 		
@D	Servin-Garciduenas, L.E.//Garrett, R.A.//Amils, R.//Martinez-Romero, E. 	Genome Sequence of the Acidophilic Bacterium Acidocella sp. Strain MX-AZ02.	Genome Announcements	2013	1		e00041-12			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. 		
@D	Servin-Garciduenas, L.E.//Martinez-Romero, E. 	Draft Genome Sequence of the Sulfolobales Archaeon AZ1, Obtained through Metagenomic Analysis of a Mexican Hot Spring.	Genome Announcements	2014	2		e00164-14			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. 		
@D	Servin-Garciduenas, L.E.//Peng, X.//Garrett, R.A.//Martinez-Romero, E. 	Genome sequence of a novel archaeal fusellovirus assembled from the metagenome of a mexican hot spring.	Genome Announcements	2013	1		e00164-13			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. 		
@D	Servin-Garciduenas, L.E.//Rogel, M.A.//Ormeno-Orrillo, E.//Delgado-Salinas, A.//Martinez-Romero, J.//Sanchez, F.//Martinez-Romero, E. 	Genome Sequence of Rhizobium sp. Strain CCGE510, a Symbiont Isolated from Nodules of the Endangered Wild Bean Phaseolus albescens.	J. Bacteriol.	2012	194		6310-6311			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. 		
@D	Servin-Garciduenas, L.E.//Rogel, M.A.//Ormeno-Orrillo, E.//Zayas-Del, M.A.//Sanchez, F.//Martinez-Romero, E. 	Complete Genome Sequence of Bradyrhizobium sp. Strain CCGE-LA001, Isolated from Field Nodules of the Enigmatic Wild Bean Phaseolus microcarpus.	Genome Announcements	2016	4		e00126-16			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. 		
@D	Servin-Garciduenas, L.E.//Sanchez-Quinto, A.//Martinez-Romero, E. 	Draft Genome Sequence of Commensalibacter papalotli MX01, a Symbiont Identified from the Guts of Overwintering Monarch Butterflies.	Genome Announcements	2014	2		e00128-14			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. 		
@D	Servos, S.//Silva, C.//Dougan, G.//Charles, I.G. 	The commercially available restriction enzyme BspHI is blocked by overlapping methylation.	Nucleic Acids Res.	1991	19		183			This report shows that BspHI is sensitive to dam methylation 		
@D	Seshadri, R. et al. 	Cultivation and sequencing of rumen microbiome members from the Hungate1000 Collection.	Nat. Biotechnol.	2018	36		359-367			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. 		
@D	Seshadri, R. et al. 	Genome sequence of the PCE-Dechlorinating bacterium Dehalococcoides ethenogenes.	Science	2005	307		105-108			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. 		
@D	Seshadri, R.//Joseph, S.W.//Chopra, A.K.//Sha, J.//Shaw, J.//Graf, J.//Haft, D.//Wu, M.//Ren, Q.//Rosovitz, M.J.//Madupu, R.//Tallon, L.//Kim, M.//Jin, S.//Vuong, H.//Stine, O.C.//Ali, A.//Horneman, A.J.//Heidelberg, J.F. 	Genome Sequence of Aeromonas hydrophila ATCC 7966T: Jack of All Trades.	J. Bacteriol.	2006	188		8272-8282			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. 		
@D	Seshasayee, A.S. 	An assessment of the role of DNA adenine methyltransferase on gene expression regulation in E coli.	PLoS ONE	2007	2		e273			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. 		
@D	Seshasayee, A.S.//Singh, P.//Krishna, S. 	Context-dependent conservation of DNA methyltransferases in bacteria.	Nucleic Acids Res.	2012	40		7066-7073			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. 		
@D	Sethmann, S.//Ceglowski, P.//Willert, J.//Iwanicka-Nowicka, R.//Trautner, T.A.//Walter, J. 	M.PhiBssHII, a novel cytosine-C5-DNA-methyltransferase with target-recognizing domains at separated locations of the enzyme.	EMBO J.	1999	18		3502-3508			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. 		
@D	Sethuraman, J.//Majer, A.//Friedrich, N.C.//Edgell, D.R.//Hausner, G. 	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.	Mol. Biol. Evol.	2009	26		2299-2315			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. 		
@D	Setubal, J.C. et al. 	Genome sequence of Azotobacter vinelandii, an obligate aerobe specialized to support diverse anaerobic metabolic processes.	J. Bacteriol.	2009	191		4534-4545			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. 		
@D	Seurinck, J.//Van de Voorde, A.//Van Montagu, M. 	A new restriction endonuclease from Acetobacter pasteurianus.	Nucleic Acids Res.	1983	11		4409-4415			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. 		
@D	Seuylemezian, A.//Cooper, K.//Schubert, W.//Vaishampayan, P. 	Draft Genome Sequences of 12 Dry-Heat-Resistant Bacillus Strains Isolated from the Cleanrooms Where the Viking Spacecraft Were Assembled.	Genome Announcements	2018	6		e00094-18			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. 		
@D	Seuylemezian, A.//Singh, N.K.//Vaishampayan, P.//Venkateswaran, K. 	Draft Genome Sequence of Solibacillus kalamii, Isolated from an Air Filter Aboard the International Space Station.	Genome Announcements	2017	5		e00696-17			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%. 		
@D	Seuylemezian, A.//Vaishampayan, P.//Cooper, K.//Venkateswaran, K. 	Draft Genome Sequences of Acinetobacter and Bacillus Strains Isolated from Spacecraft-Associated Surfaces.	Genome Announcements	2018	6		e01554-17			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. 		
@D	Sevigny, J.L.//LaJoie, J.//Shehata, S.//Christensen, E.//Cornfield, S.//Koziol, L. 	Whole-Genome Sequences of Two Pseudomonas fluorescens Strains Isolated from Roots of Tomato and Cucumber Plants.	Microbiol. Resour. Announc.	2018	7		e00974-18			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. 		
@D	Shabarova, Z.A.//Sheflyan, G.Y.//Kuznetsova, S.A.//Kubareva, E.A.//Sysoev, O.N.//Ivanovskaya, M.G.//Gromova, E.S. 	Affinity modification of restriction-endonuclease EcoRII by DNA duplex containing a monosubstituted pyrophosphate internucleotide bond.	Bioorg. Khim.	1994	20		413-419			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. 		
@D	Shafie, N.A.//Lau, N.S.//Ramachandran, H.//Amirul, A.A. 	Complete Genome Sequences of Three Cupriavidus Strains Isolated from Various Malaysian Environments.	Genome Announcements	2017	5		e01498-16			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. 		
@D	Shah, B.//Jain, K.//Patel, N.//Pandit, R.//Patel, A.//Joshi, C.G.//Madamwar, D. 	Draft Genome Sequence of Paenibacillus sp. Strain DMB20, Isolated from Alang Ship-Breaking Yard, Which Harbors Genes for Xenobiotic Degradation.	Genome Announcements	2015	3		e00554-15			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. 		
@D	Shah, D.H.//Jones, L.P.//Paul, N.//Davis, M.A. 	Draft Genome Sequences of 12 Clinical and Environmental Methicillin-Resistant Staphylococcus pseudintermedius Strains Isolated from a Veterinary Teaching  Hospital in Washington State.	Genome Announcements	2018	6		e00290-18			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. 		
@D	Shah, D.H.//Paul, N.C.//Guard, J. 	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.	Genome Announcements	2018	6		e00125-18			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). 		
@D	Shah, G.R.//Karunakaran, R.//Kumar, G.N. 	In vivo restriction endonuclease activity of the Anabaena PCC 7120 XisA protein in Escherichia coli.	Res. Microbiol.	2007	158		679-684			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. 		
@D	Shah, M.R.//Ulyanova, V.//Malanin, S.//Dudkina, E.//Vershinina, V.//Ilinskaya, O. 	Draft Whole-Genome Sequence of Bacillus altitudinis Strain B-388, a Producer of Extracellular RNase.	Genome Announcements	2015	3		e01502-14			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. 		
@D	Shah, N.R.//Moksa, M.//Novikov, A.//Perry, M.B.//Hirst, M.//Caroff, M.//Fernandez, R.C. 	Draft Genome Sequences of Bordetella hinzii and Bordetella trematum.	Genome Announcements	2013	1		e00838-13			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. 		
@D	Shah, V.//Morris, R.M. 	Genome Sequence of 'Candidatus Thioglobus autotrophica' Strain EF1, a Chemoautotroph from the SUP05 Clade of Marine Gammaproteobacteria.	Genome Announcements	2015	3		e01156-15			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. 		
@D	Shahinas, D.//Tamber, G.S.//Arya, G.//Wong, A.//Lau, R.//Jamieson, F.//Ma, J.H.//Alexander, D.C.//Low, D.E.//Pillai, D.R. 	Whole-Genome Sequence of Streptococcus pseudopneumoniae Isolate IS7493.	J. Bacteriol.	2011	193		6102-6103			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. 		
@D	Shajani, Z.//Varani, G. 	C-13 relaxation studies of the DNA target sequence for HhaI methyltransferase reveal unique motional properties.	Biochemistry	2008	47		7617-7625			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. 		
@D	Shambat, S.//Nadig, S.//Prabhakara, S.//Bes, M.//Etienne, J.//Arakere, G. 	Clonal complexes and virulence factors of Staphylococcus aureus from several cities in India.	BMC Microbiol.	2012	12		64			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. 		
@D	Shamseldin, A.//Nelson, M.S.//Staley, C.//Guhlin, J.//Sadowsky, M.J. 	Draft Genome Sequences of Four Novel Thermal- and Alkaline-Tolerant Egyptian Rhizobium Strains Nodulating Berseem Clover.	Genome Announcements	2016	4		e00988-16			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). 		
@D	Shan, D.//Li, X.//Gu, Z.//Wei, G.//Gao, Z.//Shao, Z. 	Draft Genome Sequence of the Agar-Degrading Bacterium Catenovulum sp. Strain DS-2, Isolated from Intestines of Haliotis diversicolor.	Genome Announcements	2014	2		e00144-14			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. 		
@D	Shan, D.//Ying, J.//Li, X.//Gao, Z.//Wei, G.//Shao, Z. 	Draft Genome Sequence of the Carrageenan-Degrading Bacterium Cellulophaga sp. Strain KL-A, Isolated from Decaying Marine Algae.	Genome Announcements	2014	2		e00145-14			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. 		
@D	Shan, W.//Liu, H.//Zhou, Y.//Yu, X. 	Draft Genome Sequence of Streptomyces sp. XY006, an Endophyte Isolated from Tea (Camellia sinensis).	Genome Announcements	2017	5		e00971-17			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. 		
@D	Shan, W.//Yang, X.//Ma, W.//Yang, Y.//Guo, X.//Guo, J.//Zheng, H.//Li, G.//Xie, B. 	Draft Genome Sequence of Ralstonia solanacearum Race 4 Biovar 4 Strain SD54.	Genome Announcements	2013	1		e00890-13			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. 		
@D	Shanak, S.//Helms, V. 	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.	J. Chem. Phys.	2014	141		22D512			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. 		
@D	Shane, J.L.//Bongio, N.J.//Favia, G.//Lampe, D.J. 	Draft Genome Sequence of Asaia sp. Strain SF2.1, an Important Member of the Microbiome of Anopheles Mosquitoes.	Genome Announcements	2014	2		e01202-13			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. 		
@D	Shang, N.//Zhu, Q.//Dai, M.//Zhao, G. 	Complete Genome Sequence of the Heavy-Metal-Tolerant Endophytic Type Strain of Salinicola tamaricis.	Genome Announcements	2018	6		e00358-18			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. 		
@D	Shang, Y.//Zhang, N.//Zhu, P.//Luo, Y.//Huang, K.//Tian, W.//Xu, W. 	Restriction enzyme cutting site distribution regularity for DNA looping technology.	Gene	2014	534		222-228			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. 		
@D	Shankar, C.//Nabarro, L.E.//Devanga, R.N.K.//Muthuirulandi, S.D.P.//Daniel, J.L.//Doss, C.G.P.//Veeraraghavan, B. 	Draft Genome Sequences of Three Hypervirulent Carbapenem-Resistant Klebsiella pneumoniae Isolates from Bacteremia.	Genome Announcements	2016	4		e01081-16			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. 		
@D	Shankar, C.//Santhanam, S.//Kumar, M.//Gupta, V.//Devanga, R.N.K.//Veeraraghavan, B. 	Draft Genome Sequence of an Extended-Spectrum-beta-Lactamase-Positive Hypervirulent Klebsiella pneumoniae Strain with Novel Sequence Type 2318 Isolated  from a Neonate.	Genome Announcements	2016	4		e01273-16			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). 		
@D	Shankar, M.//Mageswari, A.//Suganthi, C.//Gunasekaran, P.//Gothandam, K.M.//Karthikeyan, S. 	Genome Sequence of a Moderately Halophilic Bacillus cereus Strain, TS2, Isolated  from Saltern Sediments.	Microbiol. Resour. Announc.	2018	7		e00873-18			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. 		
@D	Shankar, M.//Ponraj, P.//Ilakiam, D.//Rajendhran, J.//Gunasekaran, P. 	Genome Sequence of the Plant Growth-Promoting Bacterium Enterobacter cloacae GS1.	J. Bacteriol.	2012	194		4479			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. 		
@D	Shankar, S.//Tyagi, A.K. 	Purification and characterization of restriction endonuclease MgoI from Mycobacterium gordonae.	Gene	1993	131		153-154			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. 		
@D	Shankar, S.//Tyagi, A.K. 	MchAI and MchAII, two class-II restriction endonucleases from Mycobacterium chelonei.	Gene	1993	132		119-123			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. 		
@D	Shankar, S.//Tyagi, A.K. 	MhaAI, a novel isoschizomer of PstI from Mycobacterium habana recognizing 5'-CTGCA/G-3'.	Nucleic Acids Res.	1992	20		2891			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. 		
@D	Shankar, S.//Tyagi, A.K. 	MfoAI, a novel isoschizomer of HaeIII from Mycobacterium fortuitum recognizing 5'-GG/CC-3' .	Nucleic Acids Res.	1992	20		2890			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. 		
@D	Shankarappa, B.//Vijayananda, K.//Ehrlich, G. 	Silmut: A Computer Program for the Identification of Regions Suitable for Silent Mutagenesis to Introduce Restriction Enzyme Recognition Sequences.	Biotechniques	1992	12		882-884			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. 		
@D	Shao, C.//Wang, C.//Zang, J. 	Structural basis for the substrate selectivity of PvuRts1I, a 5-hydroxymethylcytosine DNA restriction endonuclease.	Acta Crystallogr. D Biol. Crystallogr.	2014	70		2477-2486			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. 		
@D	Shao, Y.//Xu, M.-Q.//Paulus, H. 	Protein splicing: Evidence for an N-O acyl rearrangement as the initial step in the splicing process.	Biochemistry	1996	35		3810-3815			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. 		
@D	Shao, Y.//Xu, M.-Q.//Paulus, H. 	Protein splicing: characterization of the aminosuccinimide residue at the carboxyl terminus of the excised intervening sequence.	Biochemistry	1995	34		10844-10850			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. 		
@D	Shapiro, L.R.//Scully, E.D.//Roberts, D.//Straub, T.J.//Geib, S.M.//Park, J.//Stephenson, A.G.//Salaau, R.E.//Liu, Q.//Beattie, G.//Gleason, M.//De Moraes, C.M.//Mescher, M.C.//Fleischer, S.G.//Kolter, R.//Pierce, N.//Zhaxybayeva, O. 	Draft Genome Sequence of Erwinia tracheiphila, an Economically Important Bacterial Pathogen of Cucurbits.	Genome Announcements	2015	3		e00482-15			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. 		
@D	Shapovalova, N.I.//Ivanov, L.Y.//Matvienko, N.I. 	Site-specific endonuclease BstM6I from the natural isolate Bacillus stearothermophilus M6.	Bioorg. Khim.	1992	18		1186-1189			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. 		
@D	Shapovalova, N.I.//Zheleznaja, L.A.//Matvienko, N.I. 	BspKT6I, a new site-specific endonuclease which cleaves the GATC site producing two nucleotide 5'-protruding ends.	Nucleic Acids Res.	1993	21		5794			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. 		
@D	Shapovalova, N.I.//Zheleznaya, L.A.//Matvienko, N.I. 	New site-specific endonuclease and methylase from the thermophilic strain Bacillus species KT6.	Biokhimiia	1994	59		1730-1738			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. 		
@D	Shapovalova, N.I.//Zheleznaya, L.A.//Matvienko, N.N.//Matvienko, N.I. 	A new site-specific endonuclease BspKT5I.	Biokhimiia	1994	59		485-493			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. 		
@D	Sharath, A.N.//Weinhold, E.//Bhagwat, A.S. 	Reviving a dead enzyme: cytosine deaminations promoted by an inactive DNA methyltransferase and an S-adenosylmethionine analogue.	Biochemistry	2000	39		14611-14616			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. 		
@D	Sharko, F.S.//Shapovalova, A.A.//Tsygankova, S.V.//Komova, A.V.//Boulygina, E.S.//Teslyuk, A.B.//Gotovtsev, P.M.//Namsaraev, Z.B.//Khijniak, T.V.//Nedoluzhko, A.V.//Vasilov, R.G. 	Draft Genome Sequence of 'Halomonas chromatireducens' Strain AGD 8-3, a Haloalkaliphilic Chromate- and Selenite-Reducing Gammaproteobacterium.	Genome Announcements	2016	4		e00160-16			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. 		
@D	Sharkova, E.V.//Nikolskaya, I.I.//Shomodi, P.//Feldesh, I.//Debov, S.S. 	Effect of various conditions on stability of DNA-methylases from cells of Mycobacterium smegmatis butyricum.	Vopr. Med. Khim.	1986	32		125-129			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. 		
@D	Sharkova, E.V.//Nikolskaya, I.I.//Shomodi, P.//Feldesh, I.//Debov, S.S. 	Isolation and fractionation of DNA-methylases from Mycobacterium butyricum.	Vopr. Med. Khim.	1984	30		72-76			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. 		
@D	Sharma, A.//Hira, P.//Shakarad, M.//Lal, R. 	Draft Genome Sequence of Cellulosimicrobium sp. Strain MM, Isolated from Arsenic-Rich Microbial Mats of a Himalayan Hot Spring.	Genome Announcements	2014	2		e01020-14			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%. 		
@D	Sharma, G.//Khatri, I.//Subramanian, S. 	Draft Genome Sequence of Kocuria palustris PEL.	Genome Announcements	2014	2		e01261-13			We report the 2.9-Mb draft genome sequence of an actinobacterium, Kocuria palustris PEL, of the family Micrococcaceae. 		
@D	Sharma, G.//Khatri, I.//Subramanian, S. 	Complete Genome of the Starch-Degrading Myxobacteria Sandaracinus amylolyticus DSM 53668T.	Genome Biol. Evol.	2016	8		2520-2529			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. 		
@D	Sharma, M.//Ellis, R.L.//Hinton, D.M. 	Identification of a family of bacteriophage T4 genes encoding proteins similar to those present in group I introns of fungi and phage.	Proc. Natl. Acad. Sci. U. S. A.	1992	89		6658-6662			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. 		
@D	Sharma, M.//Hinton, D.M. 	Purification and characterization of the SegA protein of bacteriophage T4, an endonuclease related to proteins encoded by group I introns.	J. Bacteriol.	1994	176		6439-6448			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. 		
@D	Sharma, P.//D'Souza, D.R.//Bhandari, D.//Parashar, V.//Capalash, N. 	Demonstration of the principles of restriction endonuclease cleavage reactions using thermostable BflI from Anoxybacillus flavithermus.	Biochem. Mol. Biol. Educ.	2003	31		392-396			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. 		
@D	Sharma, P.//Diene, S.M.//Gimenez, G.//Robert, C.//Rolain, J.M. 	Genome Sequence of Microbacterium yannicii, a Bacterium Isolated from a Cystic Fibrosis Patient.	J. Bacteriol.	2012	194		4785			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. 		
@D	Sharma, P.//Gupta, S.K.//Adenipekun, E.O.//Barrett, J.B.//Hiott, L.M.//Woodley, T.A.//Iwalokun, B.A.//Oyedeji, K.S.//Oluwadun, A.//Ramadan, H.//Frye, J.G.//Jackson, C.R. 	Draft Genome Sequence Analysis of Multidrug-Resistant Escherichia coli Strains Isolated in 2013 from Humans and Chickens in Nigeria.	Genome Announcements	2017	5		e01073-17			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. 		
@D	Sharma, P.//Gupta, S.K.//Barrett, J.B.//Hiott, L.M.//House, S.L.//Woodley, T.A.//Frye, J.G.//Jackson, C.R. 	Draft Genome Sequences of Eight Streptogramin-Resistant Enterococcus Species Isolated from Animal and Environmental Sources in the United States.	Genome Announcements	2017	5		e01287-17			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. 		
@D	Sharma, P.//Killmaster, L.F.//Volkening, J.D.//Cardenas-Garcia, S.//Shittu, I.//Meseko, C.A.//Sulaiman, L.K.//Joannis, T.M.//Miller, P.J.//Afonso, C.L. 	Draft Genome Sequences of Five Novel Ochrobactrum spp. Isolated from Different Avian Hosts in Nigeria.	Genome Announcements	2018	6		e00063-18			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. 		
@D	Sharma, P.//Killmaster, L.F.//Volkening, J.D.//Cardenas-Garcia, S.//Wajid, A.//Rehmani, S.F.//Basharat, A.//Miller, P.J.//Afonso, C.L. 	Draft Genome Sequences of Three Ochrobactrum spp. Isolated from Different Avian Hosts in Pakistan.	Genome Announcements	2018	6		e00269-18			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. 		
@D	Sharma, P.//Reddy, D.P.//Kumar, P.A.//Gadicherla, R.//George, N.//Bhandari, V. 	Draft Genome Sequence of a Staphylococcus aureus Strain Isolated from a Cow with  Clinical Mastitis.	Genome Announcements	2015	3		e00914-15			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. 		
@D	Sharma, P.K.//Fu, J.//Cicek, N.//Sparling, R.//Levin, D.B. 	Kinetics of medium-chain-length polyhydroxyalkanoate production by a novel isolate of Pseudomonas putida LS46.	Can. J. Microbiol.	2012	58		982-989			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%). 		
@D	Sharma, P.K.//Fu, J.//Zhang, X.//Fristensky, B.W.//Davenport, K.//Chain, P.S.//Sparling, R.//Levin, D.B. 	Draft Genome Sequence of Medium-Chain-Length Polyhydroxyalkanoate-Producing Pseudomonas putida Strain LS46.	Genome Announcements	2013	1		e00151-13			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. 		
@D	Sharma, R.//Singh, R.K.M.//Malik, G.//Deveshwar, P.//Tyagi, A.K.//Kapoor, S.//Kapoor, M. 	Rice cytosine DNA methyltransferases - gene expression profiling during reproductive development and abiotic stress.	FEBS J.	2009	276		6301-6311			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. 		
@D	Sharma, V.//Midha, S.//Ranjan, M.//Pinnaka, A.K.//Patil, P.B. 	Genome Sequence of Xanthomonas axonopodis pv. punicae Strain LMG 859.	J. Bacteriol.	2012	194		2395			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. 		
@D	Sharma, V.//Singh, P.K.//Midha, S.//Ranjan, M.//Korpole, S.//Patil, P.B. 	Genome Sequence of Brevibacillus laterosporus Strain GI-9.	J. Bacteriol.	2012	194		1279			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. 		
@D	Sharma, V.//Youngblood, B.//Reich, N. 	Residues distal from the active site that alter enzyme function in M.HhaI DNA cytosine methyltransferase.	J. Biomol. Struct. Dyn.	2005	22		533-543			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. 		
@D	Sharma, V.K.//Bayles, D.O.//Alt, D.P.//Looft, T. 	Complete Genome Sequences of Curli-Negative and Curli-Positive Isolates of Foodborne Escherichia coli O157:H7 Strain 86-24.	Genome Announcements	2016	4		e01323-16			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. 		
@D	Sharmin, D.//Guo, Y.//Nishizawa, T.//Ohshima, S.//Sato, Y.//Takashima, Y.//Narisawa, K.//Ohta, H. 	Comparative Genomic Insights into Endofungal Lifestyles of Two Bacterial Endosymbionts, Mycoavidus cysteinexigens and Burkholderia rhizoxinica.	Microbes Environ.	2018	33		66-76			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. 		
@D	Sharp, C.E. et al. 	Draft Genome Sequence of the Moderately Halophilic Methanotroph Methylohalobius crimeensis Strain 10Ki.	Genome Announcements	2015	3		e00644-15			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. 		
@D	Sharp, P.A.//Sugden, B.//Sambrook, J. 	Detection of two restriction endonuclease activities in Haemophilus parainfluenzae using analytical agarose-ethidium bromide electrophoresis.	Biochemistry	1973	12		3055-3063			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. 		
@D	Sharp, P.M. 	Molecular evolution of bacteriophages: Evidence of selection against the recognition sites of host restriction enzymes.	Mol. Biol. Evol.	1986	3		75-83			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. 		
@D	Sharp, P.M.//Kelleher, J.E.//Daniel, A.S.//Cowan, G.M.//Murray, N.E. 	Roles of selection and recombination in the evolution of type I restriction-modification systems in enterobacteria.	Proc. Natl. Acad. Sci. U. S. A.	1992	89		9836-9840			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. 		
@D	Sharpe, R.M.//Koepke, T.//Harper, A.//Grimes, J.//Galli, M.//Satoh-Cruz, M.//Kalyanaraman, A.//Evans, K.//Kramer, D.//Dhingra, A. 	CisSERS: Customizable In Silico Sequence Evaluation for Restriction Sites.	PLoS ONE	2016	11		e0152404			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. 		
@D	Sharrocks, A.D.//Hornby, D.P. 	Transcriptional analysis of the restriction and modification genes of bacteriophage P1.	Mol. Microbiol.	1991	5		685-694			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. 		
@D	Shaw, P.C.//Clark, D.R.//Kam, K.M.//Mok, Y.K. 	Isolation and characterization of thermophilic restriction endonucleases.	Abstr. Gen. Meet. Am. Soc. Microbiol.	1991	91		199			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. 		
@D	Shaw, P.C.//Mok, Y.K. 	XcmI as a universal restriction enzyme for single-stranded DNA.	Gene	1993	133		85-89			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. 		
@D	Shaw, Y.J.//Chen, C.S. 	Structure-activity relationship study of (-)-epicatechin analogues as DNA methyltransferase inhibitors.	ACS Abstracts	2005	229		U186-U187			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. 		
@D	She, Q. et al. 	The complete genome of the crenarchaeon Sulfolobus solfataricus P2.	Proc. Natl. Acad. Sci. U. S. A.	2001	98		7835-7840			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. 		
@D	She, X.//Tang, Y.//He, Z.//Lan, G. 	Genome Sequencing of Ralstonia solanacearum Race 4, Biovar 4, and Phylotype I, Strain YC45, Isolated from Rhizoma kaempferiae in Southern China.	Genome Announcements	2015	3		e01110-15			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. 		
@D	Shearman, C.//Godon, J.-J.//Gasson, M. 	Splicing of a group II intron in a functional transfer gene of Lactococcus lactis.	Mol. Microbiol.	1996	21		45-53			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. 		
@D	Sheflyan, G.Y.//Kubareva, E.A.//Gromova, E.S.//Shabarova, Z.A. 	Conformational transition of restriction endonuclease MvaI-substrate complex under the influence of Mg2+ probed by DNA-protein linking studies.	Bioconjugate Chem.	1998	9		703-707			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. 		
@D	Sheflyan, G.Y.//Kubareva, E.A.//Gromova, E.S.//Shabarova, Z.A. 	Hydrolysis of 5-fluorodeoxycytidine-containing DNA duplexes using restriction endonucleases.	Biokhimiia	1993	58		1806-1811			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. 		
@D	Sheflyan, G.Y.//Kubareva, E.A.//Kuznetsova, S.A.//Karyagina, A.S.//Nikolskaya, I.I.//Gromova, E.S.//Shabarova, Z.A. 	Cross-linking of SsoII restriction endonuclease to cognate and non-cognate DNAs.	FEBS Lett.	1996	390		307-310			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. 		
@D	Sheflyan, G.Y.//Kubareva, E.A.//Volkov, E.M.//Oretskaya, T.S.//Gromova, E.S.//Shabarova, Z.A. 	Chemical cross-linking of MvaI and EcoRII enzymes to DNA duplexes containing monosubstituted pyrophosphate internucleotide bond.	Gene	1995	157		187-190			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. 		
@D	Sheflyan, G.Y.//Tashlitskii, V.N.//Kubareva, E.A. 	Interaction of restriction endonuclease MvaI with synthetic DNA duplexes.	Vestn. Mosk. Univ.	1993	34		516-520					
@D	Sheh, A.//Piazuelo, M.B.//Wilson, K.T.//Correa, P.//Fox, J.G. 	Draft Genome Sequences of Helicobacter pylori Strains Isolated from Regions of Low and High Gastric Cancer Risk in Colombia.	Genome Announcements	2013	1		e00736-13			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. 		
@D	Sheh, A.//Shen, Z.//Fox, J.G. 	Draft Genome Sequences of Eight Enterohepatic Helicobacter Species Isolated from  Both Laboratory and Wild Rodents.	Genome Announcements	2014	2		e01218-14			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. 		
@D	Sheik, C.S.//Sieber, J.R.//Badalamenti, J.P.//Carden, K.//Olson, A. 	Complete Genome Sequence of Desulfovibrio desulfuricans Strain G11, a Model Sulfate-Reducing, Hydrogenotrophic, and Syntrophic Partner Organism.	Genome Announcements	2017	5		e01207-17			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. 		
@D	Sheikhnejad, G.//Brank, A.//Christman, J.K.//Goddard, A.//Alvarez, E.//Ford, H. Jr.//Marquez, V.E.//Marasco, C.J.//Sufrin, J.R.//O'Gara, M.//Cheng, X. 	Mechanism of inhibition of DNA (cytosine C5)-methyltransferases by oligodeoxyribonucleotides containing 5,6-dihydro-5-azacytosine.	J. Mol. Biol.	1999	285		2021-2034			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. 		
@D	Sheikhnejad, G.//Marasco, C.//Sufrin, J.//Christman, J.K. 	Comparison of substrate specificity of mammalian and bacterial CpG DNA methyltransferases (MTases).	Biomed. Pharmacother.	1992	46		24			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. 		
@D	Shell, S.S.//Prestwich, E.G.//Baek, S.H.//Shah, R.R.//Sassetti, C.M.//Dedon, P.C.//Fortune, S.M. 	DNA methylation impacts gene expression and ensures hypoxic survival of Mycobacterium tuberculosis.	PLoS Pathog.	2013	9		e1003419			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. 		
@D	Sheluho, D.//Khariwala, S.//Yebra, M.J.//Bhagwat, A.S. 	Ability of cytosine methyltransferases to bind substrates containing mismatches is not sufficient for causing C to T mutations.	FASEB J.	1996	10		A965			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. 		
@D	Sheluho, D.//Yebra, M.J.//Shariwala, S.S.//Bhagwat, A.S. 	Lack of correlation between binding of EcoRII methyltransferase to DNA duplexes containing mismatches and the promotion of C to T mutations.	Mol. Gen. Genet.	1997	255		54-59			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. 		
@D	Shemer, R.//Birger, Y.//Riggs, A.D.//Razin, A. 	Structure of the imprinted mouse Snrpn gene and establishment of its parental-specific methylation pattern.	Proc. Natl. Acad. Sci. U. S. A.	1997	94		10267-10272			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. 		
@A	Shemer, R.//Razin, A. 		Establishment of imprinted methylation patterns during development.			Russo, V.E.A.//Martienssen, R.A.//Riggs, A.D. 		Epigenetic Mechanisms of Gene Regulation				Cold Spring Harbor	Cold Spring Harbor Laboratory Press	1996		0		215-229									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. 		
@D	Shemesh, M.//Pasvolsky, R.//Sela, N.//Green, S.J.//Zakin, V. 	Draft Genome Sequence of Alicyclobacillus acidoterrestris Strain ATCC 49025.	Genome Announcements	2013	1		e00638-13			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. 		
@D	Shen, B.W.//Heiter, D.F.//Chan, S.H.//Wang, H.//Xu, S.Y.//Morgan, R.D.//Wilson, G.G.//Stoddard, B.L. 	Unusual target site disruption by the rare-cutting HNH restriction endonuclease PacI.	Structure	2010	18		734-743			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. 		
@D	Shen, B.W.//Lambert, A.//Walker, B.C.//Stoddard, B.L.//Kaiser, B.K. 	The Structural Basis of Asymmetry in DNA Binding and Cleavage as Exhibited by the I-SmaMI LAGLIDADG Meganuclease.	J. Mol. Biol.	2016	428		206-220			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. 		
@D	Shen, B.W.//Landthaler, M.//Shub, D.A.//Stoddard, B.L. 	DNA binding and cleavage by the HNH homing endonuclease I-HmuI.	J. Mol. Biol.	2004	342		43-56			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. 		
@D	Shen, B.W.//Xu, D.//Chan, S.H.//Zheng, Y.//Zhu, Z.//Xu, S.Y.//Stoddard, B.L. 	Characterization and crystal structure of the type IIG restriction endonuclease RM.BpuSI.	Nucleic Acids Res.	2011	39		8223-8236			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. 		
@D	Shen, J.//Rideout, W.M. III//Jones, P.A. 	High frequency mutagenesis by a DNA methyltransferase.	Cell	1992	71		1073-1080			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. 		
@D	Shen, J.//Rideout, W.M. III//Jones, P.A. 	The rate of hydrolytic deamination of 5-methylctyosine in double-stranded DNA.	Nucleic Acids Res.	1994	22		972-976			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. 		
@D	Shen, J.-C.//Zingg, J.-M.//Yang, A.S.//Schmutte, C.//Jones, P.A. 	A mutant HpaII methyltransferase functions as a mutator enzyme.	Nucleic Acids Res.	1995	23		4275-4282			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. 		
@D	Shen, K. et al. 	Extensive genomic plasticity in Pseudomonas aeruginosa revealed by identification and distribution studies of novel genes among clinical isolates.	Infect. Immun.	2006	74		5272-5283			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. 		
@D	Shen, L.//Gao, G.//Zhang, Y.//Zhang, H.//Ye, Z.//Huang, S.//Huang, J.//Kang, J. 	A single amino acid substitution confers enhanced methylation activity of mammalian Dnmt3b on chromatin DNA.	Nucleic Acids Res.	2010	38		6054-6064			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. 		
@D	Shen, P.//Jiang, Y.//Zhou, Z.//Zhang, J.//Yu, Y.//Li, L. 	Complete nucleotide sequence of pKP96, a 67 850 bp multiresistance plasmid encoding qnrA1, aac(6')-Ib-cr and blaCTX-M-24 from Klebsiella pneumoniae.	J. Antimicrob. Chemother.	2008	62		1252-1256			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. 		
@D	Shen, S.//Li, Q.//Yan, P.//Zhou, B.//Ye, S.//Lu, Y.//Wang, D. 	Restriction endonucleases from three strains of Haemophilus influenzae.	Sci. Sin.	1980	23		1435-1442			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. 		
@D	Shen, W.Y.//Lo, W.S.//Lai, Y.C.//Kuo, C.H. 	Complete Genome Sequence of Spiroplasma helicoides TABS-2T (DSM 22551), a Bacterium Isolated from a Horsefly (Tabanus abactor).	Genome Announcements	2016	4		e01201-16			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. 		
@D	Shen, X.//Chen, M.//Hu, H.//Wang, W.//Peng, H.//Xu, P.//Zhang, X. 	Genome Sequence of Pseudomonas chlororaphis GP72, a Root-Colonizing Biocontrol Strain.	J. Bacteriol.	2012	194		1269-1270			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. 		
@D	Shen, X.//Wang, Q.//Xia, L.//Zhu, X.//Zhang, Z.//Liang, Y.//Cai, H.//Zhang, E.//Wei, J.//Chen, C.//Song, Z.//Zhang, H.//Yu, D.//Hai, R. 	Complete Genome Sequences of Yersinia pestis from Natural Foci in China.	J. Bacteriol.	2010	192		3551-3552			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. 		
@D	Shen, Z.//Sheh, A.//Young, S.K.//Abouelliel, A.//Ward, D.V.//Earl, A.M.//Fox, J.G. 	Draft genome sequences of six enterohepatic helicobacter species isolated from humans and one from rhesus macaques.	Genome Announcements	2014	2		e00857-14			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. 		
@D	Shendure, J.//Porreca, G.J.//Reppas, N.B.//Lin, X.//McCutcheon, J.P.//Rosenbaum, A.M.//Wang, M.D.//Zhang, K.//Mitra, R.D.//Church, G.M. 	Accurate multiplex polony sequencing of an evolved bacterial genome.	Science	2005	309		1728-1732			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. 		
@D	Sheng, B.//Ni, J.//Gao, C.//Ma, C.//Xu, P. 	Draft Genome Sequence of the Gluconobacter oxydans Strain DSM 2003, an Important  Biocatalyst for Industrial Use.	Genome Announcements	2014	2		e00417-14			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. 		
@D	Sheng, H.//Duan, M.//Hunter, S.S.//Minnich, S.A.//Settles, M.L.//New, D.D.//Chase, J.R.//Fagnan, M.W.//Hovde, C.J. 	High-Quality Complete Genome Sequences of Three Bovine Shiga Toxin-Producing Escherichia coli O177:H- (fliCH25) Isolates Harboring Virulent stx2 and Multiple   Plasmids.	Genome Announcements	2018	6		e01592-17			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. 		
@D	Sheng, L.//Zhang, Y.//Minton, N.P. 	Complete Genome Sequence of Geobacillus thermoglucosidasius NCIMB 11955, the Progenitor of a Bioethanol Production Strain.	Genome Announcements	2016	4		e01065-16			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. 		
@D	Shenoy, S.//Daigle, K.//Ehrlich, K.C.//Gehrke, C.W.//Ehrlich, M. 	Hydrolysis by restriction endonucleases at their DNA recognition sequences substituted with mismatched base pairs.	Nucleic Acids Res.	1986	14		4407-4420			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. 		
@D	Shepard, S.M.//Danzeisen, J.L.//Isaacson, R.E.//Seemann, T.//Achtman, M.//Johnson, T.J. 	Genome sequences and phylogenetic analysis of K88- and F18-positive porcine enterotoxigenic Escherichia coli.	J. Bacteriol.	2012	194		395-405			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. 		
@D	Sheppard, A.E.//Poehlein, A.//Rosenstiel, P.//Liesegang, H.//Schulenburg, H. 	Complete Genome Sequence of Bacillus thuringiensis Strain 407 Cry-.	Genome Announcements	2013	1		e00158-12			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. 		
@D	Sheppard, A.E.//Stoesser, N.//Sebra, R.//Kasarskis, A.//Deikus, G.//Anson, L.//Walker, A.S.//Peto, T.E.//Crook, D.W.//Mathers, A.J. 	Complete Genome Sequence of KPC-Producing Klebsiella pneumoniae Strain CAV1193.	Genome Announcements	2016	4		e01649-15			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. 		
@D	Sherburne, C.K.//Lawley, T.D.//Gilmour, M.W.//Blattner, F.R.//Burland, V.//Grotbeck, E.//Rose, D.J.//Taylor, D.E. 	The complete DNA sequence and analysis of R27, a large IncHI plasmid from Salmonella typhi that is temperature sensitive for transfer.	Nucleic Acids Res.	2000	28		2177-2186			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. 		
@D	Sheth, A.//Ravikumar, M.//Hosur, R.V.//Govil, G. 	Two dimensional NMR studies on the solution structure of d-CTCGAGCTCGAG.	Biochem. Biophys. Res. Commun.	1987	144		26-34			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. 		
@D	Shetty, A.R. et al. 	Complete genome sequence of the phenanthrene-degrading soil bacterium Delftia acidovorans Cs1-4.	Standards in Genomic Sciences	2015	10		55			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. 		
@D	Shetty, D.//Grigoryan, A.A.//Alshalchi, S.//Withana, G.N.//Roy, J.//Lawrence, J.R.//Vidovic, S.//Korber, D.R. 	Draft Genome Sequences of Biofilm-Forming and Non-Biofilm-Forming Nontyphoidal Salmonella enterica Serovars.	Genome Announcements	2017	5		e01061-17			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. 		
@D	Shetty, S.A.//Marathe, N.P.//Munot, H.//Antony, C.P.//Dhotre, D.P.//Murrell, J.C.//Shouche, Y.S. 	Draft Genome Sequence of Methylophaga lonarensis MPLT, a Haloalkaliphilic (Non-Methane-Utilizing) Methylotroph.	Genome Announcements	2013	1		e00202-13			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)). 		
@D	Shetty, S.A.//Ritari, J.//Paulin, L.//Smidt, H.//De Vos, W.M. 	Complete Genome Sequence of Eubacterium hallii Strain L2-7.	Genome Announcements	2017	5		e01167-17			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. 		
@D	Shetty, V.//Lamichhane, B.//Chua, E.G.//Ballal, M.//Tay, C.Y. 	Draft Genome Sequences of 42 Helicobacter pylori Isolates from Rural Regions of South India.	Genome Announcements	2018	6		e01486-17			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. 		
@D	Shevchuk, T.//Kretzner, L.//Munson, K.//Axume, J.//Clark, J.//Dyachenko, O.V.//Caudill, M.//Buryanov, Y.//Smith, S.S. 	Transgene-induced CCWGG methylation does not alter CG methylation patterning in human kidney cells.	Nucleic Acids Res.	2005	33		6124-6136			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. 		
@D	Shevchuk, T.V.//Buryanov, Y.I. 	DNA methyltransferase-based assay for the cytosine methylation level in the DNA sequence CCWGG.	Bioorg. Khim.	1999	25		630-633			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. 		
@D	Shevchuk, T.V.//Zakharchenko, N.S.//Dyachenko, O.V.//Buryanov, Y.I. 	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.	Russ. J. Plant Physiol.	2001	48		478-482			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. 		
@D	Shevtsov, A.//Tarlykov, P.//Zholdybayeva, E.//Momynkulov, D.//Sarsenova, A.//Moldagulova, N.//Momynaliev, K. 	Draft Genome Sequence of Rhodococcus erythropolis DN1, a Crude Oil Biodegrader.	Genome Announcements	2013	1		e00846-13			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. 		
@D	Shevtsov, A.//Tarlykov, P.//Zholdybayeva, E.//Shevtsova, E.//Momynkulov, D.//Sytnik, I.//Karibaev, T.//Chsherbakov, A.//Momynaliev, K. 	Draft Genome Sequence of the Live Vaccine Strain Brucella abortus 82.	Genome Announcements	2013	1		e01101-13			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. 		
@D	Shi, C.Y.//Jia, K.T.//Yang, B.//Huang, J. 	Complete genome sequence of a Megalocytivirus (family Iridoviridae) associated with turbot mortality in China.	Virol. J.	2010	7		159			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. 		
@D	Shi, L.//Suetake, I.//Kawakami, T.//Aimoto, S.//Tajima, S. 	Xenopus Eggs Express an Identical DNA Methyltransferase, Dnmt1, to Somatic Cells.	J. Biochem. (Tokyo)	2001	130		359-366			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. 		
@D	Shi, W.//Lu, W.//Liu, Q.//Zhi, Y.//Zhou, P. 	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.	Funct. Integr. Genomics	2014	14		219-227			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. 		
@D	Shi, X.//Yu, M.//Yan, S.//Dong, S.//Zhang, X.H. 	Genome Sequence of the Thermostable-Agarase-Producing Marine Bacterium Catenovulum agarivorans YM01T, Which Reveals the Presence of a Series of  Agarase-Encoding Genes.	J. Bacteriol.	2012	194		5484			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. 		
@D	Shi, X.//Zhu, Y.//Li, Y.//Jiang, M.//Lin, Y.//Qiu, Y.//Chen, Q.//Yuan, Y.//Ni, P.//Hu, Q.//Huang, S. 	Genome Sequence of Proteus mirabilis Clinical Isolate C05028.	Genome Announcements	2014	2		e00167-14			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. 		
@D	Shi, Y.//Chen, Y.//Li, Z.//Yang, L.//Chen, W.//Mu, Z. 	Complete Genome Sequence of Streptococcus thermophilus MN-BM-A02, a Rare Strain with a High Acid-Producing Rate and Low Post-Acidification Ability.	Genome Announcements	2015	3		e00979-15			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%. 		
@D	Shi, Y.//Tian, Z.//Leclercq, S.O.//Zhang, H.//Yang, M.//Zhang, Y. 	Genetic characterization and potential molecular dissemination mechanism of tet (31) gene in Aeromonas caviae from an oxytetracycline wastewater treatment system.	J. Environ. Sci. (China)	2019	76		259-266			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. 		
@D	Shi, Y.H.//Ren, L.//Jia, Y.//Yan, Y.C. 	Genome Sequence of Organophosphorus Pesticide-Degrading Bacterium Pseudomonas stutzeri Strain YC-YH1.	Genome Announcements	2015	3		e00192-15			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. 		
@D	Shi, Z.//Kaldhone, P.R.//Khajanchi, B.K.//Foley, S.L.//Ricke, S.C. 	Draft Genome Sequences of Salmonella enterica Serovar Enteritidis and Kentucky Isolates from Retail Poultry Sources.	Genome Announcements	2018	6		e00193-18			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. 		
@D	Shibata, T.//Ando, T. 	The restriction endonucleases in Bacillus amyloliquefaciens N strain.  Substrate specificities.	Biochim. Biophys. Acta	1976	442		184-196			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. 		
@D	Shibata, T.//Ando, T. 	In vitro Modification and Restriction of Phage Phi105C DNA with Bacillus subtilis N Cell-free Extract.	Mol. Gen. Genet.	1975	138		269-279			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. 		
@D	Shibata, T.//Ando, T. 	Host controlled modification and restriction in Bacillus subtilis.	Mol. Gen. Genet.	1974	131		275-280			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. 		
@D	Shibata, T.//Hayase, E.//Ando, T. 	Simultaneous preparation of a DNA ligase and restriction endonucleases from Bacillus amyloliquefaciens N.	Agric. Biol. Chem.	1978	42		1613-1615			None 		
@A	Shibata, T.//Ikawa, S.//Ando, T. 		Genetic study of restriction endonucleases in Bacillus subtilis.			Schlessinger, D. 		Microbiology-1982				Washington	American Society for Microbiology	1982		0		71-74									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. 		
@D	Shibata, T.//Ikawa, S.//Kim, C.//Ando, T. 	Site-specific Deoxyribonucleases in Bacillus subtilis and other Bacillus strains.	J. Bacteriol.	1976	128		473-476			We systematically studied site-specific deoxyribonucleases in Bacillus strains and detected deoxyribonuclease activities in 20 of 62 strains tested. 		
@D	Shibata, T.//Ikawa, S.//Komatsu, Y.//Ando, T.//Saito, H. 	Introduction of host-controlled modification and restriction systems of Bacillus subtilis IAM1247 into Bacillus subtilis 168.	J. Bacteriol.	1979	139		308-310			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. 		
@D	Shibata, T.//Morishima, N. 	Genetic recombination and site-specific endonucleases in mitochondria.	Tanpakushitsu Kakusan Koso	1994	39		589-600					
@D	Shibata, T.//Morishima, N.//Nakagawa, K. 	A mitochondrial multi-site specific endonuclease, endo SceI of Saccharomyces cerevisiae.	J. Cell Biochem. Suppl.	1993	17C		154			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. 		
@D	Shibata, T.//Nakagawa, K.-I.//Morishima, N. 	Multi-site-specific endonucleases and the initiation of homologous genetic recombination in yeast.	Adv. Biophys.	1995	31		77-91			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. 		
@D	Shibata, T.//Watabe, H.//Kaneko, T.//Iino, T.//Ando, T. 	On the nucleotide sequence recognized by a eukaryotic site-specific endonuclease, Endo.SceI from yeast.	J. Biol. Chem.	1984	259		10499-10506			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. 		
@D	Shibata, T.F.//Maeda, T.//Nikoh, N.//Yamaguchi, K.//Oshima, K.//Hattori, M.//Nishiyama, T.//Hasebe, M.//Fukatsu, T.//Kikuchi, Y.//Shigenobu, S. 	Complete Genome Sequence of Burkholderia sp. Strain RPE64, Bacterial Symbiont of  the Bean Bug Riptortus pedestris.	Genome Announcements	2013	1		e00441-13			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. 		
@D	Shieh, F.K.//Reich, N.O. 	AdoMet-dependent Methyl-transfer: Glu(119) Is Essential for DNA C5-Cytosine Methyltransferase M.HhaI.	J. Mol. Biol.	2007	373		1157-1168			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. 		
@D	Shieh, F.K.//Youngblood, B.//Reich, N.O. 	The Role of Arg165 Towards Base Flipping, Base Stabilization and Catalysis in M.HhaI.	J. Mol. Biol.	2006	362		516-527			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. 		
@D	Shields, S.L.//Burbank, D.E.//Grabherr, R.//Van Etten, J.L. 	Cloning and sequencing the cytosine methyltransferase gene M. CviJI from Chlorella virus IL-3A.	Virology	1990	176		16-24			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. 		
@D	Shields, S.L.//Burbank, D.E.//Van Etten, J.L. 	Molecular cloning and characterization of the gene encoding the cytosine methyltransferase.	J. Cell Biochem. Suppl.	1989	13D		214			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. 		
@D	Shields-Menard, S.A.//Brown, S.D.//Klingeman, D.M.//Indest, K.//Hancock, D.//Wewalwela, J.J.//French, W.T.//Donaldson, J.R. 	Draft Genome Sequence of Rhodococcus rhodochrous Strain ATCC 21198.	Genome Announcements	2014	2		e00054-14			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. 		
@D	Shier, V.K. 	Characterization and inhibition of an essential adenine DNA methyltransferase from Caulobacter crescentus.	Diss. Abstr.	2002	62		3185-3186			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. 		
@D	Shier, V.K.//Hancey, C.J.//Benkovic, S.J. 	Identification of the active oligomeric state of an essential adenine DNA methyltransferase from Caulobacter crescentus.	J. Biol. Chem.	2001	276		14744-14751			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. 		
@D	Shigdel, U.K. 	Developing DNA probes to trap DNA cytosine-5 methyltransferases involved in promoter hypermethylation in cancer.	Ph.D. Thesis, Univ. of Chicago	2009			1-90			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. 		
@D	Shigdel, U.K.//He, C. 	A New 1'-Methylenedisulfide Deoxyribose that Forms an Efficient Cross-Link to DNA Cytosine-5 Methyltransferase (DNMT).	J. Am. Chem. Soc.	2008	130		17634-17635			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. 		
@D	Shigemoto, N.//Kuwahara, R.//Kayama, S.//Shimizu, W.//Onodera, M.//Yokozaki, M.//Hisatsune, J.//Kato, F.//Ohge, H.//Sugai, M. 	Emergence in Japan of an imipenem-susceptible, meropenem-resistant Klebsiella pneumoniae carrying blaIMP-6.	Diagn. Microbiol. Infect. Dis.	2012	72		109-112			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. 		
@D	Shigenobu, S.//Watanabe, H.//Hattori, M.//Sakaki, Y.//Ishikawa, H. 	Genome sequence of the endocellular bacterial symbiont of aphids Buchnera sp. APS.	Nature	2000	407		81-86			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. 		
@D	Shih, P.M. et al. 	Improving the coverage of the cyanobacterial phylum using diversity-driven genome sequencing.	Proc. Natl. Acad. Sci. U. S. A.	2013	110		1053-1058			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. 		
@D	Shikara, M. 	Identification of a restriction endonuclease (SacC1) from Saccharomyces cerevisiae.	J. Yeast Fungal Res.	2010	1		127-135			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. 		
@D	Shikara, M. 	A specific inhibitory protein to a restriction enzyme from Saccharomyces cerevisiae.	J. Yeast Fungal Res.	2010	1		174-182			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. 		
@D	Shilov, I.//Tashlitsky, V.//Khodoun, M.//Vasilev, S.//Alekseev, Y.//Kuzubov, A.//Kubareva, E.//Karyagina, A. 	DNA-methyltransferase SsoII interaction with own promoter region binding site.	Nucleic Acids Res.	1998	26		2659-2664			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. 		
@D	Shimizu, M.//Goda, H.//Yamasaki, K.//Oshima, S.//Ohnishi, K.//Osaki, Y.//Kataoka, S.//Imajoh, M. 	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.	Genome Announcements	2016	4		e01762-15			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. 		
@D	Shimizu, T.//Ohtani, K.//Hirakawa, H.//Ohshima, K.//Yamashita, A.//Shiba, T.//Ogasawara, N.//Hattori, M.//Kuhara, S.//Hayashi, H. 	Complete genome sequence of Clostridium perfringens, an anaerobic flesh-eater.	Proc. Natl. Acad. Sci. U. S. A.	2002	99		996-1001			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. 		
@D	Shimizu-Kadota, M.//Kato, H.//Shiwa, Y.//Oshima, K.//Machii, M.//Araya-Kojima, T.//Zendo, T.//Hattori, M.//Sonomoto, K.//Yoshikawa, H. 	Genomic Features of Lactococcus lactis IO-1, a Lactic Acid Bacterium That Utilizes Xylose and Produces High Levels of L-Lactic Acid.	Biosci. Biotechnol. Biochem.	2013	77		1804-1808			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. 		
@D	Shimizu-Kadota, M.//Shibahara-Sone, H. 	M.HhaI-methylated DNA is resistant to cleavage by R.BbeI.	Agric. Biol. Chem.	1989	53		2841-2842			Shows that BbeI can cleave GGCG5mCC, GGCGC5mC, but not GG5mCGCC. 		
@D	Shimoda, N.//Yamakoshi, K.//Miyake, A.//Takeda, H. 	Identification of a gene required for de novo DNA methylation of the zebrafish no tail gene.	Dev. Dyn.	2005	233		1509-1516			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. 		
@D	Shimoda, Y.//Hirakawa, H.//Sato, S.//Saeki, K.//Hayashi, M. 	Whole-Genome Sequence of the Nitrogen-Fixing Symbiotic Rhizobium Mesorhizobium loti Strain TONO.	Genome Announcements	2016	4		e01016-16			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. 		
@D	Shimodaira, J.//Kamimura, N.//Hosoyama, A.//Yamazoe, A.//Fujita, N.//Masai, E. 	Draft Genome Sequence of Comamonas sp. Strain E6 (NBRC 107749), a Degrader of Phthalate Isomers through the Protocatechuate 4,5-Cleavage Pathway.	Genome Announcements	2015	3		e00643-15			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. 		
@D	Shimodaira, J.//Yonezuka, K.//Tabata, M.//Nagase, S.//Kasai, D.//Hosoyama, A.//Yamazoe, A.//Fujita, N.//Fukuda, M. 	Draft Genome Sequence of Comamonas thiooxydans Strain PHE2-6 (NBRC 110656), a Chlorinated-Ethene-Degrading Bacterium.	Genome Announcements	2016	4		e00487-16			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. 		
@D	Shimotsu, H.//Takahashi, H.//Saito, H. 	Site-specific endonucleases in Streptomyces strains.	Agric. Biol. Chem.	1980	44		1665-1666			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. 		
@D	Shimotsu, H.//Takahashi, H.//Saito, H. 	A new site-specific endonuclease StuI from Streptomyces tubercidicus.	Gene	1980	11		219-225			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. 		
@D	Shimura, Y.//Hirose, Y.//Misawa, N.//Wakazuki, S.//Fujisawa, T.//Nakamura, Y.//Kanesaki, Y.//Yamaguchi, H.//Kawachi, M. 	Complete Genome Sequence of a Coastal Cyanobacterium, Synechococcus sp. Strain NIES-970.	Genome Announcements	2017	5		e00139-17			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. 		
@D	Shin, H.//Lee, J.H.//Ahn, C.S.//Ryu, S.//Cho, B.C. 	Complete genome sequence of marine bacterium Pseudoalteromonas phenolica bacteriophage TW1.	Arch. Virol.	2014	159		159-162			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. 		
@D	Shin, H.//Lee, J.H.//Choi, Y.//Ryu, S. 	Complete Genome Sequence of the Opportunistic Food-Borne Pathogen Cronobacter sakazakii ES15.	J. Bacteriol.	2012	194		4438-4439			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. 		
@D	Shin, H.//Lee, J.H.//Kim, Y.//Ryu, S. 	Complete Genome Sequence of Cronobacter sakazakii Bacteriophage CR3.	J. Virol.	2012	86		6367-6368			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. 		
@D	Shin, H.//Lee, J.H.//Lim, J.A.//Kim, H.//Ryu, S. 	Complete Genome Sequence of Salmonella enterica Serovar Typhimurium Bacteriophage SPN1S.	J. Virol.	2012	86		1284-1285			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. 		
@D	Shin, J.//Soo-Ko, K. 	Single origin of three plasmids bearing blaCTX-M-15 from different Klebsiella pneumoniae clones.	J. Antimicrob. Chemother.	2013	69		969-972			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. 		
@D	Shin, J.E.//Lin, C.//Lim, H.N. 	Horizontal transfer of DNA methylation patterns into bacterial chromosomes.	Nucleic Acids Res.	2016	44		460-471			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. 		
@D	Shin, N.R.//Whon, T.W.//Roh, S.W.//Kim, M.S.//Jung, M.J.//Lee, J.//Bae, J.W. 	Genome Sequence of Corynebacterium nuruki S6-4T, Isolated from Alcohol Fermentation Starter.	J. Bacteriol.	2011	193		4257			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%). 		
@D	Shin, S.C.//Ahn, D.H.//Lee, J.K.//Kim, S.J.//Hong, S.G.//Kim, E.H.//Park, H. 	Genome Sequence of Sphingomonas sp. Strain PAMC 26605, Isolated from Arctic Lichen (Ochrolechia sp.).	J. Bacteriol.	2012	194		1607			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. 		
@D	Shin, S.C.//Kim, S.J.//Ahn, D.H.//Lee, J.K.//Lee, H.//Lee, J.//Hong, S.G.//Lee, Y.M.//Park, H. 	Genome Sequence of a Salinibacterium sp. Isolated from Antarctic Soil.	J. Bacteriol.	2012	194		2404			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. 		
@D	Shin, S.C.//Kim, S.J.//Ahn-do, H.//Lee, J.K.//Park, H. 	Draft Genome Sequence of Sphingomonas echinoides ATCC 14820.	J. Bacteriol.	2012	194		1843			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. 		
@D	Shin, S.C.//Kim, S.J.//Hong, S.G.//Ahn-do, H.//Lee, Y.M.//Lee, H.//Lee, J.//Park, H. 	Genome Sequence of Pseudomonas sp. Strain PAMC 25886, Isolated from Alpine Glacial Cryoconite.	J. Bacteriol.	2012	194		1844			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. 		
@D	Shin, S.H.//Kim, S.//Kim, J.Y.//Lee, S.//Um, Y.//Oh, M.K.//Kim, Y.R.//Lee, J.//Yang, K.S. 	Complete Genome Sequence of the 2,3-Butanediol-Producing Klebsiella pneumoniae Strain KCTC 2242.	J. Bacteriol.	2012	194		2736-2737			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]). 		
@D	Shin, S.H.//Kim, S.//Kim, J.Y.//Lee, S.//Um, Y.//Oh, M.K.//Kim, Y.R.//Lee, J.//Yang, K.S. 	Complete Genome Sequence of Klebsiella oxytoca KCTC 1686, Used in Production of 2,3-Butanediol.	J. Bacteriol.	2012	194		2371-2372			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. 		
@D	Shin, S.H.//Kim, S.//Kim, J.Y.//Lee, S.//Um, Y.//Oh, M.K.//Kim, Y.R.//Lee, J.//Yang, K.S. 	Complete Genome Sequence of Enterobacter aerogenes KCTC 2190.	J. Bacteriol.	2012	194		2373-2374			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. 		
@D	Shin, S.H.//Kim, S.//Kim, J.Y.//Song, H.Y.//Cho, S.J.//Kim, D.R.//Lee, K.I.//Lim, H.K.//Park, N.J.//Hwang, I.T.//Yang, K.S. 	Genome Sequence of Paenibacillus terrae HPL-003, a Xylanase-Producing Bacterium Isolated from Soil Found in Forest Residue.	J. Bacteriol.	2012	194		1266			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. 		
@D	Shin, S.H.//Um, Y.//Beak, J.H.//Kim, S.//Lee, S.//Oh, M.K.//Kim, Y.R.//Lee, J.//Yang, K.S. 	Complete Genome Sequence of Raoultella ornithinolytica Strain B6, a 2,3-Butanediol-Producing Bacterium Isolated from Oil-Contaminated Soil.	Genome Announcements	2013	1		e00395-13			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. 		
@D	Shin, S.K.//Goo, H.//Cho, Y.J.//Kwon, S.//Yong, D.//Yi, H. 	Non-contiguous finished genome sequence and description of the gliding bacterium  Flavobacterium seoulense sp. nov.	Standards in Genomic Sciences	2014	9		34			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. 		
@D	Shin, Y.W.//Choi, M.M.//Chun, J.H.//Yu, J.Y.//Kim, D.W.//Rhie, G.E. 	Draft Genome Sequence of the First South Korean Clinical Isolate of Burkholderia  pseudomallei, H0901.	Genome Announcements	2018	6		e00336-18			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. 		
@D	Shinjo, R.//Uesaka, K.//Ihara, K.//Loshakova, K.//Mizuno, Y.//Yano, K.//Tanaka, A. 	Complete Genome Sequence of Kosakonia sacchari Strain BO-1, an Endophytic Diazotroph Isolated from a Sweet Potato.	Genome Announcements	2016	4		e00868-16			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. 		
@D	Shinomiya, T.//Kobayashi, M.//Sato, S. 	A second site specific endonuclease from Thermus thermophilus 111, Tth111II.	Nucleic Acids Res.	1980	8		3275-3285			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. 		
@D	Shinomiya, T.//Kobayashi, M.//Sato, S. 	A second site specific endonuclease from Thermus thermophilus 111, Tth111II.	Nucleic Acids Symp. Ser.	1980	SS8		S181-S184			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. 		
@D	Shinomiya, T.//Kobayashi, M.//Sato, S.//Uchida, T. 	A new aspect of a restriction endonuclease Tth111I.  It has a degenerated specificity (Tth111I*).	J. Biochem. (Tokyo)	1982	92		1823-1832			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. 		
@D	Shinomiya, T.//Sato, S. 	A site specific endonuclease from Thermus thermophilus 111, Tth111I.	Nucleic Acids Res.	1980	8		43-56			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. 		
@D	Shintani, M.//Hosoyama, A.//Ohji, S.//Tsuchikane, K.//Takarada, H.//Yamazoe, A.//Fujita, N.//Nojiri, H. 	Complete Genome Sequence of the Carbazole Degrader Pseudomonas resinovorans Strain CA10 (NBRC 106553).	Genome Announcements	2013	1		e00488-13			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. 		
@D	Shintani, M.//Ohtsubo, Y.//Fukuda, K.//Hosoyama, A.//Ohji, S.//Yamazoe, A.//Fujita, N.//Nagata, Y.//Tsuda, M.//Hatta, T.//Kimbara, K. 	Complete Genome Sequence of the Thermophilic Polychlorinated Biphenyl Degrader Geobacillus sp. Strain JF8 (NBRC 109937).	Genome Announcements	2014	2		e01213-13			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. 		
@D	Shirai, M.//Hirakawa, H.//Kimoto, M.//Tabuchi, M.//Kishi, F.//Ouchi, K.//Shiba, T.//Ishii, K.//Hattori, M.//Kuhara, S.//Nakazawa, T. 	Comparison of whole genome sequences of Chlamydia pneumoniae J138 from Japan and CWL029 from USA.	Nucleic Acids Res.	2000	28		2311-2314			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. 		
@D	Shiraishi, H.//Tabuse, Y. 	The AplI Restriction-Modification System in an Edible Cyanobacterium, Arthrospira (Spirulina) platensis NIES-39, Recognizes the Nucleotide Sequence 5'-CTGCAG-3'.	Biosci. Biotechnol. Biochem.	2013	77		782-788			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. 		
@D	Shirane, K.//Toh, H.//Kobayashi, H.//Miura, F.//Chiba, H.//Ito, T.//Kono, T.//Sasaki, H. 	Mouse Oocyte Methylomes at Base Resolution Reveal Genome-Wide Accumulation of Non-CpG Methylation and Role of DNA Methyltransferases.	PLoS Genet.	2013	9		e1003439			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. 		
@D	Shiratori-Takano, H.//Takano, H.//Ueda, K. 	Whole-Genome Sequence of Filimonas lacunae, a Bacterium of the Family Chitinophagaceae Characterized by Marked Colony Growth under a High-CO2  Atmosphere.	Genome Announcements	2016	4		e00667-16			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. 		
@D	Shiroma, A.//Terabayashi, Y.//Nakano, K.//Shimoji, M.//Tamotsu, H.//Ashimine, N.//Ohki, S.//Shinzato, M.//Teruya, K.//Satou, K.//Hirano, T. 	First Complete Genome Sequences of Staphylococcus aureus subsp. aureus Rosenbach  1884 (DSM 20231T), Determined by PacBio Single-Molecule Real-Time Technology.	Genome Announcements	2015	3		e00800-15			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%). 		
@D	Shirshikov, F.V.//Korzhenkov, A.A.//Miroshnikov, K.K.//Kabanova, A.P.//Barannik, A.P.//Ignatov, A.N.//Miroshnikov, K.A. 	Draft Genome Sequences of New Genomospecies 'Candidatus Pectobacterium maceratum' Strains, Which Cause Soft Rot in Plants.	Genome Announcements	2018	6		e00260-18			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.' 		
@D	Shiryaev, S.A.//Zheleznaya, L.A.//Matvienko, N.I. 	Three site-specific endonucleases from Thermophilic strain Bacillus species LA are isoschizomers of HhaI, AsuII, and HindIII.	Biokhimiia	1997	62		280-290			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. 		
@D	Shiryaev, S.A.//Zheleznyakova, E.N.//Matvienko, N.N.//Zheleznaya, L.A.//Matvienko, N.I. 	Two new site-specific endonucleases from Staphylococcus species strain D5.	Biokhimiia	2000	65		553-561			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). 		
@D	Shishido, K.//Berg, P. 	Restriction endonuclease from Haemophilus gallinarum (HgaI) cleaves polyoma DNA at four locations.	J. Virol.	1976	18		793-798			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. 		
@D	Shishido, T.K.//Jokela, J.//Fewer, D.P.//Wahlsten, M.//Fiore, M.F.//Sivonen, K. 	Simultaneous Production of Anabaenopeptins and Namalides by the Cyanobacterium Nostoc sp. CENA543.	ACS Chem. Biol.	2017	12		2746-2755			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. 		
@D	Shivaji, S.//Ara, S.//Bandi, S.//Singh, A.//Kumar, P.A. 	Draft Genome Sequence of Arthrobacter gangotriensis Strain Lz1yT, Isolated from a Penguin Rookery Soil Sample Collected in Antarctica, near the Indian Station  Dakshin Gangotri.	Genome Announcements	2013	1		e00347-13			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. 		
@D	Shivaji, S.//Ara, S.//Begum, Z.//Ruth, M.//Singh, A.//Kumar, P.A. 	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.	Genome Announcements	2013	1		e00346-13			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. 		
@D	Shivaji, S.//Ara, S.//Begum, Z.//Srinivas, T.N.//Singh, A.//Kumar, P.A. 	Draft Genome Sequence of Cesiribacter andamanensis Strain AMV16T, Isolated from a Soil Sample from a Mud Volcano in the Andaman Islands, India.	Genome Announcements	2013	1		e00240-13			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. 		
@D	Shivaji, S.//Ara, S.//Prasad, S.//Manasa, B.P.//Begum, Z.//Singh, A.//Kumar, P.A. 	Draft Genome Sequence of Arcticibacter svalbardensis Strain MN12-7T, a Member of  the Family Sphingobacteriaceae Isolated from an Arctic Soil Sample.	Genome Announcements	2013	1		e00484-13			The 4.69-Mb genome sequence of Arcticibacter svalbardensis strain MN12-7(T), isolated from an Arctic soil sample, is reported. 		
@D	Shivaji, S.//Ara, S.//Singh, A.//Kumar, P.A. 	Draft Genome Sequence of Cyclobacterium qasimii Strain M12-11BT, Isolated from Arctic Marine Sediment.	Genome Announcements	2013	1		e00642-13			A 6.29-Mb genome sequence of Cyclobacterium qasimii strain M12-11B(T), isolated from an Arctic marine sediment sample, is reported. 		
@D	Shivaji, S.//Ara, S.//Singh, A.//Pinnaka, A.K. 	Draft Genome Sequence of Cecembia lonarensis Strain LW9T, Isolated from Lonar Lake, a Haloalkaline Lake in India.	J. Bacteriol.	2012	194		6631			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. 		
@D	Shivaji, S.//Ara, S.//Singh, S.K.//Bandi, S.//Singh, A.//Pinnaka, A.K. 	Draft Genome Sequence of Bacillus isronensis Strain B3W22, Isolated from the Upper Atmosphere.	J. Bacteriol.	2012	194		6624-6625			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. 		
@D	Shivapriya, R.//Prasad, R.//Narayanan, I.L.//Krishnaswamy, S.//Dharmalingam, K. 	Expression of the mcrA gene of Escherichia coli is regulated post-transcriptionally, possibly by sequestration of the Shine-Dalgarno region.	Gene	1995	157		201-207			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. 		
@D	Shiwa, Y.//Atarashi, H.//Tanaka, N.//Okada, S.//Yoshikawa, H.//Endo, A.//Miyaji, T.//Nakagawa, J. 	Genome Sequences of Three Strains of Lactobacillus paracasei of Different Origins and with Different Cholate Sensitivities.	Genome Announcements	2015	3		e00178-15			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. 		
@D	Shkoporov, A.N.//Efimov, B.A.//Khokhlova, E.V.//Chaplin, A.V.//Kafarskaya, L.I.//Durkin, A.S.//McCorrison, J.//Torralba, M.//Gillis, M.//Sutton, G.//Weibel, D.B.//Nelson, K.E.//Smeianov, V.V. 	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.	Genome Announcements	2013	1		e00234-13			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. 		
@D	Shlyapnikov, S.V.//Lunin, V.V.//Blagova, E.V.//Abaturov, L.V.//Perbandt, M.//Betzel, C.//Mikhailov, A.M. 	A comparative structure-function analysis and molecular mechanism of action of endonucleases from Serratia marcescens and Physarum  polycephalum.	Bioorg. Khim.	2002	28		23-31			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. 		
@D	Shock, L.S.//Thakkar, P.V.//Peterson, E.J.//Moran, R.G.//Taylor, S.M. 	DNA methyltransferase 1, cytosine methylation, and cytosine hydroxymethylation in mammalian mitochondria.	Proc. Natl. Acad. Sci. U. S. A.	2011	108		3630-3635			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. 		
@D	Shoemaker, W.R.//Muscarella, M.E.//Lennon, J.T. 	Genome Sequence of the Soil Bacterium Janthinobacterium sp. KBS0711.	Genome Announcements	2015	3		e00689-15			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. 		
@D	Shome, R.//Krithiga, N.//Muttannagouda, R.B.//Veeregowda, B.M.//Swati, S.//Shome, B.R.//Vishnu, U.//Sankarasubramanian, J.//Sridhar, J.//Gunasekaran, P.//Rahman, H.//Rajendhran, J. 	Draft Genome Sequence of Brucella melitensis Strain ADMAS-G1, Isolated from Placental Fluids of an Aborted Goat.	Genome Announcements	2013	1		e00809-13			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. 		
@D	Shome, R.//Krithiga, N.//Padmashree, B.S.//Sankarasubramanian, J.//Vishnu, U.S.//Sridhar, J.//Gunasekaran, P.//Rajendhran, J.//Rahman, H. 	Draft Genome Sequence of Brucella abortus S99: Designated Antigenic Smooth Reference Strain Used in Diagnostic Tests in India.	Genome Announcements	2014	2		e00824-14			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. 		
@D	Shore, A.//Rossney, A.S.//Keane, C.T.//Enright, M.C.//Coleman, D.C. 	Seven Novel Variants of the Staphylococcal Chromosomal Cassette mec in Methicillin-Resistant Staphylococcus aureus Isolates from Ireland.	Antimicrob. Agents Chemother.	2005	49		2070-2083			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. 		
@D	Shore, A.C.//Rossney, A.S.//O'Connell, B.//Herra, C.M.//Sullivan, D.J.//Humphreys, H.//Coleman, D.C. 	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.	Antimicrob. Agents Chemother.	2008	52		4407-4419			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. 		
@D	Shorning, B.Y.//Vanyushin, B.F. 	Putative DNA-(amino)methyltransferases in eucaryotes.	Biokhimiia	2001	66		753-762			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. 		
@D	Shouche, Y.S.//Ramesh, N.//Brahmachari, S.K. 	Probing of unusual DNA structures in topologically constrained form V DNA: use of restriction enzymes as structural probes.	Nucleic Acids Res.	1990	18		267-275			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. 		
@D	Showmaker, K.C.//Arick, M.A.I.I.//Hsu, C.Y.//Martin, B.E.//Wang, X.//Jia, J.//Wubben, M.J.//Nichols, R.L.//Allen, T.W.//Peterson, D.G.//Lu, S.E. 	The genome of the cotton bacterial blight pathogen Xanthomonas citri pv. malvacearum strain MSCT1.	Standards in Genomic Sciences	2017	12		42			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. 		
@D	Shrestha, P.M.//Kube, M.//Reinhardt, R.//Liesack, W. 	Transcriptional activity of paddy soil bacterial communities.	Environ. Microbiol.	2008	11		960-970			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. 		
@D	Shrestha, R.//Park, D.H.//Cho, J.M.//Cho, S.//Wilson, C.//Hwang, I.//Hur, J.H.//Lim, C.K. 	Genetic organization of the hrp genes cluster in Erwinia pyrifoliae and characterization of HR active domains in HrpNEp protein by mutational analysis.	Mol. Cells	2008	25		30-42			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. 		
@D	Shrestha, S.D.//Guttman, D.S.//Perron, G.G. 	Draft Genome Sequences of 10 Environmental Pseudomonas aeruginosa Strains Isolated from Soils, Sediments, and Waters.	Genome Announcements	2017	5		e00804-17			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. 		
@D	Shridhar, P.B.//Patel, I.R.//Gangiredla, J.//Mammel, M.K.//Noll, L.//Shi, X.//Bai, J.//Elkins, C.A.//Strockbine, N.//Nagaraja, T.G. 	Draft Genome Sequences of Escherichia coli O104 Strains of Bovine and Human Origin.	Genome Announcements	2017	5		e00630-17			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). 		
@D	Shtratnikova, V.Y.//Bragin, E.Y.//Dovbnya, D.V.//Pekov, Y.A.//Schelkunov, M.I.//Strizhov, N.//Ivashina, T.V.//Ashapkin, V.V.//Donova, M.V. 	Complete Genome Sequence of Sterol-Transforming Mycobacterium neoaurum Strain VKM Ac-1815D.	Genome Announcements	2014	2		e01177-13			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. 		
@D	Shtratnikova, V.Y.//Schelkunov, M.I.//Dovbnya, D.V.//Pekov, Y.A.//Bragin, E.Y.//Ashapkin, V.V.//Donova, M.V. 	Complete Genome Sequence of Mycobacterium sp. Strain VKM Ac-1817D, Capable of Producing 9alpha-Hydroxy-androst-4-ene-3,17-dione from Phytosterol.	Genome Announcements	2015	3		e01447-14			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. 		
@D	Shtratnikova, V.Y.//Schelkunov, M.I.//Pekov, Y.A.//Fokina, V.V.//Logacheva, M.D.//Sokolov, S.L.//Bragin, E.Y.//Ashapkin, V.V.//Donova, M.V. 	Complete Genome Sequence of Steroid-Transforming Nocardioides simplex VKM Ac-2033D.	Genome Announcements	2015	3		e01406-14			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. 		
@D	Shu, H.W.//Liu, T.T.//Chan, H.I.//Liu, Y.M.//Wu, K.M.//Shu, H.Y.//Tsai, S.F.//Hsiao, K.J.//Hu, W.S.//Ng, W.V. 	Genome Sequence of the Repetitive-Sequence-Rich Mycoplasma fermentans Strain M64.	J. Bacteriol.	2011	193		4302-4303			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. 		
@D	Shub, D.A.//Goodrich-Blair, H. 	Protein introns: A new home for endonucleases.	Cell	1992	71		183-186			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. 		
@D	Shub, D.A.//Goodrich-Blair, H. 	Amino acid sequence motif of group I intron endonucleases is conserved in open reading frames of group II introns.	Trends Biochem. Sci.	1994	19		402-404			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. 		
@D	Shub, D.A.//Gott, J.M.//Xu, M.Q.//Lang, B.F.//Michel, F.//Tomashewski, J.//Pedersen-Lane, J.//Belfort, M. 	Structural conservation among three homologous introns of bacteriophage T4 and the group I introns of eukaryotes.	Proc. Natl. Acad. Sci. U. S. A.	1988	85		1151-1155			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. 		
@D	Shub, D.A.//Xu, M.-Q.//Gott, J.M.//Zeeh, A.//Wilson, L.D. 	A family of autocatalytic group I introns in bacteriophage T4.	Cold Spring Harb. Symp. Quant. Biol.	1987	52		193-200			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. 		
@D	Shukla, H.//Kobayashi, Y.//Arenstorf, H.//Yasukochi, Y.//Weissman, S.M. 	Purification of BsuE methyltransferase and its application in genome mapping.	Nucleic Acids Res.	1991	19		4233-4239			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. 		
@D	Shulman, M.J. 	Model for wandering restriction enzymes.	Nature	1974	252		76-78			None 		
@D	Shumkova, E.S.//Olsson, B.E.//Kudryavtseva, A.V.//Plotnikova, E.G. 	Draft Genome Sequence of Rhodococcus ruber Strain P25, an Active Polychlorinated  Biphenyl Degrader.	Genome Announcements	2015	3		e00990-15			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. 		
@D	Shur, K.V.//Klimina, K.M.//Zakharevich, N.V.//Maslov, D.A.//Bekker, O.B.//Zaychikova, M.V.//Kamaev, E.Y.//Kravchenko, M.A.//Skornyakov, S.N.//Zhang, Y.//Danilenko, V.N. 	Draft Genome Sequence of Mycobacterium tuberculosis Strain E186hv of Beijing B0/W Lineage with Reduced Virulence.	Genome Announcements	2015	3		e00403-15			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. 		
@D	Shyaka, A.//Kusumoto, A.//Asakura, H.//Kawamoto, K. 	Whole-Genome Sequences of Eight Campylobacter jejuni Isolates from Wild Birds.	Genome Announcements	2015	3		e00315-15			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. 		
@D	Sibley, M.H.//Raleigh, E.A. 	Cassette-like variation of restriction enzyme genes in Escherichia coli C and relatives.	Nucleic Acids Res.	2004	32		522-534			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. 		
@D	Sibponkrung, S.//Kondo, T.//Tanaka, K.//Tittabutr, P.//Boonkerd, N.//Teaumroong, N.//Yoshida, K.I. 	Genome Sequence of Bacillus velezensis S141, a New Strain of Plant Growth-Promoting Rhizobacterium Isolated from Soybean Rhizosphere.	Genome Announcements	2017	5		e01312-17			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. 		
@D	Sidamonidze, K.//Hang, J.//Yang, Y.//Dzavashvili, G.//Zhgenti, E.//Trapaidze, N.//Imnadze, P.//Nikolich, M.P. 	Genome Sequences of Human and Livestock Isolates of Brucella melitensis and Brucella abortus from the Country of Georgia.	Genome Announcements	2017	5		e01518-16			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. 		
@D	Siddaramappa, S. et al. 	Complete genome sequence of Dehalogenimonas lykanthroporepellens type strain (BL-DC-9(T)) and comparison to 'Dehalococcoides' strains.	Standards in Genomic Sciences	2012	6		251-264			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. 		
@D	Siddavattam, D.//Karegoudar, T.B.//Mudde, S.K.//Kumar, N.//Baddam, R.//Avasthi, T.S.//Ahmed, N. 	Genome of a Novel Isolate of Paracoccus denitrificans Capable of Degrading N,N-Dimethylformamide.	J. Bacteriol.	2011	193		5598-5599			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. 		
@D	Siddharth, J.//Membrez, M.//Chakrabarti, A.//Betrisey, B.//Chou, C.J.//Parkinson, S.J. 	Complete Genome Sequence of Escherichia coli Strain M8, Isolated from ob/ob Mice.	Genome Announcements	2017	5		e00449-17			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. 		
@D	Siddique, A.//Jurkowska, R.Z.//Jurkowski, T.P.//Jeltsch, A. 	Auto-methylation of the mouse DNA-(cytosine C5)-methyltransferase Dnmt3a at its active site cysteine residue.	FEBS J.	2011	278		2055-2063			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. 		
@D	Siddiqui, F.M.//Ibrahim, M.//Noureen, N.//Noreen, Z.//Titball, R.W.//Champion, O.L.//Wren, B.W.//Studholme, D.//Bokhari, H. 	Draft Genome Sequence of the Enteropathogenic Bacterium Campylobacter jejuni Strain cj255.	Genome Announcements	2015	3		e01223-15			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. 		
@D	Siddiqui, H.//Yoder-Himes, D.R.//Mizgalska, D.//Nguyen, K.A.//Potempa, J.//Olsen, I. 	Genome Sequence of Porphyromonas gingivalis Strain HG66 (DSM 28984).	Genome Announcements	2014	2		e00947-14			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%. 		
@D	Siddiqui, M.A.//Rashid, N.//Ayyampalayam, S.//Whitman, W.B. 	Draft Genome Sequence of Geobacillus thermopakistaniensis Strain MAS1.	Genome Announcements	2014	2		e00559-14			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. 		
@D	Sidjabat, H.E.//Cottrell, K.//Cervin, A. 	Draft Genome Sequences of Burkholderia pseudomallei and Staphylococcus aureus, Isolated from a Patient with Chronic Rhinosinusitis.	Genome Announcements	2015	3		e01075-15			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. 		
@D	Sidjabat, H.E.//Grahn, H.E.//Cervin, A. 	Draft Genome Sequence of the Oral Commensal Streptococcus oralis 89a with Interference Activity against Respiratory Pathogens.	Genome Announcements	2016	4		e01546-15			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. 		
@D	Sidjabat, H.E.//Robson, J.//Paterson, D.L. 	Draft Genome Sequences of Two IMP-4-Producing Escherichia coli Sequence Type 131  Isolates in Australia.	Genome Announcements	2015	3		e00983-15			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. 		
@D	Sidorova, N.//Muradymov, S.//Rau, D.C. 	Specific versus Nonspecific DNA Binding of the Restriction Endonuclease EcoRV Measured by Self-Cleavage Assay.	J. Biomol. Struct. Dyn.	2009	26		896-897					
@A	Sidorova, N.//Rau, D.C. 		The role of water in the EcoRI-DNA binding.			Pingoud, A. 		Nucleic Acids Mol. Biol.				Berlin Heidelberg	Springer-Verlag	2004		14		319-337									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. 		
@D	Sidorova, N.Y.//Muradymov, S.//Rau, D.C. 	Differences in hydration coupled to specific and nonspecific competitive binding and to specific DNA binding of the restriction endonuclease BamHI.	J. Biol. Chem.	2006	281		35656-35666			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. 		
@D	Sidorova, N.Y.//Muradymov, S.//Rau, D.C. 	A novel self-cleavage assay for measuring DNA binding of restriction endonucleases.	FEBS J.	2005	272		565			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. 		
@D	Sidorova, N.Y.//Muradymov, S.//Rau, D.C. 	Solution parameters modulating DNA binding specificity of the restriction endonuclease EcoRV.	FEBS J.	2011	278		2713-2727			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. 		
@D	Sidorova, N.Y.//Muradymov, S.R.//Royal, R.M.//Rau, D.C. 	Unusual DNA-Binding Kinetics of the Restriction Endonuclease EcoRV.	Biophys. J.	2011	100		72			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. 		
@D	Sidorova, N.Y.//Rau, D.C. 	Self-footprint of the restriction endonuclease EcoRI.	Biophys. J.	2000	78		299A			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. 		
@D	Sidorova, N.Y.//Rau, D.C. 	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.	J. Mol. Biol.	2001	310		801-816			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. 		
@D	Sidorova, N.Y.//Rau, D.C. 	Differences in water release for the binding of EcoRI to specific and nonspecific DNA sequences.	Proc. Natl. Acad. Sci. U. S. A.	1996	93		12272-12277			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. 		
@D	Sidorova, N.Y.//Rau, D.C. 	Removing water from an EcoRI-noncognate DNA complex with osmotic stress.	J. Biomol. Struct. Dyn.	1999	17		19-31			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. 		
@D	Sidorova, N.Y.//Rau, D.C. 	The dissociation rate of the EcoRI-DNA-specific complex is linked to water activity.	Biopolymers	2000	53		363-368			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. 		
@D	Siebers, B.//Zaparty, M.//Raddatz, G.//Tjaden, B.//Albers, S.V.//Bell, S.D.//Blombach, F.//Kletzin, A.//Kyrpides, N.//Lanz, C.//Plagens, A.//Rampp, M.//Rosinus, A.//von Jan, M.//Makarova, K.S.//Klenk, H.P.//Schuster, S.C.//Hensel, R. 	The Complete Genome Sequence of Thermoproteus tenax: A Physiologically Versatile Member of the Crenarchaeota.	PLoS ONE	2011	6		E24222			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. 		
@D	Siedlecki, P.//Boy, R.G.//Comagic, S.//Schirrmacher, R.//Wiessler, M.//Zielenkiewicz, P.//Suhai, S.//Lyko, F. 	Establishment and functional validation of a structural homology model for human DNA methyltransferase 1.	Biochem. Biophys. Res. Commun.	2003	306		558-563			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. 		
@D	Siedlecki, P.//Boy, R.G.//Musch, T.//Brueckner, B.//Suhai, S.//Lyko, F.//Zielenkiewicz, P. 	Discovery of two novel, small-molecule inhibitors of DNA methylation.	J. Med. Chem.	2006	49		678-683			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. 		
@D	Siegl, T.//Petzke, L.//Welle, E.//Luzhetskyy, A. 	I-SceI endonuclease: a new tool for DNA repair studies and genetic manipulations in streptomycetes.	Appl. Microbiol. Biotechnol.	2010	87		1525-1532			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. 		
@D	Sievert, S.M.//Scott, K.M.//Klotz, M.G.//Chain, P.S.//Hauser, L.J.//Hemp, J.//Hugler, M.//Land, M.//Lapidus, A.//Larimer, F.W.//Lucas, S.//Malfatti, S.A.//Meyer, F.//Paulsen, I.T.//Ren, Q.//Simon, J.//USF, G.C. 	Genome of the epsilonproteobacterial chemolithoautotroph Sulfurimonas denitrificans.	Appl. Environ. Microbiol.	2008	74		1145-1156			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. 		
@D	Sievert, U. 	Determination of the specific recognition sequence of the restriction enzyme Rlu-1I from Rhizobium lupini.	Ph.D. Thesis, Erlangen University, W. Germany	1982			1-109			This is the enzyme RluI. 		
@D	Siezen, R.J.//Bayjanov, J.//Renckens, B.//Wels, M.//van Hijum, S.A.//Molenaar, D.//van Hylckama, V.J.E. 	Complete genome sequence of Lactococcus lactis subsp. lactis KF147, a plant-associated lactic acid bacterium.	J. Bacteriol.	2010	192		2649-2650			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. 		
@D	Siezen, R.J.//Francke, C.//Renckens, B.//Boekhorst, J.//Wels, M.//Kleerebezem, M.//van Hijum, S.A.F.T. 	Complete resequencing and reannotation of the Lactobacillus plantarum WCFS1 genome.	J. Bacteriol.	2011	194		195-196			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. 		
@D	Siezen, R.J.//Renckens, B.//van Swam, I.//Peters, S.//van Kranenburg, R.//Kleerebezem, M.//de Vos, W.M. 	Complete Sequences of Four Plasmids of Lactococcus lactis subsp. cremoris SK11 Reveal Extensive Adaptation to the Dairy Environment.	Appl. Environ. Microbiol.	2005	71		8371-8382			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. 		
@D	Siezen, R.J.//Starrenburg, M.J.C.//Boekhorst, J.//Renckens, B.//Molenaar, D.//van Hylckama-Vlieg, J.E.T. 	Genome-scale genotype-phenotype matching of two Lactococcus lactis isolates from plants identifies mechanisms of adaptation to the plant niche.	Appl. Environ. Microbiol.	2008	74		424-436			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. 		
@D	Sikora, A.E.//Smith, J.R.//Campbell, S.A.//Firman, K. 	AFM protein-protein interactions within the EcoR124I molecular motor.	Soft Matter	2012	8		6358-6363			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. 		
@D	Sikorski, J. et al. 	Complete genome sequence of Sulfurospirillum deleyianum type strain (5175).	Standards in Genomic Sciences	2010	2		149-157			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. 		
@D	Sikorski, J. et al. 	Complete genome sequence of Segniliparus rotundus type strain (CDC 1076).	Standards in Genomic Sciences	2010	2		203-211			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. 		
@D	Sikorski, J. et al. 	Complete genome sequence of Meiothermus silvanus type strain (VI-R2).	Standards in Genomic Sciences	2010	3		37-46			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. 		
@D	Sikorski, J. et al. 	Complete genome sequence of Acetohalobium arabaticum type strain (Z-7288).	Standards in Genomic Sciences	2010	3		57-65			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. 		
@D	Sikorski, J. et al. 	Complete genome sequence of Sulfurimonas autotrophica type strain (OK10).	Standards in Genomic Sciences	2010	3		194-202			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. 		
@D	Sikorski, J. et al. 	Complete genome sequence of Ilyobacter polytropus type strain (CuHbu1).	Standards in Genomic Sciences	2010	3		304-314			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. 		
@D	Sikorski, J. et al. 	Complete genome sequence of Mahella australiensis type strain (50-1 BON).	Standards in Genomic Sciences	2011	4		331-341			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. 		
@D	Siksnys, V.//Grazulis, S.//Huber, R. 	Structure and function of the tetrameric restriction enzymes.	Nucleic Acids Mol. Biol.	2004	14		237-259			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. 		
@D	Siksnys, V.//Pleckaityte, M. 	Catalytic and binding properties of restriction endonuclease Cfr9I.	Eur. J. Biochem.	1993	217		411-419			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. 		
@D	Siksnys, V.//Pleckaityte, M. 	Role of the reactive cysteine residue in restriction endonuclese Cfr9I.	Biochim. Biophys. Acta	1992	1160		199-205			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. 		
@D	Siksnys, V.//Skirgaila, R.//Sasnauskas, G.//Urbanke, C.//Cherny, D.//Grazulis, S.//Huber, R. 	The Cfr10I restriction enzyme is functional as a tetramer.	J. Mol. Biol.	1999	291		1105-1118			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. 		
@D	Siksnys, V.//Tamulaitis, G.//Zaremba, M.//Szczepanowski, R.//Bochtler, M. 	How do restriction enzymes acquire specificities for different target sites?	FEBS J.	2008	275		10			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. 		
@D	Siksnys, V.//Timinskas, A.//Klimasauskas, S.//Butkus, V.//Janulaitis, A. 	Sequence similarity among type-II restriction endonucleases, related by their recognized 6-bp target and tetranucleotide-overhang cleavage.	Gene	1995	157		311-314			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. 		
@D	Siksnys, V.//Zareckaja, N.//Vaisvila, R.//Timinskas, A.//Stakenas, P.//Butkus, V.//Janulaitis, A. 	CAATTG-specific restriction-modification munI genes from Mycoplasma: sequence similarities between R.MunI and R.EcoRI.	Gene	1994	142		1-8			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. 		
@D	Silanskas, A.//Foss, M.//Wende, W.//Urbanke, C.//Lagunavicius, A.//Pingoud, A.//Siksnys, V. 	Photocaged Variants of the MunI and PvuII Restriction Enzymes.	Biochemistry	2011	50		2800-2807			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. 		
@D	Silanskas, A.//Zaremba, M.//Sasnauskas, G.//Siksnys, V. 	Catalytic Activity Control of Restriction Endonuclease-Triplex Forming Oligonucleotide Conjugates.	Bioconjugate Chem.	2012	23		203-211					
@D	Silber, K.R.//Polisson, C.//Rees, P.A.//Benner, J.S. 	Cloning, purification and characterization of the M.NdeI methyltransferase from Neisseria denitrificans.	Gene	1988	74		43-44			Meeting Abstract 		
@D	Silberstein, Z.//Shalit, M.//Cohen, A. 	Heteroduplex strand-specificity in restriction-stimulated recombination by the RecE pathway of Escherichia coli.	Genetics	1993	133		439-448			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. 		
@D	Silo-Suh, L.A.//Suh, S.J.//Ohman, D.E.//Wozniak, D.J.//Pridgeon, J.W. 	Complete Genome Sequence of Pseudomonas aeruginosa Mucoid Strain FRD1, Isolated from a Cystic Fibrosis Patient.	Genome Announcements	2015	3		e00153-15			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. 		
@D	Silva, A. et al. 	Complete Genome Sequence of Corynebacterium pseudotuberculosis I-19, strain isolated from Israel Bovine mastitis.	J. Bacteriol.	2010	193		323-324			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. 		
@D	Silva, A. et al. 	Complete genome sequence of Corynebacterium pseudotuberculosis Cp31, isolated from an Egyptian buffalo.	J. Bacteriol.	2012	194		6663-6664			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. 		
@D	Silva, A.S.//Barauna, R.A.//de Sa, P.C.//das Gracas, D.A.//Carneiro, A.R.//Thouvenin, M.//Azevedo, V.//Badell, E.//Guiso, N.//da Silva, A.L.//Ramos, R.T. 	Draft Genome Sequence of Corynebacterium ulcerans FRC58, Isolated from the Bronchitic Aspiration of a Patient in France.	Genome Announcements	2014	2		e01132-13			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. 		
@D	Silva, B.S.//Nobrega, M.S.//Leomil, L.//Tschoeke, D.A.//Garcia, G.D.//Dias, G.//Thompson, C.C.//Thompson, F.L. 	Draft Genome Sequence of Pseudoalteromonas sp. Strain PAB 2.2 Isolated from Abrolhos Bank (Brazil).	Genome Announcements	2017	5		e00016-17			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%. 		
@D	Silva, C.//Calva, E.//Calva, J.J.//Wiesner, M.//Fernandez-Mora, M.//Puente, J.L.//Vinuesa, P. 	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.	Genome Announcements	2015	3		e01323-15			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. 		
@D	Silva, C.//Calva, E.//Puente, J.L.//Zaidi, M.B.//Vinuesa, P. 	Complete Genome Sequence of Salmonella enterica Serovar Typhimurium Strain SO2 (Sequence Type 302) Isolated from an Asymptomatic Child in Mexico.	Genome Announcements	2016	4		e00253-16			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. 		
@D	Silva, C.//Calva, E.//Puente, J.L.//Zaidi, M.B.//Vinuesa, P. 	Complete Genome Sequence of Salmonella enterica Serovar Typhimurium Strain YU15 (Sequence Type 19) Harboring the Salmonella Genomic Island 1 and Virulence  Plasmid pSTV.	Genome Announcements	2016	4		e00252-16			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. 		
@D	Silva, C.A.//Blondel, C.J.//Quezada, C.P.//Porwollik, S.//Andrews-Polymenis, H.L.//Toro, C.S.//Zaldivar, M.//Contreras, I.//McClelland, M.//Santiviago, C.A. 	Infection of Mice by Salmonella enterica Serovar Enteritidis Involves Additional Genes That Are Absent in the Genome of Serovar Typhimurium.	Infect. Immun.	2012	80		839-849			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. 		
@D	Silva, D.M.//da Silva, M.P.//Vidigal, P.M.//Barcelos, R.M.//Klein, R.C.//Aguilar, A.P.//Fabres-Klein, M.H.//Oliveira, G.//Ribon, A.O. 	Draft Genome Sequences of Staphylococcus aureus Strains Isolated from Subclinical Bovine Mastitis in Brazil.	Genome Announcements	2016	4		e01594-15			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. 		
@D	Silva, G.H.//Belfort, M. 	Analysis of the LAGLIDADG interface of the monomeric homing endonuclease I-DmoI.	Nucleic Acids Res.	2004	32		3156-3168			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. 		
@D	Silva, G.H.//Belfort, M.//Wende, W.//Pingoud, A. 	From monomeric to homodimeric endonucleases and back: Engineering novel specificity of LAGLIDADG enzymes.	J. Mol. Biol.	2006	361		744-754			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. 		
@D	Silva, G.H.//Dalgaard, J.Z.//Belfort, M.//Van Roey, P. 	Crystal structure of the thermostable archaeal intron-encoded endonuclease I-DmoI.	J. Mol. Biol.	1999	286		1123-1136			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. 		
@D	Silva, I.N.//Duarte, S.//Moreira, L.M.//Monteiro, G.A. 	Draft Genome Sequence of the Plasmid-Free Lactococcus lactis subsp. lactis Strain LMG 19460.	Genome Announcements	2017	5		e00210-17			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. 		
@D	Silva, I.N.//Santos, P.M.//Moreira, L.M. 	Draft Genome Sequences of Two Burkholderia multivorans Sequential Isolates from a Chronic Lung Infection of a Cystic Fibrosis Patient.	Genome Announcements	2015	3		e01531-14			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. 		
@D	Silva, S.G.//Lago-Leston, A.//Costa, R.//Keller-Costa, T. 	Draft Genome Sequence of Sphingorhabdus sp. Strain EL138, a Metabolically Versatile Alphaproteobacterium Isolated from the Gorgonian Coral Eunicella labiata.	Genome Announcements	2018	6		e00142-18			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. 		
@D	Silva-Junior, W.J.//Farias, A.R.G.//Lima, N.B.//Benko-Iseppon, A.M.//Aburjaile, F.//Balbino, V.Q.//Falcao, R.M.//Leitao, P.J.S.S.//Sousa-Paula, L.C.//Mariano, R.L.R.//Souza, E.B.//Gama, M.A.S. 	Complete Genome Sequence of Xanthomonas citri pv. anacardii Strain IBSBF2579 from Brazil.	Genome Announcements	2018	6		e01574-17			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. 		
@D	Silveira, M.//Albano, R.//Asensi, M.//Assef, A.P. 	The draft genome sequence of multidrug-resistant Pseudomonas aeruginosa strain CCBH4851, a nosocomial isolate belonging to clone SP (ST277) that is prevalent in Brazil.	Memorias do Instituto Oswaldo Cruz	2014	109		1086-1087			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. 		
@D	Simala-Grant, J.L.//Lam, E.//Keelan, M.//Taylor, D.E. 	Characterization of the DNA adenine 5 '-GATC-3 ' methylase HpyIIIM from Helicobacter pylori.	Curr. Microbiol.	2004	49		47-54			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. 		
@D	Simbochova, G.//Timko, J.//Zelinkova, E.//Zelinka, J. 	Properties and recognition sequence of site-specific endonuclease from Streptomyces aureofaciens.	Biologia (Bratisl)	1986	41		357-365			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. 		
@D	Simbochova, G.//Timko, J.//Zelinkova, E.//Zelinka, J. 	Some physical and chemical properties of site-specific endonuclease Sau3239I from Streptomyces aureofaciens.	Biologia (Bratisl)	1987	42		1129-1136			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. 		
@D	Simcox, T.G.//Fabian, L.//Kretz, K.//Hedden, V.//Simcox, M.E.C. 	SanDI, a new type-II restriction endonuclease that recognizes 5'-GG/GWCCC-3'.	Gene	1995	155		129-130			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. 		
@D	Simcox, T.G.//Marsh, S.J.//Gross, E.A.//Lernhardt, W.//Davis, S.//Simcox, M.E.C. 	SrfI, a new type-II restriction endonuclease that recognizes the octanucleotide sequence,.	Gene	1991	109		121-123			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. 		
@D	Simmon, V.F.//Lederberg, S. 	Degradation of bacteriophage lambda deoxyribonucleic acid after restriction by Escherichia coli K-12.	J. Bacteriol.	1972	112		161-169			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. 		
@D	Simmons, W.L.//Daubenspeck, J.M.//Osborne, J.D.//Balish, M.F.//Waites, K.B.//Dybvig, K. 	Type 1 and type 2 strains of Mycoplasma pneumoniae form different biofilms.	Microbiology	2013	159		737-747			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. 		
@D	Simoliunas, E.//Kaliniene, L.//Truncaite, L.//Klausa, V.//Zajanckauskaite, A.//Meskys, R. 	Genome of Klebsiella sp.-Infecting Bacteriophage vB_KleM_RaK2.	J. Virol.	2012	86		5406			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. 		
@D	Simon, D.//Grunert, F.//Acken, U.V.//Doring, H.P.//Kroger, H. 	DNA-methylase from regenerating rat liver: purification and characterisation.	Nucleic Acids Res.	1978	5		2153-2167			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. 		
@D	Simoncsits, A.//Tjornhammar, M.L.//Rasko, T.//Kiss, A.//Pongor, S. 	Covalent joining of the subunits of a homodimeric type II restriction endonuclease: single-chain PvuII endonuclease.	J. Mol. Biol.	2001	309		89-97			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. 		
@D	Simons, M.//Diffin, F.M.//Szczelkun, M.D. 	ClpXP protease targets long-lived DNA translocation states of a helicase-like motor to cause restriction alleviation.	Nucleic Acids Res.	2014	42		12082-12091			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. 		
@D	Simons, M.//Szczelkun, M.D. 	Recycling of protein subunits during DNA translocation and cleavage by Type I restriction-modification enzymes.	Nucleic Acids Res.	2011	39		7656-7666			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. 		
@D	Simpson, A.J. et al. 	The genome sequence fo the plant pathogen Xylella fastidiosa.	Nature	2000	406		151-157			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. 		
@D	Simpson, J.T.//Workman, R.E.//Zuzarte, P.C.//David, M.//Dursi, L.J.//Timp, W. 	Detecting DNA cytosine methylation using nanopore sequencing.	Nat. Methods	2017	14		407-410			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. 		
@D	Sims, D. et al. 	Complete genome sequence of Kytococcus sedentarius type strain (541).	Standards in Genomic Sciences	2009	1		12-20			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. 		
@D	Simuth, J.//Trnovsky, J.//Jelokova, J. 	Inhibition of bacterial DNA-dependent RNA polymerases and restriction endonuclease by UV-absorbing components from Propolis.	Pharmazie	1986	41		131-132			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. 		
@D	Sineva, E.V.//Zakharova, G.G.//Tarutina, Z.E.//Kravetz, A.N.//Solonin, A.S. 	Class II restriction-modification systems in Enterobacter cloacae.	Mol. Gen. Mikrobiol. Virusol.	1993	0		10-13			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. 		
@D	Sing, W.D.//Klaenhammer, T.R. 	Plasmid-induced abortive infection in Lactococci: a review.	J. Dairy Sci.	1990	73		2239-2251			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. 		
@D	Sing, W.D.//Klaenhammer, T.R. 	Characteristics of phage abortion conferred in lactococci by the conjugal plasmid pTR2030.	J. Gen. Microbiol.	1990	136		1807-1815			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. 		
@D	Sing, W.D.//Klaenhammer, T.R. 	Characterization of a recombinant plasmid, pTRK12, encoding restriction/modification and proteolytic activities in lactic streptococci.	Abstr. Gen. Meet. Am. Soc. Microbiol.	1988	88		147			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+. 		
@D	Sing, W.D.//Klaenhammer, T.R. 	Characterization of restriction-modification plasmids from Lactococcus lactis ssp. cremoris and their effects when combined with pTR2030.	J. Dairy Sci.	1991	74		1133-1144			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. 		
@D	Sing, W.D.//Klaenhammer, T.R. 	Conjugal transfer of bacteriophage resistance determinants on pTR2030 into Streptococcus cremoris strains.	Appl. Environ. Microbiol.	1986	51		1264-1271			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. 		
@D	Sing, W.D.//Klaenhammer, T.R. 	A strategy for rotation of different bacteriophage defenses in a lactococcal single-strain started culture system.	Appl. Environ. Microbiol.	1993	59		365-372			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. 		
@D	Singh, A.//Jangir, P.K.//Kumari, C.//Sharma, R. 	Genome Sequence of Nitratireductor aquibiodomus Strain RA22.	J. Bacteriol.	2012	194		6307			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. 		
@D	Singh, A.//Kumar, J.P.//Sharma, R.//Singh, A.//Kumar, P.A.//Shivaji, S. 	Draft Genome Sequence of Indibacter alkaliphilus Strain LW1T, Isolated from Lonar Lake, a Haloalkaline Lake in the Buldana District of Maharashtra, India.	Genome Announcements	2013	1		e00513-13			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. 		
@D	Singh, A.//Sreenivas, A.//Sathyanarayana, R.G.//Pinnaka, A.K.//Shivaji, S. 	Draft Genome Sequence of Lutibaculum baratangense Strain AMV1T, Isolated from a Mud Volcano in Andamans, India.	Genome Announcements	2014	2		e00735-14			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. 		
@D	Singh, A.//Zubko, E.//Meyer, P. 	Cooperative activity of DNA methyltransferases for maintenance of symmetrical and non-symmetrical cytosine methylation in Arabidopsis thaliana.	Plant J.	2008	56		814-823			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. 		
@D	Singh, A.K.//Chaudhary, P.//Macwan, A.S.//Diwedi, U.N.//Kumar, A. 	Selective loss of lin genes from hexachlorocyclohexane-degrading Pseudomonas aeruginosa ITRC-5 under different growth conditions.	Appl. Microbiol. Biotechnol.	2007	76		895-901			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. 		
@D	Singh, A.K.//Chettri, B.//Ghosh, A.//Chikara, S.K.//Tripathi, T. 	Draft Genome Sequence of the Hydrocarbon-Degrading Bacterium Acinetobacter pittii Strain ABC Isolated from Noonmati Refinery, Assam, India.	Genome Announcements	2017	5		e01264-17			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. 		
@D	Singh, A.K.//Chettri, B.//Ghosh, A.//Chikara, S.K.//Tripathi, T. 	Draft Genome Sequence of Novosphingobium panipatense Strain P5:ABC, Isolated from Hydrocarbon-Contaminated Soil from Noonmati Refinery, Assam, India.	Genome Announcements	2017	5		e01265-17			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. 		
@D	Singh, A.K.//Karaulia, P.//Chopra, S.//Dasgupta, A. 	Draft Genome Sequence of Mycobacterium fortuitum Isolated from Murine Brain.	Genome Announcements	2016	4		e00191-16			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. 		
@D	Singh, A.K.//Sangwan, N.//Sharma, A.//Gupta, V.//Khurana, J.P.//Lal, R. 	Draft Genome Sequence of Sphingobium quisquiliarum Strain P25T, a Novel Hexachlorocyclohexane (HCH)-Degrading Bacterium Isolated from an HCH Dumpsite.	Genome Announcements	2013	1		e00717-13			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. 		
@D	Singh, D.//Chandrababunaidu, M.M.//Panda, A.//Sen, D.//Bhattacharyya, S.//Adhikary, S.P.//Tripathy, S. 	Draft Genome Sequence of Cyanobacterium Hassallia byssoidea Strain VB512170, Isolated from Monuments in India.	Genome Announcements	2015	3		e00064-15			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. 		
@D	Singh, D.K.//Kumar, A.//Tiwari, A.K.//Sankarasubramanian, J.//Vishnu, U.S.//Sridhar, J.//Gunasekaran, P.//Rajendhran, J. 	Draft Genome Sequence of Brucella abortus Virulent Strain 544.	Genome Announcements	2015	3		e00419-15			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. 		
@D	Singh, I.//Beuck, C.//Bhattacharya, A.//Hecker, W.//Parmar, V.S.//Weinhold, E.//Seitz, O. 	Abasic site stabilization by aromatic DNA base surrogates: High-affinity binding to a base-flipping DNA-methyltransferase.	Pure Appl. Chem.	2004	76		1563-1570			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. 		
@D	Singh, J.//Klar, A.J.S. 	Active genes in budding yeast display enhanced in vivo accessibility to foreign DNA methylases: a novel in vivo probe for chromatin structure of yeast.	Genes Dev.	1992	6		186-196			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. 		
@D	Singh, M.//Sasaki, T.//Matsuo, M.//Morimoto, Y.//Aiba, Y.//Hiramatsu, K. 	Complete Genome Sequence of the Drug-Naive Classical Staphylococcus aureus Strain FDA209P.	Genome Announcements	2015	3		e01343-15			We report the complete genome sequence of the methicillin-sensitive Staphylococcus aureus (MSSA) strain FDA209P (ATCC 6538P and NCTC 7447). 		
@D	Singh, M.P.//Lown, J.W. 	Inhibitory effects of a GC-sequence- and minor groove-binding Hoechst 33258 analogue on DNA cleavage by selected restriction endonucleases.	J. Biomol. Struct. Dyn.	1995	12		A220			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. 		
@D	Singh, N.//Duenas-Gonzalez, A.//Lyko, F.//Medina-Franco, J.L. 	Molecular Modeling and Molecular Dynamics Studies of Hydralazine with Human DNA Methyltransferase 1.	ChemMedChem	2009	4		792-799			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. 		
@D	Singh, N.K.//Carlson, C.//Sani, R.K.//Venkateswaran, K. 	Draft Genome Sequences of Thermophiles Isolated from Yates Shaft, a Deep-Subsurface Environment.	Genome Announcements	2017	5		e00405-17			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. 		
@D	Singh, N.K.//Kumar, S.//Raghava, G.P.//Mayilraj, S. 	Draft Genome Sequence of Acinetobacter baumannii Strain MSP4-16.	Genome Announcements	2013	1		e0013713			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. 		
@D	Singh, N.N.//Lambowitz, A.M. 	Interaction of a group II intron ribonucleoprotein endonuclease with its DNA target site investigated by DNA footprinting and modification interference.	J. Mol. Biol.	2001	309		361-386			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. 		
@D	Singh, P.//Aronoff, D.M.//Davies, H.D.//Manning, S.D. 	Draft Genome Sequence of an Invasive Streptococcus agalactiae Isolate Lacking Pigmentation.	Genome Announcements	2016	4		e00015-16			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. 		
@D	Singh, P.//Kapse, N.//Roy, U.//Singh, S.M.//Dhakephalkar, P.K. 	Draft Genome Sequence of Permafrost Bacterium Nesterenkonia sp. Strain PF2B19, Revealing a Cold Adaptation Strategy and Diverse Biotechnological Potential.	Genome Announcements	2017	5		e00133-17			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. 		
@D	Singh, P.//Kumari, R.//Mukherjee, U.//Saxena, A.//Sood, U.//Lal, R. 	Draft Genome Sequence of Rifamycin Derivatives Producing Amycolatopsis mediterranei Strain DSM 46096/S955.	Genome Announcements	2014	2		e00837-14			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. 		
@D	Singh, P.//Mosci, R.//Rudrik, J.T.//Manning, S.D. 	Draft Genome Sequence of a Diarrheagenic Morganella morganii Isolate.	Genome Announcements	2015	3		e01165-15			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. 		
@D	Singh, P.//Springman, A.C.//Davies, H.D.//Manning, S.D. 	Whole-Genome Shotgun Sequencing of a Colonizing Multilocus Sequence Type 17 Streptococcus agalactiae Strain.	J. Bacteriol.	2012	194		6005			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. 		
@D	Singh, P.//Tripathi, P.//Muniyappa, K. 	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.	Protein Sci.	2010	19		111-123			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. 		
@D	Singh, P.//Tripathi, P.//Silva, G.H.//Pingoud, A.//Muniyappa, K. 	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.	J. Biol. Chem.	2009	284		25912-25928			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. 		
@D	Singh, R.//Gradnigo, J.//White, D.//Lipzen, A.//Martin, J.//Schackwitz, W.//Moriyama, E.//Blum, P. 	Complete Genome Sequence of an Evolved Thermotoga maritima Isolate.	Genome Announcements	2015	3		e00557-15			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. 		
@D	Singh, R.N.//Gaba, S.//Yadav, A.N.//Gaur, P.//Gulati, S.//Kaushik, R.//Saxena, A.K. 	First high quality draft genome sequence of a plant growth promoting and cold active enzyme producing psychrotrophic Arthrobacter agilis strain L77.	Standards in Genomic Sciences	2016	11		54			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. 		
@D	Singh, R.N.//Saldanha, R.J.//D'Souza, L.M.//Lambowitz, A.M. 	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.	J. Mol. Biol.	2002	318		287-303			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. 		
@D	Singh, S.K.//Major, S.R.//Cai, H.//Chen, F.//Hill, R.T.//Li, Y. 	Draft Genome Sequences of Cloacibacterium normanense IMET F, a Microalgal Growth-Promoting Bacterium, and Aeromonas jandaei IMET J, a Microalgal  Growth-Inhibiting Bacterium.	Genome Announcements	2018	6		e00503-18			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. 		
@D	Singh, S.V.//Kumar, N.//Singh, S.N.//Bhattacharya, T.//Sohal, J.S.//Singh, P.K.//Singh, A.V.//Singh, B.//Chaubey, K.K.//Gupta, S.//Sharma, N.//Kumar, S.//Raghava, G.P. 	Genome Sequence of the 'Indian Bison Type' Biotype of Mycobacterium avium subsp.  paratuberculosis Strain S5.	Genome Announcements	2013	1		e00005-13			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. 		
@D	Singh, T.R.//Pardasani, K.R. 	In silico Analysis of Evolutionary Patterns in Restriction Endonucleases.	In Silico Biology	2009	9		45-53			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. 		
@D	Singh-Moodley, A.//Perovic, O.//Mtshali, S.//Ismail, A.//Allam, M. 	Draft Genome Sequence of a Multidrug-Resistant Serratia marcescens Strain, Isolated from a Patient with Peritoneal Cancer in South Africa.	Genome Announcements	2017	5		e00580-17			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. 		
@D	Singha, H.//Malik, P.//Saini, S.//Khurana, S.K.//Elschner, M.C.//Mertens, K.//Barth, S.A.//Tripathi, B.N.//Singh, R.K. 	Draft Genome Sequences of Two Clinical Isolates of Burkholderia mallei Obtained from Nasal Swabs of Glanderous Equines in India.	Genome Announcements	2017	5		e00063-17			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. 		
@D	Singha, L.P.//Kotoky, R.//Pandey, P. 	Draft Genome Sequence of Pseudomonas fragi Strain DBC, Which Has the Ability To Degrade High-Molecular-Weight Polyaromatic Hydrocarbons.	Genome Announcements	2017	5		e01347-17			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. 		
@D	Singleton, D.R.//Dickey, A.N.//Scholl, E.H.//Wright, F.A.//Aitken, M.D. 	Complete Genome Sequence of a Novel Bacterium within the Family Rhodocyclaceae That Degrades Polycyclic Aromatic Hydrocarbons.	Genome Announcements	2015	3		e00251-15			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. 		
@D	Singleton, D.R.//Dickey, A.N.//Scholl, E.H.//Wright, F.A.//Aitken, M.D. 	Complete Genome Sequence of a Bacterium Representing a Deep Uncultivated Lineage  within the Gammaproteobacteria Associated with the Degradation of Polycyclic  Aromatic Hydrocarbons.	Genome Announcements	2016	4		e01086-16			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. 		
@D	Sinha, D.//Bakhshi, M.R.//Vora, R.K.//Kirby, E.P.//Budzynski, A.Z. 	Engineering DNA and protein chimeras utilizing coding sequences of restriction sites.	Anal. Biochem.	1996	238		205-208			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. 		
@D	Sinha, D.//Shamayeva, K.//Ramasubramani, V.//Reha, D.//Bialevich, V.//Khabiri, M.//Guzanova, A.//Milbar, N.//Weiserova, M.//Csefalvay, E.//Carey, J.//Ettrich, R. 	Interdomain communication in the endonuclease/motor subunit of type I restriction-modification enzyme EcoR124I.	J. Mol. Model.	2014	20		2334			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. 		
@D	Sinha, R.K.//Krishnan, K.P.//Kurian, P.J. 	Draft Genome Sequence of Idiomarina sp. Strain 5.13, a Highly Stress-Resistant Bacterium Isolated from the Southwest Indian Ridge.	Genome Announcements	2017	5		e01747-16			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. 		
@D	Siozios, S.//Cestaro, A.//Kaur, R.//Pertot, I.//Rota-Stabelli, O.//Anfora, G. 	Draft Genome Sequence of the Wolbachia Endosymbiont of Drosophila suzukii.	Genome Announcements	2013	1		e00032-13			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 . 		
@D	Siqueira, F.M.//Cibulski, S.P.//Teixeira, T.F.//Mayer, F.Q.//Roehe, P.M. 	Draft Genome Sequence of Acholeplasma laidlawii, a Common Contaminant of Cell Cultures.	Genome Announcements	2017	5		e01578-16			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. 		
@D	Siqueira, F.M.//Thompson, C.E.//Virginio, V.G.//Gonchoroski, T.//Reolon, L.//Almeida, L.G.//da Fonseca, M.M.//de Souza, R.//Prosdocimi, F.//Schrank, I.S.//Ferreira, H.B.//de Vasconcelos, A.T.//Zaha, A. 	New insights on the biology of swine respiratory tract mycoplasmas from a comparative genome analysis.	BMC Genomics	2013	14		175			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. 		
@D	Sirota-Madi, A.//Olender, T.//Helman, Y.//Brainis, I.//Finkelshtein, A.//Roth, D.//Hagai, E.//Leshkowitz, D.//Brodsky, L.//Galatenko, V.//Nikolaev, V.//Gutnick, D.L.//Lancet, D.//Ben-Jacob, E. 	Genome Sequence of the Pattern-Forming Social Bacterium Paenibacillus dendritiformis C454 Chiral Morphotype.	J. Bacteriol.	2012	194		2127-2128			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. 		
@D	Sirota-Madi, A.//Olender, T.//Helman, Y.//Ingham, C.//Brainis, I.//Roth, D.//Hagi, E.//Brodsky, L.//Leshkowitz, D.//Galatenko, V.//Nikolaev, V.//Mugasimangalam, R.C.//Bransburg-Zabary, S.//Gutnick, D.L.//Lancet, D.//Ben-Jacob, E. 	Genome sequence of the pattern forming Paenibacillus vortex bacterium reveals potential for thriving in complex environments.	BMC Genomics	2010	11		710			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. 		
@D	Sisakova, E.//Seidel, R.//Szczelkun, M.//Weiserova, M. 	Study of DNA translocation by EcoR124I type I RM enzyme.	FEBS J.	2007	274		305			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. 		
@D	Sisakova, E.//Stanley, L.K.//Weiserova, M.//Szczelkun, M.D. 	A RecB-family nuclease motif in the Type I restriction endonuclease EcoR124I.	Nucleic Acids Res.	2008	36		3939-3949			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. 		
@D	Sisakova, E.//van Aelst, K.//Diffin, F.M.//Szczelkun, M.D. 	The Type ISP Restriction-Modification enzymes LlaBIII and LlaGI use a translocation-collision mechanism to cleave non-specific DNA distant from their  recognition sites.	Nucleic Acids Res.	2013	41		1071-1080			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. 		
@D	Sisakova, E.//Weiserova, M. 	Mutagenic analysis of the HsdR motor subunit of type IC restriction modification enzyme EcoR124I.	FEBS J.	2005	272		336			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. 		
@D	Sisakova, E.//Weiserova, M.//Dekker, C.//Seidel, R.//Szczelkun, M.D. 	The Interrelationship of Helicase and Nuclease Domains during DNA Translocation by the Molecular Motor EcoR124I.	J. Mol. Biol.	2008	384		1273-1286			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. 		
@D	Sistla, S.//Krishnamurthy, V.//Rao, D.N. 	Single-stranded DNA binding and methylation by EcoP1I DNA methyltransferase.	Biochem. Biophys. Res. Commun.	2004	314		159-165			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. 		
@D	Sistla, S.//Rao, D.N. 	S-adenosyl-L-methionine-dependent restriction enzyme.	Crit. Rev. Biochem. Mol. Biol.	2004	39		1-19			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. 		
@D	Sit, C.S.//Van Arnam, E.B.//Ramadhar, T.R. 	Variable genetic architectures produce virtually identical molecules in bacterial symbionts of fungus-growing ants.	Proc. Natl. Acad. Sci. U. S. A.	2015	112		13150-13154			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. 		
@D	Sitaraman, R. 	Helicobacter pylori DNA methyltransferases and the epigenetic field effect in cancerization.	Front. Microbiol.	2014	5		115			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%. 		
@D	Sitaraman, R.//Dybvig, K. 	Restriction-modification systems and chromosomal rearrangements in mycoplasmas.	Mol. Biol. Pathog. Mycoplasmas	2002	0		371-390			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. 		
@D	Sitaraman, R.//Dybvig, K. 	The hsd loci of Mycoplasma pulmonis: organization, rearrangements and expression of genes.	Mol. Microbiol.	1997	26		109-120			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. 		
@D	Sitaraman, R.//Dybvig, K. 	Functional analysis of a unique site-specific recombinase from Mycoplasma pulmonis.	Abstr. Gen. Meet. Am. Soc. Microbiol.	2001	101		388			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. 		
@D	Sitaraman, R.//Leppla, S.H. 	Methylation-dependent DNA restriction in Bacillus anthracis.	Gene	2012	494		44-50			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. 		
@D	Sitbon, E.//Pietrokovski, S. 	New types of conserved sequence domains in DNA-binding regions of homing endonucleases.	Trends Biochem. Sci.	2003	28		473-477			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). 		
@D	Sivaraman, G.K.//Vanik, D.//Visnuvinayagam, S.//Prasad, M.M.//Murugadas, V.//Nadella, R.K.//Ravishankar, C.N. 	Draft Genome Sequence of a Methicillin-Resistant Sequence Type 39 Staphylococcal  Isolate Obtained from Seafood.	Genome Announcements	2017	5		e01193-17			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. 		
@D	Sivaraman, G.K.//Vanik, D.//Visnuvinayagam, S.//Prasad, M.M.//Ravishankar, C.N. 	Draft Genome Sequence of a Methicillin-Resistant Staphylococcus aureus Isolate (Sequence Type 1) from Seafood.	Genome Announcements	2017	5		e00776-17			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. 		
@D	Siwek, W.//Czapinska, H.//Bochtler, M.//Bujnicki, J.M.//Skowronek, K. 	Crystal structure and mechanism of action of the N6-methyladenine-dependent type  IIM restriction endonuclease R.DpnI.	Nucleic Acids Res.	2012	40		7563-7572			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. 		
@D	Sizova, I.A.//Glibin, E.N.//Ginzburg, O.F.//Tereshin, I.M. 	Inhibition of the restriction of DNA by endonucleases in the presence of Actinomycin D, Distamycin A, and their analogs.	Bioorg. Khim.	1982	8		470-477			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. 		
@D	Sizova, M.V.//Chilaka, A.//Earl, A.M.//Doerfert, S.N.//Muller, P.A.//Torralba, M.//McCorrison, J.M.//Durkin, A.S.//Nelson, K.E.//Epstein, S.S. 	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.	Standards in Genomic Sciences	2015	10		37			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)). 		
@D	Sjodin, A.//Ohrman, C.//Backman, S.//Larkeryd, A.//Granberg, M.//Lundmark, E.//Karlsson, E.//Nilsson, E.//Vallesi, A.//Tellgren-Roth, C.//Stenberg, P.//Thelaus, J. 	Complete Genome Sequence of Francisella endociliophora Strain FSC1006, Isolated from a Laboratory Culture of the Marine Ciliate Euplotes raikovi.	Genome Announcements	2014	2		e01227-14			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). 		
@D	Sjolund-Karlsson, M.//Reimer, A.//Folster, J.P.//Walker, M.//Dahourou, G.//Batra, D.G.//Martin, I.//Joyce, K.//Parsons, M.B.//Boncy, J.//Whichard, J.M.//Gilmour, M.W. 	Drug-Resistance Mechanisms in Vibrio cholerae O1 Outbreak Strain, Haiti, 2010.	Emerg. Infect. Dis.	2011	17		2151-2154			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. 		
@D	Sjostrom, J.E.//Lofdahl, S.//Philipson, L. 	Biological characteristics of a Type I restriction-modification system in Staphylococcus aureus.	J. Bacteriol.	1978	133		1144-1149			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. 		
@D	Skarin, H.//Hafstrom, T.//Westerberg, J.//Segerman, B. 	Clostridium botulinum group III: a group with dual identity shaped by plasmids, phages and mobile elements.	BMC Genomics	2011	12		185			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. 		
@D	Skavronskaya, A.G.//Aleshkin, G.I.//Demkin, V.V. 	Specificity of modification-restriction of bacteriophages P1 and lambda in strains of Escherichia coli K-12 controlled by the R124 plasmid.	Genetika	1979	15		1719-1723			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. 		
@D	Skennerton, C.T.//Angly, F.E.//Breitbart, M.//Bragg, L.//He, S.//McMahon, K.D.//Hugenholtz, P.//Tyson, G.W. 	Phage Encoded H-NS: A Potential Achilles Heel in the Bacterial Defence System.	PLoS ONE	2011	6		e20095			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. 		
@D	Skirgaila, R.//Grazulis, S.//Bozic, D.//Huber, R.//Siksnys, V. 	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.	J. Mol. Biol.	1998	279		473-481			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. 		
@D	Skirgaila, R.//Siksnys, V. 	Ca2+-ions stimulate DNA binding specificity of Cfr10I restriction enzyme.	Biol. Chem.	1998	379		595-598			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. 		
@D	Sklar, R.//Altman, D.//Sager, R. 	An endonuclease from Chlamydomonas reinhardtii that cleaves the sequence TATA.	J. Biol. Chem.	1986	261		6806-6810			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. 		
@D	Skoglund, A.//Bjorkholm, B.//Nilsson, C.//Andersson, A.F.//Jernberg, C.//Schirwitz, K.//Enroth, C.//Krabbe, M.//Engstrand, L. 	Functional analysis of the M.HpyAIV DNA methyltransferase of Helicobacter pylori.	J. Bacteriol.	2007	189		8914-8921			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. 		
@D	Skoglund, A.//Bjorkholm, B.//Nilsson, C.//Krabbe, M.//Engstrand, L. 	Are hsdS-subunits in restriction-modification systems involved in Helicobacter pylori virulence?	Helicobacter	2003	8		492			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. 		
@D	Skoglund, A.//Bjorkholm, B.//Nilsson, C.//Krabbe, M.//Engstrand, L. 	Are hsdS-subunits in restriction-modification systems involved in Helicobacter pylori virulence?	Int. J. Med. Microbiol.	2003	293		125			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. 		
@D	Skoglund, A.//Engstrand, L.//Krabbe, M.E. 	DNA methyltransferases in Helicobacter pylori.	Int. J. Med. Microbiol.	2001	291S		94-95			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. 		
@D	Skoglund, C.M.//Smith, H.O.//Chandrasegaran, S. 	Construction of an efficient overproducer clone of HinfI restriction endonuclease using the polymerase chain reaction.	Gene	1990	88		1-5			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. 		
@D	Skogman, G.S.//Bjork, G.R. 	Effects of the phage P1 restriction system on Coliphage PhiW: Degradation and complex formation of phage PhiW DNA.	J. Gen. Virol.	1976	31		9-20			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. 		
@D	Skov, K.A.//Adomat, H.//Konway, D.C.//Farrell, N.P. 	Assessment of DNA binding of platinum-radio-sensitizer complexes by inhibition of restriction enzymes.	Chem. Biol. Interact.	1987	62		117-129			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. 		
@D	Skowron, P.//Kaczorowski, T.//Tucholski, J.//Podhajska, A.J. 	Atypical DNA-binding properties of class-IIS restriction endonucleases:evidence for recognition of the cognate sequence by a FokI monomer.	Gene	1993	125		1-10			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. 		
@D	Skowron, P.M.//Anton, B.P.//Czajkowska, E.//Zebrowska, J.//Sulecka, E.//Krefft, D.//Jezewska-Frackowiak, J.//Zolnierkiewicz, O.//Witkowska, M.//Morgan, R.D.//Wilson, G.G.//Fomenkov, A.//Roberts, R.J.//Zylicz-Stachula, A. 	The third restriction-modification system from Thermus aquaticus YT-1: solving the riddle of two TaqII specificities.	Nucleic Acids Res.	2017	45		9005-9018			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. 		
@D	Skowron, P.M.//Majewski, J.//Zylicz-Stachula, A.//Rutkowska, S.M.//Jaworowska, I.//Harasimowicz-Slowinska, R.I. 	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.	Nucleic Acids Res.	2003	31		e74			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. 		
@D	Skowron, P.M.//Swaminathan, N.//McMaster, K.//George, D.//Van Etten, J.L.//Mead, D.A. 	Cloning and applications of the two/three-base restriction endonuclease R.CviJI from IL-3A virus-infected Chlorella.	Gene	1995	157		37-41			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. 		
@D	Skowron, P.M.//Vitkute, J.//Ramanauskaite, D.//Mitkaite, G.//Jezewska-Frackowiak, J.//Zebrowska, J.//Zylicz-Stachula, A.//Lubys, A. 	Three-stage biochemical selection: cloning of prototype class IIS/IIC/IIG restriction endonuclease-methyltransferase TsoI from the thermophile Thermus scotoductus.	BMC Mol. Biol.	2013	14		17			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. 		
@D	Skowronek, K.//Boniecki, M.J.//Kluge, B.//Bujnicki, J.M. 	Rational engineering of sequence specificity in R.MwoI restriction endonuclease.	Nucleic Acids Res.	2012	40		8579-8592			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. 		
@D	Skowronek, K.J.//Kosinski, J.//Bujnicki, J.M. 	Theoretical model of restriction endonuclease HpaI in complex with DNA, predicted by fold recognition and validated by site-directed mutagenesis.	Proteins	2006	63		1059-1068			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. 		
@D	Skrypina, N.A.//Kramarov, V.M.//Lyannaya, A.M.//Smolyaninov, V.V.//Goncharova, G.I. 	Restriction endonucleases from Bifidobacteria.	Mol. Gen. Mikrobiol. Virusol.	1988	0		15-16			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. 		
@D	Skrzypek, E.//Piekarowicz, A. 	The EcoDXXI restriction and modification system: cloning the genes and homology to Type I restriction and modification systems.	Plasmid	1989	21		195-204			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. 		
@D	Skvortsov, T.//Hoering, P.//Arkhipova, K.//Whitehead, R.C.//Boyd, D.R.//Allen, C.C.R. 	Draft Genome Sequences of Pseudomonas putida UV4 and UV4/95, Toluene Dioxygenase-Expressing Producers of cis-1,2-Dihydrodiols.	Genome Announcements	2018	6		e01419-17			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. 		
@D	Slaby, B.M.//Hentschel, U. 	Draft Genome Sequences of 'Candidatus Synechococcus spongiarum,' Cyanobacterial Symbionts of the Mediterranean Sponge Aplysina aerophoba.	Genome Announcements	2017	5		e00268-17			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. 		
@D	Slack, A.//Cervoni, N.//Pinard, M.//Szyf, M. 	Feedback regulation of DNA methyltransferase gene expression by methylation.	Eur. J. Biochem.	1999	264		191-199			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. 		
@D	Sladek, T.L.//Maniloff, J. 	Endonuclease from Acholeplasma laidlawii strain JA1 associated with in vivo restriction of DNA containing 5-methylcytosine.	Isr. J. Med. Sci.	1987	23		423-426			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. 		
@D	Sladek, T.L.//Nowak, J.A.//Maniloff, J. 	Mycoplasma restriction: identification of a new type of restriction specificity for DNA containing 5-methylcytosine.	J. Bacteriol.	1986	165		219-225			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. 		
@D	Slaska-Kiss, K.//Timar, E.//Kiss, A. 	Complementation between inactive fragments of SssI DNA methyltransferase.	BMC Mol. Biol.	2012	13		17			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. 		
@D	Slater, S.C. et al. 	Genome Sequences of Three Agrobacterium Biovars Help Elucidate the Evolution of Multi-Chromosome Genomes in Bacteria.	J. Bacteriol.	2009	8		2501-2511			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. 		
@D	Slatko, B.E.//Benner, J.S.//Jager-Quinton, T.//Moran, L.S.//Simcox, T.G.//VanCott, E.M.//Wilson, G.G. 	Cloning, sequencing and expression of the TaqI restriction-modification system.	Nucleic Acids Res.	1987	15		9781-9796			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. 		
@D	Slatko, B.E.//Croft, R.//Moran, L.S.//Wilson, G.G. 	Cloning and analysis of the HaeIII and HaeII methyltransferase genes.	Gene	1988	74		45-50			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'. 		
@D	Slavin, J.W.J.//Ivanisevic, A. 	Dual restriction enzyme digest of cationic-gold-coated DNA scaffolds.	Int. J. Nanomedicine	2007	2		821-825			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. 		
@D	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. 	The complete genome of the hyperthermophile Methanopyrus kandleri AV19 and monophyly of Archaeal methanogens.	Proc. Natl. Acad. Sci. U. S. A.	2002	99		4644-4649			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. 		
@D	Sletvold, H.//Johnsen, P.J.//Hamre, I.//Simonsen, G.S.//Sundsfjord, A.//Nielsen, K.M. 	Complete sequence of Enterococcus faecium pVEF3 and the detection of an omega-epsilon-zeta toxin-antitoxin module and an ABC transporter.	Plasmid	2008	60		75-85			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. 		
@D	Sloan, D.B.//Moran, N.A. 	Genome reduction and co-evolution between the primary and secondary bacterial symbionts of psyllids.	Mol. Biol. Evol.	2012	29		3781-3792			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. 		
@D	Slocum, H.//Boyer, H.W. 	Host specificity of Salmonella typhimurium deoxyribonucleic acid restriction and modification.	J. Bacteriol.	1973	113		724-726			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. 		
@D	Slocum, H.C. 	In vitro restriction of DNA.  Demonstration that the DNA of mutant phage are resistant to attack by restriction endonuclease.	Tex. Rep. Biol. Med.	1971	29		405			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. 		
@D	Slow, S.//Anderson, T.//Biggs, P.//Kennedy, M.//Murdoch, D.//Cree, S. 	Complete Genome Sequence of Legionella sainthelensi Isolated from a Patient with  Legionnaires' Disease.	Genome Announcements	2018	6		e01588-17			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. 		
@D	Slow, S.//Anderson, T.//Miller, J.//Singh, S.//Murdoch, D.//Biggs, P.J. 	Complete Genome Sequence of a Legionella longbeachae Serogroup 1 Strain Isolated  from a Patient with Legionnaires' Disease.	Genome Announcements	2017	5		e00564-17			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. 		
@D	Smajs, D.//Zobanikova, M.//Strouhal, M.//Cejkova, D.//Dugan-Rocha, S.//Pospisilova, P.//Norris, S.J.//Albert, T.//Qin, X.//Hallsworth-Pepin, K.//Buhay, C.//Muzny, D.M.//Chen, L.//Gibbs, R.A.//Weinstock, G.M. 	Complete Genome Sequence of Treponema paraluiscuniculi, Strain Cuniculi A: The Loss of Infectivity to Humans Is Associated with Genome Decay.	PLoS ONE	2011	6		e20415			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. 		
@D	Smalley, M.D.//Marinov, G.K.//Bertani, L.E.//DeSalvo, G. 	Genome Sequence of Magnetospirillum magnetotacticum Strain MS-1.	Genome Announcements	2015	3		e00233-15			Here, we report the genome sequence of Magnetospirillum magnetotacticum strain MS-1, which consists of of 36 contigs and 4,136 protein-coding genes. 		
@D	Smet, A.//Van Nieuwerburgh, F.//Ledesma, J.//Flahou, B.//Deforce, D.//Ducatelle, R.//Haesebrouck, F. 	Genome Sequence of Helicobacter heilmannii Sensu Stricto ASB1 Isolated from the Gastric Mucosa of a Kitten with Severe Gastritis.	Genome Announcements	2013	1		e00033-12			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. 		
@D	Smet, A.//Van Nieuwerburgh, F.//Vandekerckhove, T.T.//Martel, A.//Deforce, D.//Butaye, P.//Haesebrouck, F. 	Complete nucleotide sequence of CTX-M-15-plasmids from clinical Escherichia coli isolates: insertional events of transposons and insertion sequences.	PLoS ONE	2010	5		E11202			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. 		
@D	Smirnova, N.I.//Cherkasov, A.V.//Krasnov, Y.M.//Agafonov, D.A.//Kutyrev, V.V. 	Draft Whole-Genome Sequence of a New Variant of Vibrio cholerae O1 El Tor Strain  Isolated from a Cholera Patient in Russia.	Genome Announcements	2014	2		e00432-14			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. 		
@D	Smirnova, N.I.//Krasnov, Y.M.//Agafonova, E.Y.//Shchelkanova, E.Y.//Alkhova, Z.V.//Kutyrev, V.V. 	Whole-Genome Sequencing of Vibrio cholerae O1 El Tor Strains Isolated in Ukraine  (2011) and Russia (2014).	Genome Announcements	2017	5		e01640-16			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. 		
@D	Smith, A.E.//Ford, K.G. 	Specific targeting of cytosine methylation to DNA sequences in vivo.	Nucleic Acids Res.	2007	35		740-754			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. 		
@D	Smith, A.M.//Bosco, K.J.//Nicol, M.P.//Kleynhans, J.//McCulloch, M.//Duze, S.T.//Ismail, A.//Allam, M.//Tau, N.P.//Keddy, K.H. 	Genome Sequence for Shiga Toxin-Producing Escherichia coli O26:H11, Associated with a Cluster of Hemolytic-Uremic Syndrome Cases in South Africa, 2017.	Genome Announcements	2017	5		e00989-17			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. 		
@D	Smith, A.M.//Naicker, P.//Bamford, C.//Shuping, L.//McCarthy, K.M.//Sooka, A.//Smouse, S.L.//Tau, N.//Keddy, K.H. 	Genome Sequences for a Cluster of Human Isolates of Listeria monocytogenes Identified in South Africa in 2015.	Genome Announcements	2016	4		e00200-16			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. 		
@D	Smith, B.A.//Dougherty, K.M.//Baltrus, D.A. 	Complete Genome Sequence of the Highly Transformable Pseudomonas stutzeri Strain  28a24.	Genome Announcements	2014	2		e00543-14			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. 		
@D	Smith, B.R.//Unckless, R.L. 	Draft Genome Sequence of Lysinibacillus fusiformis Strain Juneja, a Laboratory-Derived Pathogen of Drosophila melanogaster.	Genome Announcements	2018	6		e01571-17			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. 		
@D	Smith, C.J.//Parker, A.//Rogers, M.B. 	Plasmid transformation of Bacteroides spp. by electroporation.	Plasmid	1990	24		100-109			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. 		
@D	Smith, D.D.//Kirzinger, M.W.//Stavrinides, J. 	Draft Genome Sequence of the Antibiotic-Producing Epiphytic Isolate Pantoea ananatis BRT175.	Genome Announcements	2013	1		e00902-13			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. 		
@D	Smith, D.D.//Kirzinger, M.W.//Stavrinides, J. 	Draft Genome Sequence of the Antibiotic-Producing Cystic Fibrosis Isolate Pantoea agglomerans Tx10.	Genome Announcements	2013	1		e00904-13			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. 		
@A	Smith, D.E.//Gemmen, G.J.//Millin, R. 		DNA looping and cleavage by restriction enzymes studied by manipulation of single DNA molecules with optical tweezers.			Dholakia, K.//Spalding, G.C. 		Proc. SPIE-Int. Soc. Opt. Eng.					SPIE-The International Society for Optical Engineering	2006		6326		1-13									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. 		
@D	Smith, D.I.//Blattner, F.R.//Davies, J. 	The isolation and partial characterization of a new restriction endonuclease from Providencia stuartii.	Nucleic Acids Res.	1976	3		343-353			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. 		
@D	Smith, D.I.//Golembieski, W.//Gilbert, J.D.//Kizyma, L.//Miller, O.J. 	Overabundance of rare-cutting restriction endonuclease sites in the human genome.	Nucleic Acids Res.	1987	15		1173-1184			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. 		
@D	Smith, D.R. 	Restriction endonuclease digestion of DNA..	Methods Mol. Biol.	1996	58		11-15			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. 		
@D	Smith, D.R. et al. 	Complete genome sequence of Methanobacterium thermoautotrophicum delta H: functional analysis and comparative genomics.	J. Bacteriol.	1997	179		7135-7155			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. 		
@D	Smith, D.W.//Crowder, S.W.//Reich, N.O. 	In vivo specificity of EcoRI DNA methyltransferase.	Nucleic Acids Res.	1992	20		6091-6096			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). 		
@D	Smith, H.//Abuyen, K.//Tremblay, J.//Savalia, P.//Perez-Rodriguez, I.//Emerson, D.//Tully, B.//Amend, J. 	Genome Sequence of Geothermobacter sp. Strain HR-1, an Iron Reducer from the Lo'ihi Seamount, Hawai'i.	Genome Announcements	2018	6		e00339-18			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. 		
@D	Smith, H.//Akiyama, T.//Foreman, C.//Franklin, M.//Woyke, T.//Teshima, H.//Davenport, K.//Daligault, H.//Erkkila, T.//Goodwin, L.//Gu, W.//Xu, Y.//Chain, P. 	Draft Genome Sequence and Description of Janthinobacterium sp. Strain CG3, a Psychrotolerant Antarctic Supraglacial Stream Bacterium.	Genome Announcements	2013	1		e00960-13			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. 		
@D	Smith, H.J.//Foreman, C.M.//Akiyama, T.//Franklin, M.J.//Devitt, N.P.//Ramaraj, T. 	Genome Sequence of Janthinobacterium sp. CG23_2, a Violacein-Producing Isolate from an Antarctic Supraglacial Stream.	Genome Announcements	2016	4		e01468-15			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. 		
@D	Smith, H.J.//Foreman, C.M.//Ramaraj, T. 	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.	Genome Announcements	2014	2		e01242-14			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. 		
@D	Smith, H.O. 	Restriction endonucleases as enzymatic tools for DNA analysis and genetic manipulation.	PAABS Revista	1976	5		313-319			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. 		
@D	Smith, H.O. 	Nucleotide sequence specificity of restriction endonucleases.	Science	1979	205		455-462			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. 		
@D	Smith, H.O. 	Restriction endonuclease from Hemophilus influenzae Rd.	Methods Mol. Biol.	1974	7		71-85			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. 		
@D	Smith, H.O.//Annau, T.M.//Chandrasegaran, S. 	Finding sequence motifs in groups of functionally related proteins.	Proc. Natl. Acad. Sci. U. S. A.	1990	87		826-830			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. 		
@D	Smith, H.O.//Birnstiel, M.L. 	A simple method for DNA restriction site mapping.	Nucleic Acids Res.	1976	9		2387-2399			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. 		
@A	Smith, H.O.//Kelly, S.V. 		Methylases of the type II restriction-modification systems.			Razin, A.//Cedar, H.//Riggs, A.D. 		DNA Methylation. Biochemistry and Biological Significance.				New York	Springer-Verlag	1984		0		39-71									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). 		
@D	Smith, H.O.//Kelly, T.J.//Roy, P.H. 	Enzymatic methods for sequence analysis applied to DNA restriction and methylation sites.	Methods Enzymol.	1974	29		282-294			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. 		
@D	Smith, H.O.//Marley, G.M. 	Purification and properties of HindII and HindIII endonucleases from Haemophilus influenzae Rd.	Methods Enzymol.	1980	65		104-108			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. 		
@D	Smith, H.O.//Nathans, D. 	A suggested nomenclature for bacterial host modification and restriction systems and their enzymes.	J. Mol. Biol.	1973	81		419-423			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. 		
@D	Smith, H.O.//Wilcox, K.W. 	A restriction enzyme from Hemophilus influenzae. I. Purification and general properties.	J. Mol. Biol.	1970	51		379-391			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. 		
@D	Smith, H.R.//Humphreys, G.O.//Willshaw, G.A.//Anderson, E.S. 	Characterisation of plasmids coding for the restriction endonuclease EcoRI.	Mol. Gen. Genet.	1976	143		319-325			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. 		
@D	Smith, H.S. 	The restriction of T2 bacteriophage by Escherichia coli, strain W.	Diss. Abstr.	1968	29		9292B			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. 		
@D	Smith, J.//Berg, J.M.//Chandrasegaran, S. 	A detailed study of the substrate specificity of a chimeric restriction enzyme.	Nucleic Acids Res.	1999	27		674-681			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. 		
@D	Smith, J.//Bibikova, M.//Whitby, F.G.//Reddy, A.R.//Chandrasegaran, S.//Carroll, D. 	Requirements for double-strand cleavage by chimeric restriction enzymes with zinc finger DNA-recognition domains.	Nucleic Acids Res.	2000	28		3361-3369			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. 		
@D	Smith, J.//Grizot, S.//Arnould, S.//Duclert, A.//Epinat, J.C.//Prieto, P.C.//Redondo, P.//Blanco, F.J.//Bravo, J.//Montoya, G.//Paques, F.//Duchateau, P. 	A combinatorial approach to create artificial homing endonucleases cleaving chosen sequences.	Nucleic Acids Res.	2006	34		e149			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. 		
@D	Smith, J.D.//Arber, W.//Kuhnlein, U. 	Host specificity of DNA by Escherichia coli. XIV.  The role of nucleotide methylation in in vivo B-specific modification.	J. Mol. Biol.	1972	63		1-8			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. 		
@D	Smith, J.L.//Goldberg, J.M.//Grossman, A.D. 	Complete Genome Sequences of Bacillus subtilis subsp. subtilis Laboratory Strains JH642 (AG174) and AG1839.	Genome Announcements	2014	2		e00663-14			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. 		
@D	Smith, L.A.//Chirikjian, J.G. 	Purification and characterization of the sequence-specific endonuclease BamHI.	J. Biol. Chem.	1979	254		1003-1006			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. 		
@D	Smith, M.A.//Mernagh, D.R.//Kneale, G.G. 	Expression and characterization of the N-terminal fragment of the hsdS subunit of M.EcoR124I.	Biol. Chem.	1998	379		505-509			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. 		
@D	Smith, M.A.//Read, C.M.//Kneale, G.G. 	Domain structure and subunit interactions in the type I DNA methyltransferase M.EcoR124I.	J. Mol. Biol.	2001	314		41-50			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. 		
@D	Smith, M.D.//Longo, M.//Gerard, G.F.//Chatterjee, D.K. 	Cloning and characterization of genes for the PvuI restriction and modification system.	Nucleic Acids Res.	1992	20		5743-5747			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. 		
@D	Smith, M.J.//Jeddeloh, J.A. 	DNA methylation in lysogens of pathogenic Burkholderia spp. requires prophage induction and is restricted to excised phage DNA.	J. Bacteriol.	2005	187		1196-1200			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. 		
@D	Smith, P.//Lindsey, R.L.//Rowe, L.A.//Batra, D.//Stripling, D.//Garcia-Toledo, L.//Drapeau, D.//Knipe, K.//Strockbine, N. 	High-Quality Whole-Genome Sequences for 21 Enterotoxigenic Escherichia coli Strains Generated with PacBio Sequencing.	Genome Announcements	2018	6		e01311-17			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. 		
@D	Smith, R.M.//Diffin, F.M.//Savery, N.J.//Josephsen, J.//Szczelkun, M.D. 	DNA cleavage and methylation specificity of the single polypeptide restriction-modification enzyme LlaGI.	Nucleic Acids Res.	2009	37		7206-7218			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). 		
@D	Smith, R.M.//Jacklin, A.J.//Marshall, J.J.//Sobott, F.//Halford, S.E. 	Organization of the BcgI restriction-modification protein for the transfer of one methyl group to DNA.	Nucleic Acids Res.	2012	41		405-417			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. 		
@D	Smith, R.M.//Josephsen, J.//Szczelkun, M.D. 	The single polypeptide restriction-modification enzyme LlaGI is a self-contained molecular motor that translocates DNA loops.	Nucleic Acids Res.	2009	37		7219-7230			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. 		
@D	Smith, R.M.//Josephsen, J.//Szczelkun, M.D. 	An Mrr-family nuclease motif in the single polypeptide restriction-modification enzyme LlaGI.	Nucleic Acids Res.	2009	37		7231-7238			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. 		
@D	Smith, R.M.//Marshall, J.J.//Jacklin, A.J.//Retter, S.E.//Halford, S.E.//Sobott, F. 	Organization of the BcgI restriction-modification protein for the cleavage of eight phosphodiester bonds in DNA.	Nucleic Acids Res.	2012	41		391-404			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. 		
@D	Smith, R.M.//Pernstich, C.//Halford, S.E. 	TstI, a Type II restriction-modification protein with DNA recognition, cleavage and methylation functions in a single polypeptide.	Nucleic Acids Res.	2014	42		5809-5822			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. 		
@D	Smith, S.A.//Krasucki, S.P.//McDowell, J.V.//Balke, V.L. 	Complete Genome Sequence of Sphingobacterium sp. Strain ML3W, Isolated from Wings of Myotis lucifugus Infected with White Nose Syndrome.	Genome Announcements	2015	3		e01477-14			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. 		
@D	Smith, S.S. 	Gilbert's conjecture: The search for DNA (cytosine-5) demethylases and the emergence of new functions for eukaryotic DNA (cytosine-5) methyltransferases.	J. Mol. Biol.	2000	302		1-7			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. 		
@D	Smith, S.S. 	Inhibition of human DNA (cytosine-5) methyltransferase by the 451nt RNA component of human telomerase.	Mol. Biol. Cell	2000	11		438a-439a			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. 		
@D	Smith, S.S. 	Stalling of DNA methyltransferase in chromosome stability and chromosome remodelling (Review).	Int. J. Mol. Med.	1998	1		147-156			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. 		
@D	Smith, S.S. 	Conformation space and the emergence of new functions for eukaryotic DNA (cytosine-5) methyltransferases.	Int. J. Mol. Med.	2000	6		S11			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. 		
@D	Smith, S.S. 	Biological implications of the mechanism of action of human DNA (cytosine-5)methyltransferase.	Prog. Nucleic Acid Res. Mol. Biol.	1994	49		65-111			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 		
@D	Smith, S.S.//Baker, D.J. 	Stalling of human methyltransferase at single-strand conformers from the Huntington's locus.	Biochem. Biophys. Res. Commun.	1997	234		73-78			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. 		
@D	Smith, S.S.//Crocitto, L. 	DNA methylation in eukaryotic chromosome stability revisited: DNA methyltransferase in the management of DNA conformation space.	Mol. Carcinog.	1999	26		1-9			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. 		
@D	Smith, S.S.//Hardy, T.A.//Baker, D.J. 	Human DNA (cytosine-5)methyltransferase selectively methylates duplex DNA containing mispairs.	Nucleic Acids Res.	1987	15		6899-6916			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. 		
@D	Smith, S.S.//Kan, J.L.C.//Baker, D.J.//Kaplan, B.E.//Dembek, P. 	Recognition of unusual DNA structures by human DNA (cytosine-5) methyltransferase.	J. Mol. Biol.	1991	217		39-51			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. 		
@D	Smith, S.S.//Kaplan, B.E.//Sowers, L.C.//Newman, E.M. 	Mechanism of human methyl-directed DNA methyltransferase and the fidelity of cytosine methylation.	Proc. Natl. Acad. Sci. U. S. A.	1992	89		4744-4748			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. 		
@D	Smith, S.S.//Kho, M.R.//Baker, D.J. 	DNA methyltransferases in the recognition and repair of hairpin loops lacking precise Watson-Crick homology.	Anticancer Res.	1995	15		1671			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. 		
@D	Smith, S.S.//Laayoun, A.//Baker, D.J.//Kho, M.R. 	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.	FASEB J.	1995	9		A1324			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. 		
@D	Smith, S.S.//Lingeman, R.G.//Kaplan, B.E. 	Recognition of foldback DNA by the human DNA (Cytosine-5-)-methyltransferase.	Biochemistry	1992	31		850-854			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. 		
@D	Smith, T. 	Restriction enzyme searches using the word processing software:  LOCOSCRIPT.	Biochemical Education	1988	16		224-226			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. 		
@D	Smith, T.J. 	Aurintricarboxylic acid inhibition of restriction endonuclease is not recognition site-specific.	FASEB J.	1988	2		A589			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. 		
@D	Smith, T.J.//Hill, K.K.//Foley, B.T.//Detter, J.C.//Munk, A.C.//Bruce, D.C.//Doggett, N.A.//Smith, L.A.//Marks, J.D.//Xie, G.//Brettin, T.S. 	Analysis of the Neurotoxin Complex Genes in Clostridium botulinum A1-A4 and B1 Strains: BoNT/A3, /Ba4 and /B1 Clusters Are Located within  Plasmids.	PLoS ONE	2007	2		e1271			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. 		
@D	Smith, T.J.//Hill, K.K.//Xie, G.//Foley, B.T.//Williamson, C.H.//Foster, J.T.//Johnson, S.L.//Chertkov, O.//Teshima, H.//Gibbons, H.S.//Johnsky, L.A.//Karavis, M.A.//Smith, L.A. 	Genomic sequences of six botulinum neurotoxin-producing strains representing three clostridial species illustrate the mobility and diversity of botulinum neurotoxin genes.	Infect. Genet. Evol.	2014	30		102-113			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. 		
@D	Smits, T.H.//Guerrero-Prieto, V.M.//Hernandez-Escarcega, G.//Blom, J.//Goesmann, A.//Rezzonico, F.//Duffy, B.//Stockwell, V.O. 	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.	Genome Announcements	2014	2		e01229-13			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. 		
@D	Smits, T.H.//Pothier, J.F.//Ruinelli, M.//Blom, J.//Frasson, D.//Koechli, C.//Fabbri, C.//Brandl, H.//Duffy, B.//Sievers, M. 	Complete Genome Sequence of the Cyanogenic Phosphate-Solubilizing Pseudomonas sp. Strain CCOS 191, a Close Relative of Pseudomonas mosselii.	Genome Announcements	2015	3		e00616-15			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. 		
@D	Smits, T.H.//Rezzonico, F.//Blom, J.//Goesmann, A.//Abelli, A.//Kron, M.R.//Vanneste, J.L.//Duffy, B. 	Draft Genome Sequence of the Commercial Biocontrol Strain Pantoea agglomerans P10c.	Genome Announcements	2015	3		e01448-15			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. 		
@D	Smits, T.H.//Rezzonico, F.//Kamber, T.//Goesmann, A.//Ishimaru, C.A.//Stockwell, V.O.//Frey, J.E.//Duffy, B. 	Genome Sequence of the Biocontrol Agent Pantoea vagans Strain C9-1.	J. Bacteriol.	2010	192		6486-6487			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. 		
@D	Smoot, J.C.//Barbian, K.D.//Van Gompel, J.J.//Smoot, L.M.//Chaussee, M.S.//Sylva, G.L.//Sturdevant, D.E.//Ricklefs, S.M.//Porcella, S.F.//Parkins, L.D.//Beres, S.B.//Campbell, D.S.//Smith, T.M.//Zhang, Q.//Kapur, V.//Daly, J.A.//Veasy, L.G. 	Genome sequence and comparative microarray analysis of serotype M18 group A Streptococcus strains associated with acute rheumatic fever outbreaks.	Proc. Natl. Acad. Sci. U. S. A.	2002	99		4668-4673			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. 		
@D	Sneider, T.W. 	The 5'-cytosine in CCGG is methylated in two eukaryotic DNAs and MspI is sensitive to methylation at this site.	Nucleic Acids Res.	1980	8		3829-3840			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. 		
@D	Snitkin, E.S.//Zelazny, A.M.//Thomas, P.J.//Stock, F.//Henderson, D.K.//Palmore, T.N.//Segre, J.A. 	Tracking a hospital outbreak of carbapenem-resistant Klebsiella pneumoniae with whole-genome sequencing.	Sci. Transl. Med.	2012	4		148RA116			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. 		
@D	Snopkova, K.//Sedlar, K.//Bosak, J.//Chaloupkova, E.//Provaznik, I.//Smajs, D. 	Complete Genome Sequence of Pragia fontium 24613, an Environmental Bacterium from the Family Enterobacteriaceae.	Genome Announcements	2015	3		e00740-15			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. 		
@D	Snounou, G.//Malcolm, A.D.B. 	Supercoiling and the mechanism of restriction endonucleases.	Eur. J. Biochem.	1984	138		275-280			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. 		
@D	Snow, A.M.//Sheardy, R.D. 	Locating cobalt-binding sites on DNA using restriction endonucleases.	Methods Enzymol.	2001	340		519-528			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. 		
@D	Soares, S.C. et al. 	Genome sequence of Corynebacterium pseudotuberculosis biovar equi strain 258 and prediction of antigenic targets to improve biotechnological vaccine production.	J. Biotechnol.	2013	167		135-141			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. 		
@D	Soares-Castro, P.//Marques, D.//Demyanchuk, S.//Faustino, A.//Santos, P.M. 	Draft Genome Sequences of Two Pseudomonas aeruginosa Clinical Isolates with Different Antibiotic Susceptibilities.	J. Bacteriol.	2011	193		5573			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. 		
@D	Soares-Castro, P.//Santos, P.M. 	Towards the Description of the Genome Catalogue of Pseudomonas sp. Strain M1.	Genome Announcements	2013	1		e00146-12			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. 		
@D	Sobell, H.M. 	Symmetry in protein-nucleic acid interaction and its genetic implications.	Adv. Genet.	1973	17		411-490			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). 		
@D	Sobotta, T.//Pingoud, A.//Jeltsch, A. 	Mapping of the functional regions of the EcoRV methyltransferase by random mutagenesis and screening for inactive mutants.	Biol. Chem. Hoppe Seyler	1995	376		S155			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. 		
@D	Sobral, B.W.S.//McClelland, M. 	Methyltransferases as tools to alter the specificity of restriction endonucleases.	Methods Mol. Biol.	1992	12		159-172			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. 		
@D	Soby, S.D. 	Draft Genome Sequence of Chromobacterium aquaticum CC-SEYA-1, a Nonpigmented Member of the Genus Chromobacterium.	Genome Announcements	2017	5		e01661-16			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. 		
@D	Soby, S.D. 	Draft Genome Sequence of Chromobacterium pseudoviolaceum LMG 3953T, an Enigmatic  Member of the Genus Chromobacterium.	Genome Announcements	2017	5		e01632-16			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. 		
@D	Soggiu, A.//Piras, C.//Gaiarsa, S.//Bendixen, E.//Panitz, F.//Bendixen, C.//Sassera, D.//Brasca, M.//Bonizzi, L.//Roncada, P. 	Draft Genome Sequence of Clostridium tyrobutyricum Strain DIVETGP, Isolated from  Cow's Milk for Grana Padano Production.	Genome Announcements	2015	3		e00213-15			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%. 		
@D	Sogutcu, E.//Emrence, Z.//Arikan, M.//Cakiris, A.//Abaci, N.//Oner, E.T.//Ustek, D.//Arga, K.Y. 	Draft Genome Sequence of Halomonas smyrnensis AAD6T.	J. Bacteriol.	2012	194		5690-5691			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. 		
@D	Soh, J.Y.K.//Russell, C.W.//Fenlon, S.N.//Chen, S.L. 	Complete Genome Sequence of Photobacterium leiognathi Strain JS01.	Genome Announcements	2018	6		e01396-17			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. 		
@D	Sohail, A.//Ives, C.L.//Brooks, J.E. 	Purification and characterization of C.BamHI, a regulator of the BamHI restriction-modification system.	Gene	1995	157		227-228			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. 		
@D	Sohail, A.//Lieb, M.//Dar, M.//Bhagwat, A.S. 	A gene required for very short patch repair in Escherichia coli is adjacent to the DNA cytosine methylase gene.	J. Bacteriol.	1990	172		4214-4221			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. 		
@D	Sohail, A.//Mushtaq, R.//Khan, E.//Maqbool, T.//Riazuddin, S. 	Discovery of two new Type II restriction enzymes.	Pak. J. Zool.	1987	19		371-391			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. 		
@D	Sohn, K.H.//Jones, J.D.//Studholme, D.J. 	Draft Genome Sequence of Pseudomonas syringae Pathovar Syringae Strain FF5, Causal Agent of Stem Tip Dieback Disease on Ornamental Pear.	J. Bacteriol.	2012	194		3733-3734			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. 		
@D	Sokolov, N.N. 	Search, isolation and study of restrictases.	Vestn. Akad. Med. Nauk SSSR	1995	2		47-51			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. 		
@D	Sokolov, N.N. 	Current approaches to the search of new restriction endonucleases.	Mol. Gen. Mikrobiol. Virusol.	1989	0		3-7			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. 		
@D	Sokolov, N.N. 	Restriction endonucleases: Isolation methods and schemes.	Mol. Gen. Mikrobiol. Virusol.	1990	0		1-6			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. 		
@D	Sokolov, N.N.//Anikeitcheva, N.V.//Fitsner, A.B.//Samko, O.T.//Khoroshutina, E.B.//Kalugin, A.A. 	Search of strains producing new restriction endonucleases.	Zh. Mikrobiol. Epidemiol. Immunobiol.	1988	9		86-89			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. 		
@D	Sokolov, N.N.//Eldarov, M.A.//Anikeitcheva, N.V.//Karpychev, I.V.//Samko, O.T.//Fitzner, A.B.//Kalugin, A.A.//Choroshoutina, E.B.//Skryabin, K.G. 	Site-specific endonuclease BbvBI from Bacillus brevis.	Bioorg. Khim.	1992	18		47-51			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. 		
@D	Sokolov, N.N.//Eldarov, M.A.//Anikeitcheva, N.V.//Karpychev, I.V.//Samko, O.T.//Fitzner, A.B.//Kalugin, A.A.//Choroshoutina, E.B.//Skryabin, K.G. 	BcoAI, a new site-specific endonuclease from Bacillus coagulans.	Bioorg. Khim.	1991	17		1188-1192			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. 		
@D	Sokolov, N.N.//Eldarov, M.A.//Rina, M.//Korolev, S.V.//Markaki, M.//Kalugin, A.A.//Omelyanuk, N.M.//Skryabin, K.G.//Bouriotis, V. 	Isolation and characterization of CspBI, a novel NotI isoschizomer from Corynebacterium species B recognizing 5'-GC/GGCCGC-3'.	Biochem. Mol. Biol. Int.	1998	44		433-441			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. 		
@D	Sokolov, N.N.//Fitsner, A.B.//Anikeitcheva, N.V.//Choroshoutina, Y.B.//Samko, O.T.//Kolosha, V.O.//Fodor, I.//Votrin, I.I. 	A site-specific endonuclease from Pseudomonas aeruginosa.	Mol. Biol. Rep.	1985	10		159-161			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. 		
@D	Sokolov, N.N.//Fitsner, A.B.//Anikeitcheva, N.V.//Khoroshutina, E.B.//Samko, O.T. 	Effect of thio-specific reagent on Pseudomonas aeruginosa PaeI and PaeII restriction endonuclease activity.	Biull. Eksp. Biol. Med.	1986	102		695-697			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. 		
@D	Sokolov, N.N.//Fitsner, A.B.//Anikeitcheva, N.V.//Samko, O.T.//Khoroshutina, E.B.//Kolosha, V.O.//Fodor, I.I. 	Pseudomonas aeruginosa restrictases:  Physico-chemical properties, substrate specificity, prospects of application.	Biotekhnologiya	1987	3		578-585			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. 		
@D	Sokolov, N.N.//Fitsner, A.B.//Anikeycheva, N.V.//Kovalenko, N.A. 	Role of bivalent cations in endonucleolysis of DNA catalyzed by restrictases.	Vopr. Med. Khim.	1989	6		66-69			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. 		
@D	Sokolov, N.N.//Fitsner, A.B.//Khoroshutina, E.B.//Kheislere, M.Y. 	Determination of restriction endonuclease activity in Toluene lysates of bacterial cells.	Biull. Eksp. Biol. Med.	1984	97		163-165			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. 		
@D	Sokolov, N.N.//Fitsner, A.B.//Samko, O.T.//Khoroshutina, E.B.//Kalugin, A.A. 	Effect of monovalent cations on activity of site-specific endonuclease PaeII.	Vopr. Med. Khim.	1990	36		65-67			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. 		
@D	Sokolov, N.N.//Fitzner, A.B.//Eldarov, M.A.//Anikeicheva, N.B.//Kalugin, A.A.//Samko, O.T.//Khoroshoutina, E.B.//Fodor, I. 	BavAI, a restriction endonuclease from Bacillus alvei.	Nucleic Acids Res.	1992	20		2897			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. 		
@D	Sokolov, N.N.//Kheislere, M.Y.//Alexandrova, S.S.//Zildere, A.M.//Ansberga, S.E. 	A systematic method to isolate restriction endonucleases.	Izv. Akad. Nauk Latv. SSR	1984	12		54-62			None 		
@D	Sokolov, N.N.//Kolosha, V.O.//Fitsner, A.B.//Anikeitcheva, N.V.//Khoroshutina, E.B.//Samko, O.T.//Fodor, I.//Votrin, I.I. 	New specific endonucleases PaeI and PaeII from Pseudomonas aeruginosa.	Mol. Gen. Mikrobiol. Virusol.	1986	0		24-26			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. 		
@D	Sokolov, N.N.//Korolev, S.V.//Rina, M.//Eldarov, M.A.//Gervaziev, Y.V.//Skryabin, K.G.//Bouriotis, V. 	New site-specific endonucleases from Brevibacterium species.	Mol. Gen. Mikrobiol. Virusol.	1998	9		35-38			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. 		
@D	Sokolov, N.N.//Maneliene, Z.P.//Butkus, V.V.//Fitzner, A.B.//Khoroshutina, E.B.//Kalugin, A.A.//Janulaitis, A. 	Site-specific endonucleases LplI and AagI.	Bioorg. Khim.	1990	16		1040-1044			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. 		
@D	Sokolov, N.N.//Samko, O.T.//Anikeitcheva, N.V.//Kalugin, A.A.//Khoroshutina, E.B.//Plutalov, O.V.//Birikh, K.R.//Berlin, Y.A. 	New site-specific endonucleases from Bacillus strains.	Bioorg. Khim.	1994	20		1334-1341			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. 		
@D	Sokolov, N.N.//Votrin, I.I. 	Restriction endonucleases as an instrument in comparative biochemical studies.	Zh. Evol. Biokhim. Fiziol.	1979	15		8-21					
@D	Sokolov, N.N.//Votrin, I.I.//Fitsner, A.B.//Anikeitcheva, N.V. 	Isolation and certain properties of restriction endonuclease from Bacillus amyloliquefaciens.	Biokhimiia	1978	43		865-871			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. 		
@D	Sokolowska, M.//Czapinska, H.//Bochtler, M. 	Crystal structure of the {beta}{beta}{alpha}-Me type II restriction endonuclease Hpy99I with target DNA.	Nucleic Acids Res.	2009	37		3799-3810			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). 		
@D	Sokolowska, M.//Czapinska, H.//Bochtler, M. 	Hpy188I-DNA pre- and post-cleavage complexes--snapshots of the GIY-YIG nuclease mediated catalysis.	Nucleic Acids Res.	2011	39		1554-1564			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. 		
@D	Sokolowska, M.//Kaus-Drobek, M.//Czapinska, H.//Tamulaitis, G.//Szczepanowski, R.H.//Urbanke, C.//Siksnys, V.//Bochtler, M. 	Monomeric Restriction Endonuclease BcnI in the Apo Form and in an Asymmetric Complex with Target DNA.	J. Mol. Biol.	2007	369		722-734			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. 		
@D	Sokolowska, M.//Kaus-Drobeka, M.//Czapinska, H.//Tamulaitis, G.//Siksnys, V.//Bochtler, M. 	Restriction endonucleases that resemble a component of the bacterial DNA repair machinery.	Cell. Mol. Life Sci.	2007	64		2351-2357			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. 		
@D	Solaiman, D.K.Y.//Somkuti, G.A. 	Isolation and characterization of a type II restriction endonuclease from Streptococcus thermophilus.	FEMS Microbiol. Lett.	1990	67		261-266			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. 		
@D	Solaiman, D.K.Y.//Somkuti, G.A. 	A type II restriction endonuclease of Streptococcus thermophilus ST117.	FEMS Microbiol. Lett.	1991	80		75-80			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. 		
@D	Solem, A.//Chatterjee, P.//Caprara, M.G. 	A novel mechanism for protein-assisted group I intron splicing.	RNA	2002	8		412-425			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. 		
@D	Soler-Bistue, A.J.//Birshan, D.//Tomaras, A.P.//Dandekar, M.//Tran, T.//Newmark, J.//Bui, D.//Gupta, N.//Hernandez, K.//Sarno, R.//Zorreguieta, A.//Actis, L.A.//Tolmasky, M.E. 	Klebsiella pneumoniae multiresistance plasmid pMET1: similarity with the Yersinia pestis plasmid pCRY and integrative conjugative elements.	PLoS ONE	2008	3		E1800			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. 		
@D	Sollner, S.//Berkner, S.//Lipps, G. 	Characterisation of the novel restriction endonuclease SuiI from Sulfolobus islandicus.	Extremophiles	2006	10		629-634			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. 		
@D	Solodukhina, L.I.//Korotayev, A.I.//Solonin, A.S.//Kuzmin, N.P. 	Cloning of genes for restriction-modification system Sfl2aI from Shigella flexneri 2a.	Genetika	1990	26		1126-1128			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. 		
@D	Solodukhina, L.I.//Manuvakhova, M.S.//Korotayev, A.I. 	Type II restriction-modification systems from Shigella strains.	Genetika	1989	25		1571-1577			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. 		
@D	Solovyeva, N.Y.//Rautenstein, Y.I. 	On the phenomenon of restriction and modification of temperate phages for the lysogenic Streptomyces hygroscopicus culture.	Mikrobiologiia	1978	47		956-959			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. 		
@D	Solovyeva, N.Y.//Rautenstein, Y.I. 	On the restriction and modification of actinophages by the cultures of Streptomyces hygroscopicus and Streptomyces levoris.	Mikrobiologiia	1980	49		512-515			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. 		
@D	Solow, B.T.//Somkuti, G.A. 	Molecular properties of Streptococcus thermophilus plasmid pER35 encoding a restriction modification system.	Curr. Microbiol.	2001	42		122-128			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. 		
@D	Soltys, K.//Vavrova, S.//Budis, J.//Palkova, L.//Minarik, G.//Grones, J. 	Draft Genome Sequence of Escherichia coli KL53.	Genome Announcements	2018	6		e00220-18			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. 		
@D	Som, S.//Bhagwat, A.S.//Friedman, S. 	Nucleotide sequence and expression of the gene encoding the EcoRII modification enzyme.	Nucleic Acids Res.	1987	15		313-332			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. 		
@D	Som, S.//Friedman, S. 	Characterization of the intergenic region which regulates the MspI restriction-modification system.	J. Bacteriol.	1997	179		964-967			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. 		
@D	Som, S.//Friedman, S. 	Inhibition of transcription in vitro by binding of DNA(cytosine-5)-methylases to DNA templates containing cytosine analogs.	J. Biol. Chem.	1994	269		25986-25991			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. 		
@D	Som, S.//Friedman, S. 	Autogenous regulation of the EcoRII methylase gene at the transcriptional level: effect of 5-azacytidine.	EMBO J.	1993	12		4297-4303			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. 		
@D	Som, S.//Friedman, S. 	Regulation of EcoRII methyltransferase: effect of mutations on gene expression and in vitro binding to the promoter region.	Nucleic Acids Res.	1994	22		5347-5353			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. 		
@D	Som, S.//Friedman, S. 	Photolabeling of the EcoRII DNA methylase with S-adenosyl-L-methionine.	FASEB J.	1988	2		A567			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. 		
@D	Som, S.//Friedman, S. 	Identification of a highly conserved domain in the EcoRII DNA methylase that can be photolabeled with S-adenosylmethionine.	FASEB J.	1990	4		A1839			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. 		
@D	Som, S.//Friedman, S. 	Identification of a highly conserved domain in the EcoRII methyltransferase which can be photolabeled with S-adenosyl-L-[methyl-3H] methionine.	J. Biol. Chem.	1991	266		2937-2945			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. 		
@D	Som, S.//Friedman, S. 	Direct photolabeling of the EcoRII methyltransferase with S-Adenosyl-L-methionine.	J. Biol. Chem.	1990	265		4278-4283			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. 		
@D	Som, S.//Yang, L.F.//Friedman, S. 	Insertion and deletion mutants in the presumed target recognition domain of the EcoRII DNA methylase.	Abstr. Gen. Meet. Am. Soc. Microbiol.	1991	91		A436			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. 		
@D	Sommer, R.//Schaller, H. 	Nucleotide sequence of the recognition site of the B-specific restriction modification system in E. coli.	Mol. Gen. Genet.	1979	168		331-335			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'. 		
@D	Song, C.X.//Yu, M.//Dai, Q.//He, C. 	Detection of 5-hydroxymethylcytosine in a combined glycosylation restriction analysis (CGRA) using restriction enzyme Taq(alpha)I.	Bioorg. Med. Chem. Lett.	2011	21		5075-5077			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. 		
@D	Song, G.T.//Chen, C.E.//Ren, J.S.//Qu, X.G. 	A Simple, Universal Colorimetric Assay for Endonuclease/Methyltransferase Activity and Inhibition Based on an  Enzyme-Responsive Nanoparticle System.	ACS NANO	2009	3		1183-1189			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. 		
@D	Song, J.//Rechkoblit, O.//Bestor, T.H.//Patel, D.J. 	Structure of DNMT1-DNA complex reveals a role for autoinhibition in maintenance DNA methylation.	Science	2011	331		1036-1040			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. 		
@D	Song, J.//Teplova, M.//Ishibe-Murakami, S.//Patel, D.J. 	Structure-based mechanistic insights into DNMT1-mediated maintenance DNA methylation.	Science	2012	335		709-712			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. 		
@D	Song, J.Y.//Hong, J.//Kwak, M.J.//Kwon, S.K.//Kim, J.F. 	Genome Sequence of Porphyrobacter dokdonensis DSW-74T, Isolated from Seawater off Dokdo in the East Sea (Sea of Korea).	Genome Announcements	2016	4		e00903-16			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. 		
@D	Song, J.Y.//Jeong, H.//Yu, D.S.//Fischbach, M.A.//Park, H.S.//Kim, J.J.//Seo, J.S.//Jensen, S.E.//Oh, T.K.//Lee, K.J.//Kim, J.F. 	Draft Genome Sequence of Streptomyces clavuligerus NRRL 3585, a Producer of Diverse Secondary Metabolites.	J. Bacteriol.	2010	192		6317-6318			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. 		
@D	Song, J.Y.//Kim, H.A.//Kim, J.S.//Kim, S.Y.//Jeong, H.//Kang, S.G.//Kim, B.K.//Kwon, S.K.//Lee, C.H.//Yu, D.S.//Kim, B.S.//Kim, S.H.//Kwon, S.Y.//Kim, J.F. 	Genome Sequence of the Plant Growth-Promoting Rhizobacterium Bacillus sp. Strain  JS.	J. Bacteriol.	2012	194		3760-3761			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. 		
@D	Song, J.Y.//Kwak, M.J.//Lee, K.Y.//Kong, H.G.//Kim, B.K.//Kwon, S.K.//Lee, S.W.//Kim, J.F. 	Draft Genome Sequence of the Antifungal-Producing Plant-Benefiting Bacterium Burkholderia pyrrocinia CH-67.	J. Bacteriol.	2012	194		6649-6650			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. 		
@D	Song, J.Y.//Yoo, R.H.//Jang, S.Y.//Seong, W.K.//Kim, S.Y.//Jeong, H.//Kang, S.G.//Kim, B.K.//Kwon, S.K.//Lee, C.H.//Yu, D.S.//Park, M.S.//Cho, S.H.//Kim, J.F. 	Genome Sequence of Enterohemorrhagic Escherichia coli NCCP15658.	J. Bacteriol.	2012	194		3749-3750			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. 		
@D	Song, L.//Ren, L.//Li, X.//Yu, D.//Yu, Y.//Wang, X.//Liu, G. 	Complete Genome Sequence of Marinobacter sp. BSs20148.	Genome Announcements	2013	1		e00236-13			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. 		
@D	Song, L.//Yu, Y.//Feng, L.//He, J.//Wang, T.//Zhu, H.//Duan, Q. 	Draft Genome Sequence of Burkholderia pseudomallei Strain 350105, Isolated in Hainan, China, in 1976.	Genome Announcements	2015	3		e01162-15			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. 		
@D	Song, L.//Yu, Y.//Feng, L.//Wang, T.//He, J.//Zhu, H.//Duan, Q. 	Draft Genome Sequence of Francisella tularensis Strain 410108 from Tibet, China.	Genome Announcements	2015	3		e01489-15			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. 		
@D	Song, P.//Xu, X.//Jiang, L.//Zhang, R.//Wang, J.//Xu, Q.//Li, S. 	Genome Sequence of Bacillus subtilis SPZ1, an Evolved Strain for Higher Uptake Rate of Tributyrin.	Genome Announcements	2013	1		e00511-13			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. 		
@D	Song, S.//Yuan, X.//Liu, S.//Zhang, N.//Wang, Y.//Ke, Y.//Xu, J.//Huang, L.//Chen, Z.//Li, Y. 	Genome Sequence of Stenotrophomonas maltophilia S028, an Isolate Harboring the AmpR-L2 Resistance Module.	J. Bacteriol.	2012	194		6696			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. 		
@D	Song, T.//Kang, B.S.//Kim, Y.M. 	XspI, a new Type II restriction endonuclease from a Xanthomonas species.	Mol. Cells	1998	8		370-373			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. 		
@D	Song, X.H.//Chen, H.X.//Zhou, W.S.//Wang, J.B.//Liu, M.F.//Wang, M.S.//Cheng, A.C.//Jia, R.Y.//Chen, S.//Sun, K.F.//Yang, Q.//Wu, Y.//Chen, X.Y.//Zhu, D.K. 	Complete Genome Sequence of Mycobacterium avium, Isolated from Commercial Domestic Pekin Ducks (Anas platyrhynchos domestica), Determined Using PacBio  Single-Molecule Real-Time Technology.	Genome Announcements	2016	4		e00769-16			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. 		
@D	Song, X.H.//Zhou, W.S.//Wang, J.B.//Liu, M.F.//Wang, M.S.//Cheng, A.C.//Jia, R.Y.//Chen, S.//Sun, K.F.//Yang, Q.//Wu, Y.//Chen, X.Y.//Zhu, D.K. 	Genome Sequence of Riemerella anatipestifer Strain RCAD0122, a Multidrug-Resistant Isolate from Ducks.	Genome Announcements	2016	4		e00332-16			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. 		
@D	Song, Y.//Cho, B.K. 	Draft Genome Sequence of Chemolithoautotrophic Acetogenic Butanol-Producing Eubacterium limosum ATCC 8486.	Genome Announcements	2015	3		e01564-14			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. 		
@D	Song, Y.//Hwang, S.//Cho, B.K. 	Draft Genome Sequence of Clostridium aceticum DSM 1496, a Potential Butanol Producer through Syngas Fermentation.	Genome Announcements	2015	3		e00258-15			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. 		
@D	Song, Y.//Jeong, Y.//Shin, H.S.//Cho, B.K. 	Draft Genome Sequence of Clostridium scatologenes ATCC 25775, a Chemolithoautotrophic Acetogenic Bacterium Producing 3-Methylindole and  4-Methylphenol.	Genome Announcements	2014	2		e00459-14			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. 		
@D	Song, Y.-H.//Rueter, T.//Geiger, R. 	DNA cleavage by AatI and StuI is sensitive to Escherichia coli dcm methylation.	Nucleic Acids Res.	1988	16		2718			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. 		
@D	Soni, D.K.//Singh, K.M.//Ghosh, A.//Chikara, S.K.//Joshi, C.G.//Dubey, S.K. 	Whole-Genome Sequence of Listeria monocytogenes Strains from Clinical and Environmental Samples from Varanasi, India.	Genome Announcements	2015	3		e01496-14			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. 		
@D	Soni, I.//Chakrapani, H.//Chopra, S. 	Draft Genome Sequence of Methicillin-Sensitive Staphylococcus aureus ATCC 29213.	Genome Announcements	2015	3		e01095-15			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. 		
@D	Sonnenschein, E.C.//Nielsen, K.F.//D'Alvise, P.//Porsby, C.H.//Melchiorsen, J.//Heilmann, J.//Kalatzis, P.G.//Lopez-Perez, M.//Bunk, B.//Sproer, C.//Middelboe, M.//Gram, L. 	Global occurrence and heterogeneity of the Roseobacter-clade species Ruegeria mobilis.	ISME J.	2017	11		569-583			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. 		
@D	Sonnenschein, E.C.//Phippen, C.B.W.//Nielsen, K.F.//Mateiu, R.V.//Melchiorsen, J.//Gram, L.//Overmann, J.//Freese, H.M. 	Phaeobacter piscinae sp. nov., a novel species of the roseobacter group and potential aquaculture probiont.	Int. J. Syst. Evol. Microbiol.	2017	67		4559-4564			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). 		
@D	Soobramoney, L.A.//Featherston, J.//Gray, V.M. 	Draft Whole-Genome Sequence of Xenorhabdus sp. Strain GDc328, Isolated from the Indigenous South African Nematode Host Steinernema khoisanae.	Genome Announcements	2015	3		e01239-15			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%. 		
@D	Soper, B.W. 	Host restriction-modification as related to gene transfer in the nitrogen-fixing cyanobacterium, Cyanothece sp.	Ph.D. Thesis, State University of New York, Binghamton, USA	1995			1-132			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. 		
@D	Soper, B.W. 	Host restriction-modification as related to gene transfer in the nitrogen-fixing cyanobacterium, cyanothece sp.	Diss. Abstr.	1996	56		3585B			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. 		
@D	Soper, B.W.//Hollister, W.R.//Reddy, K.J. 	Restriction-modification systems in the marine, aerobic, nitrogen-fixing unicellular cyanobacterium Cyanothece sp. ATCC 51142.	J. Mar. Biotechnol.	1998	6		183-185			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. 		
@D	Soper, B.W.//Hollister, W.R.//Reddy, K.J. 	Characterization of additional host restriction-modification systems in the unicellular cyanobacterium Cyanothece sp.	Biochem. Biophys. Res. Commun.	1996	223		24-30			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. 		
@D	Soper, B.W.//Reddy, K.J. 	Identification of a nuclease and host restriction-modification in the unicellular, aerobic nitrogen-fixing cyanobacterium Cyanothece sp.	J. Bacteriol.	1994	176		5565-5570			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. 		
@D	Soriano, N.//Vincent, P.//Auger, G.//Cariou, M.E.//Moullec, S.//Lagente, V.//Ygout, J.F.//Kayal, S.//Faili, A. 	Full-Length Genome Sequence of Type M/emm83 Group A Streptococcus pyogenes Strain STAB1101, Isolated from Clustered Cases in Brittany.	Genome Announcements	2015	3		e01459-14			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. 		
@D	Soriano, N.//Vincent, P.//Moullec, S.//Meygret, A.//Lagente, V.//Kayal, S.//Faili, A. 	Closed Genome Sequence of Noninvasive Streptococcus pyogenes M/emm3 Strain STAB902.	Genome Announcements	2014	2		e00792-14			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. 		
@D	Soriano, N.//Vincent, P.//Piau, C.//Moullec, S.//Gautier, P.//Lagente, V.//Faili, A.//Kayal, S. 	Complete Genome Sequence of Streptococcus pyogenes M/emm44 Strain STAB901, Isolated in a Clonal Outbreak in French Brittany.	Genome Announcements	2014	2		e01174-14			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). 		
@D	Sorokin, D.Y.//Kublanov, I.V.//Gavrilov, S.N.//Rojo, D.//Roman, P.//Golyshin, P.N.//Slepak, V.Z.//Smedile, F.//Ferrer, M.//Messina, E.//La Cono, V.//Yakimov, M.M. 	Elemental sulfur and acetate can support life of a novel strictly anaerobic haloarchaeon.	ISME J.	2016	10		240-252			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. 		
@D	Sorokin, D.Y.//Lucker, S.//Vejmelkova, D.//Kostrikina, N.A.//Kleerebezem, R.//Rijpstra, W.I.//Damste, J.S.//Le Paslier, D.//Muyzer, G.//Wagner, M.//van Loosdrecht, M.C.//Daims, H. 	Nitrification expanded: discovery, physiology and genomics of a nitrite-oxidizing bacterium from the phylum Chloroflexi.	ISME J.	2012	6		2245-2256			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. 		
@D	Sorokin, D.Y.//Messina, E.//Smedile, F.//Roman, P.//Damste, J.S.S.//Ciordia, S.//Mena, M.C.//Ferrer, M.//Golyshin, P.N.//Kublanov, I.V.//Samarov, N.I.//Toshchakov, S.V.//La Cono, V.//Yakimov, M.M. 	Discovery of anaerobic lithoheterotrophic haloarchaea, ubiquitous in hypersaline habitats.	ISME J.	2017	11		1245-1260			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. 		
@D	Sorokin, V.//Severinov, K.//Gelfand, M.S. 	Large-Scale Identification and Analysis of C-Proteins<BOOK> Computational Biology of Transcription Factor Binding.	Methods Mol. Biol.	2010	674		269-282			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. 		
@D	Sorokin, V.//Severinov, K.//Gelfand, M.S. 	Systematic prediction of control proteins and their DNA binding sites.	Nucleic Acids Res.	2009	37		441-451			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. 		
@D	Sorokulova, I.B.//Kramarov, V.M.//Reznik, S.R.//Smirnov, V.V. 	Restriction endonucleases from the genus Bacillus.	Mikrobiol. Zh.	1990	52		8-11			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. 		
@D	Sorsa, L.J.//Dufke, S.//Schubert, S. 	Identification of novel virulence-associated loci in uropathogenic Escherichia coli by suppression subtractive hybridization.	FEMS Microbiol. Lett.	2004	230		203-208			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. 		
@D	Sosio, M.//Gallo, G.//Pozzi, R.//Serina, S.//Monciardini, P.//Bera, A.//Stegmann, E.//Weber, T. 	Draft Genome Sequence of the Microbispora sp. Strain ATCC-PTA-5024, Producing the Lantibiotic NAI-107.	Genome Announcements	2014	2		e01198-13			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. 		
@D	Soslau, G.//Parker, J.//Nelson, J.W. 	Methylation and restriction endonuclease cleavage of linear Z-DNA in the presence of hexamminecobalt (III) ions.	Nucleic Acids Res.	1986	14		7237-7252			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. 		
@D	Soslau, G.//Pirollo, K. 	Selective inhibition of restriction endonuclease cleavage by DNA intercalators.	Biochem. Biophys. Res. Commun.	1983	115		484-491			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. 		
@D	Sosnovtsev, S.V.//Dedkov, V.S.//Rechkunova, N.I.//Zernov, I.P.//Degtyarev, S.K. 	Determination of substrate specificity of restriction endonuclease Mlu113I.	Sib. Biol. J.	1991	0		66-67			The recognition sequence and cleavage point of restriction endonuclease Mlu113I have been determined as 5'GG/CGCC. 		
@D	Sotnikova, E.A.//Shitikov, E.A.//Malakhova, M.V.//Kostryukova, E.S.//Ilina, E.N.//Atrasheuskaya, A.V.//Ignatyev, G.M.//Vinokurova, N.V.//Gorbachyov, V.Y. 	Complete Genome Sequence of Mycobacterium bovis Strain BCG-1 (Russia).	Genome Announcements	2016	4		e00182-16			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. 		
@D	Soule, M.//Kuhn, E.//Loge, F.//Gay, J.//Call, D.R. 	Using DNA microarrays to identify library-independent markers for bacterial source tracking.	Appl. Environ. Microbiol.	2006	72		1843-1851			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. 		
@D	Soundararajan, M.//Chang, Z.//Morgan, R.D.//Heslop, P.//Connolly, B.A. 	DNA Binding and Recognition by the IIs Restriction Endonuclease MboII.	J. Biol. Chem.	2002	277		887-895			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. 		
@D	Sousa, T.J.//Mariano, D.//Parise, D.//Parise, M.//Viana, M.V.//Guimaraes, L.C.//Benevides, L.J.//Rocha, F.//Bagano, P.//Ramos, R.//Silva, A.//Figueiredo, H.//Almeida, S.//Azevedo, V. 	Complete Genome Sequence of Corynebacterium pseudotuberculosis Strain 12C.	Genome Announcements	2015	3		e00759-15			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%. 		
@D	Sowajassatakul, A.//Coker, O.O.//Prammananan, T.//Chaiprasert, A.//Phunpruch, S. 	Draft Genome Sequence of Amikacin- and Kanamycin-Resistant Mycobacterium tuberculosis MT433 without rrs and eis Mutations.	Genome Announcements	2015	3		e01363-15			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. 		
@A	Sowers, K.R. 		Restriction-modification systems of methanogenic Archaea.			Sowers, K.R.//Schreier, H.J. 		Archaea: Methanogens: A laboratory manual.				Plainview, New York	Cold Spring Harbor Laboratory Press	1995		0		505-506									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. 		
@D	Sozhamannan, S.//Dharmalingam, K. 	Molecular cloning and identification of protein products of rglB locus of Escherichia coli.	Gene	1988	74		51-52			Meeting Abstract 		
@D	Spada, F.//Rothbauer, U.//Zolghadr, K.//Schermelleh, L.//Leonhardt, H. 	Regulation of DNA methyltransferase 1.	Adv. Enzyme Regul.	2006	46		224-234			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. 		
@D	Spang, A. et al. 	The genome of the ammonia-oxidizing Candidatus Nitrososphaera gargensis: Insights into metabolic versatility and environmental adaptations.	Environ. Microbiol.	2012	14		3122-3145			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. 		
@D	Spang, A.//Saw, J.H.//Jorgensen, S.L.//Zaremba-Niedzwiedzka, K.//Martijn, J.//Lind, A.E.//van Eijk, R.//Schleper, C.//Guy, L.//Ettema, T.J. 	Complex archaea that bridge the gap between prokaryotes and eukaryotes.	Nature	2015	521		173-179			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. 		
@D	Sparling, R.//Bhatti, A.R. 	Restriction endonuclease activities of Neisseria meningitidis.	Abstr. Gen. Meet. Am. Soc. Microbiol.	1983	83		214			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. 		
@D	Sparling, R.//Bhatti, A.R. 	NmeI, a restriction endonuclease from Neisseria meningitidis.	Microbios	1984	41		73-79			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. 		
@D	Spataro, N.//Farfan, M.//Albarral, V.//Sanglas, A.//Loren, J.G.//Fuste, M.C.//Bosch, E. 	Draft Genome Sequence of Aeromonas molluscorum Strain 848TT, Isolated from Bivalve Molluscs.	Genome Announcements	2013	1		e00382-13			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. 		
@D	Spear, M.A. 	Efficient DNA subcloning through selective restriction endonuclease digestion.	Biotechniques	2000	28		660-662			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. 		
@D	Spence, R.J.//Pavasovic, A.//Smith, J.J.//Prentis, P.J. 	Draft Genome Sequence of Enterococcus faecalis Strain PF3, Isolated from Adelie Penguin Feces from Antarctica.	Genome Announcements	2014	2		e01209-13			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. 		
@D	Spencer, D.H.//Kas, A.//Smith, E.E.//Raymond, C.K.//Sims, E.H.//Hastings, M.//Burns, J.L.//Kaul, R.//Olsen, M.V. 	Whole-genome sequence variation among multiple isolates of Pseudomonas aeruginosa.	J. Bacteriol.	2003	185		1316-1325			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. 		
@D	Speth, D.R.//Russ, L.//Kartal, B.//Op den Camp, H.J.//Dutilh, B.E.//Jetten, M.S. 	Draft Genome Sequence of Anammox Bacterium 'Candidatus Scalindua brodae,' Obtained Using Differential Coverage Binning of Sequencing Data from Two Reactor   Enrichments.	Genome Announcements	2015	3		e01415-14			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. 		
@D	Spiegel, P.C.//Chevalier, B.//Sussman, D.//Turmel, M.//Lemieux, C.//Stoddard, B.L. 	The Structure of I-CeuI Homing Endonuclease: Evolving Asymmetric DNA Recognition from a Symmetric Protein Scaffold.	Structure	2006	14		869-880			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. 		
@D	Spiess, E.//Tomassetti, A.//Hernaiz-Driever, P.//Pfeifer, G.P. 	Structure of mouse DNA (cytosine-5-)-methyltransferase.	Eur. J. Biochem.	1988	177		29-34			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. 		
@D	Spilker, T.//Darrah, R.//LiPuma, J.J. 	Complete Genome Sequences of Bordetella flabilis, Bordetella bronchialis, and 'Bordetella pseudohinzii'.	Genome Announcements	2016	4		e01132-16			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. 		
@D	Spilker, T.//LiPuma, J.J. 	Draft Genome Sequences of 63 Pseudomonas aeruginosa Isolates Recovered from Cystic Fibrosis Sputum.	Genome Announcements	2016	4		e00231-16			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. 		
@D	Spinard, E.//Kessner, L.//Gomez-Chiarri, M.//Rowley, D.C.//Nelson, D.R. 	Draft Genome Sequence of the Marine Pathogen Vibrio coralliilyticus RE22.	Genome Announcements	2015	3		e01432-15			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. 		
@D	Spinard, E.J.//Dubert, J.//Nelson, D.R.//Gomez-Chiarri, M.//Barja, J.L. 	Draft Genome Sequence of the Emerging Bivalve Pathogen Vibrio tubiashii subsp. europaeus.	Genome Announcements	2016	4		e00625-16			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. 		
@D	Spitzer, E.D. 	Restriction enzymes.  To the Editor.	Arch. Pathol. Lab. Med.	1990	114		1190			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. 		
@D	Spoerel, N.//Herrlich, P. 	Colivirus-T3-coded S-adenosylmethionine hydrolase.	Eur. J. Biochem.	1979	95		227-233			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. 		
@D	Spoerel, N.//Herrlich, P.//Bickle, T.A. 	A novel bacteriophage defence mechanism: the anti-restriction protein.	Nature	1979	278		30-34			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. 		
@D	Sprague, L.D.//Neubauer, H. 	Genome Sequence of Yersinia similis Y228T, a Member of the Yersinia pseudotuberculosis Complex.	Genome Announcements	2014	2		e00216-14			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%. 		
@D	Sprague, L.D.//Neubauer, H. 	De Novo Genome Sequence of Yersinia aleksiciae Y159T.	Genome Announcements	2015	3		e01066-15			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. 		
@D	Sprague, L.D.//Tadayon, K. 	Genome Sequence of Pasteurella multocida Razi 0002 of Avian Origin.	Genome Announcements	2017	5		e00161-17			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. 		
@D	Sprague, L.D.//Tadayon, K. 	Genome Sequence of Pasteurella multocida Strain Razi_Pm0001.	Genome Announcements	2017	5		e01532-16			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. 		
@D	Spring, S. et al. 	Complete genome sequence of the sulfate-reducing firmicute Desulfotomaculum ruminis type strain (DL(T)).	Standards in Genomic Sciences	2012	7		304-319			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. 		
@D	Spring, S. et al. 	Complete genome sequence of Desulfotomaculum acetoxidans type strain (5575).	Standards in Genomic Sciences	2009	1		242-253			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. 		
@D	Spring, S. et al. 	Complete genome sequence of Desulfohalobium retbaense type strain (HR(100)).	Standards in Genomic Sciences	2010	2		38-48			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. 		
@D	Spring, S. et al. 	Complete genome sequence of Thermosphaera aggregans type strain (M11TL).	Standards in Genomic Sciences	2010	2		245-259			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. 		
@D	Spring, S.//Bunk, B.//Sproer, C.//Schumann, P.//Rohde, M.//Tindall, B.J.//Klenk, H.P. 	Characterization of the first cultured representative of Verrucomicrobia subdivision 5 indicates the proposal of a novel phylum.	ISME J.	2016	10		2801-2816			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. 		
@D	Spring, S.//Fiebig, A.//Riedel, T.//Goker, M.//Klenk, H.P. 	Genome Sequence of Gammaproteobacterial Pseudohaliea rubra Type Strain DSM 19751, Isolated from Coastal Seawater of the Mediterranean Sea.	Genome Announcements	2014	2		e01208-14			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. 		
@D	Spuesens, E.B.//van de Kreeke, N.//Estevao, S.//Hoogenboezem, T.//Sluijter, M.//Hartwig, N.G.//van Rossum, A.M.//Vink, C. 	Variation in a surface-exposed region of the Mycoplasma pneumoniae P40 protein as a consequence of homologous DNA recombination between RepMP5  elements.	Microbiology	2011	157		473-483			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 		
@D	Spyridaki, A.//Matzen, C.//Lanio, T.//Jeltsch, A.//Simoncsits, A.//Athanasiadis, A.//Scheuring-Vanamee, E.//Kokkinidis, M.//Pingoud, A. 	Structural and Biochemical Characterization of a New Mg2+ Binding Site Near Tyr94 in the Restriction Endonuclease PvuII.	J. Mol. Biol.	2003	331		395-406			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. 		
@D	Sreenivas, A.//Sathyanarayana, R.G.//Shivaji, S. 	Draft Genome Sequence of a Psychrophilic Bacterium, Sphingomonas antarcticum, Isolated from the Soils of Schirmacher Oasis, Antarctica.	Genome Announcements	2014	2		e00696-14			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. 		
@D	Srikhanta, Y.N.//Dowideit, S.J.//Edwards, J.L.//Falsetta, M.L.//Wu, H.J.//Harrison, O.B.//Fox, K.L.//Seib, K.L.//Maguire, T.L.//Wang, A.H.J.//Maiden, M.C.//Grimmond, S.M.//Apicella, M.A.//Jennings, M.P. 	Phasevarions Mediate Random Switching of Gene Expression in Pathogenic Neisseria.	PLoS Pathog.	2009	5		e1000400			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. 		
@D	Srikhanta, Y.N.//Fox, K.L.//Jennings, M.P. 	The phasevarion: phase variation of type III DNA methyltransferases controls coordinated switching in multiple genes.	Nat. Rev. Microbiol.	2010	8		196-206			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. 		
@D	Srikhanta, Y.N.//Fung, K.Y.//Pollock, G.L.//Bennett-Wood, V.//Howden, B.P.//Hartland, E.L. 	Phasevarion-Regulated Virulence in the Emerging Pediatric Pathogen Kingella kingae.	Infect. Immun.	2017	85		e00319-17			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. 		
@D	Srikhanta, Y.N.//Gorrell, R.J.//Power, P.M.//Tsyganov, K.//Boitano, M.//Clark, T.A.//Korlach, J.//Hartland, E.L.//Jennings, M.P.//Kwok, T. 	Methylomic and phenotypic analysis of the ModH5 phasevarion of Helicobacter pylori.	Sci. Rep.	2017	7		16140			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. 		
@D	Srikhanta, Y.N.//Gorrell, R.J.//Steen, J.A.//Gawthorne, J.A.//Kwok, T.//Grimmond, S.M.//Robins-Browne, R.M.//Jennings, M.P. 	Phasevarion Mediated Epigenetic Gene Regulation in Helicobacter pylori.	PLoS ONE	2011	6		e27569			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. 		
@D	Srikhanta, Y.N.//Maguire, T.L.//Stacey, K.J.//Grimmond, S.M.//Jennings, M.P. 	The phasevarion: a genetic system controlling coordinated, random switching of expression of multiple genes.	Proc. Natl. Acad. Sci. U. S. A.	2005	102		5547-5551			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. 		
@D	Srilunchang, M.//Homchampa, P.//Proungvitaya, T.//Wongratanacheewin, S. 	Construction of a marker-free DNA adenine methylase (Dam) mutant of Burkholderia pseudomallei.	Tissue Antigens	2005	66		550			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. 		
@D	Srinivasan, V.//Metcalf, B.J.//Knipe, K.M.//Ouattara, M.//McGee, L.//Shewmaker, P.L.//Glennen, A.//Nichols, M.//Harris, C.//Brimmage, M.//Ostrowsky, B.//Park, C.J.//Schrag, S.J.//Frace, M.A.//Sammons, S.A.//Beall, B. 	vanG element insertions within a conserved chromosomal site conferring vancomycin resistance to Streptococcus agalactiae and Streptococcus anginosus.	MBio	2014	5		E01386-E01314			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. 		
@D	Srivastav, R.//Singh, A.//Jangir, P.K.//Kumari, C.//Muduli, S.//Sharma, R. 	Genome Sequence of Staphylococcus massiliensis Strain S46, Isolated from the Surface of Healthy Human Skin.	Genome Announcements	2013	1		e00553-13			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%). 		
@D	Srivastava, R.//Gopinathan, K.P.//Ramakrishnan, T. 	Deoxyribonucleic acid methylation in mycobacteria.	J. Bacteriol.	1981	148		716-719			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. 		
@D	Srivastava, S.//Moraes, C.T. 	Expression of a mitochondrially targeted restriction endonuclease in skeletal muscle causes a mitochondrial myopathy.	Mitochondrion	2003	3		158-159					
@D	Srivastava, S.//Moraes, C.T. 	Manipulating mitochondrial DNA heteroplasmy by a mitochondrially targeted restriction endonuclease.	Hum. Mol. Genet.	2001	10		3093-3099			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. 		
@D	Staab, A.//Plaut, R.D.//Pratt, C.//Lovett, S.P.//Wiley, M.R.//Biggs, T.D.//Bernhards, R.C.//Beck, L.C.//Palacios, G.F.//Stibitz, S.//Jones, K.L.//Goodwin, B.G.//Smith, M.A.//Sozhamannan, S. 	Whole-Genome Sequences of Variants of Bacillus anthracis Sterne and Their Toxin Gene Deletion Mutants.	Genome Announcements	2017	5		e01231-17			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. 		
@D	Stabler, R.A.//Negus, D.//Pain, A.//Taylor, P.W. 	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.	Genome Announcements	2013	1		e00057-12			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. 		
@D	Stacey, K.A. 	Intracellular modification of nucleic acids.	Br. Med. Bull.	1965	21		211-216			None 		
@D	Stackebrandt, E. et al. 	Complete genome sequence of Coriobacterium glomerans type strain (PW2(T)) from the midgut of Pyrrhocoris apterus L. (red soldier bug).	Standards in Genomic Sciences	2013	8		15-25			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. 		
@D	Stackebrandt, E. et al. 	Genome sequence of the free-living aerobic spirochete Turneriella parva type strain (H(T)), and emendation of the species Turneriella parva.	Standards in Genomic Sciences	2013	8		228-238			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. 		
@D	Stackebrandt, E. et al. 	High-quality-draft genome sequence of the yellow-pigmented flavobacterium Joostella marina type strain (En5(T)).	Standards in Genomic Sciences	2013	8		37-46			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. 		
@D	Stadtler, P.//von Strandmann, R.P.//Walter, T.//Frey, B.//Auer, H.//Hengstenberg, W.//Schmitz, G. 	Purification and characterisation of the restriction endonuclease ItaI from Ilyobacter tartaricus recognizing 5'-GC^NGC-3'.	Gene	1993	137		347-348			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. 		
@D	Stafford, G.P.//Chaudhuri, R.R.//Haraszthy, V.//Friedrich, V.//Schaffer, C.//Ruscitto, A.//Honma, K.//Sharma, A. 	Draft Genome Sequences of Three Clinical Isolates of Tannerella forsythia Isolated from Subgingival Plaque from Periodontitis Patients in the United  States.	Genome Announcements	2016	4		e01286-16			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. 		
@D	Stahl, B.//Barrangou, R. 	Complete Genome Sequences of Probiotic Strains Bifidobacterium animalis subsp. lactis B420 and Bi-07.	J. Bacteriol.	2012	194		4131-4132			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. 		
@D	Stahl, B.//Barrangou, R. 	Complete Genome Sequence of Probiotic Strain Lactobacillus acidophilus La-14.	Genome Announcements	2013	1		e00376-13			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. 		
@D	Stahl, F.//Wende, W.//Jeltsch, A.//Pingoud, A. 	Introduction of asymmetry in the naturally symmetric restriction endonuclease EcoRV to investigate intersubunit communication in the homodimeric protein.	Proc. Natl. Acad. Sci. U. S. A.	1996	93		6175-6180			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. 		
@D	Stahl, F.//Wende, W.//Jeltsch, A.//Pingoud, A. 	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.	Biol. Chem.	1998	379		467-473			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. 		
@D	Stahl, F.//Wende, W.//Wenz, C.//Jeltsch, A.//Pingoud, A. 	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.	Biochemistry	1998	37		5682-5688			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. 		
@D	Stakenas, P.S.//Zaretskaya, N.M.//Maneliene, Z.P.//Mauricas, M.M.//Butkus, V.V.//Yanulaitis, A.A. 	MunI mycoplasmic restriction-modification system and its possible role in pathogenesis.	Mol. Biol. (Mosk)	1992	26		546-557			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. 		
@D	Stamler, R.A.//Vereecke, D.//Zhang, Y.//Schilkey, F.//Devitt, N.//Randall, J.J. 	Complete Genome and Plasmid Sequences for Rhodococcus fascians D188 and Draft Sequences for Rhodococcus Isolates PBTS 1 and PBTS 2.	Genome Announcements	2016	4		e00495-16			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. 		
@D	Stamm, L.V.//Greene, S.R.//Barnes, N.Y.//Bergen, H.L.//Hardham, J.M. 	Identification and characterization of a Treponema pallidum subsp. pallidum gene encoding a DNA adenine methyltransferase.	FEMS Microbiol. Lett.	1997	155		115-119			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). 		
@D	Stampeggioni, E.//Palitti, F.//Carotti, D. 	A convenient assay for DNA methyltransferase.	J. Cell Biochem. Suppl.	1989	13D		226			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. 		
@D	Stamps, B.W.//Corsetti, F.A.//Spear, J.R.//Stevenson, B.S. 	Draft genome of a novel chlorobi member assembled by tetranucleotide binning of a hot spring metagenome.	Genome Announcements	2014	2		e00897-14			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. 		
@D	Stamps, B.W.//Losey, N.A.//Lawson, P.A.//Stevenson, B.S. 	Genome Sequence of Thermoanaerobaculum aquaticum MP-01T, the First Cultivated Member of Acidobacteria Subdivision 23, Isolated from a Hot Spring.	Genome Announcements	2014	2		e00570-14			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. 		
@D	Stamps, B.W.//Zingarelli, S.//Hung, C.S.//Drake, C.A.//Varaljay, V.A.//Stevenson, B.S.//Crookes-Goodson, W.J. 	Finished Genome Sequence of a Polyurethane-Degrading Pseudomonas Isolate.	Genome Announcements	2018	6		e00084-18			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. 		
@D	Stanchev, B.S.//Grokhovskii, S.L.//Khorlin, A.A.//Gottikh, B.P.//Zhuze, A.L.//Skamrov, A.V.//Bibilashvili, R.S. 	Netropsin, distamycin A, bis-netropsins as selective inhibitors of the effect of restrictases and DNaseI.	Mol. Biol. (Mosk)	1986	20		1614-1624			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. 		
@D	Stancheva, I.//Hensey, C.//Meehan, R.R. 	Loss of the maintenance methyltransferase, xDnmt1, induces apoptosis in Xenopus embryos.	EMBO J.	2001	20		1963-1973			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. 		
@D	Stancheva, I.//Koller, T.//Sogo, J.M. 	Asymmetry of Dam remethylation on the leading and lagging arms of plasmid replicative intermediates.	EMBO J.	1999	18		6542-6551			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. 		
@D	Stancheva, I.//Meehan, R.R. 	Transient depletion of xDnmt1 leads to premature gene activation in Xenopus embryos.	Genes Dev.	2000	14		313-327			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. 		
@D	Stanford, N.P.//Halford, S.E.//Baldwin, G.S. 	DNA cleavage by the EcoRV restriction endonuclease: pH dependence and proton transfers in catalysis.	J. Mol. Biol.	1999	288		105-116			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. 		
@D	Stanford, N.P.//Szczelkun, M.D.//Marko, J.F.//Halford, S.E. 	One- and three-dimensional pathways for proteins to reach specific DNA sites.	EMBO J.	2000	19		6546-6557			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. 		
@D	Stankevicius, K.//Lubys, A.//Timinskas, A.//Janulaitis, A. 	Bpu10I restriction endonuclease is composed of two nonidentical subunits.	Biologija	1996	0		51-53			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. 		
@D	Stankevicius, K.//Lubys, A.//Timinskas, A.//Vaitkevicius, D.//Janulaitis, A. 	Cloning and analysis of the four genes coding for Bpu10I restriction-modification enzymes.	Nucleic Acids Res.	1998	26		1084-1091			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. 		
@D	Stankevicius, K.//Povilionis, P.//Lubys, A.//Menkevicius, S.//Janulaitis, A. 	Cloning and characterization of the unusual restriction-modification system comprising two restriction endonucleases and one methyltransferase.	Gene	1995	157		49-53			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. 		
@D	Stankevicius, K.//Timinskas, A. 	Expression autoregulation of the Eco47II methyltransferase gene.	Biologija	1996	0		54-56			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. 		
@D	Stanley, E.//Walsh, L.//van der Zwet, A.//Fitzgerald, G.F.//van Sinderen, D. 	Identification of four loci isolated from two Streptococcus thermophilus phage genomes responsible for mediating bacteriophage resistance.	FEMS Microbiol. Lett.	2000	182		271-277			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 		
@D	Stanley, L.K.//Seidel, R.//van der Scheer, C.//Dekker, N.H.//Szczelkun, M.D.//Dekker, C. 	When a helicase is not a helicase: dsDNA tracking by the motor protein EcoR124l.	EMBO J.	2006	25		2230-2239			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. 		
@D	Stanley, L.K.//Szczelkun, M.D. 	Direct and random routing of a molecular motor protein at a DNA junction.	Nucleic Acids Res.	2006	34		4387-4394			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. 		
@D	Starikov, A.Y.//Usserbaeva, A.A.//Sinetova, M.A.//Sarsekeyeva, F.K.//Zayadan, B.K.//Ustinova, V.V.//Kupriyanova, E.V.//Los, D.A.//Mironov, K.S. 	Draft Genome Sequence of Cyanobacterium sp. Strain IPPAS B-1200 with a Unique Fatty Acid Composition.	Genome Announcements	2016	4		e01306-16			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. 		
@D	Starkenburg, S.R.//Larimer, F.W.//Stein, L.Y.//Klotz, M.G.//Chain, P.S.G.//Sayavedra-Soto, L.A.//Poret-Peterson, A.T.//Gentry, M.E.//Arp, D.J.//Ward, B.//Bottomley, P.J. 	Complete genome sequence of Nitrobacter hamburgensis X14 and comparative genomic analysis of species within the genus Nitrobactei.	Appl. Environ. Microbiol.	2008	74		2852-2863			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. 		
@D	Starkenburg, S.R.//Reitenga, K.G.//Freitas, T.//Johnson, S.//Chain, P.S.//Garcia-Pichel, F.//Kuske, C.R. 	Genome of the Cyanobacterium Microcoleus vaginatus FGP-2, a Photosynthetic Ecosystem Engineer of Arid Land Soil Biocrusts Worldwide.	J. Bacteriol.	2011	193		4569-4570			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. 		
@D	Starns, D.//Oshima, K.//Suda, W.//Iino, T.//Yuki, M.//Inoue, J.//Kitamura, K.//Iida, T.//Darby, A.//Hattori, M.//Ohkuma, M. 	Draft Genome Sequence of Cytophaga fermentans JCM 21142T, a Facultative Anaerobe  Isolated from Marine Mud.	Genome Announcements	2014	2		e00206-14			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. 		
@D	Starodumova, I.P.//Tarlachkov, S.V.//Prisyazhnaya, N.V.//Dorofeeva, L.V.//Ariskina, E.V.//Chizhov, V.N.//Subbotin, S.A.//Evtushenko, L.I.//Vasilenko, O.V. 	Draft Genome Sequence of Rathayibacter sp. Strain VKM Ac-2630 Isolated from Leaf  Gall Induced by the Knapweed Nematode Mesoanguina picridis on Acroptilon repens.	Genome Announcements	2017	5		e00650-17			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. 		
@D	Staudova, B.//Strouhal, M.//Zobanikova, M.//Cejkova, D.//Fulton, L.L.//Chen, L.//Giacani, L.//Centurion-Lara, A.//Bruisten, S.M.//Sodergren, E.//Weinstock, G.M.//Smajs, D. 	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.	PLoS Neglected Trop. Dis.	2014	8		E3261			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. 		
@D	Stecker, C.//Johann, A.//Herzberg, C.//Averhoff, B.//Gottschalk, G. 	Complete nucleotide sequence and genetic organization of the 210-Kilobase linear plasmid of Rhodococcus erythropolis BD2.	J. Bacteriol.	2003	185		5269-5274			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. 		
@D	Steczkiewicz, K.//Muszewska, A.//Knizewski, L.//Rychlewski, L.//Ginalski, K. 	Sequence, structure and functional diversity of PD-(D/E)XK phosphodiesterase superfamily.	Nucleic Acids Res.	2012	40		7016-7045			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. 		
@D	Steele, C.L.//Donaldson, J.R.//Paul, D.//Banes, M.M.//Arick, T.//Bridges, S.M.//Lawrence, M.L. 	Genome sequence of lineage III Listeria monocytogenes strain HCC23.	J. Bacteriol.	2011	193		3679-3680			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. 		
@D	Steenson, L.R.//Klaenhammer, T.R. 	Streptococcus cremoris M12R transconjugants carrying the conjugal plasmid pTR2030 are insensitive to attack by lytic bacteriophages.	Appl. Environ. Microbiol.	1985	50		851-858			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. 		
@D	Steenson, L.R.//Klaenhammer, T.R. 	Plasmid heterogeneity in Streptococcus cremoris M12R:  effects on proteolytic activity and host-dependent phage replication.	J. Dairy Sci.	1986	69		2227-2236			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. 		
@D	Stefan, C.//Xia, Y.//Van Etten, J.L. 	Molecular cloning and characterization of the gene encoding the adenine methyltransferase M.CviRI from Chlorella virus XZ-6E.	Nucleic Acids Res.	1991	19		307-311			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. 		
@D	Stefanishina, T.V.//Bogdarina, I.G.//Buryanov, Y.I. 	Search for the modification-restriction systems.	Biopol. Kletka	1987	3		128-131			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. 		
@D	Stefanovic, E.//Casey, A.//Cotter, P.//Cavanagh, D.//Fitzgerald, G.//McAuliffe, O. 	Draft Genome Sequence of Lactobacillus casei DPC6800, an Isolate with the Potential to Diversify Flavor in Cheese.	Genome Announcements	2016	4		e00063-16			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. 		
@D	Stefanovic, E.//Fitzgerald, G.//McAuliffe, O. 	Draft Genome Sequences of Three Lactobacillusparacasei Strains, Members of the Nonstarter Microbiota of Mature Cheddar Cheese.	Genome Announcements	2017	5		e00655-17			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. 		
@D	Steffani-Vallejo, J.L.//Brunck, M.E.//Acosta-Cruz, E.Y.//Montiel, R.//Barona-Gomez, F. 	Genomic insights into Mycobacterium simiae human colonization.	Standards in Genomic Sciences	2018	13		1			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. 		
@D	Steffani-Vallejo, J.L.//Zuniga, C.//Cruz-Morales, P.//Lozano, L.//Morales, M.//Licona-Cassani, C.//Revah, S.//Utrilla, J. 	Draft Genome Sequence of Sphingobacterium sp. CZ-UAM, Isolated from a Methanotrophic Consortium.	Genome Announcements	2017	5		e00792-17			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. 		
@D	Stegger, M.//Driebe, E.M.//Roe, C.//Lemmer, D.//Bowers, J.R.//Engelthaler, D.M.//Keim, P.//Andersen, P.S. 	Genome Sequence of Staphylococcus aureus Strain CA-347, a USA600 Methicillin-Resistant Isolate.	Genome Announcements	2013	1		e00517-13			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. 		
@D	Stegger, M.//Lindsay, J.A.//Moodley, A.//Skov, R.//Broens, E.M.//Guardabassi, L. 	Rapid PCR Detection of Staphylococcus aureus Clonal Complex 398 by Targeting the Restriction-Modification System Carrying sau1-hsdS1.	J. Clin. Microbiol.	2011	49		732-734			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. 		
@D	Stegger, M.//Price, L.B.//Larsen, A.R.//Gillece, J.D.//Waters, A.E.//Skov, R.//Andersen, P.S. 	Genome Sequence of Staphylococcus aureus Strain 11819-97, an ST80-IV European Community-Acquired Methicillin-Resistant Isolate.	J. Bacteriol.	2012	194		1625-1626			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. 		
@D	Steigerwald, S.D.//Pfeifer, G.P.//Riggs, A.D. 	Ligation-mediated PCR improves the sensitivity of methylation analysis by restriction enzymes and detection of specific DNA strand breaks.	Nucleic Acids Res.	1990	18		1435-1439			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. 		
@D	Stein, D.C.//Chien, R.//Seifert, S.H. 	Construction of a Neisseria gonorrhoeae MS11 derivative deficient in NgoMI restriction and modification.	J. Bacteriol.	1992	174		4899-4906			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. ] 		
@D	Stein, D.C.//Gregoire, S.//Piekarowicz, A. 	Restriction of plasmid DNA during transformation but not conjugation in Neisseria gonorrhoeae.	Infect. Immun.	1988	56		112-116			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. ] 		
@D	Stein, D.C.//Gunn, J.S.//Piekarowicz, A. 	Sequence similarities between the genes encoding the S.NgoI and HaeII restriction/modification systems.	Biol. Chem.	1998	379		575-578			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. 		
@D	Stein, D.C.//Gunn, J.S.//Radlinska, M.//Piekarowicz, A. 	Restriction and modification systems of Neisseria gonorrhoeae.	Gene	1995	157		19-22			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. 		
@D	Stein, L.Y. et al. 	Genome sequence of the methanotrophic Alphaproteobacterium, Methylocystis sp. Rockwell (ATCC 49242).	J. Bacteriol.	2011	193		2668-2669			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. 		
@D	Stein, L.Y. et al. 	Genome Sequence of the Obligate Methanotroph Methylosinus trichosporium Strain OB3b.	J. Bacteriol.	2010	192		6497-6498			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. 		
@D	Steinweg, C.//Kuenne, C.T.//Billion, A.//Mraheil, M.A.//Domann, E.//Ghai, R.//Barbuddhe, S.B.//Karst, U.//Goesmann, A.//Puhler, A.//Weisshaar, B.//Wehland, J.//Lampidis, R.//Kreft, J.//Goebel, W.//Chakraborty, T.//Hain, T. 	The complete genome sequence of L. seeligeri, a non-pathogenic member of the genus Listeria.	J. Bacteriol.	2010	192		1473-1474			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. 		
@D	Steitz, T.A. 	Structural studies of protein-nucleic acid interaction:  the source of sequence-specific binding.	Q. Rev. Biophys.	1990	23		205-280			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 		
@D	Stelling, S.C.//Techtmann, S.M.//Utturkar, S.M.//Alshibli, N.K.//Brown, S.D.//Hazen, T.C. 	Draft Genome Sequence of Thalassotalea sp. Strain ND16A Isolated from Eastern Mediterranean Sea Water Collected from a Depth of 1,055 Meters.	Genome Announcements	2014	2		e01231-14			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. 		
@D	Stenger, D.C.//Lee, M.W.//Rogers, E.E.//Chen, J. 	Plasmids of Xylella fastidiosa mulberry-infecting strains share extensive sequence identity and gene complement with pVEIS01 from the earthworm symbiont Verminephrobacter eiseniae.	Physiol. Mol. Plant Pathol.	2010	74		238-245			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. 		
@D	Stepanov, V.G.//Roberts, D.J.//Fox, G.E. 	Draft Genome Sequence of Marinobacter vinifirmus Type Strain FB1.	Genome Announcements	2017	5		e01058-17			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. 		
@D	Stepanov, V.G.//Vaishampayan, P.//Venkateswaran, K.//Fox, G.E. 	Draft Genome Sequence of Deinococcus phoenicis, a Novel Strain Isolated during the Phoenix Lander Spacecraft Assembly.	Genome Announcements	2014	2		e00301-14			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. 		
@D	Stepanov, V.G.//Xiao, Y.//Lopez, A.J.//Roberts, D.J.//Fox, G.E. 	Draft Genome Sequence of Marinobacter sp. Strain P4B1, an Electrogenic Perchlorate-Reducing Strain Isolated from a Long-Term Mixed Enrichment Culture of  Marine Bacteria.	Genome Announcements	2016	4		e01617-15			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). 		
@D	Stephan, R.//Grim, C.J.//Gopinath, G.R.//Mammel, M.K.//Sathyamoorthy, V.//Trach, L.H.//Chase, H.R.//Fanning, S.//Tall, B.D. 	Genome Sequence of Enterobacter turicensis Strain 610/05 (LMG 23731), Isolated from Fruit Powder.	Genome Announcements	2013	1		e00996-13			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. 		
@D	Stephan, R.//Lehner, A.//Tischler, P.//Rattei, T. 	Complete Genome Sequence of Cronobacter turicensis LMG 23827, a foodborne pathogen causing deaths in neonates.	J. Bacteriol.	2010	193		309-310			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. 		
@D	Stephanou, A.S.//Roberts, G.A.//Cooper, L.P.//Clarke, D.J.//Thomson, A.R.//MacKay, C.L.//Nutley, M.//Cooper, A.//Dryden, D.T. 	Dissection of the DNA mimicry of the bacteriophage T7 Ocr protein using chemical modification.	J. Mol. Biol.	2009	391		565-576			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. 		
@D	Stephanou, A.S.//Roberts, G.A.//Tock, M.R.//Pritchard, E.H.//Turkington, R.//Nutley, M.//Cooper, A.//Dryden, D.T.F. 	A mutational analysis of DNA mimicry by ocr, the gene 0.3 antirestriction protein of bacteriophage T7.	Biochem. Biophys. Res. Commun.	2009	378		129-132			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. 		
@D	Stephens, C.//Cho, P.J.//Afonso-de-Araujo, V.//Gomes, I.M.//de Azevedo-Sias, S.M.//Araujo, C.C.A.//Riley, L.W.//Aguiar-Alves, F. 	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.	Genome Announcements	2015	3		e00907-15			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. 		
@D	Stephens, C.//Reisenauer, A.//Wright, R.//Shapiro, L. 	A cell cycle-regulated bacterial DNA methyltransferase is essential for viability.	Proc. Natl. Acad. Sci. U. S. A.	1996	93		1210-1214			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. 		
@D	Stephens, C.//Shapiro, L. 	A common regulatory system controls transcription of flagellar genes and an essential DNA methyltransferase in Caulobacter.	Abstr. Gen. Meet. Am. Soc. Microbiol.	1994	94		203			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. 		
@D	Stephens, C.//Shapiro, L. 	An essential DNA methyltransferase in Caulobacter crescentus.	Abstr. Gen. Meet. Am. Soc. Microbiol.	1995	95		330			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. 		
@D	Stephens, C.M.//Skerker, J.M.//Sekhon, M.S.//Arkin, A.P.//Riley, L.W. 	Complete Genome Sequences of Four Escherichia coli ST95 Isolates from Bloodstream Infections.	Genome Announcements	2015	3		e01241-15			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. 		
@D	Stephens, C.M.//Zweiger, G.//Shapiro, L. 	Coordinate cell cycle control of a Caulobacter DNA methyltransferase and the flagellar genetic hierarchy.	J. Bacteriol.	1995	177		1662-1669			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. 		
@D	Stephens, M.A. 	Partial purification and cleavage specificity of a site-specific endonuclease, SciNI, isolated from Spiroplasma citri.	J. Bacteriol.	1982	149		508-514			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. 		
@D	Stephens, R.S.//Kalman, S.//Lammel, C.J.//Fan, J.//Marathe, R.//Aravind, L.//Mitchell, W.P.//Olinger, L.//Tatusov, R.L.//Zhao, Q.//Koonin, E.V.//Davis, R.W. 	Genome Sequence of an Obligate Intracellular Pathogen of Humans: Chlamydia trachomatis.	Science	1998	282		754-759			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 ] 		
@D	Stephenson, F.H.//Ballard, B.T.//Boyer, H.W.//Rosenberg, J.M.//Greene, P.J. 	Comparison of the nucleotide and amino acid sequences of the RsrI and EcoRI restriction endonucleases.	Gene	1989	85		1-13			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. 		
@D	Stephenson, F.H.//Greene, P.J. 	Nucleotide sequence of the gene encoding the RsrI methyltransferase.	Nucleic Acids Res.	1989	17		10503			None 		
@D	Stephenson, J.//Kumaresan, D.//Hillebrand-Voiculescu, A.M.//Brooks, E.//Whiteley, A.S.//Murrell, J.C. 	Draft Genome Sequence of the Methane-Oxidizing Bacterium 'Candidatus Methylomonas sp. LWB' Isolated from Movile Cave.	Genome Announcements	2017	5		e01491-16			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. 		
@D	Steponaviciene, D.//Maneliene, Z.//Petrusyte, M.//Janulaitis, A. 	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'.	Nucleic Acids Res.	1999	27		2644-2645			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. 		
@D	Stern, A.//Sorek, R. 	The phage-host arms race: Shaping the evolution of microbes.	Bioessays	2011	33		43-51			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. 		
@D	Sternberg, N. 	Evidence that adenine methylation influences DNA-protein interactions in Escherichia coli.	J. Bacteriol.	1985	164		490-493			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. 		
@D	Sternberg, N.//Coulby, J. 	Cleavage of the bacteriophage P1 packaging site (pac) is regulated by adenine methylation.	Proc. Natl. Acad. Sci. U. S. A.	1990	87		8070-8074			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. 		
@D	Sternglanz, H.//Bugg, C.E. 	Conformation of N6-methyladenine, a base involved in DNA modification:restriction processes.	Science	1973	182		833-834			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. 		
@D	Steuer, S.//Pingoud, V.//Pingoud, A.//Wende, W. 	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.	Chembiochem	2004	5		206-213			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. 		
@D	Stevens, D.C.//Young, J.//Carmichael, R.//Tan, J.//Taylor, R.E. 	Draft Genome Sequence of Gephyronic Acid Producer Cystobacter violaceus Strain Cb vi76.	Genome Announcements	2014	2		e01299-14			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. 		
@D	Stevens, M.//Cheng, J.B.//Li, D.//Xie, M.//Hong, C.//Maire, C.L.//Ligon, K.L.//Hirst, M.//Marra, M.A.//Costello, J.F.//Wang, T. 	Estimating absolute methylation levels at single-CpG resolution from methylation enrichment and restriction enzyme sequencing methods.	Genome Res.	2013	23		1541-1553			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. 		
@D	Stevens, M.J.//Inglin, R.C.//Meile, L. 	Complete and Assembled Genome Sequence of Vagococcus teuberi DSM 21459T, a Novel  Species Isolated from Fermented Cow Milk in Mali.	Genome Announcements	2017	5		e01514-16			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. 		
@D	Stevens, M.J.//Stephan, R.//Johler, S. 	Complete and Assembled Genome Sequence of Staphylococcus aureus RKI4, a Food-Poisoning Strain Exhibiting a Novel S. aureus Pathogenicity Island Carrying seb.	Genome Announcements	2015	3		e00769-15			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. 		
@D	Stevens, M.J.//Stephan, R.//Johler, S. 	Draft Genome Sequence of Staphylococcus aureus 1608, a Strain That Caused Toxic Mastitis in Twin Cows.	Genome Announcements	2017	5		e01438-16			Staphylococcus aureus 1608 is a strain that caused a lethal mastitis in cows. Here, the draft genome sequence of the strain is presented. 		
@D	Stevens, M.J.A.//Stephan, R.//Johler, S. 	Draft Genome Sequence of Staphylococcus aureus S681, a Tetracycline-Sensitive Livestock-Associated Methicillin-Resistant Clonal Complex 398 Strain.	Genome Announcements	2017	5		e00805-17			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. 		
@D	Stevens, M.J.A.//Zurfluh, K.//Althaus, D.//Corti, S.//Lehner, A.//Stephan, R. 	Complete and Assembled Genome Sequence of Salmonella enterica subsp. enterica Serotype Senftenberg N17-509, a Strain Lacking Salmonella Pathogen Island 1.	Genome Announcements	2018	6		e00156-18			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. 		
@D	Stevens, M.J.A.//Zurfluh, K.//Stephan, R. 	Complete and Assembled Genome Sequences of Pantoea calida DSM 22759(T) and Pantoea gaviniae DSM 22758(T).	Genome Announcements	2018	6		e00157-18			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. 		
@D	Stevens, V.//Thijs, S.//McAmmond, B.//Langill, T.//Van Hamme, J.//Weyens, N.//Vangronsveld, J. 	Draft Genome Sequence of Bacillus licheniformis VSD4, a Diesel Fuel-Degrading and Plant Growth-Promoting Phyllospheric Bacterium.	Genome Announcements	2017	5		e00027-17			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. 		
@D	Stevens, V.//Thijs, S.//McAmmond, B.//Langill, T.//Van Hamme, J.//Weyens, N.//Vangronsveld, J. 	Draft Genome Sequence of Rhodococcus erythropolis VSD3, a Diesel Fuel-Degrading and Plant Growth-Promoting Bacterium Isolated from Hedera helix Leaves.	Genome Announcements	2017	5		e01680-16			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. 		
@D	Steward, G.F.//Preston, C.M. 	Analysis of a viral metagenomic library from 200 m depth in Monterey Bay, California constructed by direct shotgun cloning.	Virol. J.	2011	8		287			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. 		
@D	Steward, N.//Kusano, T.//Sano, H. 	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.	Nucleic Acids Res.	2000	28		3250-3259			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. 		
@D	Stewart, F.//Dila, D.//Raleigh, E. 	The mechanism of action of the McrBC restriction enzyme of E. coli K-12.	J. Cell Biochem. Suppl.	1995	19A		118			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. 		
@D	Stewart, F.J.//Panne, D.//Bickle, T.A.//Raleigh, E.A. 	Methyl-specific DNA binding by McrBC, a modification-dependent restriction enzyme.	J. Mol. Biol.	2000	298		611-622			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. 		
@D	Stewart, F.J.//Raleigh, E.A. 	Dependence of McrBC cleavage on distance between recognition elements.	Biol. Chem.	1998	379		611-616			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. 		
@D	Stewart, L.//Ford, A.//Sangal, V.//Jeukens, J.//Boyle, B.//Kukavica-Ibrulj, I.//Caim, S.//Crossman, L.//Hoskisson, P.A.//Levesque, R.//Tucker, N.P. 	Draft genomes of 12 host-adapted and environmental isolates of Pseudomonas aeruginosa and their positions in the core genome phylogeny.	Pathog Dis.	2014	71		20-25			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. 		
@D	Stewart, R.M.//Wiehlmann, L.//Ashelford, K.E.//Preston, S.J.//Frimmersdorf, E.//Campbell, B.J.//Neal, T.J.//Hall, N.//Tuft, S.//Kaye, S.B.//Winstanley, C. 	Genetic characterization indicates that a specific subpopulation of Pseudomonas aeruginosa is associated with keratitis infections.	J. Clin. Microbiol.	2011	49		993-1003			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. 		
@D	Stice, S.P.//Stumpf, S.D.//Gitaitis, R.D.//Kvitko, B.H.//Dutta, B. 	Pantoea ananatis Genetic Diversity Analysis Reveals Limited Genomic Diversity as  Well as Accessory Genes Correlated with Onion Pathogenicity.	Front. Microbiol.	2018	9		184			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. 		
@D	Stiens, M.//Becker, A.//Bekel, T.//Godde, V.//Goesmann, A.//Niehaus, K.//Schneiker-Bekel, S.//Selbitschka, W.//Weidner, S.//Schluter, A.//Puhler, A. 	Comparative genomic hybridisation and ultrafast pyrosequencing revealed remarkable differences between the Sinorhizobium meliloti genomes of the model strain Rm1021 and the field isolate SM11.	J. Biotechnol.	2008	136		31-37			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. 		
@D	Stiens, M.//Schneiker, S.//Puhler, A.//Schluter, A. 	Sequence analysis of the 181-kb accessory plasmid pSmeSM11b, isolated from a dominant Sinorhizobium meliloti strain identified during a long-term field release experiment.	FEMS Microbiol. Lett.	2007	271		297-309			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. 		
@D	Stier, I.//Kiss, A. 	Cytosine-to-Uracil Deamination by SssI DNA Methyltransferase.	PLoS ONE	2013	8		e79003			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. 		
@D	Stier, I.//Kiss, A. 	The Type II restriction endonuclease MvaI has dual specificity.	Nucleic Acids Res.	2010	38		8231-8238			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. 		
@D	Stine, C.B.//Li, C.//Crosby, T.C.//Hasbrouck, N.R.//Lam, C.//Tadesse, D.A. 	Draft Whole-Genome Sequences of 18 Flavobacterium spp.	Genome Announcements	2017	5		e00865-17			We report here the draft whole-genome sequences for 18 Flavobacterium species type strains that have historically been associated with fish gill disease. 		
@D	Stine, C.B.//Li, C.//Crosby, T.C.//Hasbrouck, N.R.//Lam, C.//Tadesse, D.A. 	Draft Whole-Genome Sequences of Chryseobacterium piscicola and Chryseobacterium shigense.	Genome Announcements	2018	6		e00413-18			We report the draft whole-genome sequences for Chryseobacterium piscicola and Chryseobacterium shigense type strains, bacteria that have been associated with fish gill disease. 		
@D	Stinear, T.P. et al. 	Insights from the complete genome sequence of Mycobacterium marinum on the evolution of Mycobacterium tuberculosis.	Genome Res.	2008	18		729-741			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. 		
@D	Stipetic, L.H.//Hamilton, G.//Dalby, M.J.//Davies, R.L.//Meek, R.M.//Ramage, G.//Smith, D.G.//Burgess, K.E. 	Draft Genome Sequence of Isolate Staphylococcus aureus LHSKBClinical, Isolated from an Infected Hip.	Genome Announcements	2015	3		e00336-15			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. 		
@D	Stobberingh, E.E.//Meijers, J.A.//Van Kats-Renaud, J.H. 	The sensitivity of phage DNA and plasmid DNA for a restriction enzyme from Staphylococcus aureus.	Antonie Van Leeuwenhoek	1979	45		19-23			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. 		
@D	Stobberingh, E.E.//Schiphof, R.//Sussenbach, J.S. 	Occurrence of a Class II Restriction Endonuclease in Staphylococcus aureus.	J. Bacteriol.	1977	131		645-649			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. 		
@D	Stobberingh, E.E.//Winkler, K.C. 	Restriction-deficient mutants of Staphylococcus aureus.	J. Gen. Microbiol.	1977	99		359-367			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. 		
@D	Stoddard, B.//Belfort, M. 	Social networking between mobile introns and their host genes.	Mol. Microbiol.	2010	78		1-4			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. 		
@D	Stoddard, B.L. 	Homing endonuclease structure and function.	Q. Rev. Biophys.	2005	38		49-95			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. 		
@D	Stoddard, B.L. 	Homing endonucleases: from microbial genetic invaders to reagents for targeted DNA modification.	Structure	2011	19		7-15			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. 		
@D	Stoddard, B.L.//Jurica, M.//Heath, P.//Flick, K. 	The structure, function, and convergent evolution of intron-encoded homing endonucleases.	Biochem. Soc. Trans.	1999	27		A39			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. 		
@A	Stoddard, B.L.//Scharenberg, A.M.//Monnat, R.J. Jr. 		Advances in engineering homing endonucleases for gene targeting: ten years after structures.			Bertolotti, R.//Ozawa, K. 		Prog. Gene Ther.						2008		3		135-167									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. 		
@D	Stojanov, M.//Blanc, D.S. 	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.	Eur. J. Clin. Microbiol. Infect. Dis.	2014	33		1967-1971			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. 		
@D	Stokes, H.W.//Nesbo, C.L.//Holley, M.//Bahl, M.I.//Gillings, M.R.//Boucher, Y. 	Class 1 Integrons Potentially Predating the Association with Tn402-Like Transposition Genes Are Present in a Sediment Microbial Community.	J. Bacteriol.	2006	188		5722-5730			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." 		
@D	Stokke, R.//Hocking, W.P.//Steinsbu, B.O.//Steen, I.H. 	Complete Genome Sequence of the Thermophilic and Facultatively Chemolithoautotrophic Sulfate Reducer Archaeoglobus sulfaticallidus Strain  PM70-1T.	Genome Announcements	2013	1		e00406-13			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. 		
@D	Stolt, P.//Grampp, B.//Zillig, W. 	Genes for DNA cytosine methyltransferases and structural proteins, expressed during lytic growth by the phage Phi-H of the archaebacterium Halobacterium salinarium.	Biol. Chem. Hoppe Seyler	1994	375		747-757			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. 		
@D	Stolyar, S.//Liu, Z.//Thiel, V.//Tomsho, L.P.//Pinel, N.//Nelson, W.C.//Lindemann, S.R.//Romine, M.F.//Haruta, S.//Schuster, S.C.//Bryant, D.A.//Fredrickson, J.K. 	Genome Sequence of the Thermophilic Cyanobacterium Thermosynechococcus sp. Strain NK55a.	Genome Announcements	2014	2		e01060-13			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. 		
@D	Stone, J.K.//Johnson, S.L.//Bruce, D.C.//Detter, J.C.//Mayo, M.//Currie, B.J.//Gelhaus, H.C.//Keim, P.//Tuanyok, A. 	Complete Genome Sequence of the Encephalomyelitic Burkholderia pseudomallei Strain MSHR305.	Genome Announcements	2013	1		e00656-13			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. 		
@D	Storari, M.//Wuthrich, D.//Bruggmann, R.//Berthoud, H.//Arias-Roth, E. 	Draft Genome Sequences of Clostridium tyrobutyricum Strains FAM22552 and FAM22553, Isolated from Swiss Semihard Red-Smear Cheese.	Genome Announcements	2015	3		e00078-15			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. 		
@D	Storm, A.J.//Jensen, P.A. 	Designing Randomized DNA Sequences Free of Restriction Enzyme Recognition Sites.	Biotechnol. J.	2018	13					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). 		
@D	Stover, C.K. et al. 	Complete genome sequence of Pseudomonas aeruginosa PA01, an opportunistic pathogen.	Nature	2000	406		959-964			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. 		
@D	Stover, T.//Kohler, E.//Fagin, U.//Wende, W.//Wolfes, H.//Pingoud, A. 	Determination of the DNA bend angle induced by the restriction endonuclease EcoRV in the presence of Mg2++.	J. Biol. Chem.	1993	268		8645-8650			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. 		
@D	Strabala, T.J.//Macdonald, L.//Liu, V.//Smit, A.-M. 	Draft genome sequence of Novosphingobium nitrogenifigens Y88T.	J. Bacteriol.	2011	194		201			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. 		
@D	Strachan, C.R.//Singh, R.//VanInsberghe, D.//Ievdokymenko, K.//Budwill, K.//Mohn, W.W.//Eltis, L.D.//Hallam, S.J. 	Metagenomic scaffolds enable combinatorial lignin transformation.	Proc. Natl. Acad. Sci. U. S. A.	2014	111		10143-10148			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. 		
@D	Strapagiel, D.//Borowka, P.//Marciniak, B.//Bakula, Z.//van Ingen, J.//Safianowska, A.//Brzostek, A.//Dziadek, J.//Jagielski, T. 	Draft Genome Sequences of Mycobacterium kansasii Strains 1010001454, 1010001458,  1010001468, 1010001493, 1010001495, and 1010001469, Isolated from Environmental  Sources.	Genome Announcements	2016	4		e00456-16			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. 		
@D	Strathdee, G.//Brown, R. 	Epigenetic cancer therapies: DNA methyltransferase inhibitors.	Expert Opin. Invest. Drugs	2002	11		747-754			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. 		
@D	Strauch, E.//Goelz, G.//Knabner, D.//Konietzny, A.//Lanka, E.//Appel, B. 	A cryptic plasmid of Yersinia enterocolitica encodes a conjugative transfer system related to the regions of CloDF13 Mob and IncX Pil.	Microbiology	2003	149		2829-2845			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. 		
@D	Strauch, E.//Hammerl, J.A.//Konietzny, A.//Schneiker-Bekel, S.//Arnold, W.//Goesmann, A.//Puhler, A.//Beutin, L. 	Bacteriophage 2851 is a prototype phage for dissemination of the Shiga toxin variant gene 2c in Escherichia coli O157:H7.	Infect. Immun.	2008	76		5466-5477			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. 		
@D	Strauch, M.A. 	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.	J. Bacteriol.	1995	177		6999-7002			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. 		
@D	Strausberg, R.L. et al. 	Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences.	Proc. Natl. Acad. Sci. U. S. A.	2002	99		16899-16903			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). 		
@D	Streeck, R.E. 	Single-strand and double-strand cleavage at half-modified and fully modified recognition sites for the restriction nucleases Sau3A and TaqI.	Gene	1980	12		267-275			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. 		
@D	Streeter, S.D.//McGeehan, J.E.//Kneale, G.G. 	Overexpression, purification and preliminary X-ray diffraction analysis of the controller protein C.Csp231I from Citrobacter sp RFL231.	Acta Crystallogr. F Struct. Biol. Cryst. Commun.	2009	F65		898-901			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. 		
@D	Streeter, S.D.//Papapanagiotou, I.//McGeehan, J.E.//Kneale, G.G. 	DNA footprinting and biophysical characterization of the controller protein C.AhdI suggests the basis of a genetic switch.	Nucleic Acids Res.	2004	32		6445-6453			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. 		
@D	Streiff, M.B.//Iida, S.//Bickle, T.A. 	Expression and proteolytic processing of the darA antirestriction gene product of bacteriophage P1.	Virology	1987	157		167-171			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. 		
@D	Striebel, H.-M.//Kessler, C. 	Novel specific endonuclease activity recognizing a 10-bp sequence.	Gene	1996	172		47-48			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. 		
@D	Striebel, H.-M.//Schmitz, G.G.//Kaluza, K.//Jarsch, M.//Kessler, C. 	MamI, a novel class-II restriction endonuclease from Microbacterium ammoniaphilum recognizing 5'-GATNN^NNATC-3'.	Gene	1990	91		95-100			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*). 		
@D	Striebel, H.-M.//Seeber, S.//Jarsch, M.//Kessler, C. 	Cloning and characterization of the MamI restriction-modification system from Microbacterium ammoniaphilum in Escherichia coli.	Gene	1996	172		41-46			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. 		
@D	Strikhanov, S.N.//Aleshkin, G.I.//Skavronskaya, A.G. 	Plasmid recombination stimulated by restriction endonuclease EcoRI in vivo: specificity of recombinant plasmid formation in RecA cells of Escherichia coli.	Mol. Gen. Mikrobiol. Virusol.	1985	5		13-19			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. 		
@D	Stringer, S.C.//Carter, A.T.//Webb, M.D.//Wachnicka, E.//Crossman, L.C.//Sebaihia, M.//Peck, M.W. 	Genomic and physiological variability within Group II (non-proteolytic) Clostridium botulinum.	BMC Genomics	2013	14		333			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. 		
@D	Strittmatter, A.W. et al. 	Genome sequence of Desulfobacterium autotrophicum HRM2, a marine sulfate reducer oxidizing organic carbon completely to carbon dioxide.	Environ. Microbiol.	2009	11		1038-1055			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. 		
@D	Strnad, H.//Lapidus, A.//Paces, J.//Ulbrich, P.//Vlcek, C.//Paces, V.//Haselkorn, R. 	Complete Genome Sequence of the Photosynthetic Purple Nonsulfur Bacterium Rhodobacter capsulatus SB 1003.	J. Bacteriol.	2010	192		3545-3546			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. 		
@D	Strnad, H.//Patek, M.//Fousek, J.//Szokol, J.//Ulbrich, P.//Nesvera, J.//Paces, V.//Vlcek, C. 	Genome Sequence of Rhodococcus erythropolis Strain CCM2595, a Phenol Derivative-Degrading Bacterium.	Genome Announcements	2014	2		e00208-14			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. 		
@D	Strnad, H.//Ridl, J.//Paces, J.//Kolar, M.//Vlcek, C.//Paces, V. 	Complete Genome Sequence of the Haloaromatic Acids-degrading Bacterium Achromobacter xylosoxidans A8.	J. Bacteriol.	2010	193		791-792			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. 		
@D	Strobel, S.A.//Doucette-Stamm, L.A.//Riba, L.//Housman, D.E.//Dervan, P.B. 	Site-specific cleavage of human chromosome 4 mediated by triple-helix formation.	Science	1991	254		1639-1642			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. 		
@D	Strobel, T.//Al-Dilaimi, A.//Blom, J.//Gessner, A.//Kalinowski, J.//Luzhetska, M.//Puhler, A.//Szczepanowski, R.//Bechthold, A.//Ruckert, C. 	Complete genome sequence of Saccharothrix espanaensis DSM 44229T and comparison to the other completely sequenced Pseudonocardiaceae.	BMC Genomics	2012	13		465			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. 		
@D	Strobl, J.S.//Thompson, E.B. 	Methylation of either cytosine in the recognition sequence CGCG inhibits ThaI cleavage of DNA.	Nucleic Acids Res.	1984	12		8073-8083			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. 		
@D	Strous, M. et al. 	Deciphering the evolution and metabolism of an anammox bacterium from a community genome.	Nature	2006	440		790-794			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. 		
@D	Strzelecka, T.//Dorner, L.//Schildkraut, I.//Aggarawal, A. 	Structural studies of the BamHI restriction enzyme.	Biophys. J.	1990	57		68			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. 		
@D	Strzelecka, T.//Newman, M.//Dorner, L.F.//Knott, R.//Schildkraut, I.//Aggarwal, A.K. 	Crystallization and preliminary X-ray analysis of restriction endonuclease BamHI-DNA complex.	J. Mol. Biol.	1994	239		430-432			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. 		
@D	Stucken, K.//John, U.//Cembella, A.//Murillo, A.A.//Soto-Liebe, K.//Fuentes-Valdes, J.J.//Friedel, M.//Plominsky, A.M.//Vasquez, M.//Glockner, G. 	The smallest known genomes of multicellular and toxic cyanobacteria: comparison, minimal gene sets for linked traits and the evolutionary implications.	PLoS ONE	2010	5		E9235			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. 		
@D	Stucken, K.//Koch, R.//Dagan, T. 	Cyanobacterial defense mechanisms against foreign DNA transfer and their impact on genetic engineering.	Biol. Res.	2013	46		373-382			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. 		
@D	Stuckle, E.E.//Emmrich, C.//Grob, U.//Nielsen, P.J. 	Statistical analysis of nucleotide sequences.	Nucleic Acids Res.	1990	18		6641-6647			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. 		
@D	Studholme, D.J.//Wasukira, A.//Paszkiewicz, K.//Aritua, V.//Thwaites, R.//Smith, J.//Grant, M. 	Draft Genome Sequences of Xanthomonas sacchari and Two Banana-Associated Xanthomonads Reveal Insights into the Xanthomonas Group 1 Clade.	Genes (Basel)	2011	2		1050-1065			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. 		
@D	Studier, F.W. 	Gene 0.3 of Bacteriophage T7 Acts to Overcome the DNA Restriction System of the Host.	J. Mol. Biol.	1975	94		283-295			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. 		
@D	Studier, F.W.//Bandyopadhyay, P.K. 	Model for how type I restriction enzymes select cleavage sites in DNA.	Proc. Natl. Acad. Sci. U. S. A.	1988	85		4677-4681			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. 		
@D	Studier, F.W.//Movva, N.R. 	SAMase gene of bacteriophage T3 is responsible for overcoming host restriction.	J. Virol.	1976	19		136-145			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. 		
@D	Sturino, J.M.//Rajendran, M.//Altermann, E. 	Draft Genome Sequence of Lactobacillus animalis 381-IL-28.	Genome Announcements	2014	2		e00478-14			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. 		
@D	Sturino, J.M.//Rajendran, M.//Altermann, E. 	Draft Genome Sequence of the Pediocin-Encoding Biopreservative and Biocontrol Strain Pediococcus acidilactici D3.	Genome Announcements	2013	1		e00208-13			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. 		
@D	Sturm, G.//Buchta, K.//Kurz, T.//Rensing, S.A.//Gescher, J. 	Draft Genome Sequence of Leucobacter chromiiresistens, an Extremely Chromium-Tolerant Strain.	J. Bacteriol.	2012	194		540-541			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. 		
@D	Sturm, R.A.//Yaciuk, P. 	DNA cleavage by restriction endonucleases PflMI is inhibited in recognition sites modified by dcm methylation.	Nucleic Acids Res.	1989	17		3615			None 		
@D	Sturrock, S.S.//Dryden, D.T.//Atanasiu, C.//Dornan, J.//Bruce, S.//Cronshaw, A.//Taylor, P.//Walkinshaw, M.D. 	Crystallization and preliminary X-ray analysis of ocr, the product of gene 0.3 of bacteriophage T7.	Acta Crystallogr. D Biol. Crystallogr.	2001	57		1652-1654			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. 		
@D	Sturrock, S.S.//Dryden, D.T.F. 	A prediction of the amino acids and structures involved in DNA recognition by type I DNA restriction and modification enzymes.	Nucleic Acids Res.	1997	25		3408-3414			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. 		
@D	Stuy, J.H. 	Restriction Enzymes Do Not Play a Significant Role in Haemophilus Homospecific or Heterospecific Transformation.	J. Bacteriol.	1976	128		212-220			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. 		
@D	Stynen, A.P. et al. 	Complete Genome Sequence of Type Strain Campylobacter fetus subsp. venerealis NCTC 10354T.	J. Bacteriol.	2011	193		5871-5872			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. 		
@D	Styriak, I.//Pristas, P.//Javorsky, P. 	Lack of surface receptors not restriction-modification system determines F4 phage resistance in Streptococcus bovis II/1.	Folia Microbiol. (Praha)	1998	43		35-38			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. 		
@D	Su, C.C.//Deng, W.L.//Jan, F.J.//Chang, C.J.//Huang, H.//Chen, J. 	Draft Genome Sequence of Xylella fastidiosa Pear Leaf Scorch Strain in Taiwan.	Genome Announcements	2014	2		e00166-14			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. 		
@D	Su, F.//Hua, D.//Zhang, Z.//Wang, X.//Tang, H.//Tao, F.//Tai, C.//Wu, Q.//Wu, G.//Xu, P. 	Genome Sequence of Bacillus pumilus S-1, an Efficient Isoeugenol-Utilizing Producer for Natural Vanillin.	J. Bacteriol.	2011	193		6400-6401			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. 		
@D	Su, F.//Tao, F.//Tang, H.//Xu, P. 	Genome Sequence of the Thermophile Bacillus coagulans Hammer, the Type Strain of  the Species.	J. Bacteriol.	2012	194		6294-6295			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. 		
@D	Su, F.//Xu, K.//Zhao, B.//Tai, C.//Tao, F.//Tang, H.//Xu, P. 	Genome Sequence of the Thermophilic Strain Bacillus coagulans XZL4, an Efficient Pentose-Utilizing Producer of Chemicals.	J. Bacteriol.	2011	193		6398-6399			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. 		
@D	Su, F.//Yu, B.//Sun, J.//Ou, H.Y.//Zhao, B.//Wang, L.//Qin, J.//Tang, H.//Tao, F.//Jarek, M.//Scharfe, M.//Ma, C.//Ma, Y.//Xu, P. 	Genome Sequence of the Thermophilic Strain Bacillus coagulans 2-6, an Efficient Producer of High-Optical-Purity L-Lactic Acid.	J. Bacteriol.	2011	193		4563-4564			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. 		
@D	Su, H.//Zhang, T.//Bao, M.//Jiang, Y.//Wang, Y.//Tan, T. 	Genome Sequence of a Promising Hydrogen-Producing Facultative Anaerobic Bacterium, Brevundimonas naejangsanensis Strain B1.	Genome Announcements	2014	2		e00542-14			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. 		
@D	Su, J.//Ye, J.//Zhu, Y. 	Draft Genome Sequence of a Novel Bacterial Strain, LSJC7, Belonging to the Family Enterobacteriaceae with Dual Resistance to Arsenic and Tetracycline.	J. Bacteriol.	2012	194		7005-7006			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. 		
@D	Su, L.//Wang, T.//Zhou, L.//Wu, C.//Guo, Y.//Chang, D.//Liu, Y.//Jiang, X.//Yin, S.//Liu, C. 	Genome Sequence of Bacillus cereus Strain LCT-BC235, Carried by the Shenzhou VIII Spacecraft.	Genome Announcements	2014	2		e00665-13			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. 		
@D	Su, L.//Zhou, T.//Zhou, L.//Fang, X.//Li, T.//Wang, J.//Guo, Y.//Chang, D.//Wang, Y.//Li, D.//Liu, C. 	Draft Genome Sequence of Bacillus cereus Strain LCT-BC244.	J. Bacteriol.	2012	194		3549			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. 		
@D	Su, P.//Im, H.//Hsieh, H.//Kanga, S.//Dunn, N.W. 	LlaFI, a type III restriction and modification system in Lactococcus lactis.	Appl. Environ. Microbiol.	1999	65		686-693			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. 		
@D	Su, P.//Ng, A.//Kennelly, V.//Costello, M.//Harvey, M.//Dunn, N. 	Additive effects of two different plasmid-linked restriction and modification systems in Lactococcus.	Biotechnol. Lett.	1998	20		515-518			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. 		
@D	Su, T.-J.//Connolly, B.A.//Darlington, C.//Mallin, R.//Dryden, D.T.F. 	Unusual 2-aminopurine fluorescence from a complex of DNA and the EcoKI methyltransferase.	Nucleic Acids Res.	2004	32		2223-2230			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. 		
@D	Su, T.-J.//Tock, M.R.//Egelhaaf, S.U.//Poon, W.C.K.//Dryden, D.T.F. 	DNA bending by M.EcoKI methyltransferase is coupled to nucleotide flipping.	Nucleic Acids Res.	2005	33		3235-3244			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. 		
@D	Su, X.//Cao, G.//Kuang, D.//Zhang, J.//Chen, Y.//Allard, M.//Brown, E.//Shi, X.//Meng, J.//Xu, X. 	Draft Genome Sequences of Three Listeria monocytogenes Isolates from Foods in China.	Genome Announcements	2017	5		e00220-17			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. 		
@D	Su, Y.C.//Horhold, F.//Singh, B.//Riesbeck, K. 	Complete Genome Sequence of Encapsulated Haemophilus influenzae Type f KR494, an  Invasive Isolate That Caused Necrotizing Myositis.	Genome Announcements	2013	1		e00470-13			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. 		
@D	Suarez, N.E.//Saavedra, L.//Slozilova, I.//Bonacina, J.//Demnerova, K.//Sesma, F. 	Draft Genome Sequence of Enterococcus faecium Strain CRL 1879, Isolated from a Northwestern Argentinian Artisanal Cheese.	Genome Announcements	2013	1		e00514-13			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. 		
@D	Suarez, V.//Zago, M.//Giraffa, G.//Reinheimer, J.//Quiberoni, A. 	Evidence for the presence of restriction/modification systems in Lactobacillus delbrueckii.	J. Dairy Res.	2009	76		433-440			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. 		
@D	Suarez, V.B.//Maciel, N.//Guglielmotti, D.//Zago, M.//Giraffa, G.//Reinheimer, J. 	Phage-resistance linked to cell heterogeneity in the commercial strain Lactobacillus delbrueckii subsp lactis Ab1.	Int. J. Food Microbiol.	2008	128		401-405			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. 		
@D	Suarez-Suarez, L.Y.//Brunet-Galmes, I.//Pina-Villalonga, J.M.//Christie-Oleza, J.A.//Pena, A.//Bennasar, A.//Armengaud, J.//Nogales, B.//Bosch, R. 	Draft Genome Sequence of Citreicella aestuarii Strain 357, a Member of the Roseobacter Clade Isolated without Xenobiotic Pressure from a Petroleum-Polluted    Beach.	J. Bacteriol.	2012	194		5464-5465			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. 		
@D	Subach, F.//Kirsanova, O.//Liquier, J.//Gromova, E.S. 	Resolution of the EcoRII restriction endonuclease-DNA complex structure in solution using fluorescence spectroscopy.	Biophys. Chem.	2008	138		107-114			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. 		
@D	Subach, F.V.//Liquier, J.//Gromova, E.S. 	Investigation of restriction endonuclease EcoRII complex with DNA in solution by FTIR spectroscopy.	Russ. J. Gen. Chem.	2008	78		1103-1109			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. 		
@D	Subach, F.V.//Muller, S.//Tashlitsky, V.N.//Petrauskene, O.V.//Gromova, E.S. 	The preparation of DNA duplexes containing internucleotide phosphorothioate groups in various positions of the recognition site for the EcoRII restriction endonuclease.	Bioorg. Khim.	2003	29		623-631			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. 		
@D	Subach, O.M.//Baskunov, V.B.//Darii, M.V.//Maltseva, D.V.//Alexandrov, D.A.//Kirsanova, O.V.//Kolbanovskiy, A.//Kolbanovskiy, M.//Johnson, F.//Bonala, R.//Geacintov, N.E.//Gromova, E.S. 	Impact of benzo[a] pyrene-2 '-deoxyguanosine lesions on methylation of DNA by SssI and HhaI DNA methyltransferases.	Biochemistry	2006	45		6142-6159			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. 		
@D	Subach, O.M.//Khoroshaev, A.V.//Gerasimov, D.N.//Baskunov, V.B.//Shchyolkina, A.K.//Gromova, E.S. 	2-Pyrimidinone as a probe for studying the EcoRII DNA methyltransferase-substrate interaction.	Eur. J. Biochem.	2004	271		2391-2399			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. 		
@D	Subach, O.M.//Maltseva, D.V.//Shastry, A.//Kolbanovskiy, A.//Klimasauskas, S.//Geacintov, N.E.//Gromova, E.S. 	The stereochemistry of benzo(a)pyrene-2'-deoxyguanosine adducts affects DNA methylation by SssI and HhaI DNA methyltransferases.	FEBS J.	2007	274		2121-2134			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. 		
@D	Subhadra, B.//Krier, J.//Hofstee, K.//Monsul, N.//Berkes, E. 	Draft Whole-Genome Sequence of Lactobacillus fermentum LfQi6, Derived from the Human Microbiome.	Genome Announcements	2015	3		e00423-15			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. 		
@D	Subramaniam, R.//Wang, Y.//Mathews, C.K.//Santi, D.V. 	On the inhibition of deoxycytidylate hydroxymethylase by 5-fluoro-2'-deoxycytidine 5'-monophosphate .	Arch. Biochem. Biophys.	1989	275		11-15			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. 		
@D	Suchan, D.M.//Steve, J.J.//Pierce, A.J.//Olshefsky, S.C.//Kirzinger, M.W.B.//Perry, B.J.//Cameron, A.D.S.//Yost, C.K. 	Draft Whole-Genome Sequence of Deinococcus sp. UR1, a Putative Novel Species Isolated from an External Stainless Steel Surface in the Canadian Prairies.	Genome Announcements	2018	6		e01407-17			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%. 		
@D	Suchkov, S.V.//Lopatina, N.G.//Arutyunyan, E.E.//Nikolskaya, I.I.//Debov, S.S. 	Study of the conditions of activation and stabilization of Shigella sonnei 47 DNA methylases in the process of fractionation, purification, and during storage.	Biokhimiia	1986	51		1369-1376			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. 		
@D	Suchkov, S.V.//Nikolskaya, I.I.//Debov, S.S. 	Isoelectrofocusing of DNA-methylases from Shigella sonnei 47.	Vopr. Med. Khim.	1983	29		117-122			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. 		
@D	Suchkov, S.V.//Nikolskaya, I.I.//Debov, S.S. 	Fractionation and purification of DNA-methylases of Shigella sonnei 47 cells.	Biokhimiia	1985	50		1797-1804			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. 		
@D	Suck, D. 	Flip out and modify.	Curr. Biol.	1994	4		252-255			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. 		
@D	Sudina, A.//Volkov, E.//Oretskaya, T.//Naryshkin, N.//Ivanovskaya, M.//Kubareva, E. 	Detection of glycosylase, endonuclease and methyltransferase enzyme activities using immobilized oligonucleotides.	Life	2004	56		139-143			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. 		
@D	Sudina, A.E.//Zatsepin, T.S.//Pingoud, V.//Pingoud, A.//Oretskaya, T.S.//Kubareva, E.A. 	Affinity modification of the restriction endonuclease SsoII by 2'-aldehyde-containing double stranded DNAs.	Biochemistry	2005	70		1137-1144			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. 		
@D	Suen, G. et al. 	Complete Genome of the Cellulolytic Ruminal Bacterium Ruminococcus albus 7.	J. Bacteriol.	2011	193		5574-5575			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. 		
@D	Suenaga, H.//Yamazoe, A.//Hosoyama, A.//Kimura, N.//Hirose, J.//Watanabe, T.//Fujihara, H.//Futagami, T.//Goto, M.//Furukawa, K. 	Draft Genome Sequence of the Polychlorinated Biphenyl-Degrading Bacterium Cupriavidus basilensis KF708 (NBRC 110671) Isolated from Biphenyl-Contaminated  Soil.	Genome Announcements	2015	3		e00143-15			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. 		
@D	Suenaga, H.//Yamazoe, A.//Hosoyama, A.//Kimura, N.//Hirose, J.//Watanabe, T.//Fujihara, H.//Futagami, T.//Goto, M.//Furukawa, K. 	Draft Genome Sequence of the Polychlorinated Biphenyl-Degrading Bacterium Pseudomonas putida KF703 (NBRC 110666) Isolated from Biphenyl-Contaminated Soil.	Genome Announcements	2015	3		e00142-15			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. 		
@D	Suenaga, H.//Yamazoe, A.//Hosoyama, A.//Kimura, N.//Hirose, J.//Watanabe, T.//Fujihara, H.//Futagami, T.//Goto, M.//Furukawa, K. 	Complete Genome Sequence of the Polychlorinated Biphenyl-Degrading Bacterium Pseudomonas putida KF715 (NBRC 110667) Isolated from Biphenyl-Contaminated Soil.	Genome Announcements	2017	5		e01624-16			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. 		
@D	Suenaga, T.//Aoyagi, T.//Hosomi, M.//Hori, T.//Terada, A. 	Draft Genome Sequence of Azospira sp. Strain I13, a Nitrous Oxide-Reducing Bacterium Harboring Clade II Type nosZ.	Genome Announcements	2018	6		e00414-18			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. 		
@D	Suerbaum, S. et al. 	The complete genome sequence of the carcinogenic bacterium Helicobacter hepaticus.	Proc. Natl. Acad. Sci. U. S. A.	2003	100		7901-7906			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. 		
@D	Suetake, I.//Hayata, D.//Tajima, S. 	The amino-terminus of mouse DNA methyltransferase 1 forms an independent domain and binds to DNA with the sequence involving PCNA binding motif.	J. Biochem. (Tokyo)	2006	140		763-776			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. 		
@D	Suetake, I.//Mishima, Y.//Kimura, H.//Lee, Y.-H.//Goto, Y.//Takeshima, H.//Ikegami, T.//Tajima, S. 	Characterization of DNA-binding activity in the N-terminal domain of the DNA methyltransferase Dnmt3a.	Biochem. J.	2011	437		141-148					
@D	Suetake, I.//Miyazaki, J.//Murakami, C.//Takeshima, H.//Tajima, S. 	Distinct enzymatic properties of recombinant mouse DNA methyltransferases Dnmt3a and Dnmt3b.	J. Biochem. (Tokyo)	2003	133		737-744			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. 		
@D	Suetake, I.//Shi, L.H.//Watanabe, D.//Nakamura, M.//Tajima, S. 	Proliferation stage-dependent expression of DNA methyltransferase (Dnmt1) in mouse small intestine.	Cell Struct. Funct.	2001	26		79-86			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. 		
@D	Suetake, I.//Shinozaki, F.//Miyagawa, J.//Takeshima, H.//Tajima, S. 	DNMT3L stimulates the DNA methylation activity of Dnmt3a and Dnmt3b through a direct interaction.	J. Biol. Chem.	2004	279		27816-27823			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. 		
@D	Sugawara, M.//Hosoyama, A.//Yamazoe, A.//Morikawa, M. 	Draft Genome Sequence of Acinetobacter calcoaceticus Strain P23, a Plant Growth-Promoting Bacterium of Duckweed.	Genome Announcements	2015	3		e00026-15			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. 		
@D	Sugawara, M.//Tsukui, T.//Kaneko, T.//Ohtsubo, Y.//Sato, S.//Nagata, Y.//Tsuda, M.//Mitsui, H.//Minamisawa, K. 	Complete Genome Sequence of Bradyrhizobium diazoefficiens USDA 122, a Nitrogen-Fixing Soybean Symbiont.	Genome Announcements	2017	5		e01743-16			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. 		
@D	Sugawara, Y.//Akeda, Y.//Sakamoto, N.//Takeuchi, D.//Motooka, D.//Nakamura, S.//Hagiya, H.//Yamamoto, N.//Nishi, I.//Yoshida, H.//Okada, K.//Zin, K.N.//Aye, M.M.//Tomono, K.//Hamada, S. 	Genetic characterization of blaNDM plasmids in carbapenem-resistant Escherichia coli isolated in Myanmar.	PLoS ONE	2017	12		e184720			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. 		
@D	Sugden, B.//DeTroy, B.//Roberts, R.J.//Sambrook, J. 	Agarose slab-gel electrophoresis equipment.	Anal. Biochem.	1975	68		36-46			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. 		
@D	Sugimoto, Y.//Maruyama, F.//Suzuki, S. 	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.	Genome Announcements	2018	6		e00297-18			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. 		
@D	Sugisaki, H. 	Recognition sequence of a restriction endonuclease from Haemophilus gallinarum.	Gene	1978	3		17-28			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. 		
@D	Sugisaki, H. 	Nucleotide sequence of the gene of HgaI restriction endonuclease.	Bull. Inst. Chem. Res. Kyoto Univ.	1993	71		338-342					
@D	Sugisaki, H.//Kanazawa, S. 	New restriction endonucleases from Flavobacterium okeanokoites (FokI) and Micrococcus luteus (MluI).	Gene	1981	16		73-78			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. 		
@D	Sugisaki, H.//Kita, K.//Takanami, M. 	The FokI restriction-modification system.  II. Presence of two domains in FokI methylase responsible for modification of different DNA strands.	J. Biol. Chem.	1989	264		5757-5761			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. 		
@D	Sugisaki, H.//Maekawa, Y.//Kanazawa, S.//Takanami, M. 	New restriction endonucleases from Acetobacter aceti and Bacillus aneurinolyticus.	Nucleic Acids Res.	1982	10		5747-5752			*
 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')
 
 		
@D	Sugisaki, H.//Maekawa, Y.//Kanazawa, S.//Takanami, M. 	Screening of type II restriction endonucleases.  I.  Isolation and characterization of enzymes from fifteen bacterial strains.	Bull. Inst. Chem. Res. Kyoto Univ.	1982	60		328-335			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. 		
@D	Sugisaki, H.//Takanami, M. 	DNA Sequence restricted by restriction endonuclease AP from Haemophilus aphirophilus.	Nature New Biol.	1973	246		138-140			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. 		
@D	Sugisaki, H.//Yamamoto, K.//Takanami, M. 	The HgaI restriction-modification system contains two cytosine methylase genes responsible for modification of different DNA strands.	J. Biol. Chem.	1991	266		13952-13957			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. 		
@D	Sugiura, H.//Monno, S.//Yamashita, H.//Kato, Y.//Imajoh, M. 	Draft Genome Sequences of Two Edwardsiella piscicida Strains, JF1307 and JF1411,  Isolated from Diseased Olive Flounder (Paralichthys olivaceus) Cultured in Japan.	Genome Announcements	2018	6		e00600-18			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. 		
@D	Suhaili, Z.//Lean, S.S.//Yahya, A.//Mohd, D.M.N.//Ali, A.M.//Yeo, C.C. 	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.	Genome Announcements	2014	2		e00271-14			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. 		
@D	Sui, Z.//Zhou, W.//Yao, K.//Liu, L.//Zhang, G.//Yang, Y.//Feng, J. 	Complete Genome Sequence of Streptococcus pneumoniae Strain A026, a Clinical Multidrug-Resistant Isolate Carrying Tn2010.	Genome Announcements	2013	1		e01034-13			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. 		
@D	Sukackaite, R.//Grazulis, S.//Bochtler, M.//Siksnys, V. 	The recognition domain of the BpuJI restriction endonuclease in complex with cognate DNA at 1.3-A resolution.	J. Mol. Biol.	2008	378		1084-1093			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. 		
@D	Sukackaite, R.//Grazulis, S.//Tamulaitis, G.//Siksnys, V. 	The recognition domain of the methyl-specific endonuclease McrBC flips out 5-methylcytosine.	Nucleic Acids Res.	2012	40		7552-7562			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. 		
@D	Sukackaite, R.//Lagunavicius, A.//Stankevicius, K.//Urbanke, C.//Venclovas, C.//Siksnys, V. 	Restriction endonuclease BpuJI specific for the 5'-CCCGT sequence is related to the archaeal Holliday junction resolvase family.	Nucleic Acids Res.	2007	35		2377-2389			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. 		
@D	Sulcius, S.//Alzbutas, G.//Kvederaviciute, K.//Koreiviene, J.//Zakrys, L.//Lubys, A.//Paskauskas, R. 	Draft Genome Sequence of the Cyanobacterium Aphanizomenon flos-aquae Strain 2012/KM1/D3, Isolated from the Curonian Lagoon (Baltic Sea).	Genome Announcements	2015	3		e01392-14			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. 		
@D	Suleimanova, A.D.//Toymentseva, A.A.//Boulygina, E.A.//Kazakov, S.V.//Mardanova, A.M.//Balaban, N.P.//Sharipova, M.R. 	High-quality draft genome sequence of a new phytase-producing microorganism Pantoea sp. 3.5.1.	Standards in Genomic Sciences	2015	10		95			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. 		
@D	Sullivan, J.T.//Trzebiatowski, J.R.//Cruickshank, R.W.//Gouzy, J.//Brown, S.D.//Elliot, R.M.//Fleetwood, D.J.//McCallum, N.G.//Rossbach, U.//Stuart, G.S.//Weaver, J.E.//Webby, R.J.//de Bruijn, F.J.//Ronson, C.W. 	Comparative sequence analysis of the symbiosis island of Mesorhizobium loti strain R7A.	J. Bacteriol.	2002	184		3086-3095			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. 		
@D	Sullivan, K.M.//Macdonald, H.J.//Saunders, J.R. 	Characterization of DNA restriction and modification activities in Neisseria species.	FEMS Microbiol. Lett.	1987	44		389-393			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] 		
@D	Sullivan, K.M.//Saunders, J.R. 	Sequence analysis of the NgoPII methyltransferase gene from Neisseria gonorrhoeae P9:  homologies with other enzymes recognizing the sequence 5'-GGCC-3'.	Nucleic Acids Res.	1988	16		4369-4387			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. 		
@D	Sullivan, K.M.//Saunders, J.R. 	Nucleotide sequence and genetic organization of the NgoPII restriction-modification system of Neisseria gonorrhoeae.	Mol. Gen. Genet.	1989	216		380-387			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. 		
@A	Sullivan, K.M.//Saunders, J.R. 		Determination of the endonuclease and methylase content of Neisseria gonorrhoeae strain P9 and the cloning therefrom of two functional methylase genes.			Poolman, J.T. 		Gonococci and Meningococci				Dordrecht, The Netherlands	Kluwer Academic Publishers	1988		0		329-334									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. 		
@D	Sullivan, M.B. et al. 	Genomic analysis of oceanic cyanobacterial myoviruses compared with T4-like myoviruses from diverse hosts and environments.	Environ. Microbiol.	2010	12		3035-3056			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. 		
@D	Sullivan, M.B.//Coleman, M.L.//Weigele, P.//Rohwer, F.//Chisholm, S.W. 	Three prochlorococcus cyanophage genomes: signature features and ecological interpretations.	PLoS Biology	2005	3		E144			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. 		
@D	Sullivan, M.J.//Forde, B.M.//Prince, D.W.//Ipe, D.S.//Ben Zakour, N.L.//Davies, M.R.//Dougan, G.//Beatson, S.A.//Ulett, G.C. 	Complete Genome Sequence of Serotype III Streptococcus agalactiae Sequence Type 17 Strain 874391.	Genome Announcements	2017	5		e01107-17			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. 		
@D	Sullivan, N.L.//Septer, A.N.//Fields, A.T.//Wenren, L.M.//Gibbs, K.A. 	The Complete Genome Sequence of Proteus mirabilis Strain BB2000 Reveals Differences from the P. mirabilis Reference Strain.	Genome Announcements	2013	1		e00024-13			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. 		
@D	Sumaoka, J.//Komiyama, M. 	Super restriction enzymes for future biotechnology.	Kino Zairyo	1995	15		19-25					
@D	Sumby, P.//Porcella, S.F.//Madrigal, A.G.//Barbian, K.D.//Virtaneva, K.//Ricklefs, S.M.//Sturdevant, D.E.//Graham, M.R.//Vuopio-Varkila, J.//Hoe, N.P.//Musser, J.M. 	Evolutionary origin and emergence of a highly successful clone of serotype M1 group A Streptococcus involved multiple horizontal gene transfer   events.	J. Infect. Dis.	2005	192		771-782			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. 		
@D	Sumby, P.//Smith, M.C. 	Phase variation in the phage growth limitation system of Streptomyces coelicolor  A3(2).	J. Bacteriol.	2003	185		4558-4563			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. 		
@D	Sumby, P.//Smith, M.C. 	Genetics of the phage growth limitation (Pgl) system of Streptomyces coelicolor A3(2).	Mol. Microbiol.	2002	44		489-500			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. 		
@D	Sumegi, J.//Breedveld, D.//Hosenlopp, P.//Chambon, P. 	A rapid procedure for purification of EcoRI endonuclease.	Biochem. Biophys. Res. Commun.	1977	1		78-85			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. 		
@D	Summer, E.J.//Gonzalez, C.F.//Bomer, M.//Carlile, T.//Embry, A.//Kucherka, A.M.//Lee, J.//Mebane, L.//Morrison, W.C.//Mark, L.//King, M.D.//LiPuma, J.J.//Vidaver, A.K.//Young, R. 	Divergence and mosaicism among virulent soil phages of the Burkholderia cepacia complex.	J. Bacteriol.	2006	188		255-268			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. 		
@D	Summers, M.F.//Powell, C.//Egan, W.//Byrd, R.A.//Wilson, W.D.//Zon, G. 	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.	Nucleic Acids Res.	1986	14		7421-7436			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. 		
@D	Sumrall, E.//Klumpp, J.//Shen, Y.//Loessner, M.J. 	Genome Sequences of Five Nonvirulent Listeria monocytogenes Serovar 4 Strains.	Genome Announcements	2016	4		e00179-16			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. 		
@D	Sun, D.//Cheng, S.//Wang, A.//Huang, F.//Liu, W.//Xia, X. 	Complete Genome Sequence of Geobacter anodireducens SD-1T, a Salt-Tolerant Exoelectrogenic Microbe in Bioelectrochemical Systems.	Genome Announcements	2016	4		e00415-16			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). 		
@D	Sun, D.//Zhuo, T.//Hu, X.//Fan, X.//Zou, H. 	Identification of a Pseudomonas putida as biocontrol agent for tomato bacterial wilt disease.	Biol. Control	2017	114		45-50			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. 		
@D	Sun, D.K.//Yoo, O.J. 	Purification and characterization of a restriction endonuclease ZanI from Zymomonas anaerobia.	Korean Biochem. J.	1988	21		419-422			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. 		
@D	Sun, F.//Zhou, D.//Sun, Q.//Luo, W.//Tong, Y.//Zhang, D.//Wang, Q.//Feng, W.//Chen, W.//Fan, Y.//Xia, P. 	Genetic characterization of two fully sequenced multi-drug resistant plasmids pP10164-2 and pP10164-3 from Leclercia adecarboxylata.	Sci. Rep.	2016	6		33982			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. 		
@D	Sun, F.//Zhou, D.//Wang, Q.//Feng, J.//Feng, W.//Luo, W.//Liu, Y.//Qiu, X.//Yin, Z.//Xia, P. 	Genetic characterization of a novel blaDIM-2-carrying megaplasmid p12969-DIM from clinical Pseudomonas putida.	J. Antimicrob. Chemother.	2016	71		909-912			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. 		
@D	Sun, G.//Wang, L.//Bao, C.//Li, T.//Ma, L.//Chen, L. 	Complete Genome Sequence of Elizabethkingia meningoseptica, Isolated from a T-Cell Non-Hodgkin's Lymphoma Patient.	Genome Announcements	2015	3		e00673-15			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. 		
@D	Sun, H. et al. 	Complete genome sequence of Desulfarculus baarsii type strain (2st14).	Standards in Genomic Sciences	2010	3		276-284			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. 		
@D	Sun, H. et al. 	Complete genome sequence of Nocardiopsis dassonvillei type strain (IMRU 509).	Standards in Genomic Sciences	2010	3		325-336			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. 		
@D	Sun, J.//He, Z.//Nechushtai, R.//Chitnis, P.R. 	Molecular cloning of the PsaA and PsaB genes for the core proteins of photosystem I from the thermophilic cyanobacterium Mastigocladus Iaminosus (Accession No. AF038558).	Plant Physiol.	1998	116		1192					
@D	Sun, J.//Weinstein, H. 	The restriction enzyme BamHI is poised for sliding along DNA in a model of the nonspecific complex.	Biophys. J.	2002	82		463a			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. 		
@D	Sun, J.Q.//Xu, L.//Wang, L.J.//Wu, X.L. 	Draft genome sequence of a rhodococcus strain isolated from tannery wastewater treatment sludge.	Genome Announcements	2015	3		e01463-14			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. 		
@D	Sun, K.//Jiao, X.D.//Zhang, M.//Sun, L. 	DNA adenine methylase is involved in the pathogenesis of Edwardsiella tarda.	Vet. Microbiol.	2010	141		149-154			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. 		
@D	Sun, L. 	Kinetic studies on cleavage of adenovirus type 5 DNA by restriction endonuclease EcoRI.	Xibei Daxue Xuebao	1989	19		71-76			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. 		
@D	Sun, L.//Lu, Z.//Li, J.//Sun, F.//Huang, R. 	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.	Mol. Genet. Genomics	2018	293		265-276			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. 		
@D	Sun, L.//Schnurer, A. 	Draft Genome Sequence of the Cellulolytic Strain Clostridium sp. Bc-iso-3 Isolated from an Industrial-Scale Anaerobic Digester.	Genome Announcements	2016	4		e01188-16			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. 		
@D	Sun, L.//Wang, Y.//Yu, C.//Zhao, Y.//Gan, Y. 	Genome Sequence of Clostridium tunisiense TJ, Isolated from Drain Sediment from a Pesticide Factory.	J. Bacteriol.	2012	194		6950-6951			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. 		
@D	Sun, L.//Yin, J. 	Initial studies on chemical modification of several amino acid residues of the restriction endonuclease XhoI.	Xibei Daxue Xuebao	1990	20		65-71			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. 		
@D	Sun, L.-K.//Hong, R. 	The influence of DNA conformation and base composition flanking recognition sites on the cleavage rate of restriction.	Acta Biochim. Biophys. Sin.	1989	21		456-460			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. 		
@D	Sun, L.-K.//Ruan, H. 	Kinetics and thermodynamics of specific and non-specific interactions between BglI restriction endonuclease and pBR322-DNA.	Chinese Biochem. J.	1990	6		334-338			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. 		
@D	Sun, L.-K.//Wang, X.//Hong, R. 	Calculation of cleavage rates of restriction endonuclease on circular DNA.	Acta Biophys. Sinica	1988	4		64-66			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. 		
@D	Sun, P.//Cui, J.//Jia, X.//Wang, W. 	Complete Genome Sequence of Bacillus velezensis L-1, Which Has Antagonistic Activity against Pear Diseases.	Genome Announcements	2017	5		e01271-17			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. 		
@D	Sun, P.//Luo, H.//Zhang, X.//Xu, J.//Guo, Y.//He, S. 	Whole-Genome Sequence of Mycoplasma bovis Strain Ningxia-1.	Genome Announcements	2018	6		e01367-17			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. 		
@D	Sun, Q.//Lan, R.//Wang, Y.//Wang, J.//Wang, Y.//Li, P.//Du, P.//Xu, J. 	Isolation and genomic characterization of SfI, a serotype-converting bacteriophage of Shigella flexneri.	BMC Microbiol.	2013	13		39			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. 		
@D	Sun, S.//Yang, X.//Yuan, Y.//Dai, X.//Yan, Y.//Cao, H.//Luo, T.//Guo, R.//Wang, X.//Song, Y.//Yang, R.//Zhang, Y.//Cui, Y. 	Draft Genome Sequence of Yersinia pestis Strain 2501, an Isolate from the Great Gerbil Plague Focus in Xinjiang, China.	J. Bacteriol.	2012	194		5447-5448			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. 		
@D	Sun, X.//Meng, J.//Liu, S.//Zhang, H.//Wang, L. 	Draft Genome Sequence of Streptomyces sp. F-3.	Genome Announcements	2016	4		e00780-16			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. 		
@D	Sun, X.//Yang, Y.//Zhang, N.//Shen, Y.//Ni, J. 	Draft Genome Sequence of Dysgonomonas macrotermitis Strain JCM 19375T, Isolated from the Gut of a Termite.	Genome Announcements	2015	3		e00963-15			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. 		
@D	Sun, Y.//Li, X.//Wang, G.//Wang, Y.//Jiang, Y.//Liu, Y.//Yu, Z.//Qin, L. 	Genome Sequence of Enterococcus pernyi, a Pathogenic Bacterium for the Chinese Oak Silkworm, Antheraea pernyi.	Genome Announcements	2016	4		e01764-15			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. 		
@D	Sun, Y.//Song, Y.//Song, H.//Liu, J.//Wang, P.//Qiu, S.//Chen, S.//Zhu, L.//Ji, X.//Wang, Z.//Liu, N.//Xia, L.//Chen, W.//Feng, S. 	Complete Genome Sequence of an Acinetobacter Strain Harboring the NDM-1 Gene.	Genome Announcements	2013	1		e00023-12			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. 		
@D	Sun, Y.//Wang, K.//Caceres-Moreno, C.//Jia, W.//Chen, A.//Zhang, H.//Liu, R.//Macho, A.P. 	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.	Standards in Genomic Sciences	2017	12		29			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. 		
@D	Sun, Z. et al. 	Expanding the biotechnology potential of lactobacilli through comparative genomics of 213 strains and associated genera.	Nat. Commun.	2015	6		8322			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. 		
@D	Sun, Z.//Chen, X.//Wang, J.//Gao, P.//Zhou, Z.//Ren, Y.//Sun, T.//Wang, L.//Meng, H.//Chen, W.//Zhang, H. 	Complete genome sequence of probiotic Bifidobacterium animalis subsp. lactis strain V9.	J. Bacteriol.	2010	192		4080-4081			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. 		
@D	Sun, Z.//Chen, X.//Wang, J.//Zhao, W.//Shao, Y.//Guo, Z.//Zhang, X.//Zhou, Z.//Sun, T.//Wang, L.//Meng, H.//Zhang, H.//Chen, W. 	Complete genome sequence of Lactobacillus delbrueckii subsp. bulgaricus strain ND02.	J. Bacteriol.	2011	193		3426-3427			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. 		
@D	Sun, Z.//Chen, X.//Wang, J.//Zhao, W.//Shao, Y.//Wu, L.//Zhou, Z.//Sun, T.//Wang, L.//Meng, H.//Zhang, H.//Chen, W. 	Complete genome sequence of Streptococcus thermophilus strain ND03.	J. Bacteriol.	2010	193		793-794			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. 		
@D	Sun, Z.//Hsiang, T.//Zhou, Y.//Zhou, J. 	Draft Genome Sequence of Bacillus amyloliquefaciens XK-4-1, a Plant Growth-Promoting Endophyte with Antifungal Activity.	Genome Announcements	2015	3		e01306-15			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. 		
@D	Sun, Z.Y.//Terragni, J.//Borgaro, J.G.//Liu, Y.W.//Yu, L.//Guan, S.X.//Wang, H.//Sun, D.P.//Cheng, X.D.//Zhu, Z.Y.//Pradhan, S.//Zheng, Y. 	High-Resolution Enzymatic Mapping of Genomic 5-Hydroxymethylcytosine in Mouse Embryonic Stem Cells.	Cell Rep.	2013	3		567-576			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. 		
@D	Sung, J.S.//Chun, J.//Choi, S.//Park, W. 	Genome Sequence of the Halotolerant Staphylococcus sp. Strain OJ82, Isolated from Korean Traditional Salt-Fermented Seafood.	J. Bacteriol.	2012	194		6353-6354			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. 		
@D	Sung, K.//Khan, S.//Marasa, B.//Min, S.//Kweon, O.//Mohamed, N.//Cerniglia, C. 	Draft Genome Sequence of a vanA-Type Vancomycin-Resistant Reference Strain, Enterococcus faecium ATCC 51559.	Genome Announcements	2015	3		e01053-15			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. 		
@D	Sung, K.//Khan, S.//Marasa, B.//Min, S.//Kweon, O.//Nawaz, M.//Cerniglia, C. 	Genomic Sequence of a Clinical Vancomycin-Resistant Reference Strain, Enterococcus faecalis ATCC 51299.	Genome Announcements	2015	3		e01495-15			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. 		
@D	Suraiya, S.//Semail, N.//Ismail, M.F.//Abdullah, J.M. 	Complete Genome Sequence of Mycobacterium tuberculosis Clinical Isolate Spoligotype SIT745/EAI1-MYS.	Genome Announcements	2016	4		e00323-16			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. 		
@D	Surani, M.A. 	Imprinting and the initiation of gene silencing in the germ line.	Cell	1998	93		309-312			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. 		
@D	Surby, M.A. 	Facilitated diffusion of the EcoRI DNA methyltransferase under both catalytic and noncatalytic conditions and the potential of Z DNA disrupt protein translocation on DNA.	Diss. Abstr.	1997	57		5631B-5632B			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. 		
@D	Surby, M.A.//Reich, N.O. 	The role of nonspecific DNA in the site location kinetics of the EcoRI DNA methyltransferase.	FASEB J.	1992	6		A356			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). 		
@D	Surby, M.A.//Reich, N.O. 	The role of nonspecific DNA in the site-location kinetics of the EcoRI DNA methyltransferase.	Biochemistry	1992	31		2208			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. 		
@D	Surby, M.A.//Reich, N.O. 	Facilitated diffusion of the EcoRI DNA methyltransferase is described by a novel mechanism.	Biochemistry	1996	35		2209-2217			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. 		
@D	Surby, M.A.//Reich, N.O. 	Contribution of facilitated diffusion and processive catalysis to enzyme efficiency: Implications for the EcoRI restriction-modification system.	Biochemistry	1996	35		2201-2208			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. 		
@D	Surby, M.A.//Reich, N.O. 	The role of nonspecific DNA in the site-location kinetics of the EcoRI DNA methyltransferase.	ACS Abstracts	1992	203		110-BIOL			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. 		
@D	Suri, B.//Bickle, T.A. 	EcoA:  The first member of a new family of Type I restriction modification systems - Gene organization and enzymatic activities.	J. Mol. Biol.	1985	186		77-85			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. 		
@D	Suri, B.//Nagaraja, V.//Bickle, T.A. 	Bacterial DNA modification.	Curr. Top. Microbiol. Immunol.	1984	108		1-9			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. 		
@D	Suri, B.//Shepherd, J.C.W.//Bickle, T.A. 	The EcoA restriction and modification system of Escherichia coli 15T-: enzyme structure and DNA recognition sequence.	EMBO J.	1984	3		575-579			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. 		
@D	Suryaletha, K.//Narendrakumar, L.//John, J.//Reghunathan, D.//Prasannakumar, M.//Thomas, S. 	Genomic Insights into Biofilm-Forming Enterococcus faecalis SK460 Isolated from a Chronic Diabetic Ulcer Patient.	Genome Announcements	2018	6		e01463-17			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. 		
@D	Suryavanshi, M.V.//Paul, D.//Doijad, S.P.//Bhute, S.S.//Hingamire, T.B.//Gune, R.P.//Shouche, Y.S. 	Draft genome sequence of Lactobacillus plantarum strains E2C2 and E2C5 isolated from human stool culture.	Standards in Genomic Sciences	2017	12		15			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. 		
@D	Susanti, D. et al. 	Complete Genome Sequence of Desulfurococcus fermentans, a Hyperthermophilic Cellulolytic Crenarchaeon Isolated from a Freshwater Hot Spring in Kamchatka,  Russia.	J. Bacteriol.	2012	194		5703-5704			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. 		
@D	Susanti, D.//Johnson, E.F.//Lapidus, A.//Han, J.//Reddy, T.B.//Mukherjee, S.//Pillay, M.//Perevalova, A.A.//Ivanova, N.N.//Woyke, T.//Kyrpides, N.C.//Mukhopadhyay, B. 	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.	Genome Announcements	2017	5		e00078-17			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. 		
@D	Susanti, D.//Johnson, E.F.//Lapidus, A.//Han, J.//Reddy, T.B.//Pilay, M.//Ivanova, N.N.//Markowitz, V.M.//Woyke, T.//Kyrpides, N.C.//Mukhopadhyay, B. 	Permanent draft genome sequence of Desulfurococcus mobilis type strain DSM 2161,  a thermoacidophilic sulfur-reducing crenarchaeon isolated from acidic hot springs  of Hveravellir, Iceland.	Standards in Genomic Sciences	2016	11		3			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. 		
@D	Sussenbach, J.S.//Monfoort, C.H.//Schiphof, R.//Stobberingh, E.E. 	A restriction endonuclease from Staphylococcus aureus.	Nucleic Acids Res.	1976	3		3193-3202			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. 		
@D	Sussenbach, J.S.//Steenbergh, P.H.//Rost, J.A.//van Leeuwen, W.J.//van Embden, J.D.A. 	A second site-specific restriction endonuclease from Staphylococcus aureus.	Nucleic Acids Res.	1978	5		1153-1163			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. 		
@D	Sussman, D.//Chadsey, M.//Fauce, S.//Engel, A.//Bruett, A.//Monnat, R.//Stoddard, B.L.//Seligman, L.M. 	Isolation and characterization of new homing endonuclease specificities at individual target site positions.	J. Mol. Biol.	2004	342		31-41			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. 		
@D	Sutcliffe, B.//Midgley, D.J.//Rosewarne, C.P.//Greenfield, P.//Li, D. 	Draft Genome Sequence of Thermotoga maritima A7A Reconstructed from Metagenomic Sequencing Analysis of a Hydrocarbon Reservoir in the Bass Strait, Australia.	Genome Announcements	2013	1		e00688-13			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. 		
@D	Sutcliffe, J.G.//Church, G.M. 	The cleavage site of the restriction endonuclease AvaII.	Nucleic Acids Res.	1978	5		2313-2319			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. 		
@D	Sutherland, E.//Coe, L.//Raleigh, E.A. 	McrBC:  a multisubunit GTP-dependent restriction endonuclease.	J. Mol. Biol.	1992	225		327-358			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. 		
@D	Sutton, J.M.//Baesman, S.M.//Fierst, J.L.//Poret-Peterson, A.T.//Oremland, R.S.//Dunlap, D.S.//Akob, D.M. 	Complete Genome Sequence of the Acetylene-Fermenting Pelobacter sp. Strain SFB93.	Genome Announcements	2017	5		e01573-16			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. 		
@D	Sutton, J.M.//Baesman, S.M.//Fierst, J.L.//Poret-Peterson, A.T.//Oremland, R.S.//Dunlap, D.S.//Akob, D.M. 	Complete Genome Sequences of Two Acetylene-Fermenting Pelobacter acetylenicus Strains.	Genome Announcements	2017	5		e01572-16			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. 		
@D	Suvorova, M.A.//Tsapieva, A.N.//Bak, E.G.//Chereshnev, V.A.//Kiseleva, E.P.//Suvorov, A.N.//Arumugam, M. 	Complete Genome Sequences of emm111 Type Streptococcus pyogenes Strain GUR, with  Antitumor Activity, and Its Derivative Strain GURSA1 with an Inactivated emm  Gene.	Genome Announcements	2017	5		e00939-17			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. 		
@D	Suvorova, M.A.//Tsapieva, A.N.//Duplik, N.V.//Kramskoy, T.A.//Grabovskaya, K.B.//Kiseleva, E.P.//Chereshnev, V.A.//Suvorov, A.N. 	Construction of a Streptococcus strain mutant in the M protein gene.	Med. Akad. Z.	2016	16		235-236					
@A	Suzuki, H. 		Host-mimicking strategies in DNA methylation for improved bacterial transformation.			Anica Dricu 		Methylation - from DNA, RNa and histones to diseases and treatment				Rijeka, Croatia	InTech	2012		0		219-236									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. 		
@D	Suzuki, H.//Dapper, A.L.//Jackson, C.E.//Lee, H.//Pejaver, V.//Doak, T.G.//Lynch, M.//Preer, J.R. Jr. 	Draft Genome Sequence of Caedibacter varicaedens, a Kappa Killer Endosymbiont Bacterium of the Ciliate Paramecium biaurelia.	Genome Announcements	2015	3		e01310-15			Caedibacter varicaedens is a kappa killer endosymbiont bacterium of the ciliate Paramecium biaurelia. Here, we present the draft genome sequence of C. varicaedens. 		
@D	Suzuki, H.//Lefebure, T.//Hubisz, M.J.//Pavinski-Bitar, P.//Lang, P.//Siepel, A.//Stanhope, M.J. 	Comparative Genomic Analysis of the Streptococcus dysgalactiae Species Group: Gene Content, Molecular Adaptation, and Promoter Evolution.	Genome Biol. Evol.	2011	3		168-185			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. 		
@D	Suzuki, H.//Takahashi, S.//Osada, H.//Yoshida, K. 	Improvement of transformation efficiency by strategic circumvention of restriction barriers in Streptomyces griseus.	J. Microbiol. Biotechnol.	2011	21		675-678			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. 		
@D	Suzuki, H.//Yoshida, K. 	Genetic Transformation of Geobacillus kaustophilus HTA426 by Conjugative Transfer of Host-Mimicking Plasmids.	J. Microbiol. Biotechnol.	2012	22		1279-1287			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. 		
@D	Suzuki, K.//Aziz, F.A.//Inuzuka, Y.//Tashiro, Y.//Futamata, H. 	Draft Genome Sequence of Pseudomonas sp. LAB-08 Isolated from Trichloroethene-Contaminated Aquifer Soil.	Genome Announcements	2016	4		e00948-16			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. 		
@D	Suzuki, K.//Nagao, K.//Tokunaga, J.//Hirosawa, M.//Tsubone, H.//Uyeda, M. 	DMI-1, A new DNA methyltransferase inhibitor produced by Streptomyces sp. strain No. 560.	J. Enzym. Inhib.	1995	9		243-252			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. 		
@D	Suzuki, K.//Nagao, K.//Tokunaga, J.//Katayama, N.//Uyeda, M. 	Inhibition of DNA methyltransferase by microbial inhibitors and fatty acids.	J. Enzym. Inhib.	1996	10		271-280			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. 		
@D	Suzuki, M.//Matsui, M.//Suzuki, S.//Rimbara, E.//Asai, S.//Miyachi, H.//Takata, T.//Hiraki, Y.//Kawano, F.//Shibayama, K. 	Genome Sequences of Multidrug-Resistant Acinetobacter baumannii Strains from Nosocomial Outbreaks in Japan.	Genome Announcements	2013	1		e00476-13			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. 		
@D	Suzuki, M.//Nishio, H.//Asagoe, K.//Kida, K.//Suzuki, S.//Matsui, M.//Shibayama, K. 	Genome Sequence of a Carbapenem-Resistant Strain of Ralstonia mannitolilytica.	Genome Announcements	2015	3		e00405-15			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. 		
@D	Suzuki, M.//Suzuki, S.//Matsui, M.//Hiraki, Y.//Kawano, F.//Shibayama, K. 	Genome Sequence of a Strain of the Human Pathogenic Bacterium Pseudomonas alcaligenes That Caused Bloodstream Infection.	Genome Announcements	2013	1		e00919-13			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. 		
@D	Suzuki, N.//Okayama, S.//Nonaka, H.//Tsuge, Y.//Inui, M.//Yukawa, H. 	Large-scale engineering of the Corynebacterium glutamicum genome.	Appl. Environ. Microbiol.	2005	71		3369-3372			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. 		
@D	Suzuki, S.//Aono, T.//Lee, K.B.//Suzuki, T.//Liu, C.T.//Miwa, H.//Wakao, S.//Iki, T.//Oyaizu, H. 	Rhizobial factors required for stem nodule maturation and maintenance in Sesbania rostrata-Azorhizobium caulinodans ORS571 symbiosis.	Appl. Environ. Microbiol.	2007	73		6650-6659			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. 		
@D	Suzuki, S.//Kuenen, J.G.//Schipper, K.//van der Velde, S.//Ishii, S.//Wu, A.//Sorokin, D.Y.//Tenney, A.//Meng, X.Y.//Morrill, P.L.//Kamagata, Y.//Muyzer, G.//Nealson, K.H. 	Physiological and genomic features of highly-alkaliphilic hydrogen-utilizing Betaproteobacteria from a continental serpentinizing site.	Nat. Commun.	2014	5		3900			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'. 		
@D	Suzuki, T.//Kikuchi, M.//Konno, N.//Habu, N. 	Draft Genome Sequence of Brevundimonas sp. Strain SH203, Producing Cellouronate (beta-1,4-Linked Polyglucuronate) Lyase.	Genome Announcements	2017	5		e00262-17			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. 		
@D	Suzuki, T.//Sato, Y.//Yamada, Y.//Akagawa-Matsushita, M.//Yamasato, K. 	A restriction endonuclease (DpaI) from Deleya pacifica IAM 14115, a marine bacterium, an isoschizomer of ScaI.	Agric. Biol. Chem.	1991	55		2647-2649			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. 		
@D	Suzuki, T.//Sugimoto, E.//Tahara, Y.//Yamada, Y. 	Cloning and nucleotide sequence of ApaLI restriction-modification system from Acetobacter pasteurianus IFO 13753.	Biosci. Biotechnol. Biochem.	1996	60		1401-1405			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. 		
@D	Suzuki, T.//Sugimoto, E.//Tahara, Y.//Yamada, Y. 	Cloning and nucleotide sequence of the AgeI methylase gene from Agrobacterium gelatinovorum IAM 12617, a marine bacterium.	Biosci. Biotechnol. Biochem.	1996	60		444-447			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. 		
@D	Suzuki, T.//Yasui, K. 	Plasmid Artificial Modification: A Novel Method for Efficient DNA Transfer into Bacteria.	Methods Mol. Biol.	2011	765		309-326			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. 		
@D	Suzuki, Y.//Gilmore, J.L.//Yoshimura, S.H.//Henderson, R.M.//Lyubchenko, Y.L.//Takeyasu, K. 	Visual Analysis of Concerted Cleavage by Type IIF Restriction Enzyme SfiI in Subsecond Time Region.	Biophys. J.	2011	101		2992-2998			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. 		
@D	Svab, D.//Horvath, B.//Szucs, A.//Maroti, G.//Toth, I. 	Draft Genome Sequence of an Escherichia coli O157:H43 Strain Isolated from Cattle.	Genome Announcements	2013	1		e00263-13			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). 		
@D	Svadbina, I.V.//Matvienko, N.N.//Zheleznaya, L.A.//Matvienko, N.I. 	Location of the bases modified by M.BcoKIA and M.BcoKIB methylases in the sequence 5'-CTCTTC-3'/5'-GAAGAG-3'.	Biochemistry	2005	70		1363-1366			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'. 		
@D	Svadbina, I.V.//Zelinskaya, N.V.//Kovalevskaya, N.P.//Zheleznaya, L.A.//Matvienko, N.I. 	Isolation and characterization of site-specific DNA- methyltransferases from Bacillus coagulans K.	Biokhimiia	2004	69		372-379			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'. 		
@D	Svadbina, I.V.//Zheleznyakova, E.N.//Zheleznaya, L.A.//Matvienko, N.I. 	Bacillus species LU4 is an effective producer of thermostable site-specific endonuclease BspLU4I, an isoschizomer of AvaI.	Biokhimiia	2003	68		429-435			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. 		
@D	Svedruzic, A.M.//Reich, N.O. 	DNA cytosine C-5 methyltransferase Dnmt1: Catalysis-dependent release of allosteric inhibition.	Biochemistry	2005	44		9472-9485			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. 		
@D	Svedruzic, Z.M. 	Mammalian cytosine DNA methyltransferase Dnmt1: Enzymatic mechanism, novel mechanism-based inhibitors, and RNA-directed DNA methylation.	Curr. Med. Chem.	2008	15		92-106			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. 		
@D	Svedruzic, Z.M.//Reich, N.O. 	Enzymatic properties of mouse cytosine DNA methyltransferase DNMT1.	ACS Abstracts	2002	223		C75			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. 		
@D	Svedruzic, Z.M.//Reich, N.O. 	Mechanism of allosteric regulation of Dnmt1's processivity.	Biochemistry	2005	44		14977-14988			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). 		
@D	Svenning, M.M. et al. 	Genome Sequence of the Arctic Methanotroph Methylobacter tundripaludum SV96.	J. Bacteriol.	2011	193		6418-6419			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. 		
@D	Svensson, D.//Ohrman, C.//Backman, S.//Karlsson, E.//Nilsson, E.//Bystrom, M.//Larkeryd, A.//Myrtennas, K.//Stenberg, P.//Qu, P.H.//Trygg, J.//Scholz, H.C.//Forsman, M.//Sjodin, A. 	Complete Genome Sequence of Francisella guangzhouensis Strain 08HL01032T, Isolated from Air-Conditioning Systems in China.	Genome Announcements	2015	3		e00024-15			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. 		
@D	Swaminathan, C.P.//Sankpal, U.T.//Rao, D.N.//Surolia, A. 	Water-assisted dual mode cofactor recognition by HhaI DNA methyltransferase.	J. Biol. Chem.	2002	277		4042-4049			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. 		
@D	Swaminathan, N.//George, D.//McMaster, K.//Szablewski, J.//Van Etten, J.L.//Mead, D.A. 	Restriction generated oligonucleotides utilizing the two base recognition endonuclease CviJI.	Nucleic Acids Res.	1994	22		1470-1475			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. 		
@D	Swaminathan, N.//Mead, D.A.//McMaster, K.//George, D.//Van Etten, J.L.//Skowron, P.M. 	Molecular cloning of the three base restriction endonuclease R.CviJI from eukaryotic Chlorella virus IL-3A.	Nucleic Acids Res.	1996	24		2463-2469			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. 		
@D	Swanson, E.//Oshone, R.//Nouioui, I.//Abebe-Akele, F.//Simpson, S.//Morris, K.//Thomas, W.K.//Sen, A.//Ghodhbane-Gtari, F.//Gtari, M.//Tisa, L.S. 	Permanent Draft Genome Sequence for Frankia sp. Strain Cc1.17, a Nitrogen-Fixing  Actinobacterium Isolated from Root Nodules of Colletia cruciata.	Genome Announcements	2017	5		e00530-17			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. 		
@D	Swanson, E.//Oshone, R.//Simpson, S.//Morris, K.//Abebe-Akele, F.//Thomas, W.K.//Tisa, L.S. 	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.	Genome Announcements	2015	3		e01511-15			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. 		
@D	Swanson, E.//Oshone, R.//Simpson, S.//Morris, K.//Abebe-Akele, F.//Thomas, W.K.//Tisa, L.S. 	Permanent Draft Genome Sequence of Frankia sp. Strain ACN1ag, a Nitrogen-Fixing Actinobacterium Isolated from the Root Nodules of Alnus glutinosa.	Genome Announcements	2015	3		e01483-15			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. 		
@D	Swarbreck, D.//Wilks, C.//Lamesch, P.//Berardini, T.Z.//Garcia-Hernandez, M.//Foerster, H.//Li, D.//Meyer, T.//Muller, R.//Ploetz, L.//Radenbaugh, A.//Singh, S.//Swing, V.//Tissier, C.//Zhang, P.//Huala, E. 	The Arabidopsis Information Resource (TAIR): gene structure and function annotation.	Nucleic Acids Res.	2008	36		D1009-D1014			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. 		
@D	Swarnkar, M.K.//Salwan, R.//Kasana, R.C.//Singh, A.K. 	Draft Genome Sequence of Psychrotrophic Acinetobacter sp. Strain MN12 (MTCC 10786), Which Produces a Low-Temperature-Active and Alkaline-Stable Peptidase.	Genome Announcements	2014	2		e01167-14			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%. 		
@D	Sweetnam, K.R.//Reich, N.O. 	Construction of a mechanism-based inhibitor for EcoRI DNA methyltransferase.	Biochemistry	1992	31		2206			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. 		
@D	Sweetnam, K.R.//Reich, N.O. 	Construction of a mechanism-based inhibitor for EcoRI DNA methyltransferase.	ACS Abstracts	1992	203		102-BIOL			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. 		
@D	Swingley, W.D. et al. 	Niche adaptation and genome expansion in the chlorophyll d-producing cyanobacterium Acaryochloris marina.	Proc. Natl. Acad. Sci. U. S. A.	2008	105		2005-2010			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. 		
@D	Swingley, W.D.//Sadekar, S.//Mastrian, S.D.//Matthies, H.J.//Hao, J.//Ramos, H.//Acharya, C.R.//Conrad, A.L.//Taylor, H.L.//Dejesa, L.C.//Shah, M.K.//O'huallachain, M.E.//Lince, M.T.//Blankenship, R.E.//Beatty, J.T.//Touchman, J.W. 	The complete genome sequence of Roseobacter denitrificans reveals a mixotrophic rather than photosynthetic metabolism.	J. Bacteriol.	2007	189		683-690			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. 		
@D	Swinton, D.//Hattman, S.//Benzinger, R.//Buchanan-Wollaston, V.//Beringer, J. 	Replacement of the deoxycytidine residues in Rhizobium bacteriophage RL38JI DNA.	FEBS Lett.	1985	184		294-298			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. 		
@D	Swinton, D.//Hattman, S.//Crain, P.F.//Cheng, C.-S.//Smith, D.L.//McCloskey, J.A. 	Purification and characterization of the unusual deoxynucleoside, alpha-N-(9-beta-D-2'-deoxyribofuranosylpurin-t-yl) glycinamide, specified by the phage Mu modification function.	Proc. Natl. Acad. Sci. U. S. A.	1983	80		7400-7404			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. 		
@D	Swithers, K.S. et al. 	Genome Sequence of Thermotoga sp. Strain RQ2, a Hyperthermophilic Bacterium Isolated from a Geothermally Heated Region of the Seafloor near  Ribeira Quente, the Azores.	J. Bacteriol.	2011	193		5869-5870			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. 		
@D	Swithers, K.S.//Dipippo, J.L.//Bruce, D.C.//Detter, C.//Tapia, R.//Han, S.//Goodwin, L.A.//Han, J.//Woyke, T.//Pitluck, S.//Pennacchio, L.//Nolan, M.//Mikhailova, N.//Land, M.L.//Nesbo, C.L.//Gogarten, J.P.//Noll, K.M. 	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.	J. Bacteriol.	2011	193		5566-5567			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. 		
@D	Syazni, Y.M.//Kasuu, M.//Nakasaki, K.//Ariga, O. 	Draft Genome Sequence of the Nonmarine Agarolytic Bacterium Cellvibrio sp. OA-2007.	Genome Announcements	2015	3		e00468-15			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%. 		
@D	Syddall, R.//Stachow, C. 	A site-specific endonuclease from Caulobacter crescentus CB-13: restriction endonuclease CcrI.	Biochim. Biophys. Acta	1985	825		236-243			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. 		
@D	Sydenham, T.V.//Hasman, H.//Justesen, U.S. 	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.	Genome Announcements	2015	3		e00005-15			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. 		
@D	Sykilinda, N.N.//Bondar, A.A.//Gorshkova, A.S.//Kurochkina, L.P.//Kulikov, E.E.//Shneider, M.M.//Kadykov, V.A.//Solovjeva, N.V.//Kabilov, M.R.//Mesyanzhinov, V.V.//Vlassov, V.V.//Drukker, V.V.//Miroshnikov, K.A. 	Complete Genome Sequence of the Novel Giant Pseudomonas Phage PaBG.	Genome Announcements	2014	2		e00929-13			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. 		
@D	Szabo, Z.//Gyula, P.//Robotka, H.//Bato, E.//Galik, B.//Pach, P.//Pekker, P.//Papp, I.//Bihari, Z. 	Draft genome sequence of Methylibium sp. strain T29, a novel fuel oxygenate-degrading bacterial isolate from Hungary.	Standards in Genomic Sciences	2015	10		39			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. 		
@D	Szatmari, G.//Hua, N.M.//Vzdornov, D.//Daigle, F.//Smoragiewicz, W.//Mamet-Bratley, M.D.//Karska-Wysocki, B. 	In vitro expression of the restriction endonucleases LlaMI and ScrFI isolated from Lactococcus lactis M19 and UC503.	J. Biotechnol.	2006	121		144-153			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. 		
@D	Szczelkun, M.D. 	Kinetic models of translocation, head-on collision, and DNA cleavage by type I restriction endonucleases.	Biochemistry	2002	41		2067-2074			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. 		
@D	Szczelkun, M.D. 	Roles for Helicases as ATP-Dependent Molecular Switches.	Adv. Exp. Med. Biol.	2013	767		225-244			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. 		
@D	Szczelkun, M.D. 	Translocation, switching and gating: potential roles for ATP in long-range communication on DNA by Type III restriction endonucleases.	Biochem. Soc. Trans.	2011	39		589-594			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. 		
@A	Szczelkun, M.D. 		How do proteins move along DNA?  Lessons from type-I and type-III restriction endonucleases.			Banting, G.//Higgins, S.J. 		Essays Biochem.				London	Portland Press	2000		35		131-143									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. 		
@D	Szczelkun, M.D.//Connolly, B.A. 	Sequence-specific binding of DNA by the EcoRV restriction and modification enzymes with nucleic acid and cofactor analogues.	Biochemistry	1995	34		10724-10733			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. 		
@D	Szczelkun, M.D.//Dillingham, M.S.//Janscak, P.//Firman, K.//Halford, S.E. 	Repercussions of DNA tracking by the type IC restriction endonuclease EcoR124I on linear, circular and catenated substrates.	EMBO J.	1996	15		6335-6347			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. 		
@D	Szczelkun, M.D.//Friedhoff, P.//Seidel, R. 	Maintaining a sense of direction during long-range communication on DNA.	Biochem. Soc. Trans.	2010	38		404-409			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. 		
@D	Szczelkun, M.D.//Halford, S.E. 	Recombination by resolvase to analyse DNA communications by the SfiI restriction endonuclease.	EMBO J.	1996	15		1460-1469			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+. 		
@A	Szczelkun, M.D.//Halford, S.E. 		Restriction Endonuclease.			Brenner, S.//Miller, J. 		Encyclopaedia of Genetics				New York	Academic Press	2001		0		1693-1696									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. 		
@D	Szczelkun, M.D.//Janscak, P.//Firman, K.//Halford, S.E. 	Selection of non-specific DNA cleavage sites by the type IC restriction endonuclease EcoR124I.	J. Mol. Biol.	1997	271		112-123			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. 		
@D	Szczelkun, M.D.//Jones, H.//Connolly, B.A. 	Probing the protein-DNA interface of the EcoRV modification methyltransferase bound to its recognition sequence, GATATC.	Biochemistry	1995	34		10734-10743			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. 		
@D	Szczepanek, T.//Gora, M.//Monteilhet, C.//Wysocka, M.//Lazowska, J.//Golik, P. 	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.	FEMS Yeast Res.	2006	6		823-835			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. 		
@D	Szczepanek, T.//Jamoussi, K.//Lazowska, J. 	Critical base substitutions that affect the splicing and/or homing activities of the group I intron bi2 of yeast mitochondria.	Mol. Gen. Genet.	2000	264		137-144			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. 		
@D	Szczepanek, T.//Lazowska, J. 	Replacement of two non-adjacent amino acids in the S. cerevisiae bi2 intron-encoded RNA maturase is sufficient to gain a homing-endonuclease activity.	EMBO J.	1996	15		3758-3767			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. 		
@D	Szczepanek, T.//Macadre, C.//Meunier, B.//Lazowska, J. 	Two homologous introns from related Saccharomyces species differ in their mobility.	Gene	1994	139		1-7			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. 		
@D	Szczepanowski, R.//Eikmeyer, F.//Harfmann, J.//Blom, J.//Rogers, L.M.//Brown, C.J.//Top, E.M.//Schluter, A. 	Sequencing and comparative analysis of IncP-1alpha antibiotic resistance plasmids reveal a highly conserved backbone and differences within accessory regions.	J. Biotechnol.	2011	155		95-103			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. 		
@D	Szczepanowski, R.H.//Carpenter, M.A.//Czapinska, H.//Zaremba, M.//Tamulaitis, G.//Siksnys, V.//Bhagwat, A.S.//Bochtler, M. 	Central base pair flipping and discrimination by PspGI.	Nucleic Acids Res.	2008	36		6109-6117			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. 		
@D	Szczepek, M.//Brondani, V.//Buchel, J.//Serrano, L.//Segal, D.J.//Cathomen, T. 	Structure-based redesign of the dimerization interface reduces the toxicity of zinc-finger nucleases.	Nat. Biotechnol.	2007	25		786-793			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. 		
@D	Szczepek, M.//Mackeldanz, P.//Moncke-Buchner, E.//Alves, J.//Kruger, D.H.//Reuter, M. 	Molecular analysis of restriction endonuclease EcoRII from Escherichia coli reveals precise regulation of its enzymatic activity by autoinhibition.	Mol. Microbiol.	2009	72		1011-1021			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. 		
@D	Szczepinska, T.//Kutner, J.//Kopczynski, M.//Pawlowski, K.//Dziembowski, A.//Kudlicki, A.//Ginalski, K.//Rowicka, M. 	Probabilistic approach to predicting substrate specificity of methyltransferases.	PLOS Comp. Biol.	2014	10		e1003514			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. 		
@D	Szeberenyi, J. 	Two restriction endonucleases.	Biochem. Mol. Biol. Educ.	2006	34		228-229			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.| 		
@D	Szegedi, S.S.//Gumport, R.I. 	DNA binding properties in vivo and target recognition domain sequence alignment analyses of wild-type and mutant RsrI [N6-adenine] DNA methyltransferases.	Nucleic Acids Res.	2000	28		3972-3981			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. 		
@D	Szegedi, S.S.//Ma, Z.//Gumport, R.I. 	A novel scheme for the purification of wildtype and mutant RsrI DNA methyltransferases (MTases).	FASEB J.	1998	12		A1437			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. 		
@D	Szegedi, S.S.//Reich, N.O.//Gumport, R.I. 	Characterization of the DNA binding and kinetic properties of wild-type Rsr[N6-adenine] methyltransferase (M.RsrI).	FASEB J.	1999	13		A1367			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. 		
@D	Szegedi, S.S.//Reich, N.O.//Gumport, R.I. 	Substrate binding in vitro and kinetics of RsrI [N6-adenine] DNA methyltransferase.	Nucleic Acids Res.	2000	28		3962-3971			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. 		
@D	Szekeres, M. 	Phage-induced development of a site-specific endonuclease in Anacystis nidulans, a cyanobacterium.	Virology	1981	111		1-10			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. 		
@D	Szekeres, M.//Matveyev, A.V. 	Cleavage and sequence recognition of 2,6-diaminopurine-containing DNA by site-specific endonucleases.	FEBS Lett.	1987	222		89-94			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. 		
@D	Szekeres, M.//Szmidt, A.E.//Torok, I. 	Evidence for a restriction/modification-like system in Anacystis nidulans infected by cyanophage AS-1.	Eur. J. Biochem.	1983	131		137-141			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. 		
@D	Szeto, M.D.//Boissel, S.J.S.//Baker, D.//Thyme, S.B. 	Mining Endonuclease Cleavage Determinants in Genomic Sequence Data.	J. Biol. Chem.	2011	286		32617-32627			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. 		
@D	Szilak, L.//Der, A.//Deak, F.//Venetianer, P. 	Kinetic characterization of the EcaI methyltransferase.	Eur. J. Biochem.	1993	218		727-733			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. 		
@D	Szilak, L.//Finta, C.//Patthy, A.//Venetianer, P.//Kiss, A. 	Self-methylation of BspRI DNA-methyltransferase.	Nucleic Acids Res.	1994	22		2876-2881			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. 		
@D	Szilak, L.//Finta, C.//Patthy, A.//Venetianer, P.//Kiss, A. 	Self-methylation of the M.BspRI methyltransferase.	Gene	1995	157		105			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. 		
@D	Szilak, L.//Venetianer, P.//Kiss, A. 	Cloning and nucleotide sequence of the genes coding for the Sau96I restriction and modification enzymes.	Nucleic Acids Res.	1990	18		4659-4664			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. 		
@D	Szilak, L.//Venetianer, P.//Kiss, A. 	Purification and biochemical characterization of the EcaI DNA methyltransferase.	Eur. J. Biochem.	1992	209		391-397			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. 		
@D	Sznyter, L.A.//Brooks, J.E. 	The characterization and cloning of the NotI restriction-modification system.	Heredity	1988	61		308			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. 		
@D	Sznyter, L.A.//Brooks, J.E. 	The characterization and cloning of the EagI restriction-modification system.	Gene	1988	74		53			Meeting Abstract 		
@D	Sznyter, L.A.//Marcus, A.M.//Brooks, J.E. 	The cloning and characterization of the EagI restriction-modification system.	Abstr. Gen. Meet. Am. Soc. Microbiol.	1989	89		180			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. 		
@D	Sznyter, L.A.//Slatko, B.//Moran, L.//O'Donnell, K.H.//Brooks, J.E. 	Nucleotide sequence of the DdeI restriction-modification system and characterization of the methylase protein.	Nucleic Acids Res.	1987	15		8249-8266			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. 		
@D	Sznyter, L.A.//Vaccaro, C.M.//Jager-Quinton, T.//Wilson, G.//Brooks, J.E. 	Cloning and characterization of the SphI restriction-modification system from S. phaeochromogenes.	Abstr. Gen. Meet. Am. Soc. Microbiol.	1989	0		361			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. 		
@D	Szomolanyi, I.//Kiss, A.//Venetianer, P. 	Cloning the modification methylase gene of Bacillus sphaericus R in Escherichia coli.	Gene	1980	10		219-225			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. 		
@D	Szwagierczak, A.//Brachmann, A.//Schmidt, C.S.//Bultmann, S.//Leonhardt, H.//Spada, F. 	Characterization of PvuRts1I endonuclease as a tool to investigate genomic 5-hydroxymethylcytosine.	Nucleic Acids Res.	2011	39		5149-5156			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. 		
@D	Szybalski, W. 	Universal restriction endonucleases: designing novel cleavage specificities by combining adapter oligodeoxynucleotide and enzyme moieties.	Gene	1985	40		169-173			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. 		
@A	Szybalski, W. 		Modifying specificities of restriction enzymes.			Kamely, D.//Chakrabarty, A.M.//Kornguth, S.E. 		Biotechnology: Bridging Research and Applications				Boston	Kluwer	1991		0		371-376									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). 		
@D	Szybalski, W.//Blumenthal, R.M.//Brooks, J.E.//Hattman, S.//Raleigh, E.A. 	Nomenclature for bacterial genes coding for class-II restriction endonucleases and modification methyltransferases.	Gene	1988	74		279-280			A proposed nomenclature for restriction enzyme and methylase genes. 		
@D	Szybalski, W.//Kim, S.C.//Hasan, N.//Podhajska, A.J. 	Class-IIS restriction enzymes - a review.	Gene	1991	100		13-26			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. 		
@D	Szybalski, W.//Skalka, A. 	Nobel prizes and restriction enzymes.	Gene	1978	4		181-182			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. 		
@D	Szyf, M. 	Targeting DNA methyltransferase in cancer.	Cancer Metastasis Rev.	1998	17		219-231			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. 		
@D	Szyf, M. 	DNA methylation properties: consequences for pharmacology.	Trends Pharmacol. Sci.	1994	15		233-238			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. 		
@D	Szyf, M. 	The role of DNA methyltransferase 1 in growth control.	Front. Biosci.	2001	6		D599-D609			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. 		
@D	Szyf, M. 	DNA methylation and cancer therapy.	Drug Resistance Updates	2003	6		341-353			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. 		
@D	Szyf, M. 	The DNA methylation machinery as a therapeutic target.	Curr. Drug Targets	2000	1		101-118			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. 		
@D	Szyf, M.//Avraham-Haetzni, K.//Reifman, A.//Shlomai, J.//Kaplan, F.//Oppenheim, A.//Razin, A. 	DNA methylation pattern is determined by the intracellular level of the methylase.	Proc. Natl. Acad. Sci. U. S. A.	1984	81		3278-3282			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. 		
@D	Szyf, M.//Bigey, P. 	Oligonucleotides as inhibitors of DNA methyltransferase: novel antitumor drugs.	Curr. Res. Mol. Ther.	1998	1		93-101			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. 		
@D	Szyf, M.//Gruenbaum, Y.//Urieli-Shoval, S.//Razin, A. 	Studies on the biological role of DNA methylation:  V. The pattern of E. coli DNA methylation.	Nucleic Acids Res.	1982	10		7247-7259			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. 		
@D	Szyf, M.//Knox, D.J.//Milutinovic, S.//Slack, A.D.//Araujo, F.D. 	How does DNA methyltransferase cause oncogenic transformation?	Ann. NY Acad. Sci.	2000	910		156-174			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. 		
@D	Szyf, M.//Meisels, E.//Razin, A. 	Biological role of DNA methylation:  sequence-specific single-strand breaks associated with hypomethylation of GATC sites in Escherichia coli DNA.	J. Bacteriol.	1986	168		1487-1490			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. 		
@D	Szyf, M.//Ramchandani, S.//MacLeod, R.//Croteau, S.//von Hofe, E. 	Antisense oligonucleotides directed against DNA methyltransferase inhibit tumorigenesis.	Proc. Amer. Assoc. Cancer Res.	1996	37		353			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. 		
@D	Szyf, M.//Theberge, J. 	Mammalian cells contain a general (CpG) DNA demethylating activity.	Mol. Biol. Cell	1993	4		74a			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. 		
@D	Tabata, M.//Nakajima, K.//Nyarko, E. 	Metalloporphyrin mediated DNA cleavage by a low concentration of HaeIII restriction enzyme.	J. Inorg. Biochem.	2000	78		383-389			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. 		
@D	Tabata, M.//Ohhata, S.//Kawasumi, T.//Nikawadori, Y.//Kishida, K.//Sato, T.//Ohtsubo, Y.//Tsuda, M.//Nagata, Y. 	Complete Genome Sequence of a gamma-Hexachlorocyclohexane Degrader, Sphingobium sp. Strain TKS, Isolated from a gamma-Hexachlorocyclohexane-Degrading Microbial  Community.	Genome Announcements	2016	4		e00247-16			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. 		
@D	Tabata, M.//Ohhata, S.//Nikawadori, Y.//Sato, T.//Kishida, K.//Ohtsubo, Y.//Tsuda, M.//Nagata, Y. 	Complete Genome Sequence of a gamma-Hexachlorocyclohexane-Degrading Bacterium, Sphingobium sp. Strain MI1205.	Genome Announcements	2016	4		e00246-16			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. 		
@D	Tabata, M.//Ohtsubo, Y.//Ohhata, S.//Tsuda, M.//Nagata, Y. 	Complete Genome Sequence of the gamma-Hexachlorocyclohexane-Degrading Bacterium Sphingomonas sp. Strain MM-1.	Genome Announcements	2013	1		e00247-13			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. 		
@D	Tack, D.S.//Cole, A.C.//Shroff, R.//Morrow, B.R.//Ellington, A.D. 	Evolving Bacterial Fitness with an Expanded Genetic Code.	Sci. Rep.	2018	8		3288			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. 		
@D	Tada, I.//Saitoh, S.//Aoyama, H.//Shinzato, N.//Yamamoto, N.//Arita, M.//Ikematsu, S. 	Genome Sequence of Lactobacillus paracasei Strain LC-Ikematsu, Isolated from a Pineapple in Okinawa, Japan.	Genome Announcements	2017	5		e01583-16			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. 		
@D	Tada, T.//Kitao, T.//Miyoshi-Akiyama, T.//Kirikae, T. 	Genome Sequence of Multidrug-Resistant Pseudomonas aeruginosa NCGM1179.	J. Bacteriol.	2011	193		6397			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. 		
@D	Tadesse, D.A.//Hoffmann, M.//Sarria, S.//Lam, C.//Brown, E.//Allard, M.//McDermott, P.F. 	Complete Genome Sequences of 14 Salmonella enterica Serovar Enteritidis Strains Recovered from Human Clinical Cases between 1949 and 1995 in the United States.	Genome Announcements	2018	6		e01406-17			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. 		
@D	Tae, H.//Shallom, S.//Settlage, R.//Hawkins, G.N.//Adams, L.G.//Garner, H.R. 	Complete Genome Sequence of Brucella suis VBI22, Isolated from Bovine Milk.	J. Bacteriol.	2012	194		910			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. 		
@D	Tae, H.//Shallom, S.//Settlage, R.//Preston, D.//Adams, L.G.//Garner, H.R. 	Revised Genome Sequence of Brucella suis 1330.	J. Bacteriol.	2011	193		6410			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. 		
@D	Tagami, H.//Tayama, K.//Tohyama, T.//Fukaya, M.//Okumura, H.//Kawamura, Y.//Horinouchi, S.//Beppu, T. 	Purification and properties of a site-specific restriction endonuclease AaaI from Acetobacter aceti subsp. aceti No. 1023.	FEMS Microbiol. Lett.	1988	56		161-166			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. 		
@D	Taghavi, S.//Izquierdo, J.A.//van der Lelie, D. 	Complete Genome Sequence of Clostridium sp. Strain DL-VIII, a Novel Solventogenic Clostridium Species Isolated from Anaerobic Sludge.	Genome Announcements	2013	1		e00605-13			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. 		
@D	Tagini, F.//Pillonel, T.//Asner, S.//Prod'hom, G.//Greub, G. 	Draft Genome Sequence of a Cardiobacterium hominis Strain Isolated from Blood Cultures of a Patient with Infective Endocarditis.	Genome Announcements	2016	4		e00999-16			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. 		
@D	Tahrioui, A.//Quesada, E.//Llamas, I. 	Draft Genome Sequence of the Moderately Halophilic Gammaproteobacterium Halomonas anticariensis FP35T.	Genome Announcements	2013	1		e00497-13			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. 		
@D	Taiaroa, G.//Harbison-Price, N.//Ferguson, S.A.//Carter, G.P.//Williamson, D.A.//Macknight, R.C.//Cook, G.M.//Heikal, A. 	Complete Genome Sequence of a New Zealand Isolate of the Bovine Pathogen Streptococcus uberis.	Genome Announcements	2018	6		e00119-18			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. 		
@D	Taira, E.//Iiyama, K.//Mon, H.//Mori, K.//Akasaka, T.//Tashiro, K.//Yasunaga-Aoki, C.//Lee, J.M.//Kusakabe, T. 	Draft Genome Sequence of Entomopathogenic Serratia liquefaciens Strain FK01.	Genome Announcements	2014	2		e00609-14			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%. 		
@D	Tajima, N.//Kanesaki, Y.//Sato, S.//Yoshikawa, H.//Maruyama, F.//Kurokawa, K.//Ohta, H.//Nishizawa, T.//Asayama, M.//Sato, N. 	Complete Genome Sequence of the Nonheterocystous Cyanobacterium Pseudanabaena sp. ABRG5-3.	Genome Announcements	2018	6		e01608-17			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. 		
@D	Tajima, S. 	DNA methyltransferase and DNA methylation.	Gendai Iryo	2003	35		936-948					
@D	Tajima, S.//Tsuda, H.//Wakabayashi, N.//Asano, A.//Mizuno, S.//Nishimori, K. 	Isolation and expression of a chicken DNA methyltransferase cDNA.	J. Biochem. (Tokyo)	1995	117		1050-1057			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. 		
@D	Tak, N. et al. 	Genome sequence of Ensifer sp. TW10; a Tephrosia wallichii (Biyani) microsymbiont native to the Indian Thar Desert.	Standards in Genomic Sciences	2013	9		304-314			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. 		
@D	Takagi, M.//Nakano, A.//Toh, H.//Oshima, K.//Arakawa, K.//Nakajima, F.//Tashiro, K.//Kikusui, T.//Yanagida, F.//Morita, H. 	Draft Genome Sequence of Streptococcus orisasini SH06, Isolated from a Healthy Thoroughbred Gastrointestinal Tract.	Genome Announcements	2016	4		e01566-15			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. 		
@D	Takagi, M.//Nishioka, M.//Kakihara, H.//Kitabayashi, M.//Inoue, H.//Kawakami, B.//Oka, M.//Imanaka, T. 	Characterization of DNA polymerase from Pyrococcus sp. strain KOD1 and its application to PCR.	Appl. Environ. Microbiol.	1997	63		4504-4510			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. 		
@D	Takahashi, H.//Kojima, H.//Saito, H. 	A new site-specific endonuclease, ScaI, from Streptomyces caespitosus.	Biochem. J.	1985	231		229-232			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. 		
@D	Takahashi, H.//Saito, H.//Ikeda, Y. 	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.	J. Gen. Appl. Microbiol.	1978	24		297-306			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. 		
@D	Takahashi, H.//Shao, M.//Furuya, N.//Komano, T. 	The genome sequence of the incompatibility group Igamma plasmid R621a: Evolution of IncI plasmids.	Plasmid	2011	66		112-121			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. 		
@D	Takahashi, H.//Shimizu, M.//Saito, H.//Ikeda, Y.//Sugisaki, H. 	A new site-specific endonuclease from Streptomyces lavendulae (SlaI) .	Gene	1979	5		9-18			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. 		
@D	Takahashi, I.//Hayano, D.//Asayama, M.//Masahiro, F.//Watahiki, M.//Shirai, M. 	Restriction barrier composed of an extracellular nuclease and restriction endonuclease in the unicellular cyanobacterium Microcystis sp.	FEMS Microbiol. Lett.	1996	145		107-111			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. 		
@D	Takahashi, M.//Kobayashi, M.//Uchida, T. 	Molecular multiplicity of nuclease TT1 from Thermus thermophilus HB8.	J. Biochem. (Tokyo)	1981	90		1521-1527			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. 		
@D	Takahashi, N.//Naito, Y.//Handa, N.//Kobayashi, I. 	A DNA methyltransferase can protect the genome from postdisturbance attack by a restriction-modification gene complex.	J. Bacteriol.	2002	184		6100-6108			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. 		
@D	Takahashi, N.//Ohashi, S.//Sadykov, M.R.//Mizutani-Ui, Y.//Kobayashi, I. 	IS-Linked Movement of a Restriction-Modification System.	PLoS ONE	2011	6		e16554			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. 		
@D	Takahashi, S.//Matsuno, H.//Furusawa, H.//Okahata, Y. 	Direct monitoring of EcoRII restriction enzyme reactions on a 27MHz quartz-crystal microbalance.	Nucleic Acids Res. Suppl.	2002	2		71-72			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. 		
@D	Takahashi, S.//Matsuno, H.//Furusawa, H.//Okahata, Y. 	Direct monitoring of allosteric recognition of type IIE restriction endonuclease EcoRII.	J. Biol. Chem.	2008	283		15023-15030			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. 		
@D	Takai, D. 	Detection of DNA methylation using methylation sensitive restriction enzyme.	Jikken Igaku Bessatsu	2008	JB12		62-68					
@D	Takai, K.//Horikoshi, K. 	Molecular phylogenetic analysis of archaeal intron-containing genes coding for rRNA obtained from a deep-subsurface geothermal water pool.	Appl. Environ. Microbiol.	1999	65		5586-5589			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. 		
@D	Takami, H.//Nakasone, K.//Takaki, Y.//Maeno, G.//Sasaki, R.//Masui, N.//Fuji, F.//Hirama, C.//Nakamura, Y.//Ogasawara, N.//Kuhara, S.//Horikoshi, K. 	Complete genome sequence of the alkaliphilic bacterium Bacillus halodurans and genomic sequence comparison with Bacillus subtilis.	Nucleic Acids Res.	2000	28		4317-4331			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. 		
@D	Takami, H.//Takaki, Y.//Chee, G.-J.//Nishi, S.//Shimamura, S.//Suzuki, H.//Matsui, S.//Uchiyama, I. 	Thermoadaptation trait revealed by the genome sequence of thermophilic Geobacillus kaustophilus.	Nucleic Acids Res.	2004	32		6292-6303			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. 		
@D	Takami, H.//Takaki, Y.//Uchiyama, I. 	Genome sequence of Oceanobacillus iheyensis isolated from the Iheya Ridge and its unexpected adaptive capabilities to extreme environments.	Nucleic Acids Res.	2002	30		3927-3935			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. 		
@D	Takamiya, M.//Ozen, A.//Rasmussen, M.//Alter, T.//Gilbert, T.//Ussery, D.W.//Knochel, S. 	Genome Sequences of Two Stress-Tolerant Campylobacter jejuni Poultry Strains, 305 and DFVF1099.	J. Bacteriol.	2011	193		5546-5547			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. 		
@D	Takamiya, M.//Ozen, A.//Rasmussen, M.//Alter, T.//Gilbert, T.//Ussery, D.W.//Knochel, S. 	Genome Sequence of Campylobacter jejuni strain 327, a strain isolated from a turkey slaughterhouse.	Standards in Genomic Sciences	2011	4		113-122			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). 		
@D	Takanami, M. 	Specific cleavage of coliphage fd DNA by five different restriction endonucleases from Haemophilus genus.	FEBS Lett.	1973	34		318-322			None 		
@D	Takanami, M. 	Restriction endonucleases AP, GA, and H-1 from three Haemophilus strains.	Methods Mol. Biol.	1974	7		113-133			None 		
@D	Takanami, M.//Kojo, H. 	Cleavage site specificity of an endonuclease prepared from Haemophilus influenzae strain H-1.	FEBS Lett.	1973	29		267-270			None 		
@D	Takanami, M.//Okamoto, T.//Sugimoto, K.//Sugisaki, H. 	Studies on Bacteriophage fd DNA I.  A Cleavage Map of the fd Genome.	J. Mol. Biol.	1975	95		21-31			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. 		
@D	Takano, T.//Nakamura, Y.//Matsuyama, T.//Sakai, T.//Shigenobu, Y.//Sugaya, T.//Yasuike, M.//Fujiwara, A.//Kondo, H.//Hirono, I.//Fukuda, Y.//Nakayasu, C. 	Complete Genome Sequence of Ichthyobacterium seriolicida JBKA-6T, Isolated from Yellowtail (Seriola quinqueradiata) Affected by Bacterial Hemolytic Jaundice.	Genome Announcements	2017	5		e01574-16			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. 		
@D	Takano, T.//Ochi, A.//Yamamoto, N. 	Restriction enzyme from Lactobacillus fermentum.	FEMS Microbiol. Rev.	1990	7		64			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. 		
@D	Takano, T.//Watanabe, T.//Fukasawa, T. 	Mechanism of host-controlled restriction of bacteriophage lambda by R factors in Escherichia coli K12.	Virology	1968	34		290-302			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. 		
@D	Takano, T.//Watanabe, T.//Fukasawa, T. 	Specific inactivation of infectious lambda DNA by sonicates of restrictive bacteria with R factors.	Biochem. Biophys. Res. Commun.	1966	25		192-204			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. 		
@D	Takarada, H.//Sekine, M.//Kosugi, H.//Matsuo, Y.//Fujisawa, T.//Omata, S.//Kishi, E.//Shimizu, A.//Tsukatani, N.//Tanikawa, S.//Fujita, N.//Harayama, S. 	Complete genome sequence of the soil actinomycete Kocuria rhizophila.	J. Bacteriol.	2008	190		4139-4146			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. 		
@D	Takasaki, Y. 	Two forms of restriction enzyme HindIII.	J. Biochem. (Tokyo)	1994	116		1281-1286			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. 		
@D	Takasaki, Y. 	Alternation of two forms of restriction endonuclease HindIII.	Biosci. Biotechnol. Biochem.	1996	60		396-400			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. 		
@D	Takasu, Y.//Sajwan, S.//Daimon, T.//Osanai-Futahashi, M.//Uchino, K.//Sezutsu, H.//Tamura, T.//Zurovec, M. 	Efficient TALEN construction for Bombyx mori gene targeting.	PLoS ONE	2013	8		E73458			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. 		
@D	Takata, T.//Aras, R.//Tavakoli, D.//Ando, T.//Olivares, A.Z.//Blaser, M.J. 	Phenotypic and genotypic variation in methylases involved in type II restriction-modification systems in Helicobacter pylori.	Nucleic Acids Res.	2002	30		2444-2452			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. 		
@D	Takata, T.//Wassenaar, T.M.//Xu, Q.//Blaser, M.J. 	The gene product of Campylobacter jejuni gene Cj0208 is a DNA methyltransferase with specificity for GAATTC.	Abstr. Gen. Meet. Am. Soc. Microbiol.	2002	102		164			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. 		
@D	Takatani, N.//Nakanishi, M.//Meirelles, P.//Mino, S.//Suda, W.//Oshima, K.//Hattori, M.//Ohkuma, M.//Hosokawa, M.//Miyashita, K.//Thompson, F.L.//Niwa, A.//Sawabe, T.//Sawabe, T. 	Draft Genome Sequence of Marine Flavobacterium Jejuia pallidilutea Strain 11shimoA1 and Pigmentation Mutants.	Genome Announcements	2014	2		e01236-14			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. 		
@D	Takatani, N.//Nakanishi, M.//Meirelles, P.//Mino, S.//Suda, W.//Oshima, K.//Hattori, M.//Ohkuma, M.//Hosokawa, M.//Miyashita, K.//Thompson, F.L.//Niwa, A.//Sawabe, T.//Sawabe, T. 	Draft Genome Sequences of Marine Flavobacterium Algibacter lectus Strains SS8 and NR4.	Genome Announcements	2014	2		e01168-14			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. 		
@D	Takehara, I.//Kato, D.I.//Takeo, M.//Negoro, S. 	Draft Genome Sequence of the Nylon Oligomer-Degrading Bacterium Arthrobacter sp.  Strain KI72.	Genome Announcements	2017	5		e00217-17			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. 		
@D	Takeno, A.//Okamoto, A.//Tori, K.//Oshima, K.//Hirakawa, H.//Toh, H.//Agata, N.//Yamada, K.//Ogasawara, N.//Hayashi, T.//Shimizu, T.//Kuhara, S.//Hattori, M.//Ohta, M. 	Complete Genome Sequence of Bacillus cereus NC7401, Which Produces High Levels of the Emetic Toxin Cereulide.	J. Bacteriol.	2012	194		4767-4768			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. 		
@D	Takeshima, H.//Suetake, I.//Tajima, S. 	Mouse Dnmt3a Preferentially Methylates Linker DNA and Is Inhibited by Histone H1.	J. Mol. Biol.	2008	383		810-821			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. 		
@D	Takeshita, K.//Shibata, T.F.//Nikoh, N.//Nishiyama, T.//Hasebe, M.//Fukatsu, T.//Shigenobu, S.//Kikuchi, Y. 	Whole-Genome Sequence of Burkholderia sp. Strain RPE67, a Bacterial Gut Symbiont  of the Bean Bug Riptortus pedestris.	Genome Announcements	2014	2		e00556-14			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. 		
@D	Takeshita, K.//Suetake, I.//Yamashita, E.//Suga, M.//Narita, H.//Nakagawa, A.//Tajima, S. 	Structural insight into maintenance methylation by mouse DNA methyltransferase 1 (Dnmt1).	Proc. Natl. Acad. Sci. U. S. A.	2011	108		9055-9059			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. 		
@D	Takeuchi, F.//Watanabe, S.//Baba, T.//Yuzawa, H.//Ito, T.//Morimoto, Y.//Kuroda, M.//Cui, L.//Takahashi, M.//Ankai, A.//Baba, S.//Fukui, S.//Lee, J.C.//Hiramatsu, K. 	Whole-genome sequencing of Staphylococcus haemolyticus uncovers the extreme plasticity of its genome and the evolution of Human-colonizing   Staphylococcal species.	J. Bacteriol.	2005	187		7292-7308			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. 		
@D	Takeuchi, H.//Donahue, J.P.//Krishna, U.//Miller, G.G.//Peek, R.M. Jr.//Israel, D.A. 	Quantitative detection of expression of the Helicobacter pylori methyltransferase-encoding gene hpyIM in vivo and in vitro.	Abstr. Gen. Meet. Am. Soc. Microbiol.	2002	102		242			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. 		
@D	Takeuchi, H.//Israel, D.A.//Miller, G.G.//Donahue, J.P.//Krishna, U.//Gaus, K.//Peek, R.M. 	Characterization of expression of a functionally conserved Helicobacter pylori methyltransferase-encoding gene within inflamed mucosa and  during in vitro growth.	J. Infect. Dis.	2002	186		1186-1189			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. 		
@D	Takeuchi, K.//Noda, N.//Someya, N. 	Complete Genome Sequence of the Biocontrol Strain Pseudomonas protegens Cab57 Discovered in Japan Reveals Strain-Specific Diversity of This Species.	PLoS ONE	2014	9		E93683			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. 		
@D	Takeuchi, R.//Certo, M.//Caprara, M.G.//Scharenberg, A.M.//Stoddard, B.L. 	Optimization of in vivo activity of a bifunctional homing endonuclease and maturase reverses evolutionary degradation.	Nucleic Acids Res.	2009	37		877-890			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. 		
@D	Takeuchi, R.//Choi, M.//Stoddard, B.L. 	Engineering of Customized Meganucleases via In Vitro Compartmentalization and In Cellulo Optimization.	Methods Mol. Biol.	2015	1239		105-132			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. 		
@D	Takeuchi, R.//Lambert, A.R.//Mak, A.N.//Jacoby, K.//Dickson, R.J.//Gloor, G.B.//Scharenberg, A.M.//Edgell, D.R.//Stoddard, B.L. 	Tapping natural reservoirs of homing endonucleases for targeted gene modification.	Proc. Natl. Acad. Sci. U. S. A.	2011	108		13077-13082			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. 		
@D	Takiguchi, M.//Achanzar, W.E.//Qu, W.//Li, G.//Waalkes, M.P. 	Effects of cadmium on DNA-(cytosine-5) methyltransferase activity and DNA methylation status during cadmium-induced cellular transformation.	Exp. Cell Res.	2003	286		355-365			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. 		
@D	Taktakishvili, M.O.//Tabdzhun, A. 	Oligodeoxynucleotides, containing 6-O-alkylated guanine segments recognized by HaeIII restriction endonuclease.	Bioorg. Khim.	1991	17		806-808			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. 		
@D	Talukdar, M.//Das, D.//Borah, C.//Deka-Boruah, H.P.//Bora, T.C.//Singh, A.K. 	Draft Genome Sequence of Micromonospora sp. Strain HK10, Isolated from Kaziranga  National Park, India.	Genome Announcements	2016	4		e00559-15			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. 		
@D	Tamariz, J.//Llanos, C.//Seas, C.//Montenegro, P.//Lagos, J.//Fernandes, M.R.//Cerdeira, L.//Lincopan, N. 	Draft Genome Sequence of the First New Delhi Metallo-beta-Lactamase (NDM-1)-Producing Escherichia coli Strain Isolated in Peru.	Genome Announcements	2018	6		e00199-18			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. 		
@D	Tamaru, H.//Selker, E.U. 	A histone H3 methyltransferase controls DNA methylation in Neurospora crassa.	Nature	2001	414		277-283			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. 		
@D	Tamaru, Y.//Miyake, H.//Kuroda, K.//Nakanishi, A.//Kawade, Y.//Yamamoto, K.//Uemura, M.//Fujita, Y.//Doi, R.H.//Ueda, M. 	Genome Sequence of the Cellulosome-Producing Mesophilic Organism Clostridium cellulovorans 743B.	J. Bacteriol.	2010	192		901-902			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. 		
@D	Tamas, I.//Dedysh, S.N.//Liesack, W.//Stott, M.B.//Alam, M.//Murrell, J.C.//Dunfield, P.F. 	Complete Genome Sequence of Beijerinckia indica subsp. indica.	J. Bacteriol.	2010	192		4532-4533			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. 		
@D	Tamas, I.//Klasson, L.//Canback, B.//Naslund, A.K.//Eriksson, A.-S.//Wernegreen, J.J.//Sandstrom, J.P.//Moran, N.A.//Andersson, S.G.E. 	50 million years of genomic stasis in endosymbiotic bacteria.	Science	2002	296		2376-2379			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. 		
@D	Tambalo, D.D.//Perry, B.J.//Fitzgerald, S.F.//Cameron, A.D.//Yost, C.K. 	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.	Genome Announcements	2015	3		e00884-15			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. 		
@D	Tambong, J.T.//Xu, R.//Adam, Z.//Cott, M.//Rose, K.//Reid, L.M.//Daayf, F.//Briere, S.//Bilodeau, G.J. 	Draft Genome Sequence of Clavibacter michiganensis subsp. nebraskensis Strain DOAB 397, Isolated from an Infected Field Corn Plant in Manitoba, Canada.	Genome Announcements	2015	3		e00768-15			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. 		
@D	Tamhankar, A.J.//Nerkar, S.S.//Khadake, P.P.//Akolkar, D.B.//Apurwa, S.R.//Deshpande, U.//Khedkar, S.U.//Stalsby-Lundborg, C. 	Draft Genome Sequence of Enterotoxigenic Escherichia coli Strain E24377A, Obtained from a Tribal Drinking Water Source in India.	Genome Announcements	2015	3		e00225-15			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. 		
@D	Tamulaitiene, G.//Grazulis, S.//Janulaitis, A.//Janowski, R.//Bujacz, G.//Jaskolski, M. 	Crystallization and preliminary crystallographic studies of a bifunctional restriction endonuclease Eco57I.	Biochim. Biophys. Acta	2004	1698		251-254			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. 		
@D	Tamulaitiene, G.//Jakubauskas, A.//Urbanke, C.//Huber, R.//Grazulis, S.//Siksnys, V. 	The crystal structure of the rare-cutting restriction enzyme SdaI reveals unexpected domain architecture.	Structure	2006	14		1389-1400			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. 		
@D	Tamulaitiene, G.//Jovaisaite, V.//Tamulaitis, G.//Songailiene, I.//Manakova, E.//Zaremba, M.//Grazulis, S.//Xu, S.Y.//Siksnys, V. 	Restriction endonuclease AgeI is a monomer which dimerizes to cleave DNA.	Nucleic Acids Res.	2017	45		3547-3558			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. 		
@D	Tamulaitiene, G.//Siksnys, V. 	NotI Is Not Boring.	Structure	2008	16		497-498			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. 		
@D	Tamulaitiene, G.//Silanskas, A.//Grazulis, S.//Zaremba, M.//Siksnys, V. 	Crystal structure of the R-protein of the multisubunit ATP-dependent restriction  endonuclease NgoAVII.	Nucleic Acids Res.	2014	42		14022-14030			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. 		
@D	Tamulaitis, G.//Lagunavicius, A. 	DNA bending induced by MunI restriction endonuclease.	Biologija	2000	0		11-15			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. 		
@D	Tamulaitis, G.//Mucke, M.//Siksnys, V. 	Biochemical and mutational analysis of EcoRII functional domains reveals evolutionary links between restriction enzymes.	FEBS Lett.	2006	580		1665-1671			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. 		
@D	Tamulaitis, G.//Rutkauskas, M.//Zaremba, M.//Grazulis, S.//Tamulaitiene, G.//Siksnys, V. 	Functional significance of protein assemblies predicted by the crystal structure  of the restriction endonuclease BsaWI.	Nucleic Acids Res.	2015	43		8100-8110			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. 		
@D	Tamulaitis, G.//Sasnauskas, G.//Mucke, M.//Siksnys, V. 	Simultaneous Binding of Three Recognition Sites is Necessary for a Concerted Plasmid DNA Cleavage by EcoRII Restriction Endonuclease.	J. Mol. Biol.	2006	358		406-419			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. 		
@D	Tamulaitis, G.//Solonin, A.S.//Siksnys, V. 	Alternative arrangements of catalytic residues at the active sites of restriction enzymes.	FEBS Lett.	2002	518		17-22			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. 		
@D	Tamulaitis, G.//Zaremba, M.//Szczepanowski, R.H.//Bochtler, M.//Siksnys, V. 	How PspGI, catalytic domain of EcoRII and Ecl18kI acquire specificities for different DNA targets.	Nucleic Acids Res.	2008	36		6101-6108			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. 		
@D	Tamulaitis, G.//Zaremba, M.//Szczepanowski, R.H.//Bochtler, M.//Siksnys, V. 	Nucleotide flipping by restriction enzymes analyzed by 2-aminopurine steady-state fluorescence.	Nucleic Acids Res.	2007	35		4792-4799			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. 		
@D	Tamura, T.//Araki, Y.//Yamaoka, S.//Inagaki, K.//Tanaka, H. 	Determination of methylation specificity of sequence-specific DNA methyltransferases using matrix assisted laser desorption/ionization time-of-flight mass spectrometry.	Nucleic Acids Res.	1997	25		4162-4164			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. 		
@D	Tamura, T.//Kataoka, A.//Shu, L.Y.//Ashida, A.//Tanaka, H.//Inagaki, K. 	An in vitro Screening Method for DNA Cytosine-C5-Methylase Inhibitor.	Nat. Prod. Lett.	2002	16		25-27			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. 		
@D	Tan, A.//Atack, J.M.//Jennings, M.P.//Seib, K.L. 	The Capricious Nature of Bacterial Pathogens: Phasevarions and Vaccine Development.	Front. Immunol.	2016	7		586			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. 		
@D	Tan, A.//Blakeway, L.V.//Bakaletz, L.O.//Boitano, M.//Clark, T.A.//Korlach, J.//Jennings, M.P.//Peak, I.R.//Seib, K.L. 	Complete Genome Sequence of Moraxella catarrhalis Strain CCRI-195ME, Isolated from the Middle Ear.	Genome Announcements	2017	5		e00384-17			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. 		
@D	Tan, A.//Hill, D.M.//Harrison, O.B.//Srikhanta, Y.N.//Jennings, M.P.//Maiden, M.C.//Seib, K.L. 	Distribution of the type III DNA methyltransferases modA, modB and modD among Neisseria meningitidis genotypes: implications for gene regulation and virulence.	Sci. Rep.	2016	6		21015			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. 		
@D	Tan, B.//Charchuk, R.//Li, C.//Nesbo, C.//Abu, L.N.//Foght, J. 	Draft Genome Sequence of Uncultivated Firmicutes (Peptococcaceae SCADC) Single Cells Sorted from Methanogenic Alkane-Degrading Cultures.	Genome Announcements	2014	2		e00909-14			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. 		
@D	Tan, B.//de Araujo, E.S.R.//Rozycki, T.//Nesbo, C.//Foght, J. 	Draft Genome Sequences of Three Smithella spp. Obtained from a Methanogenic Alkane-Degrading Culture and Oil Field Produced Water.	Genome Announcements	2014	2		e01085-14			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. 		
@D	Tan, B.//Foght, J. 	Draft genome sequences of campylobacterales (epsilonproteobacteria) obtained from methanogenic oil sands tailings pond metagenomes.	Genome Announcements	2014	2		e01034-14			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. 		
@D	Tan, B.F.//Te, S.H.//Boo, C.Y.//Gin, K.Y.//Thompson, J.R. 	Insights from the draft genome of the subsection V (Stigonematales) cyanobacterium Hapalosiphon sp. Strain MRB220 associated with 2-MIB production.	Standards in Genomic Sciences	2016	11		58			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. 		
@D	Tan, B.F.//Te, S.H.//Gin, K.Y.//Thompson, J.R. 	Draft Genome Sequence of a Tropical Freshwater Cyanobacterium, Limnothrix sp. Strain P13C2.	Genome Announcements	2016	4		e01117-16			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. 		
@D	Tan, C.//Xu, Z.//Zheng, H.//Liu, W.//Tang, X.//Shou, J.//Wu, B.//Wang, S.//Zhao, G.P.//Chen, H. 	Genome Sequence of Porcine Extraintestinal Pathogenic Escherichia coli strain.	J. Bacteriol.	2011	193		5038			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. 		
@D	Tan, E.//Chen, Y.//Kuan, J.//Lin, C.//Jagoda, S.S.//Lin, F.//Tzou, W.//Kinoshita, S.//Watabe, S.//Asakawa, S.//Liu, S. 	Draft Genome Sequence of Thermoanaerobacterium saccharolyticum Strain NTOU1, a Thermophilic Bacterium Isolated from Marine Shallow Hydrothermal Vents.	Genome Announcements	2014	2		e01019-14			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. 		
@D	Tan, H.L.//Wang, Y.//Cheng, X.Q.//Huang, Y.M.//Liu, W.//Zhang, L.J. 	Genome Sequence of a Pandrug-Resistant Pseudomonas aeruginosa Strain, YN-1.	Genome Announcements	2014	2		e01280-14			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. 		
@D	Tan, H.L.//Wang, Y.//Cheng, X.Q.//Huang, Y.M.//Liu, W.//Zhang, L.J. 	Genome Sequence of an Extensively Drug-Resistant Strain of Klebsiella pneumoniae, Strain YN-1, with Carbapenem Resistance.	Genome Announcements	2015	3		e01279-14			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. 		
@D	Tan, J.L.//Ng, H.F.//Wee, W.Y.//Ang, M.Y.//Wong, G.J.//Ngeow, Y.F.//Choo, S.W. 	First Whole-Genome Sequence of Mycobacterium iranicum, a Newly Reported Mycobacterial Species.	Genome Announcements	2013	1		e00732-13			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. 		
@D	Tan, J.Y.//Yin, W.F.//Chan, K.G. 	Gene clusters of Hafnia alvei strain FB1 important in survival and pathogenesis: a draft genome perspective.	Gut Pathog.	2014	6		29			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. 		
@D	Tan, K.H.//Sheng, K.Y.//Chang, C.Y.//Yin, W.F.//Chan, K.G. 	Draft Genome Sequence of a Quorum-Sensing Bacterium, Dickeya sp. Strain 2B12, Isolated from a Freshwater Lake.	Genome Announcements	2015	3		e01542-14			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. 		
@D	Tan, N.-W.//Li, F.F.L. 	Interaction of oligonucleotides containing 6-O-methylguanine with human DNA (cytosine-5-)-methyltransferase.	Biochemistry	1990	29		9234-9240			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. 		
@D	Tan, S.//Meng, Y.//Su, A.//Zhang, C.//Ren, Y. 	Draft Genome Sequence of Bacillus subtilis subsp. natto Strain CGMCC 2108, a High Producer of Poly-gamma-Glutamic Acid.	Genome Announcements	2016	4		e00426-16			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. 		
@D	Tan, W.//Wang, G.//Pan, Z.//Yin, Y.//Jiao, X. 	Complete Genome Sequence of Listeria monocytogenes NTSN, a Serovar 4b and Animal  Source Strain.	Genome Announcements	2015	3		e01403-14			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. 		
@D	Tan, W.G.H.//Barkman, T.J.//Gregory, C.V.//Essani, K. 	Comparative genomic analyses of frog virus 3, type species of the genus Ranavirus (family Iridoviridae).	Virology	2004	323		70-84			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. 		
@D	Tan, W.S.//Chang, C.Y.//Yin, W.F.//Chan, K.G. 	Understanding the Quorum-Sensing Bacterium Pantoea stewartii Strain M009 with Whole-Genome Sequencing Analysis.	Genome Announcements	2015	3		e01509-14			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. 		
@D	Tan, W.S.//Yin, W.F.//Chan, K.G. 	Insights into the Quorum-Sensing Activity in Aeromonas hydrophila Strain M013 as  Revealed by Whole-Genome Sequencing.	Genome Announcements	2015	3		e01372-14			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. 		
@D	Tan, W.S.//Yin, W.F.//Chang, C.Y.//Chan, K.G. 	Whole-Genome Sequencing Analysis of Quorum-Sensing Aeromonas hydrophila Strain M023 from Freshwater.	Genome Announcements	2015	3		e01548-14			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. 		
@D	Tanabe, Y.//Yamaguchi, H.//Watanabe, M.M. 	Draft Genome Sequence of 'Candidatus Phycosocius bacilliformis,' an Alphaproteobacterial Ectosymbiont of the Hydrocarbon-Producing Green Alga  Botryococcus braunii.	Genome Announcements	2018	6		e00396-18			'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. 		
@D	Tanaka, R.//Mizutani, Y.//Shibata, T.//Miyake, H.//Iehata, S.//Mori, T.//Kuroda, K.//Ueda, M. 	Genome Sequence of Formosa haliotis Strain MA1, a Brown Alga-Degrading Bacterium  Isolated from the Gut of Abalone Haliotis gigantea.	Genome Announcements	2016	4		e01312-16			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. 		
@D	Tanaka, T. 	Restriction of plasmid-mediated transformation in Bacillus subtilis 168.	Mol. Gen. Genet.	1979	175		235-237			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. 		
@A	Tandeau de Marsac, N.//Houmard, J. 		Advances in cyanobacterial molecular genetics.			Fay, P.//Van Baalen, C. 		Cyanobacteria					Elsevier	1987		0		251-302									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. 		
@D	Tandon, K.//Chiang, P.W.//Chen, W.M.//Tang, S.L. 	Draft Genome Sequence of Endozoicomonas acroporae Strain Acr-14(T), Isolated from Acropora Coral.	Genome Announcements	2018	6		e01576-17			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. 		
@D	Taneike, I.//Otsuka, T.//Dohmae, S.//Saito, K.//Ozaki, K.//Takano, M.//Higuchi, W.//Takano, T.//Yamamoto, T. 	Molecular nature of methicillin-resistant Staphylococcus aureus derived from explosive nosocomial outbreaks of the 1980s in Japan.	FEBS Lett.	2006	580		2323-2334			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. 		
@D	Tang, B.//Wang, Q.//Yang, M.//Xie, F.//Zhu, Y.//Zhuo, Y.//Wang, S.//Gao, H.//Ding, X.//Zhang, L.//Zhao, G.//Zheng, H. 	ContigScape: a Cytoscape plugin facilitating microbial genome gap closing.	BMC Genomics	2013	14		289			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. 		
@D	Tang, B.//Yu, Y.//Cen, X.//Zhu, Y.//Dai, R.//Wang, X.//Zhao, G.//Ding, X. 	Draft Genome Sequence of the Streptothricin-Producing Strain Streptomyces sp. fd2-tb.	Genome Announcements	2015	3		e01277-15			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. 		
@D	Tang, B.//Zhao, W.//Zheng, H.//Zhuo, Y.//Zhang, L.//Zhao, G.P. 	Complete Genome Sequence of Amycolatopsis mediterranei S699 Based on De Novo Assembly via a Combinatorial Sequencing Strategy.	J. Bacteriol.	2012	194		5699-5700			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. 		
@D	Tang, B.L.//Rong, J.C.//Dang, Y.R.//Xie, B.B.//Chen, X.L.//Zhang, X.Y. 	Complete Genomic Sequence of Pseudoalteromonas sp. Strain SAO4-4, a Protease-Producing Bacterium Isolated from Seawater of the Atlantic Ocean.	Genome Announcements	2018	6		e00284-18			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. 		
@D	Tang, D.//Ando, S.//Takasaki, Y.//Tadano, J. 	Mutational analyses of restriction endonuclease-HindIII mutant E86K with higher activity and altered specificity.	Protein Eng.	2000	13		283-289			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. 		
@D	Tang, G.//Cui, R.//Tian, Y.//Lin, X. 	Draft Genome Sequence of Pacificimonas aurantium Type Strain JLT2012, Isolated from the Seawater of the Pacific Ocean.	Genome Announcements	2017	5		e00755-17			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. 		
@D	Tang, H.//Yu, H.//Li, Q.//Wang, X.//Gai, Z.//Yin, G.//Su, F.//Tao, F.//Ma, C.//Xu, P. 	Genome Sequence of Pseudomonas putida Strain B6-2, a Superdegrader of Polycyclic Aromatic Hydrocarbons and Dioxin-Like Compounds.	J. Bacteriol.	2011	193		6789-6790			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. 		
@D	Tang, H.//Yu, H.//Tai, C.//Huang, K.//Liu, Y.//Wang, L.//Yao, Y.//Wu, G.//Xu, P. 	Genome Sequence of a Novel Nicotine-Degrading Strain, Pseudomonas geniculata N1.	J. Bacteriol.	2012	194		3553-3554			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. 		
@D	Tang, J.//Liu, X.//Peng, J.//Tang, Y.//Zhang, Y. 	Genome sequence and genome mining of a marine-derived antifungal bacterium Streptomyces sp. M10.	Appl. Microbiol. Biotechnol.	2015	99		2763-2772			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. 		
@D	Tang, J.//Zhang, Y.//Meng, H.//Xue, Z.//Ma, J. 	Complete Genome Sequence of Exiguobacterium sp. Strain MH3, Isolated from Rhizosphere of Lemna minor.	Genome Announcements	2013	1		e01059-13			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. 		
@D	Tang, K.//Allman, S.L.//Chen, C.H.//Chang, L.Y.//Schell, M. 	Matrix-assisted laser desorption/ionization of restriction enzyme-digested DNA.	Rapid Commun. Mass. Spectrom.	1994	8		183-186			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. 		
@D	Tang, K.//Liu, K.//Jiao, N. 	Draft Genome Sequence of Oceaniovalibus guishaninsula JLT2003T.	J. Bacteriol.	2012	194		6683			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). 		
@D	Tang, K.//Liu, K.//Li, S.//Jiao, N. 	Draft Genome Sequence of Strain JLT2015T, Belonging to the Family Sphingomonadaceae of the Alphaproteobacteria.	Genome Announcements	2013	1		e00226-13			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. 		
@D	Tang, L.Y.//Reddy, M.N.//Rasheva, V.//Lee, T.L.//Lin, M.J.//Hung, M.S.//Shen, C.K. 	The eukaryotic DNMT2 genes encode a new class of cytosine-5 DNA methyltransferases.	J. Biol. Chem.	2003	278		33613-33616			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. 		
@D	Tang, S.//Edwards, E.A. 	Complete Genome Sequence of Bacteroidales Strain CF from a Chloroform-Dechlorinating Enrichment Culture.	Genome Announcements	2013	1		e01066-13			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. 		
@D	Tang, S.L.//Nuttall, S.//Ngui, K.//Fisher, C.//Lopez, P.//Dyall-Smith, M. 	HF2: a double-stranded DNA tailed haloarchaeal virus with a mosaic genome.	Mol. Microbiol.	2002	44		283-296			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. 		
@D	Tang, W.J.//Zhou, Y.//Ye, B.C. 	Draft Genome Sequence of a Phthalate Ester-Degrading Bacterium, Rhizobium sp. LMB-1, Isolated from Cultured Soil.	Genome Announcements	2015	3		e00392-15			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. 		
@D	Tani, A.//Ogura, Y.//Hayashi, T.//Kimbara, K. 	Complete Genome Sequence of Methylobacterium aquaticum Strain 22A, Isolated from  Racomitrium japonicum Moss.	Genome Announcements	2015	3		e00266-15			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. 		
@D	Tanimoto, Y.//Tamai, S.//Matsuzaki, T.//Takeuchi, N.//Noju, T.//Yanagida, S.//Kage-Nakadai, E.//Yamaguchi, Y.//Kodama, T.//Nakamura, S.//Motooka, D.//Iida, T.//Nishikawa, Y. 	Diffusely adherent Escherichia coli strains isolated from healthy carriers suppress cytokine secretions of epithelial cells stimulated by inflammatory substances.	Infect. Immun.	2018	87		0			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. 		
@D	Tanizawa, Y.//Fujisawa, T.//Mochizuki, T.//Kaminuma, E.//Nakamura, Y.//Tohno, M. 	Draft Genome Sequence of Lactobacillus oryzae Strain SG293T.	Genome Announcements	2014	2		e00861-14			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. 		
@D	Tanizawa, Y.//Fujisawa, T.//Mochizuki, T.//Kaminuma, E.//Suzuki, Y.//Nakamura, Y.//Tohno, M. 	Draft Genome Sequence of Weissella oryzae SG25T, Isolated from Fermented Rice Grains.	Genome Announcements	2014	2		e00667-14			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. 		
@D	Tank, M.//Liu, Z.//Frigaard, N.U.//Tomsho, L.P.//Schuster, S.C.//Bryant, D.A. 	Complete Genome Sequence of the Photoautotrophic and Bacteriochlorophyll e-Synthesizing Green Sulfur Bacterium Chlorobaculum limnaeum DSM 1677T.	Genome Announcements	2017	5		e00529-17			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. 		
@D	Tanyashin, V.I.//Li, L.I.//Muijnieks, I.O.//Baev, A.A. 	New endonuclease Hind GLU in Haemophilus influenzae Rd123.	Dokl. Akad. Nauk.	1976	231		226-228			None 		
@D	Tanyashin, V.I.//Zimin, A.A.//Shlyapnikov, M.G.//Boronin, A.M. 	Transduction of plasmid antibiotic resistance determinants with pseudoT-even bacteriophages.	Genetika	2003	39		914-926			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. 		
@D	Tao, F.//Shen, Y.//Fan, Z.//Tang, H.//Xu, P. 	Genome Sequence of Pseudomonas putida S12, a Potential Platform Strain for Industrial Production of Valuable Chemicals.	J. Bacteriol.	2012	194		5985-5986			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. 		
@D	Tao, F.//Tai, C.//Liu, Z.//Wang, A.//Wang, Y.//Li, L.//Gao, C.//Ma, C.//Xu, P. 	Genome Sequence of Klebsiella pneumoniae LZ, a Potential Platform Strain for 1,3-Propanediol Production.	J. Bacteriol.	2012	194		4457-4458			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. 		
@D	Tao, F.//Tang, H.//Gai, Z.//Su, F.//Wang, X.//He, X.//Xu, P. 	Genome Sequence of Pseudomonas putida Idaho, a Unique Organic-Solvent-Tolerant Bacterium.	J. Bacteriol.	2011	193		7011-7012			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. 		
@D	Tao, F.//Wang, X.//Ma, C.//Yang, C.//Tang, H.//Gai, Z.//Xu, P. 	Genome Sequence of Xanthomonas campestris JX, an Industrially Productive Strain for Xanthan Gum.	J. Bacteriol.	2012	194		4755-4756			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. 		
@D	Tao, F.//Zhao, P.//Li, Q.//Su, F.//Yu, B.//Ma, C.//Tang, H.//Tai, C.//Wu, G.//Xu, P. 	Genome Sequence of Rhodococcus erythropolis XP, a Biodesulfurizing Bacterium with Industrial Potential.	J. Bacteriol.	2011	193		6422-6423			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. 		
@D	Tao, T. 	Characterization of the cloned PvuII type II restriction-modification system in Escherichia coli.	Diss. Abstr.	1992	53		115B			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. 		
@D	Tao, T.//Blumenthal, R.M. 	Sequence and subunit structure of restriction endonuclease PvuII.	Abstr. Gen. Meet. Am. Soc. Microbiol.	1991	91		175			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. 		
@D	Tao, T.//Blumenthal, R.M. 	Sequence and characterization of pvuIIR, the PvuII endonuclease gene, and of pvuIIC, its regulatory gene.	J. Bacteriol.	1992	174		3395-3398			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. 		
@D	Tao, T.//Bourne, J.C.//Blumenthal, R.M. 	A family of regulatory genes associated with Type II restriction-modification systems.	J. Bacteriol.	1991	173		1367-1375			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. 		
@D	Tao, T.//Walter, J.//Brennan, K.J.//Cotterman, M.M.//Blumenthal, R.M. 	Sequence, internal homology and high-level expression of the gene for a DNA-(cytosine N4)-methyltransferase, M.Pvu II.	Nucleic Acids Res.	1989	17		4161-4175			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. 		
@D	Tao, X.//Jiang, M.//Zhang, F.//Xu, F.//Wei, H. 	Draft Genome Sequence of Lactobacillus plantarum WLPL04, Isolated from Human Breast Milk.	Genome Announcements	2015	3		e01443-15			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. 		
@D	Tapia, P.//Flores, F.M.//Covarrubias, P.C.//Acuna, L.G.//Holmes, D.S.//Quatrini, R. 	Complete Genome Sequence of Temperate Bacteriophage AcaML1 from the Extreme Acidophile Acidithiobacillus caldus ATCC 51756.	J. Virol.	2012	86		12452-12453			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. 		
@D	Taranto, M.P.//Villena, J.//Salva, S.//Alvarez, S.//Savoy-de-Giori, G.//Font-de-Valdez, G.//Hebert, E.M. 	Draft Genome Sequence of Lactobacillus rhamnosus CRL1505, an Immunobiotic Strain  Used in Social Food Programs in Argentina.	Genome Announcements	2013	1		e00627-13			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. 		
@D	Tarasova, G.V.//Nayakshina, T.N.//Degtyarev, S.K. 	Substrate specificity of new methyl-directed DNA endonuclease GlaI.	BMC Mol. Biol.	2008	9		7			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. 		
@D	Tarasova, M.V.//Kuznetsov, V.V.//Netesova, N.A.//Gonchar, D.A.//Degtyarev, S.C. 	Cloning and analysis of biochemical and catalytic properties of DNA methyltransferase M1.BspACI.	Vestn. Mosk. Univ.	2011	0		38-40			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). 		
@D	Tarasova, M.V.//Kuznetsov, V.V.//Netesova, N.A.//Gonchar, D.A.//Degtyarev, S.K. 	Recombinant DNA-Methyltransferase M1.BspACI from Bacillus psychrodurans AC: Purification and Properties.	Biochemistry	2010	75		1484-1490			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). 		
@D	Tarazona, D.//Borda, V.//Galarza, M.//Agapito, J.C.//Guio, H. 	Functional Analysis Using Whole-Genome Sequencing of a Drug-Sensitive Mycobacterium tuberculosis Strain from Peru.	Genome Announcements	2014	2		e00087-14			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. 		
@D	Tarazona, D.//Padilla, C.//Caceres, O.//Montenegro, J.D.//Bailon, H.//Ventura, G.//Mendoza, G.//Anaya, E.//Guio, H. 	Whole Genome Sequencing and Comparative Analysis of Bartonella bacilliformis Strain INS, the Causative Agent of Carrion's Disease.	Genome Announcements	2013	1		e00053-12			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. 		
@D	Tardy-Planechaud, S.//Fujimoto, J.//Lin, S.S.//Sowers, L.C. 	Solid phase synthesis and restriction endonuclease cleavage of oligodeoxynucleotides containing 5-(hydroxymethyl)-cytosine.	Nucleic Acids Res.	1997	25		553-558			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. 		
@D	Tareb, R.//Bernardeau, M.//Vernoux, J.P. 	Genome Sequence of Lactobacillus rhamnosus Strain CNCM I-3698.	Genome Announcements	2015	3		e00582-15			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%. 		
@D	Tareb, R.//Bernardeau, M.//Vernoux, J.P. 	Genome Sequence of Rough and Smooth Variants of Pleomorphic Strain Lactobacillus  farciminis CNCM-I-3699.	Genome Announcements	2015	3		e01059-15			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. 		
@D	Tarkka, M.T.//Feldhahn, L.//Buscot, F.//Wubet, T. 	Genome Sequence of the Mycorrhiza Helper Bacterium Streptomyces sp. Strain AcH 505.	Genome Announcements	2015	3		e01386-14			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. 		
@D	Tarkka, M.T.//Feldhahn, L.//Kruger, D.//Arnold, N.//Buscot, F.//Wubet, T. 	Draft Genome Sequence of Streptomyces sp. Strain 150FB, a Mushroom Mycoparasite Antagonist.	Genome Announcements	2015	3		e01441-14			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. 		
@D	Tarlachkov, S.V.//Dyachenko, O.V.//Cherevatenko, A.M.//Rudenko, N.V.//Shevchuk, T.V. 	Cloning, purification and characterization of translationally fused protein DNA methyltransferase MoHhaI-EGFP.	Process. Biochem.	2014	49		2170-2173			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. 		
@D	Taron, C.H.//Van Cott, E.M.//Wilson, G.G.//Moran, L.S.//Slatko, B.E.//Hornstra, L.J.//Benner, J.S.//Kucera, R.B.//Guthrie, E.P. 	Cloning and expression of the NaeI restriction endonuclease-encoding gene and sequence analysis of the NaeI restriction-modification system.	Gene	1995	155		19-25			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. 		
@D	Taron, C.H.//Van Cott, E.M.//Wilson, G.G.//Moran, L.S.//Slatko, B.E.//Hornstra, L.J.//Benner, J.S.//Kucera, R.B.//Guthrie, E.P. 	Cloning, sequencing and overexpressing the NaeI restriction endonuclease gene from Nocardia aerocolonigenes.	J. Cell Biochem. Suppl.	1993	17C		175			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. 		
@D	Tasara, T.//Ebner, R.//Klumpp, J.//Stephan, R. 	Complete Genome Sequence of Listeria monocytogenes N2306, a Strain Associated with the 2013-2014 Listeriosis Outbreak in Switzerland.	Genome Announcements	2015	3		e00553-15			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. 		
@D	Tasara, T.//Fierz, L.//Klumpp, J.//Schmidt, H.//Stephan, R. 	Draft Genome Sequences of Five Shiga Toxin-Producing Escherichia coli Isolates Harboring the New and Recently Described Subtilase Cytotoxin Allelic Variant  subAB2-3.	Genome Announcements	2017	5		e01582-16			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. 		
@D	Tasara, T.//Klumpp, J.//Bille, J.//Stephan, R. 	Genome Sequences of Listeria monocytogenes Strains Responsible for Cheese- and Cooked Ham Product-Associated Swiss Listeriosis Outbreaks in 2005 and 2011.	Genome Announcements	2016	4		e00106-16			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. 		
@D	Tasara, T.//Morach, M.//Klumpp, J.//Stephan, R. 	Complete Genome Sequence of Anoxybacillus flavithermus Strain 52-1A Isolated from a Heat-Processed Powdered Milk Concentrate.	Genome Announcements	2017	5		e00800-17			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. 		
@D	Tasara, T.//Weinmaier, T.//Klumpp, J.//Rattei, T.//Stephan, R. 	Complete Genome Sequence of Listeria monocytogenes Lm60, a Strain with an Enhanced Cold Adaptation Capacity.	Genome Announcements	2014	2		e01248-14			The complete genome sequence of Listeria monocytogenes Lm60, a fast cold-adapting serotype 1/2a human isolate, is presented. 		
@D	Tashkandy, N. et al. 	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).	Standards in Genomic Sciences	2016	11		42			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. 		
@D	Tasse, L.//Bercovici, J.//Pizzut-Serin, S.//Robe, P.//Tap, J.//Klopp, C.//Cantarel, B.L.//Coutinho, P.M.//Henrissat, B.//Leclerc, M.//Dore, J.//Monsan, P.//Remaud-Simeon, M.//Potocki-Veronese, G. 	Functional metagenomics to mine the human gut microbiome for dietary fiber catabolic enzymes.	Genome Res.	2010	20		1605-1612			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. 		
@D	Tasseron-de Jong, J.G.//Aker, J.//Giphart-Gassler, M. 	The ability of the restriction endonuclease EcoRI to digest hemi-methylated versus fully cytosine-methylated DNA of the herpes tk promoter region.	Gene	1988	74		147-149			None 		
@D	Tateishi, Y.//Kitada, S.//Miki, K.//Maekura, R.//Ogura, Y.//Ozeki, Y.//Nishiuchi, Y.//Niki, M.//Hayashi, T.//Hirata, K.//Kobayashi, K.//Matsumoto, S. 	Whole-Genome Sequence of the Hypervirulent Clinical Strain Mycobacterium intracellulare M.i.198.	J. Bacteriol.	2012	194		6336			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. 		
@D	Tateishi, Y.//Tamaru, A.//Ogura, Y.//Niki, M.//Wada, T.//Yamamoto, T.//Hirata, K.//Hayashi, T.//Matsumoto, S. 	Whole-Genome Sequence of the Potentially Hypertransmissible Multidrug-Resistant Mycobacterium tuberculosis Beijing Strain OM-V02_005.	Genome Announcements	2013	1		e00608-13			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. 		
@D	Tatti, K.M.//Loparev, V.N.//Ranganathanganakammal, S.//Changayil, S.//Frace, M.//Weil, M.R.//Sammons, S.//Maccannell, D.//Mayer, L.W.//Tondella, M.L. 	Draft Genome Sequences of Bordetella holmesii Strains from Blood (F627) and Nasopharynx (H558).	Genome Announcements	2013	1		e0005613			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. 		
@D	Tatum, F.M.//Briggs, R.E. 	Isolation, identification, and cloning of a non-palindromic type II DNA restriction endonuclease, PhaI, from Pasteurella haemolytica.	Abstr. Gen. Meet. Am. Soc. Microbiol.	1993	93		199			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. 		
@D	Tauch, A.//Kaiser, O.//Hain, T.//Goesmann, A.//Weisshaar, B.//Albersmeier, A.//Bekel, T.//Bischoff, N.//Brune, I.//Chakraborty, T.//Kalinowski, J.//Meyer, F.//Rupp, O.//Schneiker, S.//Viehoever, P.//Puhler, A. 	Complete genome sequence and analysis of the multiresistant nosocomial pathogen Corynebacterium jeikeium K411, a lipid-requiring bacterium of the human skin flora.	J. Bacteriol.	2005	187		4671-4682			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. 		
@D	Tauch, A.//Kirchner, O.//Loffler, B.//Gotker, S.//Puhler, A.//Kalinowski, J. 	Efficient electrotransformation of Corynebacterium diphtheriae with a mini-replicon derived from the Corynebacterium glutamicum plasmid pGA1.	Curr. Microbiol.	2002	45		362-367			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. 		
@D	Tauch, A.//Kirchner, O.//Wehmeier, L.//Kalinowski, J.//Puhler, A. 	Corynebacterium glutamicum DNA is subjected to methylation-restriction in Escherichia coli.	FEMS Microbiol. Lett.	1994	123		343-347			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. 		
@D	Tauch, A.//Krieft, S.//Kalinowski, J.//Puhler, A. 	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.	Mol. Gen. Genet.	2000	263		1-11			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. 		
@D	Tauch, A.//Trost, E.//Tilker, A.//Ludewig, U.//Schneiker, S.//Goesmann, A.//Arnold, W.//Bekel, T.//Brinkrolf, K.//Brune, I.//Gotker, S.//Kalinowski, J.//Kamp, P.B.//Lobo, F.P.//Viehoever, P.//Weisshaar, B.//Soriano, F.//Droge, M.//Puhler, A. 	The lifestyle of Corynebacterium urealyticum derived from its complete genome sequence established by pyrosequencing.	J. Biotechnol.	2008	136		11-21			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. 		
@D	Tautz, N.//Kaluza, K.//Frey, B.//Jarsch, M.//Schmitz, G.G.//Kessler, C. 	SgrAI, a novel class-II restriction endonuclease from Streptomyces griseus recognizing the octanucleotide sequence 5'-CR/CCGGYG-3' .	Nucleic Acids Res.	1990	18		3087					
@D	Taveirne, M.E.//Dunham, D.T.//Miller, W.G.//Parker, C.T.//Huynh, S.//DiRita, V.J. 	Complete Genome Sequence and Annotation of a Campylobacter jejuni Strain, MTVDSCj20, Isolated from a Naturally Colonized Farm-Raised Chicken.	Genome Announcements	2014	2		e00852-14			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. 		
@D	Taveirne, M.E.//Dunham, D.T.//Perault, A.//Beauchamp, J.M.//Huynh, S.//Parker, C.T.//DiRita, V.J. 	Complete Annotated Genome Sequences of Three Campylobacter jejuni Strains Isolated from Naturally Colonized Farm-Raised Chickens.	Genome Announcements	2017	5		e01407-16			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. 		
@D	Tawfik, D.S.//Griffiths, A.D. 	Man-made cell-like compartments for molecular evolution.	Nat. Biotechnol.	1998	16		652-656			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. 		
@D	Tay, A.P.//Kaakoush, N.O.//Deshpande, N.P.//Chen, Z.//Mitchell, H.//Wilkins, M.R. 	Genome Sequence of Campylobacter showae UNSWCD, Isolated from a Patient with Crohn's Disease.	Genome Announcements	2013	1		e00193-12			Campylobacter showae UNSWCD was isolated from a patient with Crohn's disease. Here we present a 2.1 Mb draft assembly of its genome. 		
@D	Tay, M.//Roizman, D.//Cohen, Y.//Tolker-Nielsen, T.//Givskov, M.//Yang, L. 	Draft Genome Sequence of the Model Naphthalene-Utilizing Organism Pseudomonas putida OUS82.	Genome Announcements	2014	2		e01161-13			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. 		
@D	Tay, N.K.//Blaschek, H.P. 	Purification and characterization of a restriction endonuclease (CpfI) from Clostridium perfringens 10543A.	Abstr. Gen. Meet. Am. Soc. Microbiol.	1994	94		224			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. 		
@D	Taylor, C.//Ford, K.//Connolly, B.A.//Hornby, D.P. 	Determination of the order of substrate addition to MspI DNA methyltransferase using a novel mechanism-based inhibitor.	Biochem. J.	1993	291		493-504			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. 		
@D	Taylor, D.E.//Eaton, M.//Chang, N.//Salama, S.M. 	Construction of a Helicobacter pylori genome map and demonstration of diversity at the genome level.	J. Bacteriol.	1992	174		6800-6806			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. 		
@D	Taylor, G.K.//Heiter, D.F.//Pietrokovski, S.//Stoddard, B.L. 	Activity, specificity and structure of I-Bth0305I: a representative of a new homing endonuclease family.	Nucleic Acids Res.	2011	39		9705-9719			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. 		
@D	Taylor, G.K.//Petrucci, L.H.//Lambert, A.R.//Baxter, S.K.//Jarjour, J.//Stoddard, B.L. 	LAHEDES: the LAGLIDADG homing endonuclease database and engineering server.	Nucleic Acids Res.	2012	40		W110-W116			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. 		
@D	Taylor, G.K.//Stoddard, B.L. 	Structural, functional and evolutionary relationships between homing endonucleases and proteins from their host organisms.	Nucleic Acids Res.	2012	40		5189-5200			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. 		
@D	Taylor, I.//Patel, J.//Firman, K.//Kneale, G. 	Purification and biochemical characterisation of the EcoR124 type I modification methylase.	Nucleic Acids Res.	1992	20		179-186			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. 		
@D	Taylor, I.//Watts, D.//Kneale, G. 	Substrate recognition and selectivity in the type IC DNA modification methylase M.EcoR124I.	Nucleic Acids Res.	1993	21		4929-4935			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. 		
@D	Taylor, I.A. 	Biochemical characterisation of the EcoR124 type I DNA modification methylase.	Diss. Abstr.	1993	53		3942			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. 		
@D	Taylor, I.A.//Davis, K.G.//Watts, D.//Kneale, G.G. 	DNA binding induces a major structural transition in a type I methyltransferase.	EMBO J.	1994	13		5772-5778			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. 		
@D	Taylor, I.A.//Kneale, G.G. 	A competition assay for DNA binding using the fluorescent probe ANS.	Methods Mol. Biol.	2009	543		577-587			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. 		
@D	Taylor, I.A.//Webb, M.//Kneale, G.G. 	Surface labelling of the type I methyltransferase M.EcoR124I reveals lysine residues critical for DNA binding.	J. Mol. Biol.	1996	258		62-73			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. 		
@D	Taylor, J.//Moore, H.//Beaujean, N.//Gardner, J.//Wilmut, I.//Meehan, R.//Young, L. 	Cloning and Expression of Sheep DNA Methyltransferase 1 and Its Development-Specific Isoform.	Mol. Reprod. Dev.	2009	76		501-513			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. 		
@D	Taylor, J.D.//Ackroyd, A.J.//Halford, S.E. 	The gel shift assay for the analysis of DNA-protein interactions.	Methods Mol. Biol.	1994	30		263-279			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. 		
@A	Taylor, J.D.//Ackroyd, A.J.//Halford, S.E. 		The gel shift assay for the analysis of DNA-protein interactions.			Rapley, R. 		The Nucleic Acid Protocols Handbook				Totowa, NJ	Humana Press, Inc.	2000		0		745-756									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. 		
@D	Taylor, J.D.//Badcoe, I.G.//Clarke, A.R.//Halford, S.E. 	EcoRV restriction endonuclease binds all DNA sequences with equal affinity.	Biochemistry	1991	30		8743-8753			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. 		
@D	Taylor, J.D.//Goodall, A.J.//Vermote, C.L.//Halford, S.E. 	Fidelity of DNA recognition by the EcoRV restriction/modification system in vivo.	Biochemistry	1990	29		10727-10733			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. 		
@D	Taylor, J.D.//Halford, S.E. 	Discrimination between DNA sequences by the EcoRV restriction endonuclease.	Biochemistry	1989	28		6198-6207			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. 		
@D	Taylor, J.D.//Halford, S.E. 	The activity of the EcoRV restriction endonuclease is influenced by flanking DNA sequences both inside and outside the DNA-protein complex.	Biochemistry	1992	31		90-97			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. 		
@D	Taylor, J.E.//Callow, P.//Swiderska, A.//Kneale, G.G. 	Structural and functional analysis of the engineered type I DNA methyltransferase EcoR124I(NT).	J. Mol. Biol.	2010	398		391-399			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. 		
@D	Taylor, J.E.//Swiderska, A.//Artero, J.-B.//Callow, P.//Kneale, G. 	Structural and Functional Analysis of the Symmetrical Type I Restriction Endonuclease R.EcoR124I(NT).	PLoS ONE	2012	7		e35263			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. 		
@D	Taylor, J.E.//Swiderska, A.//Kneale, G.G. 	A rapid purification procedure for the HsdM protein of EcoR124I and biophysical characterization of the purified protein.	Protein Expr. Purif.	2013	87		136-140			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. 		
@D	Taylor, J.R.//Fang, M.M.//Nie, S. 	Probing specific sequences on single DNA molecules with bioconjugated fluorescent nanoparticles.	Anal. Chem.	2000	72		1979-1986			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. 		
@D	Taylor, J.W.//Schmidt, W.//Cosstick, R.//Okruszek, A.//Eckstein, F. 	The use of phosphorothioate-modified DNA in restriction enzyme reactions to prepare nicked DNA.	Nucleic Acids Res.	1985	13		8749-8763			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. 		
@D	Taylor, V.L.//Titball, R.W.//Oyston, P.C.F. 	Oral immunization with a dam mutant of Yersinia pseudotuberculosis protects against plague.	Microbiology	2005	151		1919-1926			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. 		
@D	Tchagang, C.F.//Xu, R.//Mehrtash, S.//Rahimi, S.//Sidibe, A.//Li, X.//Bromfield, E.S.//Tambong, J.T. 	Draft Genome Sequences of Two Novel Pseudomonas Strains Exhibiting Differential Hypersensitivity Reactions on Tobacco and Corn Seedlings.	Genome Announcements	2016	4		e01057-16			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. 		
@D	te Poele, E.M.//Samborskyy, M.//Oliynyk, M.//Leadlay, P.F.//Bolhuis, H.//Dijkhuizen, L. 	Actinomycete integrative and conjugative pMEA-like elements of Amycolatopsis and Saccharopolyspora decoded.	Plasmid	2008	59		202-216			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. 		
@D	Te, S.H.//Tan, B.F.//Boo, C.Y.//Thompson, J.R.//Gin, K.Y. 	Genomics insights into production of 2-methylisoborneol and a putative cyanobactin by Planktothricoides sp. SR001.	Standards in Genomic Sciences	2017	12		35			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. 		
@D	Te, S.H.//Tan, B.F.//Thompson, J.R.//Gin, K.Y. 	Draft Genome Sequences of Two Benthic Cyanobacteria, Oscillatoriales USR 001 and  Nostoc sp. MBR 210, Isolated from Tropical Freshwater Lakes.	Genome Announcements	2016	4		e01115-16			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. 		
@D	Teachman, A.M.//Gumulak-Smith, J.J.//Tu, A.T.//Simecka, J.W.//Lindsey, J.R.//Dybvig, K. 	Variations in the surface proteins and in the restriction and modification systems of Mycoplasma pulmonis in the respiratory tract of  infected rats.	Abstr. Gen. Meet. Am. Soc. Microbiol.	2001	101		386			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. 		
@D	Teatero, S.//McGeer, A.//Tyrrell, G.J.//Hoang, L.//Smadi, H.//Domingo, M.C.//Levett, P.N.//Finkelstein, M.//Dewar, K.//Plevneshi, A.//Athey, T.B.//Gubbay, J.B.//Mulvey, M.R.//Martin, I.//Demczuk, W.//Fittipaldi, N. 	Canada-Wide Epidemic of emm74 Group A Streptococcus Invasive Disease.	Open Forum Infect. Dis.	2018	5		ofy085			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. 		
@D	Tediashivili, M.I.//Goryan, T.V.//Koberidse, T.D.//Chanishvili, T.G.//Nikolskaya, I.I. 	New systems of host specificity of DNA Pae610 and Pae603.	Biull. Eksp. Biol. Med.	1991	112		91-94			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. 		
@D	Tediashvili, M.I.//Goryan, T.V.//Koberidze, T.D.//Chanishvili, T.G.//Nikolskaya, I.I. 	New host DNA specificity systems Pae 610 and Pae 603.	Bull. Exp. Biol. Med.	1991	112		91-94			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. 		
@D	Tediashvili, M.I.//Uporova, T.M.//Nikolskaya, I.I.//Debov, S.S. 	Identification of host specific system in Shigella.	Biull. Eksp. Biol. Med.	1980	90		324-325			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. 		
@D	Tedim, A.P.//Lanza, V.F.//Manrique, M.//Pareja, E.//Ruiz-Garbajosa, P.//Canton, R.//Baquero, F.//Coque, T.M.//Tobes, R. 	Complete Genome Sequences of Isolates of Enterococcus faecium Sequence Type 117,  a Globally Disseminated Multidrug-Resistant Clone.	Genome Announcements	2017	5		e01553-16			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. 		
@D	Teel, L.D.//Melton-Celsa, A.R.//Schmitt, C.K.//O'Brien, A.D. 	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.	Infect. Immun.	2002	70		4282-4291			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. 		
@D	Teerawanichpan, P.//Chandrasekharan, M.B.//Jiang, Y.M.//Narangajavana, J.//Hall, T.C. 	Characterization of two rice DNA methyltransferase genes and RNAi-mediated reactivation of a silenced transgene in rice callus.	Planta	2004	218		337-349			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. 		
@D	Teerawanichpan, P.//Jiang, Y.//Dong, J.//Hall, T.C.//Narangajavana, J. 	DNA methyltransferase and developmental processes in rice.	Plant Biol.	2001	0		155-156			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. 		
@D	Teerawanichpan, P.//Krittanai, P.//Chauvatcharin, N.//Narangajavana, J. 	Purification and characterization of rice DNA methyltransferase.	Plant Physiol. Biochem.	2009	47		671-680			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. 		
@D	Tegtmeier, D.//Belitz, A.//Radek, R.//Heimerl, T.//Brune, A. 	Ereboglobus luteus gen. nov. sp. nov. from cockroach guts, and new insights into the oxygen relationship of the genera Opitutus and Didymococcus (Verrucomicrobia: Opitutaceae).	Syst. Appl. Microbiol.	2018	41		101-112			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. 		
@D	Teh, A.H.//Lee, S.M.//Dykes, G.A. 	Draft Genome Sequences of Three Multiantibiotic-Resistant Campylobacter jejuni Strains (2865, 2868, and 2871) Isolated from Poultry at Retail Outlets in  Malaysia.	Genome Announcements	2016	4		e00331-16			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. 		
@D	Teh, B.S.//Lau, N.S.//Ng, F.L.//Abdul, R.A.Y.//Wan, X.//Saito, J.A.//Hou, S.//Teh, A.H.//Najimudin, N.//Alam, M. 	Complete genome sequence of the thermophilic Thermus sp. CCB_US3_UF1 from a hot spring in Malaysia.	Standards in Genomic Sciences	2015	10		76			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). 		
@D	Tekedar, H.C.//Karsi, A.//Akgul, A.//Kalindamar, S.//Waldbieser, G.C.//Sonstegard, T.//Schroeder, S.G.//Lawrence, M.L. 	Complete Genome Sequence of Fish Pathogen Aeromonas hydrophila AL06-06.	Genome Announcements	2015	3		e00368-15			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. 		
@D	Tekedar, H.C.//Karsi, A.//Gillaspy, A.F.//Dyer, D.W.//Benton, N.R.//Zaitshik, J.//Vamenta, S.//Banes, M.M.//Gulsoy, N.//Aboko-Cole, M.//Waldbieser, G.C.//Lawrence, M.L. 	Genome Sequence of the Fish Pathogen Flavobacterium columnare ATCC 49512.	J. Bacteriol.	2012	194		2763-2764			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. 		
@D	Tekedar, H.C.//Kumru, S.//Kalindamar, S.//Karsi, A.//Waldbieser, G.C.//Sonstegard, T.//Schroeder, S.G.//Liles, M.R.//Griffin, M.J.//Lawrence, M.L. 	Draft Genome Sequences of Three Aeromonas hydrophila Isolates from Catfish and Tilapia.	Genome Announcements	2017	5		e01509-16			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. 		
@D	Tekedar, H.C.//Kumru, S.//Karsi, A.//Waldbieser, G.C.//Sonstegard, T.//Schroeder, S.G.//Liles, M.R.//Griffin, M.J.//Lawrence, M.L. 	Draft Genome Sequence of Aeromonas hydrophila TN97-08.	Genome Announcements	2016	4		e00436-16			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. 		
@D	Tekedar, H.C.//Kumru, S.//Karsi, A.//Waldbieser, G.C.//Sonstegard, T.//Schroeder, S.G.//Liles, M.R.//Griffin, M.J.//Lawrence, M.L. 	Draft Genome Sequences of Four Virulent Aeromonas hydrophila Strains from Catfish Aquaculture.	Genome Announcements	2016	4		e00860-16			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. 		
@D	Temperton, B.//Thomas, S.//Tait, K.//Parry, H.//Emery, M.//Allen, M.//Quinn, J.//Macgrath, J.//Gilbert, J. 	Permanent draft genome sequence of Vibrio tubiashii strain NCIMB 1337 (ATCC19106).	Standards in Genomic Sciences	2011	4		183-190			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. 		
@D	Templeton, M.D.//Warren, B.A.//Andersen, M.T.//Rikkerink, E.H.//Fineran, P.C. 	Complete DNA Sequence of Pseudomonas syringae pv. actinidiae, the Causal Agent of Kiwifruit Canker Disease.	Genome Announcements	2015	3		e01054-15			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. 		
@D	Teng, L.//Deng, L.//Dong, X.//Wei, S.//Li, J.//Li, N.//Zhou, Y. 	Genome Sequence of Hypervirulent Aeromonas hydrophila Strain HZAUAH.	Genome Announcements	2017	5		e00012-17			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. 		
@D	Teng, L.//Dong, X.//Zhou, Y.//Li, Z.//Deng, L.//Chen, H.//Wang, X.//Li, J. 	Draft Genome Sequence of Hypervirulent and Vaccine Candidate Streptococcus suis Strain SC19.	Genome Announcements	2017	5		e01484-16			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. 		
@D	Teng, L.//Ginn, A.//Jeon, S.//Kang, M.//Jeong, K.C. 	Complete Genome Sequence of an Escherichia coli O157:H7 Strain Isolated from a Super-Shedder Steer.	Genome Announcements	2016	4		e00258-16			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. 		
@D	Tengs, T.//LaFramboise, T.//Den, R.B.//Hayes, D.N.//Zhang, J.//DebRoy, S.//Gentleman, R.C.//O'Neill, K.//Birren, B.//Meyerson, M. 	Genomic representations using concatenates of Type IIB restriction endonuclease digestion fragments.	Nucleic Acids Res.	2004	32		e121			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. 		
@D	Tenover, F.C.//Clark, V.L.//Young, F.E. 	Presence of methyl adenine in the DNA of some strains of Neisseria Gonorrhoeae.	Biochem. Biophys. Res. Commun.	1980	95		1796-1800			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. 		
@D	Teo, J.//Tan, S.Y.//Tay, M.//Ding, Y.//Kjelleberg, S.//Givskov, M.//Lin, R.T.//Yang, L. 	First case of E anophelis outbreak in an intensive-care unit.	Lancet	2013	382		855-856			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. 		
@D	Terabayashi, Y.//Juan, A.//Tamotsu, H.//Ashimine, N.//Nakano, K.//Shimoji, M.//Shiroma, A.//Teruya, K.//Satou, K.//Hirano, T. 	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.	Genome Announcements	2014	2		e00986-14			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. 		
@D	Teramoto, M.//Zhai, Z.//Komatsu, A.//Shibayama, K.//Suzuki, M. 	Genome Sequence of the Psychrophilic Bacterium Tenacibaculum ovolyticum Strain da5A-8 Isolated from Deep Seawater.	Genome Announcements	2016	4		e00644-16			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. 		
@D	Teran, L.C.//Coeuret, G.//Raya, R.//Champomier-Verges, M.C.//Chaillou, S. 	Draft Genome Sequence of Lactobacillus curvatus FLEC03, a Meat-Borne Isolate from Beef Carpaccio Packaged in a Modified Atmosphere.	Genome Announcements	2017	5		e00584-17			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. 		
@D	Terfehr, D.//Dahlmann, T.A.//Specht, T.//Zadra, I.//Kurnsteiner, H.//Kuck, U. 	Genome Sequence and Annotation of Acremonium chrysogenum, Producer of the beta-Lactam Antibiotic Cephalosporin C.	Genome Announcements	2014	2		e00948-14			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. 		
@D	Terpolilli, J.//Garau, G.//Hill, Y.//Tian, R.//Howieson, J.//Brau, L.//Goodwin, L.//Han, J.//Liolios, K.//Huntemann, M.//Pati, A.//Woyke, T.//Mavromatis, K.//Markowitz, V.//Ivanova, N.//Kyrpides, N.//Reeve, W. 	Genome sequence of Ensifer medicae strain WSM1369; an effective microsymbiont of  the annual legume Medicago sphaerocarpos.	Standards in Genomic Sciences	2013	9		420-430			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. 		
@D	Terpolilli, J.//Hill, Y.//Tian, R.//Howieson, J.//Brau, L.//Goodwin, L.//Han, J.//Liolios, K.//Huntemann, M.//Pati, A.//Woyke, T.//Mavromatis, K.//Markowitz, V.//Ivanova, N.//Kyrpides, N.//Reeve, W. 	Genome sequence of Ensifer meliloti strain WSM1022; a highly effective microsymbiont of the model legume Medicago truncatula A17.	Standards in Genomic Sciences	2013	9		315-324			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. 		
@D	Terpolilli, J.//Rui, T.//Yates, R.//Howieson, J.//Poole, P.//Munk, C.//Tapia, R.//Han, C.//Markowitz, V.//Tatiparthi, R.//Mavrommatis, K.//Ivanova, N.//Pati, A.//Goodwin, L.//Woyke, T.//Kyrpides, N.//Reeve, W. 	Genome sequence of Rhizobium leguminosarum bv trifolii strain WSM1689, the microsymbiont of the one flowered clover Trifolium uniflorum.	Standards in Genomic Sciences	2014	9		527-539			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. 		
@D	Terry, B.J.//Jack, W.E.//Modrich, P. 	Facilitated diffusion during catalysis by EcoRI endonuclease:  nonspecific interactions in EcoRI catalysis.	J. Biol. Chem.	1985	260		13130-13137			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. 		
@A	Terry, B.J.//Jack, W.E.//Modrich, P. 		Mechanism of specific site location and DNA cleavage by EcoRI endonuclease.			Chirikjian, J.G. 		Gene Amplif. Anal.					Elsevier North Holland	1987		5		103-118									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. 		
@D	Terry, B.J.//Jack, W.E.//Rubin, R.A.//Modrich, P. 	Thermodynamic parameters governing interaction of EcoRI endonuclease with specific and nonspecific DNA sequences.	J. Biol. Chem.	1983	258		9820-9825			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. 		
@D	Terschuren, P.-A.//Noyer-Weidner, M.//Trautner, T.A. 	Recombinant derivatives of Bacillus subtilis phage Z containing the DNA methyltransferase genes of related methylation-proficient phages.	J. Gen. Microbiol.	1987	198		945-952			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. 		
@D	Teru, Y.//Hikima, J.I.//Kono, T.//Sakai, M.//Takano, T.//Hawke, J.P.//Takeyama, H.//Aoki, T. 	Whole-Genome Sequence of Photobacterium damselae subsp. piscicida Strain 91-197,  Isolated from Hybrid Striped Bass (Morone sp.) in the United States.	Genome Announcements	2017	5		e00600-17			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. 		
@D	Tesfazgi-Mebrhatu, M.//Wywial, E.//Ghosh, A.//Michiels, C.W.//Lindner, A.B.//Taddei, F.//Bujnicki, J.M.//Van Melderen, L.//Aertsen, A. 	Evidence for an evolutionary antagonism between Mrr and Type III modification systems.	Nucleic Acids Res.	2011	39		5991-6001			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. 		
@D	Tettelin, H. et al. 	Complete genome sequence of Neisseria meningitidis serogroup B strain MC58.	Science	2000	287		1809-1815			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. 		
@D	Tettelin, H. et al. 	Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: Implications for the microbial "pan-genome".	Proc. Natl. Acad. Sci. U. S. A.	2005	102		13950			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. 		
@D	Tettelin, H. et al. 	Complete genome sequence of a virulent isolate of Streptococcus pneumoniae.	Science	2001	293		498-506			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. 		
@D	Tettelin, H.//Hooven, T.A.//Zhao, X.//Su, Q.//Sadzewicz, L.//Tallon, L.J.//Fraser, C.M.//Ratner, A.J. 	Whole-Genome Sequences of Bacteremia Isolates of Bordetella holmesii.	Genome Announcements	2017	5		e01023-17			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. 		
@D	Tettelin, H.//Sampaio, E.P.//Daugherty, S.C.//Hine, E.//Riley, D.R.//Sadzewicz, L.//Sengamalay, N.//Shefchek, K.//Su, Q.//Tallon, L.J.//Conville, P.//Olivier, K.N.//Holland, S.M.//Fraser, C.M.//Zelazny, A.M. 	Genomic Insights into the Emerging Human Pathogen Mycobacterium massiliense.	J. Bacteriol.	2012	194		5450			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. 		
@D	Tetz, G.//Tetz, V. 	Draft Genome Sequence of Acinetobacter sp. Strain VT-511 Isolated from the Stomach of a Patient with Gastric Cancer.	Genome Announcements	2015	3		e01202-15			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. 		
@D	Tetz, G.//Tetz, V. 	Draft Genome Sequence of Kluyvera intestini Strain GT-16 Isolated from the Stomach of a Patient with Gastric Cancer.	Genome Announcements	2016	4		e01432-16			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. 		
@D	Tetz, G.//Tetz, V. 	Draft Genome Sequence of Tetzosporium hominis VT-49 gen. nov., sp. nov., Isolated from the Dental Decay Plaque of a Patient with Periodontitis.	Genome Announcements	2018	6		e01541-17			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. 		
@D	Tetz, G.//Tetz, V. 	Complete Genome Sequence of Bacilli bacterium Strain VT-13-104 Isolated from the  Intestine of a Patient with Duodenal Cancer.	Genome Announcements	2015	3		e00705-15			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. 		
@D	Tetz, G.//Tetz, V. 	Draft Genome Sequence of Chryseobacterium mucoviscidosis sp. nov. Strain VT16-26, Isolated from the Bronchoalveolar Lavage Fluid of a Patient with Cystic Fibrosis.	Genome Announcements	2018	6		e01473-17			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. 		
@D	Tetz, G.//Tetz, V. 	Complete Genome Sequence of a Novel Bacillus sp. VT 712 Strain Isolated from the  Duodenum of a Patient with Intestinal Cancer.	Genome Announcements	2016	4		e00786-16			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. 		
@D	Tetz, G.//Tetz, V.//Vecherkovskaya, M. 	Complete Genome Sequence of Paenibacillus sp. Strain VT 400, Isolated from the Saliva of a Child with Acute Lymphoblastic Leukemia.	Genome Announcements	2015	3		e00894-15			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. 		
@D	Tetz, G.//Vecherkovskaya, M.//Zappile, P.//Dolgalev, I.//Tsirigos, A.//Heguy, A.//Tetz, V. 	Complete Genome Sequence of Kluyvera intestini sp. nov., Isolated from the Stomach of a Patient with Gastric Cancer.	Genome Announcements	2017	5		e01184-17			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. 		
@D	Tetz, V.//Tetz, G. 	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.	Genome Announcements	2017	5		e00489-17			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. 		
@D	Tetz, V.//Tetz, G. 	Draft Genome Sequence of Bacillus obstructivus VT-16-70 Isolated from the Bronchoalveolar Lavage Fluid of a Patient with Chronic Obstructive Pulmonary  Disease.	Genome Announcements	2017	5		e01754-16			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. 		
@D	Tetz, V.//Tetz, G. 	Draft Genome Sequence of the Uropathogenic Herbaspirillumfrisingense Strain ureolyticus VT-16-41.	Genome Announcements	2017	5		e00279-17			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. 		
@D	Tetz, V.//Tetz, G. 	Draft Genome Sequence of Bacillus respiratorii VT-16-64, Isolated from the Bronchiolar Alveolar Lavage Fluid of a Patient with Chronic Obstructive Pulmonary  Disease.	Genome Announcements	2017	5		e00264-17			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. 		
@D	Tewari, R.//Das Mitra, S.//Das, S.//Jadhao, S.//Mishra, G.//Ganaie, F.//Shome, R.//Rahman, H.//Shome, B.R. 	Draft Genome Sequence of Multidrug-Resistant Escherichia coli NIVEDI-P44, Isolated from a Chicken Fecal Sample in Northeast India.	Genome Announcements	2018	6		e00205-18			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. 		
@D	Thacker, T.C.//Lippolis, J.D.//Brunelle, B.W.//Casey, T.A.//Reinhardt, T.A.//Sacco, R.E.//Holman, D.B. 	Genome Sequences of Escherichia coli Strains That Cause Persistent and Transient  Mastitis.	Genome Announcements	2017	5		e00775-17			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. 		
@D	Thanos, D.//Scarpelis, G.//Papamatheakis, J.//Bouriotis, V. 	Isolation and identification of restriction endonuclease BseAI.	Nucleic Acids Res.	1989	17		8881			None 		
@D	Thapa, S.P.//Coaker, G. 	Genome Sequences of Two Pseudomonas syringae pv. tomato Race 1 Strains, Isolated  from Tomato Fields in California.	Genome Announcements	2016	4		e01671-15			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. 		
@D	Tharek, M.//Sim, K.S.//Khairuddin, D.//Ghazali, A.H.//Najimudin, N. 	Whole-Genome Sequence of Endophytic Plant Growth-Promoting Escherichia coli USML2.	Genome Announcements	2017	5		e00305-17			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%. 		
@D	Thatcher, L.F.//Myers, C.A.//O'Sullivan, C.A.//Roper, M.M. 	Draft Genome Sequence of Rhodococcus sp. Strain 66b.	Genome Announcements	2017	5		e00229-17			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. 		
@D	Thatcher, L.F.//Myers, C.A.//O'Sullivan, C.A.//Roper, M.M. 	Draft Genome Sequences of Streptomyces sp. Strains MH60 and 111WW2.	Genome Announcements	2018	6		e00356-18			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. 		
@D	The, A.G.I. 	Analysis of the genome sequence of the flowering plant Arabidopsis thaliana.	Nature	2000	408		796-815			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. 		
@D	Thennarasu, S.//Polireddy, D.//Antony, A.//Yada, M.R.//Algarawi, S.//Sivakumar, N. 	Draft Genome Sequence of a Highly Flagellated, Fast-Swimming Archaeon, Methanocaldococcus villosus Strain KIN24-T80 (DSM 22612).	Genome Announcements	2013	1		e00481-13			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. 		
@D	Theriault, G.//Roy, P.H. 	Cloning of Pseudomonas plasmid pMG7 and its restriction-modification system in Escherichia coli.	Gene	1982	19		355-359			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. 		
@D	Theriault, G.//Roy, P.H.//Howard, K.A.//Benner, J.S.//Brooks, J.S.//Waters, A.F.//Gingeras, T.R. 	Nucleotide sequence of the PaeR7 restriction/modification system and partial characterization of its protein products.	Nucleic Acids Res.	1985	13		8441-8461			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. 		
@D	Thiaville, J.J.//Kellner, S.M.//Yuan, Y.//Hutinet, G.//Thiaville, P.C.//Jumpathong, W.//Mohapatra, S.//Brochier-Armanet, C.//Letarov, A.V.//Hillebrand, R.//Malik, C.K.//Rizzo, C.J.//Dedon, P.C.//de Crecy-Lagard, V. 	Novel genomic island modifies DNA with 7-deazaguanine derivatives.	Proc. Natl. Acad. Sci. U. S. A.	2016	113		E1452-E1459			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. 		
@D	Thibessard, A.//Leblond, P. 	Complete Genome Sequence of Streptomyces ambofaciens DSM 40697, a Paradigm for Genome Plasticity Studies.	Genome Announcements	2016	4		e00470-16			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. 		
@D	Thiel, T.//Pratte, B.S.//Zhong, J.//Goodwin, L.//Copeland, A.//Lucas, S.//Han, C.//Pitluck, S.//Land, M.L.//Kyrpides, N.C.//Woyke, T. 	Complete genome sequence of Anabaena variabilis ATCC 29413.	Standards in Genomic Sciences	2014	9		562-573			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. 		
@D	Thiel, V.//Drautz-Moses, D.I.//Purbojati, R.W.//Schuster, S.C.//Lindemann, S.//Bryant, D.A. 	Genome Sequence of Prosthecochloris sp. Strain HL-130-GSB from the Phylum Chlorobi.	Genome Announcements	2017	5		e00538-17			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. 		
@D	Thiel, V.//Hamilton, T.L.//Tomsho, L.P.//Burhans, R.//Gay, S.E.//Ramaley, R.F.//Schuster, S.C.//Steinke, L.//Bryant, D.A. 	Draft Genome Sequence of the Moderately Thermophilic Bacterium Schleiferia thermophila Strain Yellowstone (Bacteroidetes).	Genome Announcements	2014	2		e00860-14			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. 		
@D	Thiel, V.//Hamilton, T.L.//Tomsho, L.P.//Burhans, R.//Gay, S.E.//Schuster, S.C.//Ward, D.M.//Bryant, D.A. 	Draft Genome Sequence of a Sulfide-Oxidizing, Autotrophic Filamentous Anoxygenic  Phototrophic Bacterium, Chloroflexus sp. Strain MS-G (Chloroflexi).	Genome Announcements	2014	2		e00872-14			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. 		
@D	Thiel, V.//Tank, M.//Tomsho, L.P.//Burhans, R.//Gay, S.E.//Hamilton, T.L.//Schuster, S.C.//Bryant, D.A. 	Draft Genome Sequence of Anoxybacillusayderensis Strain MT-Cab (Firmicutes).	Genome Announcements	2017	5		e00547-17			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. 		
@D	Thiel, V.//Tomsho, L.P.//Burhans, R.//Gay, S.E.//Schuster, S.C.//Ward, D.M.//Bryant, D.A. 	Draft Genome Sequence of the Deinococcus-Thermus Bacterium Meiothermus ruber Strain A.	Genome Announcements	2015	3		e00202-15			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. 		
@D	Thielking, V. 	Oligodeoxynucleotides with basepair mismatches as a substrate for EcoRI and EcoRV.	Ph.D. Thesis, Medizinische Hochscule Hannover, W. Germany	1988			1-84					
@D	Thielking, V.//Alves, J.//Fliess, A.//Maass, G.//Pingoud, A. 	Accuracy of the EcoRI restriction endonuclease:  Binding and cleavage studies with oligodeoxynucleotide substrates containing degenerate recognition sequences.	Biochemistry	1990	29		4682-4691			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. 		
@D	Thielking, V.//Du Bois, S.//Eritja, R.//Guschlbauer, W. 	Dam methyltransferase from Escherichia coli: Kinetic studies using modified DNA oligomers: nonmethylated substrates.	Biol. Chem.	1997	378		407-415			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. 		
@D	Thielking, V.//Selent, U.//Kohler, E.//Landgraf, Z.//Wolfes, H.//Alves, J.//Pingoud, A. 	Mg2+ confers DNA binding specificity to the EcoRV restriction endonuclease.	Biochemistry	1992	31		3727-3732			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. 		
@D	Thielking, V.//Selent, U.//Kohler, E.//Wolfes, H.//Pieper, U.//Geiger, R.//Urbanke, C.//Winkler, F.K.//Pingoud, A. 	Site-directed mutagenesis studies with EcoRV restriction endonuclease to identify regions involved in recognition and catalysis.	Biochemistry	1991	30		6416-6422			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. 		
@D	Thieme, F. et al. 	Insights into genome plasticity and pathogenicity of the plant pathogenic bacterium Xanthomonas campestris pv. vesicatoria revealed by the complete   genome sequence.	J. Bacteriol.	2005	187		7254-7266			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. 		
@D	Thierry, A.//Perrin, A.//Boyer, J.//Fairhead, C.//Dujon, B.//Frey, B.//Schmitz, G. 	Cleavage of yeast and bacteriophage T7 genomes at a single site using the rare cutter endonuclease I-SceI.	Nucleic Acids Res.	1991	19		189-190			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. 		
@D	Thijs, S.//Van Hamme, J.//Gkorezis, P.//Rineau, F.//Weyens, N.//Vangronsveld, J. 	Draft Genome Sequence of Raoultella ornithinolytica TNT, a Trinitrotoluene-Denitrating and Plant Growth-Promoting Strain Isolated from  Explosive-Contaminated Soil.	Genome Announcements	2014	2		e00491-14			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. 		
@D	Thion, L.//Laurine, E.//Erard, M.//Burlet-Schiltz, O.//Monsarrat, B.//Masson, J.M.//Saves, I. 	The two-step cleavage activity of PI-TfuI intein endonuclease demonstrated by matrix-assisted laser desorption ionization time-of-flight mass spectrometry.	J. Biol. Chem.	2002	277		45442-45450			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. 		
@D	Thole, S.//Kalhoefer, D.//Voget, S.//Berger, M.//Engelhardt, T.//Liesegang, H.//Wollherr, A.//Kjelleberg, S.//Daniel, R.//Simon, M.//Thomas, T.//Brinkhoff, T. 	Phaeobacter gallaeciensis genomes from globally opposite locations reveal high similarity of adaptation to surface life.	ISME J.	2012	6		2229-2244			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. 		
@D	Thomas, A.T.//Brammar, W.J.//Wilkins, B.M. 	Plasmid R16 ArdA protein preferentially targets restriction activity of the type I restriction-modification system EcoKI.	J. Bacteriol.	2003	185		2022-2025			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. 		
@D	Thomas, C.B.//Gumport, R.I. 	Dimerization of the bacterial RsrI N6-adenine DNA methyltransferase.	Nucleic Acids Res.	2006	34		806-815			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. 		
@D	Thomas, C.B.//Scavetta, R.//Churchill, M.E.A.//Gumport, R.I. 	A tale of three tails, a mutant, and a dimer: Structural studies of RsrI methyltransferase.	FASEB J.	2002	16		A923-A924			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. 		
@D	Thomas, C.B.//Scavetta, R.D.//Gumport, R.I.//Churchill, M.E.A. 	Structures of liganded and unliganded RsrI N6-adenine DNA methyltransferase: a distinct orientation for active cofactor binding.	J. Biol. Chem.	2003	278		26094-26101			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. 		
@D	Thomas, D.K.//Lone, A.G.//Selinger, L.B.//Taboada, E.N.//Uwiera, R.R.//Abbott, D.W.//Inglis, G.D. 	Comparative Variation within the Genome of Campylobacter jejuni NCTC 11168 in Human and Murine Hosts.	PLoS ONE	2014	9		E88229			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. 		
@D	Thomas, G.A.//Kubasek, W.L.//Peticolas, W.L. 	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.	Biochemistry	1989	28		2001-2009			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. 		
@D	Thomas, J.C.//Godfrey, P.A.//Feldgarden, M.//Robinson, D.A. 	Draft Genome Sequences of Staphylococcus aureus Sequence Type 34 (ST34) and ST42  Hybrids.	J. Bacteriol.	2012	194		2740-2741			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. 		
@D	Thomas, J.C.//Kong, Y.//Sabharwal, V.//Pelton, S.I.//Pettigrew, M.M. 	Streptococcus pneumoniae serotype 6C: An Intra- and Interclonal Complex Comparison.	J. Bacteriol.	2011	193		3409-3410			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. 		
@D	Thomas, J.M.//Ghebrendrias, N.//Rawat, M. 	Genome Sequences of Two Spore-Forming Bacteria Isolated from the Shore of Mono Lake, California.	Genome Announcements	2017	5		e01742-16			Here, we report the draft genome sequences of two Bacillus spore-forming Gram-positive bacteria, isolated from soil on the shore of Mono Lake. 		
@D	Thomas, M.//Davis, R.W. 	Studies on the cleavage of bacteriophage lambda DNA with EcoRI restriction endonuclease.	J. Mol. Biol.	1975	91		315-328			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. 		
@D	Thomas, M.C.//Arling, V.//Goji, N.//Janzen, T.W.//Duceppe, M.-O.//Mathews, A.//Carrillo, C.//Amoako, K. 	First complete genome sequence of Yersinia massiliensis.	Genome Announcements	2018	6		e00416-18			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. 		
@D	Thomas, M.P.//Brady, R.L.//Halford, S.E.//Sessions, R.B.//Baldwin, G.S. 	Structural analysis of a mutational hot-spot in the EcoRV restriction endonuclease: a catalytic role for a main chain carbonyl group.	Nucleic Acids Res.	1999	27		3438-3445			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. 		
@D	Thomas, P.//Semmler, T.//Eichhorn, I.//Lubke-Becker, A.//Werckenthin, C.//Abdel-Glil, M.Y.//Wieler, L.H.//Neubauer, H.//Seyboldt, C. 	First report of two complete Clostridium chauvoei genome sequences and detailed in silico genome analysis.	Infect. Genet. Evol.	2017	54		287-298			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. 		
@D	Thomm, M.//Frey, G.//Bolton, B.J.//Laue, F.//Kessler, C.//Stetter, K.O. 	MvnI: a restriction enzyme in the archaebacterium Methanococcus vannielii.	FEMS Microbiol. Lett.	1988	52		229-234			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. 		
@D	Thompson, A.J.//Herrin, D.L. 	In vitro self-splicing reactions of the chloroplast group I intron Cr.LSU from Chlamydomonas reinhardtii and in vivo manipulation via gene-replacement.	Nucleic Acids Res.	1991	19		6611-6618			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. 		
@D	Thompson, A.J.//Yuan, X.//Kudlicki, W.//Herrin, D.L. 	Cleavage and recognition pattern of a double-strand-specific endonuclease (I-CreI) endcoded by the chloroplast 23S rRNA intron of Chlamydomonas reinhardtii.	Gene	1992	119		247-251			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). 		
@D	Thompson, C.C.//Marin, M.A.//Dias, G.M.//Dutilh, B.E.//Edwards, R.A.//Iida, T.//Thompson, F.L.//Vicente, A.C. 	Genome Sequence of the Human Pathogen Vibrio cholerae Amazonia.	J. Bacteriol.	2011	193		5877-5878			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. 		
@D	Thompson, R.//Hughes, S.G.//Broda, P. 	Plasmid identification using specific endonucleases.	Mol. Gen. Genet.	1974	133		141-149			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. 		
@D	Thompson, S.A.//Hall, J.E.//Baltzegar, A.D.//Yates, B.D.//Maani, E.V.//Pajaniappan, M.//Falkow, S.//Gaynor, E.C.//Mishra, A.K.//Burns, C.M. 	Mutation of a predicted Campylobacter jejuni DNA methylase affects the expression of multiple genes.	Int. J. Med. Microbiol.	2003	293		21-22			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. 		
@D	Thoms, B.//Wackernagel, W. 	Expression of ultraviolet-induced restriction alleviation in Escherichia coli K-12.	Biochim. Biophys. Acta	1983	739		42-47			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). 		
@D	Thoms, B.//Wackernagel, W. 	UV-induced allevation of lambda restriction in Escherichia coli K-12:  Kinetics of induction and specificity of this SOS function.	Mol. Gen. Genet.	1982	186		111-117			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. 		
@D	Thomson, N.R. et al. 	The Complete Genome Sequence and Comparative Genome Analysis of the High Pathogenicity Yersinia enterocolitica Strain 8081.	PLoS Genet.	2006	2		E206			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. 		
@D	Thomson, N.R. et al. 	Comparative genome analysis of Salmonella Enteritidis PT4 and Salmonella Gallinarum 287/91 provides insights into evolutionary and host adaptation pathways.	Genome Res.	2008	18		1624-1637			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. 		
@D	Thorell, K.//Collin, B.//Hernroth, B.//Sjoling, A. 	Complete Genome Sequences of Two Marine Vibrio cholerae Strains Isolated from the South Coast of Sweden.	Genome Announcements	2016	4		e01118-16			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. 		
@D	Thorogood, H.//Grasby, J.A.//Connolly, B.A. 	Influence of the phosphate backbone on the restriction and hydrolysis of DNA by the EcoRV restriction endonuclease.	J. Biol. Chem.	1996	271		8855-8862			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. 		
@D	Thorogood, H.//Waters, T.R.//Parker, A.W.//Wharton, C.//Connolly, B.A. 	Resonance raman spectroscopy of 4-thiothymidine and oligodeoxynucleotides containing this base both free in solution and bound to the restriction endonuclease EcoRV.	Biochemistry	1996	35		8723-8733			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. 		
@A	Thorpe, P.H. 		The DNA specificity of type I restriction and modification enzymes.			 		Ph.D. Thesis				Edinburgh	University of Edinburgh	1995				1-176									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. 		
@D	Thorpe, P.H.//Ternent, D.//Murray, N.E. 	The specificity of StySKI, a type I restriction enzyme, implies a structure with rotational symmetry.	Nucleic Acids Res.	1997	25		1694-1700			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. 		
@D	Thorsted, P.B.//Macartney, D.P.//Akhtar, P.//Haines, A.S.//Ali, N.//Davidson, P.//Stafford, T.//Pocklington, M.J.//Pansegrau, W.//Wilkins, B.M.//Lanka, E.//Thomas, C.M. 	Complete sequence of the IncPbeta plasmid R751: implications for evolution and organisation of the IncP backbone.	J. Mol. Biol.	1998	282		969-990			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. 		
@D	Thrash, J.C.//Cho, J.C.//Bertagnolli, A.D.//Ferriera, S.//Johnson, J.//Vergin, K.L.//Giovannoni, S.J. 	Genome sequence of the marine Janibacter sp. strain HTCC2649.	J. Bacteriol.	2010	193		584-585			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. 		
@D	Thrash, J.C.//Cho, J.C.//Ferriera, S.//Johnson, J.//Vergin, K.L.//Giovannoni, S.J. 	Genome sequences of strains HTCC2148 and HTCC2080, belonging to the OM60/NOR5 clade of the Gammaproteobacteria.	J. Bacteriol.	2010	192		3842-3843			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. 		
@D	Thrash, J.C.//Cho, J.C.//Ferriera, S.//Johnson, J.//Vergin, K.L.//Giovannoni, S.J. 	Genome sequences of Pelagibaca bermudensis HTCC2601T and Maritimibacter alkaliphilus HTCC2654T, the type strains of two marine roseobacter genera.	J. Bacteriol.	2010	192		5552-5553			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. 		
@D	Thrash, J.C.//Cho, J.C.//Vergin, K.L.//Giovannoni, S.J. 	Genome Sequences of Oceanicola granulosus HTCC2516T and Oceanicola batsensis HTCC2597T.	J. Bacteriol.	2010	192		3549-3550			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. 		
@D	Thrash, J.C.//Cho, J.C.//Vergin, K.L.//Morris, R.M.//Giovannoni, S.J. 	Genome sequence of Lentisphaera araneosa HTCC2155T, the type species of the order Lentisphaerales in the phylum Lentisphaerae.	J. Bacteriol.	2010	192		2938-2939			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. 		
@D	Thyme, S.B.//Baker, D.//Bradley, P. 	Improved Modeling of Side-Chain-Base Interactions and Plasticity in Protein-DNA Interface Design.	J. Mol. Biol.	2012	419		255-274			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. 		
@D	Thyme, S.B.//Boissel, S.J.S.//Quadri, S.//Arshiya, N.//Tony, B.//Dean, A.//Park, R.U.//Kusak, L.//Ashworth, J.//Baker, D. 	Reprogramming homing endonuclease specificity through computational design and directed evolution.	Nucleic Acids Res.	2014	42		2564-2576			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. 		
@D	Thyme, S.B.//Jarjour, J.//Takeuchi, R.//Havranek, J.J.//Ashworth, J.//Scharenberg, A.M.//Stoddard, B.L.//Baker, D. 	Exploitation of binding energy for catalysis and design.	Nature	2009	461		1300-1304			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. 		
@D	Thyme, S.B.//Song, Y.//Brunette, T.J.//Szeto, M.D.//Kusak, L.//Bradley, P.//Baker, D. 	Massively parallel determination and modeling of endonuclease substrate specificity.	Nucleic Acids Res.	2014	42		13839-13852			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. 		
@D	Tiago, I.//Maranha, A.//Mendes, V.//Alarico, S.//Moynihan, P.J.//Clarke, A.J.//Macedo-Ribeiro, S.//Pereira, P.J.//Empadinhas, N. 	Genome Sequence of Mycobacterium hassiacum DSM 44199, a Rare Source of Heat-Stable Mycobacterial Proteins.	J. Bacteriol.	2012	194		7010-7011			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. 		
@D	Tian, B.//Moran, N.A. 	Genome Sequence of Hafnia alvei bta3_1, a Bacterium with Antimicrobial Properties Isolated from Honey Bee Gut.	Genome Announcements	2016	4		e00439-16			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. 		
@D	Tian, C.F.//Zhou, Y.J.//Zhang, Y.M.//Li, Q.Q.//Zhang, Y.Z.//Li, D.F.//Wang, S.//Wang, J.//Gilbert, L.B.//Li, Y.R.//Chen, W.X. 	Comparative genomics of rhizobia nodulating soybean suggests extensive recruitment of lineage-specific genes in adaptations.	Proc. Natl. Acad. Sci. U. S. A.	2012	109		8629-8634			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. 		
@D	Tian, G.-L.//Michel, F.//Macadre, C.//Slonimski, P.P.//Lazowska, J. 	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.	J. Mol. Biol.	1991	218		747-760			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. 		
@D	Tian, H.//Jing, C. 	Genome Sequence of the Aerobic Arsenate-Reducing Bacterium Pantoea sp. Strain IMH.	Genome Announcements	2014	2		e00267-14			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. 		
@D	Tian, J.//Xu, L.//Zhang, S.//Sun, W.//Chu, X.//Wu, N. 	Draft Genome Sequence of the Organophosphorus-Degrading Bacterium Pseudomonas sp. Strain 1-7, Isolated from Organophosphorus-Polluted Sludge.	Genome Announcements	2014	2		e00993-14			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. 		
@D	Tian, R.//Parker, M.//Seshadri, R.//Reddy, T.//Markowitz, V.//Ivanova, N.//Pati, A.//Woyke, T.//Baeshen, M.//Baeshen, N.//Kyrpides, N.//Reeve, W. 	High-quality permanent draft genome sequence of Bradyrhizobium sp. Ai1a-2; a microsymbiont of Andira inermis discovered in Costa Rica.	Standards in Genomic Sciences	2015	10		33			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. 		
@D	Tian, R.//Parker, M.//Seshadri, R.//Reddy, T.//Markowitz, V.//Ivanova, N.//Pati, A.//Woyke, T.//Baeshen, M.N.//Baeshen, N.A.//Kyrpides, N.//Reeve, W. 	High-quality permanent draft genome sequence of Bradyrhizobium sp. Tv2a.2, a microsymbiont of Tachigali versicolor discovered in Barro Colorado Island of  Panama.	Standards in Genomic Sciences	2015	10		27			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. 		
@D	Tian, R.//Parker, M.//Seshadri, R.//Reddy, T.//Markowitz, V.//Ivanova, N.//Pati, A.//Woyke, T.//Baeshen, M.N.//Baeshen, N.A.//Kyrpides, N.//Reeve, W. 	High-quality permanent draft genome sequence of Bradyrhizobium sp. Th.b2, a microsymbiont of Amphicarpaea bracteata collected in Johnson City, New York.	Standards in Genomic Sciences	2015	10		24			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. 		
@D	Tian, R.C.//Huang, W. 	Draft Genome Sequences of the Multiresistant Escherichia coli C20 Strain, Isolated from Domestic Chicken Gut Microbiota.	Genome Announcements	2017	5		e00751-17			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. 		
@D	Tian, S.//Ali, M.//Xie, L.//Li, L. 	Draft Genome Sequence of Acinetobacter johnsonii MB44, Exhibiting Nematicidal Activity against Caenorhabditis elegans.	Genome Announcements	2016	4		e01772-15			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. 		
@D	Tian, S.-M.//Gong, Z.-Z.//Xie, W.-J.//Zheng, L.//Ruan, K.-C. 	Effect of high hydrostatic pressure on activity of restriction endonucleases.	Acta Biochim. Biophys. Sin.	1999	31		523-526			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. 		
@D	Tiba-Casas, M.R.//Lemes-Marques, E.G.//Almeida, E.A.//Soares, F.B.//Camargo, C.H. 	Draft Genome Sequence of a Pathogenic Vibrio vulnificus Strain Isolated in Brazil.	Genome Announcements	2018	6		e01274-17			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. 		
@D	Tice, H. et al. 	Complete genome sequence of Nakamurella multipartita type strain (Y-104).	Standards in Genomic Sciences	2010	2		168-175			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. 		
@D	Tidona, C.A.//Schnitzler, P.//Kehm, R.//Darai, G. 	Identification of the gene encoding the DNA (cytosine-5) methyltransferase of lymphocystis disease virus.	Virus Genes	1996	12		219-229			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. 		
@D	Tielen, P.//Wibberg, D.//Blom, J.//Rosin, N.//Meyer, A.K.//Bunk, B.//Schobert, M.//Tupker, R.//Schatschneider, S.//Ruckert, C.//Albersmeier, A.//Goesmann, A.//Vorholter, F.J.//Jahn, D.//Puhler, A. 	Genome Sequence of the Small-Colony Variant Pseudomonas aeruginosa MH27, Isolated from a Chronic Urethral Catheter Infection.	Genome Announcements	2014	2		e01174-13			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. 		
@D	Tikchonenko, T.I.//Karamov, E.V.//Zavizion, B.A.//Naroditsky, B.S. 	EcoRI* activity:  Enzyme modification or activation of accompanying endonuclease?	Gene	1978	4		195-212			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. 		
@D	Tikhonova, T.N.//Malyuta, S.S.//Nesterenko, V.F. 	DNA-methyltransferases from different Bacillus subtilis and Bacillus natto strains.	Mol. Gen. Mikrobiol. Virusol.	1986	11		40-44			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. 		
@D	Tilghman, S.M. 	DNA methylation: A phoenix rises.	Proc. Natl. Acad. Sci. U. S. A.	1993	90		8761-8762			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. 		
@D	Timar, E.//Groma, G.//Kiss, A.//Venetianer, P. 	Changing the recognition specificity of a DNA-methyltransferase by in vitro evolution.	Nucleic Acids Res.	2004	32		3898-3903			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. 		
@D	Timar, E.//Venetianer, P.//Kiss, A. 	In vivo DNA protection by relaxed-specificity SinI DNA methyltransferase variants.	J. Bacteriol.	2008	190		8003-8008			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. 		
@D	Timinskas, A.//Butkus, V.//Janulaitis, A. 	Sequence motifs characteristic for DNA [cytosine-N4] and DNA [adenine-N6] methyltransferases.  Classification of all DNA methyltransferases.	Gene	1995	157		3-11			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. 		
@D	Timko, J.//Horwitz, A.H.//Zelinka, J.//Wilcox, G. 	Characterization of a site-specific restriction endonuclease from Streptomyces aureofaciens.	J. Bacteriol.	1981	145		873-877			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. 		
@D	Timko, J.//Matuskova, M.//Zelinkova, E.//Zelinka, J. 	Specific endonucleases in Streptomyces aureofaciens.	Folia Microbiol. (Praha)	1978	23		243-245			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. 		
@D	Timko, J.//Sisova, M.//Ugorcakova, J.//Zelinka, J. 	Restriction endonuclease SauI from Streptomyces aureofaciens - some physical and chemical properties.	Biologia (Bratisl)	1988	43		681-689			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. 		
@A	Timko, J.//Turna, J.//Zelinka, J. 		Site-specific restriction endonuclease SauBMKI from Streptomyces aureofaciens.			Zelinka, J.//Balan, J. 		Metabolism and Enzymology of Nucleic Acids				Bratislava	Publishing House of the Slovak Akademy of Science	1987		6		107-118									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. 		
@A	Timko, J.//Zelinka, J.//Wilcox, G. 		Properties of the restriction endonuclease Saul.			Zelinka, J.//Balan, J. 		Metabolism and Enzymology of Nucleic Acids				Bratislava	Publishing House of the Slovak Akademy of Science.	1982		4		319-324									None 		
@D	Timme, R.E.//Allard, M.W.//Luo, Y.//Strain, E.//Pettengill, J.//Wang, C.//Li, C.//Keys, C.E.//Zheng, J.//Stones, R.//Wilson, M.R.//Musser, S.M.//Brown, E.W. 	Draft Genome Sequences of 21 Salmonella enterica Serovar Enteritidis Strains.	J. Bacteriol.	2012	194		5994-5995			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. 		
@D	Timme, R.E.//Pettengill, J.B.//Allard, M.W.//Strain, E.//Barrangou, R.//Wehnes, C.//Van Kessel, J.S.//Karns, J.S.//Musser, S.M.//Brown, E.W. 	Phylogenetic diversity of the enteric pathogen Salmonella enterica subsp. enterica inferred from genome-wide reference-free SNP characters.	Genome Biol. Evol.	2013	5		2109-2123			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. 		
@D	Timms, A.R.//Cambray-Young, J.//Scott, A.E.//Petty, N.K.//Connerton, P.L.//Clarke, L.//Seeger, K.//Quail, M.//Cummings, N.//Maskell, D.J.//Thomson, N.R.//Connerton, I.F. 	Evidence for a lineage of virulent bacteriophages that target Campylobacter.	BMC Genomics	2010	11		214			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. 		
@D	Tindall, B.J. et al. 	Complete genome sequence of Halomicrobium mukohataei type strain (arg-2).	Standards in Genomic Sciences	2009	1		270-277			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. 		
@D	Tindall, B.J. et al. 	Complete genome sequence of Meiothermus ruber type strain (21T).	Standards in Genomic Sciences	2010	3		26-36			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. 		
@D	Tippelt, A.//Albersmeier, A.//Brinkrolf, K.//Ruckert, C.//Fernandez-Natal, I.//Soriano, F.//Tauch, A. 	Complete Genome Sequence of Corynebacterium ureicelerivorans DSM 45051, a Lipophilic and Urea-Splitting Isolate from the Blood Culture of a Septicemia  Patient.	Genome Announcements	2014	2		e01211-14			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. 		
@D	Tippelt, A.//Mollmann, S.//Albersmeier, A.//Jaenicke, S.//Ruckert, C.//Tauch, A. 	Mycolic Acid Biosynthesis Genes in the Genome Sequence of Corynebacterium atypicum DSM 44849.	Genome Announcements	2014	2		e00845-14			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. 		
@D	Tirumalai, M.R.//Rastogi, R.//Zamani, N.//O'Bryant-Williams, E.//Allen, S.//Diouf, F.//Kwende, S.//Weinstock, G.M.//Venkateswaran, K.J.//Fox, G.E. 	Candidate genes that may be responsible for the unusual resistances exhibited by Bacillus pumilus SAFR-032 spores.	PLoS ONE	2013	8		e66012			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. 		
@D	Tisa, L.S. et al. 	Draft Genome Sequence of Frankia sp. Strain DC12, an Atypical, Noninfective, Ineffective Isolate from Datisca cannabina.	Genome Announcements	2015	3		e00889-15			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. 		
@D	Tishchenko, E.N.//Dubrovnaya, O.V. 	Methyltransferases of plants.	Biopol. Kletka	2005	21		463-472			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. 		
@D	Titeeva, G.R.//Vinogradov, S.V.//Berlin, Y.A. 	Specific features of the restriction endonuclease BamHI interaction with oligodeoxynucleotides.	Bioorg. Khim.	1986	12		640-646			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. 		
@D	Titeeva, G.R.//Vinogradov, S.V.//Berlin, Y.A. 	Complexes of the phage single-stranded DNA with synthetic oligodeoxynucleotides and their interaction with DNA polymerase and restriction endonucleases.	Bioorg. Khim.	1986	12		1484-1491			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. 		
@D	Titheradge, A.J.//King, J.//Ryu, J.//Murray, N.E. 	Families of restriction enzymes: an analysis prompted by molecular and genetic data for type ID restriction and modification systems.	Nucleic Acids Res.	2001	29		4195-4205			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. 		
@D	Titheradge, A.J.B.//Ternent, D.//Murray, N.E. 	A third family of allelic hsd genes in Salmonella enterica: sequence comparisons with related proteins identify conserved regions implicated in restriction of DNA.	Mol. Microbiol.	1996	22		437-447			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. 		
@D	Tiwari, P.K.//Joshi, K.//Rehman, R.//Bhardwaj, V.//Shamsudheen, K.V.//Sivasubbu, S.//Scaria, V. 	Draft Genome Sequence of Urease-Producing Sporosarcina pasteurii with Potential Application in Biocement Production.	Genome Announcements	2014	2		e01256-13			We describe here the draft genome sequence of Sporosarcina pasteurii, a urease-producing bacterium with potential applications in biocement production. 		
@D	Tiwari, R.//Howieson, J.//Yates, R.//Tian, R.//Held, B.//Tapia, R.//Han, C.//Seshadri, R.//Reddy, T.B.//Huntemann, M.//Pati, A.//Woyke, T.//Markowitz, V.//Ivanova, N.//Kyrpides, N.//Reeve, W. 	Genome sequence of Bradyrhizobium sp. WSM1253; a microsymbiont of Ornithopus compressus from the Greek Island of Sifnos.	Standards in Genomic Sciences	2015	10		113			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. 		
@D	Tiwari, S. et al. 	Whole-Genome Sequence of Corynebacterium auriscanis Strain CIP 106629 Isolated from a Dog with Bilateral Otitis from the United Kingdom.	Genome Announcements	2016	4		e00683-16			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%. 		
@D	Tiwari, S.//da Costa, M.P.//Almeida, S.//Hassan, S.S.//Jamal, S.B.//Oliveira, A.//Folador, E.L.//Rocha, F.//de Abreu, V.A.//Dorella, F.//Hirata, R.//de Oliveira, D.M.//da Silva-Teixeira, M.F.//Silva, A.//Barh, D.//Azevedo, V. 	C. pseudotuberculosis Phop confers virulence and may be targeted by natural compounds.	Integr Biol (Camb)	2014	6		1088-1099			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. 		
@D	Tkachuk, J.Y.//Tkachuk, L.V.//Kvasnyuk, E.I.//Zaitseva, G.V.//Kalinichenko, E.M.//Mikhailopulo, I.O.//Matsuka, G.K. 	Functioning of EcoRI, BamHI and HindIII restriction enzymes as affected by (2',5') oligoadenylates.	Dokl. Akad. Nauk UKR SSR Ser. B Geol. Khim. Biol. Nauk	1988	10		78-81			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. 		
@D	Tkachuk, Z.Y.//Tkachuk, L.V.//Kvasyuk, E.I.//Zaitseva, G.V.//Kalinichenko, E.N.//Mikhailopulo, I.A.//Matsuka, G.K. 	Changes in functional properties of restriction enzymes under the influence of (2'-5') oligoadenylates in vitro.	Biopol. Kletka	1989	5		69-73			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. 		
@D	Tkaczuk, K.L.//Obarska, A.//Bujnicki, J.M. 	Molecular phylogenetics and comparative modeling of HEN1, a methyltransferase involved in plant microRNA biogenesis.	BMC Evol. Biol.	2006	6		6			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. 		
@D	To, T.T.//Liu, Q.//Watling, M.//Bumgarner, R.E.//Darveau, R.P.//McLean, J.S. 	Draft Genome Sequence of Low-Passage Clinical Isolate Porphyromonas gingivalis MP4-504.	Genome Announcements	2016	4		e00256-16			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. 		
@D	Tobes, R.//Codoner, F.M.//Lopez-Camacho, E.//Salanueva, I.J.//Manrique, M.//Brozynska, M.//Gomez-Gil, R.//Martinez-Blanch, J.F.//Alvarez-Tejado, M.//Pareja, E.//Mingorance, J. 	Genome Sequence of Klebsiella pneumoniae KpQ3, a DHA-1 beta-Lactamase-Producing Nosocomial Isolate.	Genome Announcements	2013	1		e00167-12			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. 		
@D	Tobes, R.//Manrique, M.//Brozynska, M.//Stephan, R.//Pareja, E.//Johler, S. 	Noncontiguous Finished Genome Sequence of Staphylococcus aureus KLT6, a Staphylococcal Enterotoxin B-Positive Strain Involved in a Food Poisoning  Outbreak in Switzerland.	Genome Announcements	2013	1		e00214-13			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. 		
@D	Tobias, N.J.//Doig, K.D.//Medema, M.H.//Chen, H.//Haring, V.//Moore, R.//Seemann, T.//Stinear, T.P. 	Complete Genome Sequence of the Frog Pathogen Mycobacterium ulcerans ecovar Liflandii.	J. Bacteriol.	2012	195		556-564			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. 		
@D	Tobias, N.J.//Mishra, B.//Gupta, D.K.//Ke, L.P.//Thines, M.//Bode, H.B. 	Draft Genome Sequence of Ochrobactrum anthropi Strain ML7 Isolated from Soil Samples in Vinhphuc Province, Vietnam.	Genome Announcements	2015	3		e00218-15			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. 		
@D	Tock, M.R.//Dryden, D.T.F. 	The biology of restriction and anti-restriction.	Curr. Opin. Microbiol.	2005	8		466-472			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. 		
@D	Toh, H.//Hayashi, J.//Oshima, K.//Nakano, A.//Takayama, Y.//Takanashi, K.//Morita, H.//Hattori, M. 	Complete Genome Sequence of Bifidobacterium dentium Strain JCM 1195T, Isolated from Human Dental Caries.	Genome Announcements	2015	3		e00284-15			Bifidobacterium dentium strain JCM 1195(T) was isolated from human dental caries. Here, we report the complete genome sequence of this organism. 		
@D	Toh, H.//Matsubara, T.//Tomida, S.//Mimura, I.//Arakawa, K.//Kikusui, T.//Morita, H. 	Draft Genome Sequence of Bifidobacterium lemurum DSM 28807T Isolated from the Gastrointestinal Tracts of Ring-Tailed Lemurs (Lemur catta).	Genome Announcements	2017	5		e01656-16			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. 		
@D	Toh, H.//Nakano, A.//Nguyen, C.T.//Mimura, I.//Arakawa, K.//Tashiro, K.//Kikusui, T.//Morita, H. 	Draft Genome Sequence of Coccoid Lactobacillus equigenerosi NRIC 0697T Isolated from the Gastrointestinal Tracts of Healthy Thoroughbreds.	Genome Announcements	2016	4		e01679-15			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. 		
@D	Toh, H.//Oshima, K.//Nakano, A.//Takahata, M.//Murakami, M.//Takaki, T.//Nishiyama, H.//Igimi, S.//Hattori, M.//Morita, H. 	Genomic adaptation of the Lactobacillus casei group.	PLoS ONE	2013	8		e75073			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. 		
@D	Toh, H.//Oshima, K.//Nakano, A.//Yamashita, N.//Iioka, E.//Kurokawa, R.//Morita, H.//Hattori, M. 	Complete Genome Sequence of Bifidobacterium scardovii Strain JCM 12489T, Isolated from Human Blood.	Genome Announcements	2015	3		e00285-15			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. 		
@D	Toh, H.//Oshima, K.//Suzuki, T.//Hattori, M.//Morita, H. 	Complete Genome Sequence of the Equol-Producing Bacterium Adlercreutzia equolifaciens DSM 19450T.	Genome Announcements	2013	1		e00742-13			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. 		
@D	Toh, H.//Oshima, K.//Toyoda, A.//Ogura, Y.//Ooka, T.//Sasamoto, H.//Park, S.H.//Iyoda, S.//Kurokawa, K.//Morita, H.//Itoh, K.//Taylor, T.D.//Hayashi, T.//Hattori, M. 	Complete genome sequence of the wild-type commensal Escherichia coli strain SE15 belonging to phylogenetic group B2.	J. Bacteriol.	2009	192		1165-1166			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. 		
@D	Toh, H.//Sharma, V.K.//Oshima, K.//Kondo, S.//Hattori, M.//Ward, F.B.//Free, A.//Taylor, T.D. 	Complete Genome Sequences of Arcobacter butzleri ED-1 and Arcobacter sp. Strain L, Both Isolated from a Microbial Fuel Cell.	J. Bacteriol.	2011	193		6411-6412			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. 		
@D	Toh, H.//Weiss, B.L.//Perkin, S.A.//Yamashita, A.//Oshima, K.//Hattori, M.//Aksoy, S. 	Massive genome erosion and functional adaptations provide insights into the symbiotic lifestyle of Sodalis glossinidius in the tsetse host.	Genome Res.	2006	16		149-156			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. 		
@D	Toh, H.//Yamazaki, Y.//Tashiro, K.//Kawarai, S.//Oshima, K.//Nakano, A.//Kim, C.N.//Mimura, I.//Arakawa, K.//Iriki, A.//Kikusui, T.//Morita, H. 	Draft Genome Sequence of Bifidobacterium aesculapii DSM 26737T, Isolated from Feces of Baby Common Marmoset.	Genome Announcements	2015	3		e01463-15			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. 		
@D	Tohya, M.//Sekizaki, T.//Miyoshi-Akiyama, T. 	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.	Genome Biol. Evol.	2018	10		1180-1184			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. 		
@D	Tokajian, S.//Eisen, J.A.//Jospin, G.//Coil, D.A. 	Draft Genome Sequences of Streptococcus pyogenes Strains Associated with Throat and Skin Infections in Lebanon.	Genome Announcements	2014	2		e00358-14			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%. 		
@D	Tokajian, S.//Eisen, J.A.//Jospin, G.//Farra, A.//Coil, D.A. 	Draft Genome Sequences of Extended-Spectrum beta-Lactamase-Producing Escherchia coli Strains Isolated from Patients in Lebanon.	Genome Announcements	2014	2		e00123-14			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. 		
@D	Tokajian, S.//Eisen, J.A.//Jospin, G.//Farra, A.//Coil, D.A. 	Draft Genome Sequence of Extended-Spectrum beta-Lactamase-Producing Klebsiella pneumoniae Isolated from a Patient in Lebanon.	Genome Announcements	2014	2		e00121-14			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. 		
@D	Tokajian, S.//Eisen, J.A.//Jospin, G.//Hamze, M.//Rafei, R.//Salloum, T.//Ibrahim, J.//Coil, D.A. 	Draft Genome Sequences of Acinetobacter baumannii Strains Harboring the blaNDM-1  Gene Isolated in Lebanon from Civilians Wounded during the Syrian Civil War.	Genome Announcements	2016	4		e01678-15			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. 		
@D	Tokajian, S.//Eisen, J.A.//Jospin, G.//Matar, G.//Araj, G.F.//Coil, D.A. 	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.	Genome Announcements	2016	4		e01632-15			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. 		
@D	Tokovenko, B.//Ruckert, C.//Kalinowski, J.//Mohammadipanah, F.//Wink, J.//Rosenkranzer, B.//Myronovskyi, M.//Luzhetskyy, A. 	Complete Draft Genome Sequence of the Actinobacterium Nocardiopsis sinuspersici UTMC102 (DSM 45277T), Which Produces Serine Protease.	Genome Announcements	2017	5		e00362-17			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. 		
@D	Toksoy, E.//Onsan, Z.I.//Kirdar, B. 	Expression of a thermostable restriction endonuclease in recombinant Escherichia coli cells and optimization of fermentation conditions.	World J. Microbiol. Biotechnol.	2002	18		23-27			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. 		
@D	Toksoy, E.//Onsan, Z.I.//Kirdar, B. 	High-level production of TaqI restriction endonuclease by three different expression systems in Escherichia coli cells using the T7 phage promoter.	Appl. Microbiol. Biotechnol.	2002	59		239-245			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. 		
@D	Toksoy, E.//Onsan, Z.I.//Kirdar, B. 	Effect of the co-expression of methyltransferase activity on extracellular production of TaqI restriction endonuclease in recombinant E. coli cells.	Process. Biochem.	2001	37		527-534			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. 		
@D	Tolen, T.N.//Xie, Y.//Hernandez, A.C.//Kuty, E.G.F. 	Complete Genome Sequence of Salmonella enterica Serovar Typhimurium Myophage Mushroom.	Genome Announcements	2015	3		e00154-15			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. 		
@D	Toliusis, P.//Tamulaitiene, G.//Grigaitis, R.//Tuminauskaite, D.//Silanskas, A.//Manakova, E.//Venclovas, C.//Szczelkun, M.D.//Siksnys, V.//Zaremba, M. 	The H-subunit of the restriction endonuclease CglI contains a prototype DEAD-Z1 helicase-like motor.	Nucleic Acids Res.	2018	46		2560-2572			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. 		
@D	Toliusis, P.//Zaremba, M.//Silanskas, A.//Szczelkun, M.D.//Siksnys, V. 	CgII cleaves DNA using a mechanism distinct from other ATP-dependent restriction  endonucleases.	Nucleic Acids Res.	2017	45		8435-8447			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. 		
@D	Tollefsbol, T.O.//Hutchinson, C.A. III 	Analysis in Escherichia coli of the effects of in vivo CpG methylation catalyzed by the cloned murine maintenance methyltransferase.	Biochem. Biophys. Res. Commun.	1998	245		670-678			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. 		
@D	Tollefsbol, T.O.//Hutchison, C.A. III 	Control of methylation spreading in synthetic DNA sequences by the murine DNA methyltransferase.	J. Mol. Biol.	1997	269		494-504			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. 		
@D	Tollefsbol, T.O.//Hutchison, C.A. III 	Mammalian DNA (cytosine-5-)-methyltransferase expressed in Escherichia coli, purified and characterized.	J. Biol. Chem.	1995	270		18543-18550			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. 		
@D	Tolstoshev, C.M.//Blakesley, R.W. 	RSITE: a computer program to predict the recognition sequence of a restriction enzyme.	Nucleic Acids Res.	1982	10		1-17			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). 		
@D	Tomaschewski, J.//Ruger, W. 	Nucleotide sequence and primary structures of gene products coded for by the T4 genome between map positions 48.266 kb and 39.166 kb.	Nucleic Acids Res.	1987	15		3632-3633			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. 		
@D	Tomassini, J.//Roychoudhury, R.//Wu, R.//Roberts, R.J. 	Recognition sequence of restriction endonuclease KpnI from Klebsiella pneumoniae.	Nucleic Acids Res.	1978	5		4055-4064			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). 		
@D	Tomb, J.-F. et al. 	The complete genome sequence of the gastric pathogen Helicobacter pylori.	Nature	1997	388		539-547			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. 		
@D	Tomihama, T.//Nishi, Y.//Sakai, M.//Ikenaga, M.//Okubo, T.//Ikeda, S. 	Draft Genome Sequences of Streptomyces scabiei S58, Streptomyces turgidiscabies T45, and Streptomyces acidiscabies a10, the Pathogens of Potato Common Scab,  Isolated in Japan.	Genome Announcements	2016	4		e00062-16			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. 		
@D	Tomilov, V.N.//Chernukhin, V.A.//Abdurashitov, M.A.//Gonchar, D.A.//Degtyarev, S.K. 	Cleavage of mammalian chromosomal DNA by restriction enzymes in silico.	FEBS J.	2007	274		73			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. 		
@D	Tomilova, J.E.//Chernukhin, V.A.//Degtyarev, S.K. 	Dependence of site-specific endonuclease GlaI activity on quantity and location of methylcytosines in the recognition sequence 5'-GCGC-3'.	Ovchinnikov Bull. Biotechnol. Phys. Chem. Biol.	2006	2		30-39			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. 		
@D	Tomilova, J.E.//Kuznetsov, V.V.//Abdurashitov, M.A.//Netesova, N.A.//Degtyarev, S.K. 	Recombinant DNA-methyltransferase M1.Bst19I from Bacillus stearothermophilus 19: Purification, properties, and amino acid sequence analysis.	Mol. Biol. (Mosk)	2010	44		606-615			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. 		
@D	Tomilova, Y.E.//Abdurashitov, M.A.//Golikova, L.N.//Netesova, N.A.//Degtyarev, S.K. 	Cloning of the genes for DNA methyltransferases of the SfaNI and Bst19I restriction-modification systems and primary structure analysis of  protein products.	Mol. Biol. (Mosk)	2004	38		850-856			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. 		
@D	Tomilova, Y.E.//Dedkov, V.S.//Shinkarenko, N.M.//Popichenko, D.V.//Degtyarev, S.K. 	Restriction endonuclease Bst19I from Bacillus stearothermophilus recognizing the 5'-GCATC-3' DNA sequence.	Biotekhnologiya	2002	6		17-20			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. 		
@D	Tomkins, J.P.//Wood, T.C.//Stacey, M.G.//Loh, J.T.//Judd, A.//Goicoechea, J.L.//Stacey, G.//Sadowsky, M.J.//Wing, R.A. 	A marker-dense, sequence-ready map of the Bradyrhizobium japonicum genome.	Genome Res.	2001	11		1434-1440			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. 		
@D	Tompa, R.//McCallum, C.M.//Delrow, J.//Henikoff, J.G.//van Steensel, B.//Henikoff, S. 	Genome-Wide Profiling of DNA Methylation Reveals Transposon Targets of CHROMOMETHYLASE3.	Curr. Biol.	2002	12		65-68			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. 		
@D	Tompkins, T.A.//Barreau, G.//Broadbent, J.R. 	Complete Genome Sequence of Lactobacillus helveticus R0052, a Commercial Probiotic Strain.	J. Bacteriol.	2012	194		6349			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. 		
@D	Tompkins, T.A.//Barreau, G.//de Carvalho, V.G. 	Draft Genome Sequence of Probiotic Strain Lactobacillus rhamnosus R0011.	J. Bacteriol.	2012	194		902			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. 		
@D	Tong, H.//Shang, N.//Liu, L.//Wang, X.//Cai, J.//Dong, X. 	Complete Genome Sequence of an Oral Commensal, Streptococcus oligofermentans Strain AS 1.3089.	Genome Announcements	2013	1		e00353-13			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. 		
@D	Tong, T.//Chen, S.//Wang, L.//Tang, Y.//Ryu, J.Y.//Jiang, S.//Wu, X.//Chen, C.//Luo, J.//Deng, Z.//Li, Z.//Lee, S.Y.//Chen, S. 	Occurrence, evolution, and functions of DNA phosphorothioate epigenetics in bacteria.	Proc. Natl. Acad. Sci. U. S. A.	2018	115		E2988-E2996			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. 		
@D	Tong, Y.J.//Ji, X.J.//Liu, L.G.//Shen, M.Q.//Huang, H. 	Genome Sequence of Paenibacillus polymyxa ATCC 12321, a Promising Strain for Optically Active (R,R)-2,3-Butanediol Production.	Genome Announcements	2013	1		e00572-13			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. 		
@D	Tong, Y.J.//Ji, X.J.//Liu, L.G.//Shen, M.Q.//Huang, H. 	Genome Sequence of Klebsiella pneumoniae CICC10011, a Promising Strain for High 2,3-Butanediol Production.	Genome Announcements	2015	3		e00802-15			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. 		
@D	Tonomura, M.//Ehara, A.//Suzuki, H.//Amachi, S. 	Draft Genome Sequence of Anaeromyxobacter sp. Strain PSR-1, an Arsenate-Respiring Bacterium Isolated from Arsenic-Contaminated Soil.	Genome Announcements	2015	3		e00472-15			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. 		
@D	Too, C.C.//Ong, K.S.//Ankenbrand, M.J.//Lee, S.M.//Yule, C.M.//Keller, A. 	Draft Genome Sequence of Paraburkholderia sp. Strain C35, Isolated from a Malaysian Tropical Peat Swamp Forest.	Genome Announcements	2018	6		e00561-18			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. 		
@D	Too, C.C.//Ong, K.S.//Ankenbrand, M.J.//Lee, S.M.//Yule, C.M.//Keller, A. 	Draft Genome Sequence of Klebsiella sp. Strain C31 Isolated from a Malaysian Tropical Peat Swamp Forest.	Genome Announcements	2018	6		e00560-18			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. 		
@D	Too, C.C.//Ong, K.S.//Lee, S.M.//Yule, C.M.//Keller, A. 	Draft Genome Sequence of Dyella sp. Strain C11, Isolated from a Malaysian Tropical Peat Swamp Forest.	Genome Announcements	2018	6		e00459-18			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. 		
@D	Too, P.H.//Zhu, Z.//Chan, S.H.//Xu, S.Y. 	Engineering Nt.BtsCI and Nb.BtsCI nicking enzymes and applications in generating long overhangs.	Nucleic Acids Res.	2010	38		1294-1303			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. 		
@D	Toothman, P. 	Restriction alleviation by bacteriophages lambda and lambda reverse.	J. Virol.	1981	38		621-631			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. 		
@D	Topal, M.D.//Conrad, M. 	Changing endonuclease EcoRII Tyr308 to Phe abolishes cleavage but not recognition: possible homology with the Int-family of recombinases.	Nucleic Acids Res.	1993	21		2599-2603			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. 		
@D	Topal, M.D.//Thresher, R.J.//Conrad, M.//Griffith, J. 	NaeI endonuclease binding to pBR322 DNA induces looping.	Biochemistry	1991	30		2006-2010			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. 		
@D	Topel, M.//Pinder, M.I.M.//Johansson, O.N.//Kourtchenko, O.//Godhe, A.//Clarke, A.K. 	Complete Genome Sequence of Loktanella vestfoldensis Strain SMR4r, a Novel Strain Isolated from a Culture of the Chain-Forming Diatom Skeletonema marinoi.	Genome Announcements	2018	6		e01558-17			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. 		
@D	Topel, M.//Pinder, M.I.M.//Johansson, O.N.//Kourtchenko, O.//Godhe, A.//Clarke, A.K. 	Genome Sequence of Roseovarius mucosus Strain SMR3, Isolated from a Culture of the Diatom Skeletonema marinoi.	Genome Announcements	2017	5		e00394-17			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). 		
@D	Topin, A.N.//Gritsenko, O.M.//Brevnov, M.G.//Gromova, E.S.//Korshunova, G.A. 	Synthesis of a new photo-cross-linking nucleoside analogue containing an Aryl(trifluoromethyl)Diazirine group: Application for EcoRII and MvaI restriction-modification enzymes.	Nucleosides and Nucleotides	1998	17		1163-1175			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. 		
@D	Toro, M.//Cao, G.//Rump, L.//Nagaraja, T.G.//Meng, J.//Gonzalez-Escalona, N. 	Genome Sequences of 64 Non-O157:H7 Shiga Toxin-Producing Escherichia coli Strains.	Genome Announcements	2015	3		e01067-15			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. 		
@D	Toro, M.//Retamal, P.//Allard, M.//Brown, E.W.//Evans, P.//Gonzalez-Escalona, N. 	Draft Genome Sequences of 33 Salmonella enterica Clinical and Wildlife Isolates from Chile.	Genome Announcements	2015	3		e00054-15			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. 		
@D	Toro, N.//Martinez-Abarca, F.//Nisa-Martinez, R. 	Complete Genome Sequence of the RmInt1 Group II Intronless Sinorhizobium meliloti Strain RMO17.	Genome Announcements	2014	2		e01001-14			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). 		
@D	Toropov, V.A.//Vakhitov, T.Y.//Shalaeva, O.N.//Roshchina, E.K.//Sitkin, S.I. 	Complete Genome Sequences of the Probiotic Lactic Acid Bacteria Lactobacillus helveticus D75 and D76.	Genome Announcements	2018	6		e01552-17			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. 		
@D	Torosian, M.V.//Shishkova, O.V.//Rabinkova, E.V. 	Influence of recB and recA mutations on bacteriophage restriction by different restriction modification plasmid systems of E. coli.	Mol. Gen. Mikrobiol. Virusol.	1988	0		36-41			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. 		
@D	Torosyan, M.V.//Rainkova, E.V.//Shishkova, L.A.//Naumova, L.A.//Fradkin, G.E. 	Phenomenon of restriction alleviation in Escherichia coli strains.	Mol. Gen. Mikrobiol. Virusol.	1987	10		37-40			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. 		
@D	Torreblanca, J.//Casadesus, J. 	DNA adenine methylase mutants of Salmonella typhimurium and a novel Dam-regulated locus.	Genetics	1996	144		15-26			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. 		
@D	Torreblanca, J.//Marques, S.//Casadesus, J. 	Synthesis of FinP RNA by plasmids F and pSLT is regulated by DNA adenine methylation.	Genetics	1999	151		31-45			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. 		
@D	Torres, A.C.//Suarez, N.E.//Font, G.//Saavedra, L.//Taranto, M.P. 	Draft Genome Sequence of Lactobacillus reuteri Strain CRL 1098, an Interesting Candidate for Functional Food Development.	Genome Announcements	2016	4		e00806-16			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%. 		
@D	Torres, B.//Jaenecke, S.//Timmis, K.N.//Garcia, J.L.//Diaz, E. 	A gene containment strategy based on a restriction-modification system.	Environ. Microbiol.	2000	2		555-563			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. 		
@D	Torres, B.//Jaenecke, S.//Timmis, K.N.//Garcia, J.L.//Diaz, E. 	A dual lethal system to enhance containment of recombinant micro-organisms.	Microbiology	2003	149		3595-3601			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. 		
@D	Torres, D.//Revale, S.//Obando, M.//Maroniche, G.//Paris, G.//Perticari, A.//Vazquez, M.//Wisniewski-Dye, F.//Martinez-Abarca, F.//Cassan, F. 	Genome Sequence of Bradyrhizobium japonicum E109, One of the Most Agronomically Used Nitrogen-Fixing Rhizobacteria in Argentina.	Genome Announcements	2015	3		e01566-14			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. 		
@D	Torres, T.G.//Lozano, L.//Gonzalez, V.//Bustos, P.//Romero, D.//Brom, S. 	Draft Genome Sequence of the Bean-Nodulating Sinorhizobium fredii Strain GR64.	J. Bacteriol.	2012	194		6978			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. 		
@D	Torres-Tejerizo, G.//Wibberg, D.//Winkler, A.//Ormeno-Orrillo, E.//Martinez-Romero, E.//Niehaus, K.//Puhler, A.//Kalinowski, J.//Lagares, A.//Schluter, A.//Pistorio, M. 	Genome Sequence of the Symbiotic Type Strain Rhizobium tibeticum CCBAU85039T.	Genome Announcements	2017	5		e01513-16			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. 		
@D	Toshchakov, S.V.//Korzhenkov, A.A.//Samarov, N.I.//Mazunin, I.O.//Mozhey, O.I.//Shmyr, I.S.//Derbikova, K.S.//Taranov, E.A.//Dominova, I.N.//Bonch-Osmolovskaya, E.A.//Patrushev, M.V.//Podosokorskaya, O.A.//Kublanov, I.V. 	Complete genome sequence of and proposal of Thermofilum uzonense sp. nov. a novel hyperthermophilic crenarchaeon and emended description of the genus Thermofilum.	Standards in Genomic Sciences	2015	10		122			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. 		
@D	Toth, A.//Barna, T.//Nagy, I.//Horvath, B.//Nagy, I.//Tancsics, A.//Kriszt, B.//Baka, E.//Fekete, C.//Kukolya, J. 	Draft Genome Sequence of the Lignocellulose Decomposer Thermobifida fusca Strain  TM51.	Genome Announcements	2013	1		e00482-13			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. 		
@D	Toth, E.//Huszar, K.//Bencsura, P.//Kulcsar, P.I.//Vodicska, B.//Nyeste, A.//Welker, Z.//Toth, S.//Welker, E. 	Restriction enzyme body doubles and PCR cloning: on the general use of type IIs restriction enzymes for cloning.	PLoS ONE	2014	9		e90896			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. 		
@D	Toth, J.//Bollins, J.//Szczelkun, M.D. 	Re-evaluating the kinetics of ATP hydrolysis during initiation of DNA sliding by  Type III restriction enzymes.	Nucleic Acids Res.	2015	43		10870-10881			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. 		
@D	Toth, J.//van Aelst, K.//Salmons, H.//Szczelkun, M.D. 	Dissociation from DNA of Type III Restriction-Modification enzymes during helicase-dependent motion and following endonuclease activity.	Nucleic Acids Res.	2012	40		6752-6764			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'). 		
@D	Tothova, T.//Godany, A.//Javorsky, P.//Pristas, P. 	Production of SacI and SacII isoschizomers by soil streptomycetes.	Biologia (Bratisl)	2007	62		381-385			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. 		
@D	Totsika, M.//Beatson, S.A.//Sarkar, S.//Phan, M.D.//Petty, N.K.//Bachmann, N.//Szubert, M.//Sidjabat, H.E.//Paterson, D.L.//Upton, M.//Schembri, M.A. 	Insights into a multidrug resistant Escherichia coli pathogen of the globally disseminated ST131 lineage: genome analysis and virulence mechanisms.	PLoS ONE	2011	6		E26578			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. 		
@D	Touchon, M. et al. 	Organised genome dynamics in the Escherichia coli species results in highly diverse adaptive paths.	PLoS Genet.	2009	5		e1000344			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. 		
@D	Touchon, M.//Barbier, P.//Bernardet, J.F.//Loux, V.//Vacherie, B.//Barbe, V.//Rocha, E.//Duchaud, E. 	Complete genome sequence of the fish pathogen Flavobacterium branchiophilum.	Appl. Environ. Microbiol.	2011	77		7656-7662			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. 		
@D	Tourlousse, D.M.//Honda, T.//Matsuura, N.//Ohashi, A.//Tonouchi, A.//Sekiguchi, Y. 	Draft Genome Sequence of Bacteroidales Strain 6E, Isolated from a Rice Paddy Field in Japan.	Genome Announcements	2015	3		e01167-15			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. 		
@D	Tourlousse, D.M.//Matsuura, N.//Sun, L.//Toyonaga, M.//Kuroda, K.//Ohashi, A.//Cruz, R.//Yamaguchi, T.//Sekiguchi, Y. 	Draft Genome Sequence of Bacteroidales Strain TBC1, a Novel Isolate from a Methanogenic Wastewater Treatment System.	Genome Announcements	2015	3		e01168-15			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. 		
@D	Touzain, F.//Le Devendec, L.//de Boisseson, C.//Baron, S.//Jouy, E.//Perrin-Guyomard, A.//Blanchard, Y.//Kempf, I. 	Characterization of plasmids harboring blaCTX-M and blaCMY genes in E. coli from  French broilers.	PLoS ONE	2018	13		e0188768			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. 		
@D	Tovkach, F.I. 	A study of Erwinia carotovora phage resistance with the use of temperate bacteriophage ZF40.	Mikrobiologiia	2002	71		82-88			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. 		
@D	Tovkach, F.I.//Chervatyuk, N.V. 	Phage system for studying the restriction-modification system of Erwinia carotovora.	Mikrobiol. Zh.	2006	68		27-35			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. 		
@D	Town, J.//Audy, P.//Boyetchko, S.M.//Dumonceaux, T.J. 	High-Quality Draft Genome Sequence of Bacillus subtilis Strain WAUSV36.	Genome Announcements	2016	4		e00586-16			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. 		
@D	Town, J.//Audy, P.//Boyetchko, S.M.//Dumonceaux, T.J. 	High-Quality Draft Genome Sequence of Arthrobacter sp. OY3WO11, a Strain That Inhibits the Growth of Phytophthora infestans.	Genome Announcements	2016	4		e00585-16			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. 		
@D	Town, J.//Audy, P.//Boyetchko, S.M.//Dumonceaux, T.J. 	High-Quality Draft Genome Sequence of Biocontrol Strain Pantoea sp. OXWO6B1.	Genome Announcements	2016	4		e00582-16			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. 		
@D	Town, J.//Audy, P.//Boyetchko, S.M.//Dumonceaux, T.J. 	Genome Sequence of Pseudomonas chlororaphis Strain 189.	Genome Announcements	2016	4		e00581-16			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. 		
@D	Town, J.//Cui, N.//Audy, P.//Boyetchko, S.//Dumonceaux, T.J. 	Improved High-Quality Draft Genome Sequence of Pseudomonas fluorescens KENGFT3.	Genome Announcements	2016	4		e00428-16			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. 		
@D	Town, J.//Dumonceaux, T.J. 	High-Quality Draft Genome Sequences of Pantoea agglomerans Isolates Exhibiting Antagonistic Interactions with Wheat Seed-Associated Fungi.	Genome Announcements	2016	4		e00511-16			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. 		
@D	Town, J.R.//Dumonceaux, T.J. 	Laboratory-scale bioaugmentation relieves acetate accumulation and stimulates methane production in stalled anaerobic digesters.	Appl. Microbiol. Biotechnol.	2016	100		1009-1017			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. 		
@D	Townsley, L.//Caro, L.//Kelkar, H.//Shank, E.A. 	Draft Genome Sequence of Bacillus luciferensis Isolated from Soil.	Genome Announcements	2016	4		e01140-16			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. 		
@D	Townson, S.A.//Samuelson, J.C.//Bao, Y.//Xu, S.Y.//Aggarwal, A.K. 	BstYI Bound to Noncognate DNA Reveals a "Hemispecific" Complex: Implications for DNA Scanning.	Structure	2007	15		449-459			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. 		
@D	Townson, S.A.//Samuelson, J.C.//Vanamee, E.S.//Edwards, T.A.//Escalante, C.R.//Xu, S.-Y.//Aggarwal, A.K. 	Crystal structure of BstYI at 1.85 .ANG. resolution: A thermophilic restriction endonuclease with overlapping specificities to BamHI and  BglII.	J. Mol. Biol.	2004	338		725-733			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. 		
@D	Townson, S.A.//Samuelson, J.C.//Xu, S.-Y.//Aggarwal, A.K. 	Implications for switching restriction enzyme specificities from the structure of BstYI bound to a BglII DNA sequence.	Structure	2005	13		791-801			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. 		
@D	Toymentseva, A.A.//Suleimanova, A.D.//Boulygina, E.A.//Kazakov, S.V.//Baranova, D.S.//Akhmetova, A.I.//Mardanova, A.M.//Sharipova, M.R. 	Draft Genome Sequence of Bacillus ginsengihumi Strain M2.11 with Phytase Activity.	Genome Announcements	2015	3		e00851-15			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. 		
@D	Trachtenberg, A.M.//Carney, J.G.//Linnane, J.D.//Rheaume, B.A.//Pitts, N.L.//Mykles, D.L.//MacLea, K.S. 	Draft Genome Sequence of the Salt Water Bacterium Oceanospirillum linum ATCC 11336T.	Genome Announcements	2017	5		e00395-17			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. 		
@D	Trachtenberg, A.M.//Goen, A.E.//MacLea, K.S. 	Genome Sequences for Three Strains of Kocuria rosea, Including the Type Strain.	Genome Announcements	2018	6		e00594-18			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. 		
@D	Traglia, G.//Vilacoba, E.//Almuzara, M.//Diana, L.//Iriarte, A.//Centron, D.//Ramirez, M.S. 	Draft Genome Sequence of an Extensively Drug-Resistant Acinetobacter baumannii Indigo-Pigmented Strain.	Genome Announcements	2014	2		e01146-14			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. 		
@D	Traglia, G.M.//Almuzara, M.//Barberis, C.//Montana, S.//Schramm, S.T.//Enriquez, B.//Mussi, M.A.//Vay, C.//Iriarte, A.//Ramirez, M.S. 	Draft genome sequence of a taxonomically unique acinetobacter clinical strain with proteolytic and hemolytic activities.	Genome Announcements	2015	3		e00030-15			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. 		
@D	Traglia, G.M.//Dixon, C.//Chiem, K.//Almuzara, M.//Barberis, C.//Montana, S.//Merino, C.//Mussi, M.A.//Tolmasky, M.E.//Iriarte, A.//Vay, C.//Ramirez, M.S. 	Draft Genome Sequence of Empedobacter (Formerly Wautersiella) falsenii comb. nov. Wf282, a Strain Isolated from a Cervical Neck Abscess.	Genome Announcements	2015	3		e00235-15			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. 		
@D	Tragut, V.//Xiao, J.//Bylina, E.J.//Borthakur, D. 	Characterization of DNA restriction-modification systems in Spirulina platensis strain pacifica.	J. Appl. Phycol.	1995	7		561-564			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. 		
@D	Tran, P.H. 	X-ray crystal structure of N-6 adenine deoxyribose nucleic acid methyltransferase from Streptococcus pneumoniae.	Diss. Abstr.	2001	61		4801-B-4802-B			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. 		
@D	Tran, P.H.//Korszun, Z.R.//Cerritelli, S.//Springhorn, S.S.//Lacks, S.A. 	Crystal structure of the DpnM DNA adenine methyltransferase from the DpnII restriction system of Streptococcus pneumoniae bound to S-adenosylmethionine.	Structure	1998	6		1563-1575			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. 		
@D	Tran, P.N.//Tan, N.E.//Lee, Y.P.//Gan, H.M.//Polter, S.J.//Dailey, L.K.//Hudson, A.O.//Savka, M.A. 	Whole-Genome Sequence and Classification of 11 Endophytic Bacteria from Poison Ivy (Toxicodendron radicans).	Genome Announcements	2015	3		e01319-15			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. 		
@D	Tran, T.D.//Huynh, S.//Parker, C.T.//Hnasko, R.//Gorski, L.//McGarvey, J.A. 	Complete Genome Sequences of Three Bacillus amyloliquefaciens Strains That Inhibit the Growth of Listeria monocytogenes In Vitro.	Genome Announcements	2018	6		e00579-18			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. 		
@D	Tran-Betcke, A.//Behrens, B.//Noyer-Weidner, M.//Trautner, T.A. 	DNA methyltransferase genes of Bacillus subtilis phages: comparison of their nucleotide sequences.	Gene	1986	42		89-96			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. 		
@D	Tran-Nguyen, L.T.//Kube, M.//Schneider, B.//Reinhardt, R.//Gibb, K.S. 	Comparative genome analysis of "Candidatus Phytoplasma australiense" (subgroup tuf-Australia I; rp-A) and "Ca. Phytoplasma asteris" Strains  OY-M and AY-WB.	J. Bacteriol.	2008	190		3979-3991			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. 		
@D	Trasler, J.M.//Alcivar, A.A.//Hake, L.E.//Bestor, T.//Hecht, N.B. 	DNA methyltransferase is developmentally expressed in replicating and non-replicating male germ cells.	Nucleic Acids Res.	1992	20		2541-2545			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. 		
@D	Trasler, J.M.//Trasler, D.G.//Beston, T.H.//Li, E.//Ghibu, F. 	DNA methyltransferase in normal and Dnmtn/Dnmtn mouse embryos.	Dev. Dyn.	1996	206		239-247			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. 		
@D	Trautmann, D.//Voss, B.//Wilde, A.//Al-Babili, S.//Hess, W.R. 	Microevolution in cyanobacteria: re-sequencing a motile substrain of Synechocystis sp. PCC 6803.	DNA Res.	2012	19		435-448			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. 		
@D	Trautner, T.A.//Balganesh, T.//Wilke, K.//Noyer-Weidner, M.//Rauhut, E.//Lauster, R.//Behrens, B.//Pawlek, B. 	Organization of target-recognizing domains in the multispecific DNA (cytosine-5) methyltransferases of Bacillus subtilis phages SPR and Phi-3T.	Gene	1988	74		267			Meeting Abstract 		
@D	Trautner, T.A.//Balganesh, T.S.//Pawlek, B. 	Chimeric multispecific DNA methyltransferases with novel combinations of target recognition.	Nucleic Acids Res.	1988	16		6649-6658			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. 		
@A	Trautner, T.A.//Noyer-Weidner, M. 		Restriction/modification and methylation systems in Bacillus subtilis, related species, and their phages.			Hoch, J.A.//Losick, R. 		Bacillus subtilis and other gram-positive bacteria: Biochemistry, Physiology, and Molecular Genetics				Washington D.C.	American Society for Microbiology	1993		0		539-552									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. 		
@D	Trautner, T.A.//Pawlek, B.//Behrens, B.//Willert, J. 	Exact size and organization of DNA target-recognizing domains of multispecific DNA-(cytosine-C5)-methyltransferases.	EMBO J.	1996	15		1434-1442			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. 		
@D	Trautner, T.A.//Pawlek, B.//Bron, S.//Anagnostopoulos, C. 	Restriction and Modification in B. subtilis.	Mol. Gen. Genet.	1974	131		181-191			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. 		
@D	Trautner, T.A.//Pawlek, B.//Gunthert, U.//Canosi, U.//Jentsch, S.//Freund, M. 	Restriction and modification in Bacillus subtilis: Identification of a gene in the temperate phage SPbeta coding for a BsuR specific modification methyltransferase.	Mol. Gen. Genet.	1980	180		361-367			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. 		
@D	Travis, A.J.//Kelly, D.//Flint, H.J.//Aminov, R.I. 	Complete Genome Sequence of the Human Gut Symbiont Roseburia hominis.	Genome Announcements	2015	3		e01286-15			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. 		
@D	Travis, J. 	DNA flips out!  Enzymes repair and modify DNA in a surprising way.	Sci. News	1995	148		188-189			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. 		
@D	Travisany, D.//Di Genova, A.//Sepulveda, A.//Bobadilla-Fazzini, R.A.//Parada, P.//Maass, A. 	Draft Genome Sequence of the Sulfobacillus thermosulfidooxidans Cutipay Strain, an Indigenous Bacterium Isolated from a Naturally Extreme Mining Environment in  Northern Chile.	J. Bacteriol.	2012	194		6327-6328			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. 		
@D	Treangen, T.J.//Maybank, R.A.//Enke, S.//Friss, M.B.//Diviak, L.F.//Karaolis, D.K.//Koren, S.//Ondov, B.//Phillippy, A.M.//Bergman, N.H.//Rosovitz, M.J. 	Complete Genome Sequence of the Quality Control Strain Staphylococcus aureus subsp. aureus ATCC 25923.	Genome Announcements	2014	2		e01110-14			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. 		
@D	Trees, E.//Strockbine, N.//Changayil, S.//Ranganathan, S.//Zhao, K.//Weil, R.//MacCannell, D.//Sabol, A.//Schmidtke, A.//Martin, H.//Stripling, D.//Ribot, E.M.//Gerner-Smidt, P. 	Genome Sequences of 228 Shiga Toxin-Producing Escherichia coli Isolates and 12 Isolates Representing Other Diarrheagenic E. coli Pathotypes.	Genome Announcements	2014	2		e00718-14			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. 		
@D	Trefault, N.//De la Iglesia, R.//Molina, A.M.//Manzano, M.//Ledger, T.//Perez-Pantoja, D.//Sanchez, M.A.//Stuardo, M.//Gonzalez, B. 	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.	Environ. Microbiol.	2004	6		655-668			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. 		
@D	Treml, S.//Draveling, C.//Huang, C.//Heaster, J.//Walker, D.//DiFrancesco, R.//Jolly, J. 	Ambient-temperature-stable restriction endonucleases for use in forensic DNA applications.	Clin. Chem.	1994	40		1092			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. 		
@D	Treu, L.//de Diego-Diaz, B.//Papadimitriou, K.//Tsakalidou, E.//Giacomini, A.//Corich, V. 	Whole-Genome Sequences of Three Streptococcus macedonicus Strains Isolated from Italian Cheeses in the Veneto Region.	Genome Announcements	2017	5		e01358-17			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. 		
@D	Treu, L.//Vendramin, V.//Bovo, B.//Campanaro, S.//Corich, V.//Giacomini, A. 	Genome Sequences of Streptococcus thermophilus Strains MTH17CL396 and M17PTZA496  from Fontina, an Italian PDO Cheese.	Genome Announcements	2014	2		e00067-14			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. 		
@D	Treu, L.//Vendramin, V.//Bovo, B.//Campanaro, S.//Corich, V.//Giacomini, A. 	Whole-Genome Sequences of Streptococcus thermophilus Strains TH1435 and TH1436, Isolated from Raw Goat Milk.	Genome Announcements	2014	2		e01129-13			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. 		
@D	Treu, L.//Vendramin, V.//Bovo, B.//Campanaro, S.//Corich, V.//Giacomini, A. 	Genome Sequences of Four Italian Streptococcus thermophilus Strains of Dairy Origin.	Genome Announcements	2014	2		e00126-14			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. 		
@D	Treu, L.//Vendramin, V.//Bovo, B.//Giacomini, A.//Corich, V.//Campanaro, S. 	Genome Sequence of Lactobacillus fabifermentans Strain T30PCM01, Isolated from Fermenting Grape Marc.	Genome Announcements	2014	2		e00060-14			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. 		
@D	Treuner-Lange, A.//Bruckskotten, M.//Rupp, O.//Goesmann, A.//Sogaard-Andersen, L. 	Complete Genome Sequence of the Fruiting Myxobacterium Myxococcus macrosporus Strain DSM 14697, Generated by PacBio Sequencing.	Genome Announcements	2017	5		e01127-17			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. 		
@D	Treuner-Lange, A.//Bruckskotten, M.//Rupp, O.//Goesmann, A.//Sogaard-Andersen, L. 	Draft Genome Sequence of the Fruiting Myxobacterium Nannocystis exedens DSM 71.	Genome Announcements	2017	5		e01227-17			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%. 		
@D	Treuner-Lange, A.//Bruckskotten, M.//Rupp, O.//Goesmann, A.//Sogaard-Andersen, L. 	Complete Genome Sequence of the Fruiting Myxobacterium Melittangium boletus DSM 14713.	Genome Announcements	2017	5		e01262-17			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. 		
@D	Treuner-Lange, A.//Bruckskotten, M.//Rupp, O.//Goesmann, A.//Sogaard-Andersen, L. 	Whole-Genome Sequence of the Fruiting Myxobacterium Cystobacter fuscus DSM 52655.	Genome Announcements	2017	5		e01196-17			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. 		
@D	Treven, P.//Trmcic, A.//Bogovic, M.B.//Rogelj, I. 	Improved Draft Genome Sequence of Probiotic Strain Lactobacillus gasseri K7.	Genome Announcements	2014	2		e00725-14			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. 		
@D	Trevors, J.T. 	Review: Bacterial population genetics.	World J. Microbiol. Biotechnol.	1998	14		1-5			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. 		
@D	Trevors, J.T. 	Molecular evolution in bacteria: genome size, cell size, restriction-modification and recognition.	Bull. Inst. Pasteur	1998	96		25-33			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. 		
@D	Trevors, J.T. 	Molecular evolution in bacteria.	Antonie Van Leeuwenhoek	1995	67		315-324			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. 		
@D	Tribelli, P.M.//Raiger, I.L.J.//Catone, M.V.//Di Martino, C.//Revale, S.//Mendez, B.S.//Lopez, N.I. 	Genome Sequence of the Polyhydroxybutyrate Producer Pseudomonas extremaustralis,  a Highly Stress-Resistant Antarctic Bacterium.	J. Bacteriol.	2012	194		2381-2382			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. 		
@D	Trieu-Cuot, P.//Derlot, E.//Courvalin, P. 	Enhanced conjugative transfer of plasmid DNA from Escherichia coli to Staphylococcus aureus and Listeria monocytogenes.	FEMS Microbiol. Lett.	1993	109		19-23			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. 		
@D	Trimble, W.L.//Phung, L.T.//Meyer, F.//Gilbert, J.A.//Silver, S. 	Draft Genome Sequence of Agrobacterium albertimagni Strain AOL15.	J. Bacteriol.	2012	194		6986-6987			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. 		
@D	Trimble, W.L.//Phung, L.T.//Meyer, F.//Silver, S.//Gilbert, J.A. 	Draft Genome Sequence of Achromobacter piechaudii Strain HLE.	J. Bacteriol.	2012	194		6355			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. 		
@D	Trinh, S.A.//Leyn, S.A.//Rodionov, I.D.//Godzik, A.//Satchell, K.J.F. 	Draft Genome Sequences of Two Vibrio parahaemolyticus Strains Associated with Gastroenteritis after Raw Seafood Ingestion in Colorado.	Genome Announcements	2018	6		e01387-17			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. 		
@D	Tripathi, C.//Mahato, N.K.//Rani, P.//Singh, Y.//Kamra, K.//Lal, R. 	Draft genome sequence of Lampropedia cohaerens strain CT6(T) isolated from arsenic rich microbial mats of a Himalayan hot water spring.	Standards in Genomic Sciences	2016	11		64			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. 		
@D	Trivedi, V.D.//Jangir, P.K.//Sharma, R.//Phale, P.S. 	Draft Genome Sequence of Carbaryl-Degrading Soil Isolate Pseudomonas sp. Strain C5pp.	Genome Announcements	2016	4		e00526-16			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. 		
@D	Trotsenko, Y.A.//Shmareva, M.N.//Doronina, N.V.//Tarlachkov, S.V.//Mustakhimov, I.I.//Vasilenko, O.V. 	Draft Genome Sequence of Methylophaga muralis Bur 1, a Haloalkaliphilic (Non-Methane-Utilizing) Methylotroph Isolated from a Soda Lake.	Genome Announcements	2016	4		e01227-16			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. 		
@D	Trotter, M.//McAuliffe, O.//Callanan, M.//Edwards, R.//Fitzgerald, G.F.//Coffey, A.//Ross, R.P. 	Genome analysis of the obligately lytic bacteriophage 4268 of Lactococcus lactic provides insight into its adaptable nature.	Gene	2006	366		189-199			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. 		
@D	Trotter, M.//Ross, R.P.//Fitzgerald, G.F.//Coffey, A. 	Lactococcus lactis DPC5598, a plasmid-free derivative of a commercial starter, provides a valuable alternative host for culture improvement studies.	J. Appl. Microbiol.	2002	93		134-143			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. 		
@D	Trouillet-Assant, S. et al. 	Adaptive processes of Staphylococcus aureus isolates during the progression from acute to chronic bone and joint infections in patients.	Cell. Microbiol.	2016	18		1405-1414			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. 		
@D	Trowbridge, J.J.//Snow, J.W.//Kim, J.//Orkin, S.H. 	DNA Methyltransferase 1 Is Essential for and Uniquely Regulates Hematopoietic Stem and Progenitor Cells.	Cell Stem Cell	2009	5		442-449			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. 		
@D	Troxell, B.//Fink, R.C.//Dickey, A.N.//Scholl, E.H.//Hassan, H.M. 	Complete Genome Sequence of NC983, a Live Attenuated Strain of Salmonella enterica Serovar Typhimurium.	Genome Announcements	2016	4		e01074-16			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. 		
@D	Trubitsyn, D.//Abreu, F.//Ward, F.B.//Taylor, T.//Hattori, M.//Kondo, S.//Trivedi, U.//Staniland, S.//Lins, U.//Bazylinski, D.A. 	Draft Genome Sequence of Magnetovibrio blakemorei Strain MV-1, a Marine Vibrioid  Magnetotactic Bacterium.	Genome Announcements	2016	4		e01330-16			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. 		
@D	Trubitsyn, D.//Geurink, C.//Pikuta, E.//Lefevre, C.T.//McShan, W.M.//Gillaspy, A.F.//Bazylinski, D.A. 	Draft Genome Sequence of the Obligately Alkaliphilic Sulfate-Reducing Bacterium Desulfonatronum thiodismutans Strain MLF1.	Genome Announcements	2014	2		e00741-14			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. 		
@D	Trujillo, L.E.//Brito, J.E.//Reyes, G.//Garcia, O. 	Purification of SmaI restriction enzyme.	Biotecnol. Apl.	1990	7		326-332			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. 		
@D	Trujillo, L.E.//Pupo, E.//Miranda, F.//Perez, E.//Gonzalez, E. 	Correspondence between radioactive and functional methods in the quality control of DNA restriction and modifying enzymes.	Rev. Latinoam. Microbiol.	1996	38		31-37			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. 		
@D	Trujillo, L.E.//Reyes, G.//Bayolo, E.//Vazquez, M.M.//Garcia, O. 	Purification of NciI restriction endonuclease.	Biotecnol. Apl.	1990	7		320-325			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. 		
@D	Tsai, R.//Correa, I.R.//Xu, M.Y.//Xu, S.Y. 	Restriction and modification of deoxyarchaeosine (dG+)-containing phage 9 g DNA.	Sci. Rep.	2017	7		8348			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. 		
@D	Tsai, S.P.//Hartin, R.J.//Ryu, J.-I. 	Transformation in restriction-deficient Salmonella typhimurium LT2.	J. Gen. Microbiol.	1989	135		2561-2567			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. 		
@D	Tsai, Y.C.//Conlan, S.//Deming, C.//Segre, J.A.//Kong, H.H.//Korlach, J.//Oh, J. 	Resolving the Complexity of Human Skin Metagenomes Using Single-Molecule Sequencing.	MBio	2016	7		e01948-15			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. 		
@D	Tsai, Y.M.//Lo, W.S.//Kuo, C.H. 	Complete Genome Sequence of Spiroplasma corruscae EC-1T (DSM 19793), a Bacterium  Isolated from a Lampyrid Beetle (Ellychnia corrusca).	Genome Announcements	2017	5		e00964-17			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. 		
@D	Tsai, Y.M.//Lo, W.S.//Wu, P.S.//Cho, S.T.//Kuo, C.H. 	Complete Genome Sequence of Spiroplasma monobiae MQ-1(T) (ATCC 33825), a Bacterium Isolated from the Vespid Wasp (Monobia quadridens).	Genome Announcements	2018	6		e00347-18			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. 		
@D	Tsai, Y.M.//Wu, P.S.//Lo, W.S.//Kuo, C.H. 	Complete Genome Sequence of Spiroplasma floricola 23-6(T) (ATCC 29989), a Bacterium Isolated from a Tulip Tree (Liriodendron tulipifera L.).	Genome Announcements	2018	6		e00302-18			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. 		
@D	Tsang, H.L.//Huang, J.L.//Lin, Y.H.//Huang, K.F.//Lu, P.L.//Lin, G.H.//Khine, A.A.//Hu, A.//Chen, H.P. 	Borneol dehydrogenase from Pseudomonas sp. TCU-HL1 catalyzes the oxidation of (+)-borneol and its isomers to camphor.	Appl. Environ. Microbiol.	2016	82		6378-6385			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. 		
@D	Tsao, D.H.H.//Maki, A.H. 	Optically detected magnetic resonance study of the interaction of an Arsenic(III) derivative of cacodylic acid with EcoRI methyl transferase.	Biochemistry	1991	30		4565-4572			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]. 		
@D	Tschoeke, D.A.//Moreira, A.P.//Chimetto, T.L.A.//de Mesquita, M.M.//Gregoracci, G.B.//Gomez-Gil, B.//Valle, R.//Thompson, C.C.//Thompson, F.L. 	Exploring the Genome of Cheese Starter Lactic Acid Bacterium Lactococcus lactis subsp. lactis CECT 4433.	Genome Announcements	2014	2		e01142-14			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. 		
@D	Tse, H.//Tsoi, H.W.//Leung, S.P.//Lau, S.K.//Woo, P.C.//Yuen, K.Y. 	Complete Genome Sequence of Staphylococcus lugdunensis strain HKU09-01.	J. Bacteriol.	2010	192		1471-1472			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. 		
@D	Tse, H.//Tsoi, H.W.//Leung, S.P.//Urquhart, I.J.//Lau, S.K.//Woo, P.C.//Yuen, K.Y. 	Complete genome sequence of the veterinary pathogen Staphylococcus pseudintermedius strain HKU10-03 isolated from a case of canine pyoderma.	J. Bacteriol.	2011	193		1783-1784			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. 		
@D	Tseng, S.P.//Hsueh, P.R.//Tsai, J.C.//Teng, L.J. 	Tn6001, a Transposon-Like Element Containing the blaVIM-3-Harboring Integron In450.	Antimicrob. Agents Chemother.	2007	51		4187-4190			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. 		
@D	Tsirigos, A.//Rigoutsos, I. 	A new computational method for the detection of horizontal gene transfer events.	Nucleic Acids Res.	2005	33		922-933			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/. 		
@D	Tsonos, J.//Adriaenssens, E.M.//Klumpp, J.//Hernalsteens, J.P.//Lavigne, R.//De Greve, H. 	Complete Genome Sequence of the Novel Escherichia coli Phage phAPEC8.	J. Virol.	2012	86		13117-13118			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. 		
@D	Tsubouchi, T.//Kaneko, Y. 	Draft Genome Sequence of the Arsenic-Resistant Bacterium Brevundimonas denitrificans TAR-002T.	Genome Announcements	2017	5		e01326-17			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. 		
@D	Tsubouchi, T.//Nishi, S.//Maruyama, T.//Hatada, Y. 	Draft Genome Sequence of Aneurinibacillus tyrosinisolvens LL-002T, Which Possesses Some Pseudouridine Synthases.	Genome Announcements	2015	3		e00529-15			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. 		
@D	Tsubouchi, T.//Nishi, S.//Usui, K.//Shimane, Y.//Takaki, Y.//Maruyama, T.//Hatada, Y. 	Draft Genome Sequence of the Dimorphic Prosthecate Bacterium Brevundimonas abyssalis TAR-001T.	Genome Announcements	2013	1		e00826-13			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. 		
@D	Tsuchida, S.//Nezuo, M.//Tsukahara, M.//Ogura, Y.//Hayashi, T.//Ushida, K. 	Draft Genome Sequence of Lactobacillus gorillae Strain KZ01T, Isolated from a Western Lowland Gorilla.	Genome Announcements	2015	3		e01196-15			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. 		
@D	Tsuge, K.//Matsui, K.//Itaya, M. 	One step assembly of multiple DNA fragments with a designed order and orientation in Bacillus subtilis plasmid.	Nucleic Acids Res.	2003	31		e133			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. 		
@D	Tsui, C.K.M.//Wong, D.//Narula, G.//Gardy, J.L.//Hsiao, W.W.H.//Av-Gay, Y. 	Genome Sequences of the Mycobacterium tuberculosis H37Rv-ptkA Deletion Mutant and Its Parental Strain.	Genome Announcements	2017	5		e01156-17			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. 		
@D	Tsui, W.-C.//Elgar, G.//Merrill, C.//Maunders, M. 	RspX I:  a new restriction endonuclease with a recognition sequence of 5'T^CATGA3'.	Nucleic Acids Res.	1988	16		4178			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. 		
@D	Tsujimoto, Y.//Saito, R.//Sahara, T.//Kimura, N.//Tsuruoka, N.//Shigeri, Y.//Watanabe, K. 	Draft Genome Sequence of Caenibacillus caldisaponilyticus B157T, a Thermophilic and Phospholipase-Producing Bacterium Isolated from Acidulocompost.	Genome Announcements	2017	5		e00089-17			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. 		
@D	Tsukahara, K.//Kita, A.//Nakashimada, Y.//Hoshino, T.//Murakami, K. 	Genome-guided analysis of transformation efficiency and carbon dioxide assimilation by Moorella thermoacetica Y72.	Gene	2014	535		150-155			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. 		
@D	Tsukahara, S.//Kim, S.-G.//Takaku, H. 	Inhibition of restriction endonuclease cleavage site via triple helix formation by homopyrimidine phosphorothioate oligonucleotides.	Biochem. Biophys. Res. Commun.	1993	196		990-996			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). 		
@D	Tsukahara, S.//Yamakawa, H.//Takai, K.//Takaku, H. 	Inhibition of restriction enzyme Ksp632I via triple helix formation by phosphorothioate oligonucleotides.	Nucleosides and Nucleotides	1994	13		1617-1626			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). 		
@D	Tsukatani, Y.//Hirose, Y.//Harada, J.//Misawa, N.//Mori, K.//Inoue, K.//Tamiaki, H. 	Complete Genome Sequence of the Bacteriochlorophyll b-Producing Photosynthetic Bacterium Blastochloris viridis.	Genome Announcements	2015	3		e01006-15			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. 		
@D	Tsumura, A.//Hayakawa, T.//Kumaki, Y.//Takebayashi, S.//Sakaue, M.//Matsuoka, C.//Shimotohno, K.//Ishikawa, F.//Li, E.//Ueda, H.R.//Nakayama, J.//Okano, M. 	Maintenance of self-renewal ability of mouse embryonic stem cells in the absence of DNA methyltransferases Dnmt1, Dnmt3a and Dnmt3b.	Genes Cells	2006	11		805-814			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. 		
@D	Tsuru, T.//Kawai, M.//Mizutani-Ui, Y.//Uchiyama, I.//Kobayashi, I. 	Evolution of paralogous genes: Reconstruction of genome rearrangements through comparison of multiple genomes within Staphylococcus aureus.	Mol. Biol. Evol.	2006	23		1269-1285			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. 		
@D	Tsurumaru, H.//Kanesaki, Y.//Hashimoto, S.//Okizaki, K.//Yoshikawa, H.//Yamakawa, T. 	Draft Genome Sequence of Bradyrhizobium japonicum Is-34, Which Is Incompatible with Rj4 Genotype Soybeans.	Genome Announcements	2014	2		e01316-14			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. 		
@D	Tsutakawa, S.E.//Jingami, H.//Morikawa, K. 	Recognition of a TG mismatch: The crystal structure of very short patch repair endonuclease in complex with a DNA duplex.	Cell	1999	99		615-623			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. 		
@D	Tsutakawa, S.E.//Morikawa, K. 	The structural basis of damaged DNA recognition and endonucleolytic cleavage for very short patch repair endonuclease.	Nucleic Acids Res.	2001	29		3775-3783			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. 		
@A	Tsutakawa, S.E.//Morikawa, K. 		New recognition mode for a TG mismatch: The atomic structure of a very short patch repair endonuclease-DNA complex.			 		Cold Spring Harb. Symp. Quant. Biol.				Cold Spring Harbor	Cold Spring Harbor Laboratory Press	2000		65		233-239									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. 		
@D	Tsutakawa, S.E.//Muto, T.//Kawate, T.//Jingami, H.//Kunishima, N.//Ariyoshi, M.//Kohda, D.//Nakagawa, M.//Morikawa, K. 	Crystallographic and functional studies of very short patch repair endonuclease.	Mol. Cell	1999	3		621-628			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. 		
@D	Tsvetkova, N.V. 	Development of rational schemes of the purification of restriction endonucleases.	Zh. Mikrobiol. Epidemiol. Immunobiol.	1987	7		77-81			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. 		
@D	Tsvetkova, N.V.//Mileikovskaya, M.M.//Gruber, I.M.//Polyachenko, V.M.//Butkus, V.V.//Janulaitis, A.//Sudzhyuvene, O.F.//Tarasov, A.P. 	Purification and determination of the substrate specificity of restriction endonuclease BcmI.	Mol. Gen. Mikrobiol. Virusol.	1987	0		19-22			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. 		
@D	Tsymbal, N.V.//Samoilenko, V.A.//Tovkach, F.I. 	Site-specific endonuclease activity of filamentous cyanobacterium Plectonema boryanum.	Dopov. Nats. Akad. Nauk Ukr.	2011	0		146-149			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. 		
@D	Tu, C.-P.D.//Jay, E.//Bahl, C.P.//Wu, R. 	A reliable mapping method for sequence determination of oligodeoxyribonucleotides by mobility shift analysis.	Anal. Biochem.	1976	74		73-93			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. 		
@D	Tu, C.-P.D.//Roychoudhury, R.//Wu, R. 	Nucleotide recognition sequence at the cleavage site of Haemophilus aegyptius II (HaeII) restriction endonuclease.	Biochem. Biophys. Res. Commun.	1976	72		355-362			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. 		
@D	Tucholski, J.//Skowron, P.M.//Podhajska, A.J. 	MmeI, a class-IIS restriction endonuclease: purification and characterization.	Gene	1995	157		87-92			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. 		
@D	Tucholski, J.//Zmijewski, J.W.//Podhajska, A.J. 	Two intertwined methylation activities of the MmeI restriction-modification class-IIS system from Methylophilus methylotrophus.	Gene	1998	223		293-302			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. 		
@D	Tucker, K.L. 	A genetic investigation of the establishment of genomic imprinting.	Ph.D. Thesis, MIT, USA	1997			1-80			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. 		
@D	Tucker, K.L.//Beard, C.//Dausman, J.//Jackson-Grusby, L.//Laird, P.W.//Lei, H.//Li, E.//Jaenisch, R. 	Germ-line passage is required for establishment of methylation and expression patterns of imprinted but not of nonimprinted genes.	Genes Dev.	1996	10		1008-1020			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. 		
@D	Tucker, K.L.//Talbot, D.//Lee, M.A.//Leonhardt, H.//Jaenisch, R. 	Complementation of methylation deficiency in embryonic stem cells by a DNA methyltransferase minigene.	Proc. Natl. Acad. Sci. U. S. A.	1996	93		12920-12925			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. 		
@D	Tufariello, J.M.//Kerantzas, C.A.//Vilcheze, C.//Calder, R.B.//Nordberg, E.K.//Fischer, J.A.//Hartman, T.E.//Yang, E.//Driscoll, T.//Cole, L.E.//Sebra, R.//Maqbool, S.B.//Wattam, A.R.//Jacobs, W.R. Jr. 	The Complete Genome Sequence of the Emerging Pathogen Mycobacterium haemophilum Explains Its Unique Culture Requirements.	MBio	2015	6		e01313-15			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. 		
@D	Tuffery, P.//Dessen, P.//Mugnier, C.//Hazout, S. 	Restriction map construction using a 'complete sentences compatibility' algorithm.	Comput. Appl. Biosci.	1988	4		103-110			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. 		
@D	Tukel, C.//Sanlibaba, P.//Ozden, B.//Akcelik, M. 	Identification of adsorption inhibition, restriction/modification and abortive infection type phage resistance systems in Lactococcus lactis strains.	Acta Biol. Hung.	2006	57		377-385			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. 		
@D	Tully, B.//Savalia, P.//Abuyen, K.//Baughan, C.//Romero, E.//Ronkowski, C.//Torres, B.//Tremblay, J.//Trujillo, A.//Tyler, M.//Perez-Rodriguez, I.//Amend, J. 	Genome Sequence of Geothermobacter sp. Strain EPR-M, a Deep-Sea Hydrothermal Vent Iron Reducer.	Genome Announcements	2017	5		e00424-17			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. 		
@D	Tumbula, D.L.//Makula, R.A.//Whitman, W.B. 	Transformation of Methanococcus maripaludis and identification of a PstI-like restriction system.	FEMS Microbiol. Lett.	1994	121		309-314			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. 		
@D	Tummings, S.//Panescu, J.//Daly, R.A.//Wrighton, K.C.//Mouser, P.J. 	Draft Genome Sequences of Marinobacter Strains Recovered from Utica Shale-Produced Fluids.	Genome Announcements	2018	6		e00155-18			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. 		
@D	Tuohimaa, A.//Riipinen, K.A.//Brandt, K.//Alatossava, T. 	The genome of the virulent phage Lc-Nu of probiotic Lactobacillus rhamnosus, and comparative genomics with Lactobacillus casei phages.	Arch. Virol.	2006	151		947-965			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. 		
@D	Tupa, P.R.//Masuda, H. 	Draft Genome Sequence of a Propanotroph, Rhodococcus sp. Strain ENV425, Capable of Degrading Methyl tert-Butyl Ether and N-Nitrosodimethylamine.	Genome Announcements	2018	6		e00051-18			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. 		
@D	Tupikin, A.E.//Kalmykova, A.I.//Kabilov, M.R. 	Draft Genome Sequence of the Probiotic Bifidobacterium longum subsp. longum Strain MC-42.	Genome Announcements	2016	4		e01411-16			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. 		
@D	Turk, P.W.//Laayoun, A.//Smith, S.S.//Weitzman, S.A. 	DNA adduct 8-hydroxyl-2'-deoxyguanosine (8-hydroxyguanine) affects function of human DNA methyltransferase.	Carcinogenesis	1995	16		1253-1255			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. 		
@D	Turk, P.W.//Weitzman, S.A. 	Free radical DNA adduct 8-OH-deoxyguanosine affects activity of HpaII and MspI restriction endonuclease.	Free Radic. Res.	1995	23		255-258			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. 		
@D	Turmel, M.//Boulanger, J.//Schnare, M.N.//Gray, M.W.//Lemieux, C. 	Six group I introns and three internal transcribed spacers in the chloroplast large subunit ribosomal RNA gene of the green alga Chlamydomonas eugametos.	J. Mol. Biol.	1991	218		293-311			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. 		
@D	Turmel, M.//Cote, V.//Otis, C.//Mercier, J.-P.//Gray, M.W.//Lonergan, K.M.//Lemieux, C. 	Evolutionary transfer of ORF-containing group I introns between different subcellular compartments (chloroplast and mitochondrion).	Mol. Biol. Evol.	1995	12		533-545			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. 		
@D	Turmel, M.//Gutell, R.R.//Mercier, J.-P.//Otis, C.//Lemieux, C. 	Analysis of the chloroplast large subunit ribosomal RNA gene from 17 Chlamydomonas taxa.	J. Mol. Biol.	1993	232		446-467			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. 		
@D	Turmel, M.//Mercier, J.-P.//Cote, V.//Otis, C.//Lemieux, C. 	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+.	Nucleic Acids Res.	1995	23		2519-2525			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. 		
@D	Turmel, M.//Otis, C.//Cote, V.//Lemieux, C. 	Evolutionarily conserved and functionally important residues in the I-CeuI homing endonuclease.	Nucleic Acids Res.	1997	25		2610-2619			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. 		
@D	Turna, J.//Mikulasova, D.//Timko, J.//Zelinka, J. 	Purification of restriction endonuclease SauBMKI.	Biologia (Bratisl)	1990	45		281-288			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. 		
@D	Turner, D.P.//Connolly, B.A. 	Interaction of the E-coli DNA G : T-mismatch endonuclease (vsr protein) with oligonucleotides containing its target sequence.	J. Mol. Biol.	2000	304		765-778			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. 		
@D	Turner, P.C.//Yomano, L.P.//Jarboe, L.R.//York, S.W.//Baggett, C.L.//Moritz, B.E.//Zentz, E.B.//Shanmugam, K.T.//Ingram, L.O. 	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.	J. Ind. Microbiol. Biotechnol.	2012	39		629-639			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. 		
@D	Turroni, F. et al. 	Genome analysis of Bifidobacterium bifidum PRL2010 reveals metabolic pathways for host-derived glycan foraging.	Proc. Natl. Acad. Sci. U. S. A.	2010	107		19514-19519			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. 		
@D	Tushar, L.//Sasi, J.T.S.//Sasikala, C.//Ramana, C.V. 	Draft Genome Sequence of Antimicrobial-Producing Clostridium sp. JC272, Isolated  from Marine Sediment.	Genome Announcements	2015	3		e00650-15			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. 		
@D	Tushar, L.//Sravanthi, T.//Sasikala, C.//Ramana, C.V. 	Draft Genome Sequence of Spirochaeta sp. Strain JC202, an Endosymbiont of the Termite (Isoptera) Gut.	Genome Announcements	2015	3		e01481-14			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. 		
@D	Tuzikov, F.V.//Tuzikova, N.A.//Naumochkin, A.N.//Zinovev, V.V.//Malygin, E.G. 	Study of the equilibrium interation of T4 phage Dam-DNA-(N-adenine)-methyltransferase with substrates and ligands by fluorescence quenching method.	Mol. Biol. (Mosk)	1997	31		86-90					
@D	Tuzikov, F.V.//Tuzikova, N.A.//Naumochkin, A.N.//Zinovev, V.V.//Malygin, E.G. 	Fluorescence quenching study of equilibrium binding of phage T4 dam DNA-[N6-adenine]-methyltransferase with substrates and ligands.	Mol. Biol. (Mosk)	1997	31		73-76			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. 		
@D	Tuzikov, F.V.//Zinovev, V.V.//Vavilin, V.I.//Malygin, E.G.//Buryanov, Y.I.//Baev, A.A. 	Interaction between Ecodam methylase and double-stranded oligodeoxyribonucleotides.	Dokl. Akad. Nauk.	1989	304		231-234			None 		
@D	Tweedie, S.//Ng, H.-H.//Barlow, A.L.//Turner, B.M.//Hendrich, B.//Bird, A. 	Vestiges of a DNA methylation system in Drosophila melanogaster?	Nat. Genet.	1999	23		389-390			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. 		
@D	Twomey, D.P.//Davis, R.//Daly, C.//Fitzgerald, G.F. 	Sequence of the gene encoding a second ScrFI m5C methyltransferase of Lactococcus lactis.	Gene	1993	136		205-209			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. 		
@D	Twomey, D.P.//Davis, R.//Daly, C.//Fitzgerald, G.F. 	Molecular characterisation of the ScrFI restriction-modification system.	Irish J. Agr. Food Res.	1993	32		217			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. 		
@D	Twomey, D.P.//De Urraza, P.J.//McKay, L.L.//O'Sullivan, D.J. 	Characterization of AbiR, a novel multicomponent abortive infection mechanism encoded by plasmid pKR223 of Lactococcus lactis subsp. lactis KR2.	Appl. Environ. Microbiol.	2000	66		2647-2651			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. 		
@D	Twomey, D.P.//Gabillet, N.//Daly, C.//Fitzgerald, G.F. 	Molecular characterization of the restriction endonuclease gene (scrFIR) associated with the ScrFI restriction/modification system from Lactococcus lactis subsp. cremoris UC503.	Microbiology	1997	143		2277-2286			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. 		
@D	Twomey, D.P.//McKay, L.L.//O'Sullivan, D.J. 	Molecular characterization of the Lactococcus lactis LlaKR2I restriction-modification system and effect of an IS982 element positioned between the restriction and modification genes.	J. Bacteriol.	1998	180		5844-5854			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. 		
@D	Twomey, D.P.//McKay, L.L.//O'Sullivan, D.J. 	Molecular characterization of the LlaKR2I restriction and modification system from Lactococcus lactis ssp. lactis KR2.	Abstr. Gen. Meet. Am. Soc. Microbiol.	1997	97		426			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. 		
@D	Tyndall, C.//Lehnherr, H.//Sandmeier, U.//Kulik, E.//Bickle, T.A. 	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.	Mol. Microbiol.	1997	23		729-736			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. 		
@D	Tyndall, C.//Meister, J.//Bickle, T.A. 	The Escherichia coli prr region encodes a functional type IC DNA restriction system closely integrated with an anticodon nuclease gene.	J. Mol. Biol.	1994	237		266-274			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. 		
@D	Tyson, G.W.//Chapman, J.//Hugenholtz, P.//Allen, E.E.//Ram, R.J.//Richardson, P.M.//Solovyev, V.V.//Rubin, E.M.//Rokhsar, D.S.//Banfield, J.F. 	Community structure and metabolism through reconstruction of microbial genomes from the environment.	Nature	2004	428		37-43			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. 		
@D	Tytgat, H.L.//Douillard, F.P.//Laine, P.K.//Paulin, L.//Willems, R.J.//de Vos, W.M. 	Complete Genome Sequence of Enterococcus faecium Commensal Isolate E1002.	Genome Announcements	2016	4		e00113-16			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. 		
@D	Uchida, K.//Pyle, A.M.//Morii, T.//Barton, J.K. 	High resolution footprinting of EcoRI and distamycin with Rh(phi)2(bpy)3+, a new photofootprinting reagent.	Nucleic Acids Res.	1989	17		10259-10279			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. 		
@D	Uchimura, Y.//Wyss, M.//Brugiroux, S.//Limenitakis, J.P.//Stecher, B.//McCoy, K.D.//Macpherson, A.J. 	Complete Genome Sequences of 12 Species of Stable Defined Moderately Diverse Mouse Microbiota 2.	Genome Announcements	2016	4		e00951-16			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. 		
@D	Uchino, Y.//Miura, T.//Hosoyama, A.//Ohji, S.//Yamazoe, A.//Ito, M.//Takahata, Y.//Suzuki, K.//Fujita, N. 	Complete genome sequencing of Dehalococcoides sp. strain UCH007 using a differential reads picking method.	Standards in Genomic Sciences	2015	10		102			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. 		
@D	Uebe, R.//Schuler, D.//Jogler, C.//Wiegand, S. 	Reevaluation of the Complete Genome Sequence of Magnetospirillum gryphiswaldense  MSR-1 with Single-Molecule Real-Time Sequencing Data.	Genome Announcements	2018	6		e00309-18			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. 		
@D	Ueda, K.//Yamashita, A.//Ishikawa, J.//Shimada, M.//Watsuji, T.-o.//Morimura, K.//Ikeda, H.//Hattori, M.//Beppu, T. 	Genome sequence of Symbiobacterium thermophilum, an uncultivable bacterium that depends on microbial commensalisms.	Nucleic Acids Res.	2004	32		4937-4944			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. 		
@D	Ueno, H.//Kato, I.//Ishino, Y. 	Cloning and expression of the BalI restriction-modification system.	Nucleic Acids Res.	1996	24		2268-2270			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. 		
@D	Ueno, H.//Kita, A.//Miyahara, M.//Ishiwata, N.//Mise, K.//Kato, I.//Ishino, Y. 	Production of new restriction endonuclease VpaK11BI recognizing sequence 5'-GGWCC-3' in a Haemolysin-less mutant of Vibrio parahaemolyticus.	Biosci. Biotechnol. Biochem.	1997	61		2129-2130			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. 		
@D	Ueno, T.//Ito, H.//Kimizuka, F.//Kotani, H.//Nakajima, K. 	Gene structure and expression of the MboI restriction-modification system.	Nucleic Acids Res.	1993	21		2309-2313			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. 		
@D	Ueno, T.//Ito, H.//Kotani, H.//Kimizuka, F.//Nakajima, K. 	Cloning and expression of the NspV restriction modification genes of Nostoc sp. strain PCC7524.	Nucleic Acids Res.	1993	21		3899			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. 		
@D	Ueno, T.//Ito, I.//Kotani, H.//Nakajima, K. 	Nsp7524V restriction-modification genes.	Biotech. Advances	1996	14		465			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. 		
@D	Uetake, H.//Toyama, S.//Hagiwara, S. 	On the mechanism of host-induced modification:  Multiplicity activation and thermolabile factor responsible for phage growth restriction.	Virology	1964	22		202-213			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. 		
@D	Ugalde, J.A.//Narasingarao, P.//Kuo, S.//Podell, S.//Allen, E.E. 	Draft Genome Sequence of 'Candidatus Halobonum tyrrellensis' Strain G22, Isolated from the Hypersaline Waters of Lake Tyrrell, Australia.	Genome Announcements	2013	1		e01001-13			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. 		
@D	Uhlemann, A.C.//Porcella, S.F.//Trivedi, S.//Sullivan, S.B.//Hafer, C.//Kennedy, A.D.//Barbian, K.D.//McCarthy, A.J.//Street, C.//Hirschberg, D.L.//Lipkin, W.I.//Lindsay, J.A.//DeLeo, F.R.//Lowy, F.D. 	Identification of a highly transmissible animal-independent Staphylococcus aureus ST398 clone with distinct genomic and cell adhesion properties.	MBio	2012	3		e00027-12			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. 		
@D	Uhlich, G.A.//Paoli, G.C.//Chen, C.Y.//Cottrell, B.J.//Zhang, X.//Yan, X. 	Whole-Genome Sequence of Escherichia coli Serotype O157:H7 Strain EDL932 (ATCC 43894).	Genome Announcements	2016	4		e00647-16			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. 		
@D	Uhlich, G.A.//Paoli, G.C.//Zhang, X.//Dudley, E.G.//Figler, H.M.//Cottrell, B.J.//Andreozzi, E. 	Whole-Genome Sequence of Escherichia coli Serotype O157:H7 Strain PA20.	Genome Announcements	2017	5		e01460-16			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. 		
@D	Uhlich, G.A.//Reichenberger, E.R.//Cottrell, B.J.//Fratamico, P.//Andreozzi, E. 	Whole-Genome Sequence of Escherichia coli Serotype O157:H7 Strain B6914-ARS.	Genome Announcements	2017	5		e01191-17			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. 		
@D	Uhlig, R.//Poehlein, A.//Fischer, R.J.//Daniel, R.//Bahl, H. 	Genome Sequence of the Autotrophic Acetogen Clostridium magnum DSM 2767.	Genome Announcements	2016	4		e00464-16			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. 		
@D	Ukanis, M.//Sapranauskas, R.//Lubys, A. 	Screening for catalytically active Type II restriction endonucleases using segregation-induced methylation deficiency.	Nucleic Acids Res.	2012	40		e149			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. 		
@D	Ulge, U.Y.//Baker, D.A.//Monnat, R.J. Jr. 	Comprehensive computational design of mCreI homing endonuclease cleavage specificity for genome engineering.	Nucleic Acids Res.	2011	39		4330-4339			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. 		
@D	Ullrich, S.R.//Poehlein, A.//Voget, S.//Hoppert, M.//Daniel, R.//Leimbach, A.//Tischler, J.S.//Schlomann, M.//Muhling, M. 	Permanent draft genome sequence of Acidiphilium sp. JA12-A1.	Standards in Genomic Sciences	2015	10		56			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. 		
@D	Ulyanova, V.//Shah, M.R.//Dudkina, E.//Vershinina, V.//Ilinskaya, O. 	Draft Whole Genome Sequence of Bacillus pumilus Strain 3-19, a Chemical Mutant Overproducing Extracellular Ribonuclease.	Genome Announcements	2014	2		e00724-14			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. 		
@D	Um, J.//Park, C.//Lee, K. 	Alteration of specificity of restriction endonuclease EcoRI in organic solvent.	Korean Biochem. J.	1994	27		401-407			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. 		
@D	Umezawa, K.//Watanabe, T.//Miura, A.//Kojima, H.//Fukui, M. 	The complete genome sequences of sulfur-oxidizing Gammaproteobacteria Sulfurifustis variabilis skN76(T) and Sulfuricaulis limicola HA5(T).	Standards in Genomic Sciences	2016	11		71			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. 		
@D	Undabarrena, A.//Beltrametti, F.//Claverias, F.P.//Gonzalez, M.//Moore, E.R.//Seeger, M.//Camara, B. 	Exploring the Diversity and Antimicrobial Potential of Marine Actinobacteria from the Comau Fjord in Northern Patagonia, Chile.	Front. Microbiol.	2016	7		1135			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. 		
@D	Undabarrena, A.//Ugalde, J.A.//Castro-Nallar, E.//Seeger, M.//Camara, B. 	Genome Sequence of Streptomyces sp. H-KF8, a Marine Actinobacterium Isolated from a Northern Chilean Patagonian Fjord.	Genome Announcements	2017	5		e01645-16			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. 		
@D	Underhill, P.A.//Johnson, P.H. 	Site-specific mutagenesis of the EcoRI restriction endonuclease: substitution of cysteine-217 with glycine affects in vivo but not in vitro enzyme function.	Fed. Proc.	1986	45		1875			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. 		
@D	Unverferth, C.A.//Santisteban, I.C.//Setterdahl, A.T. 	Draft Genome Sequence of the Novel Black-Pigmented Planococcus sp. Strain CAU13.	Genome Announcements	2014	2		e01160-14			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. 		
@D	Unzaga, T.V.//Diaz-Ricci, J.C.//Rhee, J.I.//Hernandez, M.R.//Schugerl, K. 	Modeling of the controlled expression of a harmful protein by a three-plasmid harboring system.	Biotechnol. Bioeng.	2002	80		544-551			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. 		
@D	Uozumi, T.//Hoshino, T.//Miwa, K.//Horinouchi, S.//Beppu, T.//Arima, K. 	Restriction and modification in Bacillus species.	Mol. Gen. Genet.	1977	152		65-69			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. 		
@D	Upadrasta, A.//Pitta, S.//Madempudi, R.S. 	Draft Genome Sequence of Bacillus clausii UBBC07, a Spore-Forming Probiotic Strain.	Genome Announcements	2016	4		e00235-16			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. 		
@D	Upadrasta, A.//Pitta, S.//Madempudi, R.S. 	Draft Genome Sequence of the Spore-Forming Probiotic Strain Bacillus coagulans Unique IS-2.	Genome Announcements	2016	4		e00225-16			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. 		
@D	Uporova, T.M.//Kartasheva, I.M.//Skripkin, E.A.//Lopareva, E.N.//Nikolskaya, I.I.//Debov, S.S. 	Restricting endonucleases from Shigella sonnei 47.	Vopr. Med. Khim.	1985	31		131-136			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. 		
@D	Uporova, T.M.//Nikolskaya, I.I.//Rubtsova, E.N.//Debov, S.S. 	Purification and identification of Eco CK restrictional endonuclease.	Vestn. Akad. Med. Nauk SSSR	1981	2		21-26			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. 		
@D	Urakawa, H.//Garcia, J.C.//Nielsen, J.L.//Le, V.Q.//Kozlowski, J.A.//Stein, L.Y.//Lim, C.K.//Pommerening-Roser, A.//Martens-Habbena, W.//Stahl, D.A.//Klotz, M.G. 	Nitrosospira lacus sp. nov., a psychrotolerant, ammonia-oxidizing bacterium from sandy lake sediment.	Int. J. Syst. Evol. Microbiol.	2015	65		242-250			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)). 		
@D	Urbanczyk, H.//Ogura, Y.//Hayashi, T. 	Contrasting inter- and intraspecies recombination patterns in the 'Harveyi clade' Vibrio collected over large spatial and temporal scales.	Genome Biol. Evol.	2014	7		71-80			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. 		
@D	Urbanczyk, H.//Ogura, Y.//Hendry, T.A.//Gould, A.L.//Kiwaki, N.//Atkinson, J.T.//Hayashi, T.//Dunlap, P.V. 	Genome Sequence of Photobacterium mandapamensis svers. 1.1., Bioluminescent Symbiont of the Cardinalfish Siphamia versicolor.	J. Bacteriol.	2011	193		3144-3145			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. 		
@D	Urbieta, M.S.//Rascovan, N.//Castro, C.//Revale, S.//Giaveno, M.A.//Vazquez, M.//Donati, E.R. 	Draft Genome Sequence of the Novel Thermoacidophilic Archaeon Acidianus copahuensis Strain ALE1, Isolated from the Copahue Volcanic Area in Neuquen,  Argentina.	Genome Announcements	2014	2		e00259-14			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. 		
@D	Urieli-Shoval, S.//Gruenbaum, Y.//Razin, A. 	Sequence and substrate specificity of isolated DNA methylases from Escherichia coli C.	J. Bacteriol.	1983	153		274-280			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. 		
@D	Urig, S.//Gowher, H.//Hermann, A.//Beck, C.//Fatemi, M.//Humeny, A.//Jeltsch, A. 	The Escherichia coli Dam DNA methyltransferase modifies DNA in a highly processive reaction.	J. Mol. Biol.	2002	319		1085-1096			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. 		
@D	Uritani, M.//Takai, M.//Yoshinaga, K. 	Protective effect of disaccharides on restriction endonucleases during drying under vacuum.	J. Biochem. (Tokyo)	1995	117		774-779			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. 		
@D	Uron, P.//Giachini, A.J.//Glick, B.R.//Rossi, M.J.//Nascimento, F.X. 	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.	Genome Announcements	2018	6		e00242-18			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%. 		
@D	Uroz, S.//Oger, P. 	Draft Genome Sequence of Burkholderia sp. Strain PML1(12), an Ectomycorrhizosphere-Inhabiting Bacterium with Effective Mineral-Weathering  Ability.	Genome Announcements	2015	3		e00798-15			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). 		
@D	Uroz, S.//Tech, J.J.//Sawaya, N.A.//Frey-Klett, P.//Leveau, J.H.J. 	Structure and function of bacterial communities in ageing soils: insights from the Mendocino ecological staircase.	Soil Biol. Biochem.	2014	69		265-274					
@D	Urshev, Z.//Hajo, K.//Lenoci, L.//Bron, P.A.//Dijkstra, A.//Alkema, W.//Wels, M.//Siezen, R.J.//Minkova, S.//van Hijum, S.A. 	Draft Genome Sequence of Lactobacillus delbrueckii subsp. bulgaricus LBB.B5.	Genome Announcements	2016	4		e01090-16			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. 		
@D	Urushibara, N.//Kawaguchiya, M.//Kobayashi, N. 	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.	J. Antimicrob. Chemother.	2012	67		1828-1834			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. 		
@D	Useh, N.M.//Ngbede, E.O.//Akange, N.//Thomas, M.//Foley, A.//Keena, M.C.//Nelson, E.//Christopher-Hennings, J.//Tomita, M.//Suzuki, H.//Scaria, J. 	Draft Genome Sequences of 37 Salmonella enterica Strains Isolated from Poultry Sources in Nigeria.	Genome Announcements	2016	4		e00315-16			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. 		
@D	Ushakova, T.A.//Puchkova, L.I.//Gutorov, V.V.//Kuvshinov, V.N.//Repin, V.E. 	Restriction endonuclease Sst12I from a strain of Streptomyces - Recognizing the nucleotide sequence 5 '-CTGCAG-3 '.	Prikl. Biokhim. Mikrobiol.	2002	38		25-28			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. 		
@D	Ushakova, T.A.//Puchkova, L.I.//Gutorov, V.V.//Totmenina, O.D.//Repin, V.E. 	Restriction endonuclease Asi256I recognizes and cuts the nucleotide sequence 5'-GATC-3'.	Prikl. Biokhim. Mikrobiol.	2008	44		28-31			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. 		
@D	Ushakova, T.A.//Puchkova, L.I.//Radionenko, Y.V.//Gutorov, V.V.//Kuvshinov, V.N.//Repin, V.E. 	Restriction endonuclease SpmI recognizing the 5'-AT/CGAT-3' nucleotide sequence.	Biotekhnologiya	2004	0		38-42			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. 		
@D	Ushakova, T.A.//Puchkova, L.I.//Radionenko, Y.V.//Kuvshinov, V.N.//Repin, V.E. 	Restriction endonuclease Bst221 from Bacillus stearothermophilus 22 strain recognizing the 5'-CCNNNNN^NNGG-3' nucleotide sequence.	Biotekhnologiya	2003	0		11-15			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. 		
@D	Ushay, H.M.//Tullius, T.D.//Lippard, S.J. 	Inhibition of the BamHI cleavage and unwinding of pBR322 deoxyribonucleic acid by the antitumor drug cis-dichlorodiammineplatinum(II).	Biochemistry	1981	20		3744-3748			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-. 		
@D	Ushida, K.//Tsuchida, S.//Ogura, Y.//Hayashi, T.//Sawada, A.//Hanya, G. 	Draft Genome Sequences of Sarcina ventriculi Strains Isolated from Wild Japanese  Macaques in Yakushima Island.	Genome Announcements	2016	4		e01694-15			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. 		
@D	Ushijima, B.//Videau, P.//Aeby, G.S.//Callahan, S.M. 	Draft Genome Sequence of Vibrio coralliilyticus Strain OCN008, Isolated from Kane'ohe Bay, Hawai'i.	Genome Announcements	2013	1		e00786-13			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. 		
@D	Ushijima, B.//Videau, P.//Poscablo, D.//Vine, V.//Salcedo, M.//Aeby, G.//Callahan, S.M. 	Complete Genome Sequence of Vibrio coralliilyticus Strain OCN014, Isolated from a Diseased Coral at Palmyra Atoll.	Genome Announcements	2014	2		e01318-14			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. 		
@D	Ushijima, K.//Ishibashi, T.//Tsukahara, S.//Takai, K.//Takaku, H. 	Inhibition of restriction endonuclease cleavage by triplex formation with oligo-2'-O-methyl-ribonucleotides containing 8-oxo-2'-O-methyladenosine in place of cytidine.	Heterocycles	2000	52		389-398			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. 		
@D	Ushijima, K.//Ishibashi, T.//Yamakawa, H.//Tsukahara, S.//Takai, K.//Maruyama, T.//Takaku, H. 	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.	Biochemistry	1999	38		6570-6575			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. 		
@D	Ustinova, V.//Smirnova, T.//Blagodatskikh, K.//Varlamov, D.//Sochivko, D.//Larionova, E.//Andreevskaya, S.//Andrievskaya, I.//Chernousova, L. 	First Draft Genome Sequence of a Mycobacterium gordonae Clinical Isolate.	Genome Announcements	2016	4		e00638-16			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. 		
@D	Ustinova, V.//Smirnova, T.//Varlamov, D.//Monakhova, Y.//Larionova, E.//Andreevskaya, S.//Andrievskaya, I.//Chernousova, L.//Ergeshov, A. 	Draft Genome Sequence of a Mycobacterium heckeshornense Clinical Isolate.	Genome Announcements	2018	6		e00178-18			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. 		
@D	Utter, B.//Deutsch, D.R.//Schuch, R.//Winer, B.Y.//Verratti, K.//Bishop-Lilly, K.//Sozhamannan, S.//Fischetti, V.A. 	Beyond the Chromosome: The Prevalence of Unique Extra-Chromosomal Bacteriophages with Integrated Virulence Genes in Pathogenic Staphylococcus aureus.	PLoS ONE	2014	9		E100502			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). 		
@D	Utturkar, S.M. et al. 	Application of Long Sequence Reads To Improve Genomes for Clostridium thermocellum AD2, Clostridium thermocellum LQRI, and Pelosinus fermentans R7.	Genome Announcements	2016	4		e01043-16			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. 		
@D	Utturkar, S.M.//Bollmann, A.//Brzoska, R.M.//Klingeman, D.M.//Epstein, S.E.//Palumbo, A.V.//Brown, S.D. 	Draft Genome Sequence for Caulobacter sp. Strain OR37, a Bacterium Tolerant to Heavy Metals.	Genome Announcements	2013	1		e00322-13			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. 		
@D	Utturkar, S.M.//Bollmann, A.//Brzoska, R.M.//Klingeman, D.M.//Epstein, S.E.//Palumbo, A.V.//Brown, S.D. 	Draft Genome Sequence for Ralstonia sp. Strain OR214, a Bacterium with Potential  for Bioremediation.	Genome Announcements	2013	1		e00321-13			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. 		
@D	Utturkar, S.M.//Huber, H.//Leptihn, S.//Loh, B.//Brown, S.D.//Stetter, K.O.//Podar, M. 	Draft Genome Sequence of Pyrodictium occultum PL19T, a Marine Hyperthermophilic Species of Archaea That Grows Optimally at 105 degrees C.	Genome Announcements	2016	4		e00016-16			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. 		
@D	Uyar, A.//Kurkcuoglu, O.//Nilsson, L.//Doruker, P. 	The elastic network model reveals a consistent picture on intrinsic functional dynamics of type II restriction endonucleases.	Phys. Biol.	2011	8		056001			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. 		
@D	Uyen, N.T.//Nishi, K.//Park, S.Y.//Choi, J.W.//Lee, H.J.//Kim, J.S. 	Crystallization and preliminary X-ray diffraction analysis of the HsdR subunit of a putative type I restriction enzyme from Vibrio vulnificus YJ016.	Acta Crystallogr. F Struct. Biol. Cryst. Commun.	2008	64		926-928			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%. 		
@D	Uyen, N.T.//Park, S.Y.//Choi, J.W.//Lee, H.J.//Nishi, K.//Kim, J.S. 	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.	Nucleic Acids Res.	2009	37		6960-6969			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. 		
@D	Uzelac, G.//Bertani, I.//Kojic, M.//Paszkiewicz, K.H.//Studholme, D.J.//Passos-da-Silva, D.//Venturi, V. 	Draft Genome Sequence of Beneficial Rice Rhizosphere Isolate Pseudomonas aeruginosa PUPa3.	Genome Announcements	2014	2		e00654-14			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. 		
@D	Vacheron, J.//Dubost, A.//Chapulliot, D.//Prigent-Combaret, C.//Muller, D. 	Draft Genome Sequence of Chryseobacterium sp. JV274 Isolated from Maize Rhizosphere.	Genome Announcements	2017	5		e00122-17			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). 		
@D	Vader, A.//Nielsen, H.//Johansen, S. 	In vivo expression of the nucleolar group I intron-encoded I-DirI homing endonuclease involves the removal of a spliceosomal intron.	EMBO J.	1999	18		1003-1013			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. 		
@D	Vaid, R.K.//Jindal, N.//Anand, T.//Bera, B.C.//Riyesh, T.//Virmani, N.//Barua, S.//Gupta, R.//Mahajan, N.K.//Joshi, C.G.//Singh, R.K. 	First Draft Genome Sequence of Salmonella enterica Serovar Gallinarum Strain VTCCBAA614, Isolated from Chicken in India.	Genome Announcements	2015	3		e01221-15			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. 		
@D	Vaid, R.K.//Shanmugasundaram, K.//Boora, A.//Bera, B.C.//Shukla, B.N.//Anand, T.//Singha, H.//Riyesh, T.//Virmani, N.//Barua, S.//Ahir, V.B.//Koringa, P.G.//Sajnani, M.R.//Bhat, V.D.//Rana, N.//Singh, K.P.//Malik, P.//Singh, R.K.//Joshi, C.G. 	Draft Genome Sequence of Pasteurella multocida subsp. multocida B:2 Strain VTCCBAA264 Isolated from Bubalus bubalis in North India.	Genome Announcements	2014	2		e00755-14			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. 		
@D	Vairapandi, M.//Duker, N.J. 	Enzymic removal of 5-methylcytosine from DNA by a hyman DNA-glycosylase.	Nucleic Acids Res.	1993	21		5323-5327			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. 		
@D	Vaishampayan, P.A.//Kuehl, J.V.//Froula, J.L.//Morgan, J.L.//Ochman, H.//Francino, M.P. 	Comparative metagenomics and population dynamics of the gut microbiota in mother and infant.	Genome Biol. Evol.	2010	2		53-66			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. 		
@D	Vaisvila, R.//Rasmussen, L.J.//Lobner-Olesen, A.//von Freiesleben, U.//Marinus, M.G. 	The LipB protein is a negative regulator of dam gene expression in Escherichia coli.	Biochim. Biophys. Acta	2000	1494		43-53			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. 		
@D	Vaisvila, R.//Sliesaraviciute, Z.//Kulakauskas, S.//Janulaitis, A. 	Cloning of the ppu21IM gene using a in vivo selection method.	Gene	1995	157		55-57			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. 		
@D	Vaisvila, R.//Vilkaitis, G.//Janulaitis, A. 	Identification of a gene encoding a DNA invertase-like enzyme adjacent to the PaeR7I restriction-modification system.	Gene	1995	157		81-84			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. 		
@D	Vaitkevicius, D.//Naureckiene, S.//Janulaitis, A. 	Advanced method for obtaining highly purified restriction enzyme preparations.	Biotekhnologiya	1991	1		35-41			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. 		
@D	Valat, C.//Goldstone, R.J.//Hirchaud, E.//Haenni, M.//Smith, D.G.//Madec, J.Y. 	Draft Genome Sequences of Enterohemorrhagic Escherichia coli Encoding Extended-Spectrum Beta-Lactamases.	Genome Announcements	2016	4		e01633-15			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. 		
@D	Valderrama, K.//Soto-Davila, M.//Santander, J. 	Draft Genome Sequence of the Type Strain Aeromonas salmonicida subsp. salmonicida ATCC 33658.	Genome Announcements	2017	5		e01064-17			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. 		
@D	Valdes, J.//Ossandon, F.//Quatrini, R.//Dopson, M.//Holmes, D.S. 	Draft Genome Sequence of the Extremely Acidophilic Biomining Bacterium Acidithiobacillus thiooxidans ATCC 19377 Provides Insights into the  Evolution of the Acidithiobacillus Genus.	J. Bacteriol.	2011	193		7003-7004			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. 		
@D	Valdes, J.//Quatrini, R.//Hallberg, K.//Dopson, M.//Valenzuela, P.D.//Holmes, D.S. 	Draft genome sequence of the extremely acidophilic bacterium Acidithiobacillus caldus ATCC 51756 reveals metabolic versatility in the genus Acidithiobacillus.	J. Bacteriol.	2009	191		5877-5878			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. 		
@D	Valdes, N.//Rivera-Araya, J.//Bijman, J.//Escudero, L.//Demergasso, C.//Fernandez, S.//Ferrer, A.//Chavez, R.//Levican, G. 	Draft Genome Sequence of Nitrincola sp. Strain A-D6, an Arsenic-Resistant Gammaproteobacterium Isolated from a Salt Flat.	Genome Announcements	2014	2		e01144-14			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. 		
@D	Valdes, N.//Soto, P.//Cottet, L.//Alarcon, P.//Gonzalez, A.//Castillo, A.//Corsini, G.//Tello, M. 	Draft genome sequence of strain MTR reveals its mechanism of capnophilic behavior.	Standards in Genomic Sciences	2015	10		110			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. 		
@D	Valdezate, S.//Monzon, S.//Garrido, N.//Zaballos, A.//Medina-Pascual, M.J.//Azcona-Gutierrez, J.M.//Vilar, B.//Cuesta, I. 	First Insight into the Genome Sequences of Two Linezolid-Resistant Nocardia farcinica Strains Isolated from Patients with Cystic Fibrosis.	Genome Announcements	2017	5		e01212-17			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. 		
@D	Vale, A.//Vitor, J. 	Helicobacter pylori genomic DNA methylation status: strain typing.	Int. J. Med. Microbiol.	2003	293		109			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). 		
@D	Vale, F.F.//Encarnacao, P.//Vitor, J.M.B. 	A new algorithm for cluster analysis of genomic methylation: the Helicobacter pylori case.	Bioinformatics	2008	24		383-388			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. 		
@D	Vale, F.F.//Megraud, F.//Vitor, J.M. 	Geographic distribution of methyltransferases of Helicobacter pylori: evidence of human host population isolation and migration.	BMC Microbiol.	2009	9		193			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. 		
@D	Vale, F.F.//Vitor, J.M. 	Genomic Methylation: a Tool for Typing Helicobacter pylori Isolates.	Appl. Environ. Microbiol.	2007	73		4243-4249			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. 		
@D	Vale, F.F.//Vitor, J.M.B. 	Genomic methylation status for discrimination among Helicobacter species: A bioinformatics approach.	J. Proteomics Bioinformatics	2008	1		258-266			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. 		
@D	Valenzuela, C.//Ugalde, J.A.//Mora, G.C.//Alvarez, S.//Contreras, I.//Santiviago, C.A. 	Draft Genome Sequence of Salmonella enterica Serovar Typhi Strain STH2370.	Genome Announcements	2014	2		e00104-14			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. 		
@D	Valera, M.J.//Poehlein, A.//Torija, M.J.//Haack, F.S.//Daniel, R.//Streit, W.R.//Mateo, E.//Mas, A. 	Draft Genome Sequence of Komagataeibacter europaeus CECT 8546, a Cellulose-Producing Strain of Vinegar Elaborated by the Traditional Method.	Genome Announcements	2015	3		e01231-15			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. 		
@D	Valeriani, F.//Biagini, T.//Giampaoli, S.//Crognale, S.//Santoni, D.//Romano, S.V. 	Draft Genome Sequence of Tepidimonas taiwanensis Strain VT154-175.	Genome Announcements	2016	4		e00942-16			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. 		
@D	Valinluck, B. 	Characterization of restriction-modification systems in Klebsiella pneumoniae.	Diss. Abstr.	1992	53		2701B			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. 		
@D	Valinluck, B.//Lee, N.S.//Ryu, J. 	A new restriction-modification system, KpnBI, recognized in Klebsiella pneumoniae.	Gene	1995	167		59-62			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. 		
@D	Valinluck, B.//Reyno, M.//Ryu, J. 	Two new restriction-modification systems, KpnA and KpnB, in Klebsiella pneumoniae.	Abstr. Gen. Meet. Am. Soc. Microbiol.	1989	89		180			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. 		
@D	Valinluck, V.//Sowers, L.C. 	Endogenous cytosine damage products alter the site selectivity of human DNA maintenance methyltransferase DNMT1.	Cancer Res.	2007	67		946-950			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. 		
@D	Valinluck, V.//Wu, W.//Liu, P.F.//Neidigh, J.W.//Sowers, L.C. 	Impact of cytosine 5-halogens on the interaction of DNA with restriction endonucleases and methyltransferase.	Chem. Res. Toxicol.	2006	19		556-562			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. 		
@D	Vallenet, D. et al. 	Comparative analysis of Acinetobacters: three genomes for three lifestyles.	PLoS ONE	2008	3		e1805			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. 		
@D	Vallone, P.M.//Benight, A.S. 	Thermodynamic, spectroscopic, and equilibrium binding studies of DNA sequence context effects in four 40 base pair deoxyoligonucleotides.	Biochemistry	2000	39		7835-7846			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. 		
@D	Valot, B.//Rohmer, L.//Jacobs, M.A.//Miller, S.I.//Bertrand, X.//Hocquet, D. 	Comparative Genomic Analysis of Two Multidrug-Resistant Clinical Isolates of ST395 Epidemic Strain of Pseudomonas aeruginosa Obtained 12 Years Apart.	Genome Announcements	2014	2		e00515-14			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. 		
@D	Valseth, K.//Nesbo, C.L.//Easterday, W.R.//Turner, W.C.//Olsen, J.S.//Stenseth, N.C.//Haverkamp, T.H. 	Draft Genome Sequences of Two Bacillus anthracis Strains from Etosha National Park, Namibia.	Genome Announcements	2016	4		e00861-16			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. 		
@D	Valton, J.//Daboussi, F.//Leduc, S.//Molina, R.//Redondo, P.//Macmaster, R.//Montoya, G.//Duchateau, P. 	5 '-Cytosine-Phosphoguanine (CpG) Methylation Impacts the Activity of Natural and Engineered Meganucleases.	J. Biol. Chem.	2012	287		30139-30150			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. 		
@D	van Aalten, D.M.F.//Erlanson, D.A.//Verdine, G.L.//Joshua-Tor, L. 	A structural snapshot of base-pair opening in DNA.	Proc. Natl. Acad. Sci. U. S. A.	1999	96		11809-11814			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. 		
@D	van Aelst, K.//Saikrishnan, K.//Szczelkun, M.D. 	Mapping DNA cleavage by the Type ISP restriction-modification enzymes following long-range communication between DNA sites in different orientations.	Nucleic Acids Res.	2015	43		10430-10443			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. 		
@D	van Aelst, K.//Sisakova, E.//Szczelkun, M.D. 	DNA cleavage by Type ISP Restriction-Modification enzymes is initially targeted to the 3'-5' strand.	Nucleic Acids Res.	2013	41		1081-1090			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. 		
@D	van Aelst, K.//Toth, J.//Ramanathan, S.P.//Schwarz, F.W.//Seidel, R.//Szczelkun, M.D. 	Type III restriction enzymes cleave DNA by long-range interaction between sites in both head-to-head and tail-to-tail inverted repeat.	Proc. Natl. Acad. Sci. U. S. A.	2010	107		9123-9128			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. 		
@D	van Belkum, A.//Jacobs, B.//van Beek, E.//Louwen, R.//van Rijs, W.//Debruyne, L.//Gilbert, M.//Li, J.//Jansz, A.//Megraud, F.//Endtz, H. 	Can Campylobacter coli induce Guillain-Barre syndrome?	Eur. J. Clin. Microbiol. Infect. Dis.	2009	28		557-560			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. 		
@D	van Belkum, M.J.//Lohans, C.T.//Vederas, J.C. 	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.	Genome Announcements	2015	3		e00372-15			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. 		
@D	van Bemmel, D.M.//Brank, A.S.//Eritja, R.//Marquez, V.E.//Christman, J.K. 	DNA (Cytosine-C5) methyltransferase inhibition by oligodeoxyribonucleotides containing 2-(1H)-pyrimidinone (zebularine aglycon) at the enzymatic target site.	Biochem. Pharmacol.	2009	78		633-641			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. 		
@D	Van Bemmel, D.M.//Marquez, V.E.//Christman, J.K. 	Characterization of the cytidine analog zebularine as an inhibitor of mammalian DNA (cytosine C5)-methyltransferase.	Proc. Amer. Assoc. Cancer Res.	2003	44		430			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. 		
@D	van Blokland, R.//Ross, S.//Corrado, G.//Scollan, C.//Meyer, P. 	Developmental abnormalities associated with deoxyadenosine methylation in transgenic tobacco.	Plant J.	1998	15		543-551			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. 		
@D	van Boven, C.P.A. 	Restriction and modification of phages in Staphylococcal phage typing.	Ann. NY Acad. Sci.	1974	236		376-388			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. 		
@D	Van Cleve, M.//Gumport, R.I. 	Effect of flanking sequence length on EcoRI endonuclease reaction.	Fed. Proc.	1987	46		2041			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. 		
@D	Van Cleve, M.//Gumport, R.I. 	Effect of flanking sequence length on EcoRI endonuclease reaction.	J. Cell Biol.	1988	107		403a			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. 		
@D	Van Cleve, M.D.//Gumport, R.I. 	Influence of enzyme-substrate contacts located outside the EcoRI recognition site on cleavage of duplex oligodeoxyribonucleotide substrates by EcoRI endonuclease.	Biochemistry	1992	31		334-339			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. 		
@D	Van Cott, E.M.//Wilson, G.G. 	Cloning the FnuDI, NaeI, NcoI and XbaI restriction-modification systems.	Gene	1988	74		55-59			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. 		
@D	van de Guchte, M. et al. 	The complete genome sequence of Lactobacillus bulgaricus reveals extensive and ongoing reductive evolution.	Proc. Natl. Acad. Sci. U. S. A.	2006	103		9274-9279			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. 		
@D	van den Bogert, B.//Boekhorst, J.//Smid, E.J.//Zoetendal, E.G.//Kleerebezem, M. 	Draft Genome Sequence of Enterococcus sp. Strain HSIEG1, Isolated from the Human  Small Intestine.	Genome Announcements	2013	1		e01013-13			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. 		
@D	van den Bogert, B.//Boekhorst, J.//Smid, E.J.//Zoetendal, E.G.//Kleerebezem, M. 	Draft Genome Sequence of Veillonella parvula HSIVP1, Isolated from the Human Small Intestine.	Genome Announcements	2013	1		e00977-13			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. 		
@D	van den Broek, B.//Noom, M.C.//Wuike, G.J.L. 	DNA-tension dependence of restriction enzyme cleavage reveals details of the reaction pathway.	Biophys. J.	2005	88		184A			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. 		
@D	van den Broek, B.//Noom, M.C.//Wuite, G.J.L. 	DNA-tension dependence of restriction enzyme activity reveals mechanochemical properties of the reaction pathway.	Nucleic Acids Res.	2005	33		2676-2684			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. 		
@D	van den Broek, B.//Schmidt, C.F.//Wuite, G.J.L. 	The effect of DNA tension on restriction-enzyme cutting rates studied with optical tweezers.	Biophys. J.	2003	84		141a			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, 		
@D	van den Broek, B.//Vanzi, F.//Normanno, D.//Pavone, F.S.//Wuite, G.J.L. 	Real-time observation of DNA looping dynamics of Type IIE restriction enzymes NaeI and NarI.	Nucleic Acids Res.	2006	34		167-174			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. 		
@D	van den Broek, B.//Wuite, G.J.L. 	Single molecule study of DNA tension on restriction enzyme cleavage activity.	Biophys. J.	2002	82		51a			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. 		
@D	van den Hondel, C.A.M.J.J.//van Leen, R.W.//van Arkel, G.A.//Duyvesteyn, M.//de Waard, A. 	Sequence-specific nucleases from the cyanobacterium Fremyella diplosiphon, and a peculiar resistance of its chromosomal DNA towards cleavage by other restriction enzymes.	FEMS Microbiol. Lett.	1983	16		7-12			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. 		
@D	Van den Wyngaert, I.//Sprengel, J.//Kass, S.U.//Luyten, W.H.M.L. 	Cloning and analysis of a novel human putative DNA methyltransferase.	FEBS Lett.	1998	426		283-289			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. 		
@D	Van der Auwera, G.A.//Feldgarden, M.//Kolter, R.//Mahillon, J. 	Whole-Genome Sequences of 94 Environmental Isolates of Bacillus cereus Sensu Lato.	Genome Announcements	2013	1		e00380-13			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. 		
@D	van der Graaf-van, B.L.//Miller, W.G.//Yee, E.//Bono, J.L.//Rijnsburger, M.//Campero, C.//Wagenaar, J.A.//Duim, B. 	First Closed Genome Sequence of Campylobacter fetus subsp. venerealis bv. intermedius.	Genome Announcements	2014	2		e01246-13			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. 		
@D	van der Gun, B.T.F.//Maluszynska-Hoffman, M.//Kiss, A.//Arendzen, A.J.//Ruiters, M.H.J.//McLaughlin, P.M.J.//Weinhold, E.//Rots, M.G. 	Targeted DNA Methylation by a DNA Methyltransferase Coupled to a Triple Helix Forming Oligonucleotide To Down-Regulate the Epithelial Cell Adhesion Molecule.	Bioconjugate Chem.	2010	21		1239-1245			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. 		
@D	van der Mee-Marquet, N.//Hernandez, D.//Bertrand, X.//Quentin, R.//Corvaglia, A.R.//Francois, P. 	Whole-Genome Sequence of the Ancestral Animal-Borne ST398 Staphylococcus aureus Strain S123.	Genome Announcements	2013	1		e00692-13			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. 		
@D	van der Ploeg, L.H.T.//Flavell, R.A. 	DNA methylation in the human cdb-globin locus in Erythroid and Nonerythroid tissues.	Cell	1980	19		947-958			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. 		
@D	van der Woerd, M.J.//Pelletier, J.J.//Xu, S.-Y.//Friedman, A.M. 	Restriction enzyme BsoBI-DNA complex: A tunnel for recognition of degenerate DNA sequences and potential histidine catalysis.	Structure	2001	9		133-144			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. 		
@D	van der Woude, M.//Hale, W.B.//Low, D.A. 	Formation of DNA methylation patterns: Nonmethylated GATC sequences in gut and pap operons.	J. Bacteriol.	1998	180		5913-5920			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. 		
@D	van der Woude, M.W. 	Some types of bacterial phase variation are epigenetic.	Microbe	2008	3		21-26			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. 		
@D	van der Woude, M.W.//Baumler, A.J. 	Phase and antigenic variation in bacteria.	Clin. Microbiol. Rev.	2004	17		581-611			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. 		
@D	van der Woude, M.W.//Braaten, B.A.//Low, D.A. 	Evidence for global regulatory control of pilus expression in Escherichia coli by Lrp and DNA methylation: model building based on analysis of pap.	Mol. Microbiol.	1992	6		2429-2435			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. 		
@D	Van Dongen, W.M.A.M.//Van Vlerken, M.M.A.//De Graaf, F.K. 	Nucleotide sequence of a DNA fragment encoding a Vibrio cholerae haemagglutinin.	Genetics (Life Sci. Adv.)	1987	6		85-91					
@D	Van Emburgh, B.O.//Robertson, K.D. 	Modulation of Dnmt3b function in vitro by interactions with Dnmt3L, Dnmt3a and Dnmt3b splice variants.	Nucleic Acids Res.	2011	39		4984-5002			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. 		
@A	Van Emburgh, B.O.//Robertson, K.D. 		DNA methyltransferases and methyl-CPG binding proteins as multifunctional regulators of chromatin structure and development in mammalian cells.			Tost, J. 		EPIGENETICS					Caister Academic Press	2008		0		23-61									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. 		
@D	Van Etten, J.L. 	DNA methyltransferases and DNA site-specific endonucleases encoded by Chlorella viruses.	J. Phycol.	1991	27		74			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. 		
@D	Van Etten, J.L.//Meints, R.H. 	Giant viruses infecting algae.	Annu. Rev. Microbiol.	1999	53		447-494			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. 		
@D	Van Etten, J.L.//Schuster, A.M.//Girton, L.//Burbank, D.E.//Swinton, D.//Hattman, S. 	DNA methylation of viruses infecting a eukaryotic Chlorella-like green alga.	Nucleic Acids Res.	1985	13		3471-3478			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. 		
@D	Van Etten, J.L.//Xia, Y.//Burbank, D.E. 	Viruses infecting a eukaryotic green alga are a new source of DNA methyltransferases and DNA site-specific endonucleases.	J. Cell Biochem. Suppl.	1989	13D		199			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. 		
@D	Van Etten, J.L.//Xia, Y.//Burbank, D.E.//Narva, K.E. 	Chlorella viruses code for restriction and modification enzymes.	Gene	1988	74		113-115			Meeting Abstract 		
@D	Van Heuverswyn, H.//Fiers, W. 	Recognition sequence for the restriction endonuclease BglI from Bacillus globigii.	Gene	1980	9		195-203			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. 		
@D	van Hijum, S.A.//Szalowska, E.//van der Maarel, M.J.//Dijkhuizen, L. 	Biochemical and molecular characterization of a levansucrase from Lactobacillus reuteri.	Microbiology	2004	150		621-630			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. 		
@D	Van Horn, C.//Chang, C.J.//Chen, J. 	De Novo Whole-Genome Sequence of Xylella fastidiosa subsp. multiplex Strain BB01  Isolated from a Blueberry in Georgia, USA.	Genome Announcements	2017	5		e01598-16			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. 		
@D	Van Houdt, R.//Van der Lelie, D.//Izquierdo, J.A.//Aertsen, A.//Masschelein, J.//Lavigne, R.//Michiels, C.W.//Taghavi, S. 	Genome Sequence of Serratia plymuthica RVH1, Isolated from a Raw Vegetable-Processing Line.	Genome Announcements	2014	2		e00021-14			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. 		
@D	van Ingen, J. et al. 	Global outbreak of severe Mycobacterium chimaera disease after cardiac surgery: a molecular epidemiological study.	Lancet Infect Dis	2017	17		1033-1041			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). 		
@D	van Kranenburg, R.//de Vos, W.M. 	Characterization of multiple regions involved in replication and mobilization of plasmid pNZ4000 coding for exopolysaccharide production in   Lactococcus lactis.	J. Bacteriol.	1998	180		5285-5290			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. 		
@D	van Kranenburg, R.//Kleerebezem, M.//de Vos, W.M. 	Nucleotide sequence analysis of the lactococcal EPS plasmid pNZ4000.	Plasmid	2000	43		130-136			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. 		
@D	Van Laar, T.A.//Chen, T.//Childers, B.M.//Chen, P.//Abercrombie, J.J.//Leung, K.P. 	Genome Sequence of a Multidrug-Resistant Strain of Klebsiella pneumoniae, BAMC 07-18, Isolated from a Combat Injury Wound.	Genome Announcements	2014	2		e01230-14			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. 		
@D	van Luijk, N.//Stierli, M.P.//Schwenninger, S.M.//Herve, C.//Dasen, G.//Jore, J.P.M.//Pouwels, P.H.//van der Werf, M.J.//Teuber, M.//Meile, L. 	Genetics and molecular biology of propionibacteria.	Lait	2002	82		45-57			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. 		
@D	van Mastrigt, O.//Abee, T.//Smid, E.J. 	Complete Genome Sequences of Lactococcus lactis subsp. lactis bv. diacetylactis FM03 and Leuconostoc mesenteroides FM06 Isolated from Cheese.	Genome Announcements	2017	5		e00633-17			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. 		
@D	van Noort, J.//van der Heijden, T.//Dutta, F.C.//Firman, K.//Dekker, C. 	Initiation of translocation by Type I restriction-modification enzymes is associated with a short DNA extrusion.	Nucleic Acids Res.	2004	32		6540-6547			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. 		
@D	van Noort, J.//van der Heijden, T.//van der Scheer, C.//Firman, K.//Dekker, C. 	Single molecule characterization of DNA translocation by the type I restriction enzyme EcoR124I.	Biophys. J.	2003	84		304a			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. 		
@D	van Ormondt, H.//Gorter, J.//Havelaar, K.J.//de Waard, A. 	Specificity of a deoxyribonucleic acid transmethylase induced by bacteriophage T2.  I. Nucleotide sequences isolated from Micrococcus luteus DNA methylated in vitro.	Nucleic Acids Res.	1975	2		1391-1400			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. 		
@D	van Ormondt, H.//Lautenberger, J.A.//Linn, S.//de Waard, A. 	Methylated oligonucleotides derived from bacteriophage fd RF-DNA modified in vitro by E. coli B modification methylase.	FEBS Lett.	1973	33		177-180			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. 		
@D	van Passel, M.W. et al. 	Genome sequence of Victivallis vadensis ATCC BAA-548, an anaerobic bacterium from the phylum Lentisphaerae, isolated from the human  gastro-intestinal tract.	J. Bacteriol.	2011	193		2373-2374			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. 		
@D	van Passel, M.W. et al. 	Genome sequence of the Verrucomicrobium Opitutus terrae PB90-1, an abundant inhabitant of rice paddy soil ecosystems.	J. Bacteriol.	2011	193		2367-2368			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. 		
@D	Van Pel, A.//Colson, C. 	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.	Mol. Gen. Genet.	1974	135		51-60			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. 		
@A	Van Roey, P.//Belfort, M.//Derbyshire, V. 		Homing endonuclease I-TevI: An atypical zinc finger with a novel function.			Iuchi, S.//Kuldell, N. 		Zinc Finger Proteins: from Atomic Contact to Cellular Function; Molecular Biology Intelligence Unit					Landes Bioscience	2005		0		35-38									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. 		
@D	Van Roey, P.//Derbyshire, V. 	GIY-YIG homing endonucleases - beads on a string.	Nucleic Acids Mol. Biol.	2005	16		67-83			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. 		
@D	Van Roey, P.//Meehan, L.//Kowalski, J.C.//Belfort, M.//Derbyshire, V. 	Catalytic domain structure and hypothesis for function of GIY-YIG intron endonuclease I-TevI.	Nat. Struct. Biol.	2002	9		806-811			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. 		
@D	Van Roey, P.//Waddling, C.A.//Fox, K.M.//Belfort, M.//Derbyshire, V. 	Intertwined structure of the DNA-binding domain of intron endonuclease I-TevI with its substrate.	EMBO J.	2001	20		3631-3637			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. 		
@D	van Schaik, W.//Top, J.//Riley, D.R.//Boekhorst, J.//Vrijenhoek, J.E.//Schapendonk, C.M.//Hendrickx, A.P.//Nijman, I.J.//Bonten, M.J.//Tettelin, H.//Willems, R.J. 	Pyrosequencing-based comparative genome analysis of the nosocomial pathogen Enterococcus faecium and identification of a large transferable pathogenicity island.	BMC Genomics	2010	11		239			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. 		
@D	Van Sluys, M.A. et al. 	Comparative analyses of the complete genome sequences of Pierce's disease and citrus variegated chlorosis strains of Xylella fastidiosa.	J. Bacteriol.	2003	185		1018-1026			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. 		
@D	van Soolingen, D.//de Haas, P.E.W.//Blumenthal, R.M.//Kremer, K.//Sluijter, M.//Pijnenburg, J.E.M.//Schouls, L.M.//Thole, J.E.R.//Desens-Kroon, M.W.G.//van Embden, J.D.A.//Hermans, P.W.M. 	Host-mediated modification of PvuII restriction in Mycobacterium tuberculosis.	J. Bacteriol.	1996	178		78-84			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. 		
@D	van Steensel, B.//Henikoff, S. 	Epigenomic profiling using microarrays.	Biotechniques	2003	35		346-357			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. 		
@D	van Steensel, B.//Henikoff, S. 	Identification of in vivo DNA targets of chromatin proteins using tethered Dam methyltransferase.	Nat. Biotechnol.	2000	18		424-428			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. 		
@D	van Zyl, L.J.//Deane, S.M.//Louw, L.A.//Rawlings, D.E. 	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.	Appl. Environ. Microbiol.	2008	74		4300-4308			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. 		
@D	van Zyl, L.J.//Matobole, R.//Augustin, N.B.F.//Klein, T.//Kirby, B.//Trindade, M. 	Draft Genome Sequences of Three Bacillus Species from South African Marine Sponges.	Genome Announcements	2016	4		e00143-16			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. 		
@D	Vanamee, E.S.//Aggarwal, A.K. 	Metal-dependent type II restriction endonucleases.	Handbook of Metalloproteins	2004	3		742-756			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. 		
@D	Vanamee, E.S.//Berriman, J.//Aggarwal, A.K. 	An EM View of the FokI Synaptic Complex by Single Particle Analysis.	J. Mol. Biol.	2007	370		207-212			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. 		
@D	Vanamee, E.S.//Hsieh, P.C.//Zhu, Z.Y.//Yates, D.//Garman, E.//Xu, S.Y.//Aggarwal, A.K. 	Glucocorticoid receptor-like Zn(Cys)(4) motifs in BslI restriction endonuclease.	J. Mol. Biol.	2003	334		595-603			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. 		
@D	Vanamee, E.S.//Santagata, S.//Aggarwal, A.K. 	FokI requires two specific DNA sites for cleavage.	J. Mol. Biol.	2001	309		69-78			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. 		
@D	Vanamee, E.S.//Viadiu, H.//Chan, S.H.//Ummat, A.//Hartline, A.M.//Xu, S.Y.//Aggarwal, A.K. 	Asymmetric DNA recognition by the OkrAI endonuclease, an isoschizomer of BamHI.	Nucleic Acids Res.	2011	39		712-719			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. 		
@D	Vanamee, E.S.//Viadiu, H.//Kucera, R.//Dorner, L.//Picone, S.//Schildkraut, I.//Aggarwal, A.K. 	A view of consecutive binding events from structures of tetrameric endonuclease SfiI bound to DNA.	EMBO J.	2005	24		4198-4208			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. 		
@D	Vanat, I.//Pristas, P.//Kutejova, E.//Judova, J.//Godany, A.//Jovorsky, P. 	SbvI restriction endonuclease from Streptococcus bovis.	Lett. Appl. Microbiol.	1993	17		297-299			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. 		
@D	Vanat, I.//Pristas, P.//Rybosoval, E.//Godany, A.//Javorsky, P. 	SruI restriction endonuclease from Selenomonas ruminantium.	FEMS Microbiol. Lett.	1993	113		129-132			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. 		
@D	Vancheva, T.//Bogatzevska, N.//Moncheva, P.//Lefeuvre, P.//Koebnik, R. 	Draft Genome Sequences of Two Xanthomonas vesicatoria Strains from the Balkan Peninsula.	Genome Announcements	2015	3		e01558-14			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. 		
@D	Vancheva, T.//Lefeuvre, P.//Bogatzevska, N.//Moncheva, P.//Koebnik, R. 	Draft Genome Sequences of Two Xanthomonas euvesicatoria Strains from the Balkan Peninsula.	Genome Announcements	2015	3		e01528-14			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. 		
@D	Vandecandelaere, I.//Van Nieuwerburgh, F.//Deforce, D.//Nelis, H.J.//Coenye, T. 	Draft Genome Sequence of Methicillin-Resistant Staphylococcus epidermidis Strain  ET-024, Isolated from an Endotracheal Tube Biofilm of a Mechanically Ventilated  Patient.	Genome Announcements	2014	2		e00527-14			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). 		
@D	Vandenbogaert, M.//Makeev, V. 	Analysis of bacterial RM-systems through genome-scale analysis and related taxonomy issues.	In Silico Biology	2003	3		127-143			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. 		
@D	Vandersteegen, K.//Kropinski, A.M.//Nash, J.H.//Noben, J.P.//Hermans, K.//Lavigne, R. 	Romulus and Remus, Two Phage Isolates Representing a Distinct Clade within the Twortlikevirus Genus, Display Suitable Properties for Phage Therapy Applications.	J. Virol.	2013	87		3237-3247			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. 		
@D	Vandzurova, A.//Hraskova, I.//Judova, J.//Javorsky, P.//Pristas, P. 	Antibiotic resistance and restriction endonucleases in fecal enterococci of chamois (Rupicapra rupicapra Linnaeus, 1758).	Folia Microbiol. (Praha)	2012	57		355-358			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. 		
@D	Vanek, P.G. 	Cloning and characterization of the BamHI restriction-modification methylase gene from Bacillus amyloliquefaciens.	Ph.D. Thesis, Georgetown University, USA	1991			1-195			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). 		
@D	Vanek, P.G.//Connaughton, J.F.//Kaloss, W.D.//Chirikijian, G. 	Comparison of cellular and viral methyltransferase genes from Bacillus amyloliquefaciens.	FASEB J.	1990	4		A2295			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. 		
@D	Vanek, P.G.//Connaughton, J.F.//Kaloss, W.D.//Chirikjian, J.G. 	The complete sequence of the Bacillus amyloliquefaciens strain H, cellular BamHI methylase gene.	Nucleic Acids Res.	1990	18		6145			None 		
@D	Vannier, P.//Marteinsson, V.T.//Fridjonsson, O.H.//Oger, P.//Jebbar, M. 	Complete Genome Sequence of the Hyperthermophilic, Piezophilic, Heterotrophic, and Carboxydotrophic Archaeon Thermococcus barophilus MP.	J. Bacteriol.	2011	193		1481-1482			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. 		
@D	VanWagoner, T.M.//Morton, D.J.//Seale, T.W.//Mussa, H.J.//Cole, B.K.//Whitby, P.W.//Stull, T.L. 	Draft Genome Sequences of Six Nontypeable Haemophilus influenzae Strains That Establish Bacteremia in the Infant Rat Model of Invasive Disease.	Genome Announcements	2015	3		e00899-15			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. 		
@D	Vanyushin, B.F. 	Enzymatic DNA methylation is an epigenetic control for genetic functions of the cell.	Biochemistry	2005	70		598-611			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. 		
@D	Vanyushin, B.F. 	A view of an elemental naturalist at the DNA world (base composition, sequences, methylation).	Biochemistry	2007	72		1289-1298			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. 		
@A	Vanyushin, B.F. 		DNA methylation in plants.			Doerfler, W.//Bohm, P. 		Curr. Top. Microbiol. Immunol.				Berlin, Germany	Springer-Verlag	2006		301		67-122									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. 		
@D	Vanyushin, B.F.//Aleksandrushkina, N.I.//Agarkova, O.A. 	Cytokinins do not markedly affect the methylation of DNA adenine residues in cell cultures of Escherichia coli B.	Biokhimiia	1989	54		1666-1672			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. 		
@D	Vanyushin, B.F.//Buryanov, Y.I.//Belozersky, A.N. 	Distribution of N6-methyladenine in DNA of T2 phage and its host Escherichia coli B.	Nature New Biol.	1971	230		25-27			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. 		
@D	Vanyushin, B.F.//Danilevich, V.N. 	Location of 5-methylcytosine in Escherichia coli and phage DD7 DNA.	Biokhimiia	1974	39		1293-1301			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... 		
@D	Vanyushin, B.F.//Dobritsa, A.P. 	On the nature of the cytosine-methylated sequence in DNA of Bacillus brevis var. G.-B.	Biochim. Biophys. Acta	1975	407		61-72			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. 		
@D	Vanyushin, B.F.//Dobritsa, A.P. 	Specificity of the methylation of the cytosine residues in the DNA of Bacillus brevis var. G-B.	Mol. Biol. (Mosk)	1975	9		283-295			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. 		
@D	Vanyushin, B.F.//Poirier, L.A. 	Drosophila melanogaster genomic DNA sequence homologous to mammalian cytosine DNA-methyltransferase gene.	Biochem. Mol. Biol. Int.	1996	39		353-358			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. 		
@D	Varani, A.M.//Lemos, M.V.//Fernandes, C.C.//Lemos, E.G.//Alves, E.C.//Desiderio, J.A. 	Draft Genome Sequence of Bacillus thuringiensis var. thuringiensis Strain T01-328, a Brazilian Isolate That Produces a Soluble Pesticide Protein, Cry1Ia.	Genome Announcements	2013	1		e00817-13			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. 		
@D	Vardimon, L.//Gunthert, U.//Doerfler, W. 	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.	Mol. Cell. Biol.	1982	2		1574-1580			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. 		
@D	Vardimon, L.//Rich, A. 	In Z-DNA the sequence G-C-G-C is neither methylated by HhaI methyltransferase nor cleaved by HhaI restriction endonuclease.	Proc. Natl. Acad. Sci. U. S. A.	1984	81		3268-3272			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. 		
@D	Varga, J.J.//Losada, L.//Zelazny, A.M.//Brinkac, L.//Harkins, D.//Radune, D.//Hostetler, J.//Sampaio, E.P.//Ronning, C.M.//Nierman, W.C.//Greenberg, D.E.//Holland, S.M.//Goldberg, J.B. 	Draft Genome Sequence Determination for Cystic Fibrosis and Chronic Granulomatous Disease Burkholderia multivorans Isolates.	J. Bacteriol.	2012	194		6356-6357			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. 		
@D	Varga, J.J.//Losada, L.//Zelazny, A.M.//Kim, M.//McCorrison, J.//Brinkac, L.//Sampaio, E.P.//Greenberg, D.E.//Singh, I.//Heiner, C.//Ashby, M.//Nierman, W.C.//Holland, S.M.//Goldberg, J.B. 	Draft Genome Sequences of Burkholderia cenocepacia ET12 Lineage Strains K56-2 and BC7.	Genome Announcements	2013	1		e00841-13			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. 		
@D	Varni, V.//Koval, A.//Nagel, A.//Ruybal, P.//Caimi, K.//Amadio, A.F. 	First Genome Sequence of Leptospira interrogans Serovar Pomona, Isolated from a Bovine Abortion.	Genome Announcements	2016	4		e00345-16			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. 		
@D	Varshney, H.//Iqbal, J.//Seleemuddin, M. 	Immobilization of the restriction endonuclease EcoRI.  Usefulness of a polyclonal antibody support.	Enzyme Microb. Technol.	1999	25		172-176			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. 		
@D	Varshney, H.//Saleemuddin, M.//Rhee, J.I.//Schugerl, K. 	Immobilization of SpA::EcoRI on IgG support improves the thermal stability of restriction activity.	Process. Biochem.	2001	37		275-278			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. 		
@D	Varshney, R.K. et al. 	Draft genome sequence of chickpea (Cicer arietinum) provides a resource for trait improvement.	Nat. Biotechnol.	2013	31		240-246			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. 		
@D	Vasconcellos, R.L.//Mendes, R.//Taketani, R.G.//Zucchi, T.D.//Melo, I.S. 	Draft Genome Sequence of Pseudomonas sp. Strain CMAA 1215, a Plant Growth-Promoting Bacterium Isolated from a Brazilian Mangrove.	Genome Announcements	2013	1		e00995-13			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. 		
@D	Vasconcelos, A.T. et al. 	Swine and Poultry Pathogens: the Complete Genome Sequences of Two Strains of Mycoplasma hyopneumoniae and a Strain of Mycoplasma synoviae.	J. Bacteriol.	2005	187		5568-5577			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. 		
@D	Vasilenko, O.V.//Doronina, N.V.//Shmareva, M.N.//Tarlachkov, S.V.//Trotsenko, Y.A. 	Draft Genome Sequence of Methyloligella halotolerans capital ES, Cyrillic2T, a New Halotolerant Methylotroph, Accumulating Poly-3-Hydroxybutyrate and Ectoine.	Genome Announcements	2016	4		e01189-16			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). 		
@D	Vasilenko, O.V.//Starodumova, I.P.//Tarlachkov, S.V.//Dorofeeva, L.V.//Avtukh, A.N.//Evtushenko, L.I. 	Draft Genome Sequence of 'Rathayibacter tanaceti' Strain VKM Ac-2596 Isolated from Tanacetum vulgare Infested by a Foliar Nematode.	Genome Announcements	2016	4		e00512-16			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. 		
@D	Vasiljeva, L.Y.//Zheleznaya, L.A.//Matvienko, N.I. 	A site-specific endonuclease BspR7I from Thermophilic strain.	Biokhimiia	1996	61		2147-2157			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. 		
@D	Vasiljeva, L.Y.//Zheleznaya, L.A.//Matvienko, N.I. 	Cloning and expression of a new site-specific methyltransferase M.SscL1I from Staphylococcus sp. L1.	Biokhimiia	2000	65		565-570			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'. 		
@D	Vasiljeva, L.Y.//Zheleznaya, L.A.//Matvienko, N.I. 	Site-specific endonuclease SscL1I from strain Staphylococcus species L1.	Biokhimiia	1998	63		212-218			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. 		
@D	Vasilyev, I.//Siniagina, M.//Malanin, S.//Boulygina, E.//Grygoryeva, T.//Yarullina, D.//Ilinskaya, O. 	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.	Genome Announcements	2015	3		e01383-15			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. 		
@D	Vasquez, C. 	Isolation and partial characterization of BstVI, a thermostable isoschizomer of XhoI.	Biochem. Int.	1985	10		655-662			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. 		
@D	Vasquez, C. 	Structural and biochemical characterization of the modification-restriction system of Bacillus stearothermophilus V.	Arch. Biol. Med. Exp. (Santiago)	1988	21		r338			None 		
@D	Vasquez, C.//Adasme, A.//Gonzalez, E. 	Aislamiento Y caracterizacion de endonucleasas termoestables:  BstVI, un isosquizomero de XhoI (isolation and characterization of thermostable endonucleases:  BstVI, an isoschizomer of XhoI).	Arch. Biol. Med. Exp. (Santiago)	1985	18		r371			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. 		
@D	Vasquez, C.//Saavedra, C.//Gonzalez, E. 	Cloning the BstVI restriction-modification system in Escherichia coli.	Gene	1991	102		83-85			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. 		
@D	Vasquez, C.//Vicuna, R. 	The genus Thermus: restriction endonucleases and modification methylases.	Arch. Biol. Med. Exp. (Santiago)	1982	15		417-421			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. 		
@D	Vasquez, C.C.//Saavedra, C.P.//Pichuantes, S.E. 	Nucleotide sequence of the gene encoding the BstLVI DNA methyltransferase: comparison with other amino-DNA methyltransferases.	Curr. Microbiol.	2000	40		114-118			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. 		
@D	Vasu, K.//Nagamalleswari, E.//Nagaraja, V. 	Promiscuous restriction is a cellular defense strategy that confers fitness advantage to bacteria.	Proc. Natl. Acad. Sci. U. S. A.	2012	109		E1287-1293			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.' 		
@D	Vasu, K.//Nagamalleswari, E.//Zahran, M.//Imhof, P.//Xu, S.Y.//Zhu, Z.//Chan, S.H.//Nagaraja, V. 	Increasing cleavage specificity and activity of restriction endonuclease KpnI.	Nucleic Acids Res.	2013	41		9812-9824			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. 		
@D	Vasu, K.//Nagaraja, V. 	Diverse Functions of Restriction-Modification Systems in Addition to Cellular Defense.	Microbiol. Mol. Biol. Rev.	2013	77		53-72			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. 		
@D	Vasu, K.//Saravanan, M.//Bujnicki, J.M.//Nagaraja, V. 	Structural integrity of the Beta Beta Alpha-Metal finger motif is required for DNA binding and stable protein-DNA complex formation in R.KpnI.	Biochim. Biophys. Acta	2008	1784		269-275			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. 		
@D	Vasu, K.//Saravanan, M.//Rajendra, B.V.R.N.//Nagaraja, V. 	Generation of a Manganese Specific Restriction Endonuclease with Nicking Activity.	Biochemistry	2010	49		8425-8433			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. 		
@D	Vasudev, V.//Obe, G. 	Evidence for a receptor-mediated endocytosis of AluI in chinese hamster ovary cells.	Mutat. Res.	1988	197		109-116			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. 		
@D	Vater, A. et al. 	Draft Genome Sequences of Shewanella sp. Strain UCD-FRSP16_17 and Nine Vibrio Strains Isolated from Abalone Feces.	Genome Announcements	2016	4		e00977-16			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. 		
@D	Vatlin, A.A.//Bekker, O.B.//Lysenkova, L.N.//Danilenko, V.N. 	Draft Genome Sequence of Streptomyces fradiae olg1-1, a Strain Resistant to Nitrone-Oligomycin.	Genome Announcements	2015	3		e01252-15			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. 		
@D	Vaughn, J.C.//Mason, M.T.//Sper-Whitis, G.L.//Kuhlman, P.//Palmer, J.D. 	Fungal origin by horizontal transfer of a plant mitochondrial group I intron in the chimeric CoxI gene of Peperomia.	J. Mol. Evol.	1995	41		563-572			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. 		
@D	Vaz-Moreira, I.//Tamames, J.//Martinez, J.L.//Manaia, C.M. 	Draft Genome Sequences of Two Ralstonia pickettii Strains with Different Aminoglycoside Resistance Phenotypes.	Genome Announcements	2016	4		e01257-16			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. 		
@D	Vazquez, R.//Brito, J.//Guerra, M. 	Purification of the restriction endonuclease SacI, free of SacII and SacIII contaminants.	Biotecnol. Apl.	1996	13		21-24			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. 		
@D	Vazquez, R.//Martinez, D.//Reyes, G.//Marquez, G.//Ryes, N.//Diaz, Y.//Luis, M.//Gonzalez, B.//Gonzalez, N. 	Purification of NcoI restriction endonuclease free of exonucleases and contaminant endonucleases.	Biotecnol. Apl.	1996	13		289-290					
@D	Vazquez-Gutierrez, P.//Lacroix, C.//Chassard, C.//Klumpp, J.//Jans, C.//Stevens, M.J. 	Complete and Assembled Genome Sequence of Bifidobacterium kashiwanohense PV20-2,  Isolated from the Feces of an Anemic Kenyan Infant.	Genome Announcements	2015	3		e01467-14			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. 		
@D	Vazquez-Gutierrez, P.//Lacroix, C.//Chassard, C.//Klumpp, J.//Stevens, M.J.//Jans, C. 	Bifidobacterium pseudolongum Strain PV8-2, Isolated from a Stool Sample of an Anemic Kenyan Infant.	Genome Announcements	2015	3		e01469-14			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. 		
@D	Vazquez-Hernandez, M.//Ceapa, C.D.//Rodriguez-Luna, S.D.//Rodriguez-Sanoja, R.//Sanchez, S. 	Draft Genome Sequence of Streptomyces scabrisporus NF3, an Endophyte Isolated from Amphipterygium adstringens.	Genome Announcements	2017	5		e00267-17			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. 		
@D	Vecherkovskaya, M.F.//Tetz, G.V.//Tetz, V.V. 	Complete Genome Sequence of the Streptococcus sp. Strain VT 162, Isolated from the Saliva of Pediatric Oncohematology Patients.	Genome Announcements	2014	2		e00647-14			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. 		
@D	Vedantam, G.//Hecht, D.W. 	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.	J. Bacteriol.	2002	184		728-738			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. 		
@D	Vedler, E.//Vahter, M.//Heinaru, A. 	The Completely Sequenced Plasmid pEST4011 Contains a Novel IncP1 Backbone and a Catabolic Transposon Harboring tfd Genes for 2,4-Dichlorophenoxyacetic Acid Degradation.	J. Bacteriol.	2004	186		7161-7174			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. 		
@D	Veeraraghavan, B.//Anandan, S.//Ragupathi, N.K.//Vijayakumar, S.//Sethuvel, D.P.//Biswas, I. 	Draft Genome Sequence of Colistin-Resistant Acinetobacter baumannii Strain VB22595 Isolated from a Central Line-Associated Bloodstream Infection.	Genome Announcements	2016	4		e00835-16			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. 		
@D	Veeraraghavan, B.//Anandan, S.//Rajamani, S.S.K.//Gopi, R.//Devanga, R.N.K.//Ramesh, S.//Verghese, V.P.//Korulla, S.//Mathai, S.//Sangal, L.//Joshi, S. 	First Report on the Draft Genome Sequences of Corynebacterium diphtheriae Isolates from India.	Genome Announcements	2016	4		e01316-16			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. 		
@D	Veeraraghavan, B.//Neeravi, A.R.//Devanga, R.N.K.//Inbanathan, F.Y.//Pragasam, A.K.//Verghese, V.P. 	Whole-Genome Shotgun Sequencing of the First Observation of Neisseria meningitidis Sequence Type 6928 in India.	Genome Announcements	2016	4		e01232-16			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. 		
@D	Veeraraghavan, B.//Perumalla, S.K.//Devanga, R.N.K.//Pragasam, A.K.//Muthuirulandi, S.D.P.//Inian, S.//Inbanathan, F.Y. 	Coexistence of Fosfomycin and Colistin Resistance in Klebsiella pneumoniae: Whole-Genome Shotgun Sequencing.	Genome Announcements	2016	4		e01303-16			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. 		
@D	Veiga, H.//Pinho, M.G. 	Inactivation of the SauI Type I Restriction-Modification System Is Not Sufficient To Generate Staphylococcus aureus Strains Capable of Efficiently Accepting Foreign DNA.	Appl. Environ. Microbiol.	2009	75		3034-3038			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. 		
@D	Veith, B.//Herzberg, C.//Steckel, S.//Feesche, J.//Maurer, K.H.//Ehrenreich, P.//Baumer, S.//Henne, A.//Liesegang, H.//Merkl, R.//Ehrenreich, A.//Gottschalk, G. 	The complete genome sequence of Bacillus licheniformis DSM13, an organism with great industrial potential.	J. Mol. Microbiol. Biotechnol.	2004	7		204-211			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. 		
@D	Veitinger, S.//Schmitz, G.G.//Kaluza, K.//Jarsch, M.//Braun, V.//Kessler, C. 	SfuI, a novel AsuII isoschizomer from Streptomyces fulvissimus recognizing 5'-TT/CGAA-3'.	Nucleic Acids Res.	1990	18		3424			None 		
@D	Vejarano, F.//Suzuki-Minakuchi, C.//Ohtsubo, Y.//Tsuda, M.//Okada, K.//Nojiri, H. 	Complete Genome Sequence of the Marine Carbazole-Degrading Bacterium Erythrobacter sp. Strain KY5.	Microbiol. Resour. Announc.	2018	7		e00935-18			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. 		
@D	Velasco-Bucheli, R.//Del Cerro, C.//Hormigo, D.//Acebal, C.//Arroyo, M.//Garcia, J.L.//de la Mata, I. 	Draft Genome Sequence of Actinoplanes utahensis NRRL 12052, a Microorganism Involved in Industrial Production of Pharmaceutical Intermediates.	Genome Announcements	2015	3		e01411-14			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. 		
@D	Velichko, N.//Rayko, M.//Chernyaeva, E.//Lapidus, A.//Pinevich, A. 	Draft genome of Prochlorothrix hollandica CCAP 1490/1T (CALU1027), the chlorophyll a/b-containing filamentous cyanobacterium.	Standards in Genomic Sciences	2016	11		82			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. 		
@D	Velkov, V.V. 	How environmental factors regulate mutagenesis and gene transfer in microorganisms.	J. Biosci.	1999	24		529-559			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. 		
@D	Vellarikkal, S.K.//Singh, A.V.//Singh, P.K.//Garg, P.//Katoch, V.M.//Katoch, K.//Chauhan, D.S.//Sivasubbu, S.//Scaria, V. 	Draft Genome Sequence of a Multidrug-Resistant Clinical Isolate of Mycobacterium  tuberculosis Belonging to a Novel Spoligotype.	Genome Announcements	2013	1		e00965-13			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. 		
@D	Vellarikkal, S.K.//Singh, A.V.//Singh, P.K.//Garg, P.//Katoch, V.M.//Katoch, K.//Chauhan, D.S.//Sivasubbu, S.//Scaria, V. 	Draft Genome Sequence of Multidrug-Resistant Mycobacterium tuberculosis Clinical  Isolate OSDD515, Belonging to the Uganda I Genotype.	Genome Announcements	2013	1		e00750-13			We describe the genome sequencing and analysis of a clinical isolate of the multidrug-resistant Mycobacterium tuberculosis Uganda I genotype (OSDD515) from India. 		
@D	Velly, H.//Renault, P.//Abraham, A.L.//Loux, V.//Delacroix-Buchet, A.//Fonseca, F.//Bouix, M. 	Genome Sequence of the Lactic Acid Bacterium Lactococcus lactis subsp. lactis TOMSC161, Isolated from a Nonscalded Curd Pressed Cheese.	Genome Announcements	2014	2		e01121-14			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. 		
@D	Velusamy, N.//Prakash, L.//Sivakumar, N.//Antony, A.//Prajna, L.//Mohankumar, V.//Devarajan, B. 	Draft Genome Sequences of Staphylococcus aureus AMRF1 (ST22) and AMRF2 (ST672), Ocular Methicillin-Resistant Isolates.	Genome Announcements	2014	2		e00168-14			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. 		
@D	Venclovas, C.//Siksnys, V. 	Different enzymes with similar structures involved in Mg2+-mediated polynucleotidyl transfer.	Nat. Struct. Biol.	1995	2		838-841			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). 		
@D	Venclovas, C.//Timinskas, A.//Siksnys, V. 	Five-stranded beta-sheet sandwiched with two a-helices: a structural link between restriction endonucleases EcoRI and EcoRV.	Proteins	1994	20		279-282			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. 		
@D	Venditti, S.//Wells, R.D. 	A DNA conformational alteration induced by a neighboring oligopurine tract on GAATTA enables nicking by EcoRI.	J. Biol. Chem.	1991	266		16786-16790			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. 		
@D	Vendramin, V.//Treu, L.//Bovo, B.//Campanaro, S.//Corich, V.//Giacomini, A. 	Whole-Genome Sequence of Streptococcus macedonicus Strain 33MO, Isolated from the Curd of Morlacco Cheese in the Veneto Region (Italy).	Genome Announcements	2014	2		e00746-14			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. 		
@D	Venegas, A.//Motles, M.//Vasquez, C.//Vicuna, R. 	Conditions affecting DNA cleavage by TthI at a TthI endonuclease-dam methylase overlapping sequence.	FEBS Lett.	1981	130		272-274			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. 		
@D	Venegas, A.//Vicuna, R.//Alonso, A.//Valdes, F.//Yudelevich, A. 	A rapid procedure for purifying a restriction endonuclease from Thermus thermophilus (TthI).	FEBS Lett.	1980	109		156-158			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. 		
@D	Venetianer, P. 	Purification and properties of the Bsp endonuclease.	Methods Enzymol.	1980	65		109-112			None 		
@A	Venetianer, P.//Kiss, A. 		The restriction-modification enzymes of Bacillus sphaericus R.			Chirikjian, J.G. 		Gene Amplif. Anal.					Elsevier North Holland	1981		1		209-215									*
   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
 
 		
@D	Venetianer, P.//Orosz, A. 	BcefI, a new type IIS restriction endonuclease.	Nucleic Acids Res.	1988	16		3053-3060			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. 		
@D	Venetianer, P.//Orosz, A. 	Isolation and characterization of two new restriction endonucleases (BepI and BcefI) .	Gene	1988	74		99			Meeting Abstract 		
@D	Venetianer, P.//Orosz, A. 	BepI restriction endonuclease, a new isoschizomer of FnuDII.	Nucleic Acids Res.	1988	16		350			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. 		
@D	Venkatesan, M.M.//Goldberg, M.B.//Rose, D.J.//Grotbeck, E.J.//Burland, V.//Blattner, F.R. 	Complete DNA sequence and analysis of the large virulence plasmid of Shigella flexneri.	Infect. Immun.	2001	69		3271-3285			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. 		
@D	Venkateswaran, K. et al. 	Draft Genome Sequences from a Novel Clade of Bacillus cereus Sensu Lato Strains,  Isolated from the International Space Station.	Genome Announcements	2017	5		e00680-17			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). 		
@D	Venkatramanan, R.//Prakash, O.//Woyke, T.//Chain, P.//Goodwin, L.A.//Watson, D.//Brooks, S.//Kostka, J.E.//Green, S.J. 	Genome sequences for three denitrifying bacterial strains isolated from a uranium- and nitrate-contaminated subsurface environment.	Genome Announcements	2013	1		e00449-13			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. 		
@D	Venter, J.C. et al. 	Environmental Genome Shotgun Sequencing of the Sargasso Sea.	Science	2004	304		66-74			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. 		
@D	Ventura, M. et al. 	The Bifidobacterium dentium Bd1 genome sequence reflects its genetic adaptation to the human oral cavity.	PLoS Genet.	2009	5		e1000785			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. 		
@D	Venturini, C.//Beatson, S.A.//Djordjevic, S.P.//Walker, M.J. 	Multiple antibiotic resistance gene recruitment onto the enterohemorrhagic Escherichia coli virulence plasmid.	FASEB J.	2010	24		1160-1166			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. 		
@D	Venturini, C.//Hassan, K.A.//Roy-Chowdhury, P.//Paulsen, I.T.//Walker, M.J.//Djordjevic, S.P. 	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.	PLoS ONE	2013	8		E78862			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. 		
@D	Venyaminov, S.Y.//Kosykh, V.G.//Kholodkov, O.A.//Buryanov, Y.I. 	UV- and CD-spectra of restriction endonuclease EcoRII and DNA-methylase EcoRII.	Bioorg. Khim.	1990	16		47-51			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. 		
@D	Vera-Cabrera, L.//Ortiz-Lopez, R.//Elizondo-Gonzalez, R.//Campos-Rivera, M.P.//Gallardo-Rocha, A.//Molina-Torres, C.A.//Ocampo-Candiani, J. 	Draft Genome Sequence of Actinomadura madurae LIID-AJ290, Isolated from a Human Mycetoma Case.	Genome Announcements	2014	2		e00201-14			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. 		
@D	Vera-Cabrera, L.//Ortiz-Lopez, R.//Elizondo-Gonzalez, R.//Perez-Maya, A.A.//Ocampo-Candiani, J. 	Complete Genome Sequence of Nocardia brasiliensis HUJEG-1.	J. Bacteriol.	2012	194		2761-2762			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. 		
@D	Verce, M.//De Vuyst, L.//Weckx, S. 	Complete and Annotated Genome Sequence of the Sourdough Lactic Acid Bacterium Lactobacillus fermentum IMDO 130101.	Genome Announcements	2018	6		e00256-18			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. 		
@D	Verdet, C.//Gautier, V.//Chachaty, E.//Ronco, E.//Hidri, N.//Decre, D.//Arlet, G. 	Genetic context of plasmid-carried blaCMY-2-like genes in Enterobacteriaceae.	Antimicrob. Agents Chemother.	2009	53		4002-4006			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. 		
@D	Verdine, G. 	The flip side of DNA methylation.	Cell	1994	76		197-200			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). 		
@D	Verdine, G.L.//Bruner, S.D. 	How do DNA repair proteins locate damaged bases in the genome?	Chem. Biol.	1997	4		329-334			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? 		
@D	Vereijken, J.M.//van Mansfeld, A.D.M.//Baas, P.D.//Jansz, H.S. 	Arthrobacter luteus Restriction endonuclease Cleavage Map of PhiX174 RF DNA.	Virology	1975	68		221-233			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). 		
@D	Veress, A.//Wilk, T.//Kiss, J.//Olasz, F.//Papp, P.P. 	Draft Genome Sequences of Saccharibacter sp. Strains 3.A.1 and M18 Isolated from  Honey and a Honey Bee (Apis mellifera) Stomach.	Genome Announcements	2017	5		e00744-17			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. 		
@D	Veress, A.//Wilk, T.//Kiss, J.//Papp, P.P.//Olasz, F. 	Two Draft Genome Sequences of Sphingobacterium sp. Strains Isolated from Honey.	Genome Announcements	2017	5		e01364-17			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. 		
@D	Verhoef, J.//van Boven, C.P.A.//Holtrigter, B. 	Restriction and modification of phages in coagulase-negative staphylococci.	Antonie Van Leeuwenhoek	1971	37		256-267			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. 		
@D	Verhoef, J.//van Boven, C.P.A.//Holtrigter, B. 	Host-controlled modification and restriction of phages in coagulase-negative Staphylococci.	J. Gen. Microbiol.	1972	71		231-239			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. 		
@A	Verhoef, J.//van Boven, C.P.A.//Holtrigter, B. 		Restriction and modification of phages in Staphylococcus epidermidis.			Ledoux, L. 		Informative molecules in biological systems.				Amsterdam	North Holland.	1971		0		213-220									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. 		
@D	Verma, M.//Kaur, J.//Kumar, M.//Kumari, K.//Saxena, A.//Anand, S.//Nigam, A.//Ravi, V.//Raghuvanshi, S.//Khurana, P.//Tyagi, A.K.//Khurana, J.P.//Lal, R. 	Whole Genome Sequence of the Rifamycin B-Producing Strain Amycolatopsis mediterranei S699.	J. Bacteriol.	2011	193		5562-5563			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. 		
@D	Vermersch, P.S.//Bennett, G.N. 	The use of a selectable FokI cassette in DNA replacement mutagenesis of the R388 dihydrofolate reductase gene.	Gene	1987	54		229-238			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. 		
@D	Vermote, C.L.M.//Halford, S.E. 	EcoRV restriction endonuclease:  communication between catalytic metal ions and DNA recognition.	Biochemistry	1992	31		6082-6089			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. 		
@D	Vermote, C.L.M.//Vipond, I.B.//Halford, S.E. 	EcoRV restriction endonuclease:  communication between DNA recognition and catalysis.	Biochemistry	1992	31		6089-6097			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. 		
@D	Vertes, A.A.//Inui, M.//Kobayashi, M.//Kurusu, Y.//Yukawa, H. 	Presence of mrr- and mcr-like restriction systems in coryneform bacteria.	Res. Microbiol.	1993	144		181-185			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. 		
@A	Vertino, P.M. 		Eukaryotic DNA methyltransferases.			Cheng, X.//Blumenthal, R.M. 		S-Adenosylmethionine-dependent Methyltransferases: Structures and Functions.				Singapore	World Scientific Publishing	1999		0		341-372									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. 		
@D	Vertino, P.M.//Coll, J.M.//Applegren, N.//Malkas, L.H. 	Identification of DNA (cytosine-5)-methyltransferase as a component of a multiprotein DNA replication complex isolated from human cells.	Proc. Amer. Assoc. Cancer Res.	1998	39		92			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. 		
@D	Vertino, P.M.//Yen, R.-W.C.//Gao, J.//Baylin, S.B. 	De Novo methylation of CpG island sequences in human fibroblasts overexpressing DNA (cytosine-5-)-methyltransferase.	Mol. Cell. Biol.	1996	16		4555-4565			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. 		
@D	Veseli, I.A.//Mascarenhas, D.S.A.C.//Juarez, O.//Stark, B.C.//Pombert, J.F. 	Complete Genome Sequence of Vitreoscilla sp. Strain C1, Source of the First Bacterial Hemoglobin.	Microbiol. Resour. Announc.	2018	7		e00922-18			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. 		
@D	Veseli, I.A.//Tang, C.//Pombert, J.F. 	Complete Genome Sequence of Staphylococcus lutrae ATCC 700373, a Potential Pathogen Isolated from Deceased Otters.	Genome Announcements	2017	5		e00572-17			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. 		
@D	Veselkov, A.G.//Demidov, V.V.//Nielsen, P.E.//Frank-Kamenetskii, M.D. 	A new class of genome rare cutters.	Nucleic Acids Res.	1996	24		2483-2487			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. 		
@D	Vesely, Z.//Muller, A.//Schmitz, G.G.//Kaluza, K.//Jarsch, M.//Kessler, C. 	RleAI: a novel class-IIS restriction endonuclease from Rhizobium leguminosarum recognizing 5'-CCCACA(N)12-3' and 3'-GGGTGT(N)9-5'.	Gene	1990	95		129-131			The novel class-IIS restriction endonuclease, RleAI, has the 5'-CCCACA(N)12-3' 3'-GGGTGT(N)9-5' specificity. 		
@D	Vesely, Z.//Schmitz, G.G.//Jarsch, M.//Kessler, C. 	BbrPI, a novel PmaCI isoschizomer from Bacillus brevis recognizing 5'-CAC/GTG-3'.	Nucleic Acids Res.	1990	18		3423			None 		
@D	Vettath, V.K. et al. 	Complete Genome Sequence of Bacillus altitudinis Type Strain SGAir0031 Isolated from Tropical Air Collected in Singapore.	Genome Announcements	2017	5		e01260-17			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. 		
@D	Vettath, V.K. et al. 	Complete Genome Sequence of Acinetobacter indicus Type Strain SGAir0564 Isolated  from Tropical Air Collected in Singapore.	Genome Announcements	2018	6		e00230-18			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. 		
@D	Veyrier, F.J.//Ecobichon, C.//Boneca, I.G. 	Draft Genome Sequence of Strain X47-2AL, a Feline Helicobacter pylori Isolate.	Genome Announcements	2013	1		e01095-13			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. 		
@D	Veyrier, F.J.//Hong, E.//Deghmane, A.E.//Taha, M.K. 	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.	Genome Announcements	2013	1		e00795-13			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. 		
@D	Viadiu, H.//Aggarwal, A.K. 	Structure of BamHI bound to nonspecific DNA: A model for DNA sliding.	Mol. Cell	2000	5		889-895			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. 		
@D	Viadiu, H.//Aggarwal, A.K. 	The role of metals in catalysis by the restriction endonuclease BamHI.	Nat. Struct. Biol.	1998	5		910-916			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. 		
@D	Viadiu, H.//Kucera, R.//Schildkraut, I.//Aggarwal, A.K. 	Crystallization of Restriction Endonuclease BamHI with Nonspecific DNA.	J. Struct. Biol.	2000	130		81-85			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. 		
@D	Viadiu, H.//Vanamee, E.S.//Jacobson, E.M.//Schildkraut, I.//Aggarwal, A.K. 	Crystallization of restriction endonuclease SfiI in complex with DNA.	Acta Crystallogr. D Biol. Crystallogr.	2003	59		1493-1495			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. 		
@D	Viadiu-Ilarraza, H. 	Structural study of specificity and catalysis by restriction endonuclease BamHI.	Diss. Abstr.	2000	60		5978			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. 		
@D	Viana, M.V.//Wattam, A.R.//Govil, B.D.//Boisvert, S.//Brettin, T.S.//Frace, M.//Xia, F.//Azevedo, V.//Tiller, R.//Hoffmaster, A.R. 	Genome Sequences of Two Brucella suis Strains Isolated from the Same Patient, 8 Years Apart.	Genome Announcements	2017	5		e01687-16			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. 		
@D	Viana, M.V.//Wattam, A.R.//Govil, B.D.//Boisvert, S.//Brettin, T.S.//Frace, M.//Xia, F.//Azevedo, V.//Tiller, R.//Hoffmaster, A.R. 	Genome Sequences of Three Brucella canis Strains Isolated from Humans and a Dog.	Genome Announcements	2017	5		e01688-16			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. 		
@D	Viberg, L.T.//Price, E.P.//Kidd, T.J.//Bell, S.C.//Currie, B.J.//Sarovich, D.S. 	Whole-Genome Sequences of Five Burkholderia pseudomallei Isolates from Australian Cystic Fibrosis Patients.	Genome Announcements	2015	3		e00254-15			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. 		
@D	Victoria, A.J.//Cao, E.//Salmaso, N.//Segata, N.//Donati, C. 	Draft Genome Sequence of the Cadmium-Resistant Strain JJU2, Belonging to the Family Hapalosiphonaceae of the Cyanobacteria.	Microbiol. Resour. Announc.	2018	7		e00876-18			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. 		
@D	Victoria, J.G.//Kapoor, A.//Li, L.//Blinkova, O.//Slikas, B.//Wang, C.//Naeem, A.//Zaidi, S.//Delwart, E. 	Metagenomic analyses of viruses in stool samples from children with acute flaccid paralysis.	J. Virol.	2009	83		4642-4651			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. 		
@D	Vida, C.//de Vicente, A.//Cazorla, F.M. 	Draft Genome Sequence of the Rhizobacterium Pseudomonas chlororaphis PCL1601, Displaying Biocontrol against Soilborne Phytopathogens.	Genome Announcements	2017	5		e00130-17			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. 		
@D	Viedma, E.//Juan, C.//Otero, J.R.//Oliver, A.//Chaves, F. 	Draft Genome Sequence of VIM-2-Producing Multidrug-Resistant Pseudomonas aeruginosa ST175, an Epidemic High-Risk Clone.	Genome Announcements	2013	1		e00112-13			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. 		
@D	Viedma, E.//Villa, J.//Juan, C.//Oliver, A.//Chaves, F. 	Draft Genome Sequence of Colistin-Only-Susceptible Pseudomonas aeruginosa Strain  ST235, a Hypervirulent High-Risk Clone in Spain.	Genome Announcements	2014	2		e01097-14			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. 		
@D	Vienozinskis, M.T.//Nesterenko, V.F.//Kanopkaite, S.I.//Buryanov, Y.I. 	Effect of 5-azacytidine on E. coli cells with different DNA methylases.	Biokhimiia	1985	50		749-754			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. 		
@D	Vijaykumar, S.//Balaji, V.//Biswas, I. 	Complete Genome Sequence of Acinetobacter baumannii Strain B8300, Which Displays  High Twitching Motility.	Genome Announcements	2015	3		e00956-15			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. 		
@D	Vijaykumar, S.//Balaji, V.//Biswas, I. 	Complete Genome Sequence of Acinetobacter baumannii Strain B8342, a Motility-Positive Clinical Isolate.	Genome Announcements	2015	3		e00925-15			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. 		
@D	Vijesurier, R.M. 	Regulation of the gene expression of the PvuII restriction-modification system.	Diss. Abstr.	1997	57		7379B-7380B			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. 		
@D	Vijesurier, R.M.//Carlock, L.//Blumenthal, R.M.//Dunbar, J.C. 	Role and mechanism of action of C.PvuII, a regulatory protein conserved among restriction-modification systems.	J. Bacteriol.	2000	182		477-487			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. 		
@D	Vikram, S.//Kumar, S.//Subramanian, S.//Raghava, G.P. 	Draft Genome Sequence of the Nitrophenol-Degrading Actinomycete Rhodococcus imtechensis RKJ300.	J. Bacteriol.	2012	194		3543			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. 		
@D	Vikram, S.//Kumar, S.//Vaidya, B.//Pinnaka, A.K.//Raghava, G.P. 	Draft Genome Sequence of the 2-Chloro-4-Nitrophenol-Degrading Bacterium Arthrobacter sp. Strain SJCon.	Genome Announcements	2013	1		e0005813			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. 		
@D	Vilacoba, E.//Deraspe, M.//Traglia, G.M.//Roy, P.H.//Ramirez, M.S.//Centron, D. 	Draft Genome Sequence of an International Clonal Lineage 1 Acinetobacter baumannii Strain from Argentina.	Genome Announcements	2014	2		e01190-14			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. 		
@D	Vilain, A.//Apiou, F.//Dutrillaux, B.//Malfoy, B. 	Assignment  of candidate DNA methyltransferase gene (DNMT2) to human chromosome band 10p15.1 by in situ hybridization.	Cytogenet. Cell Genet.	1998	82		120			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. 		
@D	Vilas-Boas, L.A.//Headley, S.A.//Goncalves, K.B.//Scarpassa, J.A.//Pretto-Giordano, L.G. 	Complete Genome Sequence of Streptococcus iniae UEL-Si1, Isolated in Diseased Nile Tilapia (Oreochromis niloticus) from Northern Parana, Southern Brazil.	Genome Announcements	2017	5		e01458-16			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. 		
@D	Vilchez, J.I.//Tang, Q.//Kaushal, R.//Chen, S.//Liu, R.//Zhang, H. 	Genome Sequence of Bacillus cereus Strain TG1-6, a Plant-Beneficial Rhizobacterium That Is Highly Salt Tolerant.	Genome Announcements	2018	6		e00351-18			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). 		
@D	Vilchez, J.I.//Tang, Q.//Kaushal, R.//Wang, W.//Lv, S.//He, D.//Chu, Z.//Zhang, H.//Liu, R.//Zhang, H. 	Genome Sequence of Bacillus megaterium Strain YC4-R4, a Plant Growth-Promoting Rhizobacterium Isolated from a High-Salinity Environment.	Genome Announcements	2018	6		e00527-18			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). 		
@D	Vilkaitis, G.//Dong, A.//Weinhold, E.//Cheng, X.//Klimasauskas, S. 	Functional roles of the conserved threonine 250 in the target recognition domain of HhaI DNA methyltransferase.	J. Biol. Chem.	2000	275		38722-38730			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. 		
@D	Vilkaitis, G.//Klimasauskas, S. 	Bisulfite sequencing protocol displays both 5-methylcytosine and N4-methylcytosine.	Anal. Biochem.	1999	271		116-119			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. 		
@D	Vilkaitis, G.//Lubys, A.//Merkiene, E.//Timinskas, A.//Janulaitis, A.//Klimasauskas, S. 	Circular permutation of DNA cytosine-N4 methyltransferases: in vivo coexistence in the BcnI system and in vitro probing by hybrid formation.	Nucleic Acids Res.	2002	30		1547-1557			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. 		
@D	Vilkaitis, G.//Merkiene, E.//Serva, S.//Weinhold, E.//Klimasauskas, S. 	The mechanism of DNA cytosine-5 methylation. Kinetic and mutational dissection of HhaI methyltransferase.	J. Biol. Chem.	2001	276		20924-20934			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. 		
@D	Vilkaitis, G.//Suetake, I.//Klimasauskas, S.//Tajima, S. 	Processive methylation of hemimethylated CpG sites by mouse Dnmt1 DNA methyltransferase.	J. Biol. Chem.	2005	280		64-72			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. 		
@D	Villa, A.A.//Kropinski, A.M.//Abbasifar, R.//Griffiths, M.W. 	Complete Genome Sequence of Vibrio parahaemolyticus Bacteriophage vB_VpaM_MAR.	J. Virol.	2012	86		13138-13139			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. 		
@D	Villa, J.//Viedma, E.//Branas, P.//Mingorance, J.//Chaves, F. 	Draft Whole-Genome Sequence of OXA-48-Producing Multidrug-Resistant Klebsiella pneumoniae KP_ST11_OXA-48.	Genome Announcements	2014	2		e00737-14			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. 		
@D	Villa, J.//Viedma, E.//Otero, J.R.//Chaves, F. 	Draft Whole-Genome Sequence of VIM-1-Producing Multidrug-Resistant Enterobacter cloacae EC_38VIM1.	Genome Announcements	2013	1		e00694-13			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. 		
@D	Villa, L.//Feudi, C.//Fortini, D.//Iacono, M.//Bonura, C.//Endimiani, A.//Mammina, C.//Carattoli, A. 	Complete Genome Sequence of KPC-3- and CTX-M-15-Producing Klebsiella pneumoniae Sequence Type 307.	Genome Announcements	2016	4		e00213-16			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. 		
@D	Villamizar, G.A.//Daniel, R.//Poehlein, A. 	First Insights into the Genome Sequence of the Strictly Anaerobic Homoacetogenic  Sporomusa sphaeroides Strain E (DSM 2875).	Genome Announcements	2017	5		e00037-17			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). 		
@D	Villanueva, J.//Switala, J.//Ivancich, A.//Loewen, P.C. 	Genome Sequence of Bacillus pumilus MTCC B6033.	Genome Announcements	2014	2		e00327-14			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. 		
@D	Villarma, A.//Gulvik, C.A.//Rowe, L.A.//Sheth, M.//Juieng, P.//Nicholson, A.C.//Loparev, V.N.//McQuiston, J.R. 	Twelve Complete Reference Genomes of Clinical Isolates in the Capnocytophaga Genus.	Genome Announcements	2017	5		e01186-17			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. 		
@D	Villena, J.//Masumizu, Y.//Iida, H.//Ikeda-Ohtsubo, W.//Albarracin, L.//Makino, S.//Ohkawara, S.//Kimura, K.//Saavedra, L.//Hebert, E.M.//Kitazawa, H. 	Draft Genome Sequence of the Immunobiotic Strain Lactobacillus jensenii TL2937.	Genome Announcements	2017	5		e00005-17			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. 		
@D	Villena, J.//Saavedra, L.//Hebert, E.M.//Masumizu, Y.//Sato, N.//Humayun, K.A.K.//Albarracin, L.//Ikeda-Ohtsubo, W.//Makino, S.//Kimura, K.//Ohkawara, S.//Kitazawa, H. 	Draft Genome Sequence of Lactobacillus plantarum TL2766, a Strain with the Ability To Ferment Wakame.	Genome Announcements	2016	4		e01328-16			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. 		
@D	Villena, J.//Saavedra, L.//Hebert, E.M.//Suda, Y.//Masumizu, Y.//Albarracin, L.//Clua, P.//Ikeda-Ohtsubo, W.//Kitazawa, H. 	Draft Genome Sequence of Lactobacillus plantarum MPL16, a Wakame-Utilizing Immunobiotic Strain Isolated from Swine Feces.	Genome Announcements	2017	5		e00006-17			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. 		
@D	Villeneuve, C.//Martineau, C.//Mauffrey, F.//Villemur, R. 	Complete Genome Sequences of Methylophaga sp. Strain JAM1 and Methylophaga sp. Strain JAM7.	J. Bacteriol.	2012	194		4126-4127			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. 		
@D	Villion, M.//Chopin, M.C.//Deveau, H.//Ehrlich, S.D.//Moineau, S.//Chopin, A. 	P087, a lactococcal phage with a morphogenesis module similar to an Enterococcus faecalis prophage.	Virology	2009	388		49-56			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. 		
@D	Vilo, C.//Benedik, M.J.//Ilori, M.//Dong, Q. 	Draft Genome Sequence of Cupriavidus sp. Strain SK-3, a 4-Chlorobiphenyl- and 4-Clorobenzoic Acid-Degrading Bacterium.	Genome Announcements	2014	2		e00664-14			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. 		
@D	Vilo, C.//Benedik, M.J.//Ilori, M.//Dong, Q. 	Draft Genome Sequence of Cupriavidus sp. Strain SK-4, a di-ortho-Substituted Biphenyl-Utilizing Bacterium Isolated from Polychlorinated Biphenyl-Contaminated   Sludge.	Genome Announcements	2014	2		e00474-14			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. 		
@D	Vilo, C.//Galetovic, A.//Araya, J.E.//Gomez-Silva, B.//Dong, Q. 	Draft Genome Sequence of a Bacillus Bacterium from the Atacama Desert Wetlands Metagenome.	Genome Announcements	2015	3		e00955-15			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. 		
@D	Vilpo, J.A.//Vilpo, L.M. 	Restriction, methylation and ligation of 5-hydroxymethyluracil-containing DNA.	Mutat. Res.	1995	316		123-131			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. 		
@D	Vincent, A.T.//Charette, S.J. 	Completion of genome of Aeromonas salmonicida subsp. salmonicida 01-B526 reveals how sequencing technologies can influence sequence quality and result interpretations.	New Microbes New Infect.	2018	25		24-26			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. 		
@D	Vincent, A.T.//Freschi, L.//Jeukens, J.//Kukavica-Ibrulj, I.//Emond-Rheault, J.G.//Leduc, A.//Boyle, B.//Jean-Pierre, F.//Groleau, M.C.//Deziel, E.//Barbeau, J.//Charette, S.J.//Levesque, R.C. 	Genomic characterisation of environmental Pseudomonas aeruginosa isolated from dental unit waterlines revealed the insertion sequence ISPa11 as a chaotropic element.	FEMS Microbiol. Ecol.		93		fix106			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. 		
@D	Vincent, A.T.//Rouleau, F.D.//Moineau, S.//Charette, S.J. 	Study of mesophilic Aeromonas salmonicida A527 strain sheds light on the species lifestyles and taxonomic dilemma.	FEMS Microbiol. Lett.	2017	364		fnx239			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. 		
@D	Vincent, A.T.//Trudel, M.V.//Paquet, V.E.//Boyle, B.//Tanaka, K.H.//Dallaire-Dufresne, S.//Daher, R.K.//Frenette, M.//Derome, N.//Charette, S.J. 	Detection of Variants of the pRAS3, pAB5S9, and pSN254 Plasmids in Aeromonas salmonicida subsp. salmonicida: Multidrug Resistance, Interspecies Exchanges, and Plasmid Reshaping.	Antimicrob. Agents Chemother.	2014	58		7367-7374			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. 		
@D	Vincze, T.//Posfai, J.//Roberts, R.J. 	NEBcutter: a program to cleave DNA with restriction enzymes.	Nucleic Acids Res.	2003	31		3688-3691			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. 		
@D	Vinella, D.//Jaffe, A.//D'Ari, R.//Kohiyama, M.//Hughes, P. 	Chromosome partitioning in Escherichia coli in the absence of Dam-directed methylation.	J. Bacteriol.	1992	174		2388-2390			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. 		
@D	Vinogradova, M.N.//Gromova, E.S.//Gryaznova, O.I.//Isagulyants, M.D.//Kuznetsova, S.A.//Kosych, V.G.//Shabarova, Z.A. 	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.	Bioorg. Khim.	1987	13		1194-1204			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. 		
@D	Vinogradova, M.N.//Gromova, E.S.//Kosykh, V.G.//Buryanov, Y.I.//Shabarova, Z.A. 	Interaction of EcoRII restriction and modification enzymes with synthetic DNA fragments.  XI. Determination of the EcoRII binding site.	Mol. Biol. (Mosk)	1990	24		847-850			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. 		
@D	Vinogradova, M.N.//Gromova, E.S.//Purmal, A.A.//Kosykh, V.G.//Shabarova, Z.A. 	Interaction of restriction and modification enzymes EcoRII with synthetic fragments of DNA.	Mol. Biol. (Mosk)	1986	20		1329-1336			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. 		
@D	Vinogradova, M.N.//Gromova, E.S.//Uporova, T.M.//Nikolskaya, I.I.//Shabarova, Z.A. 	Restriction endonuclease SsoII:  interaction with modified substrates.	Dokl. Akad. Nauk.	1987	295		732-736			None 		
@D	Vinuesa, P.//Ochoa-Sanchez, L.E. 	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.	Genome Announcements	2015	3		e01433-15			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. 		
@D	Vinuesa, P.//Ochoa-Sanchez, L.E.//Contreras-Moreira, B. 	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.	Front. Microbiol.	2018	9		771			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. 		
@D	Vinuesa, P.//Puente, J.L.//Calva, E.//Zaidi, M.B.//Silva, C. 	Complete Genome Sequence of Salmonella enterica Serovar Typhimurium Strain SO3 (Sequence Type 302) Isolated from a Baby with Meningitis in Mexico.	Genome Announcements	2016	4		e00285-16			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). 		
@D	Vipond, B.//Halford, S.E. 	Structure-function correlation for the EcoRV restriction enzyme: from non-specific binding to specific DNA cleavage.	Mol. Microbiol.	1993	9		225-231			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. 		
@D	Vipond, I.B.//Baldwin, G.S.//Halford, S.E. 	Divalent metal ions at the active sites of the EcoRV and EcoRI restriction endonucleases.	Biochemistry	1995	34		697-704			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. 		
@D	Vipond, I.B.//Baldwin, G.S.//Oram, M.//Erskine, S.G.//Wentzell, L.M.//Szczelkun, M.D.//Nobbs, T.J.//Halford, S.E. 	A general assay for restriction endonucleases and other DNA-modifying enzymes with plasmid substrates.	Mol. Biotechnol.	1995	4		259-268			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. 		
@D	Vipond, I.B.//Halford, S.E. 	Random mutagenesis targeted to the active site of the EcoRV restriction endonuclease.	Biochemistry	1996	35		1701-1711			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. 		
@D	Vipond, I.B.//Halford, S.E. 	Specific DNA recognition by EcoRV restriction endonuclease induced by Calcium ions.	Biochemistry	1995	34		1113-1119			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. 		
@D	Vipond, I.B.//Moon, B.-J.//Halford, S.E. 	An isoleucine to leucine mutation that switches the cofactor requirement of the EcoRV restriction endonuclease from magnesium to manganese.	Biochemistry	1996	35		1712-1721			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. 		
@D	Vipond, I.B.//Moon, B.J.//Halford, S.E. 	An Ile-to-Leu mutant of the EcoRV restriction endonuclease that requires Mn2+ as catalytic cofactor.	Biochem. Soc. Trans.	1994	22		301S			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. 		
@D	Viprey, V.//Rosenthal, A.//Broughton, W.J.//Perret, X. 	Genetic snapshots of the Rhizobium species NGR234 genome.	Genome Biology	2000	1		RESEARCH0014			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. 		
@D	Viratyosin, W.//Kulawonganunchai, S.//Smittipat, N.//Juthayothin, T.//Penpassakarn, P.//Pasomsub, E.//Chantratita, W.//Chaiprasert, A.//Palittapongarnpim, P. 	Draft Genome Sequence of the Mycobacterium tuberculosis Strain 43-16836, Belonging to the Indo-Oceanic Lineage, Isolated From Tuberculous Meningitis in  Thailand.	Genome Announcements	2013	1		e00801-13			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. 		
@D	Vishnivetskaya, T.A. et al. 	Draft genome sequences of 10 strains of the genus exiguobacterium.	Genome Announcements	2014	2		e01058-14			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. 		
@D	Visnovsky, S.B.//Fiers, M.//Lu, A.//Panda, P.//Taylor, R.//Pitman, A.R. 	Draft Genome Sequences of 18 Strains of Pseudomonas Isolated from Kiwifruit Plants in New Zealand and Overseas.	Genome Announcements	2016	4		e00061-16			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. 		
@D	Visnovsky, S.B.//Lu, A.//Panda, P.//Taylor, R.//Pitman, A.R. 	Draft Genome Sequences of 14 Strains of Pseudomonas Isolated from Prunus sp. Plants.	Genome Announcements	2018	6		e01481-17			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. 		
@D	Visnovsky, S.B.//Panda, P.//Taylor, R.//Pitman, A.R. 	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.	Genome Announcements	2017	5		e00104-17			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. 		
@D	Vissel, B.//Choo, K.H. 	Altered activity of restriction endonuclease MnlI cleavage of mouse satellite DNA.	Nucleic Acids Res.	1988	16		4731			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. 		
@D	Visser, M. et al. 	Genome analyses of the carboxydotrophic sulfate-reducers Desulfotomaculum nigrificans and Desulfotomaculum carboxydivorans and reclassification of  Desulfotomaculum caboxydivorans as a later synonym of Desulfotomaculum  nigrificans.	Standards in Genomic Sciences	2014	9		655-675			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. 		
@D	Visser, M. et al. 	Genome analysis of Desulfotomaculum kuznetsovii strain 17(T) reveals a physiological similarity with Pelotomaculum thermopropionicum strain SI(T).	Standards in Genomic Sciences	2013	8		69-87			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. 		
@D	Vitkute, J.//Maneliene, Z.//Janulaitis, A. 	AbeI, a restriction endonuclease from Azotobacter beijerinckii, which recognizes the asymmetric heptanucleotide sequence 5'-CCTCAGC-3'(-5/-2).	Nucleic Acids Res.	1998	26		4917-4918			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. 		
@D	Vitkute, J.//Maneliene, Z.//Janulaitis, A. 	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.	FEMS Microbiol. Lett.	2001	204		253-257			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. 		
@D	Vitkute, J.//Maneliene, Z.//Petrusyte, M.//Janulaitis, A. 	BplI, a new BcgI-like restriction endonuclease, which recognizes a symmetric sequence.	Nucleic Acids Res.	1997	25		4444-4446			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. 		
@D	Vitkute, J.//Maneliene, Z.//Petrusyte, M.//Janulaitis, A. 	BfiI, a restriction endonuclease from Bacillus firmus S8120, which recognizes the novel non-palindromic sequence 5'-ACTGGG(N)5/4-3'.	Nucleic Acids Res.	1998	26		3348-3349			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. 		
@D	Vitkute, J.//Stankevicius, K.//Tamulaitiene, G.//Maneliene, Z.//Timinskas, A.//Berg, D.E.//Janulaitis, A. 	Specificities of eleven different DNA methyltransferases of Helicobacter pylori strain 26695.	J. Bacteriol.	2001	183		443-450			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. 		
@D	Vitkute, J.//Tamulaitiene, G.//Chalkauskas, H.//Janulaitis, A. 	Potential of H. pylori to produce R-M enzymes and their possible biological role.	Int. J. Med. Microbiol.	2001	291S		95			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. 		
@A	Vitor, J.M.B. 		Restriction and modification systems in Campylobacter jejuni and Campylobacter coli.			 		Ph.D. Thesis, University of Lisbon				Lisbon		1999				1-220									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. 		
@A	Vitor, J.M.B.//Alves, P.//Marques, M.//Vital, J. 		Helicobacter pylori type IIG restriction and modification loci.			 		Helicobacter					Blackwell Publishing Ltd.	2011		16		98									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. 		
@D	Vitor, J.M.B.//Costa, L.//Pires, I.//Cabrita, J.//Correia, R.V. 	Restriction enzymes in Campylobacter strains.	Microb. Ecol. Health Dis.	1991	4		S50			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. 		
@D	Vitor, J.M.B.//Morgan, R.D. 	Two novel restriction endonucleases from Campylobacter jejuni.	Gene	1995	157		109-110			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. 		
@D	Vitor, J.M.B.//Polisson, C.//Cabrita, J.//Silva, R.V.C. 	Restriction enzymes from Campylobacter coli strains.	Acta Gastroenterol. Belg.	1993	56		41			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. 		
@D	Vitoriano, I.//Vitor, J.M.B.//Oleastro, M.//Roxo-Rosa, M.//Vale, F.F. 	Proteome variability among Helicobacter pylori isolates clustered according to genomic methylation.	J. Appl. Microbiol.	2013	114		1817-1832			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. 		
@D	Vizoso, P.//Pacheco, N.//Bastias-Molina, M.//Meneses, C.//Poblete-Castro, I. 	Draft Genome Sequence of the Phenol-Degrading Bacterium Pseudomonas putida H.	Genome Announcements	2015	3		e00936-15			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. 		
@D	Vizoso-Pinto, M.G.//Saavedra, L.//Hebert, E.M.//Raya, T.F.//Albarracin, L.//Alvarez, S.//Kitazawa, H.//Villena, J. 	Draft Genome Sequence of Immunobiotic Lactobacillus rhamnosus Strain IBL027, a Potential Adjuvant for Mucosal Vaccine Development.	Genome Announcements	2017	5		e01268-17			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. 		
@D	Vizzotto, C.S.//Lopes, F.A.C.//Green, S.J.//Steindorff, A.S.//Walter, J.M.//Thompson, F.L.//Kruger, R.H. 	Draft Genome Sequence of Muricauda sp. Strain K001 Isolated from a Marine Cyanobacterial Culture.	Genome Announcements	2018	6		e00451-18			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. 		
@D	Vlasova, T.I.//Demidenko, Z.N.//Kirnos, M.//Vanyushin, B.F. 	In vitro DNA methylation by wheat nuclear cytosine DNA methyltransferase: effect of phytohormones.	Gene	1995	157		279-281			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. 		
@D	Vlasova, T.I.//Kirnos, M.D.//Vanyushin, B.F. 	Cytosine DNA-methyltransferase from wheat seedlings.	Biokhimiia	1996	61		774-780			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. 		
@D	Vlasova, T.I.//Vanyushin, B.F. 	DNA methylation by wheat cytosine DNA methyltransferase: modulation by protease inhibitor E-64.	Biochem. Mol. Biol. Int.	1998	45		145-153			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. 		
@D	Vlatakis, G.//Bouriotis, V. 	Affinity partitioning of restriction endonucleases:  Application to the purification of EcoRI and EcoRV.	J. Chromatogr.	1991	538		311-321			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. 		
@D	Vlatakis, G.//Bouriotis, V. 	Sequence-specific DNA affinity chromatography:  Application to the purification of EcoRI and SphI.	Anal. Biochem.	1991	195		352-357			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. 		
@D	Vlatakis, G.//Clark, D.//Bouriotis, V. 	Isolation and identification of restriction endonuclease BshFI.	Nucleic Acids Res.	1989	17		8882			None 		
@D	Vlatakis, G.//Skarpelis, G.//Stratidaki, I.//Bouriotis, V. 	Dye-ligand chromatography for the resolution and purification of restriction endonucleases.	Appl. Biochem. Biotechnol.	1987	15		201-212			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. 		
@D	Vockler, C.J.//Greenfield, P.//Tran-Dinh, N.//Midgley, D.J. 	Draft Genome Sequence of Bacillus pumilus Fairview, an Isolate Recovered from a Microbial Methanogenic Enrichment of Coal Seam Gas Formation Water from Queensland, Australia.	Genome Announcements	2014	2		e00279-14			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. 		
@D	Voelker, L.L.//Dybvig, K. 	Gene transfer in Mycoplasma arthritidis: Transformation, conjugal transfer of Tn916, and evidence for a restriction system recognizing AGCT.	J. Bacteriol.	1996	178		6078-6081			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). 		
@D	Voelker, L.L.//Dybvig, K. 	Sequence analysis of the Mycoplasma arthritidis bacteriophage MAV1 genome identifies the putative virulence factor.	Gene	1999	233		101-107			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. 		
@D	Voet, J.G.//Voet, D. 	DNA structure and restriction/modification visualized with kinemages.	FASEB J.	1997	11		A843			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. 		
@D	Voeykova, T.A.//Lomovskaya, N.D. 	Restriction and modification of Actinophage omega-C31.	Genetika	1981	17		1132-1135			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). 		
@D	Voeykova, T.A.//Slavinskaya, E.V.//Orechov, A.V.//Lomovskaya, N.D. 	Identification of restriction and modification systems in Streptomyces strains.	Genetika	1979	15		1746-1754			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. 		
@D	Vogel, V.//Falquet, L.//Calderon-Copete, S.P.//Basset, P.//Blanc, D.S. 	Short term evolution of a highly transmissible methicillin-resistant Staphylococcus aureus clone (ST228) in a tertiary care hospital.	PLoS ONE	2012	7		E38969			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. 		
@D	Vogelsang-Wenke, H.//Oesterhelt, D. 	Isolation of a halobacterial phage with a fully cytosine-methylated genome.	Mol. Gen. Genet.	1988	211		407-414			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. 		
@D	Vogensen, F.K.//Pedersen, B.M.//Nielsen, E.W.//Josephsen, J. 	Genetic and biological evidence for 5 different plasmid-encoded restriction and modification systems in Streptococcus cremoris strains.	FEMS Microbiol. Rev.	1987	46		44			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. 		
@D	Voget, S.//Billerbeck, S.//Simon, M.//Daniel, R. 	Closed Genome Sequence of Octadecabacter temperatus SB1, the First Mesophilic Species of the Genus Octadecabacter.	Genome Announcements	2015	3		e01051-15			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. 		
@D	Voget, S.//Bruns, H.//Wagner-Dobler, I.//Schulz, S.//Daniel, R. 	Draft Genome Sequence of Roseovarius tolerans EL-164, a Producer of N-Acylated Alanine Methyl Esters and N-Acylhomoserine Lactones.	Genome Announcements	2015	3		e01096-15			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. 		
@D	Voget, S.//Diaz, V.S.M.//von Hoyningen-Huene, A.J.//Nattramilarasu, P.K.//Vollheyde, K.//Xiao, S.//Daniel, R. 	Genome Sequence of Jannaschia aquimarina GSW-M26, a Member of the Roseobacter Clade.	Genome Announcements	2015	3		e00353-15			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. 		
@D	Voget, S.//Klippel, B.//Daniel, R.//Antranikian, G. 	Complete Genome Sequence of Carnobacterium sp. 17-4.	J. Bacteriol.	2011	193		3403-3404			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. 		
@D	Voget, S.//Wemheuer, B.//Brinkhoff, T.//Vollmers, J.//Dietrich, S.//Giebel, H.A.//Beardsley, C.//Sardemann, C.//Bakenhus, I.//Billerbeck, S.//Daniel, R.//Simon, M. 	Adaptation of an abundant Roseobacter RCA organism to pelagic systems revealed by genomic and transcriptomic analyses.	ISME J.	2015	9		371-384			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. 		
@D	Voigt, J.M.//Topal, M.D. 	O6 methylguanine in place of guanine causes asymmetric single-strand cleavage of DNA by some restriction enzymes.	Biochemistry	1990	29		1632-1637			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. 		
@D	Voing, K.//Harrison, A.//Soby, S.D. 	Draft Genome Sequence of Chromobacterium vaccinii, a Potential Biocontrol Agent against Mosquito (Aedes aegypti) Larvae.	Genome Announcements	2015	3		e00477-15			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. 		
@D	Voing, K.//Harrison, A.//Soby, S.D. 	Draft Genome Sequence of Chromobacterium subtsugae MWU12-2387 Isolated from a Wild Cranberry Bog in Truro, Massachusetts.	Genome Announcements	2017	5		e01633-16			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. 		
@D	Voing, K.//Harrison, A.//Soby, S.D. 	Draft Genome Sequences of Three Chromobacterium subtsugae Isolates from Wild and  Cultivated Cranberry Bogs in Southeastern Massachusetts.	Genome Announcements	2015	3		e00998-15			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. 		
@D	Volland, S.//Rachinger, M.//Strittmatter, A.//Daniel, R.//Gottschalk, G.//Meyer, O. 	Complete genome sequences of the chemolithoautotrophic Oligotropha carboxidovorans strains OM4 and OM5.	J. Bacteriol.	2011	193		5043			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). 		
@D	Volna, P.//Jarjour, J.//Baxter, S.//Roffler, S.R.//Monnat, R.J. Jr.//Stoddard, B.L.//Scharenberg, A.M. 	Flow cytometric analysis of DNA binding and cleavage by cell surface-displayed homing endonucleases.	Nucleic Acids Res.	2007	35		2748-2758			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. 		
@D	Volozhantsev, N.V.//Kislichkina, A.A.//Lev, A.I.//Mukhina, T.N.//Bogun, A.A.//Ershova, O.N.//Alexandrova, I.A.//Fursova, N.K. 	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.	Genome Announcements	2017	5		e01173-17			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. 		
@D	von Jan, M. et al. 	Complete genome sequence of Archaeoglobus profundus type strain (AV18).	Standards in Genomic Sciences	2010	2		327-346			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. 		
@D	Vongs, A.//Kakutani, T.//Martienssen, R.A.//Richards, E.J. 	Arabidopis thaliana DNA methylation mutants.	Science	1993	260		1926-1928			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. 		
@D	Vongsawan, A.A.//Kapatral, V.//Vaisvil, B.//Burd, H.//Serichantalergs, O.//Venkatesan, M.M.//Mason, C.J. 	The genome of Shigella dysenteriae strain Sd1617 comparison to representative strains in evaluating pathogenesis.	FEMS Microbiol. Lett.	2015	362		fnv011			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. 		
@D	Voo, K.//Carlone, D.//Jacobsen, B.//Flodin, A.//Skalnik, D. 	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.	Blood	1999	0		469a			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. 		
@D	Vorholt, J.A.//Vaupel, M.//Thauer, R.K. 	A selenium-dependent and a selenium-independent formylmethanofuran dehydrogenase and their transcriptional regulation in the hyperthermophilic Methanopyrus kandleri.	Mol. Microbiol.	1997	23		1033-1042			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. 		
@D	Vorholter, F.J.//Arnold, M.//Wibberg, D.//Blom, J.//Winkler, A.//Viehoever, P.//Albersmeier, A.//Goesmann, A.//Zange, S.//Heesemann, J.//Puhler, A.//Hogardt, M. 	Draft Genome Sequence of Pseudomonas aeruginosa Strain WS394, a Multidrug-Resistant and Highly Cytotoxic Wound Isolate from Chronic Ulcus Cruris.	Genome Announcements	2014	2		e01325-14			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. 		
@D	Vorholter, F.J.//Schneiker, S.//Goesmann, A.//Krause, L.//Bekel, T.//Kaiser, O.//Linke, B.//Patschkowski, T.//Ruckert, C.//Schmid, J.//Sidhu, V.K.//Sieber, V.//Tauch, A.//Watt, S.A.//Weisshaar, B.//Becker, A.//Niehaus, K.//Puhler, A. 	The genome of Xanthomonas campestris pv. campestris B100 and its use for the reconstruction of metabolic pathways involved in xanthan biosynthesis.	J. Biotechnol.	2008	134		33-45			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. 		
@D	Vorholter, F.J.//Tielen, P.//Wibberg, D.//Narten, M.//Schobert, M.//Tupker, R.//Blom, J.//Schatschneider, S.//Winkler, A.//Albersmeier, A.//Goesmann, A.//Puhler, A.//Jahn, D. 	Genome Sequence of the Urethral Catheter Isolate Pseudomonas aeruginosa MH19.	Genome Announcements	2015	3		e00115-15			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. 		
@D	Vorobeva, O.V.//Karyagina, A.S.//Volkov, E.M.//Viryasov, M.B.//Oretskaya, T.S.//Kubareva, E.A. 	An analysis of methyltransferase SsoII-DNA contacts in the enzyme-substrate complex.	Bioorg. Khim.	2002	28		402-410			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. 		
@D	Vorobeva, O.V.//Romanenkov, A.S.//Metelev, V.G.//Karyagina, A.S.//Lavrova, N.V.//Oretskaya, T.S.//Kubareva, E.A. 	Crosslinking of Cys142 of Methyltransferase SsoII with DNA Duplexes Containing a Single Internucleotide Phosphoryldisulfide Link.	Mol. Biol. (Mosk)	2003	37		906-915			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. 		
@D	Vorobeva, O.V.//Vasilev, S.A.//Karyagina, A.S.//Oretskaya, T.S.//Kubareva, E.A. 	Analysis of DNA-protein contacts in a complex between methyltransferase SsoII and a promoter region of the SsoII restriction-modification genes.	Mol. Biol. (Mosk)	2000	34		1074-1080			. 		
@D	Voros, A.//Horvath, B.//Hunyadkurti, J.//McDowell, A.//Barnard, E.//Patrick, S.//Nagy, I. 	Complete Genome Sequences of Three Propionibacterium acnes Isolates from the Type IA2 Cluster.	J. Bacteriol.	2012	194		1621-1622			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). 		
@D	Vorwerk, H.//Huber, C.//Mohr, J.//Bunk, B.//Bhuju, S.//Wensel, O.//Sproer, C.//Fruth, A.//Flieger, A.//Schmidt-Hohagen, K.//Schomburg, D.//Eisenreich, W.//Hofreuter, D. 	A transferable plasticity region in Campylobacter coli allows isolates of an otherwise non-glycolytic food-borne pathogen to catabolize glucose.	Mol. Microbiol.	2015	98		809830			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. 		
@D	Vosberg, H.-P.//Eckstein, F. 	Effect of deoxynucleoside phosphorothioates incorporated in DNA on cleavage by restriction enzymes.	J. Biol. Chem.	1982	257		6595-6599			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. 		
@D	Voss, B.//Bolhuis, H.//Fewer, D.P.//Kopf, M.//Moke, F.//Haas, F.//El-Shehawy, R.//Hayes, P.//Bergman, B.//Sivonen, K.//Dittmann, E.//Scanlan, D.J.//Hagemann, M.//Stal, L.J.//Hess, W.R. 	Insights into the physiology and ecology of the brackish-water-adapted Cyanobacterium Nodularia spumigena CCY9414 based on a genome-transcriptome analysis.	PLoS ONE	2013	8		E60224			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. 		
@D	Vovis, G.F.//Horiuchi, K.//Hartman, N.//Zinder, N.D. 	Restriction endonuclease B and f1 heteroduplex DNA.	Nature New Biol.	1973	246		13-16			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. 		
@D	Vovis, G.F.//Horiuchi, K.//Zinder, N.D. 	Endonuclease R.EcoRII restriction of bacteriophage f1 DNA in vitro:  Ordering of genes V and VII, location of an RNA promotor for Gene VIII.	J. Virol.	1975	16		674-684			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. 		
@D	Vovis, G.F.//Horiuchi, K.//Zinder, N.D. 	Kinetics of methylation of DNA by a restriction endonuclease from Escherichia coli B.	Proc. Natl. Acad. Sci. U. S. A.	1974	71		3810-3813			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. 		
@D	Vovis, G.F.//Lacks, S. 	Complementary action of restriction enzymes Endo R.DpnI and Endo R.DpnII on bacteriophage f1 DNA.	J. Mol. Biol.	1977	115		525-538			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. 		
@D	Vovis, G.F.//Zinder, N.D. 	Methylation of f1 DNA by a restriction endonuclease from Escherichia coli B.	J. Mol. Biol.	1975	95		557-568			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. 		
@D	Vranken, C.//Deen, J.//Dirix, L.//Stakenborg, T.//Dehaen, W.//Leen, V.//Hofkens, J.//Neely, R.K. 	Super-resolution optical DNA Mapping via DNA methyltransferase-directed click chemistry.	Nucleic Acids Res.	2014	42		e50			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). 		
@D	Vuilleumier, S. et al. 	Methylobacterium genome sequences: a reference blueprint to investigate microbial metabolism of C1 compounds from natural and industrial sources.	PLoS ONE	2009	4		E5584			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. 		
@D	Vuilleumier, S. et al. 	Genome Sequence of the Haloalkaliphilic Methanotrophic Bacterium Methylomicrobium alcaliphilum 20Z.	J. Bacteriol.	2012	194		551-552			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. 		
@D	Vuilleumier, S.//Nadalig, T.//Ul-Haque, M.F.//Magdelenat, G.//Lajus, A.//Roselli, S.//Muller, E.E.//Gruffaz, C.//Barbe, V.//Medigue, C.//Bringel, F. 	Complete Genome Sequence of the Chloromethane-Degrading Hyphomicrobium sp. Strain MC1.	J. Bacteriol.	2011	193		5035-5036			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. 		
@D	Vyle, J.S.//Connolly, B.A.//Kemp, D.//Cosstick, R. 	Sequence- and strand-specific cleavage in oligodeoxyribonucleotides and DNA containing 3'-thiothymidine.	Biochemistry	1992	31		3012-3018			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. 		
@D	Waalwijk, C.//Flavell, R.A. 	MspI, an isochizomer of HpaII which cleaves both unmethylated and methylated HpaII sites.	Nucleic Acids Res.	1978	5		3231-3236			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. 		
@D	Wachino, J.//Shibayama, K.//Kurokawa, H.//Kimura, K.//Yamane, K.//Suzuki, S.//Shibata, N.//Ike, Y.//Arakawa, Y. 	Novel plasmid-mediated 16S rRNA m1A1408 methyltransferase, NpmA, found in a clinically isolated Escherichia coli strain resistant to structurally diverse  aminoglycosides.	Antimicrob. Agents Chemother.	2007	51		4401-4409			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. 		
@D	Wachsman, J.T. 	DNA methylation and the association between genetic and epigenetic changes: relation to carcinogenesis.	Mutat. Res.	1997	375		1-8			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. 		
@D	Wada, T.//Hijikata, M.//Maeda, S.//Hang, N.T.L.//Thuong, P.H.//Hoang, N.P.//Hung, N.V.//Keicho, N. 	Complete Genome Sequence of a Mycobacterium tuberculosis Strain Belonging to the  East African-Indian Family in the Indo-Oceanic Lineage, Isolated in Hanoi,  Vietnam.	Genome Announcements	2017	5		e00509-17			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. 		
@D	Wada, T.//Hijikata, M.//Maeda, S.//Hang, N.T.L.//Thuong, P.H.//Hoang, N.P.//Hung, N.V.//Keicho, N. 	Complete Genome Sequences of Three Representative Mycobacterium tuberculosis Beijing Family Strains Belonging to Distinct Genotype Clusters in Hanoi, Vietnam, during 2007 to 2009.	Genome Announcements	2017	5		e00510-17			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. 		
@D	Wada, Y. 	Physiological functions of plant DNA methyltransferases.	Plant Biotechnol.	2005	22		71-80			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. 		
@D	Wada, Y. 	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.	J. Mass Spectrom.	1998	33		187-192			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. 		
@D	Wada, Y.//Ohya, H.//Yamaguchi, Y.//Koizumi, N.//Sano, H. 	Preferential de novo methylation of cytosine residues in non-CpG sequences by a domains rearranged DNA methyltransferase from tobacco plants.	J. Biol. Chem.	2003	278		42386-42393			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. 		
@D	Wafula, E.N.//Brinks, E.//Becker, B.//Huch, M.//Trierweiler, B.//Mathara, J.M.//Oguntoyinbo, F.A.//Cho, G.S.//Franz, C.M.A.P. 	Draft Genome Sequence of Lactobacillus fermentum BFE 6620, a Potential Starter Culture for African Vegetable Foods, Isolated from Fermented Cassava.	Genome Announcements	2017	5		e00801-17			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). 		
@D	Wagenfuhr, K.//Pieper, S.//Mackeldanz, P.//Linscheid, M.//Kruger, D.H.//Reuter, M. 	Structural domains in the type III restriction endonuclease EcoP15I: Characterization by limited proteolysis, mass spectrometry and insertional mutagenesis.	J. Mol. Biol.	2007	366		93-102			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. 		
@D	Wagner, E.//Schmitz, G.G.//Kaluza, K.//Jarsch, M.//Gotz, F.//Kessler, C. 	BmyI, a novel SduI isoschizomer from Bacillus mycoides recognizing 5'-GDGCH/C-3'.	Nucleic Acids Res.	1990	18		3088			None 		
@D	Wah, D.A. 	Structural study of the type IIs restriction endonuclease FokI.	Ph.D. Thesis, Columbia University	1998			1-108			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. 		
@D	Wah, D.A. 	Structural study of the type IIs restriction endonuclease FokI.	Diss. Abstr.	1998	58		6439B			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. 		
@D	Wah, D.A.//Bitinaite, J.//Schildkraut, I.//Aggarwal, A.K. 	Structure of FokI has implications for DNA cleavage.	Proc. Natl. Acad. Sci. U. S. A.	1998	95		10564-10569			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. 		
@D	Wah, D.A.//Hirsch, J.A.//Dorner, L.F.//Schildkraut, I.//Aggarwal, A.K. 	Structure of the multimodular endonuclease FokI bound to DNA.	Nature	1997	388		97-100			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. 		
@D	Wahab, T.//Ferrari, S.//Lindberg, M.//Backman, S.//Kaden, R. 	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.	Genome Announcements	2014	2		e00783-14			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. 		
@D	Wahnon, D.C.//Shier, V.K.//Benkovic, S.J. 	Mechanism-based inhibition of an essential bacterial adenine DNA methyltransferase: Rationally designed antibiotics.	J. Am. Chem. Soc.	2001	123		976-977			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. 		
@D	Wailan, A.M.//Paterson, D.L.//Caffery, M.//Sowden, D.//Sidjabat, H.E. 	Draft Genome Sequence of NDM-5-Producing Escherichia coli Sequence Type 648 and Genetic Context of blaNDM-5 in Australia.	Genome Announcements	2015	3		e00194-15			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). 		
@D	Waite-Rees, P.A.//Keating, C.J.//Moran, L.S.//Slatko, B.E.//Hornstra, L.J.//Benner, J.S. 	Characterization and expression of the Escherichia coli Mrr restriction system.	J. Bacteriol.	1991	173		5207-5219			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. 		
@D	Wajima, T.//Sabui, S.//Kano, S.//Ramamurthy, T.//Chatterjee, N.S.//Hamabata, T. 	Entire sequence of the colonization factor coli surface antigen 6-encoding plasmid pCss165 from an enterotoxigenic Escherichia coli clinical isolate.	Plasmid	2013	70		343-352			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 		
@D	Wakefield, R.I.D.//Smith, B.O.//Nan, X.//Free, A.//Soteriou, A.//Uhrin, D.//Bird, A.P.//Barlow, P.N. 	The solution structure of the domain from MeCP2 that binds to methylated DNA.	J. Mol. Biol.	1999	291		1055-1065			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. 		
@D	Walczak, A.B.//Yee, N.//Young, L.Y. 	Draft genome sequence of Bosea sp. WAO an arsenite and sulfide oxidizer isolated  from a pyrite rock outcrop in New Jersey.	Standards in Genomic Sciences	2018	13		6			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. 		
@D	Walder, R.//Walder, J.//Donelson, J. 	The DNA Sequence and Organization of the PstI Restriction-Modification Genes.	Fed. Proc.	1981	40		1647			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. 		
@A	Walder, R.Y. 		The cloning and sequence organization of the PstI restriction-modification system.			 		Ph.D. Thesis				none	The University of Iowa, Department of Biology	1984				1-228									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. 		
@D	Walder, R.Y.//Hartley, J.L.//Donelson, J.E.//Walder, J.A. 	Cloning and expression of the PstI restriction-modification system in Escherichia coli.	Proc. Natl. Acad. Sci. U. S. A.	1981	78		1503-1507			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. 		
@A	Walder, R.Y.//Hartley, J.L.//Donelson, J.E.//Walder, J.A. 		Cloning of the PstI restriction-modification system.			Chirikjian, J.G. 		Gene Amplif. Anal.					Elsevier North Holland	1981		1		217-226									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 		
@D	Walder, R.Y.//Langtimm, C.J.//Catterjee, R.//Walder, J.A. 	Cloning of the MspI modification enzyme.	J. Biol. Chem.	1983	258		1235-1241			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. 		
@D	Walder, R.Y.//Langtimm, C.J.//Chatterjee, R.//Walder, J.A. 	Cloning of the MspI modification enzyme:  the site of modification and its effects on cleavage by MspI and HpaII.	Fed. Proc.	1982	41		1199			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. 		
@A	Walder, R.Y.//Walder, J.A. 		The organization and control of expression of the PstI restriction modification system.			Chirikjian, J.G. 		Gene Amplif. Anal.					Elsevier North Holland	1987		5		209-226									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. 		
@D	Walder, R.Y.//Walder, J.A.//Donelson, J.E. 	The Organization and Complete Nucleotide Sequence of the PstI Restriction-Modification System.	J. Biol. Chem.	1984	259		8015-8026			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. 		
@D	Waldman, B.-A.H.//Yerushalmi, R.//Wachtel, C.//Barbiro-Michaely, E.//Sompolinsky, D.//Gerber, D. 	Draft Genome Sequence of the Suttonellaornithocola Bacterium.	Genome Announcements	2017	5		e01592-16			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. 		
@D	Waldman-Ben-Asher, H.//Yerushalmi, R.//Wachtel, C.//Barbiro-Michaely, E.//Sompolinsky, D.//Gerber, D. 	Draft Genome Sequence of a New Bacterium Named Rappaport israeli, gen. nov., sp.  nov., Isolated from a Blood Culture.	Genome Announcements	2017	5		e01595-16			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. 		
@D	Waldron, D.E.//Lindsay, J.A. 	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.	J. Bacteriol.	2006	188		5578-5585			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. 		
@D	Waldron, D.E.//Owen, P.//Dorman, C.J. 	Competitive interaction of the OxyR DNA-binding protein and the Dam methylase at the antigen 43 gene regulatory region in Escherichia coli.	Mol. Microbiol.	2002	44		509-520			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. 		
@D	Waleron, K.//Nakonieczna, J.//Waleron, M.//Podhajska, A.J. 	50 years of studies of restriction - modification systems (Systemy restrykcyjno-modyfikacyjne - 50 lat badan).	Biotechnologia (Poznan)	2006	2		65-88			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. 		
@D	Waleron, K.//Waleron, M.//Osipiuk, J.//Podhajska, A.J.//Lojkowska, E. 	Identification of a DNA restriction-modification system in Pectobacterium carotovorum strains isolated from Poland.	J. Appl. Microbiol.	2006	100		343-351			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. 		
@D	Walker, C.A.//Mannering, S.A.//Shields, S.//Blake, D.P.//Brownlie, J. 	Complete Genome Sequence of Mycoplasma cynos Strain C142.	Genome Announcements	2013	1		e00196-12			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. 		
@D	Walker, C.B. et al. 	Nitrosopumilus maritimus genome reveals unique mechanisms for nitrification and autotrophy in globally distributed marine crenarchaea.	Proc. Natl. Acad. Sci. U. S. A.	2010	107		8818-8823			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. 		
@D	Walker, G.T.//Little, M.C.//Nadeau, J.G.//Shank, D.D. 	Isothermal in vitro amplification of DNA by a restriction enzyme/DNA polymerase system.	Proc. Natl. Acad. Sci. U. S. A.	1992	89		392-396			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. 		
@D	Walker, J.N.B.//Dean, P.D.G.//Saunders, J.R. 	Identification and characterisation of PmaCI an endonuclease of novel specificity from Pseudomonas maltophila.	Nucleic Acids Res.	1986	14		1293-1301			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. 		
@D	Walker, R.//Watkin, E.//Tian, R.//Brau, L.//O'Hara, G.//Goodwin, L.//Han, J.//Lobos, E.//Huntemann, M.//Pati, A.//Woyke, T.//Mavromatis, K.//Markowitz, V.//Ivanova, N.//Kyrpides, N.//Reeve, W. 	Genome sequence of the acid-tolerant Burkholderia sp. strain WSM2230 from Karijini National Park, Australia.	Standards in Genomic Sciences	2014	9		551-561			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. 		
@D	Walker, R.//Watkin, E.//Tian, R.//Brau, L.//O'Hara, G.//Goodwin, L.//Han, J.//Reddy, T.//Huntemann, M.//Pati, A.//Woyke, T.//Mavromatis, K.//Markowitz, V.//Ivanova, N.//Kyrpides, N.//Reeve, W. 	Genome sequence of the acid-tolerant Burkholderia sp. strain WSM2232 from Karijini National Park, Australia.	Standards in Genomic Sciences	2014	9		1168-1180			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. 		
@A	Walker, S.A.//Klaenhammer, T.R. 		The Genetics of Phage Resistance in Lactococcus lactis.			Wood, B.J.B.//Warner, P.J. 		Genetics of Phage Resistance				NY	Kluwer Academic/Plenum Publishers	2003		3		291-315											
@D	Walkinshaw, M.D.//Taylor, P.//Sturrock, S.S.//Atanasiu, C.//Berge, T.//Henderson, R.M.//Edwardson, J.M.//Dryden, D.T. 	Structure of Ocr from bacteriophage T7, a protein that mimics B-form DNA.	Mol. Cell	2002	9		187-194			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. 		
@D	Wall, L.G. et al. 	Draft Genome Sequence of Frankia sp. Strain BCU110501, a Nitrogen-Fixing Actinobacterium Isolated from Nodules of Discaria trinevis.	Genome Announcements	2013	1		e00503-13			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. 		
@D	Wall, T.//Bath, K.//Britton, R.A.//Jonsson, H.//Versalovic, J.//Roos, S. 	The Early Response to Acid Shock in Lactobacillus reuteri Involves the ClpL Chaperone and a Putative Cell Wall-Altering Esterase.	Appl. Environ. Microbiol.	2007	73		3924-3935			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. 		
@D	Wallace, C.J.A. 	The curious case of protein splicing: mechanistic insights suggested by protein semisynthesis.	Protein Sci.	1993	2		697-705			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. 		
@D	Wallace, J.G.//Breaker, R.R. 	Improved genetic transformation methods for the model alkaliphile Bacillus halodurans C-125.	Lett. Appl. Microbiol.	2011	52		430-432			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. 		
@D	Walsh, C.P.//Bestor, T.H. 	Cytosine methylation and mammalian development.	Genes Dev.	1999	13		26-34			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. 		
@A	Walsh, C.P.//Xu, G.L. 		Cytosine methylation and DNA repair.			Doerfler, W.//Bohm, P. 		Curr. Top. Microbiol. Immunol.				Berlin, Germany	Springer-Verlag	2006		301		283-315									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. 		
@D	Walsh, D.A.//Zaikova, E.//Howes, C.G.//Song, Y.C.//Wright, J.J.//Tringe, S.G.//Tortell, P.D.//Hallam, S.J. 	Metagenome of a versatile chemolithoautotroph from expanding oceanic dead zones.	Science	2009	326		578-582			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. 		
@D	Walsh, D.A.//Zaikova, E.//Howes, C.L.//Song, Y.C.//Wright, J.//Tringe, S.G.//Tortell, P.D.//Hallam, S.J. 	Metagenome of a versatile chemolithoautotroph from expanding oxygen minimum zones.	Science	2009	326		578-582			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. 		
@D	Walsh, P.//Bekaert, M.//Carroll, J.//Manning, T.//Kelly, B.//O'Driscoll, A.//Lu, X.//Smith, C.//Dickinson, P.//Templeton, K.//Ghazal, P.//Sleator, R.D. 	Draft Genome Sequences of Six Different Staphylococcus epidermidis Clones, Isolated Individually from Preterm Neonates Presenting with Sepsis at Edinburgh's  Royal Infirmary.	Genome Announcements	2015	3		e00471-15			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. 		
@D	Walter, F.//Hartmann, M.//Roth, M. 	Purification and characterization of a site specific endonuclease from Streptomyces hygroscopicus.	Abstracts of 12th FEBS Symposium, Dresden.	1978	0		648			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. 		
@D	Walter, J.//Noyer-Weidner, M.//Trautner, T.A. 	The amino acid sequence of the CCGG recognizing DNA methyltransferase M.BsuFI: implications for the analysis of sequence recognition by cytosine DNA methyltransferases.	EMBO J.	1990	9		1007-1013			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. 		
@D	Walter, J.//Trautner, T.A.//Noyer-Weidner, M. 	High plasticity of multispecific DNA methyltransferases in the region carrying DNA target recognizing enzyme modules.	EMBO J.	1992	11		4445-4450			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. 		
@D	Wambui, J.//Stevens, M.//Njage, P.M.K.//Wuthrich, D.//Egli, A.//Stephan, R.//Tasara, T. 	Draft Genome Sequences of Enterococcus mundtii Strains Isolated from Beef Slaughterhouses in Kenya.	Genome Announcements	2018	6		e00446-18			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. 		
@D	Wan, K.H.//Yu, C.//Park, S.//Hammonds, A.S.//Booth, B.W.//Celniker, S.E. 	Complete Genome Sequence of Acetobacter pomorum Oregon-R-modENCODE Strain BDGP5,  an Acetic Acid Bacterium Found in the Drosophila melanogaster Gut.	Genome Announcements	2017	5		e01333-17			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. 		
@D	Wan, K.H.//Yu, C.//Park, S.//Hammonds, A.S.//Booth, B.W.//Celniker, S.E. 	Complete Genome Sequence of Bacillus kochii Oregon-R-modENCODE Strain BDGP4, Isolated from Drosophila melanogaster Gut.	Genome Announcements	2017	5		e01074-17			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. 		
@D	Wan, K.H.//Yu, C.//Park, S.//Hammonds, A.S.//Booth, B.W.//Celniker, S.E. 	Complete Genome Sequence of Enterococcus durans Oregon-R-modENCODE Strain BDGP3,  a Lactic Acid Bacterium Found in the Drosophila melanogaster Gut.	Genome Announcements	2017	5		e01041-17			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. 		
@D	Wan, K.H.//Yu, C.//Park, S.//Hammonds, A.S.//Booth, B.W.//Celniker, S.E. 	Complete Genome Sequence of Lactobacillus plantarum Oregon-R-modENCODE Strain BDGP2 Isolated from Drosophila melanogaster Gut.	Genome Announcements	2017	5		e01155-17			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. 		
@D	Wan, K.H.//Yu, C.//Park, S.//Hammonds, A.S.//Booth, B.W.//Celniker, S.E. 	Complete Genome Sequence of Acetobacter tropicalis Oregon-R-modENCODE Strain BDGP1, an Acetic Acid Bacterium Found in the Drosophila melanogaster Gut.	Genome Announcements	2017	5		e01020-17			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. 		
@D	Wan, T.W.//Higuchi, W.//Khokhlova, O.E.//Hung, W.C.//Iwao, Y.//Wakayama, M.//Inomata, N.//Takano, T.//Lin, Y.T.//Peryanova, O.V.//Kojima, K.K.//Salmina, A.B.//Teng, L.J.//Yamamoto, T. 	Genomic comparison between Staphylococcus aureus GN strains clinically isolated from a familial infection case: IS1272 transposition through a novel inverted repeat-replacing mechanism.	PLoS ONE	2017	12		E0187288			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. 		
@D	Wan, T.W.//Khokhlova, O.E.//Iwao, Y.//Higuchi, W.//Hung, W.C.//Reva, I.V.//Singur, O.A.//Gostev, V.V.//Sidorenko, S.V.//Peryanova, O.V.//Salmina, A.B.//Reva, G.V.//Teng, L.J.//Yamamoto, T. 	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.	PLoS ONE	2016	11		E0164168			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. 		
@D	Wan, X.//Dasilveira, L.//Hou, S.//Saito, J.A.//Donachie, S.P. 	Draft Genome Sequence of Terasakiispira papahanaumokuakeensis PH27AT, a Spiral Bacterium from the Northwestern Hawaiian Islands.	Genome Announcements	2016	4		e01166-16			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. 		
@D	Wan, X.//Hou, S.//Burns, S.L.//Saito, J.A.//Donachie, S.P. 	Draft Genome Sequence of a Novel Marinobacter sp. Strain from Honolulu Harbor, Hawai'i.	Genome Announcements	2016	4		e01354-16			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. 		
@D	Wan, X.//Hou, S.//Hayashi, K.//Anderson, J.//Donachie, S.P. 	Genome Sequence of Rheinheimera salexigens sp. nov. Isolated from a Fishing Hook  off O'ahu, Hawai'i.	Genome Announcements	2016	4		e01390-16			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%. 		
@D	Wan, X.//Hou, S.//Phan, N.//Malone, M.J.S.//Donachie, S.P.//Alam, M. 	Draft Genome Sequence of Pantoea anthophila Strain 11-2 from Hypersaline Lake Laysan, Hawaii.	Genome Announcements	2015	3		e00321-15			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. 		
@D	Wan, X.//Hou, S.//Saito, J.A.//Kaneshiro, K.Y.//Donachie, S.P. 	Genome Sequence of Flavobacterium akiainvivens IK-1T, Isolated from Decaying Wikstroemia oahuensis, an Endemic Hawaiian Shrub.	Genome Announcements	2015	3		e01222-15			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. 		
@D	Wan, X.//Lee, A.J.//Hou, S.//Ushijima, B.//Nguyen, Y.P.//Thawley, J.A.//Donachie, S.P. 	Draft Genome Sequence of Piscirickettsia litoralis, Isolated from Seawater.	Genome Announcements	2016	4		e01252-16			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. 		
@D	Wan, X.//Miller, J.M.//Rowley, S.J.//Hou, S.//Donachie, S.P. 	Draft Genome Sequence of a Novel Luteimonas sp. Strain from Coral Mucus, Hawai'i.	Genome Announcements	2016	4		e01228-16			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. 		
@D	Wan, X.//Qian, L.//Hou, S.//Drees, K.P.//Foster, J.T.//Douglas, J.T. 	Complete Genome Sequences of Beijing and Manila Family Strains of Mycobacterium tuberculosis.	Genome Announcements	2014	2		e01135-14			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. 		
@D	Wan, Y.//Gorrie, C.L.//Jenney, A.//Mirceta, M.//Holt, K.E. 	Draft Genome Sequence of a Clinical Isolate of Serratia marcescens, Strain AH0650_Sm1.	Genome Announcements	2015	3		e01007-15			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. 		
@D	Wanchanthuek, P.//Bellgard, M.I.//La, T.//Ryan, K.//Moolhuijzen, P.//Chapman, B.//Black, M.//Schibeci, D.//Hunter, A.//Barrero, R.//Phillips, N.D.//Hampson, D.J. 	The Complete Genome Sequence of the Pathogenic Intestinal Spirochete Brachyspira pilosicoli and Comparison with Other Brachyspira Genomes.	PLoS ONE	2010	5		E11455			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. 		
@D	Wanees, A.E.//Zaslow, S.J.//Potter, S.J.//Hsieh, B.P.//Boss, B.L.//Izquierdo, J.A. 	Draft Genome Sequence of the Plant Growth-Promoting Sphingobium sp. Strain AEW4,  Isolated from the Rhizosphere of the Beachgrass Ammophila breviligulata.	Genome Announcements	2018	6		e00410-18			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. 		
@D	Wang, A.//Pattemore, J.//Ash, G.//Williams, A.//Hane, J. 	Draft Genome Sequence of Bacillus thuringiensis Strain DAR 81934, Which Exhibits  Molluscicidal Activity.	Genome Announcements	2013	1		e0017512			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. 		
@D	Wang, B.//Jian, J.//Lu, Y.//Cai, S.//Huang, Y.//Tang, J.//Wu, Z. 	Complete Genome Sequence of Streptococcus agalactiae ZQ0910, a Pathogen Causing Meningoencephalitis in the GIFT Strain of Nile Tilapia (Oreochromis niloticus).	J. Bacteriol.	2012	194		5132-5133			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. 		
@D	Wang, B.//Liu, H.//Ma, H.//Wang, C.//Liu, K.//Li, Y.//Hou, Q.//Ge, R.//Zhang, T.//Liu, F.//Ma, J.//Wang, Y.//Wang, H.//Xu, B.//Yao, G.//Xu, W.//Fan, L.//Ding, Y.//Du, B. 	Complete Genome Sequence of Biocontroller Bacillus velezensis Strain JTYP2, Isolated from Leaves of Echeveria laui.	Genome Announcements	2017	5		e00505-17			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. 		
@D	Wang, C.//Chen, Q.//Wang, R.//Shi, C.//Yan, X.//He, J.//Hong, Q.//Li, S. 	A Novel Angular Dioxygenase Gene Cluster, Encoding 3-Phenoxybenzoate 1', 2' -Dioxygenase in Sphingobium wenxiniae JZ-1.	Appl. Environ. Microbiol.	2014	80		3811-3818			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. 		
@D	Wang, C.//Hu, X.//Liu, K.//Hou, Q.//Yang, Q.//Ding, Y.//Du, B. 	Draft Genome Sequence of Bacillus methylotrophicus FKM10, a Plant Growth-Promoting Rhizobacterium Isolated from Apple Rhizosphere.	Genome Announcements	2016	4		e01739-15			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. 		
@D	Wang, C.M.//Wu, Z.Y.//Shia, W.Y.//Jhou, Y.J.//Tung, K.C.//Shyu, C.L. 	Complete Genome Sequence of Campylobacter fetus subsp. testudinum Strain Pet-3, Isolated from a Lizard (Hydrosaurus pustulatus).	Genome Announcements	2015	3		e01420-14			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. 		
@D	Wang, C.X.//Zhu, S.L.//Wang, X.Y.//Feng, Y.//Li, B.//Li, Y.G.//Johnston, R.N.//Liu, G.R.//Zhou, J.//Liu, S.L. 	Complete genome sequence of Salmonella enterica subspecies arizonae str. RKS2983.	Standards in Genomic Sciences	2015	10		30			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. 		
@D	Wang, D.//Boukhalfa, H.//Ware, D.S.//Daligault, H.E. 	Draft Genome Sequence of a Chromium-Reducing Strain, Pseudomonas fluorescens S613, Isolated from a Chromium-Contaminated Aquifer in Los Alamos, New Mexico.	Genome Announcements	2017	5		e00241-17			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. 		
@D	Wang, D.//Boukhalfa, H.//Ware, D.S.//Reimus, P.W.//Daligault, H.E.//Gleasner, C.D.//Johnson, S.L.//Li, P.E. 	Genome Sequence of a Chromium-Reducing Strain, Bacillus cereus S612.	Genome Announcements	2015	3		e01392-15			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. 		
@D	Wang, D.//Han, C.S.//Dichosa, A.E.//Gleasner, C.D.//Johnson, S.L.//Daligault, H.E.//Davenport, K.W.//Li, P.E.//Pierson, E.A.//Pierson, L.S.I.I.I. 	Draft Genome Sequence of Enterobacter cloacae Strain S611.	Genome Announcements	2014	2		e00710-14			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. 		
@D	Wang, D.//Han, C.S.//Dichosa, A.E.//Gleasner, C.D.//Johnson, S.L.//Daligault, H.E.//Davenport, K.W.//Li, P.E.//Pierson, E.A.//Pierson, L.S.I.I.I. 	Draft Genome Sequence of Pseudomonas putida Strain S610, a Seed-Borne Bacterium of Wheat.	Genome Announcements	2013	1		e01048-13			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. 		
@D	Wang, D.//Hildebrand, F.//Ye, L.//Wei, Q.//Ma, L.Z. 	Genome Sequence of Mucoid Pseudomonas aeruginosa Strain FRD1.	Genome Announcements	2015	3		e00376-15			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. 		
@D	Wang, D.//Miyazono, K.I.//Tanokura, M. 	Tetrameric structure of the restriction DNA glycosylase R.PabI in complex with nonspecific double-stranded DNA.	Sci. Rep.	2016	6		35197			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. 		
@D	Wang, D.//Zhu, F.//Zhu, X.//Zheng, S.//Wang, R.//Wang, G. 	Draft genomic sequence of a selenite-reducing bacterium, Paenirhodobacter enshiensis DW2-9(T).	Standards in Genomic Sciences	2015	10		38			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. 		
@D	Wang, F.//Elmquist, C.E.//Rizzo, C.J.//Stone, M.P. 	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.	ACS Abstracts	2005	230		U1858-U1859			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. 		
@D	Wang, F.//Gong, L.//Zhou, L.//Liang, J. 	Complete Genome Sequence of the Poly-gamma-Glutamate-Synthesizing Bacterium Bacillus subtilis Bs-115.	Genome Announcements	2018	6		e00197-18			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. 		
@D	Wang, F.//Wang, J.//Jian, H.//Zhang, B.//Li, S.//Wang, F.//Zeng, X.//Gao, L.//Bartlett, D.H.//Yu, J.//Hu, S.//Xiao, X. 	Environmental adaptation: genomic analysis of the piezotolerant and psychrotolerant deep-sea iron reducing bacterium Shewanella piezotolerans WP3.	PLoS ONE	2008	3		E1937			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. 		
@D	Wang, G.//Barrett, N.H.//McCarthy, P.J. 	Draft Genome Sequence of Deep-Sea Alteromonas sp. Strain V450 Isolated from the Marine Sponge Leiodermatium sp.	Genome Announcements	2017	5		e01508-16			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. 		
@D	Wang, G.H. 	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.	Appl. Environ. Microbiol.	2013	79		7476-7481					
@D	Wang, G.L.//Zhou, L.Y.//Luo, H.Q.//Li, N.B. 	Electrochemical strategy for sensing DNA methylation and DNA methyltransferase activity.	Anal. Chim. Acta	2013	768		76-81			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. 		
@D	Wang, H.//Chen, Y.//Ayers, S.//Melka, D.//Laasri, A.//Payne, J.S.//Zheng, J.//Son, I.//Timme, R.//Kastanis, G.//Hammack, T.S.//Strain, E.//Allard, M.W.//Evans, P.S.//Brown, E.W. 	Draft Genome Sequence of Salmonella enterica subsp. enterica Serovar Give, Isolated from an Imported Chili Powder Product.	Genome Announcements	2015	3		e00726-15			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). 		
@D	Wang, H.//Guan, S.//Quimby, A.//Cohen-Karni, D.//Pradhan, S.//Wilson, G.//Roberts, R.J.//Zhu, Z.//Zheng, Y. 	Comparative characterization of the PvuRts1I family of restriction enzymes and their application in mapping genomic 5-hydroxymethylcytosine.	Nucleic Acids Res.	2011	39		9294-9305			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. 		
@D	Wang, H.//Li, H.//Shao, Z.//Liao, S.//Johnstone, L.//Rensing, C.//Wang, G. 	Genome Sequence of Deep-Sea Manganese-Oxidizing Bacterium Marinobacter manganoxydans MnI7-9.	J. Bacteriol.	2012	194		899-900			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. 		
@D	Wang, H.//Lin, H.//Tran-Dinh, N.//Li, D.//Greenfield, P.//Midgley, D.J. 	Draft Genome Sequence of Ruminoclostridium sp. Ne3, Clostridia from an Enrichment Culture Obtained from Australian Subterranean Termite, Nasutitermes exitiosus.	Genome Announcements	2015	3		e00305-15			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. 		
@D	Wang, H.//Lin, H.//Tran-Dinh, N.//Li, D.//Greenfield, P.//Midgley, D.J. 	Draft Genome Sequence of Clostridium sp. Ne2, Clostridia from an Enrichment Culture Obtained from Australian Subterranean Termite, Nasutitermes exitiosus.	Genome Announcements	2015	3		e00304-15			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. 		
@D	Wang, H.//Lin, H.//Tran-Dinh, N.//Li, D.//Greenfield, P.//Midgley, D.J. 	Draft Genome Sequence of Clostridium beijerinckii Ne1, Clostridia from an Enrichment Culture Obtained from Australian Subterranean Termite, Nasutitermes  exitiosus.	Genome Announcements	2015	3		e00303-15			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. 		
@D	Wang, H.//Sivonen, K.//Rouhiainen, L.//Fewer, D.P.//Lyra, C.//Rantala-Ylinen, A.//Vestola, J.//Jokela, J.//Rantasarkka, K.//Li, Z.//Liu, B. 	Genome-derived insights into the biology of the hepatotoxic bloom-forming cyanobacterium Anabaena sp. strain 90.	BMC Genomics	2012	13		613			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. 		
@D	Wang, H.//Wang, L.//Ju, J.//Yu, B.//Ma, Y. 	Genome Sequence of Sporolactobacillus laevolacticus DSM442, an Efficient Polymer-Grade D-Lactate Producer from Agricultural Waste Cottonseed as a Nitrogen  Source.	Genome Announcements	2013	1		e01100-13			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. 		
@D	Wang, H.//Zheng, J.//Ayers, S.//Melka, D.C.//Curry, P.E.//Payne, J.S.//Laasri, A.//Wang, C.//Hammack, T.S.//Brown, E.W. 	Draft Genome Sequences of Salmonella enterica subsp. enterica Serovars Typhimurium and Nottingham Isolated from Food Products.	Genome Announcements	2016	4		e00699-16			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. 		
@D	Wang, H.-L.//Wang, H.-R.//Zhang, W.-W.//Sun, L. 	Cloning and analysis of the Vibrio harveyi dam gene.	Wei Sheng Wu Xue Bao	2007	47		855-859			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. 		
@D	Wang, H.C.//Cheng, F.C.//Wu, M.S.//Shu, H.Y.//Sun, H.S.//Wang, Y.C.//Su, I.J.//Wu, C.J. 	Genome Sequences of Three Helicobacter pylori Strains from Patients with Gastric  Mucosa-Associated Lymphoid Tissue Lymphoma.	Genome Announcements	2015	3		e00229-15			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. 		
@D	Wang, H.C.//Ko, W.C.//Shu, H.Y.//Chen, P.L.//Wang, Y.C.//Wu, C.J. 	Genome Sequence of Aeromonas taiwanensis LMG 24683T, a Clinical Wound Isolate from Taiwan.	Genome Announcements	2014	2		e00579-14			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. 		
@D	Wang, H.F.//Muren, N.B.//Ordinario, D.//Gorodetsky, A.A.//Barton, J.K.//Nuckolls, C. 	Transducing methyltransferase activity into electrical signals in a carbon nanotube-DNA device.	Chem. Sci.	2012	3		62-65			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. 		
@D	Wang, H.X.//Wang, Y.S. 	6-Thioguanine Perturbs Cytosine Methylation at the CpG Dinucleotide Site by DNA Methyltransferases in Vitro and Acts as a DNA Demethylating Agent in Vivo.	Biochemistry	2009	48		2290-2299			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. 		
@D	Wang, H.Z.//Wong, M.M.L.//O'Toole, D.//Mak, M.M.H.//Wu, R.S.S.//Kong, R.Y.C. 	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.	Appl. Environ. Microbiol.	2006	72		4455-4460			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. 		
@D	Wang, J.//Geng, K.//Farhan, Ul.H.M.//Crombie, A.//Street, L.E.//Wookey, P.A.//Ma, K.//Murrell, J.C.//Pratscher, J. 	Draft Genome Sequence of Methylocella silvestris TVC, a Facultative Methanotroph  Isolated from Permafrost.	Genome Announcements	2018	6		e00040-18			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). 		
@D	Wang, J.//Hevi, S.//Kurash, J.K.//Lei, H.//Gay, F.//Bajko, J.//Su, H.//Sun, W.//Chang, H.//Xu, G.//Gaudet, F.//Li, E.//Chen, T. 	The lysine demethylase LSD1 (KDM1) is required for maintenance of global DNA methylation.	Nat. Genet.	2009	41		125-129			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. 		
@D	Wang, J.//Hu, W.//Lux, R.//He, X.//Li, Y.//Shi, W. 	Natural Transformation of Myxococcus xanthus.	J. Bacteriol.	2011	193		2122-2132			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. 		
@D	Wang, J.//Hurley, D.//McGrath, K.//Bai, L.//Hachler, H.//Stephan, R.//Fanning, S. 	Draft Genome Sequence of Escherichia coli 26R 793, a Plasmid-Free Recipient Strain Commonly Used in Conjugation Assays.	Genome Announcements	2016	4		e00707-16			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. 		
@D	Wang, J.//Jiang, Y.//Vincent, M.//Sun, Y.//Yu, H.//Wang, J.//Bao, Q.//Kong, H.//Hu, S. 	Complete genome sequence of bacteriophage T5.	Virology	2005	332		45-65			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. 		
@D	Wang, J.//Kim, H.-H.//Yuan, X.//Herrin, D.L. 	Purification, biochemical characterization and protein-DNA interactions of the I-CreI endonuclease produced in Escherichia coli.	Nucleic Acids Res.	1997	25		3767-3776			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. 		
@D	Wang, J.//Kuenzel, S.//Baines, J.F. 	Draft Genome Sequences of 11 Staphylococcus epidermidis Strains Isolated from Wild Mouse Species.	Genome Announcements	2014	2		e01148-13			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. 		
@D	Wang, J.//Li, X.//Li, J.//Hurley, D.//Bai, X.//Yu, Z.//Cao, Y.//Wall, E.//Fanning, S.//Bai, L. 	Complete genetic analysis of a Salmonella enterica serovar Indiana isolate accompanying four plasmids carrying mcr-1, ESBL and other resistance genes in China.	Vet. Microbiol.	2017	210		142-146			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. 		
@D	Wang, J.//Li, Y.//Guo, J.//Zhang, X.//Guo, Y.//Chang, D.//Li, T.//Xu, G.//Dai, W.//Liu, C. 	Genome Sequence of Staphylococcus aureus Strain LCT-SA67, a Space Flight Strain with Altered Carbon Source Utilization Properties.	Genome Announcements	2014	2		e00095-14			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. 		
@D	Wang, J.//Liu, Y.//Wan, D.//Fang, X.//Li, T.//Guo, Y.//Chang, D.//Su, L.//Wang, Y.//Zhao, J.//Liu, C. 	Whole-Genome Sequence of Staphylococcus aureus Strain LCT-SA112.	J. Bacteriol.	2012	194		4124			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. 		
@D	Wang, J.//McIntosh, F.//Radomski, N.//Dewar, K.//Simeone, R.//Enninga, J.//Brosch, R.//Rocha, E.P.//Veyrier, F.J.//Behr, M.A. 	Insights on the emergence of Mycobacterium tuberculosis from the analysis of Mycobacterium kansasii.	Genome Biol. Evol.	2015	7		856-870			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. 		
@D	Wang, J.//Niu, Y.D.//Chen, J.//McAllister, T.A.//Stanford, K. 	Complete Genome Sequence of Escherichia coli O145:NM Bacteriophage vB_EcoM_AYO145A, a New Member of O1-Like Phages.	Genome Announcements	2015	3		e00539-15			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. 		
@D	Wang, J.//Song, L.//Jiao, Q.//Yang, S.//Gao, R.//Lu, X.//Zhou, G. 	Comparative genome analysis of jujube witches'-broom Phytoplasma, an obligate pathogen that causes jujube witches'-broom disease.	BMC Genomics	2018	19		689			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. 		
@D	Wang, J.//Stephan, R.//Power, K.//Yan, Q.//Hachler, H.//Fanning, S. 	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.	J. Antimicrob. Chemother.	2014	69		2658-2668			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. 		
@D	Wang, J.//Wang, L.//Cao, G.//Zhang, M.//Guo, Y. 	Draft Genome Sequence of Leifsonia xyli subsp. xyli Strain gdw1.	Genome Announcements	2016	4		e01128-16			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. 		
@D	Wang, J.P.//Liu, B.//Liu, G.H.//Che, J.M.//Chen, Z.//Chen, M.//Shi, H. 	Draft Genome Sequence of Brevibacillus choshinensis HPD52T (DSM 8552), a Bacterial Host for Efficient Expression of Heterologous Proteins.	Genome Announcements	2016	4		e01688-15			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. 		
@D	Wang, J.P.//Liu, B.//Liu, G.H.//Chen, D.J.//Chen, Q.Q.//Zhu, Y.J.//Chen, Z.//Che, J.M. 	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.	Genome Announcements	2015	3		e01451-15			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%. 		
@D	Wang, J.P.//Liu, B.//Liu, G.H.//Chen, D.J.//Ge, C.B.//Chen, Z.//Che, J.M. 	Genome Sequence of Brevibacillus reuszeri NRRL NRS-1206T, an l-N-Carbamoylase-Producing Bacillus-Like Bacterium.	Genome Announcements	2015	3		e01063-15			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. 		
@D	Wang, J.P.//Liu, B.//Liu, G.H.//Chen, D.J.//Xiao, R.F.//Zheng, X.F.//Shi, H.//Ge, C.B. 	Genome Sequence of Bacillus butanolivorans K9T (DSM 18926), an n-Butanol-Consuming Bacterium Isolated from Soil.	Genome Announcements	2015	3		e01228-15			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. 		
@D	Wang, J.P.//Liu, B.//Liu, G.H.//Chen, D.J.//Zhu, Y.J.//Chen, Z.//Che, J.M. 	Genome Sequence of Virgibacillus pantothenticus DSM 26T (ATCC 14576), a Mesophilic and Halotolerant Bacterium Isolated from Soil.	Genome Announcements	2015	3		e01064-15			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. 		
@D	Wang, J.P.//Liu, B.//Liu, G.H.//Chen, Q.//Pan, Z.//Zheng, X.F.//Chen, M. 	Draft Genome Sequence of Bacillus muralis LMG 20238T (DSM 16288), a Spore-Forming Bacterium Isolated from Deteriorated Mural Paintings.	Genome Announcements	2016	4		e01691-15			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. 		
@D	Wang, J.P.//Liu, B.//Liu, G.H.//Chen, Q.Q.//Zhu, Y.J.//Chen, Z.//Che, J.M. 	Genome Sequence of Brevibacillus formosus F12T for a Genome-Sequencing Project for Genomic Taxonomy and Phylogenomics of Bacillus-Like Bacteria.	Genome Announcements	2015	3		e00753-15			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. 		
@D	Wang, J.P.//Liu, B.//Liu, G.H.//Ge, C.B.//Chen, Q.Q.//Che, J.M.//Chen, D.J. 	Draft Genome Sequence of Bacillus cecembensis PN5T (DSM 21993), a Psychrotolerant Bacterium Isolated from Soil Samples near the Pindari Glacier.	Genome Announcements	2016	4		e01687-15			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. 		
@D	Wang, J.P.//Liu, B.//Liu, G.H.//Ge, C.B.//Chen, Q.Q.//Zhu, Y.J.//Chen, Z. 	Genome Sequence of Anaerobacillus macyae JMM-4T (DSM 16346), the First Genomic Information of the Newly Established Genus Anaerobacillus.	Genome Announcements	2015	3		e00922-15			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. 		
@D	Wang, J.P.//Liu, B.//Liu, G.H.//Ge, C.B.//Xiao, R.F.//Zheng, X.F.//Shi, H. 	Draft Genome Sequence of Bacillus farraginis R-6540T (DSM 16013), a Spore-Forming Bacterium Isolated at Dairy Farms.	Genome Announcements	2016	4		e00562-16			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. 		
@D	Wang, J.P.//Liu, B.//Liu, G.H.//Ge, C.B.//Xiao, R.F.//Zheng, X.F.//Shi, H. 	Draft Genome Sequence of Bacillus plakortidis P203T (DSM 19153), an Alkali- and Salt-Tolerant Marine Bacterium.	Genome Announcements	2016	4		e01690-15			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. 		
@D	Wang, J.P.//Liu, B.//Liu, G.H.//Ge, C.B.//Xiao, R.F.//Zheng, X.F.//Shi, H. 	Draft Genome Sequence of Bacillus shackletonii LMG 18435T, Isolated from Volcanic Mossy Soil.	Genome Announcements	2016	4		e01689-15			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. 		
@D	Wang, J.P.//Liu, B.//Liu, G.H.//Ge, C.B.//Xiao, R.F.//Zheng, X.F.//Shi, H. 	High-Quality Draft Genome Sequence of Aneurinibacillus migulanus ATCC 9999T (DSM  2895), a Gramicidin S-Producing Bacterium Isolated from Garden Soil.	Genome Announcements	2015	3		e01227-15			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. 		
@D	Wang, J.P.//Liu, B.//Liu, G.H.//Pan, Z.//Xiao, R.F.//Chen, M.//Chen, D.J. 	Draft Genome Sequence of Bacillus humi LMG 22167T (DSM 16318), an Endospore-Forming Bacterium Isolated from Soil.	Genome Announcements	2016	4		e01692-15			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. 		
@D	Wang, J.P.//Liu, B.//Liu, G.H.//Xiao, R.F.//Zheng, X.F.//Shi, H.//Ge, C.B. 	Draft Genome Sequence of Bacillus pseudalcaliphilus PN-137T (DSM 8725), an Alkaliphilic Halotolerant Bacterium Isolated from Garden Soils.	Genome Announcements	2015	3		e00919-15			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. 		
@D	Wang, J.P.//Liu, B.//Liu, G.H.//Xiao, R.F.//Zheng, X.F.//Shi, H.//Ge, C.B. 	Draft Genome Sequence of Sporosarcina globispora W 25T (DSM 4), a Psychrophilic Bacterium Isolated from Soil and River Water.	Genome Announcements	2015	3		e01230-15			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. 		
@D	Wang, J.P.//Liu, B.//Liu, G.H.//Xiao, R.F.//Zheng, X.F.//Shi, H.//Ge, C.B. 	Draft Genome Sequence of Bacillus murimartini LMG 21005T, an Alkalitolerant Bacterium Isolated from a Church Wall Mural in Germany.	Genome Announcements	2015	3		e01229-15			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. 		
@D	Wang, K.//Chen, J.//Yao, H.//Lu, C. 	Whole-Genome Sequence of Streptococcus suis Serotype 3 Strain YB51.	Genome Announcements	2013	1		e00884-13			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. 		
@D	Wang, K.//Chen, J.//Yao, H.//Lu, C. 	Whole-Genome Sequence of Streptococcus suis Serotype 4 Reference Strain 6407.	Genome Announcements	2014	2		e00770-14			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. 		
@D	Wang, K.//Fan, W.//Cai, L.//Huang, B.//Lu, C. 	Genetic analysis of the capsular polysaccharide synthesis locus in 15 Streptococcus suis serotypes.	FEMS Microbiol. Lett.	2011	324		117-124					
@D	Wang, K.//Yao, H.//Lu, C.//Chen, J. 	Complete Genome Sequence of Streptococcus suis Serotype 16 Strain TL13.	Genome Announcements	2013	1		e00394-13			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. 		
@D	Wang, K.-Y.//Chen, C.-C.//Shen, C.-Kun.J. 	Active DNA demethylation of the vertebrate genomes by DNA methyltransferases: deaminase, dehydroxymethylase or demethylase?	Epigenomics	2014	6		353-363			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. 		
@D	Wang, K.Y.//Liu, T.//Wang, J.//Chen, D.F.//Wu, X.J.//Jiang, J.//Liu, J.X. 	Complete Genome Sequence of the Fish Pathogen Yersinia ruckeri Strain SC09, Isolated from Diseased Ictalurus punctatus in China.	Genome Announcements	2015	3		e01327-14			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. 		
@A	Wang, L.//Chen, S.//Deng, Z. 		Phosphorothioation:  An unusual post-replicative modification on the DNA backbone.			Herve Seligmann 		DNA Replication-Current Advances					InTech	2011				57-74									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. 		
@D	Wang, L.//Chen, S.//Vergin, K.L.//Giovannoni, S.J.//Chan, S.W.//Demott, M.S.//Taghizadeh, K.//Cordero, O.X.//Cutler, M.//Timberlake, S.//Alm, E.J.//Polz, M.F.//Pinhassi, J.//Deng, Z.//Dedon, P.C. 	DNA phosphorothioation is widespread and quantized in bacterial genomes.	Proc. Natl. Acad. Sci. U. S. A.	2011	108		2963-2968			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. 		
@D	Wang, L.//Chen, S.//Xu, T.//Taghizadeh, K.//Wishnok, J.S.//Zhou, X.//You, D.//Deng, Z.//Dedon, P.C. 	Phosphorothioation of DNA in bacteria by dnd genes.	Nat. Chem. Biol.	2007	3		709-710			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. 		
@D	Wang, L.//Gao, C.//Tang, N.//Hu, S.//Wu, Q. 	Identification of genetic variations associated with epsilon-poly-lysine biosynthesis in Streptomyces albulus ZPM by genome sequencing.	Sci. Rep.	2015	5		9201			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. 		
@D	Wang, L.//Hatem, A.//Catalyurek, U.V.//Morrison, M.//Yu, Z. 	Metagenomic insights into the carbohydrate-active enzymes carried by the microorganisms adhering to solid digesta in the rumen of cows.	PLoS ONE	2013	8		E78507			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. 		
@D	Wang, L.//Qiu, Y.//Chen, Z.//Xu, J.//Wang, Z.//Ke, Y.//Li, T.//Wang, D.//Huang, L.//Yu, Y.//Zhen, Q. 	Draft Genome Sequence of Brucella abortus BCB027, a Strain Isolated from a Domestic Deer.	Genome Announcements	2013	1		e00130-12			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. 		
@D	Wang, L.//Wang, S.//He, Q.//Yu, T.//Li, Q.//Hong, B. 	Draft Genome Sequence of Streptomyces globisporus C-1027, Which Produces an Antitumor Antibiotic Consisting of a Nine-Membered Enediyne with a Chromoprotein.	J. Bacteriol.	2012	194		4144			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. 		
@D	Wang, L.//Xie, Y.//Li, Q.//He, N.//Yao, E.//Xu, H.//Yu, Y.//Chen, R.//Hong, B. 	Draft Genome Sequence of Streptomyces sp. Strain SS, Which Produces a Series of Uridyl Peptide Antibiotic Sansanmycins.	J. Bacteriol.	2012	194		6988-6989			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. 		
@D	Wang, N.//Ng, I.S.//Chen, P.T.//Li, Y.//Chen, Y.C.//Chen, B.Y.//Lu, Y. 	Draft Genome Sequence of the Bioelectricity-Generating and Dye-Decolorizing Bacterium Proteus hauseri Strain ZMd44.	Genome Announcements	2014	2		e00992-13			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. 		
@D	Wang, P.//Brank, A.S.//Banavali, N.K.//Nicklaus, M.C.//Marquez, V.E.//Christman, J.K.//MacKerell, A.D. Jr. 	Use of oligodeoxyribonucleotides with conformationally constrained abasic sugar targets to probe the mechanism of base flipping by HhaI DNA (cytosine C5)-methyltransferase.	J. Am. Chem. Soc.	2000	122		12422-12434			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. 		
@D	Wang, P.//Harvey, S.S.//Sims, P.F.G.//Broda, P. 	The construction of Streptomyces cyaneus genomic libraries in Escherichia coli is dependent upon the use of Mcr-deficient strains.	Gene	1992	119		127-129			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. 		
@D	Wang, P.//Li, L.//Chen, X.//Jiang, N.//Liu, G.//Chen, L.//Xu, J.//Song, H.//Chen, Z.//Ma, Y. 	Draft Genome Sequence of Alicyclobacillus hesperidum Strain URH17-3-68.	J. Bacteriol.	2012	194		6348			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. 		
@D	Wang, Q.//Shao, Z.//Wang, X.//Gao, Y.//Li, M.//Xu, L.//Xu, J.//Wang, L. 	Genetic Study of Capsular Switching between Neisseria meningitidis Sequence Type 7 Serogroup A and C Strains.	Infect. Immun.	2010	78		3883-3888			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. 		
@D	Wang, Q.//Tsukahara, S.//Yamakawa, H.//Takai, K.//Takaku, H. 	pH-independent inhibition of restriction endonuclease cleavage via triple helix formation by oligonucleotides containing 8-oxo-2'-deoxyadenosine.	FEBS Lett.	1994	355		11-14			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. 		
@D	Wang, Q.//Yang, M.//Xiao, J.//Wu, H.//Wang, X.//Lv, Y.//Xu, L.//Zheng, H.//Wang, S.//Zhao, G.//Liu, Q.//Zhang, Y. 	Genome sequence of the versatile fish pathogen Edwardsiella tarda provides insights into its adaptation to broad host ranges and intracellular niches.	PLoS ONE	2009	4		E7646			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. 		
@D	Wang, Q.Y.//Xie, N.Z.//Huang, Y.Y.//Song, L.F.//Du, Q.S.//Yu, B.//Chen, D.//Huang, R.B. 	Genome Sequence of Tumebacillus flagellatus GST4, the First Genome Sequence of a  Species in the Genus Tumebacillus.	Genome Announcements	2014	2		e01189-14			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. 		
@D	Wang, R.//Jin, Y.//Norris, D. 	Identification of a protein that binds to the HO endonuclease recognition sequence at the yeast mating type locus.	Mol. Cell. Biol.	1997	17		770-777			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. 		
@D	Wang, R.//Li, L.//Luo, F.//Liang, W.//Gan, X.//Chen, M. 	Genome Sequence of Streptococcus agalactiae Strain H002, Serotype III, Isolated in China from a Pregnant Woman.	Genome Announcements	2015	3		e01109-15			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. 		
@D	Wang, R.//Tekedar, H.C.//Lawrence, M.L.//Chouljenko, V.N.//Kim, J.//Kim, N.//Kousoulas, K.G.//Hawke, J.P. 	Draft Genome Sequences of Edwardsiella ictaluri Strains LADL11-100 and LADL11-194 Isolated from Zebrafish Danio rerio.	Genome Announcements	2015	3		e01449-15			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. 		
@D	Wang, R.Y.-H.//Shedlarski, J.G.//Farber, M.B.//Kuebbing, D.//Ehrlich, M. 	Two sequence-specific endonucleases from Xanthomonas oryzae.  Characterization and unusual properties.	Biochim. Biophys. Acta	1980	606		371-385			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. 		
@D	Wang, R.Y.-H.//Shenoy, S.//Ehrlich, M. 	DNA methylation inhibits the transfecting activity of replicative-form PhiX174 DNA.	J. Virol.	1984	49		674-679			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. 		
@D	Wang, R.Y.-H.//Zhang, X.-Y.//Ehrlich, M. 	A human DNA-binding protein is methylation-specific and sequence-specific.	Nucleic Acids Res.	1986	14		1599-1614			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. 		
@D	Wang, R.Y.-H.//Zhang, X.-Y.//Khan, R.//Zhou, Y.//Huang, L.-H.//Ehrlich, M. 	Methylated DNA-binding protein from human placenta recognizes specific methylated sites on several prokaryotic DNAs.	Nucleic Acids Res.	1986	14		9843-9860			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. 		
@D	Wang, S.//Chng, K.R.//Wilm, A.//Zhao, S.//Yang, K.L.//Nagarajan, N.//He, J. 	Genomic characterization of three unique Dehalococcoides that respire on persistent polychlorinated biphenyls.	Proc. Natl. Acad. Sci. U. S. A.	2014	111		12103-12108			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. 		
@D	Wang, S.//Chng, K.R.//Wu, C.//Wilm, A.//Nagarajan, N.//He, J. 	Draft Genome Sequence of Polychlorinated Biphenyl-Dechlorinating Dehalococcoides  mccartyi Strain SG1, Which Carries a Circular Putative Plasmid.	Genome Announcements	2014	2		e00901-14			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. 		
@D	Wang, S.//Dong, L.//Zhao, B.//Xu, S.//Wu, K.//Wang, H. 	Draft Genome Sequence of Bacillus sp. Strain YSP-3, a Halophilic, Alkaliphilic Bacterium Isolated from a Salt Lake.	Microbiol. Resour. Announc.	2018	7		e00882-18			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. 		
@D	Wang, S.//Feng, L.//Zhang, D.//Xue, Y.//Xun, Y.//Ke, Y.//Zhu, H. 	Genome Sequence of Lactobacillus plantarum JMCC0013, Isolated from Traditional Chinese Fermented Milk.	Genome Announcements	2018	6		e00407-18			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. 		
@D	Wang, S.//Hao, B.//Li, J.//Gu, H.//Peng, J.//Xie, F.//Zhao, X.//Frech, C.//Chen, N.//Ma, B.//Li, Y. 	Whole-genome sequencing of Mesorhizobium huakuii 7653R provides molecular insights into host specificity and symbiosis island dynamics.	BMC Genomics	2014	15		440			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. 		
@D	Wang, S.//Zhu, H.//He, F.//Luo, Y.//Kang, Z.//Lu, C.//Feng, L.//Lu, X.//Xue, Y.//Wang, H. 	Whole Genome Sequence of the Probiotic Strain Lactobacillus paracasei N1115, Isolated from Traditional Chinese Fermented Milk.	Genome Announcements	2014	2		e00059-14			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. 		
@D	Wang, S.Y.//Wei, J.Q.//Chen, H. 	Complete Genome Sequence of a Putative New Bacterial Strain, I507, Isolated from  the Indian Ocean.	Genome Announcements	2018	6		e00246-18			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. 		
@D	Wang, T.//Sun, B.//Yang, Y.//Zhao, T. 	Genome Sequence of Acidovorax citrulli Group 1 Strain pslb65 Causing Bacterial Fruit Blotch of Melons.	Genome Announcements	2015	3		e00327-15			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%. 		
@D	Wang, T.//Yang, Y.//Zhao, T. 	Genome Sequence of a Pseudomonas syringae pv. tabaci Strain, yuexi-1, Causing Wildfire Disease in Tobacco.	Genome Announcements	2015	3		e00180-15			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%. 		
@D	Wang, T.//Yang, Y.//Zhao, T. 	Genome Sequence of a Copper-Resistant Strain of Acidovorax citrulli Causing Bacterial Fruit Blotch of Melons.	Genome Announcements	2015	3		e00310-15			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%. 		
@D	Wang, T.-S. 	PflI, a restriction endonuclease from Pseudomonas fluorescens Migula.	K'o Hsueh T'ung Pao	1981	26		815-817			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. 		
@D	Wang, W.//Liu, F.//Peng, Z.//Li, F.//Ma, A. 	Complete Genome Sequence of Salmonella enterica subsp. enterica Serovar Indiana C629, a Carbapenem-Resistant Bacterium Isolated from Chicken Carcass in China.	Genome Announcements	2016	4		e00662-16			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. 		
@D	Wang, W.//Ma, T.//Ren, Y.//Li, G. 	Draft Genome Sequence of a Benzothiophene-Desulfurizing Bacterium, Gordona terrae Strain C-6.	Genome Announcements	2013	1		e00381-13			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. 		
@D	Wang, W.//Zheng, S.S.//Sharshov, K.//Sun, H.//Wu, X.Q.//Yang, F.//Wang, X.L.//Li, L.X. 	Draft Genome Sequence of Staphylococcus hominis BHG17 Isolated from Wild Bar-Headed Goose (Anser indicus) Feces.	Genome Announcements	2017	5		e01552-16			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. 		
@D	Wang, W.//Zheng, S.S.//Sun, H.//Cao, J.//Yang, F.//Wang, X.L.//Li, L.X. 	Draft Genome Sequence of Bacillus megaterium BHG1.1, a Strain Isolated from Bar-Headed Goose (Anser indicus) Feces on the Qinghai-Tibet Plateau.	Genome Announcements	2016	4		e00317-16			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. 		
@D	Wang, X.//Chen, M.//Xiao, J.//Hao, L.//Crowley, D.E.//Zhang, Z.//Yu, J.//Huang, N.//Huo, M.//Wu, J. 	Genome Sequence Analysis of the Naphthenic Acid Degrading and Metal Resistant Bacterium Cupriavidus gilardii CR3.	PLoS ONE	2015	10		E0132881			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. 		
@D	Wang, X.//Ding, C.//Han, X.//Wang, S.//Yue, J.//Hou, W.//Cao, S.//Zou, J.//Yu, S. 	Complete Genome Sequence of Riemerella anatipestifer Serotype 1 Strain CH3.	Genome Announcements	2015	3		e01594-14			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. 		
@D	Wang, X.//Ding, C.//Wang, S.//Han, X.//Yu, S. 	Whole-Genome Sequence Analysis and Genome-Wide Virulence Gene Identification of Riemerella anatipestifer Strain Yb2.	Appl. Environ. Microbiol.	2015	81		5093-5102			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. 		
@D	Wang, X.//Gao, Z.//Xu, X.//Ruan, L. 	Complete Genome Sequence of Thermococcus sp. Strain 4557, a Hyperthermophilic Archaeon Isolated from a Deep-Sea Hydrothermal Vent  Area.	J. Bacteriol.	2011	193		5544-5545			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%. 		
@D	Wang, X.//Greenfield, P.//Li, D.//Hendry, P.//Volk, H.//Sutherland, T.D. 	Complete Genome Sequence of a Nonculturable Methanococcus maripaludis Strain Extracted in a Metagenomic Survey of Petroleum Reservoir Fluids.	J. Bacteriol.	2011	193		5595			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. 		
@D	Wang, X.//Hao, H.//Xu, Z.//Zheng, H.//Liu, C.//Wei, L.//Zhang, R.//Bi, D.//Chen, H.//Tan, C. 	Plasmid-mediated multidrug resistance and virulence in an avian pathogenic Escherichia coli strain isolated in China.	J. Glob. Antimicrob. Resist.	2014	2		57-58			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). 		
@D	Wang, X.//Hinshaw, K.C.//Macdonald, S.J.//Chandler, J.R. 	Draft Genome Sequence of Chromobacterium violaceum Strain CV017.	Genome Announcements	2016	4		e00080-16			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. 		
@D	Wang, X.//Jin, D.//Zhou, L.//Wu, L.//An, W.//Chen, Y.//Zhao, L. 	Draft Genome Sequence of Brevibacillus panacihumi Strain W25, a Halotolerant Hydrocarbon-Degrading Bacterium.	Genome Announcements	2014	2		e01215-13			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. 		
@D	Wang, X.//Jin, D.//Zhou, L.//Wu, L.//An, W.//Zhao, L. 	Draft Genome Sequence of Gordonia alkanivorans Strain CGMCC6845, a Halotolerant Hydrocarbon-Degrading Bacterium.	Genome Announcements	2014	2		e01274-13			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. 		
@D	Wang, X.//Jin, D.//Zhou, L.//Wu, L.//An, W.//Zhao, L. 	Draft Genome Sequence of Advenella kashmirensis Strain W13003, a Polycyclic Aromatic Hydrocarbon-Degrading Bacterium.	Genome Announcements	2014	2		e00003-14			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. 		
@D	Wang, X.//Jin, D.//Zhou, L.//Wu, L.//Qi, L.//Li, C.//An, W.//Chen, Y. 	Draft Genome Sequence of Halotolerant Polycyclic Aromatic Hydrocarbon-Degrading Pseudomonas bauzanensis Strain W13Z2.	Genome Announcements	2014	2		e01049-14			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. 		
@D	Wang, X.//Jin, D.//Zhou, L.//Zhang, Z. 	Draft Genome Sequence of Aquamicrobium defluvii Strain W13Z1, a Psychrotolerant Halotolerant Hydrocarbon-Degrading Bacterium.	Genome Announcements	2015	3		e00984-15			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. 		
@D	Wang, X.//Jin, D.//Zhou, L.//Zhang, Z. 	Draft Genome Sequence of Ochrobactrum anthropi Strain W13P3, a Halotolerant Polycyclic Aromatic Hydrocarbon-Degrading Bacterium.	Genome Announcements	2015	3		e00867-15			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. 		
@D	Wang, X.//Jin, D.//Zhou, L.//Zhang, Z. 	Draft Genome Sequence of Pannonibacter phragmitetus Strain CGMCC9175, a Halotolerant Polycyclic Aromatic Hydrocarbon-Degrading Bacterium.	Genome Announcements	2016	4		e01675-15			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. 		
@D	Wang, X.//Li, Y.//Jing, H.//Ren, Y.//Zhou, Z.//Wang, S.//Kan, B.//Xu, J.//Wang, L. 	Complete Genome Sequence of a Yersinia enterocolitica 'Old World' (3/O:9) Strain and Comparison with the 'New World' (1B/O:8) Strain.	J. Clin. Microbiol.	2011	49		1251-1259			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. 		
@D	Wang, X.//Liu, X.//Hou, T.//Li, W.//Li, F. 	Highly sensitive homogeneous electrochemical assay for methyltransferase activity based on methylation-responsive exonuclease III-assisted signal amplification.	Sens. Actuators B Chem.	2015	208		575-580			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. 		
@D	Wang, X.//Luo, C.//Chen, Z. 	Genome Sequence of the Plant Growth-Promoting Rhizobacterium Bacillus sp. Strain  916.	J. Bacteriol.	2012	194		5467-5468			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. 		
@D	Wang, X.//Luo, Y.//Liu, D.//Wang, J.//Wei, S.//Zhao, L. 	Complete genome sequence of the Robinia pseudoacacia L. symbiont Mesorhizobium amorphae CCNWGS0123.	Standards in Genomic Sciences	2018	13		18			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. 		
@D	Wang, X.//Tao, F.//Gai, Z.//Tang, H.//Xu, P. 	Genome Sequence of the Welan Gum-Producing Strain Sphingomonas sp. ATCC 31555.	J. Bacteriol.	2012	194		5989-5990			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. 		
@D	Wang, X.//Wang, Q.//Zhang, W.//Wang, Y.//Li, L.//Wen, T.//Zhang, T.//Zhang, Y.//Xu, J.//Hu, J.//Li, S.//Liu, L.//Liu, J.//Jiang, W.//Tian, J.//Li, Y.//Schuler, D.//Wang, L.//Li, J. 	Complete Genome Sequence of Magnetospirillum gryphiswaldense MSR-1.	Genome Announcements	2014	2		e00171-14			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. 		
@D	Wang, X.//Wei, L.//Wang, B.//Zhang, R.//Liu, C.//Bi, D.//Chen, H.//Tan, C. 	Complete genome sequence and characterization of avian pathogenic Escherichia coli field isolate ACN001.	Standards in Genomic Sciences	2016	11		13			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. 		
@D	Wang, X.//Zhang, Z.//Hao, Q.//Wu, J.//Xiao, J.//Jing, H. 	Complete Genome Sequence of Acinetobacter baumannii ZW85-1.	Genome Announcements	2014	2		e01083-13			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. 		
@D	Wang, X.//Zhang, Z.//Jin, D.//Zhou, L.//Wu, L.//Li, C.//Zhao, L.//An, W.//Chen, Y. 	Draft Genome Sequence of Brachybacterium phenoliresistens Strain W13A50, a Halotolerant Hydrocarbon-Degrading Bacterium.	Genome Announcements	2014	2		e00899-14			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. 		
@D	Wang, X.//Zhu, D.//Wang, M.//Cheng, A.//Jia, R.//Zhou, Y.//Chen, Z.//Luo, Q.//Liu, F.//Wang, Y.//Chen, X.Y. 	Complete Genome Sequence of Riemerella anatipestifer Reference Strain.	J. Bacteriol.	2012	194		3270-3271			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%. 		
@D	Wang, X.J.//Yan, Y.J.//Zhang, B.//An, J.//Wang, J.J.//Tian, J.//Jiang, L.//Chen, Y.H.//Huang, S.X.//Yin, M.//Zhang, J.//Gao, A.L.//Liu, C.X.//Zhu, Z.X.//Xiang, W.S. 	Genome Sequence of the Milbemycins-producing Bacterium Streptomyces bingchenggensis.	J. Bacteriol.	2010	192		4526-4527			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. 		
@D	Wang, X.Q.//Showmaker, K.C.//Yu, X.Q.//Bi, T.//Hsu, C.Y.//Baird, S.M.//Peterson, D.G.//Li, X.D.//Lu, S.E. 	Draft Genome Sequence of Burkholderia pyrrocinia Lyc2, a Biological Control Strain That Can Suppress Multiple Plant Microbial Pathogens.	Genome Announcements	2014	2		e00991-14			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. 		
@D	Wang, Y.//Chen, C.//Ai, L.//Zhou, F.//Zhou, Z.//Wang, L.//Zhang, H.//Chen, W.//Guo, B. 	Complete genome sequence of probiotic Lactobacillus plantarum ST-III.	J. Bacteriol.	2010	193		313-314			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. 		
@D	Wang, Y.//Chen, W.//He, L.//Wang, Q.//Sheng, X.F. 	Draft Genome Sequence of Ensifer adhaerens M78, a Mineral-Weathering Bacterium Isolated from Soil.	Genome Announcements	2016	4		e00969-16			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. 		
@D	Wang, Y.//Du, Y.//Yuan, Y.//Guo, Y.//Wang, J.//Li, T.//Chang, D.//Liu, Y.//Jiang, X.//Dai, W.//Liu, C. 	Draft Genome Sequence of Serratia marcescens Strain LCT-SM166, a Space Flight Strain with a Specific Carbon Source Utilization Pattern.	Genome Announcements	2014	2		e00069-14			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. 		
@D	Wang, Y.//He, K.//Jiang, Y.//Shen, J.//Yu, B. 	Complete Genome Sequence of Pontibacter akesuensis Strain AKS 1T, Which Exhibits  Robust Nutrient Metabolism in Harsh Environments.	Genome Announcements	2016	4		e00997-16			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. 		
@D	Wang, Y.//Jorda, M.//Jones, P.L.//Maleszka, R.//Ling, X.//Robertson, H.M.//Mizzen, C.A.//Peinado, M.A.//Robinson, G.E. 	Functional CpG methylation system in a social insect.	Science	2006	314		645-647			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. 		
@D	Wang, Y.//Ke, Y.//Gao, G.//Zhen, Q.//Yuan, X.//Wang, Z.//Xu, J.//Li, T.//Wang, D.//Huang, L.//Xu, X.//Chen, Z. 	Complete Genome Sequence of Brucella abortus 134, a Biovar 1 Strain Isolated from Human.	J. Bacteriol.	2012	194		6658			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. 		
@D	Wang, Y.//Ke, Y.//Zhen, Q.//Yuan, X.//Xu, J.//Qiu, Y.//Wang, Z.//Li, T.//Wang, D.//Huang, L.//Chen, Z. 	Complete Genome Sequence of Brucella canis BCB018, a Strain Isolated from a Human Patient.	J. Bacteriol.	2012	194		6697-6698			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. 		
@D	Wang, Y.//Li, C.//Gao, C.//Ma, C.//Xu, P. 	Genome Sequence of the Nonpathogenic Pseudomonas aeruginosa Strain ATCC 15442.	Genome Announcements	2014	2		e00421-14			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. 		
@D	Wang, Y.//Liu, H.//Liu, K.//Wang, C.//Ma, H.//Li, Y.//Hou, Q.//Liu, F.//Zhang, T.//Wang, H.//Wang, B.//Ma, J.//Ge, R.//Xu, B.//Yao, G.//Xu, W.//Fan, L.//Ding, Y.//Du, B. 	Complete Genome Sequence of Bacillus paralicheniformis MDJK30, a Plant Growth-Promoting Rhizobacterium with Antifungal Activity.	Genome Announcements	2017	5		e00577-17			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. 		
@D	Wang, Y.//Luo, X.//Zhang, L. 	Draft Genome Sequence of Glycomyces fuscus TRM 49117, Isolated from a Hypersaline Soil Sample.	Genome Announcements	2017	5		e01258-17			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. 		
@D	Wang, Y.//Qin, Y.//Kot, W.//Zhang, F.//Zheng, S.//Wang, G.//Hansen, L.H.//Rensing, C. 	Genome Sequence of Selenium-Solubilizing Bacterium Caulobacter vibrioides T5M6.	Genome Announcements	2016	4		e01721-15			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. 		
@D	Wang, Y.//Ran, S.//Yang, G. 	Single molecular investigation of DNA looping and aggregation by restriction endonuclease BspMI.	Sci. Rep.	2014	4		5897			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). 		
@D	Wang, Y.//Rocha, E.P.C.//Leung, F.C.C.//Danchin, A. 	Cytosine methylation is not the major factor inducing CpG dinucleotide deficiency in bacterial genomes.	J. Mol. Evol.	2004	58		692-700			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. 		
@D	Wang, Y.//Roos, K.P.//Taylor, D.E. 	Transformation of Helicobacter pylori  by chromosomal metronidazole resistance and by a plasmid with a selectable chloramphenicol resistance marker.	J. Gen. Microbiol.	1993	139		2485-2493			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. 		
@D	Wang, Y.//Tao, F.//Li, C.//Li, L.//Xu, P. 	Genome Sequence of Klebsiella pneumoniae Strain ATCC 25955, an Oxygen-Insensitive Producer of 1,3-Propanediol.	Genome Announcements	2013	1		e00587-13			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. 		
@D	Wang, Y.//Tao, F.//Tang, H.//Xu, P. 	Genome Sequence of Clostridium diolis Strain DSM 15410, a Promising Natural Producer of 1,3-Propanediol.	Genome Announcements	2013	1		e00542-13			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. 		
@D	Wang, Y.//Wang, J.//Ahmed, Z.//Bai, X.//Wang, J. 	Complete Genome Sequence of Lactobacillus kefiranofaciens ZW3.	J. Bacteriol.	2011	193		4280-4281			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. 		
@D	Wang, Y.//Wang, X.//Greenfield, P.//Jin, D.//Bai, Z. 	Draft Genome Sequence of Bacillus amyloliquefaciens EBL11, a New Strain of Plant  Growth-Promoting Bacterium Isolated from Rice Rhizosphere.	Genome Announcements	2014	2		e00732-14			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). 		
@D	Wang, Y.//Wang, Y.//Lang, C.//Wei, D.//Xu, P.//Xie, J. 	Genome Sequence of Lactobacillus curieae CCTCC M 2011381T, a Novel Producer of Gamma-aminobutyric Acid.	Genome Announcements	2015	3		e00552-15			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. 		
@D	Wang, Y.//Yuan, Y.//Zhou, L.//Su, Q.//Fang, X.//Li, T.//Wang, J.//Chang, D.//Su, L.//Xu, G.//Guo, Y.//Yang, R.//Liu, C. 	Draft Genome Sequence of Serratia marcescens Strain LCT-SM213.	J. Bacteriol.	2012	194		4477-4478			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. 		
@D	Wang, Y.//Zhang, R.//Zheng, Q.//Jiao, N. 	Draft Genome Sequences of Two Marine Phototrophic Bacteria, Erythrobacter longus  Strain DSM 6997 and Erythrobacter litoralis Strain DSM 8509.	Genome Announcements	2014	2		e00677-14			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. 		
@D	Wang, Y.//Zhang, T.//Lin, W.//Zhang, B.//Cai, Y.//Yang, C.//Li, J.//Xu, H.//Pan, Y. 	Complete Genome Sequence of Magnetospirillum sp. Strain XM-1, Isolated from the Xi'an City Moat, China.	Genome Announcements	2016	4		e01171-16			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. 		
@D	Wang, Y.//Zheng, Y.//Wang, M.//Gao, Y.//Xiao, Y.//Peng, H. 	Non-contiguous finished genome sequence of Anoxybacillus flavithermus subsp. yunnanensis type strain (E13(T)), a strictly thermophilic and organic  solvent-tolerant bacterium.	Standards in Genomic Sciences	2014	9		735-743			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. 		
@D	Wang, Y.//Zhuang, X.//Zhong, Y.//Zhang, C.//Zhang, Y.//Zeng, L.//Zhu, Y.//He, P.//Dong, K.//Pal, U.//Guo, X.//Qin, J. 	Distribution of Plasmids in Distinct Leptospira Pathogenic Species.	PLoS Neglected Trop. Dis.	2015	9		E0004220			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. 		
@D	Wang, Y.H.//He, X.X.//Wang, K.M.//Su, J.//Chen, Z.F.//Yan, G.P.//Du, Y.D. 	A label-free electrochemical assay for methyltransferase activity detection based on the controllable assembly of single wall carbon nanotubes.	Biosensors and Bioelectronics	2013	41		238-243			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. 		
@D	Wang, Y.P.//Jarjour, J.//Boissel, S.//Thyme, S.//Khan, I.//Pangallo, J.//Baker, D.//Stoddard, B.//Scharenberg, A.M.//Rawlings, D.J. 	Engineering an XID-Site Specific I-AniI Homing Endonuclease through Combination of Rational Design and Directed Evolution.	Mol. Ther.	2013	21		S122-S123			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. 		
@D	Wang, Z.//Chang, X.//Yang, X.//Pan, L.//Dai, J. 	Draft Genome Sequence of Polaromonas glacialis Strain R3-9, a Psychrotolerant Bacterium Isolated from Arctic Glacial Foreland.	Genome Announcements	2014	2		e00695-14			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. 		
@D	Wang, Z.//Eddie, B.J.//Malanoski, A.P.//Hervey, W.J. IV//Lin, B.//Strycharz-Glaven, S.M. 	Complete Genome Sequence of Marinobacter sp. CP1, Isolated from a Self-Regenerating Biocathode Biofilm.	Genome Announcements	2015	3		e01103-15			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. 		
@D	Wang, Z.//Eddie, B.J.//Malanoski, A.P.//Hervey, W.J. IV//Lin, B.//Strycharz-Glaven, S.M. 	Complete Genome Sequence of Labrenzia sp. Strain CP4, Isolated from a Self-Regenerating Biocathode Biofilm.	Genome Announcements	2016	4		e00354-16			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. 		
@D	Wang, Z.//Hervey, W.J. IV//Kim, S.//Lin, B.//Vora, G.J. 	Complete Genome Sequence of the Bioluminescent Marine Bacterium Vibrio harveyi ATCC 33843 (392 [MAV]).	Genome Announcements	2015	3		e01493-14			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]). 		
@D	Wang, Z.//Kadouri, D.//Wu, M. 	Genomic Insights into An Obligate Epibiotic Bacterial Predator: Micavibrio aeruginosavorus ARL-13.	BMC Genomics	2011	12		453			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. 		
@D	Wang, Z.//Lin, B.//Hervey, W.J. IV//Vora, G.J. 	Draft Genome Sequence of the Fast-Growing Marine Bacterium Vibrio natriegens Strain ATCC 14048.	Genome Announcements	2013	1		e00589-13			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. 		
@D	Wang, Z.//Wu, M. 	Complete Genome Sequence of the Endosymbiont of Acanthamoeba Strain UWC8, an Amoeba Endosymbiont Belonging to the 'Candidatus Midichloriaceae' Family in  Rickettsiales.	Genome Announcements	2014	2		e00791-14			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. 		
@D	Wang, Z.-G.//Wu, J.-X. 	DNA methyltransferases: classification, functions and research progress.	Yichuan	2009	31		903-912			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. 		
@D	Wang, Z.G.//Wu, Z.//Xu, S.L.//Zha, J. 	Genome Sequence of the Human-Pathogenetic Bacterium Vibrio vulnificus B2.	J. Bacteriol.	2012	194		7019			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. 		
@D	Wani, A.A.//Stephens, R.E.//D'Ambrosio, S.M.//Hart, R.W. 	A new sequence-specific endonuclease from Micrococcus radiodurans.	Fed. Proc.	1981	40		1848			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. 		
@D	Wani, A.A.//Stephens, R.E.//D'Ambrosio, S.M.//Hart, R.W. 	A sequence specific endonuclease from Micrococcus radiodurans.	Biochim. Biophys. Acta	1982	697		178-184			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. 		
@D	Wank, H.//SanFilippo, J.//Singh, R.N.//Matsuura, M.//Lambowitz, A.M. 	A reverse transcriptase/maturase promotes splicing by binding at its own coding segment in a group II intron RNA.	Mol. Cell	1999	4		239-250			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. 		
@D	Wannemuehler, M.J.//Overstreet, A.M.//Ward, D.V.//Phillips, G.J. 	Draft genome sequences of the altered schaedler flora, a defined bacterial community from gnotobiotic mice.	Genome Announcements	2014	2		e00287-14			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. 		
@D	Wanzala, S.I.//Nakavuma, J.//Travis, D.A.//Kia, P.//Ogwang, S.//Sreevatsan, S. 	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.	Genome Announcements	2015	3		e01102-15			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. 		
@D	Ward, A.C.//Davidson, B.E.//Hillier, A.J.//Powell, I.B. 	Conjugally transferable phage resistance activities from Lactococcus lactis DRC1.	J. Dairy Sci.	1992	75		683-691			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. 		
@D	Ward, B. 	Type IIS restriction enzyme footprint I.  Measurement of a triple helix dissociation constant with Eco57I at 25oC.	Nucleic Acids Res.	1996	24		2435-2440			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. 		
@D	Ward, C.M.//Baxter, S.W. 	Draft Genome Assembly of a Wolbachia Endosymbiont of Plutella australiana.	Genome Announcements	2017	5		e01134-17			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). 		
@D	Ward, L.J.H.//Heap, H.A.//Kelly, W.J. 	Characterization of closely related lactococcal starter strains which show differing patterns of bacteriophage sensitivity.	J. Appl. Microbiol.	2004	96		144-148			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. 		
@D	Ward, L.M.//Hemp, J.//Pace, L.A.//Fischer, W.W. 	Draft Genome Sequence of Leptolinea tardivitalis YMTK-2, a Mesophilic Anaerobe from the Chloroflexi Class Anaerolineae.	Genome Announcements	2015	3		e01356-15			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. 		
@D	Ward, L.M.//Hemp, J.//Pace, L.A.//Fischer, W.W. 	Draft Genome Sequence of Herpetosiphon geysericola GC-42, a Nonphototrophic Member of the Chloroflexi Class Chloroflexia.	Genome Announcements	2015	3		e01352-15			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. 		
@D	Ward, L.M.//McGlynn, S.E.//Fischer, W.W. 	Draft Genome Sequence of a Divergent Anaerobic Member of the Chloroflexi Class Ardenticatenia from a Sulfidic Hot Spring.	Genome Announcements	2018	6		e00571-18			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. 		
@D	Ward, L.M.//McGlynn, S.E.//Fischer, W.W. 	Draft Genome Sequences of Two Basal Members of the Anaerolineae Class of Chloroflexi from a Sulfidic Hot Spring.	Genome Announcements	2018	6		e00570-18			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. 		
@D	Ward, L.M.//McGlynn, S.E.//Fischer, W.W. 	Draft Genome Sequence of Chloracidobacterium sp. CP2_5A, a Phototrophic Member of the Phylum Acidobacteria Recovered from a Japanese Hot Spring.	Genome Announcements	2017	5		e00821-17			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. 		
@D	Ward, L.M.//McGlynn, S.E.//Fischer, W.W. 	Draft Genome Sequences of a Novel Lineage of Armatimonadetes Recovered from Japanese Hot Springs.	Genome Announcements	2017	5		e00820-17			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. 		
@D	Ward, N. et al. 	Genomic Insights into Methanotrophy: The Complete Genome Sequence of Methylococcus capsulatus (Bath).	PLoS Biology	2004	2		1616-1628			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. 		
@D	Ward, N.L. et al. 	Three genomes from the phylum Acidobacteria provide insight into the lifestyles of these microorganisms in soils.	Appl. Environ. Microbiol.	2009	75		2046-2056			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. 		
@D	Waring, R.B.//Davies, R.W.//Scazzocchio, C.//Brown, T.A. 	Internal structure of the mitochondrial intron of Aspergillus nidulans.	Proc. Natl. Acad. Sci. U. S. A.	1982	79		6332-6336			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. 		
@D	Warncke, S.//Gegout, A.//Carell, T. 	Phosphorothioation of Oligonucleotides Strongly Influences the Inhibition of Bacterial (M.Hhal) and Human (Dnmt1) DNA Methyltransferases.	Chembiochem	2009	10		728-734			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. 		
@D	Warnecke, F. et al. 	Metagenomic and functional analysis of hindgut microbiota of a wood-feeding higher termite.	Nature	2007	450		560-565			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. 		
@D	Warnecke, P.M.//Bestor, T.H. 	Cytosine methylation and human cancer.	Curr. Opin. Oncol.	2000	12		68-73			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. 		
@D	Warnecke, P.M.//Biniszkiewicz, D.//Jaenisch, R.//Frommer, M.//Clark, S.J. 	Sequence-specific methylation of the Mouse H19 gene in embryonic cells deficient in the Dnmt-1 gene.	Dev. Genet.	1998	22		111-121			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. 		
@D	Warren, R.A.J. 	Modified Bases in Bacteriophage DNAs.	Annu. Rev. Microbiol.	1980	34		137-158			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. 		
@D	Warren, W.//Merion, M. 	Rapid HPLC purification of a restriction enzyme from Sphaerotilus sp.	BioChromatography	1988	3		225-230			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. 		
@D	Waschkau, B.//Waldeck, J.//Wieland, S.//Eichstadt, R.//Meinhardt, F. 	Generation of readily transformable Bacillus licheniformis mutants.	Appl. Microbiol. Biotechnol.	2008	78		181-188			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. 		
@D	Wasels, F.//Barbanti, F.//Spigaglia, P. 	Draft Genome Sequence of Clostridium difficile Strain IT1118, an Epidemic Isolate Belonging to the Emerging PCR Ribotype 018.	Genome Announcements	2016	4		e00717-16			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. 		
@D	Wasels, F.//Clement, B.//Lopes, F.N. 	Draft Genome Sequence of the Butyric Acid Producer Clostridium tyrobutyricum Strain CIP I-776 (IFP923).	Genome Announcements	2016	4		e00048-16			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. 		
@D	Wassenegger, M. 	RNA-directed DNA methylation.	Plant Mol. Biol.	2000	43		203-220			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. 		
@D	Watabe, H.//Iino, T.//Kaneko, T.//Shibata, T.//Ando, T. 	A new class of site-specific endodeoxyribonucleases.	J. Biol. Chem.	1983	258		4663-4665			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. 		
@D	Watabe, H.//Shibata, T.//Ando, T. 	Site-specific endo-deoxyribonucleases in eukaryotes: endonucleases of yeasts, Saccharomyces and Pichia.	J. Biochem. (Tokyo)	1981	90		1623-1632			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. 		
@D	Watabe, H.-O.//Shibata, T.//Iino, T.//Ando, T. 	Purification of a eukaryotic site-specific endonuclease, Endo.SceI, from Saccharomyces cerevisiae and effectors on its specificity and activity.	J. Biochem. (Tokyo)	1984	95		1677-1690			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. 		
@D	Watahiki, S.//Kimura, N. 	Draft Genome Sequence of a Caffeine-Utilizing Bacterium, Cupriavidus sp. Strain D384.	Genome Announcements	2017	5		e00370-17			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. 		
@D	Watanabe, K.//Suzuki, H.//Nakao, R.//Shimizu, T.//Watarai, M. 	Draft Genome Sequences of Five Legionella pneumophila Strains Isolated from Environmental Water Samples.	Genome Announcements	2015	3		e00474-15			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. 		
@D	Watanabe, K.I.//Ehara, M.//Inagaki, Y.//Ohama, T. 	Distinctive origins of group I introns found in the COXI genes of three green algae.	Gene	1998	213		1-7			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. 		
@D	Watanabe, M.//Kojima, H.//Fukui, M. 	Draft genome sequence of Desulfoplanes formicivorans Pf12BT, a sulfate-reducing bacterium of the family Desulfomicrobiaceae.	Standards in Genomic Sciences	2017	12		34			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. 		
@D	Watanabe, M.//Tokizawa, R.//Kojima, H.//Fukui, M. 	High-quality draft genome sequence of Effusibacillus lacus strain skLN1(T), facultative anaerobic spore-former isolated from freshwater lake sediment.	Standards in Genomic Sciences	2017	12		76			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%. 		
@D	Watanabe, M.//Yuzawa, H.//Handa, N.//Kobayashi, I. 	Hyperthermophilic DNA methyltransferase M.Pabl from the archaeon Pyrococcus abyssi.	Appl. Environ. Microbiol.	2006	72		5367-5375			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. 		
@D	Watanabe, N.//Takasaki, Y.//Sato, C.//Ando, S.//Tanaka, I. 	Structures of restriction endonuclease HindIII in complex with its cognate DNA and divalent cations.	Acta Crystallogr. D Biol. Crystallogr.	2009	65		1326-1333			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. 		
@D	Watanabe, S.//Sasahara, T.//Arai, N.//Sasaki, K.//Aiba, Y.//Sato'o, Y.//Cui, L. 	Complete Genome Sequence of Streptococcus pyogenes Strain JMUB1235 Isolated from  an Acute Phlegmonous Gastritis Patient.	Genome Announcements	2016	4		e01133-16			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. 		
@D	Watanabe, S.//Shiwa, Y.//Itaya, M.//Yoshikawa, H. 	Complete Sequence of the First Chimera Genome Constructed by Cloning the Whole Genome of Synechocystis Strain PCC6803 into the Bacillus subtilis 168 Genome.	J. Bacteriol.	2012	194		7007			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. 		
@D	Watanabe, T.//Kojima, H.//Fukui, M. 	Draft Genome Sequence of Mizugakiibacter sediminis skMP5T.	Genome Announcements	2015	3		e01185-15			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). 		
@D	Watanabe, T.//Kojima, H.//Fukui, M. 	Draft Genome Sequence of a Sulfur-Oxidizing Autotroph, Sulfuricella sp. Strain T08, Isolated from a Freshwater Lake.	Genome Announcements	2015	3		e00498-15			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. 		
@D	Watanabe, T.//Kojima, H.//Fukui, M. 	Draft genome sequence of a psychrotolerant sulfur-oxidizing bacterium, Sulfuricella denitrificans skB26, and proteomic insights into cold adaptation.	Appl. Environ. Microbiol.	2012	78		6545-6549			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. 		
@D	Watanabe, T.//Maruyama, F.//Nozawa, T.//Aoki, A.//Okano, S.//Shibata, Y.//Oshima, K.//Kurokawa, K.//Hattori, M.//Nakagawa, I.//Abiko, Y. 	Complete Genome Sequence of the Bacterium Porphyromonas gingivalis TDC60, Which Causes Periodontal Disease.	J. Bacteriol.	2011	193		4259-4260			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. 		
@D	Watanabe, T.//Nishida, H.//Ogata, C.//Arai, T.//Sato, S. 	Episome-mediated transfer of drug resistance in enterobacteriaceae.  VII.  Two types of naturally occurring R factors.	J. Bacteriol.	1964	88		716-726			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. 		
@D	Watanabe, T.//Takano, T.//Arai, T.//Nishida, H.//Sato, S. 	Episome-mediated transfer of drug resistance in Enterobacteriaceae.   X.  Restriction and modification of phages by fi- R factors.	J. Bacteriol.	1966	92		477-486			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. 		
@D	Watanabe, T.//Yamazoe, A.//Hosoyama, A.//Fujihara, H.//Suenaga, H.//Hirose, J.//Futagami, T.//Goto, M.//Kimura, N.//Furukawa, K. 	Draft Genome Sequence of Pseudomonas toyotomiensis KF710, a Polychlorinated Biphenyl-Degrading Bacterium Isolated from Biphenyl-Contaminated Soil.	Genome Announcements	2015	3		e00223-15			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. 		
@D	Watanabe, T.//Yamazoe, A.//Hosoyama, A.//Fujihara, H.//Suenaga, H.//Hirose, J.//Futagami, T.//Goto, M.//Kimura, N.//Furukawa, K. 	Draft Genome Sequence of Cupriavidus pauculus Strain KF709, a Biphenyl-Utilizing  Bacterium Isolated from Biphenyl-Contaminated Soil.	Genome Announcements	2015	3		e00222-15			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. 		
@D	Waterbury, P.G.//Rehfuss, R.P.//Carroll, W.T.//Smardon, A.M.//Faldasz, B.D.//Huckaby, C.S.//Lane, M.J. 	Specific cleavage of the yeast genome at 5'-ATCGATCGAT-3'.	Nucleic Acids Res.	1989	17		9493			M.ClaI followed by DpnI cleavage.  Conditions are described for complete cleavage of yeast DNA. 		
@D	Waterman, S.R.//Hackett, J.//Manning, P.A. 	Isolation of a restriction-less mutant and development of a shuttle vector for the genetic analysis of Campylobacter hyointestinalis.	Gene	1993	125		19-24			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. 		
@D	Waters, E. et al. 	The genome of Nanoarchaeum equitans: Insights into early archaeal evolution and derived parasitism.	Proc. Natl. Acad. Sci. U. S. A.	2003	100		12984-12988			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. 		
@D	Waters, T.R.//Connolly, B.A. 	Continuous spectrophotometric assay for restriction endonucleases using synthetic oligodeoxynucleotides and based on the hyperchromic effect.	Anal. Biochem.	1992	204		204-209			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. 		
@D	Waters, T.R.//Connolly, B.A. 	Interaction of the restriction endonuclease EcoRV with the deoxyguanosine and deoxycytidine bases in its recognition sequence.	Biochemistry	1994	33		1812-1819			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. 		
@D	Watrob, H.//Liu, W.//Chen, Y.//Bartlett, S.G.//Jen-Jacobson, L.//Barkley, M.D. 	Solution conformation of EcoRI restriction endonuclease changes upon binding of cognate DNA and Mg2+ cofactor.	Biochemistry	2001	40		683-692			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. 		
@D	Watson, M.A.//Gowers, D.M.//Halford, S.E. 	Alternative geometries of DNA looping: an analysis using the SfiI endonuclease.	J. Mol. Biol.	2000	298		461-475			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. 		
@D	Watson, M.E.//Jarisch, J.//Smith, A.L. 	Inactivation of deoxyadenosine methyltransferase (dam) attenuates Haemophilus influenzae virulence.	Mol. Microbiol.	2004	53		651-664			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. 		
@D	Watson, R.//Zuker, M.//Martin, S.M.//Visentin, L.P. 	A new site-specific endonuclease from Neisseria cinerea.	FEBS Lett.	1980	118		47-50			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. 		
@D	Watson, R.J.//Schildkraut, I.//Qiang, B.-Q.//Martin, S.M.//Visentin, L.P. 	NdeI: a restriction endonuclease from Neisseria denitrificans which cleaves DNA at 5'-CATATG-3' sequences.	FEBS Lett.	1982	150		114-116			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'. 		
@D	Watt, A.E.//Browning, G.F.//Legione, A.R.//Bushell, R.N.//Stent, A.//Cutler, R.S.//Young, N.D.//Marenda, M.S. 	A novel Glaesserella sp. isolated from severe respiratory infections in pigs has a mosaic genome with virulence factors putatively acquired by horizontal transfer.	Appl. Environ. Microbiol.	2018	84		0			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. 		
@D	Watve, S.S.//Chande, A.T.//Rishishwar, L.//Marino-Ramirez, L.//Jordan, I.K.//Hammer, B.K. 	Whole-Genome Sequences of 26 Vibrio cholerae Isolates.	Genome Announcements	2016	4		e01396-16			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. 		
@D	Waugh, D.S.//Sauer, R.T. 	A novel class of FokI restriction endonuclease mutants that cleave hemi-methylated substrates.	J. Biol. Chem.	1994	269		12298-12303			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. 		
@D	Waugh, D.S.//Sauer, R.T. 	Single amino acid substitutions uncouple the DNA binding and strand scission activities of Fok I endonuclease.	Proc. Natl. Acad. Sci. U. S. A.	1993	90		9596-9600			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. 		
@D	Wawrik, C.B.//Callaghan, A.V.//Stamps, B.W.//Wawrik, B. 	Genome Sequence of Youngiibacter fragilis, the Type Strain of the Genus Youngiibacter.	Genome Announcements	2014	2		e01183-13			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. 		
@D	Wayne, J.//Holden, M.//Xu, S.-Y. 	The Tsp45I restriction-modification system is plasmid-borne within its thermophilic host.	Gene	1997	202		83-88			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. 		
@D	Webb, A.L.//Kruczkiewicz, P.//Selinger, L.B.//Inglis, G.D.//Taboada, E.N. 	Development of a comparative genomic fingerprinting assay for rapid and high resolution genotyping of Arcobacter butzleri.	BMC Microbiol.	2015	15		94			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. 		
@D	Webb, H.//Kaszubska, W.//Gumport, R.I. 	Overexpression of RsrI DNA methyltransferase in E. coli.	FASEB J.	1990	4		A1795			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. 		
@D	Webb, J.L.//King, G.//Ternent, D.//Titheradge, A.J.B.//Murray, N.E. 	Restriction by EcoKI is enhanced by cooperative interactions between target sequences and is dependent on DEAD box motifs.	EMBO J.	1996	15		2003-2009			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. 		
@D	Webb, M.//Taylor, I.A.//Firman, K.//Kneale, G.G. 	Probing the domain structure of the type IC DNA methyltransferase M.EcoR124I by limited proteolysis.	J. Mol. Biol.	1995	250		181-190			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. 		
@D	Weber, R.E.//Layer, F.//Fuchs, S.//Bender, J.K.//Fiedler, S.//Werner, G.//Strommenger, B. 	Complete Genome Sequences of Two Methicillin-Sensitive Staphylococcus aureus Isolates Representing a Population Subset Highly Prevalent in Human Colonization.	Genome Announcements	2016	4		e00716-16			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. 		
@D	Wegmann, U.//Goesmann, A.//Carding, S.R. 	Complete Genome Sequence of Bacteroides ovatus V975.	Genome Announcements	2016	4		e01335-16			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. 		
@D	Wegmann, U.//Louis, P.//Goesmann, A.//Henrissat, B.//Duncan, S.H.//Flint, H.J. 	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.	Environ. Microbiol.	2014	16		2879-2890			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. 		
@D	Wegmann, U.//Nueno, P.C.//Mayer, M.J.//Crost, E.//Narbad, A. 	Complete Genome Sequence of Desulfovibrio piger FI11049.	Genome Announcements	2017	5		e01528-16			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. 		
@D	Wegmann, U.//O'Connell-Motherway, M.//Zomer, A.//Buist, G.//Shearman, C.//Canchaya, C.//Ventura, M.//Goesmann, A.//Gasson, M.J.//Kuipers, O.P.//van Sinderen, D.//Kok, J. 	Complete genome sequence of the prototype lactic acid bacterium Lactococcus lactis subsp. cremoris MG1363.	J. Bacteriol.	2007	189		3256-3270			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. 		
@D	Wegmann, U.//Overweg, K.//Horn, N.//Goesmann, A.//Narbad, A.//Gasson, M.J.//Shearman, C. 	The complete genome sequence of Lactobacillus johnsonii FI9785, a competitive exclusion agent against pathogens in poultry.	J. Bacteriol.	2009	191		7142-7143			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. 		
@D	Wegner, C.E.//Richter-Heitmann, T.//Klindworth, A.//Klockow, C.//Richter, M.//Achstetter, T.//Glockner, F.O.//Harder, J. 	Expression of sulfatases in Rhodopirellula baltica and the diversity of sulfatases in the genus Rhodopirellula.	Marine Genomics	2012	9		51-61			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. 		
@D	Wei, D.D.//Wan, L.G.//Liu, Y. 	Draft Genome Sequence of an NDM-1- and KPC-2-Coproducing Hypervirulent Carbapenem-Resistant Klebsiella pneumoniae Strain Isolated from Burn Wound  Infections.	Genome Announcements	2018	6		e00192-18			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. 		
@D	Wei, H.//Therrien, C.//Blanchard, A.//Guan, S.//Zhu, Z. 	The Fidelity Index provides a systematic quantitation of star activity of DNA restriction endonucleases.	Nucleic Acids Res.	2008	36		e50			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. 		
@D	Wei, J.//Goldberg, M.B.//Burland, V.//Venkatesan, M.M.//Deng, W.//Fournier, G.//Mayhew, G.F.//Plunkett, G. III//Rose, D.J.//Darling, A.//Mau, B.//Perna, N.T.//Payne, S.M.//Runyen-Janecky, L.J.//Zhou, S.//Schwartz, D.C.//Blattner, F.R. 	Complete genome sequence and comparative genomics of Shigella flexneri serotype 2a strain 2457T.	Infect. Immun.	2003	71		2775-2786			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. 		
@D	Wei, S.//Guo, Z.//Li, T.//Zhang, T.//Li, X.//Zhou, Z.//Li, Z.//Liu, M.//Luo, R.//Bi, D.//Chen, H.//Zhou, R.//Jin, H. 	Genome Sequence of Mycoplasma iowae Strain 695, an Unusual Pathogen Causing Deaths in Turkeys.	J. Bacteriol.	2012	194		547-548			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. 		
@D	Wei, W.//Gao, C.//Xiong, Y.//Zhang, Y.//Liu, S.//Pu, Y. 	A fluorescence method for detection of DNA and DNA methylation based on graphene oxide and restriction endonuclease HpaII.	Talanta	2015	131		342-347			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. 		
@D	Wei, X.//Ge, X.//Li, Y.//Yu, Z. 	Draft Genome Sequence of Methylocaldum sp. SAD2, a Methanotrophic Strain That Can Convert Raw Biogas to Methanol in the Presence of Hydrogen Sulfide.	Genome Announcements	2017	5		e00716-17			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. 		
@D	Wei, X.//Ge, X.//Li, Y.//Yu, Z. 	Draft Genome Sequence of Methylocaldum sp. Strain 14B, an Obligate Hydrogen Sulfide-Tolerant Methanotrophic Strain That Can Convert Biogas to Methanol.	Genome Announcements	2017	5		e00153-17			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. 		
@D	Wei, Y.//Cao, J.//Fang, J.//Kato, C.//Cui, W. 	Complete Genome Sequence of Bacillus subtilis Strain 29R7-12, a Piezophilic Bacterium Isolated from Coal-Bearing Sediment 2.4 Kilometers below the Seafloor.	Genome Announcements	2017	5		e01621-16			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. 		
@D	Wei, Y.//Cao, J.//Fang, J.//Kato, C.//Cui, W. 	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.	Genome Announcements	2017	5		e01625-16			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. 		
@D	Wei, Y.//Yang, Y.//Zhou, L.//Liu, Z.//Wang, X.//Yang, R.//Su, Q.//Zhou, Y.//Zhao, J.//Yang, J. 	Genome Sequence of Enterobacter cancerogenus YZ1.	Genome Announcements	2013	1		e00023-13			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. 		
@D	Wei, Y.//Zhou, H.//Zhang, L.//Zhang, J.//Wang, Y.//Wang, S.//Zhou, Z.//Yan, X. 	Draft Genome Sequence of Clostridium ultunense Strain BS (DSMZ 10521), Recovered  from a Mixed Culture.	Genome Announcements	2014	2		e01269-13			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. 		
@D	Wei, Y.X.//Zhang, Z.Y.//Liu, C.//Zhu, Y.Z.//Zhu, Y.Q.//Zheng, H.J.//Zhao, G.P.//Wang, S.Y.//Guo, X.K. 	Complete Genome Sequence of Bifidobacterium longum JDM301.	J. Bacteriol.	2010	192		4076-4077			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. 		
@D	Weidner, S.//Baumgarth, B.//Gottfert, M.//Jaenicke, S.//Puhler, A.//Schneiker-Bekel, S.//Serrania, J.//Szczepanowski, R.//Becker, A. 	Genome Sequence of Sinorhizobium meliloti Rm41.	Genome Announcements	2013	1		e00013-12			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. 		
@D	Weidner, S.//Becker, A.//Bonilla, I.//Jaenicke, S.//Lloret, J.//Margaret, I.//Puhler, A.//Ruiz-Sainz, J.E.//Schneiker-Bekel, S.//Szczepanowski, R.//Vinardell, J.M.//Zehner, S.//Gottfert, M. 	Genome Sequence of the Soybean Symbiont Sinorhizobium fredii HH103.	J. Bacteriol.	2012	194		1617-1618			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. 		
@D	Weigand, M.R.//Changayil, S.//Kulasekarapandian, Y.//Tondella, M.L. 	Complete Genome Sequences of Two Bordetella hinzii Strains Isolated from Humans.	Genome Announcements	2015	3		e00965-15			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. 		
@D	Weigand, M.R.//Peng, Y.//Cassiday, P.K.//Loparev, V.N.//Johnson, T.//Juieng, P.//Nazarian, E.J.//Weening, K.//Tondella, M.L.//Williams, M.M. 	Complete Genome Sequences of Bordetella pertussis Isolates with Novel Pertactin-Deficient Deletions.	Genome Announcements	2017	5		e00973-17			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. 		
@D	Weigand, M.R.//Peng, Y.//Loparev, V.//Batra, D.//Bowden, K.E.//Burroughs, M.//Cassiday, P.K.//Davis, J.K.//Johnson, T.//Juieng, P.//Knipe, K.//Mathis, M.H.//Pruitt, A.M.//Rowe, L.//Sheth, M.//Tondella, M.L.//Williams, M.M. 	The History of Bordetella pertussis Genome Evolution Includes Structural Rearrangement.	J. Bacteriol.	2017	199		e00806-16			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. 		
@D	Weigand, M.R.//Peng, Y.//Loparev, V.//Batra, D.//Bowden, K.E.//Cassiday, P.K.//Davis, J.K.//Johnson, T.//Juieng, P.//Miner, C.E.//Rowe, L.//Sheth, M.//Tondella, M.L.//Williams, M.M. 	Complete Genome Sequences of Four Different Bordetella sp. Isolates Causing Human Respiratory Infections.	Genome Announcements	2016	4		e01080-16			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. 		
@D	Weigand, M.R.//Peng, Y.//Loparev, V.//Batra, D.//Burroughs, M.//Johnson, T.//Juieng, P.//Rowe, L.//Tondella, M.L.//Williams, M.M. 	Complete Genome Sequences of Bordetella pertussis Vaccine Reference Strains 134 and 10536.	Genome Announcements	2016	4		e00979-16			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. 		
@D	Weigand, M.R.//Peng, Y.//Loparev, V.//Johnson, T.//Juieng, P.//Gairola, S.//Kumar, R.//Shaligram, U.//Gowrishankar, R.//Moura, H.//Rees, J.//Schieltz, D.M.//Williamson, Y.//Woolfitt, A.//Barr, J.//Tondella, M.L.//Williams, M.M. 	Complete Genome Sequences of Four Bordetella pertussis Vaccine Reference Strains  from Serum Institute of India.	Genome Announcements	2016	4		e01404-16			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. 		
@D	Weigand, M.R.//Ryu, H.//Bozcek, L.//Konstantinidis, K.T.//Santo, D.J.W. 	Draft Genome Sequence of Catellicoccus marimammalium, a Novel Species Commonly Found in Gull Feces.	Genome Announcements	2013	1		e00019-12			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. 		
@D	Weil, M.D.//McClelland, M. 	Enzymatic cleavage of a bacterial genome at a 10-base-pair recognition site.	Proc. Natl. Acad. Sci. U. S. A.	1989	86		51-55			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. 		
@D	Weilharter, A.//Mitter, B.//Shin, M.V.//Chain, P.S.//Nowak, J.//Sessitsch, A. 	Complete genome sequence of the plant growth-promoting endophyte Burkholderia phytofirmans strain PsJN.	J. Bacteriol.	2011	193		3383-3384			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. 		
@D	Weimer, C.M.//Deitzler, G.E.//Robinson, L.S.//Park, S.//Hallsworth-Pepin, K.//Wollam, A.//Mitreva, M.//Lewis, W.G.//Lewis, A.L. 	Genome Sequences of 12 Bacterial Isolates Obtained from the Urine of Pregnant Women.	Genome Announcements	2016	4		e00882-16			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. 		
@D	Weiner, M.//Costa, G. 	New methodologies for the directional and bidirectional cloning and expression of PCR-generated DNA fragments.	Abstr. Gen. Meet. Am. Soc. Microbiol.	1994	94		249			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. 		
@D	Weingarten, R.A.//Johnson, R.C.//Conlan, S.//Ramsburg, A.M.//Dekker, J.P.//Lau, A.F.//Khil, P.//Odom, R.T.//Deming, C.//Park, M.//Thomas, P.J.//Henderson, D.K.//Palmore, T.N.//Segre, J.A.//Frank, K.M. 	Genomic Analysis of Hospital Plumbing Reveals Diverse Reservoir of Bacterial Plasmids Conferring Carbapenem Resistance.	MBio	2018	9		e02011-17			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. 		
@D	Weinmaier, T.//Riesing, M.//Rattei, T.//Bille, J.//Arguedas-Villa, C.//Stephan, R.//Tasara, T. 	Complete Genome Sequence of Listeria monocytogenes LL195, a Serotype 4b Strain from the 1983-1987 Listeriosis Epidemic in Switzerland.	Genome Announcements	2013	1		e00152-12			The complete genome sequence of Listeria monocytogenes LL195, a serotype 4b clinical strain isolated during the 1983-1987 listeriosis epidemic in Switzerland, is presented. 		
@D	Weinstock, G.M.//Robinson, G.E. 	Insights into social insects from the genome of the honeybee Apis mellifera.	Nature	2006	443		931-949			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. 		
@D	Weis, A.M.//Clothier, K.A.//Huang, B.C.//Kong, N.//Weimer, B.C. 	Draft Genome Sequences of Campylobacter jejuni Strains That Cause Abortion in Livestock.	Genome Announcements	2016	4		e01324-16			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. 		
@D	Weis, A.M.//Clothier, K.A.//Huang, B.C.//Kong, N.//Weimer, B.C. 	Draft Genome Sequence of Multidrug-Resistant Abortive Campylobacter jejuni from Northern California.	Genome Announcements	2017	5		e00171-17			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. 		
@D	Weis, A.M.//Gilpin, B.//Huang, B.C.//Kong, N.//Chen, P.//Weimer, B.C. 	Shigella Draft Genome Sequences: Resources for Food Safety and Public Health.	Genome Announcements	2017	5		e00176-17			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. 		
@D	Weis, A.M.//Huang, B.C.//Storey, D.B.//Kong, N.//Chen, P.//Arabyan, N.//Gilpin, B.//Mason, C.//Townsend, A.K.//Smith, W.A.//Byrne, B.A.//Taff, C.C.//Weimer, B.C. 	Large-Scale Release of Campylobacter Draft Genomes: Resources for Food Safety and Public Health from the 100K Pathogen Genome Project.	Genome Announcements	2017	5		e00925-16			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. 		
@D	Weisenberger, D.J.//Velicescu, M.//Cheng, J.C.//Gonzales, F.A.//Liang, G.N.//Jones, P.A. 	Role of the DNA methyltransferase variant DNMT3b3 in DNA methylation.	Mol. Cancer Res.	2004	2		62-72			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. 		
@D	Weisenberger, D.J.//Velicescu, M.//Preciado-Lopez, M.A.//Gonzales, F.A.//Tsai, Y.C.//Liang, G.//Jones, P.A. 	Identification and characterization of alternatively spliced variants of DNA methyltransferase 3a in mammalian cells.	Gene	2002	298		91-99			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. 		
@D	Weiserova, M.//Dutta, C.F.//Firman, K. 	A novel mutant of the type I restriction-modification enzyme EcoR124I is altered at a key stage of the subunit assembly pathway.	J. Mol. Biol.	2000	304		301-310			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. 		
@D	Weiserova, M.//Firman, K. 	Isolation of a non-classical mutant of the DNA recognition subunit of the type I restriction endonuclease R.EcoR124I.	Biol. Chem.	1998	379		585-589			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. 		
@D	Weiserova, M.//Janscak, P.//Benada, O.//Hubacek, J.//Vitaly, E.A.//Glover, S.W.//Firman, K. 	Cloning, production and characterization of wild type and mutant forms of the R.EcoK endonucleases.	Nucleic Acids Res.	1993	21		373-379			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. 		
@D	Weiserova, M.//Janscak, P.//Zinkevich, V.//Hubacek, J. 	Overproduction of the Hsd subunits leads to the loss of temperature-sensitive restriction and modification phenotype.	Folia Microbiol. (Praha)	1994	39		452-458			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. 		
@D	Weiserova, M.//Ryu, J.C. 	Characterization of a restriction modification system from the commensal Escherichia coli strain A0 34/86 (O83 : K24 : H31).	BMC Microbiol.	2008	8		106			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. 		
@D	Weiss, A.//Keshet, I.//Razin, A.//Cedar, H. 	DNA demethylation in vitro: Involvement of RNA.	Cell	1996	86		709-718			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. 		
@D	Weiss, M.//Kesberg, A.I.//Labutti, K.M.//Pitluck, S.//Bruce, D.//Hauser, L.//Copeland, A.//Woyke, T.//Lowry, S.//Lucas, S.//Land, M.//Goodwin, L.//Kjelleberg, S.//Cook, A.M.//Buhmann, M.//Thomas, T.//Schleheck, D. 	Permanent draft genome sequence of Comamonas testosteroni KF-1.	Standards in Genomic Sciences	2013	8		239-254			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. 		
@D	Weiss, V.A.//Faoro, H.//Tadra-Sfeir, M.Z.//Raittz, R.T.//de Souza, E.M.//Monteiro, R.A.//Cardoso, R.L.//Wassem, R.//Chubatsu, L.S.//Huergo, L.F.//Muller-Santos, M.//Steffens, M.B.//Rigo, L.U.//Pedrosa, F.O.//Cruz, L.M. 	Draft Genome Sequence of Herbaspirillum lusitanum P6-12, an Endophyte Isolated from Root Nodules of Phaseolus vulgaris.	J. Bacteriol.	2012	194		4136-4137			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. 		
@D	Weissgerber, T.//Zigann, R.//Bruce, D.//Chang, Y.-j.//Detter, J.C.//Han, C.//Hauser, L.//Jeffries, C.D.//Land, M.//Munk, A.C.//Tapia, R.//Dahl, C. 	Complete genome sequence of Allochromatium vinosum DSM 180.	Standards in Genomic Sciences	2011	5		311-330			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. 		
@D	Weitzman, C.L.//Tillett, R.L.//Sandmeier, F.C.//Tracy, C.R.//Alvarez-Ponce, D. 	High quality draft genome sequence of Mycoplasma testudineum strain BH29(T), isolated from the respiratory tract of a desert tortoise.	Standards in Genomic Sciences	2018	13		9			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. 		
@D	Welch, R.A. et al. 	Extensive mosaic structure revealed by the complete genome sequence of uropathogenic Escherichia coli.	Proc. Natl. Acad. Sci. U. S. A.	2002	99		17020-17024			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. 		
@D	Welch, S.G.//Al-Awadhi, S.//Williams, R.A.D. 	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.	Microbiology	1998	144		167-175			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. 		
@D	Welch, S.G.//Williams, R.A.D. 	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).	Biochem. J.	1995	309		595-599			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. 		
@D	Welch, S.G.//Williams, R.A.D. 	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.	Nucleic Acids Res.	1995	23		4573-4575			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. 		
@D	Welch, S.G.//Williams, R.A.D. 	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.	Biochem. J.	1995	312		505-510			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. 		
@D	Welch, S.G.//Williams, R.A.D. 	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.	Nucleic Acids Res.	1996	24		1799-1801			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. 		
@D	Welch, T.J.//Fricke, W.F.//McDermott, P.F.//White, D.G.//Rosso, M.L.//Rasko, D.A.//Mammel, M.K.//Eppinger, M.//Rosovitz, M.J.//Wagner, D.//Rahalison, L.//LeClerc, J.E.//Hinshaw, J.M.//Lindler, L.E.//Cebula, T.A.//Carniel, E.//Ravel, J. 	Multiple Antimicrobial Resistance in Plague: An Emerging Public Health Risk.	PLoS ONE	2007	2		e309			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. 		
@D	Weller, R.L.//Rajski, S.R. 	Design, synthesis, and preliminary biological evaluation of a DNA methyltransferase-directed alkylating agent.	Chembiochem	2006	7		243-245			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. 		
@D	Weller, R.L.//Rajski, S.R. 	DNA methyltransferase-moderated click chemistry.	Org. Lett.	2005	7		2141-2144			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. 		
@D	Weller-Stuart, T.//Chan, W.Y.//Coutinho, T.A.//Venter, S.N.//Smits, T.H.//Duffy, B.//Goszczynska, T.//Cowan, D.A.//de Maayer, P. 	Draft Genome Sequences of the Onion Center Rot Pathogen Pantoea ananatis PA4 and  Maize Brown Stalk Rot Pathogen P. ananatis BD442.	Genome Announcements	2014	2		e00750-14			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. 		
@A	Wells, R.D.//Klein, R.D.//Singleton, C.K. 		Type II restriction enzymes.			Boyer, P. 		The Enzymes					Academic Press	1981		14		157-191									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. 		
@A	Wells, R.D.//Neuendorf, S.K. 		Cleavage of single-stranded viral DNAs by certain restriction endonucleases.			Chirikjian, J.G. 		Gene Amplif. Anal.					Elsevier North Holland	1981		1		101-111									*
    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
 
 		
@D	Wels, M.//Backus, L.//Boekhorst, J.//Dijkstra, A.//Beerthuyzen, M.//Siezen, R.J.//Bachmann, H.//van Hijum, S.A. 	Draft Genome Sequences of 11 Lactococcus lactis subsp. cremoris Strains.	Genome Announcements	2017	5		e01739-16			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. 		
@D	Wels, M.//Serrano, L.M.//Eibrink, B.J.//Backus, L.//Bongers, R.S.//Vriesendorp, B.//Siezen, R.J.//van Hijum, S.A.//Meijer, W.C. 	Draft Genome Sequence of Streptococcus thermophilus C106, a Dairy Isolate from an Artisanal Cheese Produced in the Countryside of Ireland.	Genome Announcements	2015	3		e01377-15			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. 		
@A	Welsh, A.J.//Halford, S.E.//Scott, D.J. 		Analysis of Type II restriction endonucleases that interact with two recognition sites.			Pingoud, A. 		Nucleic Acids Mol. Biol.				Berlin Heidelberg	Springer-Verlag	2004		14		297-317									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. 		
@D	Welsh, E.A.//Liberton, M.//Stockel, J.//Loh, T.//Elvitigala, T.//Wang, C.//Wollam, A.//Fulton, R.S.//Clifton, S.W.//Jacobs, J.M.//Aurora, R.//Ghosh, B.K.//Sherman, L.A.//Smith, R.D.//Wilson, R.K.//Pakrasi, H.B. 	The genome of Cyanothece 51142, a unicellular diazotrophic cyanobacterium important in the marine nitrogen cycle.	Proc. Natl. Acad. Sci. U. S. A.	2008	105		15094-15099			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. 		
@D	Wemheuer, F.//Hollensteiner, J.//Poehlein, A.//Granzow, S.//Daniel, R.//Vidal, S.//Wemheuer, B. 	Draft Genome Sequence of Pseudomonas putida Strain GM4FR, an Endophytic Bacterium Isolated from Festuca rubra L.	Genome Announcements	2017	5		e00086-17			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. 		
@D	Wemheuer, F.//Hollensteiner, J.//Poehlein, A.//Liesegang, H.//Daniel, R.//Wemheuer, B. 	Draft Genome Sequence of the Endophyte Bacillus mycoides Strain GM6LP Isolated from Lolium perenne.	Genome Announcements	2018	6		e00011-18			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. 		
@D	Wemheuer, F.//Wemheuer, B.//Hollensteiner, J.//Daniel, R.//Poehlein, A. 	Draft Genome Sequence of the Endophyte Paenibacillus sp. Strain GM2FR Isolated from Festuca rubra.	Genome Announcements	2018	6		e00017-18			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. 		
@D	Wemhoff, S.//Meinhardt, F. 	Generation of biologically contained, readily transformable, and genetically manageable mutants of the biotechnologically important Bacillus pumilus.	Appl. Microbiol. Biotechnol.	2013	97		7805-7819			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. 		
@D	Wen, T.N.//Tung, P.H.//Chen, C.S. 	Purification and some properties of a restriction endonuclease Ccy I from Clostridium cylindrosporum.	Bot. Bull. Acad. Sinica	1989	30		91-98			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. 		
@D	Wende, W.//Grindl, W.//Christ, F.//Pingoud, A.//Pingoud, V. 	Binding, bending and cleavage of DNA substrates by the homing endonuclease PI-SceI.	Nucleic Acids Res.	1996	24		4123-4132			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. 		
@D	Wende, W.//Pingoud, A. 	Cloning, overexpression, purification and characterization of the VDE homing endonuclease.	Biol. Chem. Hoppe Seyler	1994	375		S110			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. 		
@D	Wende, W.//Schottler, S.//Grindl, W.//Christ, F.//Steuer, S.//Noel, A.J.//Pingoud, V.//Pingoud, A. 	A mutational analysis of DNA binding and cleavage by the homing endonuclease PI-SceI.	Mol. Biol. (Mosk)	2000	34		1054-1064			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. 		
@D	Wende, W.//Stahl, F.//Pingoud, A. 	The production and characterization of artificial heterodimers of the restriction endonuclease EcoRV.	Biol. Chem. Hoppe Seyler	1996	377		625-632			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. 		
@D	Weng, S.F.//Luo, A.C.//Lin, C.J.//Tseng, T.T. 	High-Quality Genome Sequence of Xanthomonas axonopodis pv. glycines Strain 12609  Isolated in Taiwan.	Genome Announcements	2017	5		e01695-16			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). 		
@D	Weng, X.B.//Mi, Z.H.//Wang, C.X.//Zhu, J.M. 	Draft Genome Sequence of a Klebsiella pneumoniae Strain (New Sequence Type 2357)  Carrying Tn3926.	Genome Announcements	2016	4		e00986-16			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. 		
@D	Weng, X.B.//Mi, Z.H.//Wang, C.X.//Zhu, J.M. 	Draft Genome Sequence of Uropathogenic Escherichia coli Strain NB8.	Genome Announcements	2016	4		e00944-16			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. 		
@D	Wenner, J.R.//Bloomfield, V.A. 	A novel kinetic mechanism for the cleavage of plasmid DNA by the restriction enzyme EcoRV accounts for nonspecific binding.	J. Biophys.	1997	72		A98			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. 		
@D	Wenner, J.R.//Bloomfield, V.A. 	Osmotic pressure effects on EcoRV cleavage and binding.	J. Biomol. Struct. Dyn.	1999	17		461-471			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. 		
@D	Wenner, J.R.//Bloomfield, V.A. 	Buffer effects on EcoRV kinetics as measured by fluorescent staining and digital imaging of plasmid cleavage.	Anal. Biochem.	1999	268		201-212			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. 		
@D	Wenren, L.M.//Sullivan, N.L.//Cardarelli, L.//Septer, A.N.//Gibbs, K.A. 	Two Independent Pathways for Self-Recognition in Proteus mirabilis Are Linked by Type VI-Dependent Export.	MBio	2013	4		e00374-13			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. 		
@D	Wentz, T.G.//Muruvanda, T.//Lomonaco, S.//Thirunavukkarasu, N.//Hoffmann, M.//Allard, M.W.//Hodge, D.R.//Pillai, S.P.//Hammack, T.S.//Brown, E.W.//Sharma, S.K. 	Closed Genome Sequence of Chryseobacterium piperi Strain CTM(T)/ATCC BAA-1782, a  Gram-Negative Bacterium with Clostridial Neurotoxin-Like Coding Sequences.	Genome Announcements	2017	5		e01296-17			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. 		
@D	Wentz, T.G.//Yao, K.//Schill, K.M.//Reddy, N.R.//Skinner, G.E.//Morrissey, T.R.//Wang, Y.//Muruvanda, T.//Manickam, G.//Pillai, C.A.//Thirunavukkarasu, N.//Hoffmann, M.//Hammack, T.S.//Brown, E.W.//Allard, M.W.//Sharma, S.K. 	Closed Genome Sequence of Clostridium botulinum Strain CFSAN064329 (62A).	Genome Announcements	2018	6		e00528-18			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). 		
@D	Wentzell, L.M.//Halford, S.E. 	DNA looping by the SfiI restriction endonuclease.	J. Mol. Biol.	1998	281		433-444			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. 		
@D	Wentzell, L.M.//Nobbs, T.J.//Halford, S.E. 	The SfiI restriction endonuclease makes a four-strand DNA break at two copies of its recognition sequence.	J. Mol. Biol.	1995	248		581-595			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. 		
@D	Wentzell, L.M.//Oram, M.//Halford, S.E. 	Purification and characterisation of the SfiI restriction endonuclease.	Biochem. Soc. Trans.	1994	22		302S			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. 		
@D	Wenz, C.//Hahn, M.//Pingoud, A. 	Engineering of variants of the restriction endonuclease EcoRV that depend in their cleavage activity on the flexibility of sequences flanking the recognition site.	Biochemistry	1998	37		2234-2242			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. 		
@D	Wenz, C.//Jeltsch, A.//Pingoud, A. 	Probing the indirect readout of the restriction enzyme EcoRV.	J. Biol. Chem.	1996	271		5565-5573			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. 		
@D	Wenz, C.//Pingoud, A. 	Probing the indirect readout of the restriction enzyme EcoRV; mutational analysis of contacts to the DNA-backbone.	Biol. Chem. Hoppe Seyler	1995	376		S168			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. 		
@D	Wenz, C.//Pingoud, A. 	Protein engineering of the restriction endonuclease EcoRV.	Biol. Chem. Hoppe Seyler	1994	375		S110			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. 		
@D	Wenz, C.//Selent, U.//Wende, W.//Jeltsch, A.//Wolfes, H.//Pingoud, A. 	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.	Biochim. Biophys. Acta	1994	1219		73-80			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. 		
@D	Wenzel, C.//Guschlbauer, W. 	Dam methyltransferase from Escherichia coli:  sequence of a peptide segment involved in S-adenosyl-methionine binding.	Nucleic Acids Res.	1993	21		4604-4609			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. 		
@D	Wenzel, C.//Moulard, M.//Lobner-Olesen, A.//Guschlbauer, W. 	Crosslinking of Dam methyltransferase with S-adenosyl-methionine.	FEBS J.	1991	280		147-151			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. 		
@D	Wenzlau, J.M.//Saldanha, R.J.//Butow, R.A.//Perlman, P.S. 	A latent intron-encoded maturase is also an endonuclease needed for intron mobility.	Cell	1989	56		421-430			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. 		
@D	Werbowy, O.//Boratynski, R.//Dekowska, A.//Kaczorowski, T. 	Genetic analysis of maintenance of pEC156, a naturally occurring Escherichia coli plasmid that carries genes of the EcoVIII restriction-modification system.	Plasmid	2015	77		39-50			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. 		
@D	Werbowy, O.//Kaczorowski, T. 	Plasmid pEC156, a Naturally Occurring Escherichia coli Genetic Element That Carries Genes of the EcoVIII Restriction-Modification System, Is Mobilizable  among Enterobacteria.	PLoS ONE	2016	11		e0148355			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. 		
@D	Werner, E.//Wende, W.//Pingoud, A.//Heinemann, U. 	High resolution crystal structure of domain I of the Saccharomyces cerevisiae homing endonuclease PI-SceI.	Nucleic Acids Res.	2002	30		3962-3971			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. 		
@D	Werner, E.A.R. 	Intracellular events following infection by bacteriophage P1:  development of host controlled modification and restriction.	Diss. Abstr.	1968	29		3420			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. 		
@D	Werner, E.R.//Christensen, J.R. 	Infection by bacteriophage P1 and development of host-controlled restriction and modification and of Lysogenic immunity.	J. Virol.	1969	3		363-368			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. 		
@D	Werner, J. et al. 	Halorhabdus tiamatea: proteogenomics and glycosidase activity measurements identify the first cultivated euryarchaeon from a deep-sea anoxic brine lake as potential polysaccharide degrader.	Environ. Microbiol.	2014	16		2525-2537			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. 		
@D	Wernette, C.//Saldanha, R.//Smith, D.//Ming, D.//Perlman, P.S.//Butow, R.A. 	Complex recognition site for the group I intron-encoded endonuclease I-SceII.	Mol. Cell. Biol.	1992	12		716-723			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 		
@D	Wernette, C.M. 	Structure and activity of the mitochondrial intron-encoded endonuclease, I-SceIV.	Biochem. Biophys. Res. Commun.	1998	248		127-133			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. 		
@D	Wernette, C.M.//Saldahna, R.//Perlman, P.S.//Butow, R.A. 	Purification of a site-specific endonuclease, I-Sce II, encoded by intron 4 alpha of the mitochondrial coxI gene of Saccharomyces cerevisiae.	J. Biol. Chem.	1990	265		18976-18982			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. 		
@D	Wernick, D.G.//Choi, K.Y.//Tat, C.A.//Lafontaine, R.J.G.//Liao, J.C. 	Genome Sequence of the Extreme Obligate Alkaliphile Bacillus marmarensis Strain DSM 21297.	Genome Announcements	2013	1		e00967-13			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. 		
@D	Wesselink, J.J.//Lopez-Camacho, E.//de la Pena, S.//Ramos-Ruiz, R.//Ruiz-Carrascoso, G.//Lusa-Bernal, S.//Fernandez-Soria, V.M.//Gomez-Gil, R.//Gomez-Puertas, P.//Mingorance, J. 	Genome Sequence of OXA-48 Carbapenemase-Producing Klebsiella pneumoniae KpO3210.	J. Bacteriol.	2012	194		6981			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. 		
@D	Westberg, J.//Persson, A.//Holmberg, A.//Goesmann, A.//Lundeberg, J.//Johansson, K.E.//Pettersson, B.//Uhlen, M. 	The Genome Sequence of Mycoplasma mycoides subsp. mycoides SC Type Strain PG1T, the Causative Agent of Contagious Bovine Pleuropneumonia (CBPP).	Genome Res.	2004	14		221-227			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. 		
@D	Westphal, L.L.//Sauvey, P.//Champion, M.M.//Ehrenreich, I.M.//Finkel, S.E. 	Genomewide Dam Methylation in Escherichia coli during Long-Term Stationary Phase.	mSystems	2016	1		e00130-16			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. 		
@D	Weyler, L.//Engelbrecht, M.//Forsberg, M.M.//Brehwens, K.//Vare, D.//Vielfort, K.//Wojcik, A.//Aro, H. 	Restriction Endonucleases from Invasive Neisseria gonorrhoeae Cause Double-Strand Breaks and Distort Mitosis in Epithelial Cells during Infection.	PLoS ONE	2014	9		e114208			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. 		
@D	Whang, Y.//Chae, K.S.//Jang, W.H.//Kim, K.T.//Yoo, O.J. 	A new restriction endonuclease from Xanthomonas citri.	Korean J. Microbiol.	1986	24		406-410			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. 		
@D	Whiley, S.J.//Lanser, J.A.//Manning, P.A.//Murray, C.//Steele, T.W. 	Plasmid profile analysis of a Salmonellosis outbreak and identification of a restriction and modification system.	Appl. Environ. Microbiol.	1988	54		1591-1594			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. 		
@D	Whitaker, R.D.//Dorner, L.F.//Schildkraut, I. 	A mutant of BamHI restriction endonuclease which requires N6-methyladenine for cleavage.	J. Mol. Biol.	1999	285		1525-1536			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. 		
@D	White, J.R.//Escobar-Paramo, P.//Mongodin, E.F.//Nelson, K.E.//DiRuggiero, J. 	Extensive genome rearrangements and multiple horizontal gene transfers in a population of pyrococcus isolates from Vulcano Island, Italy.	Appl. Environ. Microbiol.	2008	74		6447-6451			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. 		
@D	White, O. et al. 	Genome sequence of the radioresistant bacterium Deinococcus radiodurans R1.	Science	1999	286		1571-1577			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. 		
@D	White, R.A.I.I.I.//Grassa, C.J.//Suttle, C.A. 	Draft Genome Sequence of Exiguobacterium pavilionensis Strain RW-2, with Wide Thermal, Salinity, and pH Tolerance, Isolated from Modern Freshwater  Microbialites.	Genome Announcements	2013	1		e00597-13			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. 		
@D	White, R.A.I.I.I.//Grassa, C.J.//Suttle, C.A. 	First draft genome sequence from a member of the genus agrococcus, isolated from  modern microbialites.	Genome Announcements	2013	1		e00391-13			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%. 		
@D	White, R.A.I.I.I.//Suttle, C.A. 	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).	Genome Announcements	2013	1		e00598-13			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. 		
@D	Whitehead, E.P.//Taddeo, B.//Stampeggioni, E.//Palitti, F.//Carotti, D. 	Measurement of DNA methylase activity by tritium release from DNA cytosine.	Cell Biophys.	1989	15		145-147			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. 		
@D	Whitehead, P.R.//Brown, N.L. 	A simple and rapid method for screening bacteria for type II restriction endonucleases:  enzymes in Aphanothece halophytica.	Arch. Microbiol.	1985	141		70-74			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). 		
@D	Whitehead, P.R.//Brown, N.L. 	EaeI: a restriction endonuclease from Enterobacter aerogenes.	FEBS Lett.	1983	155		97-101			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. 		
@D	Whitehead, P.R.//Brown, N.L. 	Three restriction endonucleases from Anabaena flos-aquae.	J. Gen. Microbiol.	1985	131		951-958			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. 		
@D	Whitehead, P.R.//Brown, N.L. 	AhaIII: A restriction endonuclease with a recognition sequence containing only A:T basepairs.	FEBS Lett.	1982	143		296-300			None 		
@D	Whitehead, P.R.//Brown, N.L. 	The characterization of novel restriction endonuclease specificities.	Biochem. Soc. Trans.	1981	9		272P			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. 		
@D	Whitehead, P.R.//Jacobs, D.//Brown, N.L. 	Restriction endonucleases from Herpetosiphon giganteus:  an example of the evolution of DNA recognition specificity.	Nucleic Acids Res.	1986	14		7031-7045			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. 		
@D	Whiteson, K.L.//Hernandez, D.//Lazarevic, V.//Gaia, N.//Farinelli, L.//Francois, P.//Pilo, P.//Frey, J.//Schrenzel, J. 	A genomic perspective on a new bacterial genus and species from the Alcaligenaceae family, Basilea psittacipulmonis.	BMC Genomics	2014	15		169			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). 		
@D	Wiatr, C.L.//Witmer, H.J. 	Selective protection of 5'..GGCC..3' and 5'...GCNGC...3' sequences by the hypermodified oxopyrimidine in Bacillus subtilis bacteriophage SP10 DNA.	J. Virol.	1984	52		47-54			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. 		
@D	Wibberg, D.//Blom, J.//Jaenicke, S.//Kollin, F.//Rupp, O.//Scharf, B.//Schneiker-Bekel, S.//Sczcepanowski, R.//Goesmann, A.//Setubal, J.C.//Schmitt, R.//Puhler, A.//Schluter, A. 	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.	J. Biotechnol.	2011	155		50-62			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. 		
@D	Wibberg, D.//Bremges, A.//Dammann-Kalinowski, T.//Maus, I.//Igeno, M.I.//Vogelsang, R.//Konig, C.//Luque-Almagro, V.M.//Roldan, M.D.//Sczyrba, A.//Moreno-Vivian, C.//Blasco, R.//Puhler, A.//Schluter, A. 	Finished genome sequence and methylome of the cyanide-degrading Pseudomonas pseudoalcaligenes strain CECT5344 as resolved by single-molecule real-time  sequencing.	J. Biotechnol.	2016	232		61-68			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. 		
@D	Wibberg, D.//Tielen, P.//Blom, J.//Rosin, N.//Schobert, M.//Tupker, R.//Schatschneider, S.//Spilker, D.//Albersmeier, A.//Goesmann, A.//Vorholter, F.J.//Puhler, A.//Jahn, D. 	Genome Sequence of the Acute Urethral Catheter Isolate Pseudomonas aeruginosa MH38.	Genome Announcements	2014	2		e00161-14			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. 		
@D	Wibberg, D.//Tielen, P.//Narten, M.//Schobert, M.//Blom, J.//Schatschneider, S.//Meyer, A.K.//Neubauer, R.//Albersmeier, A.//Albaum, S.//Jahn, M.//Goesmann, A.//Vorholter, F.J.//Puhler, A.//Jahn, D. 	Genome Sequence of the Urethral Isolate Pseudomonas aeruginosa RN21.	Genome Announcements	2015	3		e00788-15			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. 		
@D	Wibberg, D.//Winkler, A.//Straube, E.//Karrasch, M.//Keller, P.M.//Kalinowski, J. 	Draft Genome Sequence of the Vaccination Strain Mycobacterium bovis BCG S4-Jena.	Genome Announcements	2016	4		e00296-16			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. 		
@D	Wiegand, S.//Rabausch, U.//Chow, J.//Daniel, R.//Streit, W.R.//Liesegang, H. 	Complete Genome Sequence of Geobacillus sp. Strain GHH01, a Thermophilic Lipase-Secreting Bacterium.	Genome Announcements	2013	1		e00092-13			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. 		
@D	Wiens, G.D.//LaPatra, S.E.//Welch, T.J.//Rexroad, C.I.I.I.//Call, D.R.//Cain, K.D.//LaFrentz, B.R.//Vaisvil, B.//Schmitt, D.P.//Kapatral, V. 	Complete Genome Sequence of Flavobacterium psychrophilum Strain CSF259-93, Used To Select Rainbow Trout for Increased Genetic Resistance against Bacterial Cold  Water Disease.	Genome Announcements	2014	2		e00889-14			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. 		
@D	Wiens, J.//Ho, R.//Fernando, D.//Kumar, A.//Loewen, P.C.//Brassinga, A.K.//Anderson, W.G. 	Complete Genome Sequence of a Rhodococcus Species Isolated from the Winter Skate  Leucoraja ocellata.	Genome Announcements	2016	4		e00918-16			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. 		
@D	Wiesner, M.//Calva, E.//Fernandez-Mora, M.//Cevallos, M.A.//Campos, F.//Zaidi, M.B.//Silva, C. 	Salmonella Typhimurium ST213 is associated with two types of IncA/C plasmids carrying multiple resistance determinants.	BMC Microbiol.	2011	11		9			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. 		
@D	Wigler, M.//Levy, D.//Perucho, M. 	The somatic replication of DNA methylation.	Cell	1981	24		33-40			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. 		
@D	Wijetunge, D.S.//Karunathilake, K.H.//Chaudhari, A.//Katani, R.//Dudley, E.G.//Kapur, V.//DebRoy, C.//Kariyawasam, S. 	Complete nucleotide sequence of pRS218, a large virulence plasmid, that augments pathogenic potential of meningitis-associated Escherichia coli strain RS218.	BMC Microbiol.	2014	14		203			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. 		
@D	Wijetunge, D.S.//Katani, R.//Kapur, V.//Kariyawasam, S. 	Complete Genome Sequence of Escherichia coli Strain RS218 (O18:H7:K1), Associated with Neonatal Meningitis.	Genome Announcements	2015	3		e00804-15			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. 		
@D	Wijsman, E.M. 	Optimizing selection of restriction enzymes in the search for DNA variants.	Nucleic Acids Res.	1984	12		9209-9226			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. 		
@D	Wilk, T.//Szabo, M.//Szmolka, A.//Kiss, J.//Barta, E.//Nagy, T.//Olasz, F.//Nagy, B. 	Genome Sequences of Multidrug-Resistant Salmonella enterica subsp. enterica Serovar Infantis Strains from Broiler Chicks in Hungary.	Genome Announcements	2016	4		e01400-16			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. 		
@D	Wilk, T.//Szabo, M.//Szmolka, A.//Kiss, J.//Olasz, F.//Nagy, B. 	Genome Sequences of Salmonella enterica subsp. enterica Serovar Infantis Strains  from Hungary Representing Two Peak Incidence Periods in Three Decades.	Genome Announcements	2017	5		e01735-16			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. 		
@D	Wilke, K.//Rauhut, E.//Noyer-Weidner, M.//Lauster, R.//Pawlek, B.//Behrens, B.//Trautner, T.A. 	Sequential order of target-recognizing domains in multispecific DNA-methyltransferases.	EMBO J.	1988	7		2601-2609			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. 		
@D	Wilkes, T.//Darby, A.C.//Choi, J.//Colborne, J.K.//Werren, J.H.//Hurst, G.D.D. 	The draft genome sequence of Arsenophonus nasoniae, son-killer bacterium of Nasonia vitripennis, reveals genes associated with virulence and symbiosis.	Insect Mol. Biol.	2010	19		59-73			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. 		
@D	Wilkins, B.M. 	Plasmid promiscuity: meeting the challenge of DNA immigration control.	Environ. Microbiol.	2002	4		495-500			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). 		
@D	Wilkins, B.M.//Chilley, P.M.//Thomas, A.T.//Pocklington, M.J. 	Distribution of restriction enzyme recognition sequences on broad host range plasmid RP4: molecular and evolutionary implications.	J. Mol. Biol.	1996	258		447-456			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. 		
@D	Wilkins, K.E.//Booher, N.J.//Wang, L.//Bogdanove, A.J. 	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.	Front. Plant Sci.	2015	6		1-5			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. 		
@D	Wilkinson, C.R.M.//Bartlett, R.//Nurse, P.//Bird, A.P. 	The fission yeast gene pmt1+ encodes a DNA methyltransferase homologue.	Nucleic Acids Res.	1995	23		203-210			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. 		
@D	Wilkinson, P. et al. 	Comparative genomics of the emerging human pathogen Photorhabdus asymbiotica with the insect pathogen Photorhabdus luminescens.	BMC Genomics	2009	10		302			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. 		
@D	Willcock, D.F.//Dryden, D.T.F.//Murray, N.E. 	A mutational analysis of the two motifs common to adenine methyltransferases.	EMBO J.	1994	13		3902-3908			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. 		
@D	Willems, A.//Tian, R.//Brau, L.//Goodwin, L.//Han, J.//Liolios, K.//Huntemann, M.//Pati, A.//Woyke, T.//Mavrommatis, K.//Markowitz, V.//Ivanova, N.//Kyrpides, N.//Reeve, W. 	Genome sequence of Burkholderia mimosarum strain LMG 23256(T), a Mimosa pigra microsymbiont from Anso, Taiwan.	Standards in Genomic Sciences	2014	9		484-494			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. 		
@D	Williams, B.J.//Golomb, M.//Phillips, T.//Brownlee, J.//Olson, M.V.//Smith, A.L. 	Bacteriophage HP2 of Haemophilus influenzae.	J. Bacteriol.	2002	184		6893-6905			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. 		
@D	Williams, D.M.//Benseler, F.//Eckstein, F. 	Properties of 2'-fluorothymidine-containing oligonucleotides:  Interaction with restriction endonuclease EcoRV.	Biochemistry	1991	30		4001-4009			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. 		
@D	Williams, K.//Savageau, M.A.//Blumenthal, R.M. 	A bistable hysteretic switch in an activator-repressor regulated restriction-modification system.	Nucleic Acids Res.	2013	41		6045-6057			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. 		
@D	Williams, L.E.//Baltrus, D.A.//O'Donnell, S.D.//Skelly, T.J.//Martin, M.O. 	Complete Genome Sequence of the Predatory Bacterium Ensifer adhaerens Casida A.	Genome Announcements	2017	5		e01344-17			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. 		
@D	Williams, L.E.//Detter, C.//Barry, K.//Lapidus, A.//Summers, A.O. 	Facile Recovery of Individual High-Molecular-Weight, Low-Copy-Number Natural Plasmids for Genomic Sequencing.	Appl. Environ. Microbiol.	2006	72		4899-4906			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. 		
@D	Williams, M.L.//Gillaspy, A.F.//Dyer, D.W.//Thune, R.L.//Waldbieser, G.C.//Schuster, S.C.//Gipson, J.//Zaitshik, J.//Landry, C.//Banes, M.M.//Lawrence, M.L. 	Genome Sequence of Edwardsiella ictaluri 93-146, a Strain Associated with a Natural Channel Catfish Outbreak of Enteric Septicemia of Catfish.	J. Bacteriol.	2012	194		740-741			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. 		
@D	Williams, M.M.//Sen, K.A.//Weigand, M.R.//Skoff, T.H.//Cunningham, V.A.//Halse, T.A.//Tondella, M.L. 	Bordetella pertussis strain lacking pertactin and pertussis toxin.	Emerg. Infect. Dis.	2016	22		319-322			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. 		
@D	Williams, R.J. 	Restriction endonucleases: Classification, properties, and applications.	Mol. Biotechnol.	2003	23		225-243			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. 		
@D	Williams, R.J. 	Restriction endonucleases and their uses.	Methods Mol. Biol.	2001	160		409-429			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. 		
@D	Williams, R.J. 	Isolation and characterization of an unknown restriction endonuclease.	Methods Mol. Biol.	2001	160		431-442			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. 		
@D	Williams, S.A.//Halford, S.E. 	Communications between catalytic sites in the protein-DNA synapse by the SfiI endonuclease.	J. Mol. Biol.	2002	318		387-394			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. 		
@D	Williams, S.A.//Halford, S.E. 	SfiI endonuclease activity is strongly influenced by the non-specific sequence in the middle of its recognition site.	Nucleic Acids Res.	2001	29		1476-1483			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. 		
@D	Williamson, A.//De Santi, C.//Altermark, B.//Karlsen, C.//Hjerde, E. 	Complete genome sequence of Halomonas sp. R5-57.	Standards in Genomic Sciences	2016	11		62			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. 		
@D	Williamson, M.R.//Doherty, J.P.//Woodcock, D.M. 	Modified-cytosine restriction-system-induced recombinant cloning artefacts in Escherichia coli.	Gene	1993	124		37-44			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. 		
@D	Willis, A.//Parks, M.//Burford, M.A. 	Draft Genome Assembly of Filamentous Brackish Cyanobacterium Limnoraphis robusta  Strain CS-951.	Genome Announcements	2015	3		e00846-15			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. 		
@D	Willis, D.B.//Goorha, R.//Granoff, A. 	DNA methyltransferase induced by frog virus 3.	J. Virol.	1984	49		86-91			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. 		
@D	Wilson, A.K.//Watral, V.G.//Kent, M.L.//Sharpton, T.J.//Gaulke, C.A. 	Draft Genome Sequence of Pseudomonas sp. Strain DrBHI1 (Phylum Proteobacteria).	Genome Announcements	2017	5		e01090-17			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. 		
@D	Wilson, B.D.//Strauss, M.//Stickells, B.J.//Hoal-van Helden, E.G.//van Helden, P.D. 	An assay for O6-alkylguanine-DNA alkyltransferase based on restriction endonuclease inhibition and magnetic bead separation of products.	Carcinogenesis	1994	15		2143-2148			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. 		
@D	Wilson, G.A.//Williams, M.T.//Baney, H.W.//Young, F.E. 	Characterization of temperate bacteriophages of Bacillus subtilis by the restriction endonuclease EcoRI: Evidence for three different temperate bacteriophages.	J. Virol.	1974	14		1013-1016			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. 		
@D	Wilson, G.A.//Young, F.E. 	Restriction and modification in the Bacillus subtilis genospecies:  Isolation of an endonuclease in Bacillus amyloliquefaciens.	Abstr. Gen. Meet. Am. Soc. Microbiol.	1975	75		103			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. 		
@D	Wilson, G.A.//Young, F.E. 	Isolation of a sequence-specific endonuclease (BamI) from Bacillus amyloliquefaciens H.	J. Mol. Biol.	1975	97		123-125			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. 		
@D	Wilson, G.A.//Young, F.E. 	Purification and properties of the BamHI endonuclease.	Methods Enzymol.	1980	65		147-153			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. 		
@A	Wilson, G.A.//Young, F.E. 		Restriction and modification in the Bacillus subtilis genospecies.			Schlessinger, D. 		Microbiology-1976				Washington	American Society for Microbiology	1976		0		350-357									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. 		
@D	Wilson, G.G. 	Type II restriction-modification systems.	Trends Genet.	1988	4		314-318			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. 		
@D	Wilson, G.G. 	Cloned restriction-modification systems - a review.	Gene	1988	74		281-289			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. 		
@D	Wilson, G.G. 	Organization of restriction-modification systems.	Nucleic Acids Res.	1991	19		2539-2566			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. 		
@D	Wilson, G.G. 	Amino acid sequence arrangements of DNA-methyltranferases.	Methods Enzymol.	1992	216		259-279					
@D	Wilson, G.G.//Murray, N.E. 	Restriction and Modification Systems.	Annu. Rev. Genet.	1991	25		585-627			*
 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
 
 		
@D	Wilson, G.G.//Wang, H.//Heiter, D.F.//Lunnen, K.D. 	Restriction enzymes in microbiology, biotechnology and biochemistry.	Encuentro	2012	93		19-48			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. 		
@D	Wilson, G.W.//Edgell, D.R. 	Phage T4 mobE promotes trans homing of the defunct homing endonuclease I-TevIII.	Nucleic Acids Res.	2009	37		7110-7123			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. 		
@D	Wilson, J.G.//French, W.T.//Lipzen, A.//Martin, J.//Schackwitz, W.//Woyke, T.//Shapiro, N.//Bullard, J.W.//Champlin, F.R.//Donaldson, J.R. 	Draft Genome Sequence of Enterobacter cloacae Strain JD6301.	Genome Announcements	2014	2		e00381-14			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. 		
@D	Wilson, R. et al. 	2.2 Mb of contiguous nucleotide sequence from chromosome III of C. elegans.	Nature	1994	368		32-38			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 ] 		
@D	Wilson, W.W.//Hoffman, R.M. 	Methylation of intact chromosomes by bacterial methylases in agarose plugs suitable for pulsed-field electrophoresis.	Anal. Biochem.	1990	191		370-375			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. 		
@D	Wilson, W.W.//Mebane, E.W.//Hoffman, R.M. 	Creation of ultra-rare restriction sites in intact eucaryotic chromosomes mediated by bacterial methylases: An approach to sequencing and analyzing tumor and normal genomes.	Anticancer Res.	1993	13		17-20			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. 		
@D	Winckler, K.//Bach, B.//Obe, G. 	Survival of Saccharomyces cerevisiae after treament with the restriction endonuclease AluI.	Int. J. Radiat. Biol.	1988	54		563-566			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. 		
@D	Windbichler, N.//Schroeder, R. 	Double duty.	Nat. Struct. Mol. Biol.	2004	11		910-911			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. 		
@D	Windolph, S.//Alves, J. 	Influence of divalent cations on inner-arm mutants of restriction endonuclease EcoRI.	Eur. J. Biochem.	1997	244		134-139			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. 		
@D	Windolph, S.//Fritz, A.//Oelgeschlager, T.//Wolfes, H.//Alves, J. 	Sequence context influencing cleavage activity of the K130E mutant of the restriction endonuclease EcoRI identified by a site selection assay.	Biochemistry	1997	36		9478-9485			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. 		
@D	Winegar, R.A.//Land, M.C.//Morgan, W.F. 	Increased chromosomal radiosensitivity of a Chinese hamster ovary cell line that inducibly expresses the EcoRI restriction endonuclease.	Biochem. Biophys. Res. Commun.	1989	160		1079-1084			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. 		
@D	Winegar, R.A.//Phillips, J.W.//Youngblom, J.H.//Morgan, W.F. 	Cell electroporation is a highly efficient method for introducing restriction endonucleases into cells.	Mutat. Res.	1989	225		49-53			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. 		
@D	Wines, D.R.//Talbert, P.B.//Clark, D.V.//Henikoff, S. 	Introduction of a DNA methyltransferase into Drosophila to probe chromatin structure in vivo.	Chromosoma	1996	104		332-340			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. 		
@D	Winget, D.M.//Wommack, K.E. 	Randomly amplified polymorphic DNA PCR as a tool for assessment of marine viral richness.	Appl. Environ. Microbiol.	2008	74		2612-2618			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. 		
@D	Winkle, S.A.//Aloyo, M.C.//Morales, N.//Zambrano, T.Y.//Sheardy, R.D. 	Enhanced reactivity of a B-Z junction for cleavage by the restriction enzyme MboI.	Biochemistry	1991	30		10601-10606			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. 		
@D	Winkle, S.A.//Aloyo, M.C.//Smoller, J.H.//Herrera, J.E.//Chaires, J.B.//Sheardy, R.D. 	Junctions affect the sensitivity of DNAs to reactions with enzymes.	FASEB J.	1992	6		A219			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. 		
@D	Winkle, S.A.//Thomson, H.//Aguilar, L.P.//Sheardy, R.D. 	The effects of alternate DNA structures on restriction enzyme and polymerase binding and activities with DNAS.	Biophys. J.	2002	82		463a			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. 		
@D	Winkler, F.K. 	Structure and function of restriction endonucleases.	Curr. Opin. Struct. Biol.	1992	2		93-99			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. 		
@D	Winkler, F.K. 	DNA totally flipped-out by methylase.	Structure	1994	2		79-83			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. 		
@D	Winkler, F.K. 	Restriction endonucleases, the ultimate in sequence specific DNA recognition.	J. Mol. Recognit.	1994	6		9			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. 		
@D	Winkler, F.K.//Banner, D.W.//Oefner, C.//Tsernoglou, D.//Brown, R.S.//Heathman, S.P.//Bryan, R.K.//Martin, P.D.//Petratos, K.//Wilson, K.S. 	The crystal structure of EcoRV endonuclease and of its complexes with cognate and non-cognate DNA fragments.	EMBO J.	1993	12		1781-1795			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. 		
@A	Winkler, F.K.//Brown, R.S.//Leonard, K.//Berriman, J. 		Structural studies of EcoRV endonuclease and of its complexes with short DNA fragments.			Moras, D.//Drenth, J.//Standberg, B.//Suck, D.//Wilson, K. 		Nato Advanced Studies: Crystallography in Molecular Biology				New York	Plenum Press	1987		0		345-352									None 		
@D	Winkler, F.K.//D'Arcy, A.//Blocker, H.//Frank, R.//van Boom, J.H. 	Crystallization of complexes of EcoRV endonuclease with cognate and non-cognate DNA fragments.	J. Mol. Biol.	1991	217		235-238			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. 		
@D	Winkler, F.K.//Prota, A.E. 	Structure and function of EcoRV endonuclease.	Nucleic Acids Mol. Biol.	2004	14		179-214			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. 		
@D	Winkler, K.-P. 	Isolation and characterization of a sequence specific restriction endonuclease from Rhizobium lupini.	Ph.D. Thesis, Erlangen University, W. Germany	1980			1-135			None 		
@A	Winter, M. 		Investigation of de novo methylation activity in mutants of the EcoKI methyltransferase.			 		Ph.D. Thesis, University of Edinburgh, Edinburgh, Scotland				Edinburgh		1997				1-216									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. 		
@D	Wion, D.//Casadesus, J. 	N-6-methyl-adenine: an epigenetic signal for DNA-protein interactions.	Nat. Rev. Microbiol.	2006	4		183-192			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. 		
@D	Wirth, R. et al. 	Complete genome sequence of Thermocrinis albus type strain (HI 11/12).	Standards in Genomic Sciences	2010	2		194-202			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. 		
@D	Wirth, R. et al. 	Complete genome sequence of Desulfurococcus mucosus type strain (O7/1).	Standards in Genomic Sciences	2011	4		173-182			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. 		
@D	Wise, K.S.//Calcutt, M.J.//Foecking, M.F.//Madupu, R.//Deboy, R.T.//Roske, K.//Hvinden, M.L.//Martin, T.R.//Durkin, A.S.//Glass, J.I.//Methe, B.A. 	Complete Genome Sequences of Mycoplasma leachii Strain PG50T and the Pathogenic Mycoplasma mycoides subsp. mycoides Small Colony Biotype Strain Gladysdale.	J. Bacteriol.	2012	194		4448-4449			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. 		
@D	Wisniewski-Dye, F. et al. 	Azospirillum genomes reveal transition of bacteria from aquatic to terrestrial environments.	PLoS Genet.	2011	7		e1002430			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. 		
@D	Wissuwa, J.//Bauer, S.L.//Steen, I.H.//Stokke, R. 	Complete genome sequence of Lutibacter profundi LP1T isolated from an Arctic deep-sea hydrothermal vent system.	Standards in Genomic Sciences	2017	12		5			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. 		
@D	Wissuwa, J.//Stokke, R.//Fedoy, A.E.//Lian, K.//Smalas, A.O.//Steen, I.H. 	Isolation and complete genome sequence of the thermophilic Geobacillus sp. 12AMOR1 from an Arctic deep-sea hydrothermal vent site.	Standards in Genomic Sciences	2016	11		16			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. 		
@D	Withers, B.E.//Ambroso, L.A.//Dunbar, J.C. 	Structure and evolution of the XcyI restriction-modification system.	Nucleic Acids Res.	1992	20		6267-6273			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. 		
@D	Withers, B.E.//Dunbar, J.C. 	DNA determinants in sequence-specific recognition by XmaI endonuclease.	Nucleic Acids Res.	1995	23		3571-3577			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. 		
@D	Withers, B.E.//Dunbar, J.C. 	The endonuclease isoschizomers, SmaI and XmaI bend DNA in opposite orientations.	Nucleic Acids Res.	1993	21		2571-2577			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. 		
@D	Withers, B.E.//Dunbar, J.C. 	Sequence-specific DNA recognition by the SmaI endonuclease.	J. Biol. Chem.	1995	270		6496-6504			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. 		
@D	Withers, T.R.//Johnson, S.L.//Yu, H.D. 	Draft Genome Sequence for Pseudomonas aeruginosa Strain PAO579, a Mucoid Derivative of PAO381.	J. Bacteriol.	2012	194		6617			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. 		
@D	Witmer, H.//Franks, M. 	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.	J. Virol.	1981	37		148-155			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. 		
@D	Wittmann, J.//Riedel, T.//Bunk, B.//Sproer, C.//Gronow, S.//Overmann, J. 	Complete Genome Sequence of the Novel Temperate Clostridium difficile Phage phiCDIF1296T.	Genome Announcements	2015	3		e00839-15			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. 		
@D	Wittmayer, P.K.//McKenzie, J.L.//Raines, R.T. 	Degenerate DNA recognition by I-PpoI endonuclease.	Gene	1998	206		11-21			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. 		
@D	Witzel, K.//Gwinn-Giglio, M.//Nadendla, S.//Shefchek, K.//Ruppel, S. 	Genome Sequence of Enterobacter radicincitans DSM16656T, a Plant Growth-Promoting Endophyte.	J. Bacteriol.	2012	194		5469			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. 		
@A	Wohlrab, F.//Wells, R.D. 		Enzymatic probes for left-handed Z-DNA.			Chirikjian, J.G. 		Gene Amplif. Anal.				New York	Elsevier	1987		5		247-256									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. 		
@D	Wojciechowski, M.//Czapinska, H.//Bochtler, M. 	CpG underrepresentation and the bacterial CpG-specific DNA methyltransferase M.MpeI.	Proc. Natl. Acad. Sci. U. S. A.	2013	110		105-110			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. 		
@D	Wolcke, J. 	The kinetic mechanism of the DNA methyltransferase from Thermus aquaticus and selection of a DNA binding peptide using phage display.	Ph.D. Thesis, University of Dortmund, Germany	1998			1-164					
@D	Wolcke, J.//Weinhold, E. 	A DNA-binding peptide from a phage display library.	Nucleosides Nucleotides Nucleic Acids	2001	20		1239-1241			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. 		
@D	Wolcke, J.//Weinhold, E. 	Substrate specificity of the DNA-methyltransferase from Thermus aquaticus: influence of the 3'-neighbor base.	Biol. Chem. Hoppe Seyler	1995	376		S169			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. 		
@D	Wolf, Y.I.//Rogozin, I.B.//Kondrashov, A.S.//Koonin, E.V. 	Genome alignment, evolution of prokaryotic genome organization, and prediction of gene function using genomic context.	Genome Res.	2001	11		356-372			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. 		
@D	Wolfes, H.//Alves, J.//Fliess, A.//Geiger, R.//Pingoud, A. 	Site directed mutagenesis experiments suggest that Glu 111, Glu 144 and Arg 145 are essential for endonucleolytic activity of EcoRI.	Nucleic Acids Res.	1986	14		9063-9080			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. 		
@D	Wolfes, H.//Fliess, A.//Pingoud, A. 	A comparison of the structural requirements for DNA cleavage by the isoschizomers HaeIII, BspRI and BsuRI.	Eur. J. Biochem.	1985	150		105-110			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. 		
@D	Wolfes, H.//Fliess, A.//Winkler, F.//Pingoud, A. 	Cross-linking of bromodeoxyuridine-substituted oligonucleotides to the EcoRI and EcoRV restriction endonucleases.	Eur. J. Biochem.	1986	159		267-273			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. 		
@D	Wolffe, A.P.//Jones, P.L.//Wade, P.A. 	DNA demethylation.	Proc. Natl. Acad. Sci. U. S. A.	1999	96		5894-5896			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. 		
@D	Wolk, C.P.//Kraus, J. 	Two approaches to obtaining low, extracellular deoxyribonuclease activity in cultures of heterocyst-forming cyanobacteria.	Arch. Microbiol.	1982	131		302-307			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. 		
@D	Wong, C.F.//Niu, H.//Jiang, J.//Li, J.//Chan, C.M.//Leung, D.Y.//Leung, F.C. 	Genome Sequence of Pseudomonas mendocina DLHK, Isolated from a Biotrickling Reactor.	J. Bacteriol.	2012	194		6326			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. 		
@D	Wong, D.L.//Pavlovich, J.G.//Reich, N.O. 	Electrospray ionization mass spectrometric characterization of photocrosslinked DNA-EcoRI DNA methyltransferase complexes.	Nucleic Acids Res.	1998	26		645-649			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. 		
@D	Wong, D.L.//Reich, N.O. 	Identification of tyrosine 204 as the photo-cross-linking site in the DNA - EcoRI DNA methyltransferase complex by electrospray ionization mass spectrometry.	Biochemistry	2000	39		15410-15417			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. 		
@D	Wong, D.M.//Wetmur, J.G. 	Some class-IIS restriction endonucleases can cleave across a three-way DNA junction.	Gene	1994	150		63-66			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. 		
@D	Wong, K.K.//McClelland, M. 	PCR with 5-methyl-dCTP replacing dCTP.	Nucleic Acids Res.	1991	19		1081-1085			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. 		
@D	Wong, R.M.-Y.//Wong, K.K.//Benson, N.R.//McClelland, M. 	Sample sequencing of a Salmonella typhimurium LT2 lambda library: comparison to the Escherichia coli K12 genome.	FEMS Microbiol. Lett.	1999	173		411-423			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. 		
@D	Wong, S.K.//Yoshizawa, S.//Nakajima, Y.//Ogura, Y.//Hayashi, T.//Hamasaki, K. 	Draft Genome Sequence of Lewinella sp. Strain 4G2 Isolated from the Coastal Sea Surface Microlayer.	Genome Announcements	2016	4		e00754-16			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. 		
@D	Wong, Y.L.//Choo, S.W.//Tan, J.L.//Ong, C.S.//Ng, K.P.//Ngeow, Y.F. 	Draft Genome Sequence of Mycobacterium bolletii Strain M24, a Rapidly Growing Mycobacterium of Contentious Taxonomic Status.	J. Bacteriol.	2012	194		4475			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. 		
@D	Wong, Y.M.//Juan, J.C.//Gan, H.M.//Austin, C.M. 	Draft Genome Sequence of Clostridium bifermentans Strain WYM, a Promising Biohydrogen Producer Isolated from Landfill Leachate Sludge.	Genome Announcements	2014	2		e00077-14			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. 		
@D	Wong, Y.M.//Juan, J.C.//Gan, H.M.//Austin, C.M. 	Draft Genome Sequence of Clostridium perfringens Strain JJC, a Highly Efficient Hydrogen Producer Isolated from Landfill Leachate Sludge.	Genome Announcements	2014	2		e00064-14			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. 		
@D	Wong, Y.M.//Juan, J.C.//Ting, A.//Wu, T.Y.//Gan, H.M.//Austin, C.M. 	Draft Genome Sequence of Clostridium sp. Strain Ade.TY, a New Biohydrogen- and Biochemical-Producing Bacterium Isolated from Landfill Leachate Sludge.	Genome Announcements	2014	2		e00078-14			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. 		
@D	Wons, E.//Mruk, I.//Kaczorowski, T. 	Relaxed specificity of prokaryotic DNA methyltransferases results in DNA site-specific modification of RNA/DNA heteroduplexes.	J. Appl. Genet.	2015	56		539-546			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. 		
@D	Woo, H.L. et al. 	Near-Complete Genome Sequence of Thalassospira sp. Strain KO164 Isolated from a Lignin-Enriched Marine Sediment Microcosm.	Genome Announcements	2016	4		e01297-16			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. 		
@D	Woo, H.L.//Ballor, N.R.//Hazen, T.C.//Fortney, J.L.//Simmons, B.//Davenport, K.W.//Goodwin, L.//Ivanova, N.//Kyrpides, N.C.//Mavromatis, K.//Woyke, T.//Jansson, J.//Kimbrel, J.//DeAngelis, K.M. 	Complete genome sequence of the lignin-degrading bacterium Klebsiella sp. strain  BRL6-2.	Standards in Genomic Sciences	2014	9		19			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. 		
@D	Woo, H.L.//DeAngelis, K.M.//Teshima, H.//Davenport, K.//Daligault, H.//Erkkila, T.//Goodwin, L.//Gu, W.//Lo, C.C.//Munk, C.//Scholz, M.//Xu, Y.//Chain, P.//Bruce, D.//Detter, C.//Tapia, R.//Han, C.//Simmons, B.A.//Hazen, T.C. 	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.	Genome Announcements	2017	5		e00300-17			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. 		
@D	Woo, H.L.//Utturkar, S.//Klingeman, D.//Simmons, B.A.//DeAngelis, K.M.//Brown, S.D.//Hazen, T.C. 	Draft Genome Sequence of the Lignin-Degrading Burkholderia sp. Strain LIG30, Isolated from Wet Tropical Forest Soil.	Genome Announcements	2014	2		e00637-14			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. 		
@D	Woo, P.C.//Lau, S.K.//Tse, H.//Teng, J.L.//Curreem, S.O.//Tsang, A.K.//Fan, R.Y.//Wong, G.K.//Huang, Y.//Loman, N.J.//Snyder, L.A.//Cai, J.J.//Huang, J.D.//Mak, W.//Pallen, M.J.//Lok, S.//Yuen, K.Y. 	The complete genome and proteome of Laribacter hongkongensis reveal potential mechanisms for adaptations to different temperatures and habitats.	PLoS Genet.	2009	5		E1000416			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. 		
@D	Woo, Y.H.//Rajagopalan, P.T.R.//Benkovic, S.J. 	A nonradioactive DNA methyltransferase assay adaptable to high-throughput screening.	Anal. Biochem.	2005	340		336-340			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. 		
@D	Wood, D.W. et al. 	The genome of the natural genetic engineer Agrobacterium tumefaciens C58.	Science	2001	294		2317-2323			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. 		
@D	Wood, K.M.//Daniels, L.E.//Halford, S.E. 	Long-range communications between DNA sites by the dimeric restriction endonuclease SgrAl.	J. Mol. Biol.	2005	350		240-253			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. 		
@D	Wood, R.J.//Maynard-Smith, M.D.//Robinson, V.L.//Oyston, P.C.F.//Titball, R.W.//Roach, P.L. 	Kinetic analysis of Yersinia pestis DNA adenine methyltransferase activity using a hemimethylated molecular break light oligonucleotide.	PLoS ONE	2007	2		e801			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. 		
@D	Wood, R.J.//McKelvie, J.C.//Maynard-Smith, M.D.//Roach, P.L. 	A real-time assay for CpG-specific cytosine-C5 methyltransferase activity.	Nucleic Acids Res.	2010	38		e107			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. 		
@D	Wood, V. et al. 	The genome sequence of Schizosaccharomyces pombe.	Nature	2002	415		871-880			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. 		
@D	Wood, W.B. 	Host specificity of DNA produced by Escherichia coli:  bacterial mutations affecting the restriction and modification of DNA.	J. Mol. Biol.	1966	16		118-133			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. 		
@D	Wood, W.B. 	Mutations in E. coli affecting the host-controlled modification bacteriophage lambda.	Pathol. Microbiol. (Basel)	1965	28		73-76			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. 		
@D	Woodbury, C.P. Jr.//Downey, R.L.//von Hippel, P.H. 	EcoRI Methylase: On its substrate specificity and use in radioactive labeling of DNA.	Fed. Proc.	1978	37		1415			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. 		
@D	Woodbury, C.P. Jr.//Downey, R.L.//von Hippel, P.H. 	DNA site recognition and overmethylation by the EcoRI methylase.	J. Biol. Chem.	1980	255		11526-11533			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. 		
@D	Woodbury, C.P. Jr.//Hagenbuchle, O.//von Hippel, P.H. 	DNA site recognition and reduced specificity of the EcoRI endonuclease.	J. Biol. Chem.	1980	255		11534-11546			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. 		
@A	Woodbury, C.P. Jr.//von Hippel, P.H. 		Relaxed sequence specificities of EcoRI endonuclease and methylase: Mechanisms, possible practical applications, and uses in defining protein-nucleic acid recognition mechanisms.			Chirikjian, J.G. 		Gene Amplif. Anal.					Elsevier North Holland	1981		1		181-207									*
    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
 
 		
@D	Woodcock, D.M.//Crowther, P.J.//Diver, W.P.//Graham, M.//Bateman, C.//Baker, D.J.//Smith, S.S. 	RglB facilitated cloning of highly methylated eukaryotic DNA:  the human L1 transposon, plant DNA, and DNA methylated in vitro with human DNA methyltransferase.	Nucleic Acids Res.	1988	16		4465-4482			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. 		
@D	Woodcock, D.M.//Lisenmeyer, M.E.//Warren, W.D. 	DNA methylation in mouse A-repeats in DNA methyltransferase-knockout ES cells and in normal cells determined by bisulfite genomic sequencing.	Gene	1998	206		63-67			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. 		
@D	Woodford, N.//Carattoli, A.//Karisik, E.//Underwood, A.//Ellington, M.J.//Livermore, D.M. 	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.	Antimicrob. Agents Chemother.	2009	53		4472-4482			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. 		
@D	Woodhead, J.L.//Bhave, N.//Malcolm, D.B. 	Cation dependence of restriction endonuclease EcoRI activity.	Eur. J. Biochem.	1981	115		293-296			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. 		
@D	Woodhead, J.L.//Malcolm, A.D.B. 	Restriction endonuclease EcoRI binds non-specifically to deoxyribonucleic acid.	Biochem. Soc. Trans.	1980	8		90-91			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. 		
@D	Woodhead, J.L.//Malcolm, A.D.B. 	Non-specific binding of restriction endonuclease EcoRI to DNA.	Nucleic Acids Res.	1980	8		389-402			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. 		
@D	Woodhead, J.L.//Malcolm, A.D.B. 	The essential carboxyl group in restriction endonuclease EcoRI.	Eur. J. Biochem.	1981	120		125-128			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. 		
@D	Woodhouse, J.N.//Makower, A.K.//Grossart, H.P.//Dittmann, E. 	Draft Genome Sequences of Two Uncultured Armatimonadetes Associated with a Microcystis sp. (Cyanobacteria) Isolate.	Genome Announcements	2017	5		e00717-17			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. 		
@D	Woods, D.E.//Jeddeloh, J.A.//Fritz, D.L.//DeShazer, D. 	Burkholderia thailandensis E125 harbors a temperate bacteriophage specific for Burkholderia mallei.	J. Bacteriol.	2002	184		4003-4017			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. 		
@D	Wooten, J.//Liu, X.//Miller, M.J. 	Draft Genome Sequence of Lactobacillus crispatus JCM5810, Which Can Reduce Campylobacter jejuni Colonization in Chicken Intestine.	Genome Announcements	2016	4		e00255-16			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. 		
@D	Worden, A.Z. et al. 	Green evolution and dynamic adaptations revealed by genomes of the marine picoeukaryotes Micromonas.	Science	2009	324		268-272			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. 		
@D	Workentine, M.L.//Surette, M.G.//Bernier, S.P. 	Draft Genome Sequence of Burkholderia dolosa PC543 Isolated from Cystic Fibrosis  Airways.	Genome Announcements	2014	2		e00043-14			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. 		
@D	Woudstra, C.//Brito, R.B.//Fonseca, J.A.A.//Silva, R.O.S.//Lobato, F.C.F.//Fach, P. 	Draft Genome Sequences of Five Brazilian Clostridium botulinum Group III Type D/C Strains.	Genome Announcements	2017	5		e00349-17			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. 		
@D	Woudstra, C.//Fach, P.//Chomel, B.B.//Haddad, N.//Boulouis, H.J. 	Draft Genome Sequences of 12 Feline Bartonella henselae Isolates.	Genome Announcements	2017	5		e00075-17			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. 		
@D	Woudstra, C.//Le Marechal, C.//Souillard, R.//Bayon-Auboyer, M.H.//Mermoud, I.//Desoutter, D.//Fach, P. 	Draft Genome Sequences of 17 French Clostridium botulinum Group III Strains.	Genome Announcements	2015	3		e01105-15			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. 		
@D	Woyke, T. et al. 	Complete genome sequence of the gliding freshwater bacterium Fluviicola taffensis type strain (RW262).	Standards in Genomic Sciences	2011	5		21-29			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. 		
@D	Wright, D.J.//Jack, W.E.//Modrich, P. 	The kinetic mechanism of EcoRI endonuclease.	J. Biol. Chem.	1999	274		31896-31902			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. 		
@D	Wright, D.J.//King, K.//Modrich, P. 	The negative charge of Glu-111 is required to activate the cleavage center of EcoRI endonuclease.	J. Biol. Chem.	1989	264		11816-11821			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. 		
@D	Wright, M.S.//Perez, F.//Brinkac, L.//Jacobs, M.R.//Kaye, K.//Cober, E.//van Duin, D.//Marshall, S.H.//Hujer, A.M.//Rudin, S.D.//Hujer, K.M.//Bonomo, R.A.//Adams, M.D. 	Population structure of KPC-producing Klebsiella pneumoniae isolates from midwestern U.S. hospitals.	Antimicrob. Agents Chemother.	2014	58		4961-4965			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. 		
@D	Wright, R.//Stephens, C.//Shapiro, L. 	The CcrM DNA methyltransferase is widespread in the alpha subdivision of proteobacteria, and its essential functions are conserved in Rhizobium meliloti and Caulobacter crescentus.	J. Bacteriol.	1997	179		5869-5877			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. 		
@D	Wright, R.//Stephens, C.//Zweiger, G.//Shapiro, L.//Alley, M.R.K. 	Caulobacter Lon protease has a critical role in cell-cyle control of DNA methylation.	Genes Dev.	1996	10		1532-1542			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. 		
@D	Wright, R.J.//Stephens, C.//Alley, D.//Zweiger, G.//Shapiro, L. 	Cell cycle turnover of a DNA methyltransferase in Caulobacter is dependent on the Lon protease.	Abstr. Gen. Meet. Am. Soc. Microbiol.	1996	96		527			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. 		
@D	Wright, S.//Wilson, S.//Miller, W.G.//Mandrell, R.E.//Siletzky, R.M.//Kathariou, S. 	Differences in Methylation at GATC Sites in Genomic DNA of Campylobacter coli from Turkeys and Swine.	Appl. Environ. Microbiol.	2010	76		7314-7317			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. 		
@D	Wright, S.M.//Carroll, C.//Walters, A.//Newell, P.D.//Chaston, J.M. 	Genome Sequence of Leuconostoc citreum DmW_111, Isolated from Wild Drosophila.	Genome Announcements	2017	5		e00507-17			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. 		
@D	Wrobel, A.//Ottoni, C.//Leo, J.C.//Gulla, S.//Linke, D. 	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.	J. Struct. Biol.	2018	201		171-183			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. 		
@D	Wu, A.K.//Kropinski, A.M.//Lumsden, J.S.//Dixon, B.//MacInnes, J.I. 	Complete genome sequence of the fish pathogen Flavobacterium psychrophilum ATCC 49418(T.).	Standards in Genomic Sciences	2015	10		3			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. 		
@D	Wu, Bo.//He, M.//Feng, H.//Zhang, Y.//Hu, Q.//Zhang, Y. 	Construction and Characterization of Restriction-Modification Deficient Mutants in Zymomonas mobilis ZM4.	Chin. J. Appl. Environ. Biol.	2013	19		189-197			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. 		
@D	Wu, C.-T.//Li, W.-G.//Gao, X.-S.//Zhang, X.-F. 	Bioinformatics analysis of DNA methyltransferase from plants.	Xinan Daxue Xuebao, Ziran Kexueban	2010	32		83-89			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. 		
@D	Wu, C.H.//Chen, C.Y.//Morales, C.//Kiang, D. 	Draft Genome Sequence of an ortho-Nitrophenyl-beta-d-Galactoside (ONPG)-Negative  Strain of Vibrio cholerae, Isolated from Drakes Bay, California.	Genome Announcements	2016	4		e00135-16			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. 		
@D	Wu, C.H.//Zhang, P.//Morales, C.Q.//Kiang, D. 	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.	Genome Announcements	2014	2		e01000-14			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. 		
@D	Wu, C.J.//Wang, H.C.//Chen, C.S.//Shu, H.Y.//Kao, A.W.//Chen, P.L.//Ko, W.C. 	Genome Sequence of a Novel Human Pathogen, Aeromonas aquariorum.	J. Bacteriol.	2012	194		4114-4115			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. 		
@D	Wu, D.//Raymond, J.//Wu, M.//Chatterji, S.//Ren, Q.//Graham, J.E.//Bryant, D.A.//Robb, F.//Colman, A.//Tallon, L.J.//Badger, J.H.//Madupu, R.//Ward, N.L.//Eisen, J.A. 	Complete genome sequence of the aerobic CO-oxidizing thermophile Thermomicrobium roseum.	PLoS ONE	2009	4		E4207			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. 		
@D	Wu, D.Q.//Cheng, H.//Wang, C.//Zhang, C.//Wang, Y.//Shao, J.//Duan, Q. 	Genome Sequence of Pseudomonas aeruginosa Strain AH16, Isolated from a Patient with Chronic Pneumonia in China.	J. Bacteriol.	2012	194		5976-5977			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. 		
@D	Wu, D.Q.//Ye, J.//Ou, H.Y.//Wei, X.//Huang, X.//He, Y.W.//Xu, Y. 	Genomic analysis and temperature-dependent transcriptome profiles of the rhizosphere originating strain Pseudomonas aeruginosa M18.	BMC Genomics	2011	12		438			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. 		
@D	Wu, F.//Deng, X.//Liang, G.//Huang, J.//Cen, Y.//Chen, J. 	Whole-Genome Sequence of 'Candidatus Profftella armatura' from Diaphorina citri in Guangdong, China.	Genome Announcements	2015	3		e01282-15			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. 		
@D	Wu, F.//Deng, X.//Liang, G.//Wallis, C.//Trumble, J.T.//Prager, S.//Chen, J. 	De Novo Genome Sequence of 'Candidatus Liberibacter solanacearum' from a Single Potato Psyllid in California.	Genome Announcements	2015	3		e01500-15			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. 		
@D	Wu, F.//Kumagai, L.//Liang, G.//Deng, X.//Zheng, Z.//Keremane, M.//Chen, J. 	Draft Genome Sequence of 'Candidatus Liberibacter asiaticus' from a Citrus Tree in San Gabriel, California.	Genome Announcements	2015	3		e01508-15			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. 		
@D	Wu, F.//Zheng, Z.//Deng, X.//Cen, Y.//Liang, G.//Chen, J. 	Draft Genome Sequence of 'Candidatus Liberibacter asiaticus' from Diaphorina citri in Guangdong, China.	Genome Announcements	2015	3		e01316-15			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. 		
@D	Wu, H.//Borriss, R.//Xue, P.//Liu, F.//Qiao, J.//Schneider, A.//Lasch, P.//Gao, X. 	Draft Genome Sequences of Plant-Associated Bacillus Strains Isolated from the Qinghai-Tibetan Plateau.	Genome Announcements	2018	6		e00375-18			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. 		
@D	Wu, H.//Lippmann, J.E.//Oza, J.P.//Zeng, M.//Fives-Taylor, P.//Reich, N.O. 	Inactivation of DNA adenine methyltransferase alters virulence factors in Actinobacillus actinomycetemcomitans.	Oral Microbiol. Immunol.	2006	21		238-244			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. 		
@D	Wu, H.//Qiao, J.//Blom, J.//Rueckert, C.//Reva, O.//Gao, X.//Borriss, R. 	The Rhizobacterium Bacillus amyloliquefaciens subsp. plantarum NAU-B3 Contains a  Large Inversion within the Central Portion of the Genome.	Genome Announcements	2013	1		e00941-13			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. 		
@D	Wu, H.N.//Nakura, Y.//Motooka, D.//Nakamura, S.//Nishiumi, F.//Ishino, S.//Kawai, Y.//Tanaka, T.//Takeuchi, M.//Nakayama, M.//Fujita, T.//Yanagihara, I. 	Complete Genome Sequence of Ureaplasma parvum Serovar 3 Strain SV3F4, Isolated in Japan.	Genome Announcements	2014	2		e00256-14			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. 		
@D	Wu, H.N.//Nakura, Y.//Yoshimura, M.//Gaddi-Tantengco, O.A.//Nomiyama, M.//Takayanagi, T.//Fujita, T.//Yasukawa, K.//Yanagihara, I. 	Type II restriction modification system in Ureaplasma parvum OMC-P162 strain.	PLoS ONE	2018	13		e0205328			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. 		
@D	Wu, J.//Herman, J.G.//Wilson, G.//Lee, R.Y.//Yen, R.-W.C.//Mabry, M.//de Bustros, A.//Nelkin, B.D.//Baylin, S.B. 	Expression of prokaryotic HhaI DNA methyltransferase is transforming and lethal to NIH 3T3 cells.	Cancer Res.	1996	56		616-622			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. 		
@D	Wu, J.//Issa, J.P.//Herman, J.//Bassett, D.E.//Nelkin, B.D.//Baylin, S.B. 	Expression of an exogenous eukaryotic DNA methyltransferase gene induces transformation of NIH 3T3 cells.	Proc. Natl. Acad. Sci. U. S. A.	1993	90		8891-8895			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. 		
@D	Wu, J.C.//Santi, D.V. 	Kinetic and catalytic mechanism of HhaI methyltransferase.	J. Biol. Chem.	1987	262		4778-4786			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. 		
@D	Wu, J.C.//Santi, D.V. 	High level expression and purification of HhaI methyltransferase.	Nucleic Acids Res.	1988	16		703-717			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. 		
@A	Wu, J.C.//Santi, D.V. 		On the mechanism and inhibition of DNA cytosine methyltransferases.			Cantoni, G.L.//Razin, A. 		Biochemistry and Biology of DNA Methylation					Alan R. Liss	1985		0		119-129									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. 		
@D	Wu, J.J.//de Jager, V.C.//Deng, W.L.//Leveau, J.H. 	Finished Genome Sequence of Collimonas arenae Cal35.	Genome Announcements	2015	3		e01408-14			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. 		
@D	Wu, J.J.//Issa, J.P.//Herman, J.//Nelkin, B.D.//Baylin, S.B. 	Expression of an exogenous eukaryotic DNA methyltransferase gene induces transformation of NIH 3T3 cells.	Amer. Soc. Hum. Gen.	1992	4		A74					
@D	Wu, K.-Y.//Liu, G.-R.//Liu, W.-Q.//Wang, A.Q.//Zhan, S.//Sanderson, K.E.//Johnston, R.N.//Liu, S.-L. 	The genome of Salmonella enterica serovar gallinarum: Distinct insertions/deletions and rare rearrangements.	J. Bacteriol.	2005	187		4720-4727			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. 		
@D	Wu, K.M.//Li, L.H.//Yan, J.J.//Tsao, N.//Liao, T.L.//Tsai, H.C.//Fung, C.P.//Chen, H.J.//Liu, Y.M.//Wang, J.T.//Fang, C.T.//Chang, S.C.//Shu, H.Y.//Liu, T.T.//Chen, Y.T.//Shiau, Y.R.//Lauderdale, T.L.//Su, I.J.//Kirby, R.//Tsai, S.F. 	Genome sequencing and comparative analysis of Klebsiella pneumoniae NTUH-K2044, a strain causing liver abscess and meningitis.	J. Bacteriol.	2009	191		4492-4501			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. 		
@D	Wu, M. et al. 	Phylogenomics of the reproductive parasite Wolbachia pipientis wMeI: A streamlined genome overrun by mobile genetic elements.	PLoS Biology	2004	2		327-341			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. 		
@D	Wu, M.//McNulty, N.P.//Rodionov, D.A.//Khoroshkin, M.S.//Griffin, N.W.//Cheng, J.//Latreille, P.//Kerstetter, R.A.//Terrapon, N.//Henrissat, B.//Osterman, A.L.//Gordon, J.I. 	Genetic determinants of in vivo fitness and diet responsiveness in multiple human gut Bacteroides.	Science	2015	350		AAC5992			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. 		
@D	Wu, P.//Qiu, C.//Sohail, A.//Zhang, X.//Bhagwat, A.S.//Cheng, X. 	Mismatch repair in methylated DNA. Structure and activity of the mismatch-specific thymine glycosylase domain of methyl-CpG-binding protein MBD4.	J. Biol. Chem.	2003	278		5285-5291			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. 		
@D	Wu, Q.//Liu, Z.//Li, Y.//Guan, G.//Niu, Q.//Chen, Z.//Luo, J.//Yin, H. 	Genome Sequence of Borrelia garinii Strain SZ, Isolated in China.	Genome Announcements	2014	2		e00010-14			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. 		
@D	Wu, Q.//Peng, S.//Yu, Y.//Li, Y.//Xu, Y. 	Genome Sequence of Bacillus licheniformis CGMCC3963, a Stress-Resistant Strain Isolated in a Chinese Traditional Solid-State Liquor-Making Process.	Genome Announcements	2013	1		e00060-12			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. 		
@D	Wu, Q.//Tun, H.M.//Leung, F.C.C.//Shah, N.P. 	Genomic insights into high exopolysaccharide-producing dairy starter bacterium Streptococcus thermophilus ASCC 1275.	Sci. Rep.	2014	4		4974					
@D	Wu, Q.//Zhu, L.//Jiang, L.//Xu, X.//Xu, Q.//Zhang, Z.//Huang, H. 	Genome Sequence of Paenibacillus wulumuqiensis sp. nov., a Bioflocculant-Producing Species.	Genome Announcements	2015	3		e00795-15			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. 		
@D	Wu, R.//King, C.T.//Jay, E. 	A new sequence-specific endonuclease from Streptococcus faecalis subsp. zymogenes.	Gene	1978	4		329-336			A new sequence-specific endonuclease, SfaI, has been partially purified from Streptococcus faecalis subsp. zymogenes.  SfaI recognizes the tetranucleotide sequence. 		
@D	Wu, R.S.//Hurst-Calderone, S.//Kohn, K.W. 	Measurement of O6-alkylguanine-DNA alkyltransferase activity in human cells and tumor tissues by restriction endonuclease inhibition.	Cancer Res.	1987	47		6229-6235			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. 		
@D	Wu, S.Y.//Lee, K.F.//Kam, K.M.//Shaw, P.C. 	Restriction enzyme BliHKI from a thermophilic Bacillus licheniformis strain.	Biosci. Biotechnol. Biochem.	1993	57		1193-1194			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. 		
@D	Wu, T.-H.//Grelland, E.//Boye, E.//Marinus, M.G. 	Identification of a weak promoter for the dam gene of Escherichia coli.	Biochim. Biophys. Acta	1992	1131		47-52			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. 		
@D	Wu, T.T. 	Locus determining P1 phage restriction in Escherichia coli.	J. Bacteriol.	1969	98		314			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. 		
@D	Wu, T.T.//Matsuda, A.//Cavalieri, L.F. 	The restriction and modification enzymes of Escherichia coli.	Fed. Proc.	1969	28		465			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. 		
@D	Wu, W.//Wood, D.W.//Belfort, G.//Derbyshire, V.//Belfort, M. 	Intein-mediated purification of cytotoxic endonuclease I-TevI by insertional inactivation and pH-controllable splicing.	Nucleic Acids Res.	2002	30		4864-4871			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. 		
@D	Wu, W.//Zheng, H.//Zhang, L.//Wen, Z.//Zhang, S.//Pei, H.//Yu, G.//Zhu, Y.//Cui, Z.//Hu, Z.//Wang, H.//Li, Y. 	A genome-wide analysis of multidrug-resistant and extensively drug-resistant strains of Mycobacterium tuberculosis Beijing genotype.	Mol. Genet. Genomics	2013	288		425-436			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. 		
@D	Wu, X.//Deutschbauer, A.M.//Kazakov, A.E.//Wetmore, K.M.//Cwick, B.A.//Walker, R.M.//Novichkov, P.S.//Arkin, A.P.//Chakraborty, R. 	Draft Genome Sequences of Two Janthinobacteriumlividum Strains, Isolated from Pristine Groundwater Collected from the Oak Ridge Field Research Center.	Genome Announcements	2017	5		e00582-17			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. 		
@D	Wu, X.//Zhao, C.//Guo, Z.//Hao, Y.//Li, J.//Shi, H.//Sun, Y. 	Genome Sequence of Lactobacillus johnsonii Strain W1, Isolated from Mice.	Genome Announcements	2016	4		e00561-16			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. 		
@D	Wu, Y.//Fu, Y.//Yuan, Y.//Gao, M. 	Complete Genome Sequence of Bacillus thuringiensis subsp. jinghongiensis Reference Strain YGd22-03.	Genome Announcements	2017	5		e00740-17			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. 		
@D	Wu, Y.//Wang, Y.//Li, J.//Hu, J.//Chen, K.//Wei, Y.//Bazhanov, D.P.//Bazhanova, A.A.//Yang, H. 	Draft Genome Sequence of Stenotrophomonas maltophilia Strain B418, a Promising Agent for Biocontrol of Plant Pathogens and Root-Knot Nematode.	Genome Announcements	2015	3		e00015-15			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. 		
@D	Wu, Y.//Zheng, J.//Wang, Y.//Li, S.//Jin, H.//Li, Z.//Bi, D.//Sun, M.//Liu, M. 	Draft Genome Sequence of Listeria monocytogenes LM201, Isolated from Foodstuff.	Genome Announcements	2015	3		e01417-14			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. 		
@D	Wu, Y.F.//Zhang, B.//Xing, P.//Wu, Q.L.//Liu, S.J. 	Tumebacillus algifaecis sp. nov., isolated from decomposing algal scum.	Int. J. Syst. Evol. Microbiol.	2015	65		2194-2198			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. 		
@D	Wu, Y.H.//Cheng, H.//Huo, Y.Y.//Xu, L.//Liu, Q.//Wang, C.S.//Xu, X.W. 	Complete genome sequence of esterase-producing bacterium Croceicoccus marinus E4A9(T).	Standards in Genomic Sciences	2017	12		88			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. 		
@D	Wu, Y.H.//Zhou, P.//Cheng, H.//Wang, C.S.//Wu, M.//Xu, X.W. 	Draft Genome Sequence of Microbacterium profundi Shh49T, an Actinobacterium Isolated from Deep-Sea Sediment of a Polymetallic Nodule Environment.	Genome Announcements	2015	3		e00642-15			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. 		
@D	Wu, Y.R.//Li, Y.//Yang, K.L.//He, J. 	Draft Genome Sequence of Butanol-Acetone-Producing Clostridium beijerinckii Strain G117.	J. Bacteriol.	2012	194		5470-5471			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. 		
@D	Wu, Y.R.//Lin, B.//Yu, Y. 	Draft Genome Sequence of a Xylanase-Producing Bacterial Strain, Cellvibrio mixtus J3-8.	Genome Announcements	2014	2		e01281-14			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. 		
@D	Wu, Y.W.//Shao, Y.//Khanipov, K.//Golovko, G.//Pimenova, M.//Fofanov, Y.//Chu, K.H. 	Draft Genome Sequence of Zobellella denitrificans ZD1 (JCM 13380), a Salt-Tolerant Denitrifying Bacterium Capable of Producing  Poly(3-Hydroxybutyrate).	Genome Announcements	2017	5		e00948-17			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. 		
@D	Wu, Z.//Li, F.//Liu, D.//Xue, H.//Zhao, X. 	Novel Type XII Staphylococcal Cassette Chromosome mec Harboring a New Cassette Chromosome Recombinase, CcrC2.	Antimicrob. Agents Chemother.	2015	59		7597-7601			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. 		
@D	Wu, Z.G.//Zhang, D.F.//Liu, Y.L.//Wang, F.//Jiang, X.//Li, C.//Li, S.P.//Hong, Q.//Li, W.J. 	Paracoccus zhejiangensis sp. nov., isolated from activated sludge in wastewater-treatment system.	Antonie Van Leeuwenhoek	2013	104		123-128			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)). 		
@D	Wulff, N.A.//Zhang, S.//Setubal, J.//Almeida, N.F.//Martins, E.C.//Harakava, R.//Kumar, D.//Rangel, L.T.//Foissac, X.//Bove, J.M.//Gabriel, D.W. 	The complete genome sequence of Candidatus Liberibacter americanus, associated with citrus Huanglongbing.	Mol. Plant Microbe Interact.	2014	27		163-176			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. 		
@A	Wyczechowska, D.//Fabianowska-Majewska, K. 		Does 2-chlorodeoxyadenosine contribute to alteration of DNA methyltransferase activity?			Griesmacher, A.//Chiba, P.//Muller, M.M. 		Purine and Pyrimidine Metabolism in Man IX				New York	Plenum Press	1998				595-598									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. 		
@D	Wynne, J.W.//Seemann, T.//Bulach, D.M.//Coutts, S.A.//Talaat, A.M.//Michalski, W.P. 	Resequencing the Mycobacterium avium subsp. paratuberculosis K10 Genome: Improved Annotation and Revised Genome Sequence.	J. Bacteriol.	2010	192		6319-6320			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. 		
@D	Wyres, K.L.//van Tonder, A.//Lambertsen, L.M.//Hakenbeck, R.//Parkhill, J.//Bentley, S.D.//Brueggemann, A.B. 	Evidence of antimicrobial resistance-conferring genetic elements among pneumococci isolated prior to 1974.	BMC Genomics	2013	14		500			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. 		
@D	Wyszomirski, K.H.//Curth, U.//Alves, J.//Mackeldanz, P.//Moncke-Buchner, E.//Schutkowski, M.//Kruger, D.H.//Reuter, M. 	Type III restriction endonuclease EcoP15I is a heterotrimeric complex containing  one Res subunit with several DNA-binding regions and ATPase activity.	Nucleic Acids Res.	2012	40		3610-3622			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. 		
@D	Wyszynski, M.W. 	Investigation of the molecular mechanism and mutagenic effect of C5-methyltransferases by mutational analysis.	Diss. Abstr.	1994	55		1426B-1427B			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. 		
@D	Wyszynski, M.W.//Gabbara, S.//Bhagwat, A.S. 	Substitutions of a cysteine conserved among DNA cytosine methylases result in a variety of phenotypes.	Nucleic Acids Res.	1992	20		319-326			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. 		
@D	Wyszynski, M.W.//Gabbara, S.//Kubareva, E.A.//Romanova, E.A.//Oretskaya, T.S.//Gromova, E.S.//Shabarova, Z.A.//Bhagwat, A.S. 	The cysteine conserved among DNA cytosine methylases is required for methyl transfer, but not for specific DNA binding.	Nucleic Acids Res.	1993	21		295-301			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. 		
@D	Wyszynski, W.//Garbara, S.//Bhagwat, A.S. 	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.	Proc. Natl. Acad. Sci. U. S. A.	1994	91		1574-1578			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. 		
@D	Xavier, B.B.//Lammens, C.//Butaye, P.//Goossens, H.//Malhotra-Kumar, S. 	Complete sequence of an IncFII plasmid harbouring the colistin resistance gene mcr-1 isolated from Belgian pig farms.	J. Antimicrob. Chemother.	2016	71		2342-2344			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. 		
@D	Xavier, B.B.//Vervoort, J.//Stewardson, A.//Adriaenssens, N.//Coenen, S.//Harbarth, S.//Goossens, H.//Malhotra-Kumar, S. 	Complete Genome Sequences of Nitrofurantoin-Sensitive and -Resistant Escherichia coli ST540 and ST2747 Strains.	Genome Announcements	2014	2		e00239-14			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. 		
@D	Xi, J.//Sheng, X.//He, L. 	Draft Genome Sequence of Rhizobium sp. H41, a Rock-Weathering Bacterium from a Weathered Rock Surface.	Genome Announcements	2014	2		e01127-14			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. 		
@D	Xia, E.//Khong, W.X.//Marimuthu, K.//Xu, W.//Ong, R.T.//Tan, E.L.//Krishnan, P.U.//Ang, B.S.//Lye, D.C.//Chow, A.L.//Teo, Y.Y.//Ng, O.T. 	Draft Genome Sequence of a Multidrug-Resistant New Delhi Metallo-beta-Lactamase-1 (NDM-1)-Producing Escherichia coli Isolate Obtained in Singapore.	Genome Announcements	2013	1		e01020-13			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. 		
@D	Xia, H.//Wu, S. 	Construction of DNA transfer system of Streptomyces tenebrarius.	Wei Sheng Wu Xue Bao	2002	42		181-185			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). 		
@D	Xia, L.//Cai, J.//Wang, B.//Huang, Y.//Jian, J.//Lu, Y. 	Draft Genome Sequence of Nocardia seriolae ZJ0503, a Fish Pathogen Isolated from  Trachinotus ovatus in China.	Genome Announcements	2015	3		e01223-14			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. 		
@D	Xia, X.//Li, J.//Liao, S.//Zhou, G.//Wang, H.//Li, L.//Xu, B.//Wang, G. 	Draft genomic sequence of a chromate- and sulfate-reducing Alishewanella strain with the ability to bioremediate Cr and Cd contamination.	Standards in Genomic Sciences	2016	11		48			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. 		
@D	Xia, X.//Li, J.//Zhou, Z.//Wang, D.//Huang, J.//Wang, G. 	High-quality-draft genome sequence of the multiple heavy metal resistant bacterium Pseudaminobacter manganicus JH-7(T).	Standards in Genomic Sciences	2018	13		29			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. 		
@D	Xia, Y.//Burbank, D.E.//Uher, L.//Rabussay, D.//Van Etten, J.L. 	Restriction endonuclease activity induced by PBCV-1 virus infection of a chlorella-like green alga.	Mol. Cell. Biol.	1986	6		1430-1439			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. 		
@D	Xia, Y.//Burbank, D.E.//Uher, L.//Rabussay, D.//Van Etten, J.L. 	IL-3A virus infection of a Chlorella-like green alga induces a DNA restriction endonuclease with novel sequence specificity.	Nucleic Acids Res.	1987	15		6075-6090			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. 		
@D	Xia, Y.//Burbank, D.E.//Van Etten, J.L. 	Restriction endonuclease activity induced by NC-1A virus infection of a Chlorella-like green alga.	Nucleic Acids Res.	1986	14		6017-6030			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. 		
@D	Xia, Y.//Morgan, R.//Schildkraut, I.//Van Etten, J.L. 	A site-specific single strand endonuclease activity induced by NYs-1 virus infection of a Chlorella-like green alga.	Nucleic Acids Res.	1988	16		9477-9487			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. 		
@D	Xia, Y.//Narva, K.E.//Van Etten, J.L. 	The cleavage site of the RsaI isoschizomer, CviII, is G^TAC.	Nucleic Acids Res.	1987	15		10063			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. 		
@D	Xia, Y.//Van Etten, J.L. 	DNA methyltransferase induced by PBCV-1 virus infection of a chlorella-like green alga.	Mol. Cell. Biol.	1986	6		1440-1445			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. 		
@D	Xia, Y.//Van Etten, J.L.//Dobos, P.//Ling, Y.Y.//Krell, P.J. 	Adenine DNA methyltransferase M.CviRI expression accelerates apoptosis in baculovirus-infected insect cells.	Virology	1993	196		817-824			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. 		
@D	Xia, Z.-G.//Zhu, R.-F.//Cao, X.-W.//Zou, G.-L. 	Purification and characterization of restriction endonuclease Bsp78I.	Acta Biochim. Biophys. Sin.	1987	19		27-34			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. 		
@D	Xiang, X.Y.//Chen, L.M.//Huang, X.X.//Luo, Y.M.//She, Q.X.//Huang, L. 	Sulfolobus tengchongensis spindle-shaped virus STSV1: Virus-host interactions and genomic features.	J. Virol.	2005	79		8677-8686			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. 		
@D	Xiao, J.//Luo, Y.//Xu, J. 	Genome Sequence of Serinicoccus profundi, a Novel Actinomycete Isolated from Deep-Sea Sediment.	J. Bacteriol.	2011	193		6413			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). 		
@D	Xiao, L.//Ptacek, T.//Osborne, J.D.//Crabb, D.M.//Simmons, W.L.//Lefkowitz, E.J.//Waites, K.B.//Atkinson, T.P.//Dybvig, K. 	Comparative genome analysis of Mycoplasma pneumoniae.	BMC Genomics	2015	16		610			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. 		
@D	Xie, B.//Dupras, A.A.//Duceppe, M.O.//Fattahi-Ghazi, N.//Goodridge, L.//Ogunremi, D. 	Genome Sequences of 13 Isolates of Salmonella enterica Serovar Typhimurium var. Copenhagen Obtained from Wild Pigeons in Canada.	Genome Announcements	2018	6		e00392-18			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. 		
@D	Xie, B.B.//Shu, Y.L.//Qin, Q.L.//Rong, J.C.//Zhang, X.Y.//Chen, X.L.//Shi, M.//He, H.L.//Zhou, B.C.//Zhang, Y.Z. 	Genome sequences of type strains of seven species of the marine bacterium Pseudoalteromonas.	J. Bacteriol.	2012	194		2746-2747			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. 		
@D	Xie, B.B.//Shu, Y.L.//Qin, Q.L.//Rong, J.C.//Zhang, X.Y.//Chen, X.L.//Zhou, B.C.//Zhang, Y.Z. 	Genome Sequence of the Cycloprodigiosin-Producing Bacterial Strain Pseudoalteromonas rubra ATCC 29570T.	J. Bacteriol.	2012	194		1637-1638			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. 		
@D	Xie, F. 	Mechanistic studies of specific DNA cleavage by PvuII restriction endonuclease.	Ph.D. Thesis, University of Missouri	2008						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. 		
@D	Xie, G.//Chastain-Gross, R.P.//Belanger, M.//Kumar, D.//Whitlock, J.A.//Liu, L.//Farmerie, W.G.//Daligault, H.E.//Han, C.S.//Brettin, T.S.//Progulske-Fox, A. 	Genome Sequence of Porphyromonas gingivalis Strain AJW4.	Genome Announcements	2015	3		e01304-15			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%. 		
@D	Xie, G.//Chastain-Gross, R.P.//Belanger, M.//Kumar, D.//Whitlock, J.A.//Liu, L.//Farmerie, W.G.//Zeng, C.L.//Daligault, H.E.//Han, C.S.//Brettin, T.S.//Progulske-Fox, A. 	Genome Sequence of Porphyromonas gingivalis Strain A7A1-28.	Genome Announcements	2017	5		e00021-17			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%. 		
@D	Xie, G.//Cui, Z.//Tao, Z.//Qiu, H.//Liu, H.//Ibrahim, M.//Zhu, B.//Jin, G.//Sun, G.//Almoneafy, A.//Li, B. 	Genome Sequence of the Rice Pathogen Pseudomonas fuscovaginae CB98818.	J. Bacteriol.	2012	194		5479-5480			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. 		
@D	Xie, G.//Ramirez, M.S.//Marshall, S.H.//Hujer, K.M.//Lo, C.C.//Johnson, S.//Li, P.E.//Davenport, K.//Endimiani, A.//Bonomo, R.A.//Tolmasky, M.E.//Chain, P.S. 	Genome Sequences of Two Klebsiella pneumoniae Isolates from Different Geographical Regions, Argentina (Strain JHCK1) and the United States (Strain  VA360).	Genome Announcements	2013	1		e00168-13			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. 		
@D	Xie, G.L.//Zhang, G.Q.//Liu, H.//Lou, M.M.//Tian, W.X.//Li, B.//Zhou, X.P.//Zhu, B.//Jin, G.L. 	Genome sequence of the rice-pathogenic bacterium Acidovorax avenae subsp. avenae RS-1.	J. Bacteriol.	2011	193		5013-5014			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. 		
@D	Xie, J.//Huang, J.F.//Shi, X.F.//Liu, C.Q. 	Analysis of the characteristic sequence of intein and revision of its motifs.	Chinese Sci. Bull.	2001	46		758-761			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. 		
@D	Xie, J.//Juliao, P.C.//Gilsdorf, J.R.//Ghosh, D.//Patel, M.//Marrs, C.F. 	Identification of New Genetic Regions More Prevalent in Nontypeable Haemophilus influenzae Otitis Media Strains than in Throat Strains.	J. Clin. Microbiol.	2006	44		4316-4325			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. 		
@D	Xie, J.B.//Du, Z.//Bai, L.//Tian, C.//Zhang, Y.//Xie, J.Y.//Wang, T.//Liu, X.//Chen, X.//Cheng, Q.//Chen, S.//Li, J. 	Comparative Genomic Analysis of N2-Fixing and Non-N2-Fixing Paenibacillus spp.: Organization, Evolution and Expression of the Nitrogen Fixation Genes.	PLoS Genet.	2014	10		E1004231			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. 		
@D	Xie, S.//Wang, Z.//Okano, M.//Nogami, M.//Li, Y.//He, W.-W.//Okumura, K.//Li, E. 	Cloning, expression and chromosome locations of the human DNMT3 gene family.	Gene	1999	236		87-95			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. 		
@D	Xie, X.//Yu, Y.//Liu, G.//Yuan, Z.//Song, J. 	Complexity and entropy analysis of DNA methyltransferase.	J. Data Min. Genomics Proteomics	2010	1		1000105			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. 		
@D	Xin, B.//Tao, F.//Wang, Y.//Gao, C.//Ma, C.//Xu, P. 	Genome Sequence of Clostridium butyricum Strain DSM 10702, a Promising Producer of Biofuels and Biochemicals.	Genome Announcements	2013	1		e00563-13			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. 		
@D	Xin, D.//El Karkouri, K.//Robert, C.//Raoult, D.//Fournier, P.E. 	Genomic Comparison of Rickettsia honei Strain RBT and Other Rickettsia Species.	J. Bacteriol.	2012	194		4145			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. 		
@D	Xing, P.//Hahnke, R.L.//Unfried, F.//Markert, S.//Huang, S.//Barbeyron, T.//Harder, J.//Becher, D.//Schweder, T.//Glockner, F.O.//Amann, R.I.//Teeling, H. 	Niches of two polysaccharide-degrading Polaribacter isolates from the North Sea during a spring diatom bloom.	ISME J.	2015	9		1410-1422			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. 		
@D	Xing, S.//Pan, X.//Sun, Q.//Pei, G.//An, X.//Mi, Z.//Huang, Y.//Zhao, B.//Tong, Y. 	Complete Genome Sequence of a Novel Multidrug-Resistant Klebsiella pneumoniae Phage, vB_Kpn_IME260.	Genome Announcements	2017	5		e00055-17			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. 		
@D	Xiong, J.//Deraspe, M.//Iqbal, N.//Krajden, S.//Chapman, W.//Dewar, K.//Roy, P.H. 	Complete Genome of a Panresistant Pseudomonas aeruginosa Strain, Isolated from a  Patient with Respiratory Failure in a Canadian Community Hospital.	Genome Announcements	2017	5		e00458-17			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. 		
@D	Xiong, J.//Li, D.//Li, H.//He, M.//Miller, S.J.//Yu, L.//Rensing, C.//Wang, G. 	Genome analysis and characterization of zinc efflux systems of a highly zinc-resistant bacterium, Comamonas testosteroni S44.	Res. Microbiol.	2011	162		671-679			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. 		
@D	Xiong, X.H.//Han, S.//Wang, J.H.//Jiang, Z.H.//Chen, W.//Jia, N.//Wei, H.L.//Cheng, H.//Yang, Y.X.//Zhu, B.//You, S.//He, J.Y.//Hou, W.//Chen, M.X.//Yu, C.J.//Jiao, Y.H.//Zhang, W.C. 	Complete genome sequence of the bacteria Ketogulonicigenium vulgare Y25.	J. Bacteriol.	2010	193		315-316			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. 		
@D	Xiong, X.H.//Zhi, J.J.//Yang, L.//Wang, J.H.//Zhao, Y.//Wang, X.//Cui, Y.J.//Dong, F.//Li, M.X.//Yang, Y.X.//Wei, N.//An, J.J.//Du, B.H.//Liang, L.//Zhang, J.S.//Zhou, W.//Cheng, S.F.//He, T.//Wang, L.//Chen, H.P.//Liu, D.S.//Zhang, W.C. 	Complete genome sequence of the bacterium Methylovorus sp. strain MP688, a high-level producer of pyrroloquinolone quinone.	J. Bacteriol.	2011	193		1012-1013			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. 		
@D	Xiong, Y.//Elckbush, T.H. 	Functional expression of a sequence-specific endonuclease encoded by the retrotransposon R2Bm.	Cell	1988	55		235-246			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. 		
@D	Xiong, Y.//Wang, P.//Lan, R.//Ye, C.//Wang, H.//Ren, J.//Jing, H.//Wang, Y.//Zhou, Z.//Bai, X.//Cui, Z.//Luo, X.//Zhao, A.//Wang, Y.//Zhang, S.//Sun, H.//Wang, L.//Xu, J. 	A Novel Escherichia coli O157:H7 Clone Causing a Major Hemolytic Uremic Syndrome Outbreak in China.	PLoS ONE	2012	7		E36144			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. 		
@D	Xiong, Z.//Jiang, Y.//Qi, D.//Lu, H.//Yang, F.//Yang, J.//Chen, L.//Sun, L.//Xu, X.//Xue, Y.//Zhu, Y.//Jin, Q. 	Complete genome sequence of the extremophilic Bacillus cereus strain Q1 with industrial applications.	J. Bacteriol.	2009	191		1120-1121			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. 		
@D	Xiong, Z.//Laird, P.W. 	COBRA: a sensitive and quantitative DNA methylation assay.	Nucleic Acids Res.	1997	25		2532-2534			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. 		
@D	Xiong, Z.Q.//Wang, Y. 	Draft Genome Sequence of Marine-Derived Streptomyces sp. Strain AA0539, Isolated  from the Yellow Sea, China.	J. Bacteriol.	2012	194		6622-6623			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. 		
@D	Xiong, Z.Q.//Wang, Y. 	Draft Genome Sequence of the Marine Streptomyces sp. Strain AA1529, Isolated from the Yellow Sea.	J. Bacteriol.	2012	194		5474-5475			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. 		
@D	Xu, A.//Hertrich, S.//Needleman, D.S.//Sheen, S.//Sommers, C. 	Draft Genome Sequences of Four Uropathogenic Escherichia coli Serotype O4:H5 Isolates (ATCC 700414, 700415, 700416, and 700417).	Genome Announcements	2018	6		e00134-18			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. 		
@D	Xu, A.//Johnson, J.R.//Sheen, S.//Needleman, D.S.//Sommers, C. 	Draft Genomic Sequencing of Six Potential Extraintestinal Pathogenic Escherichia  coli Isolates from Retail Chicken Meat.	Genome Announcements	2018	6		e00449-18			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. 		
@D	Xu, A.//Johnson, J.R.//Sheen, S.//Sommers, C. 	Draft Genome Sequences of Five Neonatal Meningitis-Causing Escherichia coli Isolates (SP-4, SP-5, SP-13, SP-46, and SP-65).	Genome Announcements	2018	6		e00091-18			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. 		
@D	Xu, A.//Tilman, S.//Wisser-Parker, K.//Scullen, O.J.//Sommers, C.H. 	Draft Genomic Sequences of Nine Extraintestinal Pathogenic Escherichia coli Isolates from Retail Chicken Skin.	Microbiol. Resour. Announc.	2018	7		e00859-18			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. 		
@D	Xu, C.//Song, J.//Ding, Y.//Yu, F.//Sun, L.//Tang, L.//Hu, X.//Zhang, Z.//He, J. 	Crystallization and preliminary X-ray analysis of Sau3AI/E64A mutant protein.	Protein Pept. Lett.	2007	14		505-506			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. 		
@D	Xu, D.//Cisar, J.O.//Poly, F.//Yang, J.//Albanese, J.//Dharmasena, M.//Wai, T.//Guerry, P.//Kopecko, D.J. 	Genome Sequence of Salmonella enterica Serovar Typhi Oral Vaccine Strain Ty21a.	Genome Announcements	2013	1		e00650-13			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. 		
@D	Xu, F.//Gonzalez-Escalona, N.//Drees, K.P.//Sebra, R.P.//Cooper, V.S.//Jones, S.H.//Whistler, C.A. 	Parallel evolution of two clades of a major Atlantic endemic Vibrio parahaemolyticus pathogen lineage by independent acquisition of related pathogenicity islands.	Appl. Environ. Microbiol.	2017	83		e01168-17			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. 		
@D	Xu, F.//Mao, C.//Ding, Y.//Rui, C.//Wu, L.//Shi, A.//Zhang, H.//Zhang, L.//Xu, Z. 	Molecular and Enzymatic Profiles of Mammalian DNA Methyltransferases: Structures and Targets for Drugs.	Curr. Med. Chem.	2010	17		4052-4071			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. 		
@D	Xu, F.//Miao, D.//Du, Y.//Chen, X.//Zhang, P.//Sun, H. 	Draft Genome Sequence of Avibacterium paragallinarum Strain 221.	Genome Announcements	2013	1		e00290-13			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. 		
@D	Xu, G.//Davis, M.//Glickman, F.//Reich, N. 	Purification and initial characterization of the murine cytosine DNA methyltransferase.	FASEB J.	1993	7		A1175			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. 		
@D	Xu, G.//Flynn, J.//Glickman, J.F.//Reich, N.O. 	Purification and stabilization of mouse DNA methyltransferase.	Biochem. Biophys. Res. Commun.	1995	207		544-551			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. 		
@D	Xu, G.//Hu, J.//Fang, X.//Zhang, X.//Wang, J.//Guo, Y.//Li, T.//Chen, Z.//Dai, W.//Liu, C. 	Genome Sequence of Pseudomonas aeruginosa Strain LCT-PA220, Which Was Selected after Space Flight by Using Biolog's Powerful Carbon Source Utilization  Technology.	Genome Announcements	2014	2		e00169-14			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. 		
@D	Xu, G.//Willert, J.//Kapfer, W.//Trautner, T.A. 	BsuCI, a type-I restriction-modification system in Bacillus subtilis.	Gene	1995	157		59			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. 		
@D	Xu, G.-L.//Bestor, T.H. 	Cytosine methylation targetted to pre-determined sequences.	Nat. Genet.	1997	17		376-378			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. 		
@D	Xu, G.-L.//Bestor, T.H.//Bourchis, D.//Hsieh, C.-L.//Tommerup, N.//Bugge, M.//Hulten, M.//Qu, X.//Russo, J.J.//Viegas-Pequignot, E. 	Chromosome instability and imunodeficiency syndrome caused by mutations in a DNA methyltransferase gene.	Nature	1999	402		187-191			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. 		
@D	Xu, G.L.//Kapfer, W.//Walter, J.//Trautner, T.A. 	BsuBI-an isospecific restriction and modification system of PstI: characterization of the BsuBI genes and enzymes.	Nucleic Acids Res.	1992	20		6517-6523			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. 		
@D	Xu, H.//Han, D.//Xu, Z. 	Overexpression of a lethal methylase, M.TneDI, in E-coli B1(DE3).	Biotechnol. Lett.	2014	36		1853-1859			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. 		
@D	Xu, J. et al. 	Evolution of Symbiotic Bacteria in the Distal Human Intestine.	PLoS Biology	2007	5		e156			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. 		
@D	Xu, J.//Bjursell, M.K.//Himrod, J.//Deng, S.//Carmichael, L.K.//Chiang, H.C.//Hooper, L.V.//Gordon, J.I. 	A genomic view of the human-Bacteroides thetaiotaomicron symbiosis.	Science	2003	299		2074-2076			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. 		
@D	Xu, J.//Xu, M.//Liu, K.//Peng, Q.//Tao, M. 	Complete Genome Sequence of Streptomyces sp. Sge12, Which Produces Antibacterial  and Fungicidal Activities.	Genome Announcements	2017	5		e00415-17			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. 		
@D	Xu, J.//Zheng, H.J.//Liu, L.//Pan, Z.C.//Prior, P.//Tang, B.//Xu, J.S.//Zhang, H.//Tian, Q.//Zhang, L.Q.//Feng, J. 	Complete Genome Sequence of the Plant Pathogen Ralstonia solanacearum Strain Po82.	J. Bacteriol.	2011	193		4261-4262			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. 		
@D	Xu, K.//Su, F.//Tao, F.//Li, C.//Ni, J.//Xu, P. 	Genome Sequences of Two Morphologically Distinct and Thermophilic Bacillus coagulans Strains, H-1 and XZL9.	Genome Announcements	2013	1		e00254-13			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. 		
@D	Xu, L.//Shi, W.//Zeng, X.C.//Yang, Y.//Zhou, L.//Mu, Y.//Liu, Y. 	Draft genome sequence of Arthrobacter sp. strain B6 isolated from the high-arsenic sediments in Datong Basin, China.	Standards in Genomic Sciences	2017	12		11			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. 		
@D	Xu, L.//Yin, M.//Zhu, T.//Liu, Y.//Ying, Y.//Lu, J.//Lin, C.//Ying, J.//Xu, T.//Ni, L.//Bao, Q.//Lu, S. 	Comparative Genomics Analysis of Plasmid pPV989-94 from a Clinical Isolate of Pantoea vagans PV989.	Int. J. Genomics	2018	2018		1242819			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. 		
@D	Xu, M.//Fang, Y.//Liu, J.//Chen, X.//Sun, G.//Guo, J.//Hua, Z.//Tu, Q.//Wu, L.//Zhou, J.//Liu, X. 	Draft Genome Sequence of Shewanella decolorationis S12, a Dye-Degrading Bacterium Isolated from a Wastewater Treatment Plant.	Genome Announcements	2013	1		e00993-13			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. 		
@D	Xu, M.//Kladde, M.P.//Van Etten, J.L.//Simpson, R.T. 	Cloning, characterization and expression of the gene coding for a cytosine-5-DNA methyltransferase recognizing GpC.	Nucleic Acids Res.	1998	26		3961-3966			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. 		
@D	Xu, M.-Q.//Comb, D.G.//Paulus, H.//Noren, C.J.//Shao, Y.//Perler, F.B. 	Protein splicing: an analysis of the branched intermediate and its resolution by succinimide formation.	EMBO J.	1994	13		5517-5522			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. 		
@D	Xu, M.-Q.//Perler, F.B. 	The mechanism of protein splicing and its modulation by mutation.	EMBO J.	1996	15		5146-5153			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. 		
@D	Xu, M.-Q.//Shub, D.A. 	The catalytic core of the sunY intron of bacteriophage T4.	Gene	1989	82		77-82			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. 		
@D	Xu, M.-Q.//Southworth, M.W.//Mersha, F.B.//Hornstra, L.J.//Perler, F.B. 	In vitro protein splicing of purified precursor and the identification of a branched intermediate.	Cell	1993	75		1371-1377			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. 		
@D	Xu, P.//Alves, J.M.//Kitten, T.//Brown, A.//Chen, Z.//Ozaki, L.S.//Manque, P.//Ge, X.//Serrano, M.G.//Puiu, D.//Hendricks, S.//Wang, Y.//Chaplin, M.D.//Akan, D.//Paik, S.//Peterson, D.L.//Macrina, F.L.//Buck, G.A. 	Genome of the opportunistic pathogen Streptococcus sanguinis.	J. Bacteriol.	2007	189		3166-3175			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. 		
@D	Xu, P.//Widmer, G.//Wang, Y.//Ozaki, L.S.//Alves, J.M.//Serrano, M.G.//Puiu, D.//Manque, P.//Akiyoshi, D.//Mackey, A.J.//Pearson, W.R.//Dear, P.H.//Bankier, A.T.//Peterson, D.L.//Abrahamsen, M.S.//Kapur, V.//Tzipori, S.//Buck, G.A. 	The genome of Cryptosporidium hominis.	Nature	2004	431		1107-1112			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. 		
@D	Xu, P.//Yu, H.//Chakrabarty, A.M.//Xun, L. 	Genome Sequence of the 2,4,5-Trichlorophenoxyacetate-Degrading Bacterium Burkholderia phenoliruptrix Strain AC1100.	Genome Announcements	2013	1		e00600-13			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. 		
@A	Xu, Q. 		Molecular analysis of restriction-modification systems in Helicobacter pylori.			 		Ph.D. Thesis, Vanderbilt University, Nashville, Tennessee				Nashville		1999				1-156									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. 		
@D	Xu, Q.//Blaser, M.J. 	Promoters of the CATG-specific methyltransferase gene hpyIM differ between iceA1 and iceA2 Helicobacter pylori strains.	J. Bacteriol.	2001	183		3875-3884			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. 		
@D	Xu, Q.//Morgan, R.D.//Roberts, R.J.//Blaser, M.J. 	Identification of type II restriction and modification systems in Helicobacter pylori reveals their substantial diversity among strains.	Proc. Natl. Acad. Sci. U. S. A.	2000	97		9671-9676			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. 		
@D	Xu, Q.//Morgan, R.D.//Roberts, R.J.//Xu, S.Y.//van Doorn, L.J.//Donahue, J.P.//Miller, G.G.//Blaser, M.J. 	Functional analysis of iceA1, a CATG-recognizing restriction endonuclease gene in Helicobacter pylori.	Nucleic Acids Res.	2002	30		3839-3847			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. 		
@D	Xu, Q.//Morgan, R.D.//Xu, S.Y.//van Doorn, L.J.//Donahue, J.P.//Miller, G.G.//Blaser, M.J. 	H. pylori iceA1 is capable of encoding an NlaIII-like restriction endonuclease.	Abstr. Gen. Meet. Am. Soc. Microbiol.	2000	100		291			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. 		
@D	Xu, Q.//O'Loughlin, T.J.//Kucera, R.B.//Schildkraut, I.//Guo, H.-C. 	Structural study of restriction enzyme MspI/DNA complex by x-ray crystallography.	Biophys. J.	2001	80		296a			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. 		
@D	Xu, Q.//Peek, R.//Miller, G.//Blaser, M. 	Identification of an adenine methylase gene in Helicobacter pylori.	Abstr. Gen. Meet. Am. Soc. Microbiol.	1997	97		38			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. 		
@D	Xu, Q.//Peek, R.M. Jr.//Miller, G.G.//Blaser, M.J. 	The Helicobacter pylori genome is modified at CATG by the product of hpyIM.	J. Bacteriol.	1997	179		6807-6815			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. 		
@D	Xu, Q.//Stickel, S.//Roberts, R.J.//Blaser, M.J.//Morgan, R.D. 	Purification of the Novel Endonuclease, Hpy188I, and Cloning of Its Restriction-Modification Genes Reveal Evidence of Its Horizontal Transfer to the Helicobacter pylori Genome.	J. Biol. Chem.	2000	275		17086-17093			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. 		
@A	Xu, Q.S. 		Crystal structures of restriction endonuclease MspI-DNA complex and glycosylasparaginase.			 		Ph.D. Thesis, Boston University				Boston		2003				1-161									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. 		
@D	Xu, Q.S.//Kucera, R.B.//Roberts, R.J.//Guo, H.-C. 	An asymmetric complex of restriction endonuclease MspI on its palindromic DNA recognition site.	Structure	2004	12		1741-1747			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. 		
@D	Xu, Q.S.//Roberts, R.J.//Guo, H.C. 	Two crystal forms of the restriction enzyme MspI-DNA complex show the same novel structure.	Protein Sci.	2005	14		2590-2600			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. 		
@D	Xu, S.//Schildkraut, I. 	Protecting recognition sequences on DNA by a cleavage-deficient restriction endonuclease.	Biotechniques	1993	15		310-315			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. 		
@D	Xu, S.-Y.//Fomenkov, A. 	Construction of pSC101 derivatives with Camr and Tetr for selection or LacZ' for blue/white screening.	Biotechniques	1994	17		57			Methylase genes and a mutant bamhIR gene have been cloned in the vectors described. 		
@D	Xu, S.-Y.//Schildkraut, I. 	Isolation of BamHI variants with reduced cleavage activities.	J. Biol. Chem.	1991	266		4425-4429			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. 		
@D	Xu, S.-Y.//Schildkraut, I. 	Cofactor requirements of BamHI mutant endonuclease E77K and its suppressor mutants.	J. Bacteriol.	1991	173		5030-5035			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. 		
@D	Xu, S.-Y.//Xiao, J.-P.//Ettwiller, L.//Holden, M.//Aliotta, J.//Poh, C.L.//Dalton, M.//Robinson, D.P.//Petronzio, T.R.//Moran, L.//Ganatra, M.//Ware, J.//Slatko, B.//Benner, J. 	Cloning and expression of the ApaLI, NspI, NspHI, SacI, ScaI, and SapI restriction-modification systems in Escherichia coli.	Mol. Gen. Genet.	1998	260		226-231			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. 		
@D	Xu, S.-Y.//Xiao, J.-P.//Posfai, J.//Maunus, R.//Benner, J. 	Cloning of the BssHII restriction-modification system in Escherichia coli: BssHII methyltransferase contains circularly permuted cytosine-5 methyltransferase motifs.	Nucleic Acids Res.	1997	25		3991-3994			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. 		
@D	Xu, S.Y.//Boitano, M.//Clark, T.A.//Vincze, T.//Fomenkov, A.//Kumar, S.//Too, P.H.//Gonchar, D.//Degtyarev, S.K.//Roberts, R.J. 	Complete Genome Sequence Analysis of Bacillus subtilis T30.	Genome Announcements	2015	3		e00395-15			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. 		
@D	Xu, S.Y.//Corvaglia, A.R.//Chan, S.H.//Zheng, Y.//Linder, P. 	A type IV modification-dependent restriction enzyme SauUSI from Staphylococcus aureus subsp. aureus USA300.	Nucleic Acids Res.	2011	39		5597-5610			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. 		
@D	Xu, S.Y.//Klein, P.//Degtyarev, S.K.//Roberts, R.J. 	Expression and purification of the modification-dependent restriction enzyme BisI and its homologous enzymes.	Sci. Rep.	2016	6		28579			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. 		
@D	Xu, S.Y.//Nugent, R.L.//Kasamkattil, J.//Fomenkov, A.//Gupta, Y.//Aggarwal, A.//Wang, X.//Li, Z.//Zheng, Y.//Morgan, R. 	Characterization of Type II and III restriction-modification systems from Bacillus cereus strains ATCC10987 and ATCC14579.	J. Bacteriol.	2012	194		49-60			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. 		
@D	Xu, S.Y.//Zhu, Z.//Zhang, P.//Chan, S.H.//Samuelson, J.C.//Xiao, J.//Ingalls, D.//Wilson, G.G. 	Discovery of natural nicking endonucleases Nb.BsrDI and Nb.BtsI and engineering of top-strand nicking variants from BsrDI and BtsI.	Nucleic Acids Res.	2007	35		4608-4618			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. 		
@D	Xu, T.//Liang, J.//Chen, S.//Wang, L.//He, X.//You, D.//Wang, Z.//Li, A.//Xu, Z.//Zhou, X.//Deng, Z. 	DNA phosphorothioation in Streptomyces lividans: mutational analysis of the dnd locus.	BMC Microbiol.	2009	9		41			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. 		
@D	Xu, T.//Yao, F.//Zhou, X.//Deng, Z.//You, D. 	A novel host-specific restriction system associated with DNA backbone S-modification in Salmonella.	Nucleic Acids Res.	2010	38		7133-7141			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. 		
@A	Xu, W.L.//Muller, S.J. 		Exploring both sequence detection and restriction endonuclease cleavage kinetics by recognition site via single-molecule microfluidic trapping.			 		Lab on a Chip				Cambridge	Royal Soc. Chemistry	2011		11		435-442									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. 		
@D	Xu, X.//Chen, L.//Chen, C.//Tang, Y.J.//Bai, F.W.//Su, C.//Zhao, X.Q. 	Genome mining of the marine actinomycete Streptomyces sp. DUT11 and discovery of tunicamycins as anti-complement agents.	Front. Microbiol.	2018	9		1318			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. 		
@D	Xu, X.//Jiang, L.//Zhang, Z.//Shi, Y.//Huang, H. 	Genome Sequence of a Gamma- and UV-Ray-Resistant Strain, Deinococcus wulumuqiensis R12.	Genome Announcements	2013	1		e00206-13			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. 		
@D	Xu, Y.//Kersten, R.D.//Nam, S.J.//Lu, L.//Al-Suwailem, A.M.//Zheng, H.//Fenical, W.//Dorrestein, P.C.//Moore, B.S.//Qian, P.Y. 	Bacterial Biosynthesis and Maturation of the Didemnin Anti-cancer Agents.	J. Am. Chem. Soc.	2012	134		8625-8632			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. 		
@D	Xu, Y.//Liu, J.//Zheng, Q.//Liu, Y.//Jiao, N. 	Genome Sequence of Salegentibacter salarius KCTC 12974, Isolated from a Marine Solar Saltern of the Yellow Sea in South Korea.	Genome Announcements	2016	4		e01308-16			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. 		
@D	Xu, Y.//Liu, Y.//Yao, S.//Li, J.//Cheng, C. 	Genome Sequence of Paenibacillus polymyxa Strain CICC 10580, Isolated from the Fruit of Noni (Morinda citrifolia L.) Grown in the Paracel Islands.	Genome Announcements	2014	2		e00854-14			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. 		
@D	Xu, Y.//Lunnen, K.D.//Kong, H. 	Engineering a nicking endonuclease N.AlwI by domain swapping.	Proc. Natl. Acad. Sci. U. S. A.	2001	98		12990-12995			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. 		
@D	Xu, Y.//Nagy, A.//Yan, X.//Haley, B.J.//Kim, S.W.//Liu, N.T.//Nou, X. 	Genome Sequences of Ralstonia insidiosa Type Strain ATCC 49129 and Strain FC1138, a Strong Biofilm Producer Isolated from a Fresh-Cut Produce-Processing Plant.	Genome Announcements	2016	4		e00847-16			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. 		
@D	Xu, Y.//Ren, C.//Chen, R.//Zeng, R. 	Draft Genome Sequence of Oil-Degrading Bacterium Gallaecimonas pentaromativorans  Strain YA_1 from the Southwest Indian Ocean.	Genome Announcements	2016	4		e00764-16			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. 		
@D	Xu, Y.//Tan, G.//Ke, M.//Li, J.//Tang, Y.//Meng, S.//Niu, J.//Wang, Y.//Liu, R.//Wu, H.//Bai, L.//Zhang, L.//Zhang, B. 	Enhanced lincomycin production by co-overexpression of metK1 and metK2 in Streptomyces lincolnensis.	J. Ind. Microbiol. Biotechnol.	2018	45		345-355			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. 		
@D	Xu, Y.//Wang, A.//Tao, F.//Su, F.//Tang, H.//Ma, C.//Xu, P. 	Genome Sequence of Enterobacter cloacae subsp. dissolvens SDM, an Efficient Biomass-Utilizing Producer of Platform Chemical 2,3-Butanediol.	J. Bacteriol.	2012	194		897-898			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. 		
@D	Xu, Y.//Yu, M.//Shen, A. 	Complete Genome Sequence of the Polychlorinated Biphenyl Degrader Rhodococcus sp. WB1.	Genome Announcements	2016	4		e00996-16			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. 		
@D	Xu, Z. et al. 	Genome Biology of Actinobacillus pleuropneumoniae JL03, an Isolate of Serotype 3 Prevalent in China.	PLoS ONE	2008	3		e1450			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. 		
@D	Xu, Z.//Chen, X.//Li, L.//Li, T.//Wang, S.//Chen, H.//Zhou, R. 	Comparative genomic characterization of Actinobacillus pleuropneumoniae.	J. Bacteriol.	2010	192		5625-5636			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. 		
@D	Xu, Z.//Puranik, R.//Hu, J.//Xu, H.//Han, D. 	Complete genome sequence of Thermotoga sp. strain RQ7.	Standards in Genomic Sciences	2017	12		62			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. 		
@D	Xu, Z.//Xia, J.//Feng, X.//Li, S.//Xu, H.//Bo, F.//Sun, Z. 	Genome Sequence of Streptomyces albulus PD-1, a Productive Strain for Epsilon-Poly-L-Lysine and Poly-L-Diaminopropionic Acid.	Genome Announcements	2014	2		e00297-14			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. 		
@D	Xu, Z.//Yin, H.//Tian, Z.//Zhou, Y.//Ai, S. 	Electrochemical immunoassays for the detection the activity of DNA methyltransferase by using the rolling circle amplification technique.	Microchimica Acta	2014	181		471-477			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. 		
@D	Xu, Z.//Zhang, X.Y.//Su, H.N.//Yu, Z.C.//Liu, C.//Li, H.//Chen, X.L.//Song, X.Y.//Xie, B.B.//Qin, Q.L.//Zhou, B.C.//Shi, M.//Huang, Y.//Zhang, Y.Z. 	Oceanisphaera profunda sp. nov., a marine bacterium isolated from deep-sea sediment, and emended description of the genus Oceanisphaera.	Int. J. Syst. Evol. Microbiol.	2014	64		1252-1256			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. 		
@D	Xu, Z.H.//Han, D.M.//Cao, J.J.//Saini, U. 	Cloning and characterization of the TneDI restriction-modification system of Thermotoga neapolitana.	Extremophiles	2011	15		665-672			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. 		
@D	Xue, C.//Cao, L.//Zhang, R.//He, J.//Li, S.//Hong, Q. 	Draft Genome Sequence of Sphingobium sp. Strain BHC-A, Revealing Genes for the Degradation of Hexachlorocyclohexane.	Genome Announcements	2014	2		e00254-14			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. 		
@D	Xue, J.//He, Z. 	Enzymology of BamHI DNA methylase.	Shengwu Huaxue Zazhi	1991	7		13-20			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. 		
@D	Xydas, S.//Lange, C.S.//Phil, D.//Neimark, H.C. 	Effect of methylation on the electrophoretic mobility of chromosomal DNA in pulse-field agarose gels.	Appl. Theor. Electrophor.	1996	6		43-47			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. 		
@D	Yaakop, A.S.//Chan, C.S.//Kahar, U.M.//Ee, R.//Chan, K.G.//Goh, K.M. 	Draft Genome Sequence of Erythrobacter vulgaris Strain O1, a Glycosyl Hydrolase-Producing Bacterium.	Genome Announcements	2015	3		e00457-15			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. 		
@D	Yaakop, A.S.//Chan, K.G.//Gan, H.M.//Goh, K.M. 	Draft Genome Sequence of Yellow Pigmented Jeotgalibacillus alimentarius JY-13T, the First Halophile Strain of the Genus Jeotgalibacillus.	Genome Announcements	2015	3		e01224-15			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. 		
@D	Yacoub, E.//Sirand-Pugnet, P.//Barre, A.//Blanchard, A.//Hubert, C.//Maurier, F.//Bouilhol, E.//Ben Abdelmoumen, M.B. 	Genome Sequences of Two Tunisian Field Strains of Avian Mycoplasma, M. meleagridis and M. gallinarum.	Genome Announcements	2016	4		e00558-16			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. 		
@D	Yacoub, E.//Sirand-Pugnet, P.//Blanchard, A.//Ben Abdelmoumen, M.B. 	Genome Sequence of Mycoplasma meleagridis Type Strain 17529.	Genome Announcements	2015	3		e00484-15			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. 		
@D	Yagubi, A.I.//Castle, A.J.//Kropinski, A.M.//Banks, T.W.//Svircev, A.M. 	Complete Genome Sequence of Erwinia amylovora Bacteriophage vB_EamM_Ea35-70.	Genome Announcements	2014	2		e00413-14			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. 		
@D	Yahara, K.//Furuta, Y.//Oshima, K.//Yoshida, M.//Azuma, T.//Hattori, M.//Uchiyama, I.//Kobayashi, I. 	Chromosome painting in silico in a bacterial species reveals fine population structure.	Mol. Biol. Evol.	2013	30		1454-1464			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. 		
@D	Yahara, K.//Horie, R.//Kobayashi, I.//Sasaki, A. 	Evolution of DNA double-strand break repair by gene conversion: Coevolution between a phage and a restriction-modification system.	Genetics	2007	176		513-526			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. 		
@D	Yahara, K.//Kobayashi, I. 	Evolution of selfish homing endonuclease genes in the absence of horizontal transfer.	Saibo Kogaku	2010	29		190-195					
@D	Yaharaa, K.//Fukuyo, M.//Sasaki, A.//Kobayashi, I. 	Evolutionary maintenance of selfish homing endonuclease genes in the absence of horizontal transfer.	Proc. Natl. Acad. Sci. U. S. A.	2009	106		18861-18866			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 		
@D	Yaish, M.W. 	Draft Genome Sequence of the Endophytic Bacillus aryabhattai Strain SQU-R12, Identified from Phoenix dactylifera L. Roots.	Genome Announcements	2017	5		e00718-17			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. 		
@D	Yaish, M.W. 	Draft Genome Sequence of Endophytic Bacterium Enterobacter asburiae PDA134, Isolated from Date Palm (Phoenix dactylifera L.) Roots.	Genome Announcements	2016	4		e00848-16			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. 		
@D	Yamada, T.//Chuchird, N.//Kawasaki, T.//Nishida, K.//Hiramatsu, S. 	Chlorella viruses as a source of novel enzymes.	J. Biosci. Bioeng.	1999	88		353-361			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. 		
@D	Yamada, Y.//Mizuno, H.//Sato, H.//Akagawa, M.//Yamasato, K. 	A new restriction endonuclease from Agrobacterium gelatinovorum, a marine agrobacterium (AgeI).	Agric. Biol. Chem.	1989	53		1747-1749			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. 		
@D	Yamada, Y.//Murakami, M. 	A new restriction endonuclease from Acetobacter pasteurianus (ApaI).	Agric. Biol. Chem.	1985	49		3627-3629			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. 		
@D	Yamada, Y.//Sasaki, J. 	Distribution of Restriction Enzymes in Strains of Acetobacter (Gluconoacetobacter) Liquefaciens.	J. Gen. Appl. Microbiol.	1984	30		309-312			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. 		
@D	Yamada, Y.//Sato, H. 	The manganese ion strongly activates restriction endonuclease AatII from Acetobacter aceti IFO 3281.	Agric. Biol. Chem.	1989	53		1745-1746			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+. 		
@D	Yamada, Y.//Yoshioka, H.//Sasaki, J.//Tahara, Y. 	Purification, properties and recognition sequence of site-specific restriction endonuclease from "Acetobacter liquefaciens".	J. Gen. Appl. Microbiol.	1983	29		157-166			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). 		
@D	Yamaguchi, H.//Shimura, Y.//Suzuki, S.//Yamagishi, T.//Tatarazako, N.//Kawachi, M. 	Complete Genome Sequence of Cyanobium sp. NIES-981, a Marine Strain Potentially Useful for Ecotoxicological Bioassays.	Genome Announcements	2016	4		e00736-16			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. 		
@D	Yamaguchi, H.//Suzuki, S.//Kawachi, M. 	Improved Draft Genome Sequence of Microcystis aeruginosa NIES-298, a Microcystin-Producing Cyanobacterium from Lake Kasumigaura, Japan.	Genome Announcements	2018	6		e01551-17			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. 		
@D	Yamaguchi, H.//Suzuki, S.//Kawachi, M. 	Draft Genome Sequence of Microcystis aeruginosa NIES-87, a Bloom-Forming Cyanobacterium from Lake Kasumigaura, Japan.	Genome Announcements	2018	6		e01596-17			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. 		
@D	Yamaguchi, H.//Suzuki, S.//Sano, T.//Tanabe, Y.//Nakajima, N.//Kawachi, M. 	Draft Genome Sequence of Microcystis aeruginosa NIES-98, a Non-Microcystin-Producing Cyanobacterium from Lake Kasumigaura, Japan.	Genome Announcements	2016	4		e01187-16			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. 		
@D	Yamaguchi, H.//Suzuki, S.//Tanabe, Y.//Osana, Y.//Shimura, Y.//Ishida, K.//Kawachi, M. 	Complete Genome Sequence of Microcystis aeruginosa NIES-2549, a Bloom-Forming Cyanobacterium from Lake Kasumigaura, Japan.	Genome Announcements	2015	3		e00551-15			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. 		
@D	Yamaguchi, T.//Asano, Y. 	Draft Genome Sequence of an Aldoxime Degrader, Rhodococcus sp. Strain YH3-3.	Genome Announcements	2016	4		e00406-16			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. 		
@D	Yamaguchi, T.//Asano, Y. 	Complete Genome Sequence of an Aldoxime Degrader, Bacillus sp. OxB-1.	Genome Announcements	2015	3		e00025-15			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. 		
@D	Yamaguchi, T.//Nishifuji, K.//Sasaki, M.//Fudaba, Y.//Aepfelbacher, M.//Takata, T.//Ohara, M.//Komatsuzawa, H.//Amagai, M.//Sugai, M. 	Identification of the Staphylococcus aureus etd pathogenicity island which encodes a novel exfoliative toxin, ETD, and EDIN-B.	Infect. Immun.	2002	70		5835-5845			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. 		
@D	Yamaichi, Y.//Chao, M.C.//Sasabe, J.//Clark, L.//Davis, B.M.//Yamamoto, N.//Mori, H.//Kurokawa, K.//Waldor, M.K. 	High-resolution genetic analysis of the requirements for horizontal transmission  of the ESBL plasmid from Escherichia coli O104:H4.	Nucleic Acids Res.	2015	43		348-360			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. 		
@D	Yamamoto, K.//Asano, Y. 	Genome Sequence of Microbacterium sp. Strain TPU 3598, a Lumichrome Producer.	Genome Announcements	2017	5		e00204-17			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. 		
@D	Yamamoto, K.//Tamaki, H.//Cadillo-Quiroz, H.//Imachi, H.//Kyrpides, N.//Woyke, T.//Goodwin, L.//Zinder, S.H.//Kamagata, Y.//Liu, W.T. 	Complete Genome Sequence of Methanolinea tarda NOBI-1T, a Hydrogenotrophic Methanogen Isolated from Methanogenic Digester Sludge.	Genome Announcements	2014	2		e00876-14			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. 		
@D	Yamamoto, K.//Tamaki, H.//Cadillo-Quiroz, H.//Imachi, H.//Kyrpides, N.//Woyke, T.//Goodwin, L.//Zinder, S.H.//Kamagata, Y.//Liu, W.T. 	Complete Genome Sequence of Methanoregula formicica SMSPT, a Mesophilic Hydrogenotrophic Methanogen Isolated from a Methanogenic Upflow Anaerobic Sludge   Blanket Reactor.	Genome Announcements	2014	2		e00870-14			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. 		
@D	Yamamoto, N.//Inoue, D.//Kuroda, M.//Ike, M. 	Draft Genome Sequence of Pseudonocardia sp. Strain N23, a 1,4-Dioxane-Degrading Bacterium.	Genome Announcements	2017	5		e01240-17			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. 		
@D	Yamamoto, S.//Lee, K.I.//Morita, M.//Arakawa, E.//Izumiya, H.//Ohnishi, M. 	Single Circular Chromosome Identified from the Genome Sequence of the Vibrio cholerae O1 bv. El Tor Ogawa Strain V060002.	Genome Announcements	2018	6		e00564-18			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. 		
@D	Yamamoto, Y. et al. 	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.	DNA Res.	1997	4		91-113			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. 		
@D	Yamamura, H.//Ohnishi, Y.//Ishikawa, J.//Ichikawa, N.//Ikeda, H.//Sekine, M.//Harada, T.//Horinouchi, S.//Otoguro, M.//Tamura, T.//Suzuki, K.//Hoshino, Y.//Arisawa, A.//Nakagawa, Y.//Fujita, N.//Hayakawa, M. 	Complete genome sequence of the motile actinomycete Actinoplanes missouriensis 431(T) (= NBRC 102363(T)).	Standards in Genomic Sciences	2012	7		294-303			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. 		
@D	Yamaoka, S.//Tamura, T.//Takenobu, H.//Kojo, T.//Tanaka, H.//Inagaki, K. 	Cloning and nucleotide sequence of the genes encoding restriction-modification system from acidophilic bacterium Acidocella facilis 22M.	Sci. Reports. Fac. Agric. Okayama Univ.	2003	92		9-15			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. 		
@D	Yamauchi, T.//Moritoh, S.//Johzuka-Hisatomi, Y.//Ono, A.//Terada, R.//Nakamura, I.//Iida, S. 	Alternative splicing of the rice OsMET1 genes encoding maintenance DNA methyltransferase.	J. Plant Physiol.	2008	165		1774-1782			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. 		
@D	Yamazaki, T.//Matsuo, J.//Kikuchi, M.//Miyamoto, K.//Oka, K.//Takahashi, M.//Takahashi, S.//Okubo, T.//Yamaguchi, H. 	Draft Genome Sequence of Chlamydia trachomatis Strain 54, Isolated from the Urogenital Tract of a Male in Japan.	Genome Announcements	2015	3		e01242-15			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. 		
@D	Yan, B.-X.//Li, N.//Wu, C.-X. 	The true recognizing sequence of the restriction enzyme whose recognizing sequence is nonpalindromic.	Yichuan	2002	24		420-422			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. 		
@D	Yan, J.//Deforet, M.//Boyle, K.E.//Rahman, R.//Liang, R.//Okegbe, C.//Dietrich, L.E.P.//Qiu, W.//Xavier, J.B. 	Bow-tie signaling in c-di-GMP: Machine learning in a simple biochemical network.	PLoS Comput. Biol.	2017	13		e1005677			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. 		
@D	Yan, J.//Skoko, D.//Marko, J.F. 	Near-field-magnetic-tweezer manipulation of single DNA molecules.	Phys. Rev. E Stat. Nonlin. Soft Matter Phys.	2004	70		011905			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. 		
@D	Yan, L.//Yan, M.//Xu, L.//Wei, L.//Zhang, L. 	Draft Genome Sequence of a Pseudomonas aeruginosa Strain Able To Decompose N,N-Dimethyl Formamide.	Genome Announcements	2016	4		e01609-15			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. 		
@D	Yan, P.-F.//Ye, S.-Y.//Wang, P.-Z.//Li, Q.-L.//Lu, Y.-Y.//Zhou, B. 	The restriction endonucleases from Bacillus.	Acta Biochim. Biophys. Sin.	1982	14		151-158			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. 		
@D	Yan, W.//Zhang, R.//Wei, S.//Zeng, Q.//Xiao, X.//Wang, Q.//Yan, H.//Jiao, N. 	Draft Genome Sequence of Prochlorococcus marinus Strain XMU1401, Isolated from the Western Tropical North Pacific Ocean.	Genome Announcements	2018	6		e01431-17			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. 		
@D	Yan, X.//Ge, H.//Huang, T.//Hindra, Y.D.//Teng, Q.//Crnovcic, I.//Li, X.//Rudolf, J.D.//Lohman, J.R.//Gansemans, Y.//Zhu, X.//Huang, Y.//Zhao, L.X.//Jiang, Y.//Van Nieuwerburgh, F.//Rader, C.//Duan, Y.//Shen, B. 	Strain Prioritization and Genome Mining for Enediyne Natural Products.	MBio	2016	7		e02104-16			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. 		
@D	Yan, X.J.//Xu, J.//Gu, Z.H.//Pan, C.M.//Lu, G.//Shen, Y.//Shi, J.Y.//Zhu, Y.M.//Tang, L.//Zhang, X.W.//Liang, W.X.//Mi, J.Q.//Song, H.D.//Li, K.Q.//Chen, Z.//Chen, S.J. 	Exome sequencing identifies somatic mutations of DNA methyltransferase gene DNMT3A in acute monocytic leukemia.	Nat. Genet.	2011	43		309-315			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. 		
@D	Yan, Y.//Zhao, C.W.//Zhang, Y.Z.//Zhang, Z.H.//Pan, G.L.//Liu, W.W.//Ma, Q.Y.//Hou, R.//Tan, X.M. 	Draft Genome Sequence of Enterobacter cloacae subsp. cloacae Strain 08XA1, a Fecal Bacterium of Giant Pandas.	J. Bacteriol.	2012	194		6928-6929			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. 		
@D	Yan, Y.W.//Zhang, P.P.//Zhu, T.//Quan, Z.X. 	Draft Genome Sequence of n-Alkane-Utilizing Acinetobacter sp. Strain BS1, Isolated from Ethane Oxidation Culture.	Genome Announcements	2018	6		e00465-18			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. 		
@D	Yanagisawa, Y.//Ito, E.//Yuasa, Y.//Maruyama, K. 	The human DNA methyltransferases DNMT3A and DNMT3B have two types of promoters with different CpG contents.	Biochim. Biophys. Acta	2002	1577		457			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. 		
@A	Yang, A.S.//Jones, P.A.//Shibata, A. 		The mutational burden of 5-methylcytosine.			Russo, V.E.A.//Martienssen, R.A.//Riggs, A.D. 		Epigenetic Mechanisms of Gene Regulation				Cold Spring Harbor	Cold Spring Harbor Laboratory Press	1996		0		77-94									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. 		
@D	Yang, A.S.//Shen, J.-C.//Zingg, J.-M.//Mi, S.//Jones, P.A. 	DNA (cytosine-5) methyltransferase blocks DNA repair.	Proc. Amer. Assoc. Cancer Res.	1995	36		538			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. 		
@D	Yang, A.S.//Shen, J.-C.//Zingg, J.-M.//Mi, S.//Jones, P.A. 	HhaI and HpaII DNA methyltransferases bind DNA mismatches, methylate uracil and block DNA repair.	Nucleic Acids Res.	1995	23		1380-1387			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. 		
@D	Yang, C.//Zhang, W.//Ren, M.//Song, L.//Li, T.//Zhao, J. 	Whole-Genome Sequence of Microcystis aeruginosa TAIHU98, a Nontoxic Bloom-Forming Strain Isolated from Taihu Lake, China.	Genome Announcements	2013	1		e00333-13			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. 		
@D	Yang, C.C.//Baxter, B.K.//Topal, M.D. 	DNA cleavage by NaeI: protein purification, rate-limiting step, and accuracy.	Biochemistry	1994	33		14918-14925			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. 		
@D	Yang, C.C.//Topal, M.D. 	Nonidentical DNA-binding sites of endonuclease NaeI recognize different families of sequences flanking the recognition site.	Biochemistry	1992	31		9657-9664			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. 		
@D	Yang, C.H.//Wu, C.C.//Cheng, W.S.//Chung, M.C.//Tsai, Y.C.//Chang, C.H. 	A17, the First Sequenced Strain of Lactococcus lactis subsp. cremoris with Potential Immunomodulatory Functions.	Genome Announcements	2015	3		e01563-14			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. 		
@D	Yang, F. et al. 	Genome dynamics and diversity of Shigella species, the etiologic agents of bacillary dysentery.	Nucleic Acids Res.	2005	33		6445-6458			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. 		
@D	Yang, F.//Li, H.//Zhang, S.//Wang, X. 	Draft Genome Sequence of Streptococcus agalactiae Serotype Ia Strain M19, a Multidrug-Resistant Isolate from a Cow with Bovine Mastitis.	Genome Announcements	2016	4		e01093-16			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. 		
@D	Yang, F.//Tang, C.//Wang, Y.//Zhang, H.//Yue, H. 	Genome Sequence of Mycoplasma ovipneumoniae Strain SC01.	J. Bacteriol.	2011	193		5018			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. 		
@D	Yang, G.//Chen, J.//Zhou, S. 	Novibacillus thermophilus gen. nov., sp. nov., a Gram-staining-negative and moderately thermophilic member of the family Thermoactinomycetaceae.	Int. J. Syst. Evol. Microbiol.	2015	65		2591-2597			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). 		
@D	Yang, G.//Chen, S.//Zhou, S.//Liu, Y. 	Genome sequence of a dissimilatory Fe(III)-reducing bacterium Geobacter soli type strain GSS01(T).	Standards in Genomic Sciences	2015	10		118			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. 		
@D	Yang, G.//Guo, J.//Zhuang, L.//Yuan, Y.//Zhou, S. 	Desulfotomaculum ferrireducens sp. nov., a moderately thermophilic sulfate-reducing and dissimilatory Fe(III)-reducing bacterium isolated from compost.	Int. J. Syst. Evol. Microbiol.	2016	66		3022-3028			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). 		
@D	Yang, H.//Carlson, B.//Geornaras, I.//Woerner, D.//Sofos, J.//Belk, K. 	Draft Genome Sequence of Shiga Toxin-Negative Escherichia coli O157:H7 Strain C1-057, Isolated from Feedlot Cattle.	Genome Announcements	2016	4		e00049-16			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. 		
@D	Yang, H.//Fitz-Gibbon, S.//Marcotte, E.M.//Tai, J.H.//Hyman, E.C.//Miller, J.H. 	Characterization of a thermostable DNA glycosylase specific for U/G and T/G mismatches from the hyperthermophilic archaeon Pyrobaculum aerophilum.	J. Bacteriol.	2000	182		1272-1279			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. 		
@D	Yang, H.//He, T.//Wu, W.//Zhu, W.//Lu, B.//Sun, W. 	Whole-Genome Shotgun Assembly and Analysis of the Genome of Streptomyces mobaraensis DSM 40847, a Strain for Industrial Production of Microbial  Transglutaminase.	Genome Announcements	2013	1		e0014313			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. 		
@D	Yang, H.//Liao, Y.//Wang, B.//Lin, Y.//Pan, L. 	Genome Sequence of Escherichia coli XH140A, Which Produces L-Threonine.	J. Bacteriol.	2011	193		6090-6091			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. 		
@D	Yang, H.//Liao, Y.//Wang, B.//Lin, Y.//Pan, L. 	Draft Genome Sequence of Escherichia coli XH001, a Producer of L-Threonine in Industry.	J. Bacteriol.	2011	193		6406-6407			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. 		
@D	Yang, H.//Liao, Y.//Wang, B.//Lin, Y.//Pan, L. 	Complete Genome Sequence of Bacillus amyloliquefaciens XH7, Which Exhibits Production of Purine Nucleosides.	J. Bacteriol.	2011	193		5593-5594			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. 		
@D	Yang, H.//Zhang, Z.//Yan, R.//Wang, Y.//Zhu, D. 	Draft Genome Sequence of Streptomyces sp. Strain PRh5, a Novel Endophytic Actinomycete Isolated from Dongxiang Wild Rice Root.	Genome Announcements	2014	2		e00012-14			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. 		
@D	Yang, J.//Deng, C.//Hemati, N.//Hanash, S.M.//Richardson, B.C. 	Effect of mitogenic stimulation and DNA methylation on human T cell DNA methyltransferase expression and activity.	J. Immunol.	1997	159		1303-1309			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. 		
@D	Yang, J.//Dong, C.X.//Huang, X.//Zhao, J.D. 	Sulfonation of polyvinylidene difluoride resin and its application in extraction of restriction enzymes from DNA digestion solutions.	Anal. Biochem.	2003	322		99-103			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. 		
@D	Yang, J.//Malik, H.S.//Eickbush, T.H. 	Identification of the endonuclease domain encoded by R2 and other site-specific, non-long terminal repeat retrotransposable elements.	Proc. Natl. Acad. Sci. U. S. A.	1999	96		7847-7852			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. 		
@D	Yang, J.//Mohr, G.//Perlman, P.S.//Lambowitz, A.M. 	Group II intron mobility in yeast mitochondria: target DNA-primed reverse transcription activity of aI1 and reverse splicing into DNA transposition sites in vitro.	J. Mol. Biol.	1998	282		505-523			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. 		
@D	Yang, J.//Zimmerly, S.//Perlman, P.S.//Lambowitz, A.M. 	Efficient integration of an intron RNA into double-stranded DNA by reverse splicing.	Nature	1996	381		332-335			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. 		
@D	Yang, J.A.//Kwon, K.K.//Oh, H.M. 	Complete Genome Sequence of Flavobacteriales Bacterium Strain UJ101 Isolated from a Xanthid Crab.	Genome Announcements	2017	5		e01551-16			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. 		
@D	Yang, J.L.//Guo, X.P.//Chen, Y.R.//Gao, W.//Ding, D.W. 	Draft Genome Sequence of Shewanella sp. ECSMB14102, a Mussel Recruitment-Promoting Bacterium Isolated from the East China Sea.	Genome Announcements	2015	3		e00670-15			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. 		
@D	Yang, J.L.//Guo, X.P.//Ding, D.W. 	Draft Genome Sequence of Shewanella sp. ECSMB14101, Isolated from the East China  Sea.	Genome Announcements	2015	3		e01388-14			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. 		
@D	Yang, J.M.//Deurraza, P.J.//Matvienko, N.//O'sullivan, D.J. 	Involvement of the LlaKR2I Methylase in Expression of the AbiR Bacteriophage Defense System in Lactococcus lactis subsp. lactis biovar   diacetylactis KR2.	J. Bacteriol.	2006	188		1920-1928			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. 		
@D	Yang, L.//Chen, Y.//Li, Z.//Shi, Y.//Li, Z.//Zhao, X. 	Complete Genome Sequence of Lactobacillus acidophilus MN-BM-F01.	Genome Announcements	2016	4		e01699-15			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. 		
@D	Yang, L.F.//Som, S.//Friedman, S. 	Effect of N-terminal deletions on the activity of EcoRII DNA methylase.	Abstr. Gen. Meet. Am. Soc. Microbiol.	1991	91		A436			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. 		
@D	Yang, M.//Lv, Y.//Xiao, J.//Wu, H.//Zheng, H.//Liu, Q.//Zhang, Y.//Wang, Q. 	Edwardsiella comparative phylogenomics reveal the new intra/inter-species taxonomic relationships, virulence evolution and niche adaptation mechanisms.	PLoS ONE	2012	7		E36987			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. 		
@D	Yang, M.-K.//Ser, S.-C.//Lee, C.-H. 	Involvement of E. coli dcm methylase in Tn3 transposition.	Proc. Natl. Sci. Counc. Repub. China B	1989	13		276-283			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. 		
@D	Yang, Q. et al. 	Balancing mcr-1 expression and bacterial survival is a delicate equilibrium between essential cellular defence mechanisms.	Nat. Commun.	2017	8		2054			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. 		
@D	Yang, Q.H.//Zhou, C.//Lin, Q.//Lu, Z.//He, L.B.//Guo, S.L. 	Draft Genome Sequence of Aeromonas sobria Strain 08005, Isolated from Sick Rana catesbeiana.	Genome Announcements	2017	5		e01352-16			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. 		
@D	Yang, R.//Liu, G.//Chen, T.//Zhang, W.//Zhang, G.//Chang, S. 	The complete genomic sequence of a novel cold-adapted bacterium, Planococcus maritimus Y42, isolated from crude oil-contaminated soil.	Standards in Genomic Sciences	2018	13		23			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. 		
@D	Yang, S.//Pappas, K.M.//Hauser, L.J.//Land, M.L.//Chen, G.L.//Hurst, G.B.//Pan, C.//Kouvelis, V.N.//Typas, M.A.//Pelletier, D.A.//Klingeman, D.M.//Chang, Y.J.//Samatova, N.F.//Brown, S.D. 	Improved genome annotation for Zymomonas mobilis.	Nat. Biotechnol.	2009	27		893-894			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. 		
@D	Yang, S.//Vera, J.M.//Grass, J.//Savvakis, G.//Moskvin, O.V.//Yang, Y.//McIlwain, S.J.//Lyu, Y.//Zinonos, I.//Hebert, A.S.//Coon, J.J.//Bates, D.M.//Sato, T.K.//Brown, S.D.//Himmel, M.E.//Zhang, M.//Landick, R.//Pappas, K.M.//Zhang, Y. 	Complete genome sequence and the expression pattern of plasmids of the model ethanologen Zymomonas mobilis ZM4 and its xylose-utilizing derivatives 8b and 2032.	Biotechnol. Biofuels.	2018	11		125			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. 		
@D	Yang, S.J.//Kang, I.//Cho, J.C. 	Genome Sequence of Strain IMCC14465, Isolated from the East Sea, Belonging to the PS1 Clade of Alphaproteobacteria.	J. Bacteriol.	2012	194		6952-6953			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. 		
@D	Yang, W.//Lee, J.Y.//Nowotny, M. 	Making and breaking nucleic acids: Two-Mg2+-ion catalysis and substrate specificity.	Mol. Cell	2006	22		5-13			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. 		
@D	Yang, W.//Li, N.//Li, M.//Zhang, D.//An, G. 	Complete Genome Sequence of Fish Pathogen Aeromonas hydrophila JBN2301.	Genome Announcements	2016	4		e01615-15			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. 		
@D	Yang, X. et al. 	A public genome-scale lentiviral expression library of human ORFs.	Nat. Methods	2011	8		659-661			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. 		
@D	Yang, X.//Cao, X.//Wang, N.//Wang, J.//Bie, P.//Lyu, Y.//Wu, Q. 	Complete Genome Sequences of Four Brucella Strains Isolated from China.	Genome Announcements	2017	5		e01034-17			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. 		
@D	Yang, X.//Chen, C.//Wang, D.//Yang, S.//Wu, R. 	Cloning and overexpression of the restriction gene of EcoRI.	Acta Biochim. Biophys. Sin.	1990	22		599-606			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]. 		
@D	Yang, X.//Huang, E.//Yesil, M.//Xiaoli, L.//Dudley, E.G.//Yousef, A.E. 	Draft Genome Sequence of Brevibacillus laterosporus OSY-I1, a Strain That Produces Brevibacillin, Which Combats Drug-Resistant Gram-Positive Bacteria.	Genome Announcements	2017	5		e01093-17			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. 		
@D	Yang, X.//Wang, Y.//Huo, G. 	Complete Genome Sequence of Lactococcus lactis subsp. lactis KLDS4.0325.	Genome Announcements	2013	1		e00962-13			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. 		
@D	Yang, X.//Xu, M.//Yang, S.T. 	Restriction modification system analysis and development of in vivo methylation for the transformation of Clostridium cellulovorans.	Appl. Microbiol. Biotechnol.	2016	100		2289-2299			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. 		
@D	Yang, X.//Xue, R.//Shen, C.//Li, S.//Gao, C.//Wang, Q.//Zhao, X. 	Genome sequence of Rhodococcus sp. R04, a polychlorinated biphenyl biodegrader.	J. Bacteriol.	2011	193		5032-5033			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. 		
@D	Yang, X.J.//Wang, S.//Cao, J.M.//Hou, J.H. 	Draft Genome Sequence of Klebsiella pneumoniae Strain AS Isolated from Zhejiang Provincial Hospital of TCM, China.	Genome Announcements	2016	4		e00930-16			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. 		
@D	Yang, Y.//Li, Q. 	Restriction enzyme SnaBI is sensitive to methylation of cytosine within its recognition sequence.	Nucleic Acids Res.	1990	18		3083			None 		
@D	Yang, Y.//Yu, X.//Zhang, R. 	Draft Genome Sequence of Ochrobactrum pseudogrignonense Strain CDB2, a Highly Efficient Arsenate-Resistant Soil Bacterium from Arsenic-Contaminated Cattle Dip   Sites.	Genome Announcements	2013	1		e00173-13			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. 		
@D	Yang, Y.//Zhang, R. 	Draft Genome Sequence of Bacillus sp. Strain CDB3, an Arsenic-Resistant Soil Bacterium Isolated from Cattle Dip Sites.	Genome Announcements	2017	5		e00429-17			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. 		
@D	Yang, Y.T.//Chen, I.T.//Lee, C.T.//Chen, C.Y.//Lin, S.S.//Hor, L.I.//Tseng, T.C.//Huang, Y.T.//Sritunyalucksana, K.//Thitamadee, S.//Wang, H.C.//Lo, C.F. 	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.	Genome Announcements	2014	2		e00816-14			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. 		
@D	Yang, Z.//Horton, J.R.//Maunus, R.//Wilson, G.G.//Roberts, R.J.//Cheng, X. 	Structure of HinP1I endonuclease reveals a striking similarity to the monomeric restriction enzyme MspI.	Nucleic Acids Res.	2005	33		1892-1901			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. 		
@D	Yang, Z.//Horton, J.R.//Zhou, L.//Zhang, X.J.//Dong, A.P.//Zhang, X.//Schlagman, S.L.//Kossykh, V.//Hattman, S.//Cheng, X.D. 	Structure of the bacteriophage T4 DNA adenine methyltransferase.	Nat. Struct. Biol.	2003	10		849-855			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. 		
@D	Yangtse, W.//Zhou, Y.//Lei, Y.//Qiu, Y.//Wei, X.//Ji, Z.//Qi, G.//Yong, Y.//Chen, L.//Chen, S. 	Genome Sequence of Bacillus licheniformis WX-02.	J. Bacteriol.	2012	194		3561-3562			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. 		
@D	Yankovsky, N.K.//Fonstein, M.Y.//Lashina, S.Y.//Bukanov, N.O.//Yakubovich, N.V.//Ermakova, L.M.//Rebentish, B.A.//Janulaitis, A.//Debabov, V.G. 	Phasmids as effective and simple tools for construction and analysis of gene libraries.	Gene	1989	81		203-210			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. 		
@D	Yano, H.//Iwamoto, T.//Nishiuchi, Y.//Nakajima, C.//Starkova, D.A.//Mokrousov, I.//Narvskaya, O.//Yoshida, S.//Arikawa, K.//Nakanishi, N.//Osaki, K.//Nakagawa, I.//Ato, M.//Suzuki, Y.//Maruyama, F. 	Population Structure and Local Adaptation of MAC Lung Disease Agent Mycobacterium avium subsp. hominissuis.	Genome Biol. Evol.	2017	9		2403-2417			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. 		
@D	Yanofsky, S.//Boyer, H.//Grable, J.//McClarin, J.//Rosenberg, J.//Greene, P. 	Mutational analysis of the EcoRI endonuclease.	J. Cell Biochem. Suppl.	1987	11C		211			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. 		
@D	Yanofsky, S.//Boyer, H.//Greene, P. 	Positive control of EcoRI endonuclease expression by the EcoRI methylase.	Abstr. Gen. Meet. Am. Soc. Microbiol.	1985	85		106			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. 		
@D	Yanofsky, S.D.//Love, R.//McClarin, J.A.//Rosenberg, J.M.//Boyer, H.W.//Greene, P.J. 	Clustering of null mutations in the EcoRI endonuclease.	Proteins	1987	2		273-282			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. 		
@D	Yao, K.//Muruvanda, T.//Allard, M.W.//Hoffmann, M. 	Complete Genome Sequences of Three Salmonella enterica subsp. enterica Serovar Saintpaul Isolates Associated with a 2013 Multistate Outbreak in the United  States.	Genome Announcements	2017	5		e00456-17			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. 		
@D	Yao, K.//Muruvanda, T.//Roberts, R.J.//Payne, J.//Allard, M.W.//Hoffmann, M. 	Complete Genome and Methylome Sequences of Two Salmonella enterica spp.	Genome Announcements	2016	4		e01599-15			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. 		
@D	Yao, K.//Muruvanda, T.//Roberts, R.J.//Payne, J.//Allard, M.W.//Hoffmann, M. 	Complete Genome and Methylome Sequences of Salmonella enterica subsp. enterica Serovar Panama (ATCC 7378) and Salmonella enterica subsp. enterica Serovar  Sloterdijk (ATCC 15791).	Genome Announcements	2016	4		e00133-16			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). 		
@D	Yao, K.//Roberts, R.J.//Allard, M.W.//Hoffmann, M. 	Complete Genome and Methylome Sequences of Salmonella enterica subsp. enterica Serovars Typhimurium, Saintpaul, and Stanleyville from the SARA/SARB Collection.	Genome Announcements	2017	5		e00031-17			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). 		
@D	Yao, L.//Yu, L.L.//Zhang, J.J.//Xie, X.T.//Tao, Q.//Yan, X.//Hong, Q.//Qiu, J.G.//He, J.//Ding, D.R. 	A Tetrahydrofolate-Dependent Methyltransferase Catalyzing the Demethylation of Dicamba in Sphingomonas sp. Strain Ndbn-20.	Appl. Environ. Microbiol.	2016	82		5621-5630			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. 		
@D	Yao, N.//Ren, Y.//Wang, W. 	Genome Sequence of a Thermophilic Bacillus, Geobacillus thermodenitrificans DSM465.	Genome Announcements	2013	1		e01046-13			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. 		
@D	Yao, S.//Xu, Y.//Xin, C.//Xu, L.//Liu, Y.//Li, H.//Li, J.//Zhao, J.//Cheng, C. 	Genome Sequence of Thermoactinomyces daqus H-18, a Novel Thermophilic Species Isolated from High-Temperature Daqu.	Genome Announcements	2015	3		e01394-14			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. 		
@D	Yao, X.//Sun, Q.//Liu, W.//Yin, X.//Pei, G.//Wang, Y.//An, X.//Mi, Z.//Luo, Y.//Tong, Y.//Chen, S. 	Complete Genome Sequence of Serratia rubidaea Isolated in China.	Genome Announcements	2016	4		e00283-16			We report here the first complete genome of Serratia rubidaea, isolated from a patient in China. 		
@D	Yao, Y.//Falgenhauer, L.//Kempf, V.A.//Hogardt, M.//Gottig, S.//Imirzalioglu, C.//Chakraborty, T. 	Draft Genome Sequences of Pandrug-Resistant Serratia marcescens Clinical Isolates Harboring blaNDM-1.	Genome Announcements	2017	5		e01481-16			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. 		
@D	Yao, Y.//Imirzalioglu, C.//Hain, T.//Kaase, M.//Gatermann, S.//Exner, M.//Mielke, M.//Hauri, A.//Dragneva, Y.//Bill, R.//Wendt, C.//Wirtz, A.//Domann, E.//Chakraborty, T. 	Complete Nucleotide Sequence of a Citrobacter freundii Plasmid Carrying KPC-2 in  a Unique Genetic Environment.	Genome Announcements	2014	2		e01157-14			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. 		
@D	Yao, Y.//Tang, H.//Ren, H.//Yu, H.//Wang, L.//Xu, P. 	Genome sequence of a nicotine-degrading strain of arthrobacter.	J. Bacteriol.	2012	194		5714-5715			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. 		
@D	Yao, Z.//Feng, Y.//Lin, J.//Zong, Z. 	Draft Genome Sequence of a Colistin-Resistant Klebsiella pneumoniae Clinical Strain Carrying the blaNDM-1 Carbapenemase Gene.	Genome Announcements	2017	5		e01654-16			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. 		
@D	Yao, Z.//Feng, Y.//Wei, L.//Zong, Z. 	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.	Genome Announcements	2017	5		e01549-16			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. 		
@D	Yap, H.Y.//Ghazali, K.//Wan, M.N.W.F.//Mat, I.M.N.//Zakaria, Z.//Omar, A.R. 	Draft Genome Sequence of Pasteurella multocida subsp. multocida Strain PMTB, Isolated from a Buffalo.	Genome Announcements	2013	1		e00872-13			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. 		
@D	Yap, K.P.//Gan, H.M.//Teh, C.S.//Baddam, R.//Chai, L.C.//Kumar, N.//Tiruvayipati, S.A.//Ahmed, N.//Thong, K.L. 	Genome Sequence and Comparative Pathogenomics Analysis of a Salmonella enterica Serovar Typhi Strain Associated with a Typhoid Carrier in Malaysia.	J. Bacteriol.	2012	194		5970-5971			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. 		
@D	Yap, K.P.//Teh, C.S.//Baddam, R.//Chai, L.C.//Kumar, N.//Avasthi, T.S.//Ahmed, N.//Thong, K.L. 	Insights from the Genome Sequence of a Salmonella enterica Serovar Typhi Strain Associated with a Sporadic Case of Typhoid Fever in Malaysia.	J. Bacteriol.	2012	194		5124-5125			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. 		
@D	Yarmolinsky, M.B. 	Programmed cell death in bacterial populations.	Science	1995	267		836-837			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. 		
@D	Yasar-Yildiz, S.//Kambourova, M.//Arga, K.Y.//Toksoy, O.E. 	Draft Genome Sequence of Exopolysaccharide-Producing Thermophilic Bacterium Brevibacillus thermoruber Strain 423.	Genome Announcements	2013	1		e00774-13			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. 		
@D	Yasawong, M. et al. 	Complete genome sequence of Arcanobacterium haemolyticum type strain (11018).	Standards in Genomic Sciences	2010	3		126-135			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. 		
@D	Yassin, A.F.//Lapidus, A.//Han, J.//Reddy, T.B.//Huntemann, M.//Pati, A.//Ivanova, N.//Markowitz, V.//Woyke, T.//Klenk, H.P.//Kyrpides, N.C. 	High quality draft genome sequence of Corynebacterium ulceribovis type strain IMMIB-L1395(T) (DSM 45146(T)).	Standards in Genomic Sciences	2015	10		50			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. 		
@D	Yasui, K.//Kano, Y.//Tanaka, K.//Watanabe, K.//Shimizu-Kadota, M.//Yoshikawa, H.//Suzuki, T. 	Improvement of bacterial transformation efficiency using plasmid artificial modification.	Nucleic Acids Res.	2009	37		e3			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. 		
@D	Yasuike, M.//Nakamura, Y.//Kai, W.//Fujiwara, A.//Fukui, Y.//Satomi, M.//Sano, M. 	Draft Genome Sequence of Agarivorans albus Strain MKT 106T, an Agarolytic Marine  Bacterium.	Genome Announcements	2013	1		e00367-13			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. 		
@D	Yasuike, M.//Nishiki, I.//Iwasaki, Y.//Nakamura, Y.//Fujiwara, A.//Shimahara, Y.//Kamaishi, T.//Yoshida, T.//Nagai, S.//Kobayashi, T.//Katoh, M. 	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.	PLoS ONE	2017	12		E0173198			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. 		
@D	Yates, R.//Howieson, J.//De Meyer, S.E.//Tian, R.//Seshadri, R.//Pati, A.//Woyke, T.//Markowitz, V.//Ivanova, N.//Kyrpides, N.//Loi, A.//Nutt, B.//Garau, G.//Sulas, L.//Reeve, W. 	High-quality permanent draft genome sequence of Rhizobium sullae strain WSM1592;  a Hedysarum coronarium microsymbiont from Sassari, Italy.	Standards in Genomic Sciences	2015	10		44			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. 		
@D	Yau, E.K.//Coward, J.K. 	The synthesis of complex 6'-alkynyl-6'-dethia analogs of s-adenosylhomocysteine as potential inhibitors of methyltransferases.	ACS Abstracts	1989	198		100			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. 		
@D	Yau, S.//Lauro, F.M.//DeMaere, M.Z.//Brown, M.V.//Thomas, T.//Raftery, M.J.//Andrews-Pfannkoch, C.//Lewis, M.//Hoffman, J.M.//Gibson, J.A.//Cavicchioli, R. 	Virophage control of antarctic algal host-virus dynamics.	Proc. Natl. Acad. Sci. U. S. A.	2011	108		6163-6168			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. 		
@D	Yaung, S.J.//Esvelt, K.M.//Church, G.M. 	Complete Genome Sequences of T4-Like Bacteriophages RB3, RB5, RB6, RB7, RB9, RB10, RB27, RB33, RB55, RB59, and RB68.	Genome Announcements	2015	3		e01122-14			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. 		
@A	Yazdanparast, S.//Toma, E.//Karska-Wysocki, B. 		Characterization of methicillin-resistant Staphylococcus aureus isolated at Hotel-Dieu Hospital, Montreal.			 		Ottawa Life Sciences Internl Conf. and Exhibit.				Ottawa, Ontario		2001		0		Abstract #P301									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 		
@A	Yazdanparast, S.//Toma, E.//Karska-Wysocki, B. 		Restriction enzyme activity for subgenomic discrimination of  Methicillin-resistant Staphylococcus aureus.			 		Abstracts of IBC's 7th Annual World Congress				Boston, MA		2002		0		abstract #100									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. 		
@D	Ybazeta, G.//Douglas, L.//Graham, J.//Fraleigh, N.L.//Murad, Y.//Perez, J.//Diaz-Mitoma, F.//Tilbe, K.//Nokhbeh, R. 	Complete Genome Sequence of Enterococcus thailandicus Strain a523 Isolated from Urban Raw Sewage.	Genome Announcements	2017	5		e01298-17			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. 		
@D	Ye, C.//Zheng, H.//Zhang, J.//Jing, H.//Wang, L.//Xiong, Y.//Wang, W.//Zhou, Z.//Sun, Q.//Luo, X.//Du, H.//Gottschalk, M.//Xu, J. 	Clinical, experimental, and genomic differences between intermediately pathogenic, highly pathogenic, and epidemic Streptococcus suis.	J. Infect. Dis.	2009	199		97-107			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. 		
@D	Ye, J.//Ren, C.//Shan, X.//Zeng, R. 	Draft Genome Sequence of Aldehyde-Degrading Strain Halomonas axialensis ACH-L-8.	Genome Announcements	2016	4		e00287-16			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. 		
@D	Ye, L.//Hildebrand, F.//Dingemans, J.//Ballet, S.//Laus, G.//Matthijs, S.//Berendsen, R.//Cornelis, P. 	Draft Genome Sequence Analysis of a Pseudomonas putida W15Oct28 Strain with Antagonistic Activity to Gram-Positive and Pseudomonas sp. Pathogens.	PLoS ONE	2014	9		E110038			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. 		
@D	Ye, M.//Tu, J.//Jiang, J.//Bi, Y.//You, W.//Zhang, Y.//Ren, J.//Zhu, T.//Cao, Z.//Yu, Z.//Shao, C.//Shen, Z.//Ding, B.//Yuan, J.//Zhao, X.//Guo, Q.//Xu, X.//Huang, J.//Wang, M. 	Clinical and Genomic Analysis of Liver Abscess-Causing Klebsiella pneumoniae Identifies New Liver Abscess-Associated Virulence Genes.	Front Cell Infect Microbiol	2016	6		165			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. 		
@D	Ye, P.//Luan, Y.//Chen, K.//Liu, Y.//Xiao, C.//Xie, Z. 	MethSMRT: an integrative database for DNA N6-methyladenine and N4-methylcytosine  generated by single-molecular real-time sequencing.	Nucleic Acids Res.	2017	45		D85-D89			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. 		
@D	Ye, W.//Ye, S.//Liu, J.//Chang, S.//Chen, M.//Zhu, B.//Guo, L.//An, Q. 	Genome Sequence of the Pathogenic Herbaspirillum seropedicae Strain Os34, Isolated from Rice Roots.	J. Bacteriol.	2012	194		6993-6994			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. 		
@D	Ye, Y.//Stivers, J.T. 	Fluorescence-based high-throughput assay for human DNA (cytosine-5)-methyltransferase 1.	Anal. Biochem.	2010	401		168-172			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. 		
@D	Yebra, M.J.//Bhagwat, A.S. 	A cytosine methyltransferase converts 5-methylcytosine in DNA to thymine.	Biochemistry	1995	34		14752-14757			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. 		
@D	Yebra, M.J.//Bhagwat, A.S. 	A novel repetitive sequence lies near the gene encoding a cytosine methyltransferase in the cyanobacterium Dactylococcopsis salina.	Gene	1995	164		71-74			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. 		
@D	Yebra, M.J.//Bhagwat, A.S. 	A rapid and sensitive method to measure DNA endonuclease activity.	Nucleic Acids Res.	1993	21		5797-5798			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. 		
@D	Yebra, M.J.//Novella, I.S.//Barbes, C.//Aparicio, J.F.//Martin, C.G.//Hardisson, C.//Sanchez, J. 	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.	J. Gen. Microbiol.	1991	137		1279-1284			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. 		
@D	Yebra, M.J.//Sanchez, J.//Martin, C.G.//Hardisson, C.//Barbes, C. 	The effect of sinefungin and synthetic analogues on RNA and DNA methyltransferase from Streptomyces.	J. Antibiot. (Tokyo)	1991	44		1141-1147			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. 		
@D	Yee, L.//Hosoyama, A.//Ohji, S.//Tsuchikane, K.//Shimodaira, J.//Yamazoe, A.//Fujita, N.//Suzuki-Minakuchi, C.//Nojiri, H. 	Complete Genome Sequence of a Dimethyl Sulfide-Utilizing Bacterium, Acinetobacter guillouiae Strain 20B (NBRC 110550).	Genome Announcements	2014	2		e01048-14			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. 		
@D	Yee, M.//Klinzing, D.//Wei, J.R.//Gengenbacher, M.//Rubin, E.J.//Chien, J.Y.//Hsueh, P.R.//Dick, T. 	Draft Genome Sequence of Mycobacterium avium 11.<jour_book>Genome Announc.		2017	5		e00766-17			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. 		
@D	Yee, M.//Klinzing, D.//Wei, J.R.//Gengenbacher, M.//Rubin, E.J.//Dick, T. 	Draft Genome Sequence of Mycobacterium abscessus Bamboo.	Genome Announcements	2017	5		e00388-17			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. 		
@D	Yen, Ly.H.T.//Park, S.-Y.//Kim, J.-S. 	Cloning, crystallization and preliminary X-ray diffraction analysis of an intact DNA methyltransferase of a type I restriction-modification enzyme from Vibrio vulnificus.	Acta Crystallogr. F Struct. Biol. Cryst. Commun.	2014	70		489-492			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%. 		
@D	Yen, R.-W.C.//Vertino, P.M.//Nelkin, B.D.//Yu, J.J.//El-Deiry, W.//Cumaraswamy, A.//Lennon, G.G.//Trask, B.J.//Celano, P.//Baylin, S.B. 	Isolation and characterization of the cDNA encoding human DNA methyltransferase.	Nucleic Acids Res.	1992	20		2287-2291			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. 		
@D	Yeo, C.C.//Tham, J.M.//Kwong, S.M.//Poh, C.L. 	Characterization of the Pac25I restriction-modification genes isolated from the endogenous pRA2 plasmid of Pseudomonas alcaligenes NCIB 9867.	Plasmid	1998	40		203-213			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. 		
@D	Yeo, I.C.//Lee, N.K.//Hahm, Y.T. 	Genome Sequencing of Bacillus subtilis SC-8, Antagonistic to the Bacillus cereus Group, Isolated from Traditional Korean Fermented-Soybean Food.	J. Bacteriol.	2012	194		536-537			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. 		
@D	Yeoman, C.J.//Yildirim, S.//Thomas, S.M.//Durkin, A.S.//Torralba, M.//Sutton, G.//Buhay, C.J.//Ding, Y.//Dugan-Rocha, S.P.//Muzny, D.M.//Qin, X.//Gibbs, R.A.//Leigh, S.R.//Stumpf, R.//White, B.A.//Highlander, S.K.//Nelson, K.E.//Wilson, B.A. 	Comparative genomics of Gardnerella vaginalis strains reveals substantial differences in metabolic and virulence potential.	PLoS ONE	2010	5		E12411			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. 		
@D	Yeon, S.M.//Kim, Y.C. 	Complete sequence and organization of the Sphingobium chungbukense DJ77 pSY2 plasmid.	J. Microbiol.	2011	49		684-688			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. 		
@D	Yergeau, E.//Lawrence, J.R.//Waiser, M.J.//Korber, D.R.//Greer, C.W. 	Metatranscriptomic analysis of the response of river biofilms to pharmaceutical products, using anonymous DNA microarrays.	Appl. Environ. Microbiol.	2010	76		5432-5439			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. 		
@D	Yerrapragada, S. et al. 	Extreme Sensory Complexity Encoded in the 10-Megabase Draft Genome Sequence of the Chromatically Acclimating Cyanobacterium Tolypothrix sp. PCC 7601.	Genome Announcements	2015	3		e00355-15			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. 		
@D	Yesufu, H.M.I.//Hanley, A.//Rinaldi, A.//Adams, R.L.P. 	DNA methylase from Pisum sativum.	Biochem. J.	1991	273		469-475			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. 		
@D	Yew, S.M.//Chan, C.L.//Soo-Hoo, T.S.//Na, S.L.//Ong, S.S.//Hassan, H.//Ngeow, Y.F.//Hoh, C.C.//Lee, K.W.//Yee, W.Y.//Ng, K.P. 	Draft Genome Sequence of Dematiaceous Coelomycete Pyrenochaeta sp. Strain UM 256, Isolated from Skin Scraping.	Genome Announcements	2013	1		e00158-13			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. 		
@D	Yi, C.Q.//Fong, C.C.//Chen, W.W.//Qi, S.J.//Tzang, C.H.//Lee, S.T.//Yang, M.S. 	Interactions between carbon nanotubes and DNA polymerase and restriction endonucleases.	Nanotechnol.	2007	18		025102			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. 		
@D	Yi, H.//Cho, Y.J.//Hur, H.G.//Chun, J. 	Genome sequence of Escherichia coli AA86, isolated from cow feces.	J. Bacteriol.	2011	193		3681			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. 		
@D	Yi, H.//Cho, Y.J.//Yong, D.//Chun, J. 	Genome Sequence of Escherichia coli J53, a Reference Strain for Genetic Studies.	J. Bacteriol.	2012	194		3742-3743			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). 		
@D	Yi, J.L.//Wang, J.//Li, Q.//Liu, Z.X.//Zhang, L.//Liu, A.X.//Yu, J.F. 	Draft Genome Sequence of the Bacterium Lysobacter capsici X2-3, with a Broad Spectrum of Antimicrobial Activity against Multiple Plant-Pathogenic Microbes.	Genome Announcements	2015	3		e00589-15			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. 		
@D	Yi, L.//Guo, X.//Liu, L.//Shao, C.//Lu, X. 	First Report on the Complete Genome Sequence of Lactobacillus crustorum MN047, a  Potent Probiotic Strain Isolated from Koumiss in China.	Genome Announcements	2017	5		e00048-17			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. 		
@D	Yi, L.//Tang, C.//Peng, Q.//Peng, Q.//Chai, L. 	Draft Genome Sequence of Perfluorooctane Acid-Degrading Bacterium Pseudomonas parafulva YAB-1.	Genome Announcements	2015	3		e00935-15			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. 		
@D	Yi, Y.//de Jong, A.//Spoelder, J.//Elzenga, J.T.//van Elsas, J.D.//Kuipers, O.P. 	Draft Genome Sequence of Bacillus mycoides M2E15, a Strain Isolated from the Endosphere of Potato.	Genome Announcements	2016	4		e00031-16			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. 		
@D	Yilder, C.//Onsan, Z.I.//Kirdar, B. 	Optimization of starting time and period of induction and inducer concentration in the production of the restriction enzyme EcoRI from recombinant Escherichia coli 294.	Turk. J. Chem.	1998	22		221-226			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. 		
@D	Yildirim, S.//Elhanafi, D.//Lin, W.//Hitchins, A.D.//Siletzky, R.M.//Kathariou, S. 	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.	Appl. Environ. Microbiol.	2010	76		5577-5584			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. 		
@D	Yildirim, S.//Lin, W.//Hitchins, A.D.//Jaykus, L.A.//Altermann, E.//Klaenhammer, T.R.//Kathariou, S. 	Epidemic clone I-specific genetic markers in strains of Listeria monocytogenes serotype 4b from foods.	Appl. Environ. Microbiol.	2004	70		4158-4164			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. 		
@D	Yim, A.K.//Kwok, J.S.//Yu, A.C.//Leung, A.K.//Lau, H.H.//Chan, T.F.//Ip, M.//Tsui, S.K. 	Draft Genome Sequence of Extensively Drug-Resistant Acinetobacter baumannii Strain CUAB1 from a Patient in Hong Kong, China.	Genome Announcements	2015	3		e00442-15			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. 		
@D	Yin, C.//Chen, D.S.//Zhuge, J.//McKenna, D.//Sagurton, J.//Wang, G.//Huang, W.//Dimitrova, N.//Fallon, J.T. 	Complete Genome Sequences of Four Toxigenic Clostridium difficile Clinical Isolates from Patients of the Lower Hudson Valley, New York, USA.	Genome Announcements	2018	6		e01537-17			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. 		
@D	Yin, H.//Zhang, X.//Liang, Y.//Xiao, Y.//Niu, J.//Liu, X. 	Draft Genome Sequence of the Extremophile Acidithiobacillus thiooxidans A01, Isolated from the Wastewater of a Coal Dump.	Genome Announcements	2014	2		e00222-14			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). 		
@D	Yin, H.S.//Zhou, Y.L.//Xu, Z.N.//Chen, L.J.//Zhang, D.//Ai, S.Y. 	An electrochemical assay for DNA methylation, methyltransferase activity and inhibitor screening based on methyl binding domain protein.	Biosensors and Bioelectronics	2013	41		492-497			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. 		
@D	Yin, J.//Chen, J.//Liu, G.//Yu, Y.//Song, L.//Wang, X.//Qu, X. 	Complete Genome Sequence of Glaciecola psychrophila Strain 170T.	Genome Announcements	2013	1		e00199-13			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. 		
@D	Yin, M. 	Molecular characteristics and comparative genomics analysis of a clinical Enterococcus casseliflavus with a resistance plasmid.	Infection and Drug Resistance	2018	11		2159-2167			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. 		
@D	Yin, M.//Jiang, M.//Ren, Z.//Dong, Y.//Lu, T. 	The complete genome sequence of Streptomyces autolyticus CGMCC 0516, the producer of geldanamycin, autolytimycin, reblastatin and elaiophylin.	J. Biotechnol.	2017	252		27-31			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. 		
@D	Yin, M.//Ma, Z.//Cai, Z.//Lin, G.//Zhou, J. 	Genome Sequence Analysis Reveals Evidence of Quorum-Sensing Genes Present in Aeromonas hydrophila strain KOR1, Isolated from a Mangrove Plant (Kandelia  obovata).	Genome Announcements	2015	3		e01461-15			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. 		
@D	Yin, X.//Luan, X.//Xu, A.//Li, Q.//Cui, Z.//Valentine, D.L. 	Genome Sequence of a Marine Alkane Degrader, Alcanivorax sp. Strain 97CO-6.	Genome Announcements	2018	6		e00087-18			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. 		
@D	Yin, Y.//Withers, T.R.//Govan, J.R.//Johnson, S.L.//Yu, H.D. 	Draft Genome Sequence of a Stable Mucoid Strain of Pseudomonas aeruginosa PAO581  with a mucA25 Mutation.	Genome Announcements	2013	1		e00834-13			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. 		
@D	Yin, Y.//Withers, T.R.//Johnson, S.L.//Yu, H.D. 	Draft Genome Sequence of a Mucoid Isolate of Pseudomonas aeruginosa Strain C7447m from a Patient with Cystic Fibrosis.	Genome Announcements	2013	1		e00837-13			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. 		
@D	Yin, Y.//Withers, T.R.//Niles, R.M.//Johnson, S.L.//Yu, H.D. 	Draft Genome Sequences of Two Alginate-Overproducing Variants of Pseudomonas aeruginosa, PAO1-VE2 and PAO1-VE13.	Genome Announcements	2013	1		e01031-13			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. 		
@D	Yin, Y.//Yue, G.//Gao, Q.//Wang, Z.//Peng, F.//Fang, C.//Yang, X.//Pan, L. 	Genome Sequence of Pedobacter arcticus sp. nov., a Sea Ice Bacterium Isolated from Tundra Soil.	J. Bacteriol.	2012	194		6688			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. 		
@D	Yoder, J.A.//Bestor, T.H. 	A candidate mammalian DNA methyltransferase related to pmt1p of fission yeast.	Hum. Mol. Genet.	1998	7		279-284			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. 		
@D	Yoder, J.A.//Bestor, T.H. 	Genetic analysis of genomic methylation patterns in plants and mammals.	Biol. Chem.	1996	377		605-610			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. 		
@D	Yoder, J.A.//Soman, N.S.//Verdine, G.L.//Bestor, T.H. 	DNA (cytosine-5)-methyltransferases in mouse cells and tissues.  Studies with a mechanism-based probe.	J. Mol. Biol.	1997	270		385-395			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. 		
@D	Yoder, J.A.//Walsh, C.P.//Bestor, T.H. 	Cytosine methylation and the ecology of intragenomic parasites.	Trends Genet.	1997	13		335-340			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. 		
@D	Yoder, J.A.//Yen, R.-W.C.//Vertino, P.M.//Bestor, T.H.//Baylin, S.B. 	New 5' regions of the murine and human genes for DNA (cytosine-5)-methyltransferase.	J. Biol. Chem.	1996	271		31092-31097			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. 		
@D	Yohda, M. et al. 	Isolation and genomic characterization of a Dehalococcoides strain suggests genomic rearrangement during culture.	Sci. Rep.	2017	7		2230			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. 		
@D	Yokochi, T.//Robertson, K.D. 	Preferential methylation of unmethylated DNA by mammalian de novo DNA methyltransferase Dnmt3a.	J. Biol. Chem.	2002	277		11735-11745			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. 		
@D	Yokochi, T.//Robertson, K.D. 	Dimethyl sulfoxide stimulates the catalytic activity of de novo DNA methyltransferase 3a (Dnmt3a) in vitro.	Bioorg. Chem.	2004	32		234-243			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. 		
@D	Yokochi, T.//Robertson, K.D. 	DMB (DNMT-magnetic beads) assay: Measuring DNA methyltransferase activity in vitro.	Methods Mol. Biol.	2004	287		285-296			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. 		
@D	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. 	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.	Gene	2000	258		127-139			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. 		
@D	Yokoyama, S.//Oshima, K.//Nomura, I.//Hattori, M.//Suzuki, T. 	Complete Genomic Sequence of the O-Desmethylangolensin-Producing Bacterium Clostridium rRNA Cluster XIVa Strain SY8519, Isolated from Adult Human  Intestine.	J. Bacteriol.	2011	193		5568-5569			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. 		
@D	Yokoyama, S.//Oshima, K.//Nomura, I.//Hattori, M.//Suzuki, T. 	Complete Genomic Sequence of the Equol-Producing Bacterium Eggerthella sp. Strain YY7918, Isolated from Adult Human Intestine.	J. Bacteriol.	2011	193		5570-5571			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. 		
@D	Yolov, A.A.//Gromova, E.S.//Potapov, V.K.//Shabarova, Z.A. 	Interaction of EcoRII restriction and modification enzymes with synthetic DNA fragments.  V.  Study of single-stranded cleavages.	Nucleic Acids Res.	1985	13		8969-8981			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. 		
@D	Yolov, A.A.//Gromova, E.S.//Romanova, E.A.//Oretskaya, T.S.//Oganov, A.A.//Buryanov, Y.I.//Shabarova, Z.A. 	Interaction of EcoRII restriction and modification enzymes with synthetic DNA fragments.	FEBS Lett.	1984	167		147-150			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. 		
@D	Yolov, A.A.//Gromova, E.S.//Shabarova, Z.A. 	Processive cleavage of concatemer DNA duplexes by EcoRII restriction endonuclease.	Mol. Biol. Rep.	1985	10		173-176			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. 		
@D	Yolov, A.A.//Vinogradova, M.N.//Gromova, E.S.//Rosenthal, A.//Cech, D.//Veiko, V.P.//Metelev, V.G.//Kosykh, V.G.//Buryanov, Y.I.//Vayev, A.A.//Shabarova, A.Z. 	Interaction of EcoRII restriction and modification enzymes with synthetic DNA fragments. VI.  The binding and cleavage of substrates containing nucleotide analogs.	Nucleic Acids Res.	1985	13		8983-8998			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. 		
@D	Yonezawa, A.//Sugiura, Y. 	DNA binding mode of class-IIS restriction endonuclease FokI revealed by DNA footprinting analysis.	Biochim. Biophys. Acta	1994	1219		369-379			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. 		
@D	Yonezuka, K.//Shimodaira, J.//Tabata, M.//Nagase, S.//Kasai, D.//Hosoyama, A.//Yamazoe, A.//Fujita, N.//Fukuda, M. 	Draft Genome Sequence of a Chlorinated-Ethene Degrader, Cupriavidus necator Strain PHE3-6 (NBRC 110655).	Genome Announcements	2016	4		e01743-15			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. 		
@D	Yong, B.//Yang, B.Q.//Zhao, C.W.//Feng, H. 	Draft Genome Sequence of Bacillus subtilis Strain S1-4, Which Degrades Feathers Efficiently.	Genome Announcements	2013	1		e00766-13			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. 		
@D	Yong, D.//Ee, R.//Lim, Y.L.//Chang, C.Y.//Yin, W.F.//Chan, K.G. 	Insights on Quorum-Quenching Properties of Lysinibacillus fusiformis Strain RB21, a Malaysian Municipal Solid-Waste Landfill Soil Isolate, via Complete Genome  Sequence Analysis.	Genome Announcements	2015	3		e00409-15			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. 		
@D	Yoo, H.Y.//Noshari, J.//Lapeyre, J.N. 	Subunit and functional size of human placental DNA methyltransferase involved in de novo and maintenance methylation.	J. Biol. Chem.	1987	262		8066-8070			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. 		
@D	Yoo, J.//Choi, S.//Medina-Franco, J.L. 	Molecular Modeling Studies of the Novel Inhibitors of DNA Methyltransferases SGI-1027 and CBC12: Implications for the Mechanism of Inhibition of DNMTs.	PLoS ONE	2013	8		e62152			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. 		
@D	Yoo, J.//Kim, J.H.//Robertson, K.D.//Medina-Franco, J.L. 	MOLECULAR MODELING OF INHIBITORS OF HUMAN DNA METHYLTRANSFERASE WITH A CRYSTAL STRUCTURE: DISCOVERY OF A NOVEL DNMT1 INHIBITOR.	Adv. Protein Chem. Struct. Biol.	2012	87		219-247			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. 		
@D	Yoo, J.//Medina-Franco, J.L. 	Inhibitors of DNA Methyltransferases: Insights from Computational Studies.	Curr. Med. Chem.	2012	19		3475-3487			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. 		
@D	Yoo, M.//Kim, D.//Choi, K.Y.//Chae, J.C.//Zylstra, G.J.//Kim, E. 	Draft Genome Sequence and Comparative Analysis of the Superb Aromatic-Hydrocarbon Degrader Rhodococcus sp. Strain DK17.	J. Bacteriol.	2012	194		4440			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. 		
@D	Yoo, O.J.//Agarwal, K.L. 	Isolation and characterization of two proteins possessing HpaII methylase activity.	J. Biol. Chem.	1980	255		6445-6449			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. 		
@D	Yoo, O.J.//Agarwal, K.L. 	Cleavage of single strand oligonucleotides and bacteriophage PhiX174 DNA by MspI endonuclease.	J. Biol. Chem.	1980	255		10559-10562			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. 		
@D	Yoo, O.J.//Dwyer-Hallquist, P.//Agarwal, K.L. 	Purification and properties of the HpaI methylase.	Nucleic Acids Res.	1982	10		6511-6519			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. 		
@D	Yoon, H.//Suh, H.//Han, M.H.//Yoo, O.J. 	Purification and characterization of AluI methylase.	Korean Biochem. J.	1985	18		82-87			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. 		
@D	Yoon, H.//Suh, H.//Kim, K.//Han, M.H.//Yoo, O.J. 	The specificity and catalytic properties of AluI methylase.	Korean Biochem. J.	1985	18		88-93			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. 		
@D	Yoon, H.J.//Kang, K.Y.//Ahn, H.J.//Shim, S.M.//Ha, J.Y.//Lee, S.K.//Mikami, B.//Suh, S.W. 	X-ray crystallographic studies of HemK from Thermotoga maritima, an N-5-glutamine methyltransferase.	Mol. Cells	2003	16		266-269			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%). 		
@D	Yoon, H.S.//Kang, S.C.//Yoo, O.J. 	Purification and characterization of HpaI endonuclease.	Sanop Misaengmul Hakhoe Chi	1985	13		87-91			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. 		
@D	Yoon, M.Y.//Lee, K.M.//Yoon, Y.//Go, J.//Park, Y.//Cho, Y.J.//Tannock, G.W.//Yoon, S.S. 	Functional screening of a metagenomic library reveals operons responsible for enhanced intestinal colonization by gut commensal microbes.	Appl. Environ. Microbiol.	2013	79		3829-3838			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. 		
@D	Yooseph, S. et al. 	The Sorcerer II Global Ocean Sampling Expedition: Expanding the Universe of Protein Families.	PLoS Biology	2007	5		e16			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. 		
@D	Yoshida, C.//Brumwell, S.L.//Lingohr, E.J.//Ahmad, A.//Blimkie, T.M.//Kogan, B.A.//Pilsworth, J.//Rehman, M.A.//Schleicher, K.L.//Shanmugaraj, J.//Kropinski, A.M.//Nash, J.H. 	Draft Whole-Genome Sequences of 25 Salmonella enterica Strains Representing 24 Serovars.	Genome Announcements	2016	4		e01718-15			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. 		
@D	Yoshida, H.//Ishigaki, Y.//Takizawa, A.//Moro, K.//Kishi, Y.//Takahashi, T.//Matsui, H. 	Comparative Genomics of the Mucoid and Nonmucoid Strains of Streptococcus pyogenes, Isolated from the Same Patient with Streptococcal Meningitis.	Genome Announcements	2015	3		e00221-15			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. 		
@D	Yoshida, H.//Katayama, Y.//Fukushima, Y.//Taniyama, D.//Murata, Y.//Mizutani, T.//Takahashi, T. 	Draft Genome Sequence of Streptococcus canis Clinical Strain TA4, Harboring the M-Like Protein Gene and Isolated in Japan from a Patient with Bacteremia.	Genome Announcements	2018	6		e01469-17			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. 		
@D	Yoshida, H.//Wada, T.//Taniyama, D.//Takahashi, T. 	Draft Genome Sequence of Clinical Strain TANI1 of Streptococcus suis Serotype 5 Isolated from a Bacteremia Patient in Japan.	Genome Announcements	2017	5		e00260-17			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). 		
@D	Yoshida, M.//Fukano, H.//Miyamoto, Y.//Shibayama, K.//Suzuki, M.//Hoshino, Y. 	Complete Genome Sequence of a Type Strain of Mycobacterium abscessus subsp. bolletii, a Member of the Mycobacterium abscessus Complex.	Genome Announcements	2018	6		e01530-17			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. 		
@D	Yoshida, M.//Fukano, H.//Miyamoto, Y.//Shibayama, K.//Suzuki, M.//Hoshino, Y. 	Complete Genome Sequence of Mycobacterium marinum ATCC 927(T), Obtained Using Nanopore and Illumina Sequencing Technologies.	Genome Announcements	2018	6		e00397-18			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. 		
@D	Yoshida, M.//Fukano, H.//Ogura, Y.//Kazumi, Y.//Mitarai, S.//Hayashi, T.//Hoshino, Y. 	Complete Genome Sequence of Mycobacterium shigaense.	Genome Announcements	2018	6		e00552-18			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. 		
@D	Yoshida, M.//Izumiyama, S.//Fukano, H.//Sugiyama, K.//Suzuki, M.//Shibayama, K.//Hoshino, Y. 	Draft Genome Sequence of Mycobacterium sp. Strain shizuoka-1, a Novel Mycobacterium Isolated from Groundwater of a Bathing Facility in Shizuoka, Japan.	Genome Announcements	2017	5		e01309-17			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. 		
@D	Yoshida, M.//Miyamoto, Y.//Ogura, Y.//Hayashi, T.//Hoshino, Y. 	Complete Chromosome Sequence of a Mycolactone-Producing Mycobacterium, Mycobacterium pseudoshottsii.	Genome Announcements	2017	5		e01363-17			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. 		
@D	Yoshida, M.//Nakanaga, K.//Ogura, Y.//Toyoda, A.//Ooka, T.//Kazumi, Y.//Mitarai, S.//Ishii, N.//Hayashi, T.//Hoshino, Y. 	Complete Genome Sequence of Mycobacterium ulcerans subsp. shinshuense.	Genome Announcements	2016	4		e01050-16			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. 		
@D	Yoshida, S.//Enoki, J.//Hemmi, R.//Kourist, R.//Kawakami, N.//Miyamoto, K. 	Draft Genome Sequence of Bordetella bronchiseptica KU1201, the First Isolation Source of Arylmalonate Decarboxylase.	Genome Announcements	2015	3		e00373-15			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. 		
@D	Yoshida, Y.//Mise, K. 	Occurrence of small Hsd plasmids in Salmonella typhi, Shigella boydii, and Escherichia coli.	J. Bacteriol.	1986	165		357-362			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. 		
@D	Yoshii, A.//Omatsu, T.//Katayama, Y.//Koyama, S.//Mizutani, T.//Moriyama, H.//Fukuhara, T. 	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.	Mol. Plant Pathol.	2014	16		288-300			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. 		
@D	Yoshimori, R.//Roulland-Dussoix, D.//Boyer, H.W. 	R factor-controlled restriction and modification of deoxyribonucleic acids:  restriction mutants.	J. Bacteriol.	1972	112		1275-1279			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. 		
@D	Yoshimori, R.N. 	A genetic and biochemical analysis of the restriction and modification of DNA by resistance transfer factors.	Ph.D. Thesis, University of California, San Francisco, USA	1971			1-73			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. 		
@D	Yoshimoto, H.//Takahashi, Y.//Hamada, N.//Umemoto, T. 	Genetic transformation of Porphyromonas gingivalis by electroporation.	Oral Microbiol. Immunol.	1993	8		208-212			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. 		
@D	Yoshino, T.//Honda, T.//Tanaka, M.//Tanaka, T. 	Draft Genome Sequence of Marine Cyanobacterium Synechococcus sp. Strain NKBG15041c.	Genome Announcements	2013	1		e00954-13			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. 		
@D	Yoshioka, H.//Nakamura, H.//Sasaki, J.//Tahara, Y.//Yamada, Y. 	Purification, properties and recognition sequence of site-specific restriction endonuclease from "Acetobacter xylinus".	Agric. Biol. Chem.	1983	47		2871-2879			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). 		
@D	Yoshizawa, H.//Motooka, D.//Katada, R.//Matsumoto, Y.//Nakamura, S.//Morii, E.//Iida, T.//Matsumoto, H. 	Whole-Genome Sequence of Streptococcus tigurinus Strain osk_001, Isolated from Postmortem Material.	Genome Announcements	2017	5		e00878-17			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. 		
@D	You, D.//Wang, L.//Yao, F.//Zhou, X.//Deng, Z. 	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.	Biochemistry	2007	46		6126-6133			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. 		
@D	You, D.L.//Indrakanti, R.//Cao, B.//Yao, F.//Deng, Z.X.//Dedon, P.C. 	Development of a mass spectrometry-based assay to define the biochemistry of phosphorothioate DNA modifications of DNA in bacterial restriction/modification systems.	ACS Abstracts	2011	242		0			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. 		
@D	You, X.Y.//Guo, X.//Zheng, H.J.//Zhang, M.J.//Liu, L.J.//Zhu, Y.Q.//Zhu, B.//Wang, S.Y.//Zhao, G.P.//Poetsch, A.//Jiang, C.Y.//Liu, S.J. 	Unraveling the Acidithiobacillus caldus complete genome and its central metabolisms for carbon assimilation.	J. Genetics Genomics	2011	38		243-252			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. 		
@D	You, X.Y.//Liu, C.//Wang, S.Y.//Jiang, C.Y.//Shah, S.A.//Prangishvili, D.//Liu, S.J.//Garrett, R.A. 	Genomic analyses of Acidianus hospitalis W1 a host for studying crenarchaeal virus and plasmid life cycles.	Extremophiles	2011	15		487-497			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. 		
@D	You, X.Y.//Wang, H.//Ren, G.Y.//Li, J.J.//Duan, X.//Zheng, H.J.//Jiang, Z.Q. 	Complete genome sequence of the molybdenum-resistant bacterium Bacillus subtilis  strain LM 4-2.	Standards in Genomic Sciences	2015	10		127			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. 		
@D	You, Y.//He, L.//Zhang, M.//Fu, J.//Gu, Y.//Zhang, B.//Tao, X.//Zhang, J. 	Comparative Genomics of Helicobacter pylori Strains of China Associated with Different Clinical Outcome.	PLoS ONE	2012	7		e38528			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. 		
@D	You, Y.//Liu, L.//Zhang, M.//Han, X.//He, L.//Zhu, Y.//Ni, P.//Zhang, J. 	Genome Sequences of Three Helicobacter pylori Strains Isolated from Atrophic Gastritis and Gastric Ulcer Patients in China.	J. Bacteriol.	2012	194		6314-6315			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. 		
@D	You, Y.//Liu, L.//Zhang, M.//Zhu, Y.//He, L.//Li, D.//Zhang, J. 	Genomic characterization of a Helicobacter pylori isolate from a patient with gastric cancer in China.	Gut Pathog.	2014	6		5			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. 		
@D	You, Y.//Yang, X.//Song, Y.//Yan, X.//Yuan, Y.//Li, D.//Yan, Y.//Wang, H.//Tao, X.//Li, L.//Jiang, X.//Zhou, H.//Xiao, D.//Jin, L.//Feng, Z.//Yang, R.//Luo, F.//Cui, Y.//Zhang, J. 	Draft Genome Sequences of Two Streptococcus pyogenes Strains Involved in Abnormal Sharp Raised Scarlet Fever in China, 2011.	J. Bacteriol.	2012	194		5983-5984			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. 		
@D	Youell, J.//Firman, K. 	Mechanistic insight into Type I restriction endonucleases.	Front. Biosci., Landmark Ed.	2012	17		2122-2139			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. 		
@D	Youell, J.//Firman, K. 	EcoR124I: from plasmid-encoded restriction-modification system to nanodevice.	Microbiol. Mol. Biol. Rev.	2008	72		365-377			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. 		
@D	Youn, J.H.//Moodley, A.//Park, Y.H.//Sugimoto, C. 	Genome Sequence of Methicillin-Resistant Staphylococcus pseudintermedius Sequence Type 233 (ST233) Strain K7, of Human Origin.	Genome Announcements	2013	1		e00310-13			We report the genome sequence of the methicillin-resistant Staphylococcus pseudintermedius strain K7, isolated from the nares of a veterinarian in Seoul, South Korea. 		
@D	Young, D.D.//Govan, J.M.//Lively, M.O.//Deiters, A. 	Photochemical Regulation of Restriction Endonuclease Activity.	Chembiochem	2009	10		1612-1616			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. 		
@D	Young, J.M.//Skvortsov, T.//Arkhipova, K.//Allen, C.C.R. 	Draft Genome Sequence of the Predatory Marine Bacterium Halobacteriovorax sp. Strain JY17.	Genome Announcements	2018	6		e01416-17			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. 		
@D	Young, J.P. et al. 	The genome of Rhizobium leguminosarum has recognizable core and accessory components.	Genome Biol.	2006	7		R34			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. 		
@D	Young, M. et al. 	Genome Sequence of the Fleming Strain of Micrococcus luteus, a Simple Free-Living Actinobacterium.	J. Bacteriol.	2010	192		841-860			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. 		
@D	Young, T.-S.//Kim, S.-H.//Modrich, P.//Beth, A.//Jay, E. 	Preliminary x-ray diffraction studies of EcoRI restriction endonuclease-DNA complex.	J. Mol. Biol.	1981	145		607-610			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. 		
@D	Youngblood, B.//Bonnist, E.//Dryden, D.T.//Jones, A.C.//Reich, N.O. 	Differential stabilization of reaction intermediates: specificity checkpoints for M.EcoRI revealed by transient fluorescence and  fluorescence lifetime studies.	Nucleic Acids Res.	2008	36		2917-2925			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. 		
@D	Youngblood, B.//Buller, F.//Reich, N.O. 	Determinants of sequence-specific DNA methylation: target recognition and catalysis are coupled in M.HhaI.	Biochemistry	2006	45		15563-15572			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. 		
@D	Youngblood, B.//Reich, N. 	Conformational transitions as molecular determinants of specificity for the DNA methyltransferase EcoRI.	FASEB J.	2006	20		A40			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. 		
@D	Youngblood, B.//Reich, N.O. 	Conformational transitions as determinants of specificity for the DNA methyltransferase EcoRI.	J. Biol. Chem.	2006	281		26821-26831			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. 		
@D	Youngblood, B.//Shieh, F.K.//Buller, F.//Bullock, T.//Reich, N.O. 	S-adenosyl-L-methionine-dependent methyl transfer: observable precatalytic intermediates during DNA cytosine methylation.	Biochemistry	2007	46		8766-8775			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. 		
@D	Youngblood, B.//Shieh, F.K.//De Los Rios, S.//Perona, J.J.//Reich, N.O. 	Engineered Extrahelical Base Destabilization Enhances Sequence Discrimination of DNA Methyltransferase M.HhaI.	J. Mol. Biol.	2006	362		334-346			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. 		
@D	Youngblood, B.A. 	Analysis of conformational transitions that facilitate DNA methyltransferase specificity and catalysis.	Ph.D. Thesis, Univ. of California, Santa Barbara	2007			1-190			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. 		
@D	Youngblood, B.A.//Shieh, F.-K.//Snider, S.//Perona, J.//Reich, N. 	Engineering a more specific DNA methyltransferase by inducing loop instability.	FASEB J.	2005	19		A846			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. 		
@D	Yousfi, K.//Touati, A.//Bekal, S. 	Complete Genome Sequence of an Extensively Drug-Resistant Shewanella xiamenensis  Strain Isolated from Algerian Hospital Effluents.	Genome Announcements	2016	4		e01236-16			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. 		
@D	Youssoufian, H.//Hammer, S.M.//Hirsch, M.S.//Mulder, C. 	Methylation of the viral genome in an in vitro model of herpes simplex virus latency.	Proc. Natl. Acad. Sci. U. S. A.	1982	79		2207-2210			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. 		
@D	Youssoufian, H.//Mulder, C. 	Detection of methylated sequences in eukaryotic DNA with the restriction endonucleases SmaI and XmaI.	J. Mol. Biol.	1981	150		133-136			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. 		
@D	Yousten, A.A. 	Bacteriophage typing of mosquito pathogenic strains of Bacillus sphaericus.	J. Invertebr. Pathol.	1984	43		124-125			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. 		
@D	Yu, B.//Su, F.//Wang, L.//Xu, K.//Zhao, B.//Xu, P. 	Draft Genome Sequence of Sporolactobacillus inulinus Strain CASD, an Efficient D-Lactic Acid-Producing Bacterium with High-Concentration  Lactate Tolerance Capability.	J. Bacteriol.	2011	193		5864-5865			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. 		
@D	Yu, B.//Su, F.//Wang, L.//Zhao, B.//Qin, J.//Ma, C.//Xu, P.//Ma, Y. 	Genome Sequence of Lactobacillus rhamnosus Strain CASL, an Efficient L-Lactic Acid Producer from Cheap Substrate Cassava.	J. Bacteriol.	2011	193		7013-7014			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. 		
@D	Yu, C.H.//Lu, C.K.//Su, H.M.//Chiang, T.Y.//Hwang, C.C.//Liu, T.//Chen, Y.M. 	Draft genome of Myxosarcina sp. strain GI1, a baeocytous cyanobacterium associated with the marine sponge Terpios hoshinota.	Standards in Genomic Sciences	2015	10		28			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. 		
@D	Yu, C.S.//Yim, K.Y.//Tsui, S.K.//Chan, T.F. 	Complete Genome Sequence of Bacillus subtilis Strain QB928, a Strain Widely Used  in B. subtilis Genetic Studies.	J. Bacteriol.	2012	194		6308-6309			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. 		
@D	Yu, C.Y.//Ang, G.Y.//Ngeow, Y.F.//Tee, K.K.//Yin, W.F.//Chan, K.G. 	Genome Sequences of Two Multidrug-Resistant Proteus mirabilis Strains Harboring CTX-M-65 Isolated from Malaysia.	Genome Announcements	2016	4		e01301-16			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. 		
@D	Yu, D.//Hui, Y.//Zai, X.//Xu, J.//Liang, L.//Wang, B.//Yue, J.//Li, S. 	Comparative Genomic Analysis of Brucella abortus vaccine strain 104M Reveals a Set of Candidate Genes Associated With Its Virulence Attenuation.	Virulence	2015	6		745-754			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. 		
@D	Yu, D.//Pi, B.//Chen, Y.//Wang, Y.//Ruan, Z.//Otto, M.//Yu, Y. 	Characterization of the Staphylococcal Cassette Chromosome Composite Island of Staphylococcus haemolyticus SH32, a Methicillin-Resistant Clinical Isolate from China.	PLoS ONE	2014	9		6			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. 		
@D	Yu, D.S.//Jeong, H.//Lee, D.H.//Kwon, S.K.//Song, J.Y.//Kim, B.K.//Park, M.S.//Ji, G.E.//Oh, T.K.//Kim, J.F. 	Complete Genome Sequence of the Probiotic Bacterium Bifidobacterium bifidum Strain BGN4.	J. Bacteriol.	2012	194		4757-4758			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. 		
@D	Yu, H.//Li, Y.//Tang, H.//Xu, P. 	Genome Sequence of a Newly Isolated Nicotine-Degrading Bacterium, Ochrobactrum sp. SJY1.	Genome Announcements	2014	2		e00720-14			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. 		
@D	Yu, H.//Liu, L.//Chang, Z.//Wang, S.//Wen, B.//Yin, P.//Liu, D.//Chen, B.//Zhang, J. 	Genome Sequence of the Bacterium Bifidobacterium longum Strain CMCC P0001, a Probiotic Strain Used for Treating Gastrointestinal Disease.	Genome Announcements	2013	1		e00716-13			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. 		
@D	Yu, H.//Tang, H.//Wang, L.//Yao, Y.//Wu, G.//Xu, P. 	Complete Genome Sequence of the Nicotine-Degrading Pseudomonas putida Strain S16.	J. Bacteriol.	2011	193		5541-5542			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. 		
@D	Yu, H.//Yin, Y.//Xu, L.//Yan, M.//Fang, W.//Ge, Q. 	Genome Sequence of Klebsiella pneumoniae YZUSK-4, a Bacterium Proposed as a Starter Culture for Fermented Meat Products.	Genome Announcements	2015	3		e00774-15			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. 		
@D	Yu, H.//Yuan, M.//Lu, W.//Yang, J.//Dai, S.//Li, Q.//Yang, Z.//Dong, J.//Sun, L.//Deng, Z.//Zhang, W.//Chen, M.//Ping, S.//Han, Y.//Zhan, Y.//Yan, Y.//Jin, Q.//Lin, M. 	Complete Genome Sequence of the Nitrogen-fixing and Rhizosphere-associated Bacterium Pseudomonas stutzeri Strain DSM4166.	J. Bacteriol.	2011	193		3422-3423			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. 		
@D	Yu, H.B.//Zhang, Y.L.//Lau, Y.L.//Yao, F.//Vilches, S.//Merino, S.//Tomas, J.M.//Howard, S.P.//Leung, K.Y. 	Identification and characterization of putative virulence genes and gene clusters in Aeromonas hydrophila PPD134/91.	Appl. Environ. Microbiol.	2005	71		4469-4477			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. 		
@D	Yu, J.//Ahn, S.//Kim, K.//Caetano-Anolles, K.//Lee, C.//Kang, J.//Cho, K.//Yoon, S.//Kang, D.K.//Kim, H. 	Comparative genomic analysis of Lactobacillus plantarum GB-LP1 isolated from traditional Korean fermented food.	J. Microbiol. Biotechnol.	2017	27		1419-1427			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. 		
@D	Yu, L.//Hisatsune, J.//Hirakawa, H.//Mizumachi, E.//Toyoda, A.//Yahara, K.//Sugai, M. 	Complete Genome Sequence of Super Biofilm-Elaborating Staphylococcus aureus Isolated in Japan.	Genome Announcements	2017	5		e01043-17			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. 		
@D	Yu, M.//Dai, Z.//Qu, X.//Gao, X. 	Draft Genome Sequence of Marine Bacterium Streptomyces sp. Strain CNQ431, a Producer of the Cytokine Inhibitor Splenocin.	Genome Announcements	2015	3		e01383-14			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. 		
@D	Yu, M.//Ji, L.//Neumann, D.A.//Chung, D.H.//Groom, J.//Westpheling, J.//He, C.//Schmitz, R.J. 	Base-resolution detection of N4-methylcytosine in genomic DNA using 4mC-Tet-assisted-bisulfite- sequencing.	Nucleic Acids Res.	2015	43		e148			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. 		
@D	Yu, M.//Ren, C.//Qiu, J.//Luo, P.//Zhu, R.//Zhao, Z.//Hu, C. 	Draft Genome Sequence of the Opportunistic Marine Pathogen Vibrio harveyi Strain  E385.	Genome Announcements	2013	1		e00677-13			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. 		
@D	Yu, M.//Tang, K.//Shi, X.//Zhang, X.H. 	Genome Sequence of Pseudoalteromonas flavipulchra JG1, a Marine Antagonistic Bacterium with Abundant Antimicrobial Metabolites.	J. Bacteriol.	2012	194		3735			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. 		
@D	Yu, X.//Cloutier, S.//Tambong, J.T.//Bromfield, E.S. 	Bradyrhizobium ottawaense sp. nov., a symbiotic nitrogen fixing bacterium from root nodules of soybeans in Canada.	Int. J. Syst. Evol. Microbiol.	2014	64		3202-3207			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%. 		
@D	Yu, X.//Jiang, J.//Liang, C.//Zhang, X.//Wang, J.//Shen, D.//Feng, Y. 	Indole affects the formation of multicellular aggregate structures in Pantoea agglomerans YS19.	J. Gen. Appl. Microbiol.	2016	62		31-37			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. 		
@D	Yu, X.//Kang, Y.Q.//Ji, F. 	Draft Genome Sequence of a Trimethylamine-Producing Staphylococcus Isolate from Blood of a Coronary Atherosclerotic Heart Disease Patient.	Genome Announcements	2018	6		e01563-17			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. 		
@D	Yu, Y.J.//Yang, M.T. 	A novel restriction-modification system from Xanthomonas campestris pv. vesicatoria encodes a m4C-methyltransferase and a nonfunctional  restriction endonuclease.	FEMS Microbiol. Lett.	2007	272		83-90			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. 		
@D	Yu, Z.//Gunn, L.//Brennan, E.//Reid, R.//Wall, P.G.//Gaora, O.P.//Hurley, D.//Bolton, D.//Fanning, S. 	Complete genome sequence of Clostridium estertheticum DSM 8809, a microbe identified in spoiled vacuum packed beef.	Front. Microbiol.	2016	7		1764			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. 		
@D	Yu, Z.//Ma, Y.//Zhong, W.//Qiu, J.//Li, J. 	Comparative Genomics of Methanopyrus sp. SNP6 and KOL6 Revealing Genomic Regions  of Plasticity Implicated in Extremely Thermophilic Profiles.	Front. Microbiol.	2017	8		1278			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. 		
@D	Yu, Z.//Yang, G.//Liu, X.//Wang, Y.//Zhuang, L.//Zhou, S. 	Complete genome sequence of the nitrogen-fixing bacterium Azospirillum humicireducens type strain SgZ-5(T).	Standards in Genomic Sciences	2018	13		28			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. 		
@D	Yu, Z.//Zhao, M.//Qiu, J. 	Draft Genome Sequence of Pseudoalteromonas sp. Strain R3, a Red-Pigmented l-Amino Acid Oxidase-Producing Bacterium.	Genome Announcements	2015	3		e01339-15			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. 		
@D	Yuan, J.//Li, L.//Sun, M.//Dong, J.//Hu, Q. 	Genome Sequence of Avirulent Riemerella anatipestifer Strain RA-SG.	Genome Announcements	2013	1		e0021812			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. 		
@D	Yuan, K.X.//Adam, Z.//Tambong, J.//Levesque, C.A.//Chen, W.//Lewis, C.T.//De Boer, S.H.//Li, X.S. 	Draft Genome Sequence of Pectobacterium wasabiae Strain CFIA1002.	Genome Announcements	2014	2		e00214-14			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. 		
@D	Yuan, K.X.//Cullis, J.//Levesque, C.A.//Tambong, J.//Chen, W.//Lewis, C.T.//De Boer, S.H.//Li, X.S. 	Draft Genome Sequences of Ralstonia solanacearum Race 3 Biovar 2 Strains with Different Temperature Adaptations.	Genome Announcements	2015	3		e00815-15			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. 		
@D	Yuan, M.//Chen, H.//Zhu, X.//Feng, J.//Zhan, Z.//Zhang, D.//Chen, X.//Zhao, X.//Lu, J.//Xu, J.//Zhou, D.//Li, J. 	pSY153-MDR, a p12969-DIM-related mega plasmid carrying blaIMP-45 and armA, from clinical Pseudomonas putida.	Oncotarget	2017	8		68439-68447			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. 		
@D	Yuan, R. 	Structure and mechanism of multifunctional restriction endonucleases.	Annu. Rev. Biochem.	1981	50		285-315			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. 		
@A	Yuan, R. 		The reaction mechanism of type I restriction endonucleases.			Chirikjian, J.G. 		Gene Amplif. Anal.					Elsevier North Holland	1981		1		45-72									*
    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
 
 		
@D	Yuan, R.//Bickle, T.A.//Ebbers, W.//Brack, C. 	Multiple steps in DNA recognition by restriction endonuclease from E. coli K.	Nature	1975	256		556-560			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. 		
@A	Yuan, R.//Burckhardt, J.//Weisemann, J.//Hamilton, D.L. 		The mechanism of DNA methylation by the restriction endonuclease from E. coli K.			Usdin, E.//Borchardt, R.T.//Creveling, C.R. 		Biochemistry of S-adenosylmethionine and related compounds				London	MacMillan	1981		0		239-247									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. 		
@D	Yuan, R.//Hamilton, D.L. 	Restriction and modification of DNA by a complex protein.	Am. Sci.	1982	70		61-69			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. 		
@A	Yuan, R.//Hamilton, D.L. 		Type I and Type III restriction-modification enzymes.			Razin, A.//Cedar, H.//Riggs, A.D. 		DNA Methylation. Biochemistry and Biological Significance.				New York	Springer-Verlag	1984		0		11-38									None 		
@D	Yuan, R.//Hamilton, D.L.//Burckhardt, J. 	DNA translocation by the restriction enzyme from E. coli K.	Cell	1980	20		237-244			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. 		
@D	Yuan, R.//Hamilton, D.L.//Hadi, S.M.//Bickle, T.A. 	Role of ATP in the cleavage mechanism of the EcoP15 restriction endonuclease.	J. Mol. Biol.	1980	144		501-519			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. 		
@D	Yuan, R.//Heywood, J.//Meselson, M. 	ATP hydrolysis by restriction endonuclease from E. coli K.	Nature New Biol.	1972	240		42-43			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). 		
@D	Yuan, R.//Meselson, M. 	A specific complex between a restriction endonuclease and its DNA substrate.	Proc. Natl. Acad. Sci. U. S. A.	1970	65		357-362			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. 		
@D	Yuan, R.//Reiser, J. 	Steps in the reaction mechanism of the Escherichia coli plasmid P15-specific restriction endonuclease.	J. Mol. Biol.	1978	122		433-445			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. 		
@A	Yuan, R.//Smith, H.O. 		The restriction and modification DNA methylases: An overview.			Razin, A.//Cedar, H.//Riggs, A.D. 		DNA Methylation. Biochemistry and Biological Significance.				New York	Springer-Verlag	1984		0		73-80									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. 		
@D	Yuan, Y.//Zhang, Y.//Fu, S.//Crippen, T.L.//Visi, D.K.//Benbow, M.E.//Allen, M.S.//Tomberlin, J.K.//Sze, S.H.//Tarone, A.M. 	Genome Sequence of a Proteus mirabilis Strain Isolated from the Salivary Glands of Larval Lucilia sericata.	Genome Announcements	2016	4		e00672-16			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. 		
@D	Yuan, Y.//Zhang, Y.//Fu, S.//Crippen, T.L.//Visi, D.K.//Benbow, M.E.//Allen, M.S.//Tomberlin, J.K.//Sze, S.H.//Tarone, A.M. 	Genome Sequence of a Providencia stuartii Strain Isolated from Luciliasericata Salivary Glands.	Genome Announcements	2017	5		e00250-17			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. 		
@D	Yucel, O.//Wibberg, D.//Philipp, B.//Kalinowski, J. 	Genome Sequence of the Bile Salt-Degrading Bacterium Novosphingobium sp. Strain Chol11, a Model Organism for Bacterial Steroid Catabolism.	Genome Announcements	2018	6		e01372-17			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. 		
@D	Yuichi, S.//Norton, J.M.//Bollmann, A.//Klotz, M.G.//Stein, L.Y.//Laanbroek, H.J.//Arp, D.J.//Goodwin, L.A.//Chertkov, O.//Held, B.//Bruce, D.//Detter, J.C.//Detter, J.C.//Tapia, R.//Han, C.S. 	Genome sequence of Nitrosomonas sp. strain AL212, an ammonia-oxidizing bacterium  sensitive to high levels of ammonia.	J. Bacteriol.	2011	193		5047-5048			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. 		
@D	Yukawa, H.//Omumasaba, C.A.//Nonaka, H.//Kos, P.//Okai, N.//Suzuki, N.//Suda, M.//Tsuge, Y.//Watanabe, J.//Ikeda, Y.//Vertes, A.A.//Inui, M. 	Comparative analysis of the Corynebacterium glutamicum group and complete genome sequence of strain R.	Microbiology	2007	153		1042-1058			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. 		
@D	Yuki, M.//Oshima, K.//Suda, W.//Kitahara, M.//Kitamura, K.//Iida, T.//Hattori, M.//Ohkuma, M. 	Draft Genome Sequences of Two Lactobacillus Strains, L. farraginis JCM 14108T and L. composti JCM 14202T, Isolated from Compost of Distilled Shochu Residue.	Genome Announcements	2014	2		e00257-14			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. 		
@D	Yuki, M.//Oshima, K.//Suda, W.//Oshida, Y.//Kitamura, K.//Iida, T.//Hattori, M.//Ohkuma, M. 	Draft Genome Sequences of Three Alkaliphilic Bacillus Strains, Bacillus wakoensis JCM 9140T, Bacillus akibai JCM 9157T, and Bacillus hemicellulosilyticus JCM  9152T.	Genome Announcements	2014	2		e01258-13			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. 		
@D	Yuki, M.//Oshima, K.//Suda, W.//Oshida, Y.//Kitamura, K.//Iida, T.//Hattori, M.//Ohkuma, M. 	Draft Genome Sequence of Paenibacillus pini JCM 16418T, Isolated from the Rhizosphere of Pine Tree.	Genome Announcements	2014	2		e00210-14			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. 		
@D	Yuki, M.//Oshima, K.//Suda, W.//Sakamoto, M.//Iida, T.//Hattori, M.//Ohkuma, M. 	Draft Genome Sequence of Bacteroides reticulotermitis Strain JCM 10512T, Isolated from the Gut of a Termite.	Genome Announcements	2014	2		e00072-14			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. 		
@D	Yuki, M.//Oshima, K.//Suda, W.//Sakamoto, M.//Kitamura, K.//Iida, T.//Hattori, M.//Ohkuma, M. 	Draft Genome Sequence of Clostridium straminisolvens Strain JCM 21531T, Isolated  from a Cellulose-Degrading Bacterial Community.	Genome Announcements	2014	2		e00110-14			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. 		
@D	Yuki, M.//Sakamoto, M.//Kuwahara, H.//Hongoh, Y.//Ohkuma, M. 	Draft Genome Sequence of Lactococcus sp. Strain Rs-Y01, Isolated from the Gut of  the Lower Termite Reticulitermes speratus.	Genome Announcements	2017	5		e00999-17			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. 		
@D	Yulandi, A.//Sugiokto, F.G.//Febrilina, S.A. 	Genomic Sequence of Klebsiella pneumoniae IIEMP-3, a Vitamin B12-Producing Strain from Indonesian Tempeh.	Genome Announcements	2016	4		e01724-15			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. 		
@D	Yun, J.H.//Cho, Y.J.//Chun, J.//Hyun, D.W.//Bae, J.W. 	Genome sequence of the chromate-resistant bacterium Leucobacter salsicius type strain M1-8(T.).	Standards in Genomic Sciences	2014	9		495-504			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. 		
@D	Yun, J.H.//Sung, H.//Kim, H.S.//Tak, E.J.//Kang, W.//Lee, J.Y.//Hyun, D.W.//Kim, P.S.//Bae, J.W. 	Complete genome sequence of the halophile bacterium Kushneria konosiri X49(T), isolated from salt-fermented Konosirus punctatus.	Standards in Genomic Sciences	2018	13		19			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. 		
@D	Yun, M.-S.//Bae, M. 	Purification and characterization of a thermotolerable restriction endonuclease from Streptomyces violochromogenes D2-5.	Proc. Mol. Biol. and Genet.	1993	8		73-74			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. 		
@D	Yun, M.-S.//Hwang, H.//Bae, M. 	Purification and characterization of a thermotolerable restriction endonuclease from Streptomyces violochromogenes D2-5.	J. Microbiol. Biotechnol.	1995	5		269-273			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. 		
@D	Yun, M.R.//Han, S.J.//Yoo, W.G.//Kwon, T.//Lee, S.//Lee, J.S.//Kim, D.W. 	Draft Genome Sequence of Mycobacterium tuberculosis KT-0204, Isolated in South Korea.	Genome Announcements	2016	4		e01519-15			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. 		
@D	Yunes, R.A.//Klimina, K.M.//Emelyanov, K.V.//Zakharevich, N.V.//Poluektova, E.U.//Danilenko, V.N. 	Draft Genome Sequences of Lactobacillus plantarum Strain 90sk and Lactobacillus brevis Strain 15f: Focusing on Neurotransmitter Genes.	Genome Announcements	2015	3		e00261-15			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. 		
@D	Yung, P.Y.//Burke, C.//Lewis, M.//Egan, S.//Kjelleberg, S.//Thomas, T. 	Phylogenetic screening of a bacterial, metagenomic library using homing endonuclease restriction and marker insertion.	Nucleic Acids Res.	2009	37		e144			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. 		
@D	Yunusova, A.K.//Rogulin, E.A.//Artyukh, R.I.//Zheleznaya, L.A.//Matvienko, N.I. 	Nickase and a protein encoded by an open reading frame downstream from the nickase BspD6I gene form a restriction endonuclease complex.	Biokhimiia	2006	71		1002-1008			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. 		
@D	Yussifov, T.N.//Zavilgelsky, G.B.//Delver, E.P.//Belogurov, A.A. 	Plasmid pKM101ard+-mediated alleviation of EcoK restriction.  II. Cloning of ard gene.	Mol. Biol. (Mosk)	1987	21		847-852			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. 		
@D	Zabaznaya, E.V.//Nikiforev, V.V.//Zheleznaya, L.A.//Matvienko, N.I. 	Site-specific endonuclease AbaI from Azospirillum brasilense UQ 1796 is an isoschizomer of endonuclease BclI.	Biokhimiia	1997	62		403-410			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. 		
@D	Zabaznaya, E.V.//Zheleznaya, L.A.//Matvienko, N.I. 	Site-specific endonucleases RspLKI and RspLKII from Rhodococcus species LK2 are isoschizomers of SphI and BamHI.	Biokhimiia	1997	62		1018-1028			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. 		
@D	Zabaznaya, E.V.//Zheleznaya, L.A.//Svadbina, I.V.//Matvienko, N.I. 	Site-specific endonuclease NspLKI is an isoschizomer of Endonuclease HaeIII.	Biokhimiia	1999	64		234-238			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. 		
@D	Zabeau, M.//Friedman, S.//Van Montagu, M.//Schell, J. 	The ral gene of phage lambda: I. Identification of a non-essential gene that modulates restriction and modification in E. coli.	Mol. Gen. Genet.	1980	179		63-73			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. 		
@A	Zabeau, M.//Roberts, R.J. 		The role of restriction endonucleases in molecular genetics.			Taylor, J.H. 		Molecular Genetics				New York	Academic Press, Inc.	1979		3		1-63									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). 		
@D	Zabeau, M.//Schell, J.//Van Montagu, M. 	The alleviation of host-controlled restriction of unmodified phages by functions of bacteriophage lambda.	Arch. Int. Physiol. Biochim.	1973	81		990			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. 		
@D	Zaburannyi, N.//Grosser, K.//Gasparoni, G.//Muller, R.//Schrallhammer, M.//Simon, M. 	Draft Genome Sequence and Annotation of the Obligate Bacterial Endosymbiont Caedibacter taeniospiralis, Causative Agent of the Killer Phenotype in Paramecium  tetraurelia.	Genome Announcements	2018	6		e01418-17			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. 		
@D	Zaburannyi, N.//Rabyk, M.//Ostash, B.//Fedorenko, V.//Luzhetskyy, A. 	Insights into naturally minimised Streptomyces albus J1074 genome.	BMC Genomics	2014	15		11			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. 		
@D	Zacharias, W.//Larson, J.E.//Kilpatrick, M.W.//Wells, R.D. 	HhaI methylase and restriction endonuclease as probes for B to Z DNA conformational changes in d(GCGC) sequences.	Nucleic Acids Res.	1984	12		7677-7692			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. 		
@D	Zacharias, W.//O'Connor, T.R.//Larson, J.E. 	Methylation of cytosine in the 5-position alters the structural and energetic properties of the supercoil-induced Z-helix and B-Z junctions.	Biochemistry	1988	27		2970-2978			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. 		
@D	Zachow, C.//Muller, H.//Laireiter, C.M.//Tilcher, R.//Berg, G. 	Complete genome sequence of Pseudomonas corrugata strain RM1-1-4, a stress protecting agent from the rhizosphere of an oilseed rape bait plant.	Standards in Genomic Sciences	2017	12		66			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. 		
@D	Zachow, C.//Muller, H.//Monk, J.//Berg, G. 	Complete genome sequence of Pseudomonas brassicacearum strain L13-6-12, a biological control agent from the rhizosphere of potato.	Standards in Genomic Sciences	2017	12		6			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. 		
@D	Zagorskaite, E.//Manakova, E.//Sasnauskas, G. 	Recognition of modified cytosine variants by the DNA-binding domain of methyl-directed endonuclease McrBC.	FEBS Lett.	2018	592		3335-3345			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. 		
@D	Zagorskaite, E.//Sasnauskas, G. 	Chemical Display of Pyrimidine Bases Flipped Out by Modification-Dependent Restriction Endonucleases of MspJI and PvuRts1I Families.	PLoS ONE	2014	9		e114580			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. 		
@D	Zahidi, J.M.//Ahmad, N.//Tay, B.Y.//Hashim, R.//Khoo, E.//Ahmad, N.//Yee, C.Y.//Dolhan, N.Q. 	Genome Sequences of Brucella melitensis, Isolated from Blood Samples of Brucellosis Patients in Malaysia.	Genome Announcements	2017	5		e00689-17			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. 		
@D	Zahner, V.//Priest, F.G. 	Distribution of restriction nucleases among some entomopathogenic strains of Bacillus sphaericus.	Lett. Appl. Microbiol.	1997	24		483-487			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. 		
@D	Zahradnik, J.//Kyslikova, E.//Kyslik, P. 	Draft Genome Sequence of Agrobacterium sp. Strain R89-1, a Morphine Alkaloid-Biotransforming Bacterium.	Genome Announcements	2016	4		e00196-16			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. 		
@D	Zahradnik, J.//Plackova, M.//Palyzova, A.//Maresova, H.//Kyslikova, E.//Kyslik, P. 	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.	Genome Announcements	2017	5		e00921-17			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. 		
@D	Zahran, M.//Berezniak, T.//Imhof, P.//Smith, J.C. 	Role of magnesium ions in DNA recognition by the EcoRV restriction endonuclease.	FEBS Lett.	2011	585		2739-2743			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. 		
@D	Zahran, M.//Daidone, I.//Smith, J.C.//Imhof, P. 	Mechanism of DNA Recognition by the Restriction Enzyme EcoRV.	J. Mol. Biol.	2010	401		415-432			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. 		
@D	Zain, B.S.//Roberts, R.J. 	A new specific endonuclease from Xanthomonas badrii.	J. Mol. Biol.	1977	115		249-255			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. 		
@D	Zakharevich, N.V.//Averina, O.V.//Klimina, K.M.//Kudryavtseva, A.V.//Kasianov, A.S.//Makeev, V.J.//Danilenko, V.N. 	Complete Genome Sequence of Bifidobacterium longum GT15: Unique Genes for Russian Strains.	Genome Announcements	2014	2		e01348-14			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). 		
@D	Zakharova, M.//Minakhin, L.//Solonin, A.//Severinov, K. 	Regulation of RNA polymerase promoter selectivity by covalent modification of DNA.	J. Mol. Biol.	2004	335		103-111			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. 		
@D	Zakharova, M.V.//Beletskaya, I.V.//Denjmukhametov, M.M.//Yurkova, T.V.//Semenova, L.M.//Shlyapnikov, M.G.//Solonin, A.S. 	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.	Mol. Genet. Genomics	2002	267		171-178			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. 		
@D	Zakharova, M.V.//Beletskaya, I.V.//Kravetz, A.N.//Pertzev, A.V.//Mayorov, S.G.//Shlyapnikov, M.G.//Solonin, A.S. 	Cloning and sequence anlaysis of the plasmid-borne genes encoding the Eco29kI restriction and modification enzymes.	Gene	1998	208		177-182			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. 		
@D	Zakharova, M.V.//Kravets, A.N.//Klimashina, N.V.//Solonin, A.S. 	Properties of the replicator region of natural plasmid pLG13 carrying genes of the EcoRV restriction-modification system.	Mol. Biol. (Mosk)	1991	25		1615-1625			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. 		
@D	Zakharova, M.V.//Kravetz, A.N.//Beletzkaja, I.V.//Repyk, A.V.//Solonin, A.S. 	Cloning and sequences of the genes encoding the CfrBI restriction-modification system from Citrobacter freundii.	Gene	1993	129		77-81			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. 		
@D	Zakharova, M.V.//Pertzev, A.V.//Kravetz, A.N.//Beletskaya, I.V.//Shlyapnikov, M.G.//Solonin, A.S. 	Complete nucleotide sequence of the Hsd plasmid pECO29 and identification of its functional regions.	Biochim. Biophys. Acta	1998	1398		106-112			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. 		
@D	Zaleski, P.//Piekarowicz, A. 	Characterization of a dam mutant of Haemophilus influenzae Rd.	Microbiology	2004	150		3773-3781			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. 		
@D	Zaleski, P.//Wojciechowski, M.//Piekarowicz, A. 	The role of Dam methylation in phase variation of Haemophilus influenzae genes involved in defence against phage infection.	Microbiology	2005	151		3361-3369			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. 		
@D	Zamorano, A.//Fiore, N. 	Draft Genome Sequence of 16SrIII-J Phytoplasma, a Plant Pathogenic Bacterium with a Broad Spectrum of Hosts.	Genome Announcements	2016	4		e00602-16			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%. 		
@D	Zan, J.//Fricke, W.F.//Fuqua, C.//Ravel, J.//Hill, R. 	Genome Sequence of Ruegeria sp. strain KLH11, an N-Acylhomoserine Lactone-Producing Bacterium Isolated from the Marine Sponge Mycale  laxissima.	J. Bacteriol.	2011	193		5011-5012			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. 		
@D	Zangi, R.//Arrieta, A.//Cossio, F.P. 	Mechanism of DNA Methylation: The Double Role of DNA as a Substrate and as a Cofactor.	J. Mol. Biol.	2010	400		632-644			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. 		
@D	Zarate, M.A.//Rodriguez, M.D.//Chang, E.I.//Russell, J.T.//Arndt, T.J.//Richards, E.M.//Ocasio, B.A.//Aranda, E.//Gordon, E.M.//Yu, K.//Neu, J.//Keller-Wood, M.//Triplett, E.W.//Wood, C.E. 	Post-hypoxia Invasion of the fetal brain by multidrug resistant Staphylococcus.	Sci. Rep.	2017	7		6458			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. 		
@D	Zaremba, M.//Owsicka, A.//Tamulaitis, G.//Sasnauskas, G.//Shlyakhtenko, L.S.//Lushnikov, A.Y.//Lyubchenko, Y.L.//Laurens, N.//van den Broek, B.//Wuite, G.J.//Siksnys, V. 	DNA synapsis through transient tetramerization triggers cleavage by Ecl18kI restriction enzyme.	Nucleic Acids Res.	2010	38		7142-7154			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. 		
@D	Zaremba, M.//Sasnauskas, G.//Siksnys, V. 	The link between restriction endonuclease fidelity and oligomeric state: A study with Bse634I.	FEBS Lett.	2012	586		3324-3329			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. 		
@D	Zaremba, M.//Sasnauskas, G.//Urbanke, C.//Siksnys, V. 	Allosteric communication network in the tetrameric restriction endonuclease Bse634I.	J. Mol. Biol.	2006	363		500-512			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. 		
@D	Zaremba, M.//Sasnauskas, G.//Urbanke, C.//Siksnys, V. 	Conversion of the tetrameric restriction endonuclease Bse634I into a dimer: Oligomeric structure-stability-function correlations.	J. Mol. Biol.	2005	348		459-478			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. 		
@D	Zaremba, M.//Siksnys, V. 	Molecular scissors under light control.	Proc. Natl. Acad. Sci. U. S. A.	2010	107		1259-1260			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. 		
@D	Zaremba, M.//Toliusis, P.//Grigaitis, R.//Manakova, E.//Silanskas, A.//Tamulaitiene, G.//Szczelkun, M.D.//Siksnys, V. 	DNA cleavage by CgII and NgoAVII requires interaction between N- and R-proteins and extensive nucleotide hydrolysis.	Nucleic Acids Res.	2014	42		13887-13896			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. 		
@D	Zaremba, M.//Urbanke, C.//Halford, S.E.//Siksnys, V. 	Generation of the BfiI restriction endonuclease from the fusion of a DNA recognition domain to a non-specific nuclease from the  phospholipase D superfamily.	J. Mol. Biol.	2004	336		81-92			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. 		
@D	Zarogiannis, S.G.//Filippidis, A.S. 	Resenbase: A sophisticated and user-friendly, restriction endonuclease database compilation for handheld computers.	Clin. Chim. Acta	2005	355		S360			A database of commonly used restriction enzymes was constructed and programmed into a PalmOs handheld. 		
@D	Zarrilli, R.//Giannouli, M.//Rocco, F.//Loman, N.J.//Haines, A.S.//Constantinidou, C.//Pallen, M.J.//Triassi, M.//Di Nocera, P.P. 	Genome sequences of three Acinetobacter baumannii strains assigned to ST2, ST25 and ST78 multilocus sequencing typing genotypes.	J. Bacteriol.	2011	193		2359-2360			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. 		
@D	Zarza, E.//Alcaraz, L.D.//Aguilar-Salinas, B.//Islas, A.//Olmedo-Alvarez, G. 	Complete Genome Sequence of Bacillus horikoshii Strain 20a from Cuatro Cienegas,  Coahuila, Mexico.	Genome Announcements	2017	5		e00592-17			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. 		
@D	Zarza, E.//Alcaraz, L.D.//Aguilar-Salinas, B.//Islas, A.//Olmedo-Alvarez, G. 	Complete Genome Sequences of Two Bacillus pumilus Strains from Cuatrocienegas, Coahuila, Mexico.	Genome Announcements	2018	6		e00364-18			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. 		
@D	Zatkovic, B.//Molnarova, V.//Kmet, V.//Javorsky, P.//Pristas, P. 	Diversity of DNA sequences among restriction endonucleases producing Selenomonas ruminantium isolates detected by enterobacterial repetitive intergenic consensus based polymerase chain reaction (ERIC-PCR).	Anaerobe	2000	6		299-304			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. 		
@D	Zautner, A.E.//Bunk, B.//Pfeifer, Y.//Sproer, C.//Reichard, U.//Eiffert, H.//Scheithauer, S.//Gross, U.//Overmann, J.//Bohne, W. 	Monitoring microevolution of OXA-48-producing Klebsiella pneumoniae ST147 in a hospital setting by SMRT sequencing.	J. Antimicrob. Chemother.	2017	72		2737-2744			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. 		
@D	Zautner, A.E.//Goldschmidt, A.M.//Thurmer, A.//Schuldes, J.//Bader, O.//Lugert, R.//Gross, U.//Stingl, K.//Salinas, G.//Lingner, T. 	SMRT sequencing of the Campylobacter coli BfR-CA-9557 genome sequence reveals unique methylation motifs.	BMC Genomics	2015	16		1088			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. 		
@D	Zavilgelskii, G.B.//Bakalova, T.L.//Duzhii, D.E.//Kotova, V.Y. 	The ard gene encoding the type I restriction inhibitor is present in conjugative plasmids of FII, B/O, and K groups of incompatibility.	Genetika	1994	30		1582-1586			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. 		
@D	Zavilgelskii, G.B.//Manukhov, I.V.//Rastorguev, S.M. 	Attenuation of type I restriction in Escherichia coli: effect of the ard gene in UV-irradiated cells.	Genetika	1996	32		1013-1016			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] 		
@D	Zavilgelsky, G.B. 	Antirestriction.	Mol. Biol. (Mosk)	2000	34		854-862			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. 		
@D	Zavilgelsky, G.B.//Kotova, V.Y. 	Antirestriction activity of the monomeric and dimeric forms of T7 Ocr.	Mol. Biol. (Mosk)	2014	48		150-157			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. 		
@D	Zavilgelsky, G.B.//Kotova, V.Y.//Melkina, O.E.//Pustovoit, K.S. 	Antirestriction activity of the mercury resistance nonconjugative transposon Tn5053 is controlled by the protease ClpXP.	Genetika	2014	50		910-915			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. 		
@D	Zavilgelsky, G.B.//Kotova, V.Y.//Rastorguev, S.M. 	Antirestriction and antimodification activities of T7 Ocr: Effects of amino acid substitutions in the interface.	Mol. Biol. (Mosk)	2009	43		93-100			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). 		
@D	Zavilgelsky, G.B.//Kotova, V.Y.//Rastorguev, S.M. 	Antimodification activity of the ArdA and Ocr proteins.	Genetika	2011	47		159-167			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. 		
@D	Zavilgelsky, G.B.//Kotova, V.Y.//Rastorguev, S.M. 	Comparative analysis of anti-restriction activities of ArdA (ColIb-P9) and Ocr (T7) proteins.	Biochemistry	2008	73		906-911			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. 		
@D	Zavilgelsky, G.B.//Letuchaya, T.A.//Rastorguev, S.M. 	Antirestriction and antimodification activities of the ArdA protein encoded by the IncI1 transmissive plasmids R-64 and ColIb-P9.	Genetika	2006	42		252-258			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. 		
@D	Zavilgelsky, G.B.//Letutchaja, T.A.//Rastorguev, S.M. 	Antirestriction activity of ArdA encoded by the IncI1 transmissive plasmid R64.	Mol. Biol. (Mosk)	2004	38		901-906			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). 		
@D	Zavilgelsky, G.B.//Mershavka, V.Y.//Jusifov, T.N.//Belogurov, A.A. 	Plasmid pKM101 ard+-mediated alleviation of K-restriction of bacteriophage lambda.  I. General characteristics and genetic localization of the ard gene.	Mol. Biol. (Mosk)	1984	18		1590-1596			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). 		
@D	Zavilgelsky, G.B.//Rastorguev, S.M. 	Antirestriction proteins ArdA and Ocr as efficient inhibitors of type I restriction-modification enzymes.	Mol. Biol. (Mosk)	2009	43		241-248			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. 		
@D	Zavilgelsky, G.B.//Rastorguev, S.M. 	DNA mimicry by proteins as effective mechanism for regulation of activity of DNA-dependent enzymes.	Biochemistry	2007	72		913-919			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. 		
@D	Zaw, H.A.//Kanesaki, Y.//Yoshikawa, H.//Tsurumaru, H.//Yamakawa, T. 	Draft Genome Sequences of Bradyrhizobium elkanii Strains BLY3-8 and BLY6-1, Which Are Incompatible with Rj3 Genotype Soybean Cultivars.	Genome Announcements	2016	4		e01169-16			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. 		
@D	Zdziarski, J.//Brzuszkiewicz, E.B.//Wullt, B.//Liesegang, H.//Biran, D.//Voigt, B.//Gronberg-Hernandez, J.//Ragnarsdottir, B.//Hecker, M.//Ron, E.Z.//Daniel, R.//Gottschalk, G.//Hacker, J.//Svanborg, C.//Dobrindt, U. 	Host imprints on bacterial genomes--Rapid, divergent evolution in individual patients.	PLoS Pathog.	2010	6		e1001078			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. 		
@D	Zebala, J.//Choi, J.//Barany, F. 	Recognition of base-analogue modified substrates by the TaqI restriction endonuclease.	FASEB J.	1992	6		A358			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. 		
@D	Zebala, J.//Choi, J.//Barany, F. 	Characterization of steady state, single-turnover, and binding kinetics of the TaqI restriction endonuclease.	J. Biol. Chem.	1992	267		8097-8105			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. 		
@D	Zebala, J.A. 	DNA recognition of base-analogue and chemically modified substrates by the TaqI restriction endonuclease.	Diss. Abstr.	1993	54		1394-B			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. 		
@D	Zebala, J.A.//Choi, J.//Trainor, G.L.//Barany, F. 	DNA recognition of base analogue and chemically modified substrates by the TaqI restriction endonuclease.	J. Biol. Chem.	1992	267		8106-8116			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. 		
@D	Zebrowska, J.//Zolnierkiewicz, O.//Skowron, M.A.//Zylicz-Stachula, A.//Jezewska-Frackowiak, J.//Skowron, P.M. 	A putative Type IIS restriction endonuclease GeoICI from Geobacillus sp.--A robust, thermostable alternative to mezophilic prototype BbvI.	J. Biosci.	2016	41		27-38			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. 		
@D	Zecher, K.//Suleiman, M.//Wibberg, D.//Winkler, A.//Philipp, B.//Kalinowski, J. 	Draft Genome Sequence of Donghicola sp. Strain KarMa, a Model Organism for Monomethylamine-Degrading Nonmethylotrophic Bacteria.	Genome Announcements	2017	5		e01623-16			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. 		
@D	Zedelius, J.//Rabus, R.//Grundmann, O.//Werner, I.//Brodkorb, D.//Schreiber, F.//Ehrenreich, P.//Behrends, A.//Wilkes, H.//Kube, M.//Reinhardt, R.//Widdel, F. 	Alkane degradation under anoxic conditions by a nitrate-reducing bacterium with possible involvement of the electron acceptor in substrate activation.	Environ. Microbiol. Reports	2011	3		125-135			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. 		
@D	Zehr, E.S.//Bayles, D.O.//Boatwright, W.D.//Tabatabai, L.B.//Register, K.B. 	Complete genome sequence of Ornithobacterium rhinotracheale strain ORT-UMN 88.	Standards in Genomic Sciences	2014	9		16			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. 		
@D	Zehr, E.S.//Bayles, D.O.//Boatwright, W.D.//Tabatabai, L.B.//Register, K.B. 	Non-contiguous finished genome sequence of Ornithobacterium rhinotracheale strain H06-030791.	Standards in Genomic Sciences	2014	9		14			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. 		
@D	Zehr, E.S.//Tabatabai, L.B. 	Detection of a bacteriophage gene encoding a Mu-like portal protein in Haemophilus parasuis reference strains and field isolates by nested polymerase chain reaction.	J. Vet. Diagn. Invest.	2011	23		538-542			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. 		
@D	Zehr, E.S.//Tabatabai, L.B.//Bayles, D.O. 	Genomic and proteomic characterization of SuMu, a Mu-like bacteriophage infecting Haemophilus parasuis.	BMC Genomics	2012	13		331			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. 		
@D	Zehr, J.P.//Bench, S.R.//Carter, B.J.//Hewson, I.//Niazi, F.//Shi, T.//Tripp, H.J.//Affourtit, J.P. 	Globally distributed uncultivated oceanic N2-fixing cyanobacteria lack oxygenic photosystem II.	Science	2008	322		1110-1112			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. 		
@D	Zeigler, D.R. 	Genome Sequence of Bacillus glycinifermentans TH008, Isolated from Ohio Soil.	Genome Announcements	2016	4		e01573-15			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. 		
@D	Zekic, F.//Weselowski, B.//Yuan, Z.C. 	Complete Genome Sequence of Burkholderia cenocepacia CR318, a Phosphate-Solubilizing Bacterium Isolated from Corn Root.	Genome Announcements	2017	5		e00490-17			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. 		
@D	Zelby, L.S. 	Antisense RNA and ribozymes targeting DNA methyltransferase for in vivo studies.	Diss. Abstr.	1996	57		907			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. 		
@D	Zelinkova, E.//Paulicek, M.//Zelinka, J. 	Modification methylase M. Sau3239I from Streptomyces aureofaciens 3239.	FEBS Lett.	1990	271		147-148			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. 		
@D	Zelinskaya, N.V.//Kovalevskaya, N.P.//Matvienko, N.N.//Zheleznaya, L.A.//Matvienko, N.I. 	A new site-specific endonuclease from Acinetobacter species (Strain M).	Biokhimiia	1996	61		1471-1482			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. 		
@D	Zelinskaya, N.V.//Kovalevskaya, N.P.//Matvienko, N.N.//Zheleznaya, L.A.//Matvienko, N.I. 	A site-specific endonuclease and methylase from the Thermophilic strain of Bacillus species IS4.	Biokhimiia	1995	60		1435-1448			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. 		
@D	Zelinskaya, N.V.//Matvienko, N.N.//Zheleznaya, L.A.//Matvienko, N.I. 	A new site-specific adenine DNA-methyltransferase from the strain of Bacillus species ST5.	Biokhimiia	1996	61		1006-1014			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. 		
@D	Zelinskaya, N.V.//Matvienko, N.N.//Zheleznaya, L.A.//Matvienko, N.I. 	A novel site-specific endonuclease from Bacillus species ST5.	Biokhimiia	1995	60		1999-2010			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. 		
@D	Zell, R.//Fritz, H.-J. 	DNA mismatch-repair in Escherichia coli counteracting the hydrolytic deamination of 5-methyl-cytosine residues.	EMBO J.	1987	6		1809-1815			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. 		
@D	Zeng, Q.//Wang, J.//Bertels, F.//Giordano, P.R.//Chilvers, M.I.//Huntley, R.B.//Vargas, J.M.//Sundin, G.W.//Jacobs, J.L.//Yang, C.H. 	Recombination of Virulence Genes in Divergent Acidovorax avenae Strains That Infect a Common Host.	Mol. Plant Microbe Interact.	2017	30		813-828			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. 		
@D	Zeng, Q.L.//Bonocora, R.P.//Shub, D.A. 	A Free-Standing Homing Endonuclease Targets an Intron Insertion Site in the psbA Gene of Cyanophages.	Curr. Biol.	2009	19		218-222			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. 		
@D	Zeng, W.//Chen, G.//Tang, Z.//Wu, H.//Shu, L.//Liang, Z. 	Draft Genome Sequence of Bacillus subtilis GXA-28, a Thermophilic Strain with High Productivity of Poly-gamma-Glutamic Acid.	Genome Announcements	2014	2		e01259-14			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. 		
@D	Zeng, X.//Jebbar, M.//Shao, Z. 	Complete Genome Sequence of Hyperthermophilic Piezophilic Archaeon Palaeococcus pacificus DY20341T, Isolated from Deep-Sea Hydrothermal Sediments.	Genome Announcements	2015	3		e01080-15			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. 		
@D	Zeng, Y.//Feng, F.//Liu, Y.//Li, Y.//Koblizek, M. 	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.	Genome Announcements	2013	1		e00034-13			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. 		
@D	Zeng, Y.//Kasalicky, V.//Simek, K.//Koblizek, M. 	Genome sequences of two freshwater betaproteobacterial isolates, limnohabitans species strains rim28 and rim47, indicate their capabilities as both  photoautotrophs and ammonia oxidizers.	J. Bacteriol.	2012	194		6302-6303			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. 		
@D	Zeng, Y.//Koblizek, M.//Feng, F.//Liu, Y.//Wu, Z.//Jian, J. 	Whole-Genome Sequences of an Aerobic Anoxygenic Phototroph, Blastomonas sp. Strain AAP53, Isolated from a Freshwater Desert Lake in Inner Mongolia, China.	Genome Announcements	2013	1		e0007113			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. 		
@D	Zeng, Z.//Chen, C.//Du, H.//Wang, G.//Li, M. 	High quality draft genomic sequence of Flavobacterium enshiense DK69(T) and comparison among Flavobacterium genomes.	Standards in Genomic Sciences	2015	10		92			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. 		
@D	Zeng, Z.//Dai, S.//Xie, Y.//Tian, X.//Li, J.//Wang, X. 	Genome sequences of two pseudoalteromonas strains isolated from the South china sea.	Genome Announcements	2014	2		e00305-14			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. 		
@D	Zepeda, V.//Dassa, B.//Borovok, I.//Lamed, R.//Bayer, E.A.//Cate, J.H. 	Draft Genome Sequence of the Cellulolytic Bacterium Clostridium papyrosolvens C7  (ATCC 700395).	Genome Announcements	2013	1		e00698-13			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. 		
@D	Zerillo, M.M.//Van Sluys, M.A.//Camargo, L.E.//Monteiro-Vitorello, C.B. 	Characterization of new IS elements and studies of their dispersion in two subspecies of Leifsonia xyli.	BMC Microbiol.	2008	8		127			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. 		
@D	Zernov, Y.P.//Lebedev, L.R.//Babkin, I.V.//Chizhikov, V.E. 	Determination of substrate specificity of restriction endonuclease Kpn378I.	Bioorg. Khim.	1990	16		603-604			The recognition sequence and cleavage site, CCGC^GG, of a new restriction endonuclease Kpn378I has been determined. 		
@D	Zeytun, A. et al. 	Complete genome sequence of Hydrogenobacter thermophilus type strain (TK-6).	Standards in Genomic Sciences	2011	4		131-143			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. 		
@D	Zeytun, A.//Malfatti, S.A.//Vergez, L.M.//Shin, M.//Garcia, E.//Chain, P.S. 	Complete Genome Sequence of Francisella philomiragia ATCC 25017.	J. Bacteriol.	2012	194		3266			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. 		
@D	Zhai, Y.//Cheng, B.//Hu, J.//Kyeremeh, K.//Wang, X.//Jaspars, M.//Deng, H.//Deng, Z.X.//Hong, K. 	Draft Genome Sequence of Streptomyces sp. Strain CT34, Isolated from a Ghanaian Soil Sample.	Genome Announcements	2015	3		e01508-14			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. 		
@D	Zhalnina, K.V.//Dias, R.//Leonard, M.T.//Dorr-de-Quadros, P.//Camargo, F.A.//Drew, J.C.//Farmerie, W.G.//Daroub, S.H.//Triplett, E.W. 	Genome Sequence of Candidatus Nitrososphaera evergladensis from Group I.1b Enriched from Everglades Soil Reveals Novel Genomic Features of the  Ammonia-Oxidizing Archaea.	PLoS ONE	2014	9		e101648			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. 		
@D	Zhan, B.//Angen, O.//Hedegaard, J.//Bendixen, C.//Panitz, F. 	Draft Genome Sequences of Actinobacillus pleuropneumoniae Serotypes 2 and 6.	J. Bacteriol.	2010	192		5846-5847			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). 		
@D	Zhan, Y.//Yan, Y.//Zhang, W.//Yu, H.//Chen, M.//Lu, W.//Ping, S.//Peng, Z.//Yuan, M.//Zhou, Z.//Elmerich, C.//Lin, M. 	Genome Sequence of Acinetobacter calcoaceticus PHEA-2, Isolated from Industry Wastewater.	J. Bacteriol.	2011	193		2672-2673			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. 		
@D	Zhang, A.//Yang, M.//Hu, P.//Wu, J.//Chen, B.//Hua, Y.//Yu, J.//Chen, H.//Xiao, J.//Jin, M. 	Comparative Genomic Analysis of Streptococcus suis reveals significant genomic diversity among different serotypes.	BMC Genomics	2011	12		523			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. 		
@D	Zhang, B.//Li, L.//Chen, F.//Guan, Y. 	Initial investigation on restriction modification system of Streptomyces ahygroscopicus wuzhouensis neosubsp.	Weishengwuxue Zazhi	2008	28		65-68			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. 		
@D	Zhang, B.//Tao, T.//Wilson, G.G.//Blumenthal, R.M. 	The M.AluI DNA-(cytosine C5)-methyltransferase has an unusually large, partially dispensable, variable region.	Nucleic Acids Res.	1993	21		905-911			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. 		
@D	Zhang, C.//Feng, Y.//Liu, F.//Jiang, H.//Qu, Z.//Lei, M.//Wang, J.//Zhang, B.//Hu, Y.//Ding, J.//Zhu, B. 	A phage-like IncY plasmid carrying mcr-1 gene in an Escherichia coli strain from pig farm in China.	Antimicrob. Agents Chemother.	2016	61		e02035-16			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. 		
@D	Zhang, C.//Guo, W.//Wang, Y.//Chen, X. 	Draft Genome Sequences of Two Psychrotolerant Strains, Colwellia polaris MCCC 1C00015(T) and Colwellia chukchiensis CGMCC 1.9127(T).	Genome Announcements	2018	6		e01575-17			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. 		
@D	Zhang, C.//Pang, B.//Zhou, Z.//Wang, H.//Zhou, H.//Lu, X.//Du, P.//Zhang, L.//Li, J.//Cui, Z.//Chen, C.//Stokes, H.W.//Kan, B. 	The purifying trend in the chromosomal integron in Vibrio cholerae strains during the seventh pandemic.	Infect. Genet. Evol.	2014	26C		241-249			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. 		
@D	Zhang, D.//Chang, D.//Zhang, X.//Yu, Y.//Guo, Y.//Wang, J.//Li, T.//Xu, G.//Dai, W.//Liu, C. 	Genome Sequence of Escherichia coli Strain LCT-EC52, Which Acquired Changes in Antibiotic Resistance Properties after the Shenzhou-VIII Mission.	Genome Announcements	2014	2		e00081-14			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. 		
@D	Zhang, D.//Li, L.//Zhu, S.//Zhang, N.//Yang, J.//Ma, X.//Chen, J. 	Complete Genome Sequence of Rhodococcus sp. B7740, a Carotenoid-Producing Bacterium Isolated from the Arctic Sea.	Genome Announcements	2015	3		e00333-15			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. 		
@D	Zhang, D.//Li, W.//Qin, W.//Huang, X.//Gong, X. 	Draft Genome Sequences of Acinetobacter harbinensis Strain HITLi 7T, Isolated from River Water.	Genome Announcements	2015	3		e00028-15			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. 		
@D	Zhang, D.//Xu, D.H.//Qiu, J.//Rasmussen-Ivey, C.R.//Liles, M.R.//Beck, B.H. 	Draft Genome Sequence of Pseudomonas mosselii Gil3, Isolated from Catfish and Antagonistic against Hypervirulent Aeromonas hydrophila.	Genome Announcements	2016	4		e01305-16			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. 		
@D	Zhang, D.C.//Liu, Y.X.//Huo, Y.Y.//Xu, X.W.//Li, X.Z. 	Draft Genome Sequence of Thermophilic Exiguobacterium sp. Strain JLM-2, Isolated  from Deep-Sea Ferromanganese Nodules.	Genome Announcements	2015	3		e00794-15			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. 		
@D	Zhang, F.//Lin, W.//Zhang, R.//Zheng, Q.//Jiao, N. 	Genome Sequence of Salegentibacter mishustinae KCTC 12263, Containing a Complete  Subtype I-B CRISPR-Cas System.	Genome Announcements	2016	4		e00267-16			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. 		
@D	Zhang, F.//Su, S.//Yu, G.//Zheng, B.//Shu, F.//Wang, Z.//Xiang, T.//Dong, H.//Zhang, Z.//Hou, D.//She, Y. 	High quality genome sequence and description of Enterobacter mori strain 5-4, isolated from a mixture of formation water and crude-oil.	Standards in Genomic Sciences	2015	10		9			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. 		
@D	Zhang, G.//Deng, A.//Xu, Q.//Liang, Y.//Chen, N.//Wen, T. 	Complete genome sequence of Bacillus amyloliquefaciens TA208, a strain for industrial production of guanosine and ribavirin.	J. Bacteriol.	2011	193		3142-3143			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. 		
@D	Zhang, G.//Esteve, P.O.//Chin, H.G.//Terragni, J.//Dai, N.//Correa, I.R. Jr.//Pradhan, S. 	Small RNA-mediated DNA (cytosine-5) methyltransferase 1 inhibition leads to aberrant DNA methylation.	Nucleic Acids Res.	2015	43		6112-6124			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. 		
@D	Zhang, G.//Fauzi, H.M.//Zhang, R.//Hikmawan, T.//Stingl, U. 	Draft Genome Sequences of Two Thiomicrospira Strains Isolated from the Brine-Seawater Interface of Kebrit Deep in the Red Sea.	Genome Announcements	2016	4		e00110-16			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. 		
@D	Zhang, G.//Fauzi, H.M.//Zhang, R.//Hikmawan, T.//Stingl, U. 	Draft Genome Sequence of Pseudoalteromonas sp. Strain XI10 Isolated from the Brine-Seawater Interface of Erba Deep in the Red Sea.	Genome Announcements	2016	4		e00109-16			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. 		
@D	Zhang, G.//Wang, Q.//Su, Y.//Li, S.//Liu, H. 	Genome Sequence of Staphylococcus aureus PX03, an Acetoin-Producing Strain with a Small-Sized Genome.	Genome Announcements	2017	5		e00753-17			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. 		
@D	Zhang, G.//Wang, W.//Deng, A.//Sun, Z.//Zhang, Y.//Liang, Y.//Che, Y.//Wen, T. 	A Mimicking-of-DNA-Methylation-Patterns Pipeline for Overcoming the Restriction Barrier of Bacteria.	PLoS Genet.	2012	8		e1002987			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. 		
@D	Zhang, H.//Li, X.//Zhang, B.//Liu, C. 	Draft Genome Sequence of Acinetobacter sp. Strain YZS-X1-1, a Denitrifying Bacterium Isolated from Freshwater Pond Sludge in China.	Genome Announcements	2015	3		e01579-14			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%. 		
@D	Zhang, H.//Liu, R.//Wang, M.//Wang, H.//Gao, Q.//Hou, Z.//Gao, D.//Wang, L. 	Draft Genome Sequence of Alcanivorax sp. Strain KX64203 Isolated from Deep-Sea Sediments of Iheya North, Okinawa Trough.	Genome Announcements	2016	4		e00872-16			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. 		
@D	Zhang, H.//Liu, R.//Wang, M.//Wang, H.//Gao, Q.//Hou, Z.//Zhou, Z.//Gao, D.//Wang, L. 	Draft Genome Sequences of Pseudoalteromonas telluritireducens DSM 16098 and P. spiralis DSM 16099 Isolated from the Hydrothermal Vents of the Juan de Fuca  Ridge.	Genome Announcements	2016	4		e00871-16			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. 		
@D	Zhang, H.//Shen, N.//Qin, Y.//Zhu, J.//Li, Y.//Wu, J.//Jiang, M.G. 	Complete Genome Sequence of Actinobacillus succinogenes GXAS137, a Highly Efficient Producer of Succinic Acid.	Genome Announcements	2018	6		e01562-17			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. 		
@D	Zhang, H.//Zhang, S.//Peng, Y.//Li, Y.//Chen, Z.//Zheng, W.//Xu, H.//Yu, Z.//Zheng, T. 	Draft Genome Sequence of the Anti-Algal Marine Actinomycete Streptomyces sp. JS01.	Genome Announcements	2014	2		e01261-14			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. 		
@D	Zhang, H.//Zhou, W.//Zhuang, Y.//Liang, X.//Liu, T. 	Draft Genome Sequence of Streptomyces bottropensis ATCC 25435, a Bottromycin-Producing Actinomycete.	Genome Announcements	2013	1		e0001913			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. 		
@D	Zhang, J.//Cao, G.//Xu, X.//Jin, H.//Yang, X.//Allard, M.//Brown, E.//Meng, J. 	Draft Genome Sequences of Three Salmonella enterica Serotype Agona Strains from China.	Genome Announcements	2013	1		e00203-12			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. 		
@D	Zhang, J.//Cao, G.//Xu, X.//Jin, H.//Zhang, Q.//Chen, J.//Yang, X.//Pan, H.//Zhang, X.//Allard, M.//Brown, E.//Meng, J. 	Whole-Genome Sequences of Four Salmonella enterica Serotype Newport Strains from  Humans.	Genome Announcements	2013	1		e00213-13			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. 		
@D	Zhang, J.//Hu, J.//Zhang, X.//Zeng, X. 	Draft Genome Sequence of Anaerobic Fermentative Bacterium Anaeromicrobium sediminis DY2726D.	Genome Announcements	2018	6		e00002-18			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. 		
@D	Zhang, J.//Hung, G.C.//Lei, H.//Li, T.//Li, B.//Tsai, S.//Lo, S.C. 	Draft Genome Sequence of Pantoea sp. Strain MBLJ3, Isolated in a Laboratory Environmental Control Study.	Genome Announcements	2015	3		e01595-14			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. 		
@D	Zhang, J.//Wang, J.//Wang, C. 	Complete Genome Sequence of Ehrlichia canis Strain YZ-1, Isolated from a Beagle with Fever and Thrombocytopenia.	Genome Announcements	2018	6		e00133-18			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. 		
@D	Zhang, J.//Yuan, Q.//Yang, W.//Wang, X. 	Complete Genome Sequence of Carbendazim-Degrading Mycobacterium sp. Strain djl-10.	Genome Announcements	2017	5		e01683-16			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. 		
@D	Zhang, J.X.//Lin, B.R.//Shen, H.F.//Pu, X.M. 	Genome Sequence of the Banana Pathogen Dickeya zeae Strain MS1, Which Causes Bacterial Soft Rot.	Genome Announcements	2013	1		e00317-13			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. 		
@D	Zhang, J.Y.//Guan, R.//Zhang, H.J.//Li, H.//Xiao, P.//Yu, G.L.//Du, L.//Cao, D.M.//Zhu, B.C.//Li, R.H.//Lu, Z.H. 	Complete genome sequence and genomic characterization of Microcystis panniformis  FACHB 1757 by third-generation sequencing.	Standards in Genomic Sciences	2016	11		11			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. 		
@D	Zhang, K.//McClure, J.A.//Elsayed, S.//Conly, J.M. 	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.	Antimicrob. Agents Chemother.	2009	53		531-540			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. 		
@D	Zhang, L.//Li, X.//Zhang, F.//Wang, G. 	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.	Standards in Genomic Sciences	2014	9		574-584			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. 		
@D	Zhang, L.//Morrison, M.//O'Cuiv, P.//Evans, P.//Rickard, C.M. 	Genome Sequence of Stenotrophomonas maltophilia Strain AU12-09, Isolated from an  Intravascular Catheter.	Genome Announcements	2013	1		e00195-13			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. 		
@D	Zhang, L.//Morrison, M.//O'Cuiv, P.//Evans, P.//Rickard, C.M. 	Genome Sequence of Staphylococcus epidermidis Strain AU12-03, Isolated from an Intravascular Catheter.	J. Bacteriol.	2012	194		6639			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. 		
@D	Zhang, L.//Morrison, M.//Rickard, C.M. 	Draft Genome Sequence of Ralstonia pickettii AU12-08, Isolated from an Intravascular Catheter in Australia.	Genome Announcements	2014	2		e00027-14			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. 		
@D	Zhang, L.//Si, M.//Zhu, L.//Li, C.//Wei, Y.//Shen, X. 	Draft Genome Sequence of Nafulsella turpanensis ZLM-10T, a Novel Member of the Family Flammeovirgaceae.	Genome Announcements	2014	2		e00263-14			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%. 		
@D	Zhang, L.//Skurnik, M. 	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.	J. Bacteriol.	1994	176		1756-1760			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. 		
@D	Zhang, L.//Yang, Z. 	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.	Genome Announcements	2017	5		e01418-16			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. 		
@D	Zhang, L.//Zhang, X.//Liu, C.//Li, C.//Li, S.//Li, T.//Li, D.//Zhao, Y.//Yang, Z. 	Manufacture of Cheddar cheese using probiotic Lactobacillus plantarum K25 and its cholesterol-lowering effects in a mice model.	World J. Microbiol. Biotechnol.	2013	29		127-135			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. 		
@D	Zhang, Lu.//Lu, D.-Y.//Ma, W.-Y.//Li, Y. 	Age-related changes in the localization of DNA methyltransferases during meiotic maturation in mouse oocytes.	Fertil. Steril.	2011	95		1531-1534			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. 		
@D	Zhang, M.//He, L.//Li, Q.//Sun, H.//Gu, Y.//You, Y.//Meng, F.//Zhang, J. 	Genomic characterization of the Guillain-Barre syndrome-associated Campylobacter jejuni ICDCCJ07001 Isolate.	PLoS ONE	2010	5		e15060			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. 		
@D	Zhang, M.//Ito, T.//Li, S.//Misawa, S.//Kondo, S.//Miida, T.//Ohsaka, A.//Hiramatsu, K. 	Analysis of Staphylococcal cassette chromosome mec in BD GeneOhm MRSA assay-negative strains.	Antimicrob. Agents Chemother.	2013	57		2890-2891			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. 		
@D	Zhang, M.//Li, Q.//He, L.//Meng, F.//Gu, Y.//Zheng, M.//Gong, Y.//Wang, P.//Ruan, F.//Zhou, L.//Wu, J.//Chen, L.//Fitzgerald, C.//Zhang, J. 	Association study between an outbreak of Guillain-Barre syndrome in Jilin, China, and preceding Campylobacter jejuni infection.	Foodborne Pathog. Dis.	2010	7		913-919			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. 		
@D	Zhang, M.//Ma, L.//Yang, Y.//Hu, T.//Liu, X.//Zhang, X.//Hua, Y.//Gao, Y.//Zhu, Z. 	Draft Genome Sequence of Pseudomonas stutzeri LH-42, Isolated from Petroleum-Contaminated Soil.	Genome Announcements	2017	5		e00589-17			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. 		
@D	Zhang, M.//Yang, X.//Liu, H.//Liu, X.//Huang, Y.//He, L.//Gu, Y.//Zhang, J. 	Genome Sequences of the Guillain-Barre Syndrome Outbreak-Associated Campylobacter jejuni Strains ICDCCJ07002 and ICDCCJ07004.	Genome Announcements	2013	1		e00256-13			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. 		
@D	Zhang, P.//Bao, Y.//Higgins, L.//Xu, S.Y. 	Rational design of a chimeric endonuclease targeted to NotI recognition site.	Protein Eng. Des. Sel.	2007	20		497-504			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. 		
@D	Zhang, P.H.//Too, P.H.M.//Samuelson, J.C.//Chan, S.H.//Vincze, T.//Doucette, S.//Backstrom, S.//Potamousis, K.D.//Schramm, T.M.//Forrest, D.//Schwartz, D.C.//Xu, S.Y. 	Engineering BspQI nicking enzymes and application of N.BspQI in DNA labeling and production of single-strand DNA.	Protein Expr. Purif.	2010	69		226-234			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). 		
@D	Zhang, Q.//Poehlein, A.//Hollensteiner, J.//Daniel, R. 	Draft Genome Sequence of Komagataeibacter maltaceti LMG 1529(T), a Vinegar-Producing Acetic Acid Bacterium Isolated from Malt Vinegar Brewery  Acetifiers.	Genome Announcements	2018	6		e00330-18			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. 		
@A	Zhang, Q.//Xie, J.//Wu, J.//Lu, Z. 		RESP: a tool using for selecting a set of restriction enzymes.			Zhou, G.//Lu, Z.//Takeyama, H. 		Prog. Post-Genome Technol.					Southeast University Press, Nanjing, China	2006		0		388-390									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. 		
@D	Zhang, Q.//Ye, X.//Ren, G.//Zhang, N.//Li, Lu.//Li, D. 	A new method for the purification of restriction enzyme NotI.	Zhongguo Shengwu Gongcheng Zazhi	2011	31		102-109			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. 		
@D	Zhang, Q.-M.//Sugiyama, H.//Miyabe, I.//Matsuda, S.//Kino, K.//Saito, I.//Yonei, S. 	Replication in vitro and cleavage by restriction endonuclease of 5-formyluracil- and 5-hydroxymethyluracil-containing oligonucleotides.	Int. J. Radiat. Biol.	1999	75		59-65			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. 		
@D	Zhang, Q.Y.//Xiao, F.//Xie, J.//Li, Z.Q.//Gui, J.F. 	Complete Genome Sequence of Lymphocystis Disease Virus Isolated from China.	J. Virol.	2004	78		6982-6994			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. 		
@D	Zhang, R.//Xia, H.//Xu, Q.//Dang, F.//Qin, Z. 	Recombinational cloning of the antibiotic biosynthetic gene clusters in linear plasmid SCP1 of Streptomyces coelicolor A3(2).	FEMS Microbiol. Lett.	2013	345		39-48			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. 		
@D	Zhang, S.//Flores-Cruz, Z.//Kumar, D.//Chakrabarty, P.//Hopkins, D.L.//Gabriel, D.W. 	The Xylella fastidiosa Biocontrol Strain EB92-1 Genome Is Very Similar and Syntenic to Pierce's Disease Strains.	J. Bacteriol.	2011	193		5576-5577			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. 		
@D	Zhang, S.//Jiang, W.//Li, J.//Meng, L.//Cao, X.//Hu, J.//Liu, Y.//Chen, J.//Sha, C. 	Whole genome shotgun sequence of Bacillus amyloliquefaciens TF28, a biocontrol entophytic bacterium.	Standards in Genomic Sciences	2016	11		73			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. 		
@D	Zhang, S.//Luo, X.//Cheng, J.//Peng, J.//Zhang, D.//Liu, Y. 	Genome Sequence of Pyrethroid-Degrading Bacterium Rhodopseudomonas palustris Strain JSC-3b.	Genome Announcements	2014	2		e01228-13			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. 		
@D	Zhang, S.//Wang, D.//Wang, Y.//Hasman, H.//Aarestrup, F.M.//Alwathnani, H.A.//Zhu, Y.G.//Rensing, C. 	Genome sequences of copper resistant and sensitive Enterococcus faecalis strains  isolated from copper-fed pigs in Denmark.	Standards in Genomic Sciences	2015	10		35			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. 		
@D	Zhang, S.//Xu, Y.//Zhou, Z.//Wang, S.//Yang, R.//Wang, J.//Wang, L. 	Complete genome sequence of Bordetella pertussis CS, a Chinese pertussis vaccine strain.	J. Bacteriol.	2011	193		4017-4018			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. 		
@D	Zhang, S.D.//Barbe, V.//Garel, M.//Zhang, W.J.//Chen, H.//Santini, C.L.//Murat, D.//Jing, H.//Zhao, Y.//Lajus, A.//Martini, S.//Pradel, N.//Tamburini, C.//Wu, L.F. 	Genome Sequence of Luminous Piezophile Photobacterium phosphoreum ANT-2200.	Genome Announcements	2014	2		e00096-14			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. 		
@D	Zhang, S.H.//Qiu, J.J.//Yang, R.//Shen, K.F.//Xu, G.Y.//Fu, L.Z. 	Complete Genome Sequence of Trueperella pyogenes, Isolated from Infected Farmland Goats.	Genome Announcements	2016	4		e01421-16			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. 		
@D	Zhang, T.//Bao, M.//Wang, Y.//Su, H.//Tan, T. 	Genome Sequence of Bacillus cereus Strain A1, an Efficient Starch-Utilizing Producer of Hydrogen.	Genome Announcements	2014	2		e00494-14			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. 		
@D	Zhang, T.//Zhang, R.//Luo, Q.//Wen, G.//Ai, D.//Wang, H.//Luo, L.//Wang, H.//Shao, H. 	Genome Sequence of Avirulent Riemerella anatipestifer Strain RA-JLLY.	Genome Announcements	2015	3		e00895-15			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. 		
@D	Zhang, W.//Nadirk, J.//Kossow, A.//Bielaszewska, M.//Leopold, S.R.//Witten, A.//Fruth, A.//Karch, H.//Ammon, A.//Mellmann, A. 	Phylogeny and phenotypes of clinical and environmental Shiga toxin-producing Escherichia coli O174.	Environ. Microbiol.	2014	16		963-976			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. 		
@D	Zhang, W.//Yu, D.//Sun, Z.//Wu, R.//Chen, X.//Chen, W.//Meng, H.//Hu, S.//Zhang, H. 	Complete genome sequence of Lactobacillus casei Zhang, a new probiotic strain isolated from traditional homemade koumiss in Inner Mongolia,  China.	J. Bacteriol.	2010	192		5268-5269			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. 		
@D	Zhang, W.Y.//Hu, J.//Pan, J.//Sun, C.//Wu, M.//Xu, X.W. 	Draft genome sequence of Halopiger salifodinae KCY07-B2(T), an extremly halophilic archaeon isolated from a salt mine.	Standards in Genomic Sciences	2015	10		124			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. 		
@D	Zhang, W.Y.//Yuan, Y.//Su, D.Q.//He, X.P.//Han, S.B.//Epstein, S.S.//He, S.//Wu, M. 	Gallaecimonas mangrovi sp. nov., a novel bacterium isolated from mangrove sediment.	Antonie Van Leeuwenhoek	2018	111		1855-1862			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). 		
@D	Zhang, X.//Bruice, T.C. 	The mechanism of M.HhaI DNA C5 cytosine methyltransferase enzyme: a quantum mechanics/molecular mechanics approach.	Proc. Natl. Acad. Sci. U. S. A.	2006	103		6148-6153			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. 		
@D	Zhang, X.//Hu, Q.//Yuan, W.//Shang, W.//Cheng, H.//Yuan, J.//Zhu, J.//Hu, Z.//Li, S.//Chen, W.//Hu, X.//Rao, X. 	First report of a sequence type 239 vancomycin-intermediate Staphylococcus aureus isolate in Mainland China.	Diagn. Microbiol. Infect. Dis.	2013	77		64-68			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. 		
@D	Zhang, X.//Jacobsen, S.E. 	Genetic analyses of DNA methyltransferases in Arabidopsis thaliana.	Cold Spring Harb. Symp. Quant. Biol.	2006	71		439-447			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. 		
@D	Zhang, X.//Li, G.X.//Chen, S.C.//Jia, X.Y.//Wu, K.//Cao, C.L.//Bao, P. 	Draft Genome Sequence of Desulfitobacterium hafniense Strain DH, a Sulfate-Reducing Bacterium Isolated from Paddy Soils.	Genome Announcements	2016	4		e01693-15			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. 		
@D	Zhang, X.//Ma, F.//Szewzyk, U. 	Draft Genome Sequence of a Potential Nitrate-Dependent Fe(II)-Oxidizing Bacterium, Aquabacterium parvum B6.	Genome Announcements	2016	4		e01651-15			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. 		
@D	Zhang, X.//Mathews, C.K. 	Effect of DNA cytosine methylation upon deamination-induced mutagenesis in a natural target sequence in duplex DNA.	J. Biol. Chem.	1994	269		7066-7069			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. 		
@D	Zhang, X.//Verdine, G.L. 	Mammalian DNA cytosine-5 methyltransferase interacts with p23 protein.	FEBS Lett.	1996	392		179-183			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. 		
@D	Zhang, X.//Wang, T.//Liu, W.//Guo, Y.//Wang, J.//Li, T.//Fang, X.//Zhang, X.//Dai, W.//Liu, C. 	Genome Sequence of Klebsiella pneumoniae Strain LCT-KP182, Which Acquired Hemolytic Properties after Space Flight.	Genome Announcements	2014	2		e01088-13			The Klebsiella pneumoniae strain LCT-KP182 acquired hemolytic properties after space flight. Here, we present the draft genome sequence of this strain. 		
@D	Zhang, X.//Wang, T.//Su, L.//Zhou, L.//Li, T.//Wang, J.//Liu, Y.//Jiang, X.//Wu, C.//Liu, C. 	Draft Genome Sequence of Bacillus cereus LCT-BC25, Isolated from Space Flight.	Genome Announcements	2014	2		e00667-13			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. 		
@D	Zhang, X.//Xu, J.R.//Nakatsu, C.H. 	Draft Genome Sequence of Pseudomonas fluorescens Strain TR3, a Potential Biocontrol Agent against the Rice Blast Fungus Magnaporthe oryzae.	Genome Announcements	2017	5		e01332-17			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. 		
@D	Zhang, X.//Xu, X.//Yuan, W.//Hu, Q.//Shang, W.//Hu, X.//Tong, Y.//Rao, X. 	Complete Genome Sequence of Staphylococcus aureus XN108, an ST239-MRSA-SCCmec III Strain with Intermediate Vancomycin Resistance Isolated in Mainland China.	Genome Announcements	2014	2		e00449-14			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. 		
@D	Zhang, X.//Zhao, C.//Hong, X.//Chen, S.//Yang, S. 	Genome Sequence of Marichromatium gracile YL-28, a Purple Sulfur Bacterium with Bioremediation Potential.	Genome Announcements	2016	4		e00288-16			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. 		
@D	Zhang, X.S.//Blaser, M.J. 	Natural Transformation of an Engineered Helicobacter pylori Strain Deficient in Type II Restriction Endonucleases.	J. Bacteriol.	2012	194		3407-3416			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. 		
@D	Zhang, X.Y.//Xie, B.B.//Qin, Q.L.//Liu, A.//Chen, X.L.//Zhou, B.C.//Zhang, Y.Z. 	Draft genome sequence of strain p7-3-5, a new flavobacteriaceae bacterium isolated from intertidal sand.	J. Bacteriol.	2012	194		6632			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. 		
@D	Zhang, X.Y.//Zhang, Y.J.//Qin, Q.L.//Xie, B.B.//Chen, X.L.//Zhou, B.C.//Zhang, Y.Z. 	Genome Sequence of the Protease-Producing Bacterium Rheinheimera nanhaiensis E407-8T, Isolated from Deep-Sea Sediment of the South China Sea.	J. Bacteriol.	2012	194		7001-7002			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. 		
@D	Zhang, Y.//Chen, C.//Liu, J.//Deng, H.//Pan, A.//Zhang, L.//Zhao, X.//Huang, M.//Lu, B.//Dong, H.//Du, P.//Chen, W.//Wan, K. 	Complete Genome Sequences of Mycobacterium tuberculosis Strains CCDC5079 and CCDC5080, Which Belong to the Beijing Family.	J. Bacteriol.	2011	193		5591-5592			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. 		
@D	Zhang, Y.//Nelson, M.//Nietfeldt, J.//Xia, Y.//Burbank, D.//Ropp, S.//Van Etten, J.L. 	Chlorella virus NY-2A encodes at least 12 DNA endonuclease/methyltransferase genes.	Virology	1998	240		366-375			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. 		
@D	Zhang, Y.//Nelson, M.//Nietfeldt, J.W.//Burbank, D.E.//Van Etten, J.L. 	Characterization of Chlorella virus PBCV-1 CviAII restriction and modification system.	Nucleic Acids Res.	1992	20		5351-5356			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. 		
@D	Zhang, Y.//Nelson, M.//Van Etten, J.L. 	A single amino acid change restores DNA cytosine methyltransferase activity in a cloned Chlorella virus pseudogene.	Nucleic Acids Res.	1992	20		1637-1642			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. 		
@D	Zhang, Y.//Nie, P.//Lin, L. 	Complete Genome Sequence of the Fish Pathogen Flavobacterium columnare Pf1.	Genome Announcements	2016	4		e00900-16			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. 		
@D	Zhang, Y.//Qin, F.//Qiao, J.//Li, G.//Shen, C.//Huang, T.//Hu, Z. 	Draft Genome Sequence of Rhodococcus sp. Strain P14, a Biodegrader of High-Molecular-Weight Polycyclic Aromatic Hydrocarbons.	J. Bacteriol.	2012	194		3546			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. 		
@D	Zhang, Y.//Yang, J.//Xu, L.//Zhu, Y.//Liu, B.//Shao, Z.//Zhang, X.//Jin, Q. 	Complete Genome Sequence of Neisseria meningitidis Serogroup A Strain NMA510612,  Isolated from a Patient with Bacterial Meningitis in China.	Genome Announcements	2014	2		e00360-14			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. 		
@D	Zhang, Y.//Zhao, Z.//Deng, W.//Xie, X.//Jiao, N. 	Draft Genome Sequence of Euryhalocaulis caribicus Strain JL2009T, a New Member of the Family Hyphomonadaceae Isolated from the Caribbean Sea.	Genome Announcements	2013	1		e00407-13			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. 		
@D	Zhang, Y.C.//Zhang, Y.//Zhu, B.R.//Zhang, B.W.//Ni, C.//Zhang, D.Y.//Huang, Y.//Pang, E.//Lin, K. 	Genome sequences of two closely related strains of Escherichia coli K-12 GM4792.	Standards in Genomic Sciences	2015	10		125			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. 		
@D	Zhang, Y.L.//Ong, C.T.//Leung, K.Y. 	Molecular analysis of genetic differences between virulent and avirulent strains of Aeromonas hydrophila isolated from diseased fish.	Microbiology	2000	146		999-1009			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. 		
@D	Zhang, Y.Y.//Li, Q.G.//Liang, J.X.//Zhu, Y.B. 	Hairpin probes for real-time assay of restriction endonucleases.	Acta Biochim. Biophys. Sin.	2002	34		329-332			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. 		
@D	Zhang, Z.//Chen, Y.//Fu, Y.//Jiao, N. 	Draft Genome Sequence of the Novel Exopolysaccharide-Producing Bacterium Altibacter lentus Strain JLT2010T, Isolated from Deep Seawater of the South China  Sea.	Genome Announcements	2014	2		e00954-14			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. 		
@D	Zhang, Z.//Hai, R.//Song, Z.//Xia, L.//Liang, Y.//Cai, H.//Liang, Y.//Shen, X.//Zhang, E.//Xu, J.//Yu, D.//Yu, X.J. 	Spatial variation of Yersinia pestis from Yunnan Province of China.	Am. J. Trop. Med. Hyg.	2009	81		714-717			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. 		
@D	Zhang, Z.//Liu, C.//Zhu, Y.//Zhong, Y.//Zhu, Y.//Zheng, H.//Zhao, G.P.//Wang, S.Y.//Guo, X. 	Complete genome sequence of Lactobacillus plantarum JDM1.	J. Bacteriol.	2009	191		5020-5021			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. 		
@D	Zhang, Z.//Yu, A.//Lan, J.//Zhang, Y.//Zhang, H.//Li, Y.//Hu, M.//Cheng, J.//Wei, S.//Lin, L. 	Draft Genome Sequence of an Attenuated Streptococcus agalactiae Strain Isolated from the Gut of a Nile Tilapia (Oreochromis niloticus).	Genome Announcements	2017	5		e01627-16			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. 		
@D	Zhang, Z.J.//Chen, C.Q.//Manev, H. 	Enzymatic regional methylation assay for determination of CpG methylation density.	Anal. Chem.	2004	76		6829-6832			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. 		
@D	Zhang, Z.M.//Liu, S.//Lin, K.//Luo, Y.//Perry, J.J.//Wang, Y.//Song, J. 	Crystal Structure of Human DNA Methyltransferase 1.	J. Mol. Biol.	2015	427		2520-2531			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. 		
@D	Zhang, Z.M.//Lu, R.//Wang, P.//Yu, Y.//Chen, D.//Gao, L.//Liu, S.//Ji, D.//Rothbart, S.B.//Wang, Y.//Wang, G.G.//Song, J. 	Structural basis for DNMT3A-mediated de novo DNA methylation.	Nature	2018	554		387-391			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. 		
@D	Zhang, Z.Y.//Sun, Z.Q.//Wang, Z.L.//Wen, Z.L.//Sun, Q.W.//Zhu, Z.Q.//Song, Y.Z.//Zhao, J.W.//Wang, H.H.//Zhang, S.L.//Guo, X.K. 	Complete Genome Sequence of a Novel Clinical Isolate, the Nontuberculous Mycobacterium Strain JDM601.	J. Bacteriol.	2011	193		4300-4301			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. 		
@D	Zhao, B.//Mesbah, N.M.//Dalin, E.//Goodwin, L.//Nolan, M.//Pitluck, S.//Chertkov, O.//Brettin, T.S.//Han, J.//Larimer, F.W.//Land, M.L.//Hauser, L.//Kyrpides, N.//Wiegel, J. 	Complete Genome Sequence of the Anaerobic, Halophilic Alkalithermophile Natranaerobius thermophilus JW/NM-WN-LFT.	J. Bacteriol.	2011	193		4023			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. 		
@D	Zhao, C.//Qu, K.G.//Song, Y.J.//Ren, J.S.//Qu, X.G. 	A Universal, Label-Free, and Sensitive Optical Enzyme-Sensing System for Nuclease and Methyltransferase Activity Based on Light Scattering of Carbon Nanotubes.	Adv. Funct. Mater.	2011	21		583-590			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. 		
@D	Zhao, C.W.//Wang, H.Y.//Zhang, Y.Z.//Feng, H. 	Draft Genome Sequence of Bacillus pumilus BA06, a Producer of Alkaline Serine Protease with Leather-Dehairing Function.	J. Bacteriol.	2012	194		6668-6669			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. 		
@D	Zhao, D.M.//Jin, F.//Huang, H.F. 	A review on DNA methyltransferases and early embryo development including DNA methyltransferases I (DnmT1) and DNA methyltransferases  III (DnmT3).	Zhejiang Da Xue Xue Bao Yi Xue Ban	2005	34		281-284					
@D	Zhao, F.//Bai, J.//Wu, J.//Liu, J.//Zhou, M.//Xia, S.//Wang, S.//Yao, X.//Yi, H.//Lin, M.//Gao, S.//Zhou, T.//Xu, Z.//Niu, Y.//Bao, Q. 	Sequencing and Genetic Variation of Multidrug Resistance Plasmids in Klebsiella pneumoniae.	PLoS ONE	2010	5		E10141			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. 		
@D	Zhao, F.Q.//Zhang, X.W.//Liang, C.W.//Wu, J.Y.//Bao, Q.Y.//Qin, S. 	Genome-wide analysis of restriction-modification system in unicellular and filamentous cyanobacteria.	Physiol. Genomics	2006	24		181-190			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. 		
@D	Zhao, G.//Li, J.//Tong, Z.//Zhao, B.//Mu, R.//Guan, Y. 	Enzymatic Cleavage of Type II Restriction Endonucleases on the 2 '-O-Methyl Nucleotide and Phosphorothioate Substituted DNA.	PLoS ONE	2013	8		e79415			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. 		
@D	Zhao, L. 	Characterization of bacterial homing endonuclease I-Ssp6803I.	Ph.D. Thesis, University of Washington, Seattle, USA	2008			1-142			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. 		
@D	Zhao, L.//Bao, G.//Geng, B.//Song, J.//Li, Y. 	Draft Genome Sequence of Lysinibacillus fusiformis Strain SW-B9, a Novel Strain for Biotransformation of Isoeugenol to Vanillin.	Genome Announcements	2015	3		e00289-15			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. 		
@D	Zhao, L.//Bonocora, R.P.//Shub, D.A.//Stoddard, B.L. 	The restriction fold turns to the dark side: a bacterial homing endonuclease with a PD-(D/E)-XK motif.	EMBO J.	2007	26		2432-2442			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. 		
@D	Zhao, L.//Pellenz, S.//Stoddard, B.L. 	Activity and Specificity of the Bacterial PD-(D/E)XK Homing Endonuclease I-Ssp6803I.	J. Mol. Biol.	2009	385		1498-1510			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. 		
@D	Zhao, M.//Liu, S.//He, L.//Tian, Y. 	Draft Genome Sequence of Lactobacillus plantarum XJ25 Isolated from Chinese Red Wine.	Genome Announcements	2016	4		e01216-16			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. 		
@D	Zhao, N.//Bai, Y.//Zhao, X.Q.//Yang, Z.Y.//Bai, F.W. 	Draft Genome Sequence of the Flocculating Zymomonas mobilis Strain ZM401 (ATCC 31822).	J. Bacteriol.	2012	194		7008-7009			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. 		
@D	Zhao, N.//Pan, Y.//Liu, H.//Cheng, Z. 	Draft Genome Sequence of Zymomonas mobilis ZM481 (ATCC 31823).	Genome Announcements	2016	4		e00193-16			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. 		
@D	Zhao, Q.//Hu, H.//Wang, W.//Peng, H.//Zhang, X. 	Genome Sequence of Sphingobium yanoikuyae B1, a Polycyclic Aromatic Hydrocarbon-Degrading Strain.	Genome Announcements	2015	3		e01522-14			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. 		
@D	Zhao, W.//Chen, Y.//Sun, Z.//Wang, J.//Zhou, Z.//Sun, T.//Wang, L.//Chen, W.//Zhang, H. 	Complete Genome Sequence of the Lactobacillus helveticus H10.	J. Bacteriol.	2011	193		2666-2667			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. 		
@D	Zhao, W.//Jiang, H.//Tian, Q.//Hu, J. 	Draft Genome Sequence of Pseudomonas syringae pv. persicae NCPPB 2254.	Genome Announcements	2015	3		e00555-15			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. 		
@D	Zhao, W.//Zeng, X.//Xiao, X. 	Thermococcus eurythermalis sp. nov., a conditional piezophilic hyperthermophilic archaeon with a wide temperature range isolated from an oil-immersed chimney in the Guaymas Basin.	Int. J. Syst. Evol. Microbiol.	2015	65		30-35			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). 		
@D	Zhao, X.//de Jong, A.//Zhou, Z.//Kuipers, O.P. 	Complete Genome Sequence of Bacillus amyloliquefaciens Strain BH072, Isolated from Honey.	Genome Announcements	2015	3		e00098-15			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. 		
@D	Zhao, X.//Epperson, L.E.//Hasan, N.A.//Honda, J.R.//Chan, E.D.//Strong, M.//Walter, N.D.//Davidson, R.M. 	Complete Genome Sequence of Mycobacterium avium subsp. hominissuis Strain H87 Isolated from an Indoor Water Sample.	Genome Announcements	2017	5		e00189-17			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%. 		
@D	Zhao, X.//Geng, X.//Chen, C.//Chen, L.//Jiao, W.//Yang, C. 	Draft Genome Sequence of the Marine Actinomycete Streptomyces sulphureus L180, Isolated from Marine Sediment.	J. Bacteriol.	2012	194		4482			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. 		
@D	Zhao, X.//Yang, T. 	Draft Genome Sequence of the Marine Sediment-Derived Actinomycete Streptomyces xinghaiensis NRRL B24674T.	J. Bacteriol.	2011	193		5543			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. 		
@D	Zhao, Y.//Caspers, M.P.//Abee, T.//Siezen, R.J.//Kort, R. 	Complete Genome Sequence of Geobacillus thermoglucosidans TNO-09.020, a Thermophilic Sporeformer Associated with a Dairy-Processing Environment.	J. Bacteriol.	2012	194		4118			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. 		
@D	Zhao, Y.//Chen, M.//Su, L.//Wang, T.//Liu, S.//Yang, H. 	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.	Comp. Biochem. Physiol. B, Biochem. Mol. Biol.	2013	165		26-35			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. 		
@D	Zhao, Y.//Dong, Y.//Zhang, Y.//Che, L.//Pan, H.//Zhou, H. 	Draft Genome Sequence of a Selenite- and Tellurite-Reducing Marine Bacterium, Lysinibacillus sp. Strain ZYM-1.	Genome Announcements	2016	4		e01552-15			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. 		
@D	Zhao, Y.//Tian, Y.//Li, X.//Hu, B. 	Complete Genome Sequence of a Dickeya fangzhongdai Type Strain Causing Bleeding Canker of Pear Tree Trunks.	Genome Announcements	2018	6		e00177-18			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. 		
@D	Zhao, Z.//Wang, L.//Wang, B.//Liang, H.//Ye, Q.//Zeng, M. 	Complete Genome Sequence of Cronobacter sakazakii Strain CMCC 45402.	Genome Announcements	2014	2		e01139-13			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. 		
@D	Zhao, Z.-H.//Yung, M.-H.//Cui, T.//Wang, Y.-Z.//Shaw, P.C. 	Restriction endonuclease from thermophilic bacterial species IV. Isolation and characterization of BpuB5I.	Nucleic Acids Res.	1992	20		1156			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. 		
@D	Zharmukhamedova, T.Y.//Privezencova, N.G.//Shishova, O.V.//Shiryaev, S.A.//Zheleznaya, L.A.//Matvienko, N.I. 	A site-specific endonuclease from the thermophilic strain Bacillus species F4.	Biokhimiia	1999	64		697-702			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. 		
@D	Zheleznaya, L.//Shiryaev, S.//Zheleznyakova, E.//Matvienko, N.//Matvienko, N. 	R.SspD5I is a neoschizomer of HphI producing blunt end DNA fragments.	FEBS Lett.	1999	448		38-40			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'. 		
@D	Zheleznaya, L.A.//Kainov, D.E.//Yunusova, A.K.//Matvienko, N.I. 	Regulatory C protein of the EcoRV modification-restriction system.	Biokhimiia	2003	68		125-132			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. 		
@D	Zheleznaya, L.A.//Matvienko, N.N.//Matvienko, N.I. 	Two site-specific endonucleases from the thermophilic strain of Bacillus species LU11.	Biokhimiia	1993	58		1315-1322			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. 		
@D	Zheleznaya, L.A.//Perevyazova, T.A.//Alzhanova, D.V.//Matvienko, N.I. 	Site-specific nickase from Bacillus species strain D6.	Biokhimiia	2001	66		1215-1220			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. 		
@D	Zheleznaya, L.A.//Perevyazova, T.A.//Zheleznyakova, E.N.//Matvienko, N.I. 	Some properties of site-specific nickase BspD6I and the possibility of its use in hybridization analysis of DNA.	Biokhimiia	2002	67		595-600			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. 		
@D	Zheleznyakova, E.N.//Zheleznaya, L.A.//Svadbina, I.V.//Matvienko, N.I. 	A site-specific endonuclease from thermophilic strain Bacillus species ZE is a ClaI isoschizomer.	Biokhimiia	1998	63		1675-1681			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. 		
@D	Zheng, B.//Dong, H.//Xu, H.//Lv, J.//Zhang, J.//Jiang, X.//Du, Y.//Xiao, Y.//Li, L. 	Coexistence of MCR-1 and NDM-1 in Clinical Escherichia coli Isolates.	Clin. Infect. Dis.	2016	63		1393-1395			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. 		
@D	Zheng, B.//Hu, X.//Jiang, X.//Li, A.//Yao, J.//Li, L. 	First Draft Genome Sequence of Staphylococcus condimenti F-2T.	Genome Announcements	2016	4		e00499-16			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. 		
@D	Zheng, B.//Jiang, X.//Li, A.//Yao, J.//Zhang, J.//Hu, X.//Li, L. 	Whole-Genome Sequence of Multidrug-Resistant Staphylococcus caprae Strain 9557, Isolated from Cerebrospinal Fluid.	Genome Announcements	2015	3		e00718-15			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. 		
@D	Zheng, B.//Tomita, H.//Inoue, T.//Ike, Y. 	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.	Antimicrob. Agents Chemother.	2009	53		735-747			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. 		
@D	Zheng, B.//Zhang, F.//Dong, H.//Chai, L.//Shu, F.//Yi, S.//Wang, Z.//Cui, Q.//Dong, H.//Zhang, Z.//Hou, D.//Yang, J.//She, Y. 	Draft genome sequence of Paenibacillus sp. strain A2.	Standards in Genomic Sciences	2016	11		9			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. 		
@D	Zheng, B.X.//Zhang, H.K.//Ding, K. 	Draft Genome Sequence of Rhodococcus opacus Strain 04-OD7, Which Can Mobilize Phosphate.	Genome Announcements	2018	6		e00494-18			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. 		
@D	Zheng, D.//Koller, W. 	Characterization of the mitochondrial cytochrome b gene from Venturia inaequalis.	Curr. Genet.	1997	32		361-366			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. 		
@D	Zheng, D.//Wang, X.//Wang, P.//Peng, W.//Ji, N.//Liang, R. 	Genome Sequence of Pseudomonas citronellolis SJTE-3, an Estrogen- and Polycyclic  Aromatic Hydrocarbon-Degrading Bacterium.	Genome Announcements	2016	4		e01373-16			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. 		
@D	Zheng, H.//Brune, A. 	Complete Genome Sequence of Endomicrobium proavitum, a Free-Living Relative of the Intracellular Symbionts of Termite Gut Flagellates (Phylum Elusimicrobia).	Genome Announcements	2015	3		e00679-15			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. 		
@D	Zheng, H.//Guo, L.//Du, N.//Lin, J.//Song, L.//Liu, G.//Chen, F. 	Draft Genome Sequences of Two Clinical Isolates of Streptococcus mutans.	Genome Announcements	2014	2		e00441-14			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. 		
@D	Zheng, L.//Braymer, H.D. 	Overproduction and purification of McrC protein from Escherichia coli K-12.	J. Bacteriol.	1991	173		3918-3920			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). 		
@D	Zheng, L.//Cui, Z.//Xu, L.//Sun, C.//Powell, R.J.//Hill, R.T. 	Draft Genome Sequence of Rhodobacteraceae Strain PD-2, an Algicidal Bacterium with a Quorum-Sensing System, Isolated from the Marine Microalga Prorocentrum donghaiense.	Genome Announcements	2015	3		e01549-14			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. 		
@D	Zheng, L.//Simmons, L.A.//Braymer, H.D. 	Determination of the recognition sequence for McrB restriction of E. coli K12.	Abstr. Gen. Meet. Am. Soc. Microbiol.	1991	91		175			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. 		
@D	Zheng, L.//Wang, X.//Braymer, H.D. 	Purification and N-terminal amino acid sequences of two polypeptides encoded by the mcrB gene from Escherichia coli K-12.	Gene	1992	112		97-100			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. 		
@D	Zheng, P.X.//Chung, K.T.//Chiang-Ni, C.//Wang, S.Y.//Tsai, P.J.//Chuang, W.J.//Lin, Y.S.//Liu, C.C.//Wu, J.J. 	Complete Genome Sequence of emm1 Streptococcus pyogenes A20, a Strain with an Intact Two-Component System, CovRS, Isolated from a Patient with Necrotizing  Fasciitis.	Genome Announcements	2013	1		e00149-12			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. 		
@D	Zheng, Q.//Zhang, R.//Jiao, N. 	Genome Sequence of Citromicrobium Strain JLT1363, Isolated from the South China Sea.	J. Bacteriol.	2011	193		2074-2075			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. 		
@D	Zheng, W. 	Isolation and purification of the restriction endonuclease Bsu1076I.	Weishengwuxue Tongbao	1987	14		105-108			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. 		
@D	Zheng, W.//Kathariou, S. 	Host-mediated modification of Sau3AI restriction in Listeria monocytogenes: Prevalence in epidemic-associated strains.	Appl. Environ. Microbiol.	1997	63		3085-3089			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. 		
@D	Zheng, Y.//Cohen-Karni, D.//Xu, D.//Chin, H.G.//Wilson, G.//Pradhan, S.//Roberts, R.J. 	A unique family of Mrr-like modification-dependent restriction endonucleases.	Nucleic Acids Res.	2010	38		5527-5534			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. 		
@D	Zheng, Y.//Posfai, J.//Morgan, R.D.//Vincze, T.//Roberts, R.J. 	Using shotgun sequence data to find active restriction enzyme genes.	Nucleic Acids Res.	2009	37		1-11			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. 		
@D	Zheng, Y.//Roberts, R.J. 	Selection of restriction endonucleases using artificial cells.	Nucleic Acids Res.	2007	35		e83			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. 		
@D	Zheng, Z.//Clark, N.//Keremane, M.//Lee, R.//Wallis, C.//Deng, X.//Chen, J. 	Whole-Genome Sequence of 'Candidatus Liberibacter solanacearum' Strain R1 from California.	Genome Announcements	2014	2		e01353-14			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. 		
@D	Zheng, Z.//Deng, X.//Chen, J. 	Draft Genome Sequence of 'Candidatus Liberibacter asiaticus' from California.	Genome Announcements	2014	2		e00999-14			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. 		
@D	Zheng, Z.//Deng, X.//Chen, J. 	Whole-Genome Sequence of 'Candidatus Liberibacter asiaticus' from Guangdong, China.	Genome Announcements	2014	2		e00273-14			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. 		
@D	Zheng, Z.//Jiang, T.//Lin, X.//Zhou, J.//Ouyang, J. 	Draft Genome Sequence of Bacillus coagulans NL01, a Wonderful l-Lactic Acid Producer.	Genome Announcements	2015	3		e00635-15			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. 		
@D	Zheng, Z.//Sun, X.//Deng, X.//Chen, J. 	Whole-Genome Sequence of 'Candidatus Liberibacter asiaticus' from a Huanglongbing-Affected Citrus Tree in Central Florida.	Genome Announcements	2015	3		e00169-15			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. 		
@D	Zhgenti, E.//Johnson, S.L.//Davenport, K.W.//Chanturia, G.//Daligault, H.E.//Chain, P.S.//Nikolich, M.P. 	Genome Assemblies for 11 Yersinia pestis Strains Isolated in the Caucasus Region.	Genome Announcements	2015	3		e01030-15			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. 		
@D	Zhi, Y.//Wu, Q.//Xu, Y. 	Genome and transcriptome analysis of surfactin biosynthesis in Bacillus amyloliquefaciens MT45.	Sci. Rep.	2017	7		40976			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. 		
@D	Zhilkina, O.A.//Repin, V.E.//Degtyarev, S.K. 	Effect of some cultivation parameters on the yield of restriction endonuclease SfaNI.	Prikl. Biokhim. Mikrobiol.	1991	27		486-490			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. 		
@D	Zhong, C.//Nelson, M.//Cao, G.//Sadowsky, M.J.//Yan, T. 	Complete Genome Sequence of the Triclosan- and Multidrug-Resistant Pseudomonas aeruginosa Strain B10W Isolated from Municipal Wastewater.	Genome Announcements	2017	5		e01489-16			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%. 		
@D	Zhong, X.//Du, J.//Hale, C.J.//Gallego-Bartolome, J.//Feng, S.//Vashisht, A.A.//Chory, J.//Wohlschlegel, J.A.//Patel, D.J.//Jacobsen, S.E. 	Molecular Mechanism of Action of Plant DRM De Novo DNA Methyltransferases.	Cell	2014	157		1050-1060			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. 		
@D	Zhong, X.//Hale, C.J.//Nguyen, M.//Ausin, I.//Groth, M.//Hetzel, J.//Vashisht, A.A.//Henderson, I.R.//Wohlschlegel, J.A.//Jacobsen, S.E. 	DOMAINS REARRANGED METHYLTRANSFERASE3 controls DNA methylation and regulates RNA  polymerase V transcript abundance in Arabidopsis.	Proc. Natl. Acad. Sci. U. S. A.	2015	112		911-916			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. 		
@D	Zhong, X.//Tian, Y.//Niu, G.//Tan, H. 	Assembly and features of secondary metabolite biosynthetic gene clusters in Streptomyces ansochromogenes.	Sci. China Life. Sci.	2013	56		609-618			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. 		
@D	Zhong, Y.//Chang, X.//Cao, X.J.//Zhang, Y.//Zheng, H.//Zhu, Y.//Cai, C.//Cui, Z.//Zhang, Y.//Li, Y.Y.//Jiang, X.G.//Zhao, G.P.//Wang, S.//Li, Y.//Zeng, R.//Li, X.//Guo, X.K. 	Comparative proteogenomic analysis of the Leptospira interrogans virulence-attenuated strain IPAV against the pathogenic strain 56601.	Cell Res.	2011	21		1210-1229			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. 		
@D	Zhong, Z.//Toukdarian, A.//Helinski, D.//Knauf, V.//Sykes, S.//Wilkinson, J.E.//O'Bryne, C.//Shea, T.//DeLoughery, C.//Caspi, R. 	Sequence analysis of a 101-kilobase plasmid required for agar degradation by a Microscilla isolate.	Appl. Environ. Microbiol.	2001	67		5771-5779			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. 		
@D	Zhong, Z.//Wang, L.//Chen, Y.//Wang, Z.//Wang, Y.//Cui, M.//Li, T.//Ke, Y.//Yuan, X.//Wang, D.//Chen, Z.//Peng, G. 	Complete Genome Sequence of Brucella abortus Strain BCB034, a Strain of Biovar 2  Isolated from Human.	J. Bacteriol.	2012	194		6943			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. 		
@D	Zhou, B.//Li, Q. 	Bacillus subtilis 36 a highly productive strain containing the isoschizomer of restriction enzyme MstII.	Acta Biochim. Biophys. Sin.	1987	19		537-540			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. 		
@D	Zhou, E.M. et al. 	High-quality draft genome sequence of the Thermus amyloliquefaciens type strain YIM 77409(T) with an incomplete denitrification pathway.	Standards in Genomic Sciences	2016	11		20			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. 		
@D	Zhou, E.X.//Reuter, M.//Meehan, E.J.//Chen, L. 	A new crystal form of restriction endonuclease EcoRII that diffracts to 2.8 A resolution.	Acta Crystallogr. D Biol. Crystallogr.	2002	58		1343-1345			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. 		
@D	Zhou, G.//Chen, C.//Jeon, C.O.//Wang, G.//Li, M. 	High quality draft genomic sequence of Flavihumibacter solisilvae 3-3(T).	Standards in Genomic Sciences	2015	10		66			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. 		
@D	Zhou, H.//Shatz, W.//Purdy, M.M.//Fera, N.//Dahlquist, F.W.//Reich, N.O. 	Long-range structural and dynamical changes induced by cofactor binding in DNA methyltransferase M.HhaI.	Biochemistry	2007	46		7261-7268			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. 		
@D	Zhou, H.//Wang, Y.//Yu, Y.//Bai, T.//Chen, L.//Liu, P.//Guo, H.//Zhu, C.//Tao, M.//Deng, Z. 	A non-restricting and non-methylating Escherichia coli strain for DNA cloning and high-throughput conjugation to Streptomyces coelicolor.	Curr. Microbiol.	2012	64		185-190			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. 		
@D	Zhou, H.//Yao, Z.//Shi, H.//Wang, B.//Li, D.//Hou, J.//Ma, S. 	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.	Genome Announcements	2017	5		e01521-16			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. 		
@D	Zhou, H.//Zhang, T.W.//Yu, D.L.//Pi, B.R.//Yang, Q.//Zhou, J.Y.//Hu, S.N.//Yu, Y.S. 	Genomic Analysis of the Multidrug-Resistant Acinetobacter baumannii Strain MDR-ZJ06 Widely Spread in China.	Antimicrob. Agents Chemother.	2011	55		4506-4512			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. 		
@D	Zhou, H.J.//Purdy, M.M.//Dahlquist, F.W.//Reich, N.O. 	The Recognition Pathway for the DNA Cytosine Methyltransferase M.HhaI.	Biochemistry	2009	48		7807-7816			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. 		
@D	Zhou, J.//Sun, D.//Childers, A.//McDermott, T.R.//Wang, Y.//Liles, M.R. 	Three novel virophage genomes discovered from Yellowstone Lake metagenomes.	J. Virol.	2015	89		1278-1285			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. 		
@D	Zhou, L.//Cheng, X.//Connolly, B.A.//Dickman, M.J.//Hurd, P.J.//Hornby, D.P. 	Zebularine: A novel DNA methylation inhibitor that forms a covalent complex with DNA methyltransferases.	J. Mol. Biol.	2002	321		591-599			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. 		
@D	Zhou, L.//Li, M.//Yang, J.//Wei, L.//Ji, G. 	Draft Genome Sequence of Antagonistic Agent Lysobacter antibioticus 13-6.	Genome Announcements	2014	2		e00566-14			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. 		
@D	Zhou, M.//Chen, W.//Chen, H.//Wei, G. 	Draft Genome Sequence of Mesorhizobium alhagi CCNWXJ12-2T, a Novel Salt-Resistant Species Isolated from the Desert of Northwestern China.	J. Bacteriol.	2012	194		1261-1262			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. 		
@D	Zhou, M.//Dong, B.//Liu, Q. 	Draft Genome Sequence of Psychrobacter piscatorii Strain LQ58, a Psychrotolerant  Bacterium Isolated from a Deep-Sea Hydrothermal Vent.	Genome Announcements	2016	4		e00044-16			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. 		
@D	Zhou, M.//Xie, Y.//Dong, B.//Liu, Q.//Chen, X. 	Draft Genome Sequence of Caloranaerobacter sp. TR13, an Anaerobic Thermophilic Bacterium Isolated from a Deep-Sea Hydrothermal Vent.	Genome Announcements	2015	3		e01491-15			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. 		
@D	Zhou, P.//Wu, Y.H.//Cheng, H.//Wang, C.S.//Xu, X.W. 	Draft Genome Sequence of Altererythrobacter troitsensis JCM 17037, Isolated from  the Sea Urchin Strongylocentrotus intermedius.	Genome Announcements	2016	4		e01556-15			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. 		
@D	Zhou, P.//Xie, G.//Li, X.//Liu, J.//Qi, F. 	Complete Genome Sequence of Veillonella atypica OK5, the First Transformable Strain in the Species.	Genome Announcements	2017	5		e00391-17			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. 		
@D	Zhou, S.//Li, L.//Wei, J.//Qin, Q. 	Genome Sequence of Klebsiella pneumoniae HSL4, a New Strain Isolated from Mangrove Sediment for Biosynthesis of 1,3-Propanediol.	Genome Announcements	2013	1		e00177-13			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. 		
@D	Zhou, W.//Li, M.//Zhu, L.//Hua, F.//Ji, X.//Sun, Y.//Liu, J.//Guo, X. 	Complete Genome Sequence of Wohlfahrtiimonas chitiniclastica Strain BM-Y, Isolated from the Pancreas of a Zebra in China.	Genome Announcements	2016	4		e00643-16			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. 		
@D	Zhou, W.//Niu, D.//Zhang, Z.//Liu, Y.//Ning, M.//Cao, X.//Zhang, C.//Shen, H. 	Complete Genome Sequence of Aerococcus urinaeequi Strain AV208.	Genome Announcements	2016	4		e01218-16			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. 		
@D	Zhou, X.//Deng, Z.//Firmin, J.L.//Hopwood, D.A.//Kieser, T. 	Site-specific degradation of Streptomyces lividans DNA during electrophoresis in  buffers contaminated with ferrous iron.	Nucleic Acids Res.	1988	16		4341-4352			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. 		
@D	Zhou, X.//He, X.//Liang, J.//Li, A.//Xu, T.//Kieser, T.//Helmann, J.D.//Deng, Z. 	A novel DNA modification by sulphur.	Mol. Microbiol.	2005	57		1428-1438			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. 		
@D	Zhou, X.E.//Wang, Y.//Reuter, M.//Mackeldanz, P.//Kruger, D.H.//Meehan, E.J.//Chen, L.Q. 	A single mutation of restriction endonuclease EcoRII led to a new crystal form that diffracts to 2.1 angstrom resolution.	Acta Crystallogr. D Biol. Crystallogr.	2003	59		910-912			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. 		
@D	Zhou, X.W.//Li, J.//Wang, K.M.//Tan, W.H.//Yang, X.H.//Meng, X.X.//Yan, H.F. 	An assay for the activity of DNA methylase based on a hairpin fluorescence molecular probe and its application in drug selection.	Acta Chimi. Sin.	2006	64		2096-2100			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. 		
@D	Zhou, X.Y.E.//Wang, Y.J.//Reuter, M.//Mucke, M.//Kruger, D.H.//Meehan, E.J.//Chen, L.Q. 	Crystal structure of Type IIE restriction endonuclease EcoRII reveals an autoinhibition mechanism by a novel effector-binding fold.	J. Mol. Biol.	2004	335		307-319			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. 		
@D	Zhou, Y.//Li, R.//Gao, X.Y.//Lapidus, A.//Han, J.//Haynes, M.//Lobos, E.//Huntemann, M.//Pati, A.//Ivanova, N.N.//Rohde, M.//Mavromatis, K.//Tindall, B.J.//Markowitz, V.//Woyke, T.//Klenk, H.P.//Kyrpides, N.C.//Li, W.J. 	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.	Standards in Genomic Sciences	2014	9		1020-1030			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. 		
@D	Zhou, Z.//Li, H.//Zhang, M.//Wang, Z.//Zhou, R.//Hu, S.//Li, X.//Song, X.//Zhu, Z. 	Genome Sequence of Corynebacterium pseudotuberculosis Strain XH02 Isolated from a Boer Goat in Xuanhan, China.	Genome Announcements	2016	4		e01329-16			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. 		
@D	Zhou, Z.//Li, X.//Liu, B.//Beutin, L.//Xu, J.//Ren, Y.//Feng, L.//Lan, R.//Reeves, P.R.//Wang, L. 	Derivation of Escherichia coli O157:H7 from its O55:H7 precursor.	PLoS ONE	2010	5		E8700			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. 		
@D	Zhou, Z.//McCann, A.//Litrup, E.//Murphy, R.//Cormican, M.//Fanning, S.//Brown, D.//Guttman, D.S.//Brisse, S.//Achtman, M. 	Neutral Genomic Microevolution of a Recently Emerged Pathogen, Salmonella enterica Serovar Agona.	PLoS Genet.	2013	9		E1003471			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. 		
@D	Zhou, Z.//Peng, X.//Xiao, Y.//Wang, X.//Guo, Z.//Zhu, L.//Liu, M.//Jin, H.//Bi, D.//Li, Z.//Sun, M. 	Genome Sequence of the poultry pathogen Riemerella anatipestifer Strain RA-YM.	J. Bacteriol.	2010	193		1284-1285			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. 		
@D	Zhu, B.//Chen, M.//Lin, L.//Yang, L.//Li, Y.//An, Q. 	Genome sequence of Enterobacter sp. strain SP1, an endophytic nitrogen-fixing bacterium isolated from sugarcane.	J. Bacteriol.	2012	194		6963-6964			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. 		
@D	Zhu, B.//Liu, H.//Tian, W.X.//Fan, X.Y.//Li, B.//Zhou, X.P.//Jin, G.L.//Xie, G.L. 	Genome Sequence of Stenotrophomonas maltophilia RR-10, Isolated as an Endophyte from Rice Root.	J. Bacteriol.	2012	194		1280-1281			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. 		
@D	Zhu, B.//Ye, S.//Chang, S.//Chen, M.//Sun, L.//An, Q. 	Genome Sequence of the Pathogenic Herbaspirillum seropedicae Strain Os45, Isolated from Rice Roots.	J. Bacteriol.	2012	194		6995-6996			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. 		
@D	Zhu, D.//Li, P.//Tanabe, S.H.//Sun, J. 	Genome Sequence of the Alkaliphilic Bacterial Strain Bacillus ligninesis L1, a Novel Degrader of Lignin.	Genome Announcements	2013	1		e0004213			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. 		
@D	Zhu, H.//Ni, Y.//Zhou, J.//Yu, Z.//Mao, A.//Wang, D.//He, K. 	Complete Genome Sequence of Streptococcus suis Serotype 2 Virulent Strain SS2-1.	Genome Announcements	2018	6		e00067-18			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. 		
@D	Zhu, H.//Wang, Q.//Wen, L.//Xu, J.//Shao, Z.//Chen, M.//Chen, M.//Reeves, P.R.//Cao, B.//Wang, L. 	Development of a Multiplex PCR Assay for Detection and Genogrouping of Neisseria meningitidis.	J. Clin. Microbiol.	2012	50		46-51			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. 		
@D	Zhu, J. 	Susceptibility of AatII and ApaI 3' protruding ends to exonuclease III degradation.	Biotechniques	1991	11		757-759			None 		
@D	Zhu, L.//Li, M.//Guo, S.//Wang, W. 	Draft Genome Sequence of a Thermophilic Desulfurization Bacterium, Geobacillus thermoglucosidasius Strain W-2.	Genome Announcements	2016	4		e00793-16			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. 		
@D	Zhu, L.//Yan, Z.//Zhang, Z.//Zhou, Q.//Zhou, J.//Wakeland, E.K.//Fang, X.//Xuan, Z.//Shen, D.//Li, Q.Z. 	Complete Genome Analysis of Three Acinetobacter baumannii Clinical Isolates in China for Insight into the Diversification of Drug Resistance Elements.	PLoS ONE	2013	8		E66584			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. 		
@D	Zhu, L.//Zhong, J.//Jia, X.//Liu, G.//Kang, Y.//Dong, M.//Zhang, X.//Li, Q.//Yue, L.//Li, C.//Fu, J.//Xiao, J.//Yan, J.//Zhang, B.//Lei, M.//Chen, S.//Lv, L.//Zhu, B.//Huang, H.//Chen, F. 	Precision methylome characterization of Mycobacterium tuberculosis complex (MTBC) using PacBio single-molecule real-time (SMRT) technology.	Nucleic Acids Res.	2016	44		730-743			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. 		
@D	Zhu, M.//McCully, L.M.//Silby, M.W.//Charles-Ogan, T.I.//Huang, J.//Brigham, C.J. 	Draft Genome Sequence of Ralstonia sp. MD27, a Poly(3-Hydroxybutyrate)-Degrading  Bacterium, Isolated from Compost.	Genome Announcements	2015	3		e01170-15			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. 		
@D	Zhu, P.//Morelli, G.//Achtman, M. 	The opcA and (psi)opcB regions in Neisseria: genes, pseudogenes, deletions, insertion elements and DNA islands.	Mol. Microbiol.	1999	33		635-650			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. 		
@D	Zhu, S.//Wang, H.L.//Wang, C.//Tang, L.//Wang, X.//Yu, K.J.//Liu, S.L. 	Non-contiguous finished genome sequence and description of Salmonella enterica subsp. houtenae str. RKS3027.	Standards in Genomic Sciences	2013	8		198-205			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. 		
@D	Zhu, S.//Wang, X.//Zhang, D.//Jing, X.//Zhang, N.//Yang, J.//Chen, J. 	Complete Genome Sequence of Hemolysin-Containing Carnobacterium sp. Strain CP1 Isolated from the Antarctic.	Genome Announcements	2016	4		e00690-16			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. 		
@D	Zhu, T.//Hou, S.//Lu, X.//Hess, W.R. 	Draft Genome Sequences of Nine Cyanobacterial Strains from Diverse Habitats.	Genome Announcements	2017	5		e01676-16			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. 		
@D	Zhu, W.//Huang, J.//Li, M.//Li, X.//Wang, G. 	Genomic analysis of Skermanella stibiiresistens type strain SB22 (T.).	Standards in Genomic Sciences	2014	9		1211-1220			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. 		
@D	Zhu, W.//Wang, J.//Zhu, Y.//Tang, B.//Zhang, Y.//He, P.//Zhang, Y.//Liu, B.//Guo, X.//Zhao, G.//Qin, J. 	Identification of three extra-chromosomal replicons in Leptospira pathogenic strain and development of new shuttle vectors.	BMC Genomics	2015	16		90			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. 		
@D	Zhu, X.//Wang, W.//Xu, P.//Tang, H. 	Complete Genome Sequence of Sphingomonas sp. Strain NIC1, an Efficient Nicotine-Degrading Bacterium.	Genome Announcements	2016	4		e00666-16			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. 		
@D	Zhu, Y.//Chen, P.//Bao, Y.//Men, Y.//Zeng, Y.//Yang, J.//Sun, J.//Sun, Y. 	Complete genome sequence and transcriptomic analysis of a novel marine strain Bacillus weihaiensis reveals the mechanism of brown algae degradation.	Sci. Rep.	2016	6		38248			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. 		
@D	Zhu, Y.//Fang, D.//Shi, D.//Li, A.//Lv, L.//Yan, R.//Yao, J.//Hua, D.//Hu, X.//Guo, F.//Wu, W.//Guo, J.//Chen, Y.//Jiang, X.//Chen, X.//Li, L. 	Draft Genome Sequence of Lactobacillus panis DSM 6035T, First Isolated from Sourdough.	Genome Announcements	2015	3		e00778-15			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. 		
@D	Zhu, Y.//He, Y.//Zheng, Z.//Chen, J.//Wang, Z.//Zhou, G. 	Draft Genome Sequence of Rice Orange Leaf Phytoplasma from Guangdong, China.	Genome Announcements	2017	5		e00430-17			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. 		
@D	Zhu, Y.//Shang, H.//Zhu, Q.//Ji, F.//Wang, P.//Fu, J.//Deng, Y.//Xu, C.//Ye, W.//Zheng, J.//Zhu, L.//Sun, M. 	Complete Genome Sequence of Bacillus thuringiensis serovar. finitimus Strain YBT-020.	J. Bacteriol.	2011	193		2379-2380			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. 		
@D	Zhu, Y.//Zeng, H.//Gao, X.//Lu, Z.H. 	Quantitative analysis of EcoR1 methylase-DNA complex by atomic force microscopy.	Scanning	2006	28		15-19			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. 		
@D	Zhu, Z.//Guan, S.//Robinson, D.//El Fezzazi, H.//Quimby, A.//Xu, S.Y. 	Characterization of cleavage intermediate and star sites of RM.Tth111II.	Sci. Rep.	2014	4		3838			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. 		
@D	Zhu, Z.//Pedamallu, C.S.//Fomenkov, A.//Benner, J.//Xu, S.Y. 	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.	BMC Res. Notes	2010	3		139			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. 		
@D	Zhu, Z.//Samuelson, J.C.//Zhou, J.//Dore, A.//Xu, S.-y. 	Engineering strand-specific DNA nicking enzymes from the type IIS restriction endonucleases BsaI, BsmBI, and BsmAI.	J. Mol. Biol.	2004	337		573-583			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. 		
@D	Zhu, Z.Y.//Zhou, J.//Friedman, A.M.//Xu, S.Y. 	Isolation of BsoBI restriction endonuclease variants with altered substrate specificity.	J. Mol. Biol.	2003	330		359-372			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. 		
@D	Zhu-Ge, X.//Jiang, J.//Pan, Z.//Hu, L.//Wang, S.//Wang, H.//Leung, F.C.//Dai, J.//Fan, H. 	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.	PLoS ONE	2014	9		E112048			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. 		
@D	Zhuang, W.//Zhang, S.//Xia, X.//Wang, G. 	Draft genome sequence of T26 and comparative analysis of six genomes.	Standards in Genomic Sciences	2015	10		104			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. 		
@D	Zhuo, W.//Lai, X.//Zhang, L.//Chan, S.-H.//Li, F.//Zhu, Z.//Yang, M.//Sun, D. 	Elimination of inter-domain interactions increases the cleavage fidelity of the restriction endonuclease DraIII.	Protein Cell	2014	5		357-368			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. 		
@D	Zhuo, Y.//Liu, L.//Wang, Q.//Liu, X.//Ren, B.//Liu, M.//Ni, P.//Cheng, Y.Q.//Zhang, L. 	Revised Genome Sequence of Burkholderia thailandensis MSMB43 with Improved Annotation.	J. Bacteriol.	2012	194		4749-4750			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. 		
@D	Zhuravleva, L.I.//Oreshkin, E.N. 	The effect of cultivation conditions and ultrasonic destruction of Streptomyces achromogenes ATCC 12767 cells on the yield of restriction endonucleases.	Prikl. Biokhim. Mikrobiol.	1985	21		401-406			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. 		
@D	Zhuravleva, L.I.//Oreshkin, E.N.//Bezborodov, A.M. 	Isolation and purification of restriction endonuclease SacI from Streptomyces achromogenes ATCC 12767.	Prikl. Biokhim. Mikrobiol.	1987	23		208-215			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. 		
@D	Zhurina, D.//Dudnik, A.//Waidmann, M.S.//Grimm, V.//Westermann, C.//Breitinger, K.J.//Yuan, J.//van Sinderen, D.//Riedel, C.U. 	High-Quality Draft Genome Sequence of Bifidobacterium longum E18, Isolated from a Healthy Adult.	Genome Announcements	2013	1		e01084-13			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. 		
@D	Zhurina, D.//Zomer, A.//Gleinser, M.//Brancaccio, V.F.//Auchter, M.//Waidmann, M.S.//Westermann, C.//van Sinderen, D.//Riedel, C.U. 	Complete genome sequence of Bifidobacterium bifidum S17.	J. Bacteriol.	2010	193		301-302			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. 		
@D	Zieger, M.//Patillon, M.//Roizes, G.//Lerouge, T.//Dupret, D.//Jeltsch, J.M. 	Two restriction endonucleases from Bacillus sphaericus:  BspXI and BspXII.	Nucleic Acids Res.	1987	15		3919			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. 		
@D	Ziegler, M.//Jang, H.//Gopinath, G.//Horlbog, J.A.//Stephan, R.//Guldimann, C. 	Whole-Genome Shotgun Sequencing of Three Listeria monocytogenes Strains Isolated  from a Ready-to-Eat Salad-Producing Facility in Switzerland.	Genome Announcements	2018	6		e00547-18			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. 		
@D	Zienkiewicz, M.//Kern-Zdanowicz, I.//Golebiewski, M.//Zylinska, J.//Mieczkowski, P.//Gniadkowski, M.//Bardowski, J.//Ceglowski, P. 	Mosaic Structure of p1658/97, a 125-Kilobase Plasmid Harboring an Active Amplicon with the Extended-Spectrum -Lactamase Gene blaSHV-5.	Antimicrob. Agents Chemother.	2007	51		1164-1171			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. 		
@D	Zilli, J.E.//Passos, S.R.//Leite, J.//Xavier, G.R.//Rumjaneck, N.G.//Simoes-Araujo, J.L. 	Draft Genome Sequence of Microvirga vignae Strain BR 3299T, a Novel Symbiotic Nitrogen-Fixing Alphaproteobacterium Isolated from a Brazilian Semiarid Region.	Genome Announcements	2015	3		e00700-15			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. 		
@D	Zimmerly, S.//Guo, H.//Eskes, R.//Yang, J.//Perlman, P.S.//Lambowitz, A.M. 	A group II intron RNA is a catalytic component of a DNA endonuclease involved in intron mobility.	Cell	1995	83		529-538			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. 		
@D	Zimmerly, S.//Guo, H.//Perlman, P.S.//Lambowitz, A.M. 	Group II intron mobility occurs by target DNA-primed reverse transcription.	Cell	1995	82		545-554			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. 		
@D	Zimmerly, S.//Moran, J.V.//Perlman, P.S.//Lambowitz, A.M. 	Group II intron reverse transcriptase in yeast mitochondria.  Stabilization and regulation of reverse transcriptase activity by the intron RNA.	J. Mol. Biol.	1999	289		473-490			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. 		
@D	Zimmerman, W.J.//Culley, D.E. 	Genetic variation at the apcAB, cpcAB, gvpA1, and nifH loci and in DNA methylation among N2-fixing cyanobacteria designated Nostoc punctiforme.	Microb. Ecol.	1991	21		199-209			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. 		
@D	Zimmermann, C.//Guhl, E.//Graessmann, A. 	Mouse DNA methyltransferase (MTase) deletion mutants that retain the catalytic domain display neither de novo nor maintenance methylation activity in vivo.	Biol. Chem.	1997	378		393-405			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. 		
@D	Zimmermann, K.//Schogl, D.//Mannhalter, J.W. 	Digestion of terminal restriction endonuclease recognition sites on PCR products.	Biotechniques	1998	24		582-584			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. 		
@D	Zingg, J.-M.//Jones, P.A. 	Genetic and epigenetic aspects of DNA methylation on genome expression, evolution, mutation and carcinogenesis.	Carcinogenesis	1997	18		869-882			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. 		
@D	Zingg, J.-M.//Shen, J.-C.//Jones, P.A. 	Enzyme-mediated cytosine deamination by the bacterial methyltransferase M.MspI.	Biochem. J.	1998	332		223-230			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. 		
@D	Zingg, J.-M.//Shen, J.-C.//Yang, A.S.//Rapoport, H.//Jones, P.A. 	Methylation inhibitors can increase the rate of cytosine deamination by (cytosine- 5)-DNA methyltransferase.	Nucleic Acids Res.	1996	24		3267-3275			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. 		
@D	Zinkevich, V.//Heslop, P.//Glover, S.W.//Weiserova, M.//Hubacek, J.//Firman, K. 	Mutation in the specificity polypeptide of the Type I restriction endonuclease R EcoK that affects subunit assembly.	J. Mol. Biol.	1992	227		597-601			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. 		
@D	Zinkevich, V.//Popova, L.//Kryukov, V.//Abadjieva, A.//Bogdarina, I.//Janscak, P.//Firman, K. 	The HsdR subunit of R.EcoR124II: cloning and over-expression of the gene and unexpected properties of the subunit.	Nucleic Acids Res.	1997	25		503-510			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. 		
@D	Zinkevich, V.E.//Alekseev, A.M.//Tanyashin, V.I. 	Influence of bacteriophage lambda ral gene on the level of synthesis of the restriction endonuclease EcoK beta-subunit.	Mol. Biol. (Mosk)	1986	20		1638-1644			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. 		
@D	Zinkevich, V.E.//Solonin, A.S.//Bogdarina, I.G.//Tanyashin, V.I. 	Cloning and restriction analysis of the BamHI-EcoRI fragment of DNA, containing genes of the hsd region of Escherichia coli.	Dokl. Akad. Nauk.	1981	259		216-218					
@D	Zinkevich, V.E.//Solonin, A.S.//Tanyashin, V.I.//Bayev, A.A. 	Function of hsdS gene of E. coli K in recombinant plasmid containing the regulatory lambda phage region.	Dokl. Akad. Nauk.	1982	263		717-721			None 		
@D	Zinkevich, V.E.//Weiserova, M.//Kryukov, V.M.//Hubacek, J. 	A mutation that converts serine 340 of the HsdSK polypeptide to phenylalanine and its effects on restriction and modification in Escherichia coli K-12.	Gene	1990	90		125-128			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. 		
@D	Zinkevich, V.E.//Zograf, Y.N.//Tanyashin, V.I. 	Expression of the EcoK DNA-methylase genes cloned.	Dokl. Akad. Nauk.	1985	282		993-995			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. 		
@D	Zinkevich, V.E.//Zograf, Y.N.//Tanyashin, V.I. 	The genes of EcoK DNA methylase:  cloning and expression.	Dokl. Akad. Nauk.	1984	279		1493-1496			None 		
@D	Zinn, A.R.//Butow, R.A. 	Nonreciprocal exchange between alleles of the yeast mitochondrial 21S rRNA gene:  kinetics and the involvement of a double-strand break.	Cell	1985	40		887-895			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. 		
@D	Zinovev, V.V.//Kolesnikov, V.A.//Beznedelnaya, N.L.//Gilev, A.F.//Gorbunov, Y.A.//Popov, S.G.//Malygin, E.G. 	Interaction of restrictase BamHI with synthetic substrates containing complete or partial recognition sites.	Mol. Biol. (Mosk)	1984	18		169-175			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. 		
@D	Zinovev, V.V.//Kolesnikov, V.A.//Beznedelnaya, N.L.//Gorbunov, J.A.//Popov, S.G.//Malygin, E.G. 	Restriction endonuclease BamHI interaction with a synthetic duplex containing half-size recognition sequences.	FEBS Lett.	1981	132		98-100			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. 		
@D	Zinovev, V.V.//Ovechkina, L.G.//Malygin, E.G. 	Stoichiometry of phage T4 Dam DNA (Adenine-N6)-methyltransferase binding with oligonucleotide substrates.	Mol. Biol. (Mosk)	1996	30		1203-1208			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. 		
@D	Zinovev, V.V.//Rechkunova, N.I.//Gorbunov, Y.A.//Buryanov, Y.I.//Malygin, E.G. 	The significance of internucleotide phosphates and noncomplementary substitutions in the oligonucleotide substrates on the interaction with the DNA methylase Ecodam.	Biopol. Kletka	1989	5		22-27			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. 		
@D	Zinoviev, V.V.//Evdokimov, A.A.//Gorbunov, Y.A.//Malygin, E.G.//Kossykh, V.G.//Hattman, S. 	Phage T4 DNA [N6-adenine] methyltransferase: Kinetic studies using oligonucleotides containing native or modified recognition sites.	Biol. Chem.	1998	379		481-488			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. 		
@D	Zinoviev, V.V.//Evdokimov, A.A.//Hattman, S.//Malygin, E.G. 	Molecular enzymology of phage T4 Dam DNA methyltransferase.	Mol. Biol. (Mosk)	2004	38		737-751			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. 		
@D	Zinoviev, V.V.//Evdokimov, A.A.//Malygin, E.G. 	DNA-[N4-Cytosine]-Methyltransferase from Bacillus amyloliquefaciens: Mechanism of Action Derived from Steady-State Kinetics.	Mol. Biol. (Mosk)	2003	37		128-138			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. 		
@D	Zinoviev, V.V.//Evdokimov, A.A.//Malygin, E.G.//Schlagman, S.L.//Hattman, S. 	Bacteriophage T4 dam DNA-[N6-adenine] methyltransferase: Processivity and orientation to the methylation target.	J. Biol. Chem.	2002	278		7829-7833			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. 		
@D	Zinoviev, V.V.//Evdokimov, A.A.//Malygin, E.G.//Sclavi, B.//Buckle, M.//Hattman, S. 	Differential methylation kinetics of individual target site strands by T4Dam DNA methyltransferase.	Biol. Chem.	2007	388		1199-1207			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. 		
@D	Zinoviev, V.V.//Gorbunov, J.A.//Baclanov, M.M.//Popov, S.G.//Malygin, E.G. 	Structure subtraction as an approach to investigation of the mechanism of restriction enzyme action.	FEBS Lett.	1983	154		282-284			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. 		
@D	Zinoviev, V.V.//Gorbunov, Y.A.//Popov, S.G.//Malygin, E.G.//Buryanov, J.I.//Nesterenko, V.F.//Baev, A.A.//Venoginskis, M.T. 	Interaction of EcoDam methylase with single stranded sequences and synthetic oligonucleotides.	Mol. Biol. (Mosk)	1985	19		947-954			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. 		
@D	Zinoviev, V.V.//Yakishchik, S.I.//Evdokimov, A.A.//Malygin, E.G.//Hattman, S. 	Symmetry elements in DNA structure important for recognition/methylation by DNA [amino]-methyltransferases.	Nucleic Acids Res.	2004	32		3930-3934			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. 		
@D	Zischka, M.//Kuenne, C.//Blom, J.//Dabrowski, P.W.//Linke, B.//Hain, T.//Nitsche, A.//Goesmann, A.//Larsen, J.//Jensen, L.B.//Witte, W.//Werner, G. 	Complete Genome Sequence of the Porcine Isolate Enterococcus faecalis D32.	J. Bacteriol.	2012	194		5490-5491			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. 		
@D	Zivanovic, Y.//Armengaud, J.//Lagorce, A.//Leplat, C.//Guerin, P.//Dutertre, M.//Anthouard, V.//Forterre, P.//Wincker, P.//Confalonieri, F. 	Genome analysis and genome-wide proteomics of Thermococcus gammatolerans, the most radioresistant organism known amongst the Archaea.	Genome Biol.	2009	10		R70			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. 		
@D	Zobanikova, M.//Mikolka, P.//Cejkova, D.//Pospisilova, P.//Chen, L.//Strouhal, M.//Qin, X.//Weinstock, G.M.//Smajs, D. 	Complete genome sequence of Treponema pallidum strain DAL-1.	Standards in Genomic Sciences	2012	7		12-21			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. 		
@D	Zobanikova, M.//Strouhal, M.//Mikalova, L.//Cejkova, D.//Ambrozova, L.//Pospisilova, P.//Fulton, L.L.//Chen, L.//Sodergren, E.//Weinstock, G.M.//Smajs, D. 	Whole genome sequence of the Treponema pallidum Fribourg-Blanc: Unspecified simian isolate is highly similar to the yaws subspecies.	PLoS Neglected Trop. Dis.	2013	7		E2172			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. 		
@D	Zomer, A.//de Vries, S.P.//Riesbeck, K.//Meinke, A.L.//Hermans, P.W.//Bootsma, H.J. 	Genome Sequence of Moraxella catarrhalis RH4, an Isolate of Seroresistant Lineage.	J. Bacteriol.	2012	194		6969			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. 		
@D	Zong, G.//Zhong, C.//Fu, J.//Qin, R.//Cao, G. 	Draft Genome Sequence of the Tacrolimus-Producing Bacterium Streptomyces tsukubaensis F601.	Genome Announcements	2017	5		e00385-17			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. 		
@D	Zong, G.//Zhong, C.//Fu, J.//Zhao, Z.//Cao, G. 	Complete Genome Sequence of the High-Natamycin-Producing Strain Streptomyces gilvosporeus F607.	Genome Announcements	2018	6		e01402-17			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. 		
@D	Zong, Z.//Lu, X. 	Characterization of a New SCCmec Element in Staphylococcus cohnii.	PLoS ONE	2010	5		E14016			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. 		
@D	Zoropogui, A. et al. 	Genome Sequence of the Human- and Animal-Pathogenic Strain Nocardia cyriacigeorgica GUH-2.	J. Bacteriol.	2012	194		2098-2099			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. 		
@D	Zorzetti, J.//Ricietto, A.P.//da Silva, C.R.//Wolf, I.R.//Vilas-Boas, G.T.//Neves, P.M.//Meneguim, A.M.//Vilas-Boas, L.A. 	Genome Sequence of the Mosquitocidal Bacillus thuringiensis Strain BR58, a Biopesticide Product Effective against the Coffee Berry Borer (Hypothenemus  hampei).	Genome Announcements	2015	3		e01232-15			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. 		
@D	Zotchev, S.B.//Schrempf, H.//Hutchinson, C.R. 	Identification of a methyl-specific restriction system mediated by a conjugative element from Streptomyces bambergiensis.	J. Bacteriol.	1995	177		4809-4812			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. 		
@D	Zotta, T.//Ricciardi, A.//Parente, E.//Reale, A.//Ianniello, R.G.//Bassi, D. 	Draft Genome Sequence of the Respiration-Competent Strain Lactobacillus casei N87.	Genome Announcements	2016	4		e00348-16			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. 		
@D	Zou, C.//Wang, K.//Meng, J.//Yuan, G.//Lin, W.//Peng, H.//Li, Q. 	Draft Genome Sequence of Ralstonia solanacearum Strain Rs-T02, Which Represents the Most Prevalent Phylotype in Guangxi, China.	Genome Announcements	2016	4		e00241-16			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. 		
@D	Zou, G. 	Methods for preparation and determination of the purity and activity of restriction endonucleases.	Weishengwuxue Zazhi	1987	7		63-66			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. 		
@D	Zou, G.//Cao, X.//Zhu, R. 	One step purification of restriction endonuclease PstI by sepharose affinity column separation.	Shengwu Huaxue Yu Shengwu Wuli Jinzhan	1985	62		64-66			None 		
@D	Zou, G.//Gao, C.//Pi, X. 	Kinetic studies on the irreversible inhibition of restriction endonuclease PstI by site-specific inhibitors.	Wuhan Univ. J. Natural Sciences	2001	6		859-863			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. 		
@D	Zou, G.-L.//Cao, X.-W.//Zhu, R.-F. 	The purification and some properties of restriction endonuclease PstI.	Acta Biochim. Biophys. Sin.	1985	17		268-274			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. 		
@D	Zou, G.-L.//Gao, C.-Z.//Pi, X.-C.//Hu, W.J. 	Studies on the star activity of restriction endonuclease PstI.	Wuhan Daxue Xuebao	1999	45		873-875			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. 		
@D	Zou, G.-l.//Gao, C.-Z.//Pi, X.-C.//Zhang, J.-J. 	Alteration of the specificity of PstI restriction endonuclease.	Wuhan Univ. J. Nat. Sci.	2000	5		361-365			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/. 		
@D	Zou, S.//Zhang, M.//Hong, J.//Ma, Y.//Zhang, W. 	Comparison of the electro transformation of plasmids and plasmid stability between Zymomonas mobilis ZM4 and CP4.	Afr. J. Microbiol. Res.	2011	5		2026-2033			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. 		
@D	Zschuttig, A.//Auerbach, C.//Meltke, S.//Eichhorn, C.//Brandt, M.//Blom, J.//Goesmann, A.//Jarek, M.//Scharfe, M.//Zimmermann, K.//Wassenaar, T.M.//Gunzer, F. 	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.	Genome Announcements	2015	3		e01330-14			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). 		
@D	Zubair, S.//de Villiers, E.P.//Fuxelius, H.H.//Andersson, G.//Johansson, K.E.//Bishop, R.P.//Bongcam-Rudloff, E. 	Genome Sequence of Streptococcus agalactiae Strain 09mas018883, Isolated from a Swedish Cow.	Genome Announcements	2013	1		e00456-13			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. 		
@D	Zubair, S.//de Villiers, E.P.//Younan, M.//Andersson, G.//Tettelin, H.//Riley, D.R.//Jores, J.//Bongcam-Rudloff, E.//Bishop, R.P. 	Genome Sequences of Two Pathogenic Streptococcus agalactiae Isolates from the One-Humped Camel Camelus dromedarius.	Genome Announcements	2013	1		e00515-13			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. 		
@D	Zubair, S.//Fischer, A.//Liljander, A.//Meens, J.//Hegerman, J.//Gourle, H.//Bishop, R.P.//Roebbelen, I.//Younan, M.//Mustafa, M.I.//Mushtaq, M.//Bongcam-Rudloff, E.//Jores, J. 	Complete genome sequence of Staphylococcus aureus, strain ILRI_Eymole1/1, isolated from a Kenyan dromedary camel.	Standards in Genomic Sciences	2015	10		109			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. 		
@D	Zueva, V.S.//Dmitrenko, O.A.//Gladkova, K.K.//Zueva, E.A. 	New collection of phages for typing methicillin-resistant Staphylococcus aureus.	Zh. Mikrobiol. Epidemiol. Immunobiol.	1994	2		20-23			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. 		
@D	Zueva, V.S.//Dmitrienko, O.A.//Krupina, E.A.//Belikov, N.G.//Nesterenko, L.N. 	To the mechanism of the resistance of methicillin-resistant staphylococcus aureus to phages of the international collection.	Zh. Mikrobiol. Epidemiol. Immunobiol.	1990	10		11-15			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. 		
@D	Zuljan, F.//Espariz, M.//Blancato, V.S.//Esteban, L.//Alarcon, S.//Magni, C. 	Draft Genome Sequence of Lactococcus lactis subsp. lactis bv. diacetylactis CRL264, a Citrate-Fermenting Strain.	Genome Announcements	2016	4		e01575-15			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. 		
@D	Zulkifli, M.H.//Teh, L.K.//Lee, L.S.//Zakaria, Z.A.//Salleh, M.Z. 	Draft Genome Sequence of Klebsiella pneumoniae Isolate PR04.	Genome Announcements	2013	1		e00418-13			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. 		
@D	Zuniga-Bahamon, A.//Tobar-Tosse, F.//Guillermo-Ortega, J.//Wibberg, D.//Tauch, A. 	Draft Genome Sequence of Streptococcus anginosus BVI, a New Vaginal Pathogen Candidate.	Genome Announcements	2016	4		e01417-16			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. 		
@D	Zuo, F.//Feng, X.//Sun, X.//Du, C.//Chen, S. 	Characterization of Plasmid pML21 of Enterococcus faecalis ML21 from Koumiss.	Curr. Microbiol.	2013	66		103-105					
@D	Zurawski, D.V.//Thompson, M.G.//McQueary, C.N.//Matalka, M.N.//Sahl, J.W.//Craft, D.W.//Rasko, D.A. 	Genome Sequences of Four Divergent Multidrug-Resistant Acinetobacter baumannii Strains Isolated from Patients with Sepsis or Osteomyelitis.	J. Bacteriol.	2012	194		1619-1620			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. 		
@D	Zurfluh, K.//Stephan, R.//Klumpp, J.//Nuesch-Inderbinen, M.//Hummerjohann, J.//Bagutti, C.//Marti, R. 	Complete Genome Sequence of Citrobacter freundii 705SK3, an OXA-48-Encoding Wastewater Isolate.	Genome Announcements	2017	5		e00842-17			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. 		
@D	Zurfluh, K.//Stephan, R.//Klumpp, J.//Nuesch-Inderbinen, M.//Hummerjohann, J.//Bagutti, C.//Marti, R. 	Complete Genome Sequence of Escherichia coli ABWA45, an rmtB-Encoding Wastewater  Isolate.	Genome Announcements	2017	5		e00844-17			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. 		
@D	Zurfluh, K.//Tasara, T.//Poirel, L.//Nordmann, P.//Stephan, R. 	Draft Genome Sequence of Escherichia coli S51, a Chicken Isolate Harboring a Chromosomally Encoded mcr-1 Gene.	Genome Announcements	2016	4		e00796-16			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. 		
@D	Zurfluh, K.//Tasara, T.//Stephan, R. 	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.	Genome Announcements	2016	4		e00927-16			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). 		
@D	Zweiger, G.//Marczynski, G.//Shapiro, L. 	A Caulobacter DNA methyltransferase that functions only in the predivisional cell.	J. Mol. Biol.	1994	235		472-474			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. 		
@D	Zwick, M.E.//Joseph, S.J.//Didelot, X.//Chen, P.E.//Bishop-Lilly, K.A.//Stewart, A.C.//Willner, K.//Nolan, N.//Lentz, S.//Thomason, M.K.//Sozhamannan, S.//Mateczun, A.J.//Du, L.//Read, T.D. 	Genomic characterization of the Bacillus cereus sensu lato species: Backdrop to the evolution of Bacillus anthracis.	Genome Res.	2012	22		1512-1524			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. 		
@D	Zylicz-Stachula, A.//Bujnicki, J.M.//Skowron, P.M. 	Cloning and analysis of a bifunctional methyltransferase/restriction endonuclease TspGWI, the prototype of a Thermus sp. enzyme family.	BMC Mol. Biol.	2009	10		52			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. 		
@D	Zylicz-Stachula, A.//Harasimowicz-Slowinska, R.I.//Sobolewski, I.//Skowron, P.M. 	TspGWI, a thermophilic class-IIS restriction endonuclease from Thermus sp., recognizes novel asymmetric sequence 5'-ACGGA(N11/9)-3'.	Nucleic Acids Res.	2002	30		e33			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. 		
@D	Zylicz-Stachula, A.//Jezewska-Frackowiak, J.//Skowron, P.M. 	Cofactor analogue-induced chemical reactivation of endonuclease activity in a DNA cleavage/methylation deficient TspGWI N(473)A variant in the NPPY motif.	Mol. Biol. Rep.	2014	41		2313-2323			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. 		
@D	Zylicz-Stachula, A.//Zebrowska, J.//Czajkowska, E.//Wrese, W.//Sulecka, E.//Skowron, P.M. 	Engineering TaqII bifunctional endonuclease DNA recognition fidelity: the effect  of a single amino acid substitution within the methyltransferase catalytic site.	Mol. Biol. Rep.	2016	43		269-282			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. 		
@D	Zylicz-Stachula, A.//Zolnierkiewicz, O.//Jasiecki, J.//Skowron, P.M. 	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.	BMC Genomics	2013	14		370			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. 		
@D	Zylicz-Stachula, A.//Zolnierkiewicz, O.//Jezewska-Frackowiak, J.//Skowron, P.M. 	Chemically-induced affinity star restriction specificity: a novel TspGWI/sinefungin endonuclease with theoretical 3-bp cleavage frequency.	Biotechniques	2011	50		397-406			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. 		
@D	Zylicz-Stachula, A.//Zolnierkiewicz, O.//Lubys, A.//Ramanauskaite, D.//Mitkaite, G.//Bujnicki, J.M.//Skowron, P.M. 	Related bifunctional restriction endonuclease-methyltransferase triplets: TspDTI, Tth111II/TthHB27I and TsoI with distinct specificities.	BMC Mol. Biol.	2012	13		13			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. 		
@D	Zylicz-Stachula, A.//Zolnierkiewicz, O.//Sliwinska, K.//Jezewska-Frackowiak, J.//Skowron, P.M. 	Bifunctional TaqII restriction endonuclease: redefining the prototype DNA recognition site and establishing the Fidelity Index for partial cleaving.	BMC Biochem.	2011	12		62			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. 		
@D	Zylicz-Stachula, A.//Zolnierkiewicz, O.//Sliwinska, K.//Jezewska-Frackowiak, J.//Skowron, P.M. 	Modified 'one amino acid-one codon' engineering of high GC content TaqII-coding gene from thermophilic Thermus aquaticus results in radical expression increase.	Microb. Cell Fact.	2014	13		7			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. 		
