 
REBASE version 901                                              procite.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
 

New References:

@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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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. 		
@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	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	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	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	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	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	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	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	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	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	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	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. 		
