Author Report for: DeBoy RTNo contact information in database for DeBoy RT
Ward NL, Challacombe JF, Janssen PH, Henrissat B, Coutinho PM, Wu M, Xie G, Haft DH, Sait M and Kuske CR <36 more author(s)> Ward NL, Challacombe JF, Janssen PH, Henrissat B, Coutinho PM, Wu M, Xie G, Haft DH, Sait M, Badger J, Barabote RD, Bradley B, Brettin TS, Brinkac LM, Bruce D, Creasy T, Daugherty SC, Davidsen TM, DeBoy RT, Detter JC, Dodson RJ, Durkin AS, Ganapathy A, Gwinn-Giglio M, Han CS, Khouri H, Kiss H, Kothari SP, Madupu R, Nelson KE, Nelson WC, Paulsen I, Penn K, Ren Q, Rosovitz MJ, Selengut JD, Shrivastava S, Sullivan SA, Tapia R, Thompson LS, Watkins KL, Yang Q, Yu C, Zafar N, Zhou L, Kuske CR (- 36) Ref: Applied Environmental Microbiology, 75:2046, 2009 : PubMed ESTHER: Ward_2009_Appl.Environ.Microbiol_75_2046 PubMedSearch: Ward 2009 Appl.Environ.Microbiol 75 2046 PubMedID: 19201974 Gene_locus related to this paper: korve-q1ihr9, korve-q1ii02, korve-q1iit0, korve-q1ilk4, korve-q1imj9, korve-q1ims4, korve-q1iqj0, korve-q1isy7, korve-q1itj5, korve-q1itz6, korve-q1ivc8, acic5-c1f1u6, acic5-c1f2i7, acic5-c1f4m6, acic5-c1f4y4, acic5-c1f5a7, acic5-c1f5u2, acic5-c1f7a9, acic5-c1f7x6, acic5-c1f8y9, acic5-c1f9m2, acic5-c1f594, acic5-c1f609, acic5-c1f692, acic5-c1f970, acic5-c1fa52, korve-q1iiw2, korve-q1ivn9, solue-q01nb0, solue-q01qj6, solue-q01r37, solue-q01rq8, solue-q01rz0, solue-q01t44, solue-q01t57, solue-q01ts5, solue-q01tv4, solue-q01vd8, solue-q01vr3, solue-q01vw5, solue-q01w12, solue-q01wt9, solue-q01y40, solue-q01ym8, solue-q01z24, solue-q01z97, solue-q01zl4, solue-q01zm0, solue-q01zm5, solue-q01zm7, solue-q02aa4, solue-q02ab9, solue-q02b72, solue-q02bs8, solue-q02bt7, solue-q02cp0, solue-q02d61, solue-q020h3, solue-q020i8, solue-q021i6, solue-q022b1, solue-q022p8, solue-q022q2, solue-q022q3, solue-q022x2, solue-q022x5, solue-q022x6, solue-q022x8, solue-q023e7, solue-q024d9, solue-q025c1, solue-q026j1, solue-q026k6, solue-q026r6, solue-q027p2, solue-q027r8, solue-q01zt5, korve-q1itw6, solue-q01yh7, solue-q02ad6, korve-q1imj6, korve-q1iuf6, acic5-c1f891, solue-q026h7 Abstract 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. Title: Insights into plant cell wall degradation from the genome sequence of the soil bacterium Cellvibrio japonicus DeBoy RT, Mongodin EF, Fouts DE, Tailford LE, Khouri H, Emerson JB, Mohamoud Y, Watkins K, Henrissat B and Nelson KE <1 more author(s)> DeBoy RT, Mongodin EF, Fouts DE, Tailford LE, Khouri H, Emerson JB, Mohamoud Y, Watkins K, Henrissat B, Gilbert HJ, Nelson KE (- 1) Ref: Journal of Bacteriology, 190:5455, 2008 : PubMed ESTHER: DeBoy_2008_J.Bacteriol_190_5455 PubMedSearch: DeBoy 2008 J.Bacteriol 190 5455 PubMedID: 18556790 Gene_locus related to this paper: celju-b3pei5, celju-b3pf25, celju-b3pfb5, celju-b3pgh5, celju-b3pgz5, celju-b3ph03, celju-b3pi00, celju-b3pi89, celju-b3pj26, celju-b3pju5, celju-b3pks4, celju-b3pks5, celju-b3plp7, celju-metx, celju-b3phr4, celju-b3pjj6, celju-b3pcj5, celju-b3pcu6, celju-b3pei0 Abstract 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. Title: Complete genome sequence of the N2-fixing broad host range endophyte Klebsiella pneumoniae 342 and virulence predictions verified in mice Fouts DE, Tyler HL, DeBoy RT, Daugherty S, Ren Q, Badger JH, Durkin AS, Huot H, Shrivastava S and Methe BA <8 more author(s)> Fouts DE, Tyler HL, DeBoy RT, Daugherty S, Ren Q, Badger JH, Durkin AS, Huot H, Shrivastava S, Kothari S, Dodson RJ, Mohamoud Y, Khouri H, Roesch LF, Krogfelt KA, Struve C, Triplett EW, Methe BA (- 8) Ref: PLoS Genet, 4:e1000141, 2008 : PubMed ESTHER: Fouts_2008_PLoS.Genet_4_e1000141 PubMedSearch: Fouts 2008 PLoS.Genet 4 e1000141 PubMedID: 18654632 Gene_locus related to this paper: klep3-b5xp56, klep3-b5xqp6, klep3-b5xzn5, klep3-b5xzy8, klep3-bioh, klep3-menh, klep7-a6t8q2, klep7-a6t9v6, klep7-a6tb98, klep7-mhpc, klep7-y243, klep7-y1077, klepn-c4x8q1, klepn-w8uta0, klep3-rutd Abstract 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. Title: Genome sequence and identification of candidate vaccine antigens from the animal pathogen Dichelobacter nodosus Myers GS, Parker D, Al-Hasani K, Kennan RM, Seemann T, Ren Q, Badger JH, Selengut JD, DeBoy RT and Paulsen IT <15 more author(s)> Myers GS, Parker D, Al-Hasani K, Kennan RM, Seemann T, Ren Q, Badger JH, Selengut JD, DeBoy RT, Tettelin H, Boyce JD, McCarl VP, Han X, Nelson WC, Madupu R, Mohamoud Y, Holley T, Fedorova N, Khouri H, Bottomley SP, Whittington RJ, Adler B, Songer JG, Rood JI, Paulsen IT (- 15) Ref: Nat Biotechnol, 25:569, 2007 : PubMed ESTHER: Myers_2007_Nat.Biotechnol_25_569 PubMedSearch: Myers 2007 Nat.Biotechnol 25 569 PubMedID: 17468768 Gene_locus related to this paper: dicnv-a5evg0, dicnv-a5ewn0, dicnv-a5ewp3 Abstract Dichelobacter nodosus causes ovine footrot, a disease that leads to severe economic losses in the wool and meat industries. We sequenced its 1.4-Mb genome, the smallest known genome of an anaerobe. It differs markedly from small genomes of intracellular bacteria, retaining greater biosynthetic capabilities and lacking any evidence of extensive ongoing genome reduction. Comparative genomic microarray studies and bioinformatic analysis suggested that, despite its small size, almost 20% of the genome is derived from lateral gene transfer. Most of these regions seem to be associated with virulence. Metabolic reconstruction indicated unsuspected capabilities, including carbohydrate utilization, electron transfer and several aerobic pathways. Global transcriptional profiling and bioinformatic analysis enabled the prediction of virulence factors and cell surface proteins. Screening of these proteins against ovine antisera identified eight immunogenic proteins that are candidate antigens for a cross-protective vaccine. Title: Secrets of soil survival revealed by the genome sequence of Arthrobacter aurescens TC1 Mongodin EF, Shapir N, Daugherty SC, DeBoy RT, Emerson JB, Shvartzbeyn A, Radune D, Vamathevan J, Riggs F and Sadowsky MJ <4 more author(s)> Mongodin EF, Shapir N, Daugherty SC, DeBoy RT, Emerson JB, Shvartzbeyn A, Radune D, Vamathevan J, Riggs F, Grinberg V, Khouri H, Wackett LP, Nelson KE, Sadowsky MJ (- 4) Ref: PLoS Genet, 2:e214, 2006 : PubMed ESTHER: Mongodin_2006_PLoS.Genet_2_e214 PubMedSearch: Mongodin 2006 PLoS.Genet 2 e214 PubMedID: 17194220 Gene_locus related to this paper: artat-a1r1g1, artat-a1r2c8, artat-a1r3u0, artat-a1r3x5, artat-a1r4v1, artat-a1r5d9, artat-a1r6c9, artat-a1r6v0, artat-a1r6v1, artat-a1r6y1, artat-a1r7h1, artat-a1r7q0, artat-a1r7v1, artat-a1r9g3, artat-a1r9t7, artat-a1r9u8, artat-a1r171, artat-a1r172, artat-a1r173, artat-a1r612, artat-a1r682, artat-a1ra89, artat-a1ra98, artat-a1ram7, artat-a1rb20, artat-a1rbd0, artat-a1rbi2, artat-a1rbl7, artat-a1rbz2, artat-a1r0x8, artat-a1r1x6, artat-a1r6f6 Abstract 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. Title: Skewed genomic variability in strains of the toxigenic bacterial pathogen, Clostridium perfringens Myers GS, Rasko DA, Cheung JK, Ravel J, Seshadri R, DeBoy RT, Ren Q, Varga J, Awad MM and Paulsen IT <24 more author(s)> Myers GS, Rasko DA, Cheung JK, Ravel J, Seshadri R, DeBoy RT, Ren Q, Varga J, Awad MM, Brinkac LM, Daugherty SC, Haft DH, Dodson RJ, Madupu R, Nelson WC, Rosovitz MJ, Sullivan SA, Khouri H, Dimitrov GI, Watkins KL, Mulligan S, Benton J, Radune D, Fisher DJ, Atkins HS, Hiscox T, Jost BH, Billington SJ, Songer JG, McClane BA, Titball RW, Rood JI, Melville SB, Paulsen IT (- 24) Ref: Genome Res, 16:1031, 2006 : PubMed ESTHER: Myers_2006_Genome.Res_16_1031 PubMedSearch: Myers 2006 Genome.Res 16 1031 PubMedID: 16825665 Gene_locus related to this paper: clope-CPE0307, clope-CPE0432, clope-CPE1581, clope-CPE1596, clope-CPE1989, clope-CPE2231, clope-lipa, clope-LIPB, clope-PLDB Abstract 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. Title: Major structural differences and novel potential virulence mechanisms from the genomes of multiple campylobacter species Fouts DE, Mongodin EF, Mandrell RE, Miller WG, Rasko DA, Ravel J, Brinkac LM, DeBoy RT, Parker CT and Nelson KE <11 more author(s)> Fouts DE, Mongodin EF, Mandrell RE, Miller WG, Rasko DA, Ravel J, Brinkac LM, DeBoy RT, Parker CT, Daugherty SC, Dodson RJ, Durkin AS, Madupu R, Sullivan SA, Shetty JU, Ayodeji MA, Shvartsbeyn A, Schatz MC, Badger JH, Fraser CM, Nelson KE (- 11) Ref: PLoS Biol, 3:e15, 2005 : PubMed ESTHER: Fouts_2005_PLoS.Biol_3_e15 PubMedSearch: Fouts 2005 PLoS.Biol 3 e15 PubMedID: 15660156 Gene_locus related to this paper: camje-CJ0796C, camjr-q5ht69, camjr-q5ht95, camjr-q5huc7, camjr-q5hwg6, camju-a3yll6 Abstract 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. Title: 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 Gill SR, Fouts DE, Archer GL, Mongodin EF, DeBoy RT, Ravel J, Paulsen IT, Kolonay JF, Brinkac L and Fraser CM <19 more author(s)> Gill SR, Fouts DE, Archer GL, Mongodin EF, DeBoy RT, Ravel J, Paulsen IT, Kolonay JF, Brinkac L, Beanan M, Dodson RJ, Daugherty SC, Madupu R, Angiuoli SV, Durkin AS, Haft DH, Vamathevan J, Khouri H, Utterback T, Lee C, Dimitrov G, Jiang L, Qin H, Weidman J, Tran K, Kang K, Hance IR, Nelson KE, Fraser CM (- 19) Ref: Journal of Bacteriology, 187:2426, 2005 : PubMed ESTHER: Gill_2005_J.Bacteriol_187_2426 PubMedSearch: Gill 2005 J.Bacteriol 187 2426 PubMedID: 15774886 Gene_locus related to this paper: staau-LIP, staau-lipas, staau-MW0741, staau-MW2456, staau-q6gfm6, staau-SA0011, staau-SA0569, staau-SA0572, staau-SA0897, staau-SA1143, staau-SA2240, staau-SA2306, staau-SA2367, staau-SA2422, staau-SAV0321, staau-SAV0446, staau-SAV0457, staau-SAV0655, staau-SAV1014, staau-SAV1765, staau-SAV1793, staau-SAV2188, staau-SAV2350, staau-SAV2484, staau-SAV2594, staep-lipas, staep-SE0011, staep-SE0226, staep-SE0386, staep-SE0389, staep-SE0424, staep-SE0564, staep-SE0714, staep-SE0745, staep-SE0980, staep-SE1436, staep-SE1460, staep-SE1510, staep-SE1780, staep-SE1929, staep-SERP2035, staep-SE2050, staep-SE2095, staep-SE2213, staep-SE2328 Abstract 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 approximately 2.8-Mb genome of S. aureus COL, an early methicillin-resistant isolate, and the approximately 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. Title: The psychrophilic lifestyle as revealed by the genome sequence of Colwellia psychrerythraea 34H through genomic and proteomic analyses Methe BA, Nelson KE, Deming JW, Momen B, Melamud E, Zhang X, Moult J, Madupu R, Nelson WC and Fraser CM <17 more author(s)> Methe BA, Nelson KE, Deming JW, Momen B, Melamud E, Zhang X, Moult J, Madupu R, Nelson WC, Dodson RJ, Brinkac LM, Daugherty SC, Durkin AS, DeBoy RT, Kolonay JF, Sullivan SA, Zhou L, Davidsen TM, Wu M, Huston AL, Lewis M, Weaver B, Weidman JF, Khouri H, Utterback TR, Feldblyum TV, Fraser CM (- 17) Ref: Proc Natl Acad Sci U S A, 102:10913, 2005 : PubMed ESTHER: Methe_2005_Proc.Natl.Acad.Sci.U.S.A_102_10913 PubMedSearch: Methe 2005 Proc.Natl.Acad.Sci.U.S.A 102 10913 PubMedID: 16043709 Gene_locus related to this paper: colp3-q47uc4, colp3-q47uc7, colp3-q47ut6, colp3-q47ut7, colp3-q47v81, colp3-q47vk3, colp3-q47vy9, colp3-q47w94, colp3-q47wj4, colp3-q47wr2, colp3-q47ws7, colp3-q47ws9, colp3-q47x08, colp3-q47x48, colp3-q47yd5, colp3-q47ye2, colp3-q47yq1, colp3-q47yv1, colp3-q47za7, colp3-q47zp5, colp3-q48ac9, colp3-q48aj8, colp3-q48aq9, colp3-q480e1, colp3-q481z4, colp3-q482y8, colp3-q484d8, colp3-q484k3, colp3-q485e4, colp3-q485t4, colp3-q486t5, colp3-q487b7, colp3-q487s5, colp3-q488a3, colp3-q488d2, colp3-q488d8, colp3-q488e7, colp3-q488f8, colp3-q488p2, colp3-q489b1, colp3-q489i6, colp3-q47ya3 Abstract 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. Title: The genome of Salinibacter ruber: convergence and gene exchange among hyperhalophilic bacteria and archaea Mongodin EF, Nelson KE, Daugherty S, DeBoy RT, Wister J, Khouri H, Weidman J, Walsh DA, Papke RT and Rodriguez-Valera F <8 more author(s)> Mongodin EF, Nelson KE, Daugherty S, DeBoy RT, Wister J, Khouri H, Weidman J, Walsh DA, Papke RT, Sanchez Perez G, Sharma AK, Nesbo CL, Macleod D, Bapteste E, Doolittle WF, Charlebois RL, Legault B, Rodriguez-Valera F (- 8) Ref: Proc Natl Acad Sci U S A, 102:18147, 2005 : PubMed ESTHER: Mongodin_2005_Proc.Natl.Acad.Sci.U.S.A_102_18147 PubMedSearch: Mongodin 2005 Proc.Natl.Acad.Sci.U.S.A 102 18147 PubMedID: 16330755 Gene_locus related to this paper: salrd-q2ryx4, salrd-q2ryz7, salrd-q2rz15, salrd-q2rz19, salrd-q2rz52, salrd-q2rz84, salrd-q2rzy1, salrd-q2s0e4, salrd-q2s1i8, salrd-q2s1v7, salrd-q2s1v9, salrd-q2s2d6, salrd-q2s2y7, salrd-q2s5a6, salrd-q2s5k5, salrd-q2s5u7, salrd-q2s6g6, salrd-q2s039, salrd-q2s117, salrd-q2s215, salrd-q2s287, salrd-q2s400, salrd-q2s402, salrd-q2s473, salrd-q2s516, salrd-q2s564 Abstract 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. Title: Complete genome sequence of the plant commensal Pseudomonas fluorescens Pf-5 Paulsen IT, Press CM, Ravel J, Kobayashi DY, Myers GS, Mavrodi DV, DeBoy RT, Seshadri R, Ren Q and Loper JE <19 more author(s)> Paulsen IT, Press CM, Ravel J, Kobayashi DY, Myers GS, Mavrodi DV, DeBoy RT, Seshadri R, Ren Q, Madupu R, Dodson RJ, Durkin AS, Brinkac LM, Daugherty SC, Sullivan SA, Rosovitz MJ, Gwinn ML, Zhou L, Schneider DJ, Cartinhour SW, Nelson WC, Weidman J, Watkins K, Tran K, Khouri H, Pierson EA, Pierson LS, 3rd, Thomashow LS, Loper JE (- 19) Ref: Nat Biotechnol, 23:873, 2005 : PubMed ESTHER: Paulsen_2005_Nat.Biotechnol_23_873 PubMedSearch: Paulsen 2005 Nat.Biotechnol 23 873 PubMedID: 15980861 Gene_locus related to this paper: psef5-metx, psef5-q4k3c9, psef5-q4k4b4, psef5-q4k4t4, psef5-q4k4u7, psef5-q4k4y2, psef5-q4k5b5, psef5-q4k5k6, psef5-q4k5w4, psef5-q4k6z9, psef5-q4k7i6, psef5-q4k7u9, psef5-q4k8j2, psef5-q4k9i3, psef5-q4k458, psef5-q4k713, psef5-q4k717, psef5-q4k873, psef5-q4k906, psef5-q4k982, psef5-q4k989, psef5-q4k993, psef5-q4kax4, psef5-q4kay8, psef5-q4kaz0, psef5-q4kaz4, psef5-q4kb21, psef5-q4kbd7, psef5-q4kbs3, psef5-q4kbs6, psef5-q4kc18, psef5-q4kc21, psef5-q4kcd3, psef5-q4kch8, psef5-q4kcj3, psef5-q4kck4, psef5-q4kcn8, psef5-q4kcq2, psef5-q4kcx3, psef5-q4kd54, psef5-q4kda1, psef5-q4kdb4, psef5-q4ke18, psef5-q4keh1, psef5-q4kej0, psef5-q4keq4, psef5-q4kes9, psef5-q4kf14, psef5-q4kfj4, psef5-q4kfw0, psef5-q4kfw1, psef5-q4kfx7, psef5-q4kgg3, psef5-q4kgj9, psef5-q4kgs6, psef5-q4kh30, psef5-q4kha2, psef5-q4khf1, psef5-q4khl0, psef5-q4khv5, psef5-q4ki42, psef5-q4kj24, psef5-q4kj95, psef5-q4kjk5, psef5-q4kjk7, psef5-q4kjm8, psef5-q4kjt7, psef5-q4kk20, psef5-q4kk22, psef5-q4kk59, psef5-q4kkf7, psefl-PLTG, psepf-PHAZ, psef5-q4kfd8 Abstract 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. Title: Genome sequence of the PCE-dechlorinating bacterium Dehalococcoides ethenogenes Seshadri R, Adrian L, Fouts DE, Eisen JA, Phillippy AM, Methe BA, Ward NL, Nelson WC, DeBoy RT and Heidelberg JF <15 more author(s)> Seshadri R, Adrian L, Fouts DE, Eisen JA, Phillippy AM, Methe BA, Ward NL, Nelson WC, DeBoy RT, Khouri HM, Kolonay JF, Dodson RJ, Daugherty SC, Brinkac LM, Sullivan SA, Madupu R, Nelson KE, Kang KH, Impraim M, Tran K, Robinson JM, Forberger HA, Fraser CM, Zinder SH, Heidelberg JF (- 15) Ref: Science, 307:105, 2005 : PubMed ESTHER: Seshadri_2005_Science_307_105 PubMedSearch: Seshadri 2005 Science 307 105 PubMedID: 15637277 Gene_locus related to this paper: dehm1-q3z6q3, dehm1-q3z6x9, dehm1-q3z6z2, dehm1-q3z8f3, dehm1-q3za50 Abstract 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. Title: Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial pan-genome Tettelin H, Masignani V, Cieslewicz MJ, Donati C, Medini D, Ward NL, Angiuoli SV, Crabtree J, Jones AL and Fraser CM <36 more author(s)> Tettelin H, Masignani V, Cieslewicz MJ, Donati C, Medini D, Ward NL, Angiuoli SV, Crabtree J, Jones AL, Durkin AS, DeBoy RT, Davidsen TM, Mora M, Scarselli M, Margarit y Ros I, Peterson JD, Hauser CR, Sundaram JP, Nelson WC, Madupu R, Brinkac LM, Dodson RJ, Rosovitz MJ, Sullivan SA, Daugherty SC, Haft DH, Selengut J, Gwinn ML, Zhou L, Zafar N, Khouri H, Radune D, Dimitrov G, Watkins K, O'Connor KJ, Smith S, Utterback TR, White O, Rubens CE, Grandi G, Madoff LC, Kasper DL, Telford JL, Wessels MR, Rappuoli R, Fraser CM (- 36) Ref: Proc Natl Acad Sci U S A, 102:13950, 2005 : PubMed ESTHER: Tettelin_2005_Proc.Natl.Acad.Sci.U.S.A_102_13950 PubMedSearch: Tettelin 2005 Proc.Natl.Acad.Sci.U.S.A 102 13950 PubMedID: 16172379 Gene_locus related to this paper: strag-ESTA, strag-GBS0040, strag-GBS0107, strag-GBS1828, strag-pepx, strag-q3dah6, strag-SAG0246, strag-SAG0383, strag-SAG0679, strag-SAG0680, strag-SAG0785, strag-SAG0912, strag-SAG1562, strag-SAG2132 Abstract 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. Title: The genome sequence of the anaerobic, sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough Heidelberg JF, Seshadri R, Haveman SA, Hemme CL, Paulsen IT, Kolonay JF, Eisen JA, Ward N, Methe B and Fraser CM <25 more author(s)> Heidelberg JF, Seshadri R, Haveman SA, Hemme CL, Paulsen IT, Kolonay JF, Eisen JA, Ward N, Methe B, Brinkac LM, Daugherty SC, DeBoy RT, Dodson RJ, Durkin AS, Madupu R, Nelson WC, Sullivan SA, Fouts D, Haft DH, Selengut J, Peterson JD, Davidsen TM, Zafar N, Zhou L, Radune D, Dimitrov G, Hance M, Tran K, Khouri H, Gill J, Utterback TR, Feldblyum TV, Wall JD, Voordouw G, Fraser CM (- 25) Ref: Nat Biotechnol, 22:554, 2004 : PubMed ESTHER: Heidelberg_2004_Nat.Biotechnol_22_554 PubMedSearch: Heidelberg 2004 Nat.Biotechnol 22 554 PubMedID: 15077118 Gene_locus related to this paper: desvh-q72b36, desvh-q72ed6, desvh-q728i3, desvh-q729w4, desvh-q72b15 Abstract Desulfovibrio vulgaris Hildenborough is a model organism for studying the energy metabolism of sulfate-reducing bacteria (SRB) and for understanding the economic impacts of SRB, including biocorrosion of metal infrastructure and bioremediation of toxic metal ions. The 3,570,858 base pair (bp) genome sequence reveals a network of novel c-type cytochromes, connecting multiple periplasmic hydrogenases and formate dehydrogenases, as a key feature of its energy metabolism. The relative arrangement of genes encoding enzymes for energy transduction, together with inferred cellular location of the enzymes, provides a basis for proposing an expansion to the 'hydrogen-cycling' model for increasing energy efficiency in this bacterium. Plasmid-encoded functions include modification of cell surface components, nitrogen fixation and a type-III protein secretion system. This genome sequence represents a substantial step toward the elucidation of pathways for reduction (and bioremediation) of pollutants such as uranium and chromium and offers a new starting point for defining this organism's complex anaerobic respiration. Title: Genome sequence of Silicibacter pomeroyi reveals adaptations to the marine environment Moran MA, Buchan A, Gonzalez JM, Heidelberg JF, Whitman WB, Kiene RP, Henriksen JR, King GM, Belas R and Ward N <25 more author(s)> Moran MA, Buchan A, Gonzalez JM, Heidelberg JF, Whitman WB, Kiene RP, Henriksen JR, King GM, Belas R, Fuqua C, Brinkac L, Lewis M, Johri S, Weaver B, Pai G, Eisen JA, Rahe E, Sheldon WM, Ye W, Miller TR, Carlton J, Rasko DA, Paulsen IT, Ren Q, Daugherty SC, DeBoy RT, Dodson RJ, Durkin AS, Madupu R, Nelson WC, Sullivan SA, Rosovitz MJ, Haft DH, Selengut J, Ward N (- 25) Ref: Nature, 432:910, 2004 : PubMed ESTHER: Moran_2004_Nature_432_910 PubMedSearch: Moran 2004 Nature 432 910 PubMedID: 15602564 Gene_locus related to this paper: silpo-q5lke5, silpo-q5lke7, silpo-q5lke8, silpo-q5lkk5, silpo-q5lkv2, silpo-q5lln9, silpo-q5llu0, silpo-q5llu2, silpo-q5llx5, silpo-q5lm66, silpo-q5lmb9, silpo-q5lml9, silpo-q5lnp6, silpo-q5lp28, silpo-q5lp48, silpo-q5lp56, silpo-q5lpa5, silpo-q5lpf7, silpo-q5lpy6, silpo-q5lrk1, silpo-q5lsn7, silpo-q5ltb5, silpo-q5ltk0, silpo-q5ltm5, silpo-q5ltw8, silpo-q5ltw9, silpo-q5ltx1, silpo-q5ltx5, silpo-q5lu02, silpo-q5lv12, silpo-q5lv17, silpo-q5lv53, silpo-q5lvg9, silpo-q5lw35, silpo-q5lwk9, silpo-q5lws0 Abstract 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. Title: 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 Nelson KE, Fouts DE, Mongodin EF, Ravel J, DeBoy RT, Kolonay JF, Rasko DA, Angiuoli SV, Gill SR and Fraser CM <23 more author(s)> Nelson KE, Fouts DE, Mongodin EF, Ravel J, DeBoy RT, Kolonay JF, Rasko DA, Angiuoli SV, Gill SR, Paulsen IT, Peterson J, White O, Nelson WC, Nierman W, Beanan MJ, Brinkac LM, Daugherty SC, Dodson RJ, Durkin AS, Madupu R, Haft DH, Selengut J, Van Aken S, Khouri H, Fedorova N, Forberger H, Tran B, Kathariou S, Wonderling LD, Uhlich GA, Bayles DO, Luchansky JB, Fraser CM (- 23) Ref: Nucleic Acids Research, 32:2386, 2004 : PubMed ESTHER: Nelson_2004_Nucleic.Acids.Res_32_2386 PubMedSearch: Nelson 2004 Nucleic.Acids.Res 32 2386 PubMedID: 15115801 Gene_locus related to this paper: lismc-c1l0d9, lismf-q71xq4, lismo-LMO0110, lismo-LMO0493, lismo-LMO0580, lismo-LMO0752, lismo-LMO0760, lismo-LMO0857, lismo-LMO0950, lismo-LMO0951, lismo-LMO0977, lismo-LMO1128, lismo-LMO1258, lismo-LMO1674, lismo-LMO2089, lismo-LMO2109, lismo-LMO2433, lismo-LMO2450, lismo-LMO2452, lismo-LMO2453, lismo-LMO2578, lismo-LMO2677, lismo-LMO2755, lismo-metx Abstract 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. Title: Structural flexibility in the Burkholderia mallei genome Nierman WC, DeShazer D, Kim HS, Tettelin H, Nelson KE, Feldblyum T, Ulrich RL, Ronning CM, Brinkac LM and Fraser CM <23 more author(s)> Nierman WC, DeShazer D, Kim HS, Tettelin H, Nelson KE, Feldblyum T, Ulrich RL, Ronning CM, Brinkac LM, Daugherty SC, Davidsen TD, DeBoy RT, Dimitrov G, Dodson RJ, Durkin AS, Gwinn ML, Haft DH, Khouri H, Kolonay JF, Madupu R, Mohammoud Y, Nelson WC, Radune D, Romero CM, Sarria S, Selengut J, Shamblin C, Sullivan SA, White O, Yu Y, Zafar N, Zhou L, Fraser CM (- 23) Ref: Proc Natl Acad Sci U S A, 101:14246, 2004 : PubMed ESTHER: Nierman_2004_Proc.Natl.Acad.Sci.U.S.A_101_14246 PubMedSearch: Nierman 2004 Proc.Natl.Acad.Sci.U.S.A 101 14246 PubMedID: 15377793 Gene_locus related to this paper: burma-a5j5w8, burma-a5tj72, burma-a5tq93, burma-metx, burma-q62a61, burma-q62ar2.1, burma-q62ar2.2, burma-q62ax8, burma-q62b60, burma-q62b79, burma-q62bh9, burma-q62bl4, burma-q62bl7, burma-q62c00, burma-q62cg5, burma-q62d41, burma-q62d56, burma-q62d83, burma-q62dg2, burma-q62du7, burma-q62e67, burma-q62eb8, burma-q62ed8, burma-q62f28, burma-q62fx7, burma-q62g26, burma-q62gx9, burma-q62gy2, burma-q62hq2, burma-q62i62, burma-q62ib8, burma-q62ie8, burma-q62j07, burma-q62j15, burma-q62jn5, burma-q62jy7, burma-q62kb7, burma-q62kg0, burma-q62kh9, burma-q62lp7, burma-q62m40, burma-q62mc3, burma-q62mf4, burma-q62mq7, burma-q629m1, burma-q629p4, burma-q629u0, burps-q3v7s4, burps-hboh Abstract 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. Title: Comparison of the genome of the oral pathogen Treponema denticola with other spirochete genomes Seshadri R, Myers GS, Tettelin H, Eisen JA, Heidelberg JF, Dodson RJ, Davidsen TM, DeBoy RT, Fouts DE and Paulsen IT <29 more author(s)> Seshadri R, Myers GS, Tettelin H, Eisen JA, Heidelberg JF, Dodson RJ, Davidsen TM, DeBoy RT, Fouts DE, Haft DH, Selengut J, Ren Q, Brinkac LM, Madupu R, Kolonay J, Durkin SA, Daugherty SC, Shetty J, Shvartsbeyn A, Gebregeorgis E, Geer K, Tsegaye G, Malek J, Ayodeji B, Shatsman S, McLeod MP, Smajs D, Howell JK, Pal S, Amin A, Vashisth P, McNeill TZ, Xiang Q, Sodergren E, Baca E, Weinstock GM, Norris SJ, Fraser CM, Paulsen IT (- 29) Ref: Proc Natl Acad Sci U S A, 101:5646, 2004 : PubMed ESTHER: Seshadri_2004_Proc.Natl.Acad.Sci.U.S.A_101_5646 PubMedSearch: Seshadri 2004 Proc.Natl.Acad.Sci.U.S.A 101 5646 PubMedID: 15064399 Gene_locus related to this paper: trede-q73j01, trede-q73kf5, trede-q73kp3, trede-q73ks1, trede-q73nf8, trede-q73qt5, trede-q73qv0, trede-q73ra4, trede-q73ri8, trede-Q93EK3, trede-TDE0521 Abstract We present the complete 2,843,201-bp genome sequence of Treponema denticola (ATCC 35405) an oral spirochete associated with periodontal disease. Analysis of the T. denticola genome reveals factors mediating coaggregation, cell signaling, stress protection, and other competitive and cooperative measures, consistent with its pathogenic nature and lifestyle within the mixed-species environment of subgingival dental plaque. Comparisons with previously sequenced spirochete genomes revealed specific factors contributing to differences and similarities in spirochete physiology as well as pathogenic potential. The T. denticola genome is considerably larger in size than the genome of the related syphilis-causing spirochete Treponema pallidum. The differences in gene content appear to be attributable to a combination of three phenomena: genome reduction, lineage-specific expansions, and horizontal gene transfer. Genes lost due to reductive evolution appear to be largely involved in metabolism and transport, whereas some of the genes that have arisen due to lineage-specific expansions are implicated in various pathogenic interactions, and genes acquired via horizontal gene transfer are largely phage-related or of unknown function. Title: Genomic insights into methanotrophy: the complete genome sequence of Methylococcus capsulatus (Bath) Ward N, Larsen O, Sakwa J, Bruseth L, Khouri H, Durkin AS, Dimitrov G, Jiang L, Scanlan D and Eisen JA <28 more author(s)> Ward N, Larsen O, Sakwa J, Bruseth L, Khouri H, Durkin AS, Dimitrov G, Jiang L, Scanlan D, Kang KH, Lewis M, Nelson KE, Methe B, Wu M, Heidelberg JF, Paulsen IT, Fouts D, Ravel J, Tettelin H, Ren Q, Read T, DeBoy RT, Seshadri R, Salzberg SL, Jensen HB, Birkeland NK, Nelson WC, Dodson RJ, Grindhaug SH, Holt I, Eidhammer I, Jonasen I, Vanaken S, Utterback T, Feldblyum TV, Fraser CM, Lillehaug JR, Eisen JA (- 28) Ref: PLoS Biol, 2:e303, 2004 : PubMed ESTHER: Ward_2004_PLoS.Biol_2_e303 PubMedSearch: Ward 2004 PLoS.Biol 2 e303 PubMedID: 15383840 Gene_locus related to this paper: metca-q60a38, metca-q60bu6, metca-q60cn0, metca-q605j8, metca-q606x9, metca-q607f7, metca-q607m2, metca-q609v0 Abstract 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. Title: The complete genome sequence of the Arabidopsis and tomato pathogen Pseudomonas syringae pv. tomato DC3000 Buell CR, Joardar V, Lindeberg M, Selengut J, Paulsen IT, Gwinn ML, Dodson RJ, DeBoy RT, Durkin AS and Collmer A <34 more author(s)> Buell CR, Joardar V, Lindeberg M, Selengut J, Paulsen IT, Gwinn ML, Dodson RJ, DeBoy RT, Durkin AS, Kolonay JF, Madupu R, Daugherty S, Brinkac L, Beanan MJ, Haft DH, Nelson WC, Davidsen T, Zafar N, Zhou L, Liu J, Yuan Q, Khouri H, Fedorova N, Tran B, Russell D, Berry K, Utterback T, Van Aken SE, Feldblyum TV, D'Ascenzo M, Deng WL, Ramos AR, Alfano JR, Cartinhour S, Chatterjee AK, Delaney TP, Lazarowitz SG, Martin GB, Schneider DJ, Tang X, Bender CL, White O, Fraser CM, Collmer A (- 34) Ref: Proc Natl Acad Sci U S A, 100:10181, 2003 : PubMed ESTHER: Buell_2003_Proc.Natl.Acad.Sci.U.S.A_100_10181 PubMedSearch: Buell 2003 Proc.Natl.Acad.Sci.U.S.A 100 10181 PubMedID: 12928499 Gene_locus related to this paper: pse14-q48ia0, psesm-IRP1, psesm-METX, psesm-q87y20, psesm-q88a39, psesm-q881b4, psesm-q889k3, psesy-BIOH, psesy-CFA7, psesy-CFA9, psesy-CMAT, psesy-ESTA, psesy-IRP4, psesy-PHAB, psesy-PHAC, psesy-PHAG1, psesy-PHAG2, psesy-PIP, psesy-PSPTO0162, psesy-PSPTO0421, psesy-PSPTO0508, psesy-PSPTO0675, psesy-PSPTO0715, psesy-PSPTO1154, psesy-PSPTO1504, psesy-PSPTO1559, psesy-PSPTO1580, psesy-PSPTO1604, psesy-PSPTO1677, psesy-PSPTO1766, psesy-PSPTO1863, psesy-PSPTO2042, psesy-PSPTO2134, psesy-PSPTO2150, psesy-PSPTO2209, psesy-PSPTO2217, psesy-PSPTO2218, psesy-PSPTO2293, psesy-PSPTO2495, psesy-PSPTO2674, psesy-PSPTO2830, psesy-PSPTO3135, psesy-PSPTO3138, psesy-PSPTO3264, psesy-PSPTO3282, psesy-PSPTO3306, psesy-PSPTO3485, psesy-PSPTO3572, psesy-PSPTO3911, psesy-PSPTO4089, psesy-PSPTO4178, psesy-PSPTO4277, psesy-PSPTO4430, psesy-PSPTO4519, psesy-PSPTO4540, psesy-PSPTO4699, psesy-PSPTO4708, psesy-PSPTO4781, psesy-PSPTO4843, psesy-PSPTO4964, psesy-PSPTO5218, psesy-PSPTO5299, psesy-PSPTO5448, psesy-PSPTO5537, psesy-SYLD, psesy-SYPC, psesy-SYRE, psesm-q87v84 Abstract 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. Title: Genome of Geobacter sulfurreducens: metal reduction in subsurface environments Methe BA, Nelson KE, Eisen JA, Paulsen IT, Nelson W, Heidelberg JF, Wu D, Wu M, Ward N and Fraser CM <24 more author(s)> Methe BA, Nelson KE, Eisen JA, Paulsen IT, Nelson W, Heidelberg JF, Wu D, Wu M, Ward N, Beanan MJ, Dodson RJ, Madupu R, Brinkac LM, Daugherty SC, DeBoy RT, Durkin AS, Gwinn M, Kolonay JF, Sullivan SA, Haft DH, Selengut J, Davidsen TM, Zafar N, White O, Tran B, Romero C, Forberger HA, Weidman J, Khouri H, Feldblyum TV, Utterback TR, Van Aken SE, Lovley DR, Fraser CM (- 24) Ref: Science, 302:1967, 2003 : PubMed ESTHER: Methe_2003_Science_302_1967 PubMedSearch: Methe 2003 Science 302 1967 PubMedID: 14671304 Gene_locus related to this paper: geosl-q74a54, geosl-q74ac8, geosl-q74eb1, geosl-q747u4, geosl-q747v8, geosl-q749w4 Abstract 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. Title: Complete genome sequence of the oral pathogenic Bacterium porphyromonas gingivalis strain W83 Nelson KE, Fleischmann RD, DeBoy RT, Paulsen IT, Fouts DE, Eisen JA, Daugherty SC, Dodson RJ, Durkin AS and Fraser CM <13 more author(s)> Nelson KE, Fleischmann RD, DeBoy RT, Paulsen IT, Fouts DE, Eisen JA, Daugherty SC, Dodson RJ, Durkin AS, Gwinn M, Haft DH, Kolonay JF, Nelson WC, Mason T, Tallon L, Gray J, Granger D, Tettelin H, Dong H, Galvin JL, Duncan MJ, Dewhirst FE, Fraser CM (- 13) Ref: Journal of Bacteriology, 185:5591, 2003 : PubMed ESTHER: Nelson_2003_J.Bacteriol_185_5591 PubMedSearch: Nelson 2003 J.Bacteriol 185 5591 PubMedID: 12949112 Gene_locus related to this paper: 9gamm-q4a538, porgi-DPP, porgi-q7mtk3, porgi-q7mu18, porgi-q7mub3, porgi-q7muw6, porgi-q7mvp4, porgi-q7mwa7, porgi-q7mx03 Abstract 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. Title: Role of mobile DNA in the evolution of vancomycin-resistant Enterococcus faecalis Paulsen IT, Banerjei L, Myers GS, Nelson KE, Seshadri R, Read TD, Fouts DE, Eisen JA, Gill SR and Fraser CM <22 more author(s)> Paulsen IT, Banerjei L, Myers GS, Nelson KE, Seshadri R, Read TD, Fouts DE, Eisen JA, Gill SR, Heidelberg JF, Tettelin H, Dodson RJ, Umayam L, Brinkac L, Beanan M, Daugherty S, DeBoy RT, Durkin S, Kolonay J, Madupu R, Nelson W, Vamathevan J, Tran B, Upton J, Hansen T, Shetty J, Khouri H, Utterback T, Radune D, Ketchum KA, Dougherty BA, Fraser CM (- 22) Ref: Science, 299:2071, 2003 : PubMed ESTHER: Paulsen_2003_Science_299_2071 PubMedSearch: Paulsen 2003 Science 299 2071 PubMedID: 12663927 Gene_locus related to this paper: entfa-EF0101, entfa-EF0274, entfa-EF0381, entfa-EF0449, entfa-EF0667, entfa-EF0786, entfa-EF1028, entfa-EF1236, entfa-EF1505, entfa-EF1536, entfa-EF1670, entfa-EF2618, entfa-EF2728, entfa-EF2792, entfa-EF2963, entfa-EF3191 Abstract 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. Title: The genome sequence of Bacillus anthracis Ames and comparison to closely related bacteria Read TD, Peterson SN, Tourasse N, Baillie LW, Paulsen IT, Nelson KE, Tettelin H, Fouts DE, Eisen JA and Fraser CM <42 more author(s)> Read TD, Peterson SN, Tourasse N, Baillie LW, Paulsen IT, Nelson KE, Tettelin H, Fouts DE, Eisen JA, Gill SR, Holtzapple EK, Okstad OA, Helgason E, Rilstone J, Wu M, Kolonay JF, Beanan MJ, Dodson RJ, Brinkac LM, Gwinn M, DeBoy RT, Madpu R, Daugherty SC, Durkin AS, Haft DH, Nelson WC, Peterson JD, Pop M, Khouri HM, Radune D, Benton JL, Mahamoud Y, Jiang L, Hance IR, Weidman JF, Berry KJ, Plaut RD, Wolf AM, Watkins KL, Nierman WC, Hazen A, Cline R, Redmond C, Thwaite JE, White O, Salzberg SL, Thomason B, Friedlander AM, Koehler TM, Hanna PC, Kolsto AB, Fraser CM (- 42) Ref: Nature, 423:81, 2003 : PubMed ESTHER: Read_2003_Nature_423_81 PubMedSearch: Read 2003 Nature 423 81 PubMedID: 12721629 Gene_locus related to this paper: bacan-BA0160, bacan-BA0950, bacan-BA0954, bacan-BA1019, bacan-BA1242, bacan-BA1727, bacan-BA1747, bacan-BA1866, bacan-BA1914, bacan-BA2015, bacan-BA2392, bacan-BA2417, bacan-BA2557, bacan-BA2607, bacan-BA2687, bacan-BA2694, bacan-BA2738, bacan-BA2865, bacan-BA3068, bacan-BA3165, bacan-BA3178, bacan-BA3187, bacan-BA3343, bacan-BA3372, bacan-BA3703, bacan-BA3805, bacan-BA3863, bacan-BA3877, bacan-BA3887, bacan-BA4324, bacan-BA4328, bacan-BA4338, bacan-BA4577, bacan-BA4983, bacan-BA5009, bacan-BA5110, bacan-BA5136, bacan-DHBF, bacan-q81tt2, bacce-BC0192, bacce-BC1788, bacce-BC1954, bacce-BC2141, bacce-BC2171, bacce-BC4730, bacce-BC4862, bacce-BC5130, bacce-PHAC, bacce-q72yu1, baccr-pepx Abstract 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. Title: Complete genome sequence of the Q-fever pathogen Coxiella burnetii Seshadri R, Paulsen IT, Eisen JA, Read TD, Nelson KE, Nelson WC, Ward NL, Tettelin H, Davidsen TM and Heidelberg JF <14 more author(s)> Seshadri R, Paulsen IT, Eisen JA, Read TD, Nelson KE, Nelson WC, Ward NL, Tettelin H, Davidsen TM, Beanan MJ, DeBoy RT, Daugherty SC, Brinkac LM, Madupu R, Dodson RJ, Khouri HM, Lee KH, Carty HA, Scanlan D, Heinzen RA, Thompson HA, Samuel JE, Fraser CM, Heidelberg JF (- 14) Ref: Proc Natl Acad Sci U S A, 100:5455, 2003 : PubMed ESTHER: Seshadri_2003_Proc.Natl.Acad.Sci.U.S.A_100_5455 PubMedSearch: Seshadri 2003 Proc.Natl.Acad.Sci.U.S.A 100 5455 PubMedID: 12704232 Gene_locus related to this paper: coxbu-BIOH, coxbu-CBU0752, coxbu-CBU1119, coxbu-CBU1225, coxbu-CBU1529, coxbu-CBU1769, coxbu-CBU1975 Abstract The 1,995,275-bp genome of Coxiella burnetii, Nine Mile phase I RSA493, a highly virulent zoonotic pathogen and category B bioterrorism agent, was sequenced by the random shotgun method. This bacterium is an obligate intracellular acidophile that is highly adapted for life within the eukaryotic phagolysosome. Genome analysis revealed many genes with potential roles in adhesion, invasion, intracellular trafficking, host-cell modulation, and detoxification. A previously uncharacterized 13-member family of ankyrin repeat-containing proteins is implicated in the pathogenesis of this organism. Although the lifestyle and parasitic strategies of C. burnetii resemble that of Rickettsiae and Chlamydiae, their genome architectures differ considerably in terms of presence of mobile elements, extent of genome reduction, metabolic capabilities, and transporter profiles. The presence of 83 pseudogenes displays an ongoing process of gene degradation. Unlike other obligate intracellular bacteria, 32 insertion sequences are found dispersed in the chromosome, indicating some plasticity in the C. burnetii genome. These analyses suggest that the obligate intracellular lifestyle of C. burnetii may be a relatively recent innovation. Title: Genome sequence of the dissimilatory metal ion-reducing bacterium Shewanella oneidensis Heidelberg JF, Paulsen IT, Nelson KE, Gaidos EJ, Nelson WC, Read TD, Eisen JA, Seshadri R, Ward N and Fraser CM <33 more author(s)> Heidelberg JF, Paulsen IT, Nelson KE, Gaidos EJ, Nelson WC, Read TD, Eisen JA, Seshadri R, Ward N, Methe B, Clayton RA, Meyer T, Tsapin A, Scott J, Beanan M, Brinkac L, Daugherty S, DeBoy RT, Dodson RJ, Durkin AS, Haft DH, Kolonay JF, Madupu R, Peterson JD, Umayam LA, White O, Wolf AM, Vamathevan J, Weidman J, Impraim M, Lee K, Berry K, Lee C, Mueller J, Khouri H, Gill J, Utterback TR, McDonald LA, Feldblyum TV, Smith HO, Venter JC, Nealson KH, Fraser CM (- 33) Ref: Nat Biotechnol, 20:1118, 2002 : PubMed ESTHER: Heidelberg_2002_Nat.Biotechnol_20_1118 PubMedSearch: Heidelberg 2002 Nat.Biotechnol 20 1118 PubMedID: 12368813 Gene_locus related to this paper: sheon-BIOH, sheon-LYPA, sheon-PIP, sheon-PTRB, sheon-q8ej95, sheon-SO0071, sheon-SO0614, sheon-SO0616, sheon-SO0801, sheon-SO0880, sheoe-SO0967, sheon-SO1006, sheon-SO1224, sheon-SO1310, sheon-SO1534, sheon-SO1539, sheon-SO1686, sheon-SO1743, sheon-SO1976, sheon-SO1999, sheon-SO2024, sheon-SO2047, sheon-SO2055, sheon-SO2223, sheon-SO2333, sheon-SO2473, sheon-SO2582, sheon-SO2753, sheon-SO2934, sheon-SO3025, sheon-SO3900, sheon-SO3990, sheon-SO4252, sheon-SO4400, sheon-SO4537, sheon-SO4543, sheon-SO4574, sheon-SO4618, sheon-SO4650, sheon-SOA0048, shefn-SfSFGH, sheon-ym51 Abstract 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. Title: Complete genome sequence and comparative analysis of the metabolically versatile Pseudomonas putida KT2440 Nelson KE, Weinel C, Paulsen IT, Dodson RJ, Hilbert H, Martins dos Santos VA, Fouts DE, Gill SR, Pop M and Fraser CM <33 more author(s)> Nelson KE, Weinel C, Paulsen IT, Dodson RJ, Hilbert H, Martins dos Santos VA, Fouts DE, Gill SR, Pop M, Holmes M, Brinkac L, Beanan M, DeBoy RT, Daugherty S, Kolonay J, Madupu R, Nelson W, White O, Peterson J, Khouri H, Hance I, Chris Lee P, Holtzapple E, Scanlan D, Tran K, Moazzez A, Utterback T, Rizzo M, Lee K, Kosack D, Moestl D, Wedler H, Lauber J, Stjepandic D, Hoheisel J, Straetz M, Heim S, Kiewitz C, Eisen JA, Timmis KN, Dusterhoft A, Tummler B, Fraser CM (- 33) Ref: Environ Microbiol, 4:799, 2002 : PubMed ESTHER: Nelson_2002_Environ.Microbiol_4_799 PubMedSearch: Nelson 2002 Environ.Microbiol 4 799 PubMedID: 12534463 Gene_locus related to this paper: psep1-a5wa77, psep1-a5wax1, psepk-q88nk6, psepk-q88qt0, psepu-acoc, psepu-BIOH, psepu-bpest, psepu-ESTB, psepu-LIP, psepu-METX, psepu-PHAC1, psepu-PHAC2, psepu-PHAG, psepu-PHAZ, psepu-PIP, psepu-PP0375, psepu-PP0498, psepu-PP0532, psepu-PP1064, psepu-PP1184, psepu-PP1310, psepu-PP1500, psepu-PP1617, psepu-PP1829, psepu-PP1979, psepu-PP2083, psepu-PP2201, psepu-PP2236, psepu-PP2567, psepu-PP2804, psepu-PP2934, psepu-PP3195, psepu-PP3367, psepu-PP3404, psepu-PP3645, psepu-PP3807, psepu-PP3812, psepu-PP3943, psepu-PP4164, psepu-PP4165, psepu-PP4178, psepu-PP4249, psepu-PP4540, psepu-PP4551, psepu-PP4583, psepu-PP4624, psepu-PP4634, psepu-PP4916, psepu-PP5117, psepu-PP5161, psepu-PP5167, psepu-PPSD, psepu-Q8KQK1, psepu-q9wwz4 Abstract Pseudomonas putida is a metabolically versatile saprophytic soil bacterium that has been certified as a biosafety host for the cloning of foreign genes. The bacterium also has considerable potential for biotechnological applications. Sequence analysis of the 6.18 Mb genome of strain KT2440 reveals diverse transport and metabolic systems. Although there is a high level of genome conservation with the pathogenic Pseudomonad Pseudomonas aeruginosa (85% of the predicted coding regions are shared), key virulence factors including exotoxin A and type III secretion systems are absent. Analysis of the genome gives insight into the non-pathogenic nature of P. putida and points to potential new applications in agriculture, biocatalysis, bioremediation and bioplastic production. Title: The Brucella suis genome reveals fundamental similarities between animal and plant pathogens and symbionts Paulsen IT, Seshadri R, Nelson KE, Eisen JA, Heidelberg JF, Read TD, Dodson RJ, Umayam L, Brinkac LM and Fraser CM <21 more author(s)> Paulsen IT, Seshadri R, Nelson KE, Eisen JA, Heidelberg JF, Read TD, Dodson RJ, Umayam L, Brinkac LM, Beanan MJ, Daugherty SC, DeBoy RT, Durkin AS, Kolonay JF, Madupu R, Nelson WC, Ayodeji B, Kraul M, Shetty J, Malek J, Van Aken SE, Riedmuller S, Tettelin H, Gill SR, White O, Salzberg SL, Hoover DL, Lindler LE, Halling SM, Boyle SM, Fraser CM (- 21) Ref: Proc Natl Acad Sci U S A, 99:13148, 2002 : PubMed ESTHER: Paulsen_2002_Proc.Natl.Acad.Sci.U.S.A_99_13148 PubMedSearch: Paulsen 2002 Proc.Natl.Acad.Sci.U.S.A 99 13148 PubMedID: 12271122 Gene_locus related to this paper: brume-BMEI0552, brume-BMEI0733, brume-BMEI1044, brume-BMEI1119, brume-BMEI1365, brume-BMEI1594, brume-BMEI1608, brume-BMEI1822, brume-BMEI1884, brume-BMEI1951, brume-BMEI2011, brume-BMEII0047, brume-BMEII0681, brume-BMEII0989, brume-PCAD, brusu-BR0288, brusu-BR1291, brusu-BR1327, brusu-BRA0989 Abstract 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. Title: Complete genome sequence and comparative genomic analysis of an emerging human pathogen, serotype V Streptococcus agalactiae Tettelin H, Masignani V, Cieslewicz MJ, Eisen JA, Peterson S, Wessels MR, Paulsen IT, Nelson KE, Margarit I and Fraser CM <33 more author(s)> Tettelin H, Masignani V, Cieslewicz MJ, Eisen JA, Peterson S, Wessels MR, Paulsen IT, Nelson KE, Margarit I, Read TD, Madoff LC, Wolf AM, Beanan MJ, Brinkac LM, Daugherty SC, DeBoy RT, Durkin AS, Kolonay JF, Madupu R, Lewis MR, Radune D, Fedorova NB, Scanlan D, Khouri H, Mulligan S, Carty HA, Cline RT, Van Aken SE, Gill J, Scarselli M, Mora M, Iacobini ET, Brettoni C, Galli G, Mariani M, Vegni F, Maione D, Rinaudo D, Rappuoli R, Telford JL, Kasper DL, Grandi G, Fraser CM (- 33) Ref: Proc Natl Acad Sci U S A, 99:12391, 2002 : PubMed ESTHER: Tettelin_2002_Proc.Natl.Acad.Sci.U.S.A_99_12391 PubMedSearch: Tettelin 2002 Proc.Natl.Acad.Sci.U.S.A 99 12391 PubMedID: 12200547 Gene_locus related to this paper: strag-ESTA, strag-GBS0040, strag-GBS1828, strag-pepx, strag-SAG0108, strag-SAG0246, strag-SAG0383, strag-SAG0521, strag-SAG0679, strag-SAG0680, strag-SAG0681, strag-SAG0785, strag-SAG0912, strag-SAG1040, strag-SAG1562, strag-SAG2132 Abstract The 2,160,267 bp genome sequence of Streptococcus agalactiae, the leading cause of bacterial sepsis, pneumonia, and meningitis in neonates in the U.S. and Europe, is predicted to encode 2,175 genes. Genome comparisons among S. agalactiae, Streptococcus pneumoniae, Streptococcus pyogenes, and the other completely sequenced genomes identified genes specific to the streptococci and to S. agalactiae. These in silico analyses, combined with comparative genome hybridization experiments between the sequenced serotype V strain 2603 V/R and 19 S. agalactiae strains from several serotypes using whole-genome microarrays, revealed the genetic heterogeneity among S. agalactiae strains, even of the same serotype, and provided insights into the evolution of virulence mechanisms. Title: Complete genome sequence of Caulobacter crescentus Nierman WC, Feldblyum TV, Laub MT, Paulsen IT, Nelson KE, Eisen JA, Heidelberg JF, Alley MR, Ohta N and Fraser CM <27 more author(s)> Nierman WC, Feldblyum TV, Laub MT, Paulsen IT, Nelson KE, Eisen JA, Heidelberg JF, Alley MR, Ohta N, Maddock JR, Potocka I, Nelson WC, Newton A, Stephens C, Phadke ND, Ely B, DeBoy RT, Dodson RJ, Durkin AS, Gwinn ML, Haft DH, Kolonay JF, Smit J, Craven MB, Khouri H, Shetty J, Berry K, Utterback T, Tran K, Wolf A, Vamathevan J, Ermolaeva M, White O, Salzberg SL, Venter JC, Shapiro L, Fraser CM (- 27) Ref: Proc Natl Acad Sci U S A, 98:4136, 2001 : PubMed ESTHER: Nierman_2001_Proc.Natl.Acad.Sci.U.S.A_98_4136 PubMedSearch: Nierman 2001 Proc.Natl.Acad.Sci.U.S.A 98 4136 PubMedID: 11259647 Gene_locus related to this paper: caucr-CC0087, caucr-CC0223, caucr-CC0341, caucr-CC0352, caucr-CC0355, caucr-CC0384, caucr-CC0477, caucr-CC0478, caucr-CC0525, caucr-CC0552, caucr-CC0771, caucr-CC0799, caucr-CC0847, caucr-CC0936, caucr-CC0940, caucr-CC1048, caucr-CC1053, caucr-CC1175, caucr-CC1226, caucr-CC1227, caucr-CC1229, caucr-CC1499, caucr-CC1622, caucr-CC1734, caucr-CC1867, caucr-CC1986, caucr-CC2083, caucr-CC2154, caucr-CC2185, caucr-CC2230, caucr-CC2253, caucr-CC2298, caucr-CC2313, caucr-CC2358, caucr-CC2395, caucr-CC2411, caucr-CC2515, caucr-CC2565, caucr-CC2671, caucr-CC2710, caucr-CC2763, caucr-CC2797, caucr-CC3039, caucr-CC3091, caucr-CC3099, caucr-CC3204, caucr-CC3246, caucr-CC3300, caucr-CC3308, caucr-CC3346, caucr-CC3418, caucr-CC3441, caucr-CC3442, caucr-CC3634, caucr-CC3687, caucr-CC3688, caucr-CC3723, caucr-CC3725, caucr-CC3758, caucr-PHAZ, caucr-PHBC, caucr-q9a8c1, caucr-q9aac8 Abstract 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. Title: Complete genome sequence of a virulent isolate of Streptococcus pneumoniae Tettelin H, Nelson KE, Paulsen IT, Eisen JA, Read TD, Peterson S, Heidelberg J, DeBoy RT, Haft DH and Fraser CM <29 more author(s)> Tettelin H, Nelson KE, Paulsen IT, Eisen JA, Read TD, Peterson S, Heidelberg J, DeBoy RT, Haft DH, Dodson RJ, Durkin AS, Gwinn M, Kolonay JF, Nelson WC, Peterson JD, Umayam LA, White O, Salzberg SL, Lewis MR, Radune D, Holtzapple E, Khouri H, Wolf AM, Utterback TR, Hansen CL, McDonald LA, Feldblyum TV, Angiuoli S, Dickinson T, Hickey EK, Holt IE, Loftus BJ, Yang F, Smith HO, Venter JC, Dougherty BA, Morrison DA, Hollingshead SK, Fraser CM (- 29) Ref: Science, 293:498, 2001 : PubMed ESTHER: Tettelin_2001_Science_293_498 PubMedSearch: Tettelin 2001 Science 293 498 PubMedID: 11463916 Gene_locus related to this paper: strp2-q04l35, strpj-b8zns7, strpn-AXE1, strpn-b2dz20, strpn-pepx, strpn-SP0614, strpn-SP0666, strpn-SP0777, strpn-SP0902, strpn-SP1343 Abstract 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. | |||||||
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