Author Report for: Paulsen ITNo contact information in database for Paulsen IT
Attie O, Jayaprakash A, Shah H, Paulsen IT, Morino M, Takahashi Y, Narumi I, Sachidanandam R, Satoh K and Krulwich TA <1 more author(s)> Attie O, Jayaprakash A, Shah H, Paulsen IT, Morino M, Takahashi Y, Narumi I, Sachidanandam R, Satoh K, Ito M, Krulwich TA (- 1) Ref: Genome Announc, 2:, 2014 : PubMed ESTHER: Attie_2014_Genome.Announc_2_ PubMedSearch: Attie 2014 Genome.Announc 2 PubMedID: 25395643 Gene_locus related to this paper: bacao-a0a094xfl6, bacao-a0a094wig6 Abstract Bacillus alcalophilus AV1934, isolated from human feces, was described in 1934 before microbiome studies and recent indications of novel potassium ion coupling to motility in this extremophile. Here, we report draft sequences that will facilitate an examination of whether that coupling is part of a larger cycle of potassium ion-coupled transporters. Title: Comparative genomics of plant-associated Pseudomonas spp.: insights into diversity and inheritance of traits involved in multitrophic interactions Loper JE, Hassan KA, Mavrodi DV, Davis EW, 2nd, Lim CK, Shaffer BT, Elbourne LD, Stockwell VO, Hartney SL and Paulsen IT <25 more author(s)> Loper JE, Hassan KA, Mavrodi DV, Davis EW, 2nd, Lim CK, Shaffer BT, Elbourne LD, Stockwell VO, Hartney SL, Breakwell K, Henkels MD, Tetu SG, Rangel LI, Kidarsa TA, Wilson NL, van de Mortel JE, Song C, Blumhagen R, Radune D, Hostetler JB, Brinkac LM, Durkin AS, Kluepfel DA, Wechter WP, Anderson AJ, Kim YC, Pierson LS, 3rd, Pierson EA, Lindow SE, Kobayashi DY, Raaijmakers JM, Weller DM, Thomashow LS, Allen AE, Paulsen IT (- 25) Ref: PLoS Genet, 8:e1002784, 2012 : PubMed ESTHER: Loper_2012_PLoS.Genet_8_E1002784 PubMedSearch: Loper 2012 PLoS.Genet 8 E1002784 PubMedID: 22792073 Gene_locus related to this paper: psebn-f2kd12, psefl-e2xn15, psefs-c3k632, psepf-q3k919, psebn-f2k9f6, psefl-i2br68, psefl-i4k4a8, 9psed-i4l6c7, 9psed-i4xqw9, psefl-j2epr2, 9psed-j2ew12, psefs-c3k813, psefl-w2f4e5, 9psed-s6i647, 9psed-j2wmk3, 9psed-i4kt90, 9psed-a0a068aip7, 9psed-j2nei8, 9psed-i4kw69, psefl-i2bvr1, psefl-j2mu40, 9psed-j2ync4 Abstract We provide here a comparative genome analysis of ten strains within the Pseudomonas fluorescens group including seven new genomic sequences. These strains exhibit a diverse spectrum of traits involved in biological control and other multitrophic interactions with plants, microbes, and insects. Multilocus sequence analysis placed the strains in three sub-clades, which was reinforced by high levels of synteny, size of core genomes, and relatedness of orthologous genes between strains within a sub-clade. The heterogeneity of the P. fluorescens group was reflected in the large size of its pan-genome, which makes up approximately 54% of the pan-genome of the genus as a whole, and a core genome representing only 45-52% of the genome of any individual strain. We discovered genes for traits that were not known previously in the strains, including genes for the biosynthesis of the siderophores achromobactin and pseudomonine and the antibiotic 2-hexyl-5-propyl-alkylresorcinol; novel bacteriocins; type II, III, and VI secretion systems; and insect toxins. Certain gene clusters, such as those for two type III secretion systems, are present only in specific sub-clades, suggesting vertical inheritance. Almost all of the genes associated with multitrophic interactions map to genomic regions present in only a subset of the strains or unique to a specific strain. To explore the evolutionary origin of these genes, we mapped their distributions relative to the locations of mobile genetic elements and repetitive extragenic palindromic (REP) elements in each genome. The mobile genetic elements and many strain-specific genes fall into regions devoid of REP elements (i.e., REP deserts) and regions displaying atypical tri-nucleotide composition, possibly indicating relatively recent acquisition of these loci. Collectively, the results of this study highlight the enormous heterogeneity of the P. fluorescens group and the importance of the variable genome in tailoring individual strains to their specific lifestyles and functional repertoire. Title: Comparative genomic analysis of the thermophilic biomass-degrading fungi Myceliophthora thermophila and Thielavia terrestris Berka RM, Grigoriev IV, Otillar R, Salamov A, Grimwood J, Reid I, Ishmael N, John T, Darmond C and Tsang A <29 more author(s)> Berka RM, Grigoriev IV, Otillar R, Salamov A, Grimwood J, Reid I, Ishmael N, John T, Darmond C, Moisan MC, Henrissat B, Coutinho PM, Lombard V, Natvig DO, Lindquist E, Schmutz J, Lucas S, Harris P, Powlowski J, Bellemare A, Taylor D, Butler G, de Vries RP, Allijn IE, van den Brink J, Ushinsky S, Storms R, Powell AJ, Paulsen IT, Elbourne LD, Baker SE, Magnuson J, Laboissiere S, Clutterbuck AJ, Martinez D, Wogulis M, de Leon AL, Rey MW, Tsang A (- 29) Ref: Nat Biotechnol, 29:922, 2011 : PubMed ESTHER: Berka_2011_Nat.Biotechnol_29_922 PubMedSearch: Berka 2011 Nat.Biotechnol 29 922 PubMedID: 21964414 Gene_locus related to this paper: thiha-cip2, thite-g2r8b5, thite-g2rcm8, thite-g2r192, thiha-g2qdy2, thiha-g2qh51, thite-g2rae6, thite-g2r5h0, thiha-g2qj94, thiha-g2qnb2, thite-g2rg14, myctt-g2q973, thite-g2qtu3, myctt-g2qpr0, thite-g2rhm0, 9pezi-a0a3s4b069, myctt-g2qmb4, thett-g2qur2 Abstract Thermostable enzymes and thermophilic cell factories may afford economic advantages in the production of many chemicals and biomass-based fuels. Here we describe and compare the genomes of two thermophilic fungi, Myceliophthora thermophila and Thielavia terrestris. To our knowledge, these genomes are the first described for thermophilic eukaryotes and the first complete telomere-to-telomere genomes for filamentous fungi. Genome analyses and experimental data suggest that both thermophiles are capable of hydrolyzing all major polysaccharides found in biomass. Examination of transcriptome data and secreted proteins suggests that the two fungi use shared approaches in the hydrolysis of cellulose and xylan but distinct mechanisms in pectin degradation. Characterization of the biomass-hydrolyzing activity of recombinant enzymes suggests that these organisms are highly efficient in biomass decomposition at both moderate and high temperatures. Furthermore, we present evidence suggesting that aside from representing a potential reservoir of thermostable enzymes, thermophilic fungi are amenable to manipulation using classical and molecular genetics. Title: Adherence and motility characteristics of clinical Acinetobacter baumannii isolates Eijkelkamp BA, Stroeher UH, Hassan KA, Papadimitrious MS, Paulsen IT, Brown MH Ref: FEMS Microbiology Letters, 323:44, 2011 : PubMed ESTHER: Eijkelkamp_2011_FEMS.Microbiol.Lett_323_44 PubMedSearch: Eijkelkamp 2011 FEMS.Microbiol.Lett 323 44 PubMedID: 22092679 Gene_locus related to this paper: aciba-f5iht4, aciba-a0a009wzt4 Abstract Acinetobacter baumannii continues to be a major health problem especially in hospital settings. Herein, features that may play a role in persistence and disease potential were investigated in a collection of clinical A. baumannii strains from Australia. Twitching motility was found to be a common trait in A. baumannii international clone I strains and in abundant biofilm formers, whereas swarming motility was only observed in isolates not classified within the international clone lineages. Bioinformatic analysis of the type IV fimbriae revealed a correlation between PilA sequence homology and motility. A high level of variability in adherence to both abiotic surfaces and epithelial cells was found. We report for the first time the motility characteristics of a large number of A. baumannii isolates and present a direct comparison of A. baumannii binding to nasopharyngeal and lung epithelial cells. Title: Niche of harmful alga Aureococcus anophagefferens revealed through ecogenomics Gobler CJ, Berry DL, Dyhrman ST, Wilhelm SW, Salamov A, Lobanov AV, Zhang Y, Collier JL, Wurch LL and Grigoriev IV <23 more author(s)> Gobler CJ, Berry DL, Dyhrman ST, Wilhelm SW, Salamov A, Lobanov AV, Zhang Y, Collier JL, Wurch LL, Kustka AB, Dill BD, Shah M, VerBerkmoes NC, Kuo A, Terry A, Pangilinan J, Lindquist EA, Lucas S, Paulsen IT, Hattenrath-Lehmann TK, Talmage SC, Walker EA, Koch F, Burson AM, Marcoval MA, Tang YZ, Lecleir GR, Coyne KJ, Berg GM, Bertrand EM, Saito MA, Gladyshev VN, Grigoriev IV (- 23) Ref: Proc Natl Acad Sci U S A, 108:4352, 2011 : PubMed ESTHER: Gobler_2011_Proc.Natl.Acad.Sci.U.S.A_108_4352 PubMedSearch: Gobler 2011 Proc.Natl.Acad.Sci.U.S.A 108 4352 PubMedID: 21368207 Gene_locus related to this paper: auran-f0xvq5, auran-f0xwb9, auran-f0y4x4, auran-f0y5a8, auran-f0ycl4, auran-f0ycp7, auran-f0ye99, auran-f0yge8, auran-f0yci9, auran-f0yr72, auran-f0y8q8, auran-f0y7s1 Abstract Harmful algal blooms (HABs) cause significant economic and ecological damage worldwide. Despite considerable efforts, a comprehensive understanding of the factors that promote these blooms has been lacking, because the biochemical pathways that facilitate their dominance relative to other phytoplankton within specific environments have not been identified. Here, biogeochemical measurements showed that the harmful alga Aureococcus anophagefferens outcompeted co-occurring phytoplankton in estuaries with elevated levels of dissolved organic matter and turbidity and low levels of dissolved inorganic nitrogen. We subsequently sequenced the genome of A. anophagefferens and compared its gene complement with those of six competing phytoplankton species identified through metaproteomics. Using an ecogenomic approach, we specifically focused on gene sets that may facilitate dominance within the environmental conditions present during blooms. A. anophagefferens possesses a larger genome (56 Mbp) and has more genes involved in light harvesting, organic carbon and nitrogen use, and encoding selenium- and metal-requiring enzymes than competing phytoplankton. Genes for the synthesis of microbial deterrents likely permit the proliferation of this species, with reduced mortality losses during blooms. Collectively, these findings suggest that anthropogenic activities resulting in elevated levels of turbidity, organic matter, and metals have opened a niche within coastal ecosystems that ideally suits the unique genetic capacity of A. anophagefferens and thus, has facilitated the proliferation of this and potentially other HABs. Title: Genome of alkaliphilic Bacillus pseudofirmus OF4 reveals adaptations that support the ability to grow in an external pH range from 7.5 to 11.4 Janto B, Ahmed A, Ito M, Liu J, Hicks DB, Pagni S, Fackelmayer OJ, Smith TA, Earl J and Krulwich TA <12 more author(s)> Janto B, Ahmed A, Ito M, Liu J, Hicks DB, Pagni S, Fackelmayer OJ, Smith TA, Earl J, Elbourne LD, Hassan K, Paulsen IT, Kolsto AB, Tourasse NJ, Ehrlich GD, Boissy R, Ivey DM, Li G, Xue Y, Ma Y, Hu FZ, Krulwich TA (- 12) Ref: Environ Microbiol, 13:3289, 2011 : PubMed ESTHER: Janto_2011_Environ.Microbiol_13_3289 PubMedSearch: Janto 2011 Environ.Microbiol 13 3289 PubMedID: 21951522 Gene_locus related to this paper: alkpo-d3fst0 Abstract Bacillus pseudofirmus OF4 is an extreme but facultative alkaliphile that grows non-fermentatively in a pH range from 7.5 to above 11.4 and can withstand large sudden increases in external pH. It is a model organism for studies of bioenergetics at high pH, at which energy demands are higher than at neutral pH because both cytoplasmic pH homeostasis and ATP synthesis require more energy. The alkaliphile also tolerates a cytoplasmic pH>9.0 at external pH values at which the pH homeostasis capacity is exceeded, and manages other stresses that are exacerbated at alkaline pH, e.g. sodium, oxidative and cell wall stresses. The genome of B.pseudofirmus OF4 includes two plasmids that are lost from some mutants without viability loss. The plasmids may provide a reservoir of mobile elements that promote adaptive chromosomal rearrangements under particular environmental conditions. The genome also reveals a more acidic pI profile for proteins exposed on the outer surface than found in neutralophiles. A large array of transporters and regulatory genes are predicted to protect the alkaliphile from its overlapping stresses. In addition, unanticipated metabolic versatility was observed, which could ensure requisite energy for alkaliphily under diverse conditions. Title: Complete genome sequence of the multiresistant taxonomic outlier Pseudomonas aeruginosa PA7 Roy PH, Tetu SG, Larouche A, Elbourne L, Tremblay S, Ren Q, Dodson R, Harkins D, Shay R and Paulsen IT <2 more author(s)> Roy PH, Tetu SG, Larouche A, Elbourne L, Tremblay S, Ren Q, Dodson R, Harkins D, Shay R, Watkins K, Mahamoud Y, Paulsen IT (- 2) Ref: PLoS ONE, 5:e8842, 2010 : PubMed ESTHER: Roy_2010_PLoS.ONE_5_E8842 PubMedSearch: Roy 2010 PLoS.ONE 5 E8842 PubMedID: 20107499 Gene_locus related to this paper: pseae-PA5384, psea7-a6vca5, psea7-a6v8b2, psea7-a6v754 Abstract Pseudomonas aeruginosa PA7 is a non-respiratory human isolate from Argentina that is multiresistant to antibiotics. We first sequenced gyrA, gyrB, parC, parE, ampC, ampR, and several housekeeping genes and found that PA7 is a taxonomic outlier. We report here the complete sequence of the 6,588,339 bp genome, which has only about 95% overall identity to other strains. PA7 has multiple novel genomic islands and a total of 51 occupied regions of genomic plasticity. These islands include antibiotic resistance genes, parts of transposons, prophages, and a pKLC102-related island. Several PA7 genes not present in PAO1 or PA14 are putative orthologues of other Pseudomonas spp. and Ralstonia spp. genes. PA7 appears to be closely related to the known taxonomic outlier DSM1128 (ATCC9027). PA7 lacks several virulence factors, notably the entire TTSS region corresponding to PA1690-PA1725 of PAO1. It has neither exoS nor exoU and lacks toxA, exoT, and exoY. PA7 is serotype O12 and pyoverdin type II. Preliminary proteomic studies indicate numerous differences with PAO1, some of which are probably a consequence of a frameshift mutation in the mvfR quorum sensing regulatory gene. Title: Genome of the epsilonproteobacterial chemolithoautotroph Sulfurimonas denitrificans Sievert SM, Scott KM, Klotz MG, Chain PS, Hauser LJ, Hemp J, Hugler M, Land M, Lapidus A and Simon J <6 more author(s)> Sievert SM, Scott KM, Klotz MG, Chain PS, Hauser LJ, Hemp J, Hugler M, Land M, Lapidus A, Larimer FW, Lucas S, Malfatti SA, Meyer F, Paulsen IT, Ren Q, Simon J (- 6) Ref: Applied Environmental Microbiology, 74:1145, 2008 : PubMed ESTHER: Sievert_2008_Appl.Environ.Microbiol_74_1145 PubMedSearch: Sievert 2008 Appl.Environ.Microbiol 74 1145 PubMedID: 18065616 Gene_locus related to this paper: suldn-q30ua6, suldn-q30rs9 Abstract Sulfur-oxidizing epsilonproteobacteria are common in a variety of sulfidogenic environments. These autotrophic and mixotrophic sulfur-oxidizing bacteria are believed to contribute substantially to the oxidative portion of the global sulfur cycle. In order to better understand the ecology and roles of sulfur-oxidizing epsilonproteobacteria, in particular those of the widespread genus Sulfurimonas, in biogeochemical cycles, the genome of Sulfurimonas denitrificans DSM1251 was sequenced. This genome has many features, including a larger size (2.2 Mbp), that suggest a greater degree of metabolic versatility or responsiveness to the environment than seen for most of the other sequenced epsilonproteobacteria. A branched electron transport chain is apparent, with genes encoding complexes for the oxidation of hydrogen, reduced sulfur compounds, and formate and the reduction of nitrate and oxygen. Genes are present for a complete, autotrophic reductive citric acid cycle. Many genes are present that could facilitate growth in the spatially and temporally heterogeneous sediment habitat from where Sulfurimonas denitrificans was originally isolated. Many resistance-nodulation-development family transporter genes (10 total) are present; of these, several are predicted to encode heavy metal efflux transporters. An elaborate arsenal of sensory and regulatory protein-encoding genes is in place, as are genes necessary to prevent and respond to oxidative stress. Title: Genome sequence of Babesia bovis and comparative analysis of apicomplexan hemoprotozoa Brayton KA, Lau AO, Herndon DR, Hannick L, Kappmeyer LS, Berens SJ, Bidwell SL, Brown WC, Crabtree J and Nene VM <18 more author(s)> Brayton KA, Lau AO, Herndon DR, Hannick L, Kappmeyer LS, Berens SJ, Bidwell SL, Brown WC, Crabtree J, Fadrosh D, Feldblum T, Forberger HA, Haas BJ, Howell JM, Khouri H, Koo H, Mann DJ, Norimine J, Paulsen IT, Radune D, Ren Q, Smith RK, Jr., Suarez CE, White O, Wortman JR, Knowles DP, Jr., McElwain TF, Nene VM (- 18) Ref: PLoS Pathog, 3:1401, 2007 : PubMed ESTHER: Brayton_2007_PLoS.Pathog_3_1401 PubMedSearch: Brayton 2007 PLoS.Pathog 3 1401 PubMedID: 17953480 Gene_locus related to this paper: babbo-a7amu4, babbo-a7as90, babbo-a7au28, babbo-a7avh4 Abstract Babesia bovis is an apicomplexan tick-transmitted pathogen of cattle imposing a global risk and severe constraints to livestock health and economic development. The complete genome sequence was undertaken to facilitate vaccine antigen discovery, and to allow for comparative analysis with the related apicomplexan hemoprotozoa Theileria parva and Plasmodium falciparum. At 8.2 Mbp, the B. bovis genome is similar in size to that of Theileria spp. Structural features of the B. bovis and T. parva genomes are remarkably similar, and extensive synteny is present despite several chromosomal rearrangements. In contrast, B. bovis and P. falciparum, which have similar clinical and pathological features, have major differences in genome size, chromosome number, and gene complement. Chromosomal synteny with P. falciparum is limited to microregions. The B. bovis genome sequence has allowed wide scale analyses of the polymorphic variant erythrocyte surface antigen protein (ves1 gene) family that, similar to the P. falciparum var genes, is postulated to play a role in cytoadhesion, sequestration, and immune evasion. The approximately 150 ves1 genes are found in clusters that are distributed throughout each chromosome, with an increased concentration adjacent to a physical gap on chromosome 1 that contains multiple ves1-like sequences. ves1 clusters are frequently linked to a novel family of variant genes termed smorfs that may themselves contribute to immune evasion, may play a role in variant erythrocyte surface antigen protein biology, or both. Initial expression analysis of ves1 and smorf genes indicates coincident transcription of multiple variants. B. bovis displays a limited metabolic potential, with numerous missing pathways, including two pathways previously described for the P. falciparum apicoplast. This reduced metabolic potential is reflected in the B. bovis apicoplast, which appears to have fewer nuclear genes targeted to it than other apicoplast containing organisms. Finally, comparative analyses have identified several novel vaccine candidates including a positional homolog of p67 and SPAG-1, Theileria sporozoite antigens targeted for vaccine development. The genome sequence provides a greater understanding of B. bovis metabolism and potential avenues for drug therapies and vaccine development. Title: The Chlamydomonas genome reveals the evolution of key animal and plant functions Merchant SS, Prochnik SE, Vallon O, Harris EH, Karpowicz SJ, Witman GB, Terry A, Salamov A, Fritz-Laylin LK and Grossman AR <107 more author(s)> Merchant SS, Prochnik SE, Vallon O, Harris EH, Karpowicz SJ, Witman GB, Terry A, Salamov A, Fritz-Laylin LK, Marechal-Drouard L, Marshall WF, Qu LH, Nelson DR, Sanderfoot AA, Spalding MH, Kapitonov VV, Ren Q, Ferris P, Lindquist E, Shapiro H, Lucas SM, Grimwood J, Schmutz J, Cardol P, Cerutti H, Chanfreau G, Chen CL, Cognat V, Croft MT, Dent R, Dutcher S, Fernandez E, Fukuzawa H, Gonzalez-Ballester D, Gonzalez-Halphen D, Hallmann A, Hanikenne M, Hippler M, Inwood W, Jabbari K, Kalanon M, Kuras R, Lefebvre PA, Lemaire SD, Lobanov AV, Lohr M, Manuell A, Meier I, Mets L, Mittag M, Mittelmeier T, Moroney JV, Moseley J, Napoli C, Nedelcu AM, Niyogi K, Novoselov SV, Paulsen IT, Pazour G, Purton S, Ral JP, Riano-Pachon DM, Riekhof W, Rymarquis L, Schroda M, Stern D, Umen J, Willows R, Wilson N, Zimmer SL, Allmer J, Balk J, Bisova K, Chen CJ, Elias M, Gendler K, Hauser C, Lamb MR, Ledford H, Long JC, Minagawa J, Page MD, Pan J, Pootakham W, Roje S, Rose A, Stahlberg E, Terauchi AM, Yang P, Ball S, Bowler C, Dieckmann CL, Gladyshev VN, Green P, Jorgensen R, Mayfield S, Mueller-Roeber B, Rajamani S, Sayre RT, Brokstein P, Dubchak I, Goodstein D, Hornick L, Huang YW, Jhaveri J, Luo Y, Martinez D, Ngau WC, Otillar B, Poliakov A, Porter A, Szajkowski L, Werner G, Zhou K, Grigoriev IV, Rokhsar DS, Grossman AR (- 107) Ref: Science, 318:245, 2007 : PubMed ESTHER: Merchant_2007_Science_318_245 PubMedSearch: Merchant 2007 Science 318 245 PubMedID: 17932292 Gene_locus related to this paper: chlre-a0a2k3e2k6, chlre-a8hmd4, chlre-a8hqa9, chlre-a8htq0, chlre-a8hus6.1, chlre-a8hus6.2, chlre-a8icg4, chlre-a8iwm0, chlre-a8ize5, chlre-a8j2s9, chlre-a8j5w6, chlre-a8j7f8, chlre-a8j8u9, chlre-a8j8v0, chlre-a8j9u6, chlre-a8j143, chlre-a8j248, chlre-a8jd32, chlre-a8jd42, chlre-a8jgj2, chlre-a8jhc8, chlre-a8jhe5, chlre-a8iwj1, chlre-a8j7d5, chlre-a0a2k3dii0 Abstract Chlamydomonas reinhardtii is a unicellular green alga whose lineage diverged from land plants over 1 billion years ago. It is a model system for studying chloroplast-based photosynthesis, as well as the structure, assembly, and function of eukaryotic flagella (cilia), which were inherited from the common ancestor of plants and animals, but lost in land plants. We sequenced the approximately 120-megabase nuclear genome of Chlamydomonas and performed comparative phylogenomic analyses, identifying genes encoding uncharacterized proteins that are likely associated with the function and biogenesis of chloroplasts or eukaryotic flagella. Analyses of the Chlamydomonas genome advance our understanding of the ancestral eukaryotic cell, reveal previously unknown genes associated with photosynthetic and flagellar functions, and establish links between ciliopathy and the composition and function of flagella. 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: Genome sequence of Aedes aegypti, a major arbovirus vector Nene V, Wortman JR, Lawson D, Haas B, Kodira C, Tu ZJ, Loftus B, Xi Z, Megy K and Severson DW <85 more author(s)> Nene V, Wortman JR, Lawson D, Haas B, Kodira C, Tu ZJ, Loftus B, Xi Z, Megy K, Grabherr M, Ren Q, Zdobnov EM, Lobo NF, Campbell KS, Brown SE, Bonaldo MF, Zhu J, Sinkins SP, Hogenkamp DG, Amedeo P, Arensburger P, Atkinson PW, Bidwell S, Biedler J, Birney E, Bruggner RV, Costas J, Coy MR, Crabtree J, Crawford M, Debruyn B, Decaprio D, Eiglmeier K, Eisenstadt E, El-Dorry H, Gelbart WM, Gomes SL, Hammond M, Hannick LI, Hogan JR, Holmes MH, Jaffe D, Johnston JS, Kennedy RC, Koo H, Kravitz S, Kriventseva EV, Kulp D, LaButti K, Lee E, Li S, Lovin DD, Mao C, Mauceli E, Menck CF, Miller JR, Montgomery P, Mori A, Nascimento AL, Naveira HF, Nusbaum C, O'Leary S, Orvis J, Pertea M, Quesneville H, Reidenbach KR, Rogers YH, Roth CW, Schneider JR, Schatz M, Shumway M, Stanke M, Stinson EO, Tubio JM, Vanzee JP, Verjovski-Almeida S, Werner D, White O, Wyder S, Zeng Q, Zhao Q, Zhao Y, Hill CA, Raikhel AS, Soares MB, Knudson DL, Lee NH, Galagan J, Salzberg SL, Paulsen IT, Dimopoulos G, Collins FH, Birren B, Fraser-Liggett CM, Severson DW (- 85) Ref: Science, 316:1718, 2007 : PubMed ESTHER: Nene_2007_Science_316_1718 PubMedSearch: Nene 2007 Science 316 1718 PubMedID: 17510324 Gene_locus related to this paper: aedae-ACHE, aedae-ACHE1, aedae-glita, aedae-q0iea6, aedae-q0iev6, aedae-q0ifn6, aedae-q0ifn8, aedae-q0ifn9, aedae-q0ifp0, aedae-q0ig41, aedae-q1dgl0, aedae-q1dh03, aedae-q1dh19, aedae-q1hqe6, aedae-Q8ITU8, aedae-Q8MMJ6, aedae-Q8T9V6, aedae-q16e91, aedae-q16f04, aedae-q16f25, aedae-q16f26, aedae-q16f28, aedae-q16f29, aedae-q16f30, aedae-q16gq5, aedae-q16iq5, aedae-q16je0, aedae-q16je1, aedae-q16je2, aedae-q16ks8, aedae-q16lf2, aedae-q16lv6, aedae-q16m61, aedae-q16mc1, aedae-q16mc6, aedae-q16mc7, aedae-q16md1, aedae-q16ms7, aedae-q16nk5, aedae-q16rl5, aedae-q16rz9, aedae-q16si8, aedae-q16t49, aedae-q16wf1, aedae-q16x18, aedae-q16xp8, aedae-q16xu6, aedae-q16xw5, aedae-q16xw6, aedae-q16y04, aedae-q16y05, aedae-q16y06, aedae-q16y07, aedae-q16y39, aedae-q16y40, aedae-q16yg4, aedae-q16z03, aedae-q17aa7, aedae-q17av1, aedae-q17av2, aedae-q17av3, aedae-q17av4, aedae-q17b28, aedae-q17b29, aedae-q17b30, aedae-q17b31, aedae-q17b32, aedae-q17bm3, aedae-q17bm4, aedae-q17bv7, aedae-q17c44, aedae-q17cz1, aedae-q17d32, aedae-q17g39, aedae-q17g40, aedae-q17g41, aedae-q17g42, aedae-q17g43, aedae-q17g44, aedae-q17gb8, aedae-q17gr3, aedae-q17if7, aedae-q17if9, aedae-q17ig1, aedae-q17ig2, aedae-q17is4, aedae-q17l09, aedae-q17m26, aedae-q17mg9, aedae-q17mv4, aedae-q17mv5, aedae-q17mv6, aedae-q17mv7, aedae-q17mw8, aedae-q17mw9, aedae-q17nw5, aedae-q17nx5, aedae-q17pa4, aedae-q17q69, aedae-q170k7, aedae-q171y4, aedae-q172e0, aedae-q176i8, aedae-q176j0, aedae-q177k1, aedae-q177k2, aedae-q177l9, aedae-j9hic3, aedae-q179r9, aedae-u483, aedae-j9hj23, aedae-q17d68, aedae-q177c7, aedae-q0ifp1, aedae-a0a1s4fx83, aedae-a0a1s4g2m0, aedae-q1hr49 Abstract We present a draft sequence of the genome of Aedes aegypti, the primary vector for yellow fever and dengue fever, which at approximately 1376 million base pairs is about 5 times the size of the genome of the malaria vector Anopheles gambiae. Nearly 50% of the Ae. aegypti genome consists of transposable elements. These contribute to a factor of approximately 4 to 6 increase in average gene length and in sizes of intergenic regions relative to An. gambiae and Drosophila melanogaster. Nonetheless, chromosomal synteny is generally maintained among all three insects, although conservation of orthologous gene order is higher (by a factor of approximately 2) between the mosquito species than between either of them and the fruit fly. An increase in genes encoding odorant binding, cytochrome P450, and cuticle domains relative to An. gambiae suggests that members of these protein families underpin some of the biological differences between the two mosquito species. Title: Comparative genomic evidence for a close relationship between the dimorphic prosthecate bacteria Hyphomonas neptunium and Caulobacter crescentus Badger JH, Hoover TR, Brun YV, Weiner RM, Laub MT, Alexandre G, Mrazek J, Ren Q, Paulsen IT and Ward NL <19 more author(s)> Badger JH, Hoover TR, Brun YV, Weiner RM, Laub MT, Alexandre G, Mrazek J, Ren Q, Paulsen IT, Nelson KE, Khouri HM, Radune D, Sosa J, Dodson RJ, Sullivan SA, Rosovitz MJ, Madupu R, Brinkac LM, Durkin AS, Daugherty SC, Kothari SP, Giglio MG, Zhou L, Haft DH, Selengut JD, Davidsen TM, Yang Q, Zafar N, Ward NL (- 19) Ref: Journal of Bacteriology, 188:6841, 2006 : PubMed ESTHER: Badger_2006_J.Bacteriol_188_6841 PubMedSearch: Badger 2006 J.Bacteriol 188 6841 PubMedID: 16980487 Gene_locus related to this paper: hypna-q0bwt8, hypna-q0bwv5, hypna-q0bww7, hypna-q0bxb2, hypna-q0bxr5, hypna-q0by84, hypna-q0byl3, hypna-q0bz23, hypna-q0bzi5, hypna-q0c0f7, hypna-q0c0f8, hypna-q0c2v8, hypna-q0c2w1, hypna-q0c2w4, hypna-q0c3g0, hypna-q0c4j0, hypna-q0c4n1, hypna-q0c4q9, hypna-q0c4v5, hypna-q0c386, hypna-q0c539, hypna-q0c611 Abstract The dimorphic prosthecate bacteria (DPB) are alpha-proteobacteria that reproduce in an asymmetric manner rather than by binary fission and are of interest as simple models of development. Prior to this work, the only member of this group for which genome sequence was available was the model freshwater organism Caulobacter crescentus. Here we describe the genome sequence of Hyphomonas neptunium, a marine member of the DPB that differs from C. crescentus in that H. neptunium uses its stalk as a reproductive structure. Genome analysis indicates that this organism shares more genes with C. crescentus than it does with Silicibacter pomeroyi (a closer relative according to 16S rRNA phylogeny), that it relies upon a heterotrophic strategy utilizing a wide range of substrates, that its cell cycle is likely to be regulated in a similar manner to that of C. crescentus, and that the outer membrane complements of H. neptunium and C. crescentus are remarkably similar. H. neptunium swarmer cells are highly motile via a single polar flagellum. With the exception of cheY and cheR, genes required for chemotaxis were absent in the H. neptunium genome. Consistent with this observation, H. neptunium swarmer cells did not respond to any chemotactic stimuli that were tested, which suggests that H. neptunium motility is a random dispersal mechanism for swarmer cells rather than a stimulus-controlled navigation system for locating specific environments. In addition to providing insights into bacterial development, the H. neptunium genome will provide an important resource for the study of other interesting biological processes including chromosome segregation, polar growth, and cell aging. Title: Exopolysaccharide-associated protein sorting in environmental organisms: the PEP-CTERM/EpsH system. Application of a novel phylogenetic profiling heuristic Haft DH, Paulsen IT, Ward N, Selengut JD Ref: BMC Biol, 4:29, 2006 : PubMed ESTHER: Haft_2006_BMC.Biol_4_29 PubMedSearch: Haft 2006 BMC.Biol 4 29 PubMedID: 16930487 Abstract BACKGROUND: Protein translocation to the proper cellular destination may be guided by various classes of sorting signals recognizable in the primary sequence. Detection in some genomes, but not others, may reveal sorting system components by comparison of the phylogenetic profile of the class of sorting signal to that of various protein families. 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: Genome sequence of Synechococcus CC9311: Insights into adaptation to a coastal environment Palenik B, Ren Q, Dupont CL, Myers GS, Heidelberg JF, Badger JH, Madupu R, Nelson WC, Brinkac LM and Paulsen IT <7 more author(s)> Palenik B, Ren Q, Dupont CL, Myers GS, Heidelberg JF, Badger JH, Madupu R, Nelson WC, Brinkac LM, Dodson RJ, Durkin AS, Daugherty SC, Sullivan SA, Khouri H, Mohamoud Y, Halpin R, Paulsen IT (- 7) Ref: Proc Natl Acad Sci U S A, 103:13555, 2006 : PubMed ESTHER: Palenik_2006_Proc.Natl.Acad.Sci.U.S.A_103_13555 PubMedSearch: Palenik 2006 Proc.Natl.Acad.Sci.U.S.A 103 13555 PubMedID: 16938853 Gene_locus related to this paper: syns3-q0i8r7, syns3-q0i9w2, syns3-q0i996, syns3-q0ia13, syns3-q0ia55, syns3-q0ib73, syns3-q0ibm2, syns3-q0ibp1, syns3-q0iby1, syns9-q3ax89, syns3-q0ibv4 Abstract Coastal aquatic environments are typically more highly productive and dynamic than open ocean ones. Despite these differences, cyanobacteria from the genus Synechococcus are important primary producers in both types of ecosystems. We have found that the genome of a coastal cyanobacterium, Synechococcus sp. strain CC9311, has significant differences from an open ocean strain, Synechococcus sp. strain WH8102, and these are consistent with the differences between their respective environments. CC9311 has a greater capacity to sense and respond to changes in its (coastal) environment. It has a much larger capacity to transport, store, use, or export metals, especially iron and copper. In contrast, phosphate acquisition seems less important, consistent with the higher concentration of phosphate in coastal environments. CC9311 is predicted to have differences in its outer membrane lipopolysaccharide, and this may be characteristic of the speciation of some cyanobacterial groups. In addition, the types of potentially horizontally transferred genes are markedly different between the coastal and open ocean genomes and suggest a more prominent role for phages in horizontal gene transfer in oligotrophic environments. Title: The genome of deep-sea vent chemolithoautotroph Thiomicrospira crunogena XCL-2 Scott KM, Sievert SM, Abril FN, Ball LA, Barrett CJ, Blake RA, Boller AJ, Chain PS, Clark JA and Zeruth GT <33 more author(s)> Scott KM, Sievert SM, Abril FN, Ball LA, Barrett CJ, Blake RA, Boller AJ, Chain PS, Clark JA, Davis CR, Detter C, Do KF, Dobrinski KP, Faza BI, Fitzpatrick KA, Freyermuth SK, Harmer TL, Hauser LJ, Hugler M, Kerfeld CA, Klotz MG, Kong WW, Land M, Lapidus A, Larimer FW, Longo DL, Lucas S, Malfatti SA, Massey SE, Martin DD, McCuddin Z, Meyer F, Moore JL, Ocampo LH, Jr., Paul JH, Paulsen IT, Reep DK, Ren Q, Ross RL, Sato PY, Thomas P, Tinkham LE, Zeruth GT (- 33) Ref: PLoS Biol, 4:e383, 2006 : PubMed ESTHER: Scott_2006_PLoS.Biol_4_e383 PubMedSearch: Scott 2006 PLoS.Biol 4 e383 PubMedID: 17105352 Gene_locus related to this paper: thicr-q31fm2, thicr-q31ih5 Abstract Presented here is the complete genome sequence of Thiomicrospira crunogena XCL-2, representative of ubiquitous chemolithoautotrophic sulfur-oxidizing bacteria isolated from deep-sea hydrothermal vents. This gammaproteobacterium has a single chromosome (2,427,734 base pairs), and its genome illustrates many of the adaptations that have enabled it to thrive at vents globally. It has 14 methyl-accepting chemotaxis protein genes, including four that may assist in positioning it in the redoxcline. A relative abundance of coding sequences (CDSs) encoding regulatory proteins likely control the expression of genes encoding carboxysomes, multiple dissolved inorganic nitrogen and phosphate transporters, as well as a phosphonate operon, which provide this species with a variety of options for acquiring these substrates from the environment. Thiom. crunogena XCL-2 is unusual among obligate sulfur-oxidizing bacteria in relying on the Sox system for the oxidation of reduced sulfur compounds. The genome has characteristics consistent with an obligately chemolithoautotrophic lifestyle, including few transporters predicted to have organic allocrits, and Calvin-Benson-Bassham cycle CDSs scattered throughout the genome. Title: Genome sequence of Theileria parva, a bovine pathogen that transforms lymphocytes Gardner MJ, Bishop R, Shah T, de Villiers EP, Carlton JM, Hall N, Ren Q, Paulsen IT, Pain A and Nene V <34 more author(s)> Gardner MJ, Bishop R, Shah T, de Villiers EP, Carlton JM, Hall N, Ren Q, Paulsen IT, Pain A, Berriman M, Wilson RJ, Sato S, Ralph SA, Mann DJ, Xiong Z, Shallom SJ, Weidman J, Jiang L, Lynn J, Weaver B, Shoaibi A, Domingo AR, Wasawo D, Crabtree J, Wortman JR, Haas B, Angiuoli SV, Creasy TH, Lu C, Suh B, Silva JC, Utterback TR, Feldblyum TV, Pertea M, Allen J, Nierman WC, Taracha EL, Salzberg SL, White OR, Fitzhugh HA, Morzaria S, Venter JC, Fraser CM, Nene V (- 34) Ref: Science, 309:134, 2005 : PubMed ESTHER: Gardner_2005_Science_309_134 PubMedSearch: Gardner 2005 Science 309 134 PubMedID: 15994558 Gene_locus related to this paper: thepa-q4mzr2, thepa-q4n0b4, thepa-q4n2i4, thepa-q4n4i8, thepa-q4n5d6, thepa-q4n5m4, thepa-q4n006, thepa-q4n9g7, thepa-q4n315, thepa-q4n349, thepa-q4n803 Abstract We report the genome sequence of Theileria parva, an apicomplexan pathogen causing economic losses to smallholder farmers in Africa. The parasite chromosomes exhibit limited conservation of gene synteny with Plasmodium falciparum, and its plastid-like genome represents the first example where all apicoplast genes are encoded on one DNA strand. We tentatively identify proteins that facilitate parasite segregation during host cell cytokinesis and contribute to persistent infection of transformed host cells. Several biosynthetic pathways are incomplete or absent, suggesting substantial metabolic dependence on the host cell. One protein family that may generate parasite antigenic diversity is not telomere-associated. 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: 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: 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: 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: Phylogenomics of the reproductive parasite Wolbachia pipientis wMel: a streamlined genome overrun by mobile genetic elements Wu M, Sun LV, Vamathevan J, Riegler M, Deboy R, Brownlie JC, McGraw EA, Martin W, Esser C and Eisen JA <20 more author(s)> Wu M, Sun LV, Vamathevan J, Riegler M, Deboy R, Brownlie JC, McGraw EA, Martin W, Esser C, Ahmadinejad N, Wiegand C, Madupu R, Beanan MJ, Brinkac LM, Daugherty SC, Durkin AS, Kolonay JF, Nelson WC, Mohamoud Y, Lee P, Berry K, Young MB, Utterback T, Weidman J, Nierman WC, Paulsen IT, Nelson KE, Tettelin H, O'Neill SL, Eisen JA (- 20) Ref: PLoS Biol, 2:E69, 2004 : PubMed ESTHER: Wu_2004_PLoS.Biol_2_E69 PubMedSearch: Wu 2004 PLoS.Biol 2 E69 PubMedID: 15024419 Gene_locus related to this paper: wolpm-q73gf0, wolpm-q73gx7 Abstract The complete sequence of the 1,267,782 bp genome of Wolbachia pipientis wMel, an obligate intracellular bacteria of Drosophila melanogaster, has been determined. Wolbachia, which are found in a variety of invertebrate species, are of great interest due to their diverse interactions with different hosts, which range from many forms of reproductive parasitism to mutualistic symbioses. Analysis of the wMel genome, in particular phylogenomic comparisons with other intracellular bacteria, has revealed many insights into the biology and evolution of wMel and Wolbachia in general. For example, the wMel genome is unique among sequenced obligate intracellular species in both being highly streamlined and containing very high levels of repetitive DNA and mobile DNA elements. This observation, coupled with multiple evolutionary reconstructions, suggests that natural selection is somewhat inefficient in wMel, most likely owing to the occurrence of repeated population bottlenecks. Genome analysis predicts many metabolic differences with the closely related Rickettsia species, including the presence of intact glycolysis and purine synthesis, which may compensate for an inability to obtain ATP directly from its host, as Rickettsia can. Other discoveries include the apparent inability of wMel to synthesize lipopolysaccharide and the presence of the most genes encoding proteins with ankyrin repeat domains of any prokaryotic genome yet sequenced. Despite the ability of wMel to infect the germline of its host, we find no evidence for either recent lateral gene transfer between wMel and D. melanogaster or older transfers between Wolbachia and any host. Evolutionary analysis further supports the hypothesis that mitochondria share a common ancestor with the alpha-Proteobacteria, but shows little support for the grouping of mitochondria with species in the order Rickettsiales. With the availability of the complete genomes of both species and excellent genetic tools for the host, the wMel-D. melanogaster symbiosis is now an ideal system for studying the biology and evolution of Wolbachia infections. 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: Genome sequence of Chlamydophila caviae (Chlamydia psittaci GPIC): examining the role of niche-specific genes in the evolution of the Chlamydiaceae Read TD, Myers GS, Brunham RC, Nelson WC, Paulsen IT, Heidelberg J, Holtzapple E, Khouri H, Federova NB and Fraser CM <11 more author(s)> Read TD, Myers GS, Brunham RC, Nelson WC, Paulsen IT, Heidelberg J, Holtzapple E, Khouri H, Federova NB, Carty HA, Umayam LA, Haft DH, Peterson J, Beanan MJ, White O, Salzberg SL, Hsia RC, McClarty G, Rank RG, Bavoil PM, Fraser CM (- 11) Ref: Nucleic Acids Research, 31:2134, 2003 : PubMed ESTHER: Read_2003_Nucleic.Acids.Res_31_2134 PubMedSearch: Read 2003 Nucleic.Acids.Res 31 2134 PubMedID: 12682364 Gene_locus related to this paper: chlca-CCA00443, chlca-CCA00510, chlca-CCA00609, chlca-CCA00614, chlcv-p94660 Abstract The genome of Chlamydophila caviae (formerly Chlamydia psittaci, GPIC isolate) (1 173 390 nt with a plasmid of 7966 nt) was determined, representing the fourth species with a complete genome sequence from the Chlamydiaceae family of obligate intracellular bacterial pathogens. Of 1009 annotated genes, 798 were conserved in all three other completed Chlamydiaceae genomes. The C.caviae genome contains 68 genes that lack orthologs in any other completed chlamydial genomes, including tryptophan and thiamine biosynthesis determinants and a ribose-phosphate pyrophosphokinase, the product of the prsA gene. Notable amongst these was a novel member of the virulence-associated invasin/intimin family (IIF) of Gram-negative bacteria. Intriguingly, two authentic frameshift mutations in the ORF indicate that this gene is not functional. Many of the unique genes are found in the replication termination region (RTR or plasticity zone), an area of frequent symmetrical inversion events around the replication terminus shown to be a hotspot for genome variation in previous genome sequencing studies. In C.caviae, the RTR includes several loci of particular interest including a large toxin gene and evidence of ancestral insertion(s) of a bacteriophage. This toxin gene, not present in Chlamydia pneumoniae, is a member of the YopT effector family of type III-secreted cysteine proteases. One gene cluster (guaBA-add) in the RTR is much more similar to orthologs in Chlamydia muridarum than those in the phylogenetically closest species C.pneumoniae, suggesting the possibility of horizontal transfer of genes between the rodent-associated Chlamydiae. With most genes observed in the other chlamydial genomes represented, C.caviae provides a good model for the Chlamydiaceae and a point of comparison against the human atherosclerosis-associated C.pneumoniae. This crucial addition to the set of completed Chlamydiaceae genome sequences is enabling dissection of the roles played by niche-specific genes in these important bacterial pathogens. 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: The complete genome sequence of Chlorobium tepidum TLS, a photosynthetic, anaerobic, green-sulfur bacterium Eisen JA, Nelson KE, Paulsen IT, Heidelberg JF, Wu M, Dodson RJ, Deboy R, Gwinn ML, Nelson WC and Fraser CM <25 more author(s)> Eisen JA, Nelson KE, Paulsen IT, Heidelberg JF, Wu M, Dodson RJ, Deboy R, Gwinn ML, Nelson WC, Haft DH, Hickey EK, Peterson JD, Durkin AS, Kolonay JL, Yang F, Holt I, Umayam LA, Mason T, Brenner M, Shea TP, Parksey D, Nierman WC, Feldblyum TV, Hansen CL, Craven MB, Radune D, Vamathevan J, Khouri H, White O, Gruber TM, Ketchum KA, Venter JC, Tettelin H, Bryant DA, Fraser CM (- 25) Ref: Proceedings of the National Academy of Sciences of the United States of America, 99:9509, 2002 : PubMed ESTHER: Eisen_2002_Proc.Natl.Acad.Sci.U.S.A_99_9509 PubMedSearch: Eisen 2002 Proc.Natl.Acad.Sci.U.S.A 99 9509 PubMedID: 12093901 Gene_locus related to this paper: chlte-CT0177, chlte-CT0524, chlte-CT0717, chlte-CT0947, chlte-CT1208, chlte-CT1253, chlte-CT1301, chlte-CT1312, chlte-CT1856, chlte-CT1908, chlte-CT2087, chlte-CT2271, chlte-MENH, chlte-MET2, chlte-q4w546, chlte-q8kgb8 Abstract The complete genome of the green-sulfur eubacterium Chlorobium tepidum TLS was determined to be a single circular chromosome of 2,154,946 bp. This represents the first genome sequence from the phylum Chlorobia, whose members perform anoxygenic photosynthesis by the reductive tricarboxylic acid cycle. Genome comparisons have identified genes in C. tepidum that are highly conserved among photosynthetic species. Many of these have no assigned function and may play novel roles in photosynthesis or photobiology. Phylogenomic analysis reveals likely duplications of genes involved in biosynthetic pathways for photosynthesis and the metabolism of sulfur and nitrogen as well as strong similarities between metabolic processes in C. tepidum and many Archaeal species. Title: Genome sequence of the human malaria parasite Plasmodium falciparum Gardner MJ, Hall N, Fung E, White O, Berriman M, Hyman RW, Carlton JM, Pain A, Nelson KE and Barrell B <35 more author(s)> Gardner MJ, Hall N, Fung E, White O, Berriman M, Hyman RW, Carlton JM, Pain A, Nelson KE, Bowman S, Paulsen IT, James K, Eisen JA, Rutherford K, Salzberg SL, Craig A, Kyes S, Chan MS, Nene V, Shallom SJ, Suh B, Peterson J, Angiuoli S, Pertea M, Allen J, Selengut J, Haft D, Mather MW, Vaidya AB, Martin DM, Fairlamb AH, Fraunholz MJ, Roos DS, Ralph SA, McFadden GI, Cummings LM, Subramanian GM, Mungall C, Venter JC, Carucci DJ, Hoffman SL, Newbold C, Davis RW, Fraser CM, Barrell B (- 35) Ref: Nature, 419:498, 2002 : PubMed ESTHER: Gardner_2002_Nature_419_498 PubMedSearch: Gardner 2002 Nature 419 498 PubMedID: 12368864 Gene_locus related to this paper: plaf7-c0h4q4, plaf7-q8i5y6, plaf7-q8iik5, plafa-PF10.0018, plafa-PF10.0020, plafa-PF10.0379, plafa-PF11.0211, plafa-PF11.0276, plafa-PF11.0441, plafa-PF14.0015, plafa-PF14.0017, plafa-PF14.0099, plafa-PF14.0250, plafa-PF14.0395, plafa-PF14.0737, plafa-PF14.0738, plafa-PFL2530W Abstract The parasite Plasmodium falciparum is responsible for hundreds of millions of cases of malaria, and kills more than one million African children annually. Here we report an analysis of the genome sequence of P. falciparum clone 3D7. The 23-megabase nuclear genome consists of 14 chromosomes, encodes about 5,300 genes, and is the most (A + T)-rich genome sequenced to date. Genes involved in antigenic variation are concentrated in the subtelomeric regions of the chromosomes. Compared to the genomes of free-living eukaryotic microbes, the genome of this intracellular parasite encodes fewer enzymes and transporters, but a large proportion of genes are devoted to immune evasion and host-parasite interactions. Many nuclear-encoded proteins are targeted to the apicoplast, an organelle involved in fatty-acid and isoprenoid metabolism. The genome sequence provides the foundation for future studies of this organism, and is being exploited in the search for new drugs and vaccines to fight malaria. 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. Title: The genome of the natural genetic engineer Agrobacterium tumefaciens C58 Wood DW, Setubal JC, Kaul R, Monks DE, Kitajima JP, Okura VK, Zhou Y, Chen L, Wood GE and Nester EW <41 more author(s)> Wood DW, Setubal JC, Kaul R, Monks DE, Kitajima JP, Okura VK, Zhou Y, Chen L, Wood GE, Almeida NF, Jr., Woo L, Chen Y, Paulsen IT, Eisen JA, Karp PD, Bovee D, Sr., Chapman P, Clendenning J, Deatherage G, Gillet W, Grant C, Kutyavin T, Levy R, Li MJ, McClelland E, Palmieri A, Raymond C, Rouse G, Saenphimmachak C, Wu Z, Romero P, Gordon D, Zhang S, Yoo H, Tao Y, Biddle P, Jung M, Krespan W, Perry M, Gordon-Kamm B, Liao L, Kim S, Hendrick C, Zhao ZY, Dolan M, Chumley F, Tingey SV, Tomb JF, Gordon MP, Olson MV, Nester EW (- 41) Ref: Science, 294:2317, 2001 : PubMed ESTHER: Wood_2001_Science_294_2317 PubMedSearch: Wood 2001 Science 294 2317 PubMedID: 11743193 Gene_locus related to this paper: agrt5-a9cf94, agrt5-a9cfa9, agrt5-a9cfs8, agrt5-a9cfu7, agrt5-a9cie7, agrt5-a9cj11, agrt5-a9cjp2, agrt5-a9cki2, agrt5-a9ckr2, agrt5-a9ckt2, agrt5-a9cle4, agrt5-a9clq8, agrt5-a9clq9, agrt5-q7cx24, agrt5-q7d1j0, agrt5-q7d1j3, agrt5-q7d3m5, agrt5-y5261, agrtu-ACVB, agrtu-ATTS, agrtu-ATU0253, agrtu-ATU0403, agrtu-ATU0841, agrtu-ATU1045, agrtu-ATU1102, agrtu-ATU1572, agrtu-ATU1617, agrtu-ATU1826, agrtu-ATU1842, agrtu-ATU2061, agrtu-ATU2126, agrtu-ATU2171, agrtu-ATU2409, agrtu-ATU2452, agrtu-ATU2481, agrtu-ATU2497, agrtu-ATU2576, agrtu-ATU3428, agrtu-ATU3651, agrtu-ATU3652, agrtu-ATU4238, agrtu-ATU5190, agrtu-ATU5193, agrtu-ATU5275, agrtu-ATU5296, agrtu-ATU5348, agrtu-ATU5389, agrtu-ATU5446, agrtu-ATU5495, agrtu-CPO, agrtu-DHAA, agrtu-DLHH, agrtu-EPHA, agrtu-GRST, agrtu-PCA, agrtu-PCAD, agrtu-PHBC, agrtu-PTRB, agrt5-a9cji8 Abstract The 5.67-megabase genome of the plant pathogen Agrobacterium tumefaciens C58 consists of a circular chromosome, a linear chromosome, and two plasmids. Extensive orthology and nucleotide colinearity between the genomes of A. tumefaciens and the plant symbiont Sinorhizobium meliloti suggest a recent evolutionary divergence. Their similarities include metabolic, transport, and regulatory systems that promote survival in the highly competitive rhizosphere; differences are apparent in their genome structure and virulence gene complement. Availability of the A. tumefaciens sequence will facilitate investigations into the molecular basis of pathogenesis and the evolutionary divergence of pathogenic and symbiotic lifestyles. Title: Complete genome sequence of Pseudomonas aeruginosa PAO1, an opportunistic pathogen Stover CK, Pham XQ, Erwin AL, Mizoguchi SD, Warrener P, Hickey MJ, Brinkman FS, Hufnagle WO, Kowalik DJ and Olson MV <21 more author(s)> Stover CK, Pham XQ, Erwin AL, Mizoguchi SD, Warrener P, Hickey MJ, Brinkman FS, Hufnagle WO, Kowalik DJ, Lagrou M, Garber RL, Goltry L, Tolentino E, Westbrock-Wadman S, Yuan Y, Brody LL, Coulter SN, Folger KR, Kas A, Larbig K, Lim R, Smith K, Spencer D, Wong GK, Wu Z, Paulsen IT, Reizer J, Saier MH, Hancock RE, Lory S, Olson MV (- 21) Ref: Nature, 406:959, 2000 : PubMed ESTHER: Stover_2000_Nature_406_959 PubMedSearch: Stover 2000 Nature 406 959 PubMedID: 10984043 Gene_locus related to this paper: pseae-clipa, pseae-CPO, pseae-metx, pseae-PA0201, pseae-PA0231, pseae-PA0308, pseae-PA0368, pseae-PA0480, pseae-PA0502, pseae-PA0543, pseae-PA0599, pseae-PA0829, pseae-PA1166, pseae-PA1211, pseae-PA1239, pseae-PA1291, pseae-PA1304, pseae-PA1510, pseae-PA1558, pseae-PA1597, pseae-PA1621, pseae-PA1622, pseae-PA1680, pseae-PA1771, pseae-PA1888, pseae-PA1907, pseae-PA1990, pseae-PA2086, pseae-PA2098, pseae-PA2168, pseae-PA2302, pseae-PA2411, pseae-PA2425, pseae-PA2451, pseae-PA2540, pseae-PA2682, pseae-PA2689, pseae-PA2745, pseae-PA2764, pseae-PA2927, pseae-PA2934, pseae-PA2949, pseae-PA3053, pseae-PA3132, pseae-PA3226, pseae-PA3301, pseae-PA3324, pseae-PA3327, pseae-PA3429, pseae-PA3509, pseae-PA3586, pseae-PA3628, pseae-PA3695, pseae-PA3734, pseae-PA3829, pseae-PA3859, pseae-PA3994, pseae-PA4008, pseae-PA4152, pseae-PA4440, pseae-PA4968, pseae-PA5080, pseae-PA5384, pseae-PA5513, pseae-PCHC, pseae-PCHF, pseae-PHAC1, pseae-PHAC2, pseae-phaD, pseae-phag, pseae-PVDD, pseae-q9i4b9, pseae-q9i538, pseae-rhla, pseae-Y2218, pseae-q9hyv3, pseae-q9i252, pseae-q9i6m9 Abstract Pseudomonas aeruginosa is a ubiquitous environmental bacterium that is one of the top three causes of opportunistic human infections. A major factor in its prominence as a pathogen is its intrinsic resistance to antibiotics and disinfectants. Here we report the complete sequence of P. aeruginosa strain PAO1. At 6.3 million base pairs, this is the largest bacterial genome sequenced, and the sequence provides insights into the basis of the versatility and intrinsic drug resistance of P. aeruginosa. Consistent with its larger genome size and environmental adaptability, P. aeruginosa contains the highest proportion of regulatory genes observed for a bacterial genome and a large number of genes involved in the catabolism, transport and efflux of organic compounds as well as four potential chemotaxis systems. We propose that the size and complexity of the P. aeruginosa genome reflect an evolutionary adaptation permitting it to thrive in diverse environments and resist the effects of a variety of antimicrobial substances. | |||||||
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