Author Report for: Sullivan SANo contact information in database for Sullivan SA
Tachibana S, Sullivan SA, Kawai S, Nakamura S, Kim HR, Goto N, Arisue N, Palacpac NM, Honma H and Tanabe K <14 more author(s)> Tachibana S, Sullivan SA, Kawai S, Nakamura S, Kim HR, Goto N, Arisue N, Palacpac NM, Honma H, Yagi M, Tougan T, Katakai Y, Kaneko O, Mita T, Kita K, Yasutomi Y, Sutton PL, Shakhbatyan R, Horii T, Yasunaga T, Barnwell JW, Escalante AA, Carlton JM, Tanabe K (- 14) Ref: Nat Genet, 44:1051, 2012 : PubMed ESTHER: Tachibana_2012_Nat.Genet_44_1051 PubMedSearch: Tachibana 2012 Nat.Genet 44 1051 PubMedID: 22863735 Gene_locus related to this paper: plavs-a5k3z4 Abstract P. cynomolgi, a malaria-causing parasite of Asian Old World monkeys, is the sister taxon of P. vivax, the most prevalent malaria-causing species in humans outside of Africa. Because P. cynomolgi shares many phenotypic, biological and genetic characteristics with P. vivax, we generated draft genome sequences for three P. cynomolgi strains and performed genomic analysis comparing them with the P. vivax genome, as well as with the genome of a third previously sequenced simian parasite, Plasmodium knowlesi. Here, we show that genomes of the monkey malaria clade can be characterized by copy-number variants (CNVs) in multigene families involved in evasion of the human immune system and invasion of host erythrocytes. We identify genome-wide SNPs, microsatellites and CNVs in the P. cynomolgi genome, providing a map of genetic variation that can be used to map parasite traits and study parasite populations. The sequencing of the P. cynomolgi genome is a critical step in developing a model system for P. vivax research and in counteracting the neglect of P. vivax. Title: Three genomes from the phylum Acidobacteria provide insight into the lifestyles of these microorganisms in soils Ward NL, Challacombe JF, Janssen PH, Henrissat B, Coutinho PM, Wu M, Xie G, Haft DH, Sait M and Kuske CR <36 more author(s)> Ward NL, Challacombe JF, Janssen PH, Henrissat B, Coutinho PM, Wu M, Xie G, Haft DH, Sait M, Badger J, Barabote RD, Bradley B, Brettin TS, Brinkac LM, Bruce D, Creasy T, Daugherty SC, Davidsen TM, DeBoy RT, Detter JC, Dodson RJ, Durkin AS, Ganapathy A, Gwinn-Giglio M, Han CS, Khouri H, Kiss H, Kothari SP, Madupu R, Nelson KE, Nelson WC, Paulsen I, Penn K, Ren Q, Rosovitz MJ, Selengut JD, Shrivastava S, Sullivan SA, Tapia R, Thompson LS, Watkins KL, Yang Q, Yu C, Zafar N, Zhou L, Kuske CR (- 36) Ref: Applied Environmental Microbiology, 75:2046, 2009 : PubMed ESTHER: Ward_2009_Appl.Environ.Microbiol_75_2046 PubMedSearch: Ward 2009 Appl.Environ.Microbiol 75 2046 PubMedID: 19201974 Gene_locus related to this paper: korve-q1ihr9, korve-q1ii02, korve-q1iit0, korve-q1ilk4, korve-q1imj9, korve-q1ims4, korve-q1iqj0, korve-q1isy7, korve-q1itj5, korve-q1itz6, korve-q1ivc8, acic5-c1f1u6, acic5-c1f2i7, acic5-c1f4m6, acic5-c1f4y4, acic5-c1f5a7, acic5-c1f5u2, acic5-c1f7a9, acic5-c1f7x6, acic5-c1f8y9, acic5-c1f9m2, acic5-c1f594, acic5-c1f609, acic5-c1f692, acic5-c1f970, acic5-c1fa52, korve-q1iiw2, korve-q1ivn9, solue-q01nb0, solue-q01qj6, solue-q01r37, solue-q01rq8, solue-q01rz0, solue-q01t44, solue-q01t57, solue-q01ts5, solue-q01tv4, solue-q01vd8, solue-q01vr3, solue-q01vw5, solue-q01w12, solue-q01wt9, solue-q01y40, solue-q01ym8, solue-q01z24, solue-q01z97, solue-q01zl4, solue-q01zm0, solue-q01zm5, solue-q01zm7, solue-q02aa4, solue-q02ab9, solue-q02b72, solue-q02bs8, solue-q02bt7, solue-q02cp0, solue-q02d61, solue-q020h3, solue-q020i8, solue-q021i6, solue-q022b1, solue-q022p8, solue-q022q2, solue-q022q3, solue-q022x2, solue-q022x5, solue-q022x6, solue-q022x8, solue-q023e7, solue-q024d9, solue-q025c1, solue-q026j1, solue-q026k6, solue-q026r6, solue-q027p2, solue-q027r8, solue-q01zt5, korve-q1itw6, solue-q01yh7, solue-q02ad6, korve-q1imj6, korve-q1iuf6, acic5-c1f891, solue-q026h7 Abstract The complete genomes of three strains from the phylum Acidobacteria were compared. Phylogenetic analysis placed them as a unique phylum. They share genomic traits with members of the Proteobacteria, the Cyanobacteria, and the Fungi. The three strains appear to be versatile heterotrophs. Genomic and culture traits indicate the use of carbon sources that span simple sugars to more complex substrates such as hemicellulose, cellulose, and chitin. The genomes encode low-specificity major facilitator superfamily transporters and high-affinity ABC transporters for sugars, suggesting that they are best suited to low-nutrient conditions. They appear capable of nitrate and nitrite reduction but not N(2) fixation or denitrification. The genomes contained numerous genes that encode siderophore receptors, but no evidence of siderophore production was found, suggesting that they may obtain iron via interaction with other microorganisms. The presence of cellulose synthesis genes and a large class of novel high-molecular-weight excreted proteins suggests potential traits for desiccation resistance, biofilm formation, and/or contribution to soil structure. Polyketide synthase and macrolide glycosylation genes suggest the production of novel antimicrobial compounds. Genes that encode a variety of novel proteins were also identified. The abundance of acidobacteria in soils worldwide and the breadth of potential carbon use by the sequenced strains suggest significant and previously unrecognized contributions to the terrestrial carbon cycle. Combining our genomic evidence with available culture traits, we postulate that cells of these isolates are long-lived, divide slowly, exhibit slow metabolic rates under low-nutrient conditions, and are well equipped to tolerate fluctuations in soil hydration. Title: Comparative genomics of the neglected human malaria parasite Plasmodium vivax Carlton JM, Adams JH, Silva JC, Bidwell SL, Lorenzi H, Caler E, Crabtree J, Angiuoli SV, Merino EF and Fraser-Liggett CM <30 more author(s)> Carlton JM, Adams JH, Silva JC, Bidwell SL, Lorenzi H, Caler E, Crabtree J, Angiuoli SV, Merino EF, Amedeo P, Cheng Q, Coulson RM, Crabb BS, Del Portillo HA, Essien K, Feldblyum TV, Fernandez-Becerra C, Gilson PR, Gueye AH, Guo X, Kang'a S, Kooij TW, Korsinczky M, Meyer EV, Nene V, Paulsen I, White O, Ralph SA, Ren Q, Sargeant TJ, Salzberg SL, Stoeckert CJ, Sullivan SA, Yamamoto MM, Hoffman SL, Wortman JR, Gardner MJ, Galinski MR, Barnwell JW, Fraser-Liggett CM (- 30) Ref: Nature, 455:757, 2008 : PubMed ESTHER: Carlton_2008_Nature_455_757 PubMedSearch: Carlton 2008 Nature 455 757 PubMedID: 18843361 Gene_locus related to this paper: plakh-b3lb44, plavi-a5kcq0, plavs-a5k2k6, plavs-a5k3z4, plavs-a5k4s6, plavs-a5k5e4, plavs-a5k7t5, plavs-a5k686, plavs-a5kaa1, plavs-a5kaa3, plavs-a5kas6, plavs-a5kcm2 Abstract The human malaria parasite Plasmodium vivax is responsible for 25-40% of the approximately 515 million annual cases of malaria worldwide. Although seldom fatal, the parasite elicits severe and incapacitating clinical symptoms and often causes relapses months after a primary infection has cleared. Despite its importance as a major human pathogen, P. vivax is little studied because it cannot be propagated continuously in the laboratory except in non-human primates. We sequenced the genome of P. vivax to shed light on its distinctive biological features, and as a means to drive development of new drugs and vaccines. Here we describe the synteny and isochore structure of P. vivax chromosomes, and show that the parasite resembles other malaria parasites in gene content and metabolic potential, but possesses novel gene families and potential alternative invasion pathways not recognized previously. Completion of the P. vivax genome provides the scientific community with a valuable resource that can be used to advance investigation into this neglected 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: Comparative genomics of emerging human ehrlichiosis agents Dunning Hotopp JC, Lin M, Madupu R, Crabtree J, Angiuoli SV, Eisen JA, Seshadri R, Ren Q, Wu M and Tettelin H <30 more author(s)> Dunning Hotopp JC, Lin M, Madupu R, Crabtree J, Angiuoli SV, Eisen JA, Seshadri R, Ren Q, Wu M, Utterback TR, Smith S, Lewis M, Khouri H, Zhang C, Niu H, Lin Q, Ohashi N, Zhi N, Nelson W, Brinkac LM, Dodson RJ, Rosovitz MJ, Sundaram J, Daugherty SC, Davidsen T, Durkin AS, Gwinn M, Haft DH, Selengut JD, Sullivan SA, Zafar N, Zhou L, Benahmed F, Forberger H, Halpin R, Mulligan S, Robinson J, White O, Rikihisa Y, Tettelin H (- 30) Ref: PLoS Genet, 2:e21, 2006 : PubMed ESTHER: Dunning Hotopp_2006_PLoS.Genet_2_e21 PubMedSearch: Dunning Hotopp 2006 PLoS.Genet 2 e21 PubMedID: 16482227 Gene_locus related to this paper: anapz-q2gj80, anapz-q2gle9, anapz-q2glf0, anapz-q2gln7, ehrch-q40iu0, ehrch-q40jj7, ehrcr-q2gfq9, neosm-q2gcq8, neosm-q2gdf2, neosm-q2gcn8, anapz-q2gk48, ehrcr-q2ggj6 Abstract Anaplasma (formerly Ehrlichia) phagocytophilum, Ehrlichia chaffeensis, and Neorickettsia (formerly Ehrlichia) sennetsu are intracellular vector-borne pathogens that cause human ehrlichiosis, an emerging infectious disease. We present the complete genome sequences of these organisms along with comparisons to other organisms in the Rickettsiales order. Ehrlichia spp. and Anaplasma spp. display a unique large expansion of immunodominant outer membrane proteins facilitating antigenic variation. All Rickettsiales have a diminished ability to synthesize amino acids compared to their closest free-living relatives. Unlike members of the Rickettsiaceae family, these pathogenic Anaplasmataceae are capable of making all major vitamins, cofactors, and nucleotides, which could confer a beneficial role in the invertebrate vector or the vertebrate host. Further analysis identified proteins potentially involved in vacuole confinement of the Anaplasmataceae, a life cycle involving a hematophagous vector, vertebrate pathogenesis, human pathogenesis, and lack of transovarial transmission. These discoveries provide significant insights into the biology of these obligate intracellular pathogens. Title: Evolution of sensory complexity recorded in a myxobacterial genome Goldman BS, Nierman WC, Kaiser D, Slater SC, Durkin AS, Eisen JA, Ronning CM, Barbazuk WB, Blanchard M and Kaplan HB <12 more author(s)> Goldman BS, Nierman WC, Kaiser D, Slater SC, Durkin AS, Eisen JA, Ronning CM, Barbazuk WB, Blanchard M, Field C, Halling C, Hinkle G, Iartchuk O, Kim HS, Mackenzie C, Madupu R, Miller N, Shvartsbeyn A, Sullivan SA, Vaudin M, Wiegand R, Kaplan HB (- 12) Ref: Proc Natl Acad Sci U S A, 103:15200, 2006 : PubMed ESTHER: Goldman_2006_Proc.Natl.Acad.Sci.U.S.A_103_15200 PubMedSearch: Goldman 2006 Proc.Natl.Acad.Sci.U.S.A 103 15200 PubMedID: 17015832 Gene_locus related to this paper: myxxa-q4vps9, myxxa-Q8VQX5, myxxa-Q84FB1, myxxa-Q84FE8, myxxd-q1cvh4, myxxd-q1cvn3, myxxd-q1cvz5, myxxd-q1cw78, myxxd-q1cwf6, myxxd-q1cwl7, myxxd-q1cwt9, myxxd-q1cxe9, myxxd-q1cxf0, myxxd-q1cxj1, myxxd-q1cze1, myxxd-q1czi2, myxxd-q1czk0, myxxd-q1czr4, myxxd-q1czy4, myxxd-q1d0l8, myxxd-q1d0y6, myxxd-q1d1c9, myxxd-q1d2h6, myxxd-q1d2h8, myxxd-q1d2m8, myxxd-q1d2n2, myxxd-q1d3m2, myxxd-q1d5c1, myxxd-q1d6k0, myxxd-q1d6z6, myxxd-q1d8v0, myxxd-q1d145, myxxd-q1d167, myxxd-q1d458, myxxd-q1d796, myxxd-q1da49, myxxd-q1dbk1, myxxd-q1dbn0, myxxd-q1dbn1, myxxd-q1dbn9, myxxd-q1dbp0, myxxd-q1dbs7, myxxd-q1dcd0, myxxd-q1dcj1, myxxd-q1ddx1, myxxd-q1ddx8, myxxd-q1de36, myxxd-q1det8, myxxd-q1dey9, myxxd-q1df33, myxxd-q1dfs1, myxxd-q1dfu0, myxxd-q1dfy2, myxxd-q1ddu9, myxxd-q1d1h0, myxxd-q1cwu7, myxxd-q1d790 Abstract Myxobacteria are single-celled, but social, eubacterial predators. Upon starvation they build multicellular fruiting bodies using a developmental program that progressively changes the pattern of cell movement and the repertoire of genes expressed. Development terminates with spore differentiation and is coordinated by both diffusible and cell-bound signals. The growth and development of Myxococcus xanthus is regulated by the integration of multiple signals from outside the cells with physiological signals from within. A collection of M. xanthus cells behaves, in many respects, like a multicellular organism. For these reasons M. xanthus offers unparalleled access to a regulatory network that controls development and that organizes cell movement on surfaces. The genome of M. xanthus is large (9.14 Mb), considerably larger than the other sequenced delta-proteobacteria. We suggest that gene duplication and divergence were major contributors to genomic expansion from its progenitor. More than 1,500 duplications specific to the myxobacterial lineage were identified, representing >15% of the total genes. Genes were not duplicated at random; rather, genes for cell-cell signaling, small molecule sensing, and integrative transcription control were amplified selectively. Families of genes encoding the production of secondary metabolites are overrepresented in the genome but may have been received by horizontal gene transfer and are likely to be important for predation. 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: Major structural differences and novel potential virulence mechanisms from the genomes of multiple campylobacter species Fouts DE, Mongodin EF, Mandrell RE, Miller WG, Rasko DA, Ravel J, Brinkac LM, DeBoy RT, Parker CT and Nelson KE <11 more author(s)> Fouts DE, Mongodin EF, Mandrell RE, Miller WG, Rasko DA, Ravel J, Brinkac LM, DeBoy RT, Parker CT, Daugherty SC, Dodson RJ, Durkin AS, Madupu R, Sullivan SA, Shetty JU, Ayodeji MA, Shvartsbeyn A, Schatz MC, Badger JH, Fraser CM, Nelson KE (- 11) Ref: PLoS Biol, 3:e15, 2005 : PubMed ESTHER: Fouts_2005_PLoS.Biol_3_e15 PubMedSearch: Fouts 2005 PLoS.Biol 3 e15 PubMedID: 15660156 Gene_locus related to this paper: camje-CJ0796C, camjr-q5ht69, camjr-q5ht95, camjr-q5huc7, camjr-q5hwg6, camju-a3yll6 Abstract Sequencing and comparative genome analysis of four strains of Campylobacter including C. lari RM2100, C. upsaliensis RM3195, and C. coli RM2228 has revealed major structural differences that are associated with the insertion of phage- and plasmid-like genomic islands, as well as major variations in the lipooligosaccharide complex. Poly G tracts are longer, are greater in number, and show greater variability in C. upsaliensis than in the other species. Many genes involved in host colonization, including racR/S, cadF, cdt, ciaB, and flagellin genes, are conserved across the species, but variations that appear to be species specific are evident for a lipooligosaccharide locus, a capsular (extracellular) polysaccharide locus, and a novel Campylobacter putative licABCD virulence locus. The strains also vary in their metabolic profiles, as well as their resistance profiles to a range of antibiotics. It is evident that the newly identified hypothetical and conserved hypothetical proteins, as well as uncharacterized two-component regulatory systems and membrane proteins, may hold additional significant information on the major differences in virulence among the species, as well as the specificity of the strains for particular hosts. Title: The psychrophilic lifestyle as revealed by the genome sequence of Colwellia psychrerythraea 34H through genomic and proteomic analyses Methe BA, Nelson KE, Deming JW, Momen B, Melamud E, Zhang X, Moult J, Madupu R, Nelson WC and Fraser CM <17 more author(s)> Methe BA, Nelson KE, Deming JW, Momen B, Melamud E, Zhang X, Moult J, Madupu R, Nelson WC, Dodson RJ, Brinkac LM, Daugherty SC, Durkin AS, DeBoy RT, Kolonay JF, Sullivan SA, Zhou L, Davidsen TM, Wu M, Huston AL, Lewis M, Weaver B, Weidman JF, Khouri H, Utterback TR, Feldblyum TV, Fraser CM (- 17) Ref: Proc Natl Acad Sci U S A, 102:10913, 2005 : PubMed ESTHER: Methe_2005_Proc.Natl.Acad.Sci.U.S.A_102_10913 PubMedSearch: Methe 2005 Proc.Natl.Acad.Sci.U.S.A 102 10913 PubMedID: 16043709 Gene_locus related to this paper: colp3-q47uc4, colp3-q47uc7, colp3-q47ut6, colp3-q47ut7, colp3-q47v81, colp3-q47vk3, colp3-q47vy9, colp3-q47w94, colp3-q47wj4, colp3-q47wr2, colp3-q47ws7, colp3-q47ws9, colp3-q47x08, colp3-q47x48, colp3-q47yd5, colp3-q47ye2, colp3-q47yq1, colp3-q47yv1, colp3-q47za7, colp3-q47zp5, colp3-q48ac9, colp3-q48aj8, colp3-q48aq9, colp3-q480e1, colp3-q481z4, colp3-q482y8, colp3-q484d8, colp3-q484k3, colp3-q485e4, colp3-q485t4, colp3-q486t5, colp3-q487b7, colp3-q487s5, colp3-q488a3, colp3-q488d2, colp3-q488d8, colp3-q488e7, colp3-q488f8, colp3-q488p2, colp3-q489b1, colp3-q489i6, colp3-q47ya3 Abstract The completion of the 5,373,180-bp genome sequence of the marine psychrophilic bacterium Colwellia psychrerythraea 34H, a model for the study of life in permanently cold environments, reveals capabilities important to carbon and nutrient cycling, bioremediation, production of secondary metabolites, and cold-adapted enzymes. From a genomic perspective, cold adaptation is suggested in several broad categories involving changes to the cell membrane fluidity, uptake and synthesis of compounds conferring cryotolerance, and strategies to overcome temperature-dependent barriers to carbon uptake. Modeling of three-dimensional protein homology from bacteria representing a range of optimal growth temperatures suggests changes to proteome composition that may enhance enzyme effectiveness at low temperatures. Comparative genome analyses suggest that the psychrophilic lifestyle is most likely conferred not by a unique set of genes but by a collection of synergistic changes in overall genome content and amino acid composition. Title: Complete genome sequence of the plant commensal Pseudomonas fluorescens Pf-5 Paulsen IT, Press CM, Ravel J, Kobayashi DY, Myers GS, Mavrodi DV, DeBoy RT, Seshadri R, Ren Q and Loper JE <19 more author(s)> Paulsen IT, Press CM, Ravel J, Kobayashi DY, Myers GS, Mavrodi DV, DeBoy RT, Seshadri R, Ren Q, Madupu R, Dodson RJ, Durkin AS, Brinkac LM, Daugherty SC, Sullivan SA, Rosovitz MJ, Gwinn ML, Zhou L, Schneider DJ, Cartinhour SW, Nelson WC, Weidman J, Watkins K, Tran K, Khouri H, Pierson EA, Pierson LS, 3rd, Thomashow LS, Loper JE (- 19) Ref: Nat Biotechnol, 23:873, 2005 : PubMed ESTHER: Paulsen_2005_Nat.Biotechnol_23_873 PubMedSearch: Paulsen 2005 Nat.Biotechnol 23 873 PubMedID: 15980861 Gene_locus related to this paper: psef5-metx, psef5-q4k3c9, psef5-q4k4b4, psef5-q4k4t4, psef5-q4k4u7, psef5-q4k4y2, psef5-q4k5b5, psef5-q4k5k6, psef5-q4k5w4, psef5-q4k6z9, psef5-q4k7i6, psef5-q4k7u9, psef5-q4k8j2, psef5-q4k9i3, psef5-q4k458, psef5-q4k713, psef5-q4k717, psef5-q4k873, psef5-q4k906, psef5-q4k982, psef5-q4k989, psef5-q4k993, psef5-q4kax4, psef5-q4kay8, psef5-q4kaz0, psef5-q4kaz4, psef5-q4kb21, psef5-q4kbd7, psef5-q4kbs3, psef5-q4kbs6, psef5-q4kc18, psef5-q4kc21, psef5-q4kcd3, psef5-q4kch8, psef5-q4kcj3, psef5-q4kck4, psef5-q4kcn8, psef5-q4kcq2, psef5-q4kcx3, psef5-q4kd54, psef5-q4kda1, psef5-q4kdb4, psef5-q4ke18, psef5-q4keh1, psef5-q4kej0, psef5-q4keq4, psef5-q4kes9, psef5-q4kf14, psef5-q4kfj4, psef5-q4kfw0, psef5-q4kfw1, psef5-q4kfx7, psef5-q4kgg3, psef5-q4kgj9, psef5-q4kgs6, psef5-q4kh30, psef5-q4kha2, psef5-q4khf1, psef5-q4khl0, psef5-q4khv5, psef5-q4ki42, psef5-q4kj24, psef5-q4kj95, psef5-q4kjk5, psef5-q4kjk7, psef5-q4kjm8, psef5-q4kjt7, psef5-q4kk20, psef5-q4kk22, psef5-q4kk59, psef5-q4kkf7, psefl-PLTG, psepf-PHAZ, psef5-q4kfd8 Abstract Pseudomonas fluorescens Pf-5 is a plant commensal bacterium that inhabits the rhizosphere and produces secondary metabolites that suppress soilborne plant pathogens. The complete sequence of the 7.1-Mb Pf-5 genome was determined. We analyzed repeat sequences to identify genomic islands that, together with other approaches, suggested P. fluorescens Pf-5's recent lateral acquisitions include six secondary metabolite gene clusters, seven phage regions and a mobile genomic island. We identified various features that contribute to its commensal lifestyle on plants, including broad catabolic and transport capabilities for utilizing plant-derived compounds, the apparent ability to use a diversity of iron siderophores, detoxification systems to protect from oxidative stress, and the lack of a type III secretion system and toxins found in related pathogens. In addition to six known secondary metabolites produced by P. fluorescens Pf-5, three novel secondary metabolite biosynthesis gene clusters were also identified that may contribute to the biocontrol properties of P. fluorescens Pf-5. Title: Genome sequence of the PCE-dechlorinating bacterium Dehalococcoides ethenogenes Seshadri R, Adrian L, Fouts DE, Eisen JA, Phillippy AM, Methe BA, Ward NL, Nelson WC, DeBoy RT and Heidelberg JF <15 more author(s)> Seshadri R, Adrian L, Fouts DE, Eisen JA, Phillippy AM, Methe BA, Ward NL, Nelson WC, DeBoy RT, Khouri HM, Kolonay JF, Dodson RJ, Daugherty SC, Brinkac LM, Sullivan SA, Madupu R, Nelson KE, Kang KH, Impraim M, Tran K, Robinson JM, Forberger HA, Fraser CM, Zinder SH, Heidelberg JF (- 15) Ref: Science, 307:105, 2005 : PubMed ESTHER: Seshadri_2005_Science_307_105 PubMedSearch: Seshadri 2005 Science 307 105 PubMedID: 15637277 Gene_locus related to this paper: dehm1-q3z6q3, dehm1-q3z6x9, dehm1-q3z6z2, dehm1-q3z8f3, dehm1-q3za50 Abstract Dehalococcoides ethenogenes is the only bacterium known to reductively dechlorinate the groundwater pollutants, tetrachloroethene (PCE) and trichloroethene, to ethene. Its 1,469,720-base pair chromosome contains large dynamic duplicated regions and integrated elements. Genes encoding 17 putative reductive dehalogenases, nearly all of which were adjacent to genes for transcription regulators, and five hydrogenase complexes were identified. These findings, plus a limited repertoire of other metabolic modes, indicate that D. ethenogenes is highly evolved to utilize halogenated organic compounds and H2. Diversification of reductive dehalogenase functions appears to have been mediated by recent genetic exchange and amplification. Genome analysis provides insights into the organism's complex nutrient requirements and suggests that an ancestor was a nitrogen-fixing autotroph. Title: Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial pan-genome Tettelin H, Masignani V, Cieslewicz MJ, Donati C, Medini D, Ward NL, Angiuoli SV, Crabtree J, Jones AL and Fraser CM <36 more author(s)> Tettelin H, Masignani V, Cieslewicz MJ, Donati C, Medini D, Ward NL, Angiuoli SV, Crabtree J, Jones AL, Durkin AS, DeBoy RT, Davidsen TM, Mora M, Scarselli M, Margarit y Ros I, Peterson JD, Hauser CR, Sundaram JP, Nelson WC, Madupu R, Brinkac LM, Dodson RJ, Rosovitz MJ, Sullivan SA, Daugherty SC, Haft DH, Selengut J, Gwinn ML, Zhou L, Zafar N, Khouri H, Radune D, Dimitrov G, Watkins K, O'Connor KJ, Smith S, Utterback TR, White O, Rubens CE, Grandi G, Madoff LC, Kasper DL, Telford JL, Wessels MR, Rappuoli R, Fraser CM (- 36) Ref: Proc Natl Acad Sci U S A, 102:13950, 2005 : PubMed ESTHER: Tettelin_2005_Proc.Natl.Acad.Sci.U.S.A_102_13950 PubMedSearch: Tettelin 2005 Proc.Natl.Acad.Sci.U.S.A 102 13950 PubMedID: 16172379 Gene_locus related to this paper: strag-ESTA, strag-GBS0040, strag-GBS0107, strag-GBS1828, strag-pepx, strag-q3dah6, strag-SAG0246, strag-SAG0383, strag-SAG0679, strag-SAG0680, strag-SAG0785, strag-SAG0912, strag-SAG1562, strag-SAG2132 Abstract The development of efficient and inexpensive genome sequencing methods has revolutionized the study of human bacterial pathogens and improved vaccine design. Unfortunately, the sequence of a single genome does not reflect how genetic variability drives pathogenesis within a bacterial species and also limits genome-wide screens for vaccine candidates or for antimicrobial targets. We have generated the genomic sequence of six strains representing the five major disease-causing serotypes of Streptococcus agalactiae, the main cause of neonatal infection in humans. Analysis of these genomes and those available in databases showed that the S. agalactiae species can be described by a pan-genome consisting of a core genome shared by all isolates, accounting for approximately 80% of any single genome, plus a dispensable genome consisting of partially shared and strain-specific genes. Mathematical extrapolation of the data suggests that the gene reservoir available for inclusion in the S. agalactiae pan-genome is vast and that unique genes will continue to be identified even after sequencing hundreds of genomes. Title: Life in hot carbon monoxide: the complete genome sequence of Carboxydothermus hydrogenoformans Z-2901 Wu M, Ren Q, Durkin AS, Daugherty SC, Brinkac LM, Dodson RJ, Madupu R, Sullivan SA, Kolonay JF and Eisen JA <8 more author(s)> Wu M, Ren Q, Durkin AS, Daugherty SC, Brinkac LM, Dodson RJ, Madupu R, Sullivan SA, Kolonay JF, Haft DH, Nelson WC, Tallon LJ, Jones KM, Ulrich LE, Gonzalez JM, Zhulin IB, Robb FT, Eisen JA (- 8) Ref: PLoS Genet, 1:e65, 2005 : PubMed ESTHER: Wu_2005_PLoS.Genet_1_e65 PubMedSearch: Wu 2005 PLoS.Genet 1 e65 PubMedID: 16311624 Gene_locus related to this paper: carhz-metx, carhz-q3abd5, carhz-q3adp4 Abstract We report here the sequencing and analysis of the genome of the thermophilic bacterium Carboxydothermus hydrogenoformans Z-2901. This species is a model for studies of hydrogenogens, which are diverse bacteria and archaea that grow anaerobically utilizing carbon monoxide (CO) as their sole carbon source and water as an electron acceptor, producing carbon dioxide and hydrogen as waste products. Organisms that make use of CO do so through carbon monoxide dehydrogenase complexes. Remarkably, analysis of the genome of C. hydrogenoformans reveals the presence of at least five highly differentiated anaerobic carbon monoxide dehydrogenase complexes, which may in part explain how this species is able to grow so much more rapidly on CO than many other species. Analysis of the genome also has provided many general insights into the metabolism of this organism which should make it easier to use it as a source of biologically produced hydrogen gas. One surprising finding is the presence of many genes previously found only in sporulating species in the Firmicutes Phylum. Although this species is also a Firmicutes, it was not known to sporulate previously. Here we show that it does sporulate and because it is missing many of the genes involved in sporulation in other species, this organism may serve as a "minimal" model for sporulation studies. In addition, using phylogenetic profile analysis, we have identified many uncharacterized gene families found in all known sporulating Firmicutes, but not in any non-sporulating bacteria, including a sigma factor not known to be involved in sporulation previously. 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: Structural flexibility in the Burkholderia mallei genome Nierman WC, DeShazer D, Kim HS, Tettelin H, Nelson KE, Feldblyum T, Ulrich RL, Ronning CM, Brinkac LM and Fraser CM <23 more author(s)> Nierman WC, DeShazer D, Kim HS, Tettelin H, Nelson KE, Feldblyum T, Ulrich RL, Ronning CM, Brinkac LM, Daugherty SC, Davidsen TD, DeBoy RT, Dimitrov G, Dodson RJ, Durkin AS, Gwinn ML, Haft DH, Khouri H, Kolonay JF, Madupu R, Mohammoud Y, Nelson WC, Radune D, Romero CM, Sarria S, Selengut J, Shamblin C, Sullivan SA, White O, Yu Y, Zafar N, Zhou L, Fraser CM (- 23) Ref: Proc Natl Acad Sci U S A, 101:14246, 2004 : PubMed ESTHER: Nierman_2004_Proc.Natl.Acad.Sci.U.S.A_101_14246 PubMedSearch: Nierman 2004 Proc.Natl.Acad.Sci.U.S.A 101 14246 PubMedID: 15377793 Gene_locus related to this paper: burma-a5j5w8, burma-a5tj72, burma-a5tq93, burma-metx, burma-q62a61, burma-q62ar2.1, burma-q62ar2.2, burma-q62ax8, burma-q62b60, burma-q62b79, burma-q62bh9, burma-q62bl4, burma-q62bl7, burma-q62c00, burma-q62cg5, burma-q62d41, burma-q62d56, burma-q62d83, burma-q62dg2, burma-q62du7, burma-q62e67, burma-q62eb8, burma-q62ed8, burma-q62f28, burma-q62fx7, burma-q62g26, burma-q62gx9, burma-q62gy2, burma-q62hq2, burma-q62i62, burma-q62ib8, burma-q62ie8, burma-q62j07, burma-q62j15, burma-q62jn5, burma-q62jy7, burma-q62kb7, burma-q62kg0, burma-q62kh9, burma-q62lp7, burma-q62m40, burma-q62mc3, burma-q62mf4, burma-q62mq7, burma-q629m1, burma-q629p4, burma-q629u0, burps-q3v7s4, burps-hboh Abstract The complete genome sequence of Burkholderia mallei ATCC 23344 provides insight into this highly infectious bacterium's pathogenicity and evolutionary history. B. mallei, the etiologic agent of glanders, has come under renewed scientific investigation as a result of recent concerns about its past and potential future use as a biological weapon. Genome analysis identified a number of putative virulence factors whose function was supported by comparative genome hybridization and expression profiling of the bacterium in hamster liver in vivo. The genome contains numerous insertion sequence elements that have mediated extensive deletions and rearrangements of the genome relative to Burkholderia pseudomallei. The genome also contains a vast number (>12,000) of simple sequence repeats. Variation in simple sequence repeats in key genes can provide a mechanism for generating antigenic variation that may account for the mammalian host's inability to mount a durable adaptive immune response to a B. mallei infection. Title: 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. | |||||||
|
