Haft DH

References (31)

Title : InterPro in 2022 - Paysan-Lafosse_2023_Nucleic.Acids.Res_51_D418
Author(s) : Paysan-Lafosse T , Blum M , Chuguransky S , Grego T , Pinto BL , Salazar GA , Bileschi ML , Bork P , Bridge A , Colwell L , Gough J , Haft DH , Letunic I , Marchler-Bauer A , Mi H , Natale DA , Orengo CA , Pandurangan AP , Rivoire C , Sigrist CJA , Sillitoe I , Thanki N , Thomas PD , Tosatto SCE , Wu CH , Bateman A
Ref : Nucleic Acids Research , 51 :D418 , 2023
Abstract : The InterPro database (https://www.ebi.ac.uk/interpro/) provides an integrative classification of protein sequences into families, and identifies functionally important domains and conserved sites. Here, we report recent developments with InterPro (version 90.0) and its associated software, including updates to data content and to the website. These developments extend and enrich the information provided by InterPro, and provide a more user friendly access to the data. Additionally, we have worked on adding Pfam website features to the InterPro website, as the Pfam website will be retired in late 2022. We also show that InterPro's sequence coverage has kept pace with the growth of UniProtKB. Moreover, we report the development of a card game as a method of engaging the non-scientific community. Finally, we discuss the benefits and challenges brought by the use of artificial intelligence for protein structure prediction.
ESTHER : Paysan-Lafosse_2023_Nucleic.Acids.Res_51_D418
PubMedSearch : Paysan-Lafosse_2023_Nucleic.Acids.Res_51_D418
PubMedID: 36350672

Title : Creating a specialist protein resource network: a meeting report for the protein bioinformatics and community resources retreat - Babbitt_2015_Database.(Oxford)_2015_bav063
Author(s) : Babbitt PC , Bagos PG , Bairoch A , Bateman A , Chatonnet A , Chen MJ , Craik DJ , Finn RD , Gloriam D , Haft DH , Henrissat B , Holliday GL , Isberg V , Kaas Q , Landsman D , Lenfant N , Manning G , Nagano N , Srinivasan N , O'Donovan C , Pruitt KD , Sowdhamini R , Rawlings ND , Saier MH, Jr. , Sharman JL , Spedding M , Tsirigos KD , Vastermark A , Vriend G
Ref : Database (Oxford) , 2015 :bav063 , 2015
Abstract : During 11-12 August 2014, a Protein Bioinformatics and Community Resources Retreat was held at the Wellcome Trust Genome Campus in Hinxton, UK. This meeting brought together the principal investigators of several specialized protein resources (such as CAZy, TCDB and MEROPS) as well as those from protein databases from the large Bioinformatics centres (including UniProt and RefSeq). The retreat was divided into five sessions: (1) key challenges, (2) the databases represented, (3) best practices for maintenance and curation, (4) information flow to and from large data centers and (5) communication and funding. An important outcome of this meeting was the creation of a Specialist Protein Resource Network that we believe will improve coordination of the activities of its member resources. We invite further protein database resources to join the network and continue the dialogue.
ESTHER : Babbitt_2015_Database.(Oxford)_2015_bav063
PubMedSearch : Babbitt_2015_Database.(Oxford)_2015_bav063
PubMedID: 26284514

Title : New insights into dissemination and variation of the health care-associated pathogen Acinetobacter baumannii from genomic analysis - Wright_2014_MBio_5_e00963
Author(s) : Wright MS , Haft DH , Harkins DM , Perez F , Hujer KM , Bajaksouzian S , Benard MF , Jacobs MR , Bonomo RA , Adams MD
Ref : MBio , 5 :e00963 , 2014
Abstract : Acinetobacter baumannii is a globally important nosocomial pathogen characterized by an increasing incidence of multidrug resistance. Routes of dissemination and gene flow among health care facilities are poorly resolved and are important for understanding the epidemiology of A. baumannii, minimizing disease transmission, and improving patient outcomes. We used whole-genome sequencing to assess diversity and genome dynamics in 49 isolates from one United States hospital system during one year from 2007 to 2008. Core single-nucleotide-variant-based phylogenetic analysis revealed multiple founder strains and multiple independent strains recovered from the same patient yet was insufficient to fully resolve strain relationships, where gene content and insertion sequence patterns added additional discriminatory power. Gene content comparisons illustrated extensive and redundant antibiotic resistance gene carriage and direct evidence of gene transfer, recombination, gene loss, and mutation. Evidence of barriers to gene flow among hospital components was not found, suggesting complex mixing of strains and a large reservoir of A. baumannii strains capable of colonizing patients. IMPORTANCE: Genome sequencing was used to characterize multidrug-resistant Acinetobacter baumannii strains from one United States hospital system during a 1-year period to better understand how A. baumannii strains that cause infection are related to one another. Extensive variation in gene content was found, even among strains that were very closely related phylogenetically and epidemiologically. Several mechanisms contributed to this diversity, including transfer of mobile genetic elements, mobilization of insertion sequences, insertion sequence-mediated deletions, and genome-wide homologous recombination. Variation in gene content, however, lacked clear spatial or temporal patterns, suggesting a diverse pool of circulating strains with considerable interaction between strains and hospital locations. Widespread genetic variation among strains from the same hospital and even the same patient, particularly involving antibiotic resistance genes, reinforces the need for molecular diagnostic testing and genomic analysis to determine resistance profiles, rather than a reliance primarily on strain typing and antimicrobial resistance phenotypes for epidemiological studies.
ESTHER : Wright_2014_MBio_5_e00963
PubMedSearch : Wright_2014_MBio_5_e00963
PubMedID: 24449752
Gene_locus related to this paper: aciba-f5iht4 , aciba-a0a009wzt4

Title : Genomic insights to SAR86, an abundant and uncultivated marine bacterial lineage - Dupont_2012_ISME.J_6_1186
Author(s) : Dupont CL , Rusch DB , Yooseph S , Lombardo MJ , Richter RA , Valas R , Novotny M , Yee-Greenbaum J , Selengut JD , Haft DH , Halpern AL , Lasken RS , Nealson K , Friedman R , Venter JC
Ref : Isme J , 6 :1186 , 2012
Abstract : Bacteria in the 16S rRNA clade SAR86 are among the most abundant uncultivated constituents of microbial assemblages in the surface ocean for which little genomic information is currently available. Bioinformatic techniques were used to assemble two nearly complete genomes from marine metagenomes and single-cell sequencing provided two more partial genomes. Recruitment of metagenomic data shows that these SAR86 genomes substantially increase our knowledge of non-photosynthetic bacteria in the surface ocean. Phylogenomic analyses establish SAR86 as a basal and divergent lineage of gamma-proteobacteria, and the individual genomes display a temperature-dependent distribution. Modestly sized at 1.25-1.7 Mbp, the SAR86 genomes lack several pathways for amino-acid and vitamin synthesis as well as sulfate reduction, trends commonly observed in other abundant marine microbes. SAR86 appears to be an aerobic chemoheterotroph with the potential for proteorhodopsin-based ATP generation, though the apparent lack of a retinal biosynthesis pathway may require it to scavenge exogenously-derived pigments to utilize proteorhodopsin. The genomes contain an expanded capacity for the degradation of lipids and carbohydrates acquired using a wealth of tonB-dependent outer membrane receptors. Like the abundant planktonic marine bacterial clade SAR11, SAR86 exhibits metabolic streamlining, but also a distinct carbon compound specialization, possibly avoiding competition.
ESTHER : Dupont_2012_ISME.J_6_1186
PubMedSearch : Dupont_2012_ISME.J_6_1186
PubMedID: 22170421
Gene_locus related to this paper: 9gamm-j4wzh3 , 9gamm-j4wnu4 , 9gamm-j4v6c9 , 9gamm-j4ksf8 , 9gamm-j4uzz4 , 9gamm-j5kai7

Title : Three genomes from the phylum Acidobacteria provide insight into the lifestyles of these microorganisms in soils - Ward_2009_Appl.Environ.Microbiol_75_2046
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
Ref : Applied Environmental Microbiology , 75 :2046 , 2009
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.
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

Title : Comparative genomic evidence for a close relationship between the dimorphic prosthecate bacteria Hyphomonas neptunium and Caulobacter crescentus - Badger_2006_J.Bacteriol_188_6841
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
Ref : Journal of Bacteriology , 188 :6841 , 2006
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.
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

Title : Skewed genomic variability in strains of the toxigenic bacterial pathogen, Clostridium perfringens - Myers_2006_Genome.Res_16_1031
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
Ref : Genome Res , 16 :1031 , 2006
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.
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

Title : Exopolysaccharide-associated protein sorting in environmental organisms: the PEP-CTERM\/EpsH system. Application of a novel phylogenetic profiling heuristic - Haft_2006_BMC.Biol_4_29
Author(s) : Haft DH , Paulsen IT , Ward N , Selengut JD
Ref : BMC Biol , 4 :29 , 2006
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.
RESULTS: We describe a short C-terminal homology domain, sporadically distributed in bacteria, with several key characteristics of protein sorting signals. The domain includes a near-invariant motif Pro-Glu-Pro (PEP). This possible recognition or processing site is followed by a predicted transmembrane helix and a cluster rich in basic amino acids. We designate this domain PEP-CTERM. It tends to occur multiple times in a genome if it occurs at all, with a median count of eight instances; Verrucomicrobium spinosum has sixty-five. PEP-CTERM-containing proteins generally contain an N-terminal signal peptide and exhibit high diversity and little homology to known proteins. All bacteria with PEP-CTERM have both an outer membrane and exopolysaccharide (EPS) production genes. By a simple heuristic for screening phylogenetic profiles in the absence of pre-formed protein families, we discovered that a homolog of the membrane protein EpsH (exopolysaccharide locus protein H) occurs in a species when PEP-CTERM domains are found. The EpsH family contains invariant residues consistent with a transpeptidase function. Most PEP-CTERM proteins are encoded by single-gene operons preceded by large intergenic regions. In the Proteobacteria, most of these upstream regions share a DNA sequence, a probable cis-regulatory site that contains a sigma-54 binding motif. The phylogenetic profile for this DNA sequence exactly matches that of three proteins: a sigma-54-interacting response regulator (PrsR), a transmembrane histidine kinase (PrsK), and a TPR protein (PrsT). CONCLUSION: These findings are consistent with the hypothesis that PEP-CTERM and EpsH form a protein export sorting system, analogous to the LPXTG/sortase system of Gram-positive bacteria, and correlated to EPS expression. It occurs preferentially in bacteria from sediments, soils, and biofilms. The novel method that led to these findings, partial phylogenetic profiling, requires neither global sequence clustering nor arbitrary similarity cutoffs and appears to be a rapid, effective alternative to other profiling methods.
ESTHER : Haft_2006_BMC.Biol_4_29
PubMedSearch : Haft_2006_BMC.Biol_4_29
PubMedID: 16930487

Title : Comparative genomics of emerging human ehrlichiosis agents - Dunning Hotopp_2006_PLoS.Genet_2_e21
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
Ref : PLoS Genet , 2 :e21 , 2006
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.
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

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_2005_J.Bacteriol_187_2426
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
Ref : Journal of Bacteriology , 187 :2426 , 2005
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.
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

Title : Whole-genome sequence analysis of Pseudomonas syringae pv. phaseolicola 1448A reveals divergence among pathovars in genes involved in virulence and transposition - Joardar_2005_J.Bacteriol_187_6488
Author(s) : Joardar V , Lindeberg M , Jackson RW , Selengut J , Dodson R , Brinkac LM , Daugherty SC , Deboy R , Durkin AS , Giglio MG , Madupu R , Nelson WC , Rosovitz MJ , Sullivan S , Crabtree J , Creasy T , Davidsen T , Haft DH , Zafar N , Zhou L , Halpin R , Holley T , Khouri H , Feldblyum T , White O , Fraser CM , Chatterjee AK , Cartinhour S , Schneider DJ , Mansfield J , Collmer A , Buell CR
Ref : Journal of Bacteriology , 187 :6488 , 2005
Abstract : Pseudomonas syringae pv. phaseolicola, a gram-negative bacterial plant pathogen, is the causal agent of halo blight of bean. In this study, we report on the genome sequence of P. syringae pv. phaseolicola isolate 1448A, which encodes 5,353 open reading frames (ORFs) on one circular chromosome (5,928,787 bp) and two plasmids (131,950 bp and 51,711 bp). Comparative analyses with a phylogenetically divergent pathovar, P. syringae pv. tomato DC3000, revealed a strong degree of conservation at the gene and genome levels. In total, 4,133 ORFs were identified as putative orthologs in these two pathovars using a reciprocal best-hit method, with 3,941 ORFs present in conserved, syntenic blocks. Although these two pathovars are highly similar at the physiological level, they have distinct host ranges; 1448A causes disease in beans, and DC3000 is pathogenic on tomato and Arabidopsis. Examination of the complement of ORFs encoding virulence, fitness, and survival factors revealed a substantial, but not complete, overlap between these two pathovars. Another distinguishing feature between the two pathovars is their distinctive sets of transposable elements. With access to a fifth complete pseudomonad genome sequence, we were able to identify 3,567 ORFs that likely comprise the core Pseudomonas genome and 365 ORFs that are P. syringae specific.
ESTHER : Joardar_2005_J.Bacteriol_187_6488
PubMedSearch : Joardar_2005_J.Bacteriol_187_6488
PubMedID: 16159782
Gene_locus related to this paper: pse14-q48cb3 , pse14-q48ck7 , pse14-q48cs3 , pse14-q48ct2 , pse14-q48d82 , pse14-q48da3 , pse14-q48dj9 , pse14-q48dq5 , pse14-q48e33 , pse14-q48es1 , pse14-q48f84 , pse14-q48fg2 , pse14-q48g47 , pse14-q48g51 , pse14-q48gq9 , pse14-q48h40 , pse14-q48ha4 , pse14-q48hb4 , pse14-q48he1 , pse14-q48hq0 , pse14-q48hq2 , pse14-q48ia0 , pse14-q48im0 , pse14-q48j48 , pse14-q48ji2 , pse14-q48k54 , pse14-q48k55 , pse14-q48k63 , pse14-q48kc1 , pse14-q48kt9 , pse14-q48ku0 , pse14-q48lb6 , pse14-q48lj1 , pse14-q48ln2 , pse14-q48m56 , pse14-q48mh5 , pse14-q48mq7 , pse14-q48nt0 , pse14-q48p24 , pse14-q48pi7 , pse14-q48pi8 , pse14-q48pi9 , pse14-q48pq2 , pse14-q48pq5 , psesm-METX , psesm-q87y20 , psesm-q889k3 , psesy-PIP , psesy-PSPTO0162 , psesy-PSPTO1766 , psesy-PSPTO2134 , psesy-PSPTO3135 , pseu2-q4zwv7 , psesg-e7p3i0

Title : Life in hot carbon monoxide: the complete genome sequence of Carboxydothermus hydrogenoformans Z-2901 - Wu_2005_PLoS.Genet_1_e65
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
Ref : PLoS Genet , 1 :e65 , 2005
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.
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

Title : Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial pan-genome - Tettelin_2005_Proc.Natl.Acad.Sci.U.S.A_102_13950
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
Ref : Proc Natl Acad Sci U S A , 102 :13950 , 2005
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.
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

Title : The genome sequence of the anaerobic, sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough - Heidelberg_2004_Nat.Biotechnol_22_554
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
Ref : Nat Biotechnol , 22 :554 , 2004
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.
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

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_2004_Nucleic.Acids.Res_32_2386
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
Ref : Nucleic Acids Research , 32 :2386 , 2004
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.
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

Title : Genome sequence of Silicibacter pomeroyi reveals adaptations to the marine environment - Moran_2004_Nature_432_910
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
Ref : Nature , 432 :910 , 2004
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.
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

Title : Comparison of the genome of the oral pathogen Treponema denticola with other spirochete genomes - Seshadri_2004_Proc.Natl.Acad.Sci.U.S.A_101_5646
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
Ref : Proc Natl Acad Sci U S A , 101 :5646 , 2004
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.
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

Title : Structural flexibility in the Burkholderia mallei genome - Nierman_2004_Proc.Natl.Acad.Sci.U.S.A_101_14246
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
Ref : Proc Natl Acad Sci U S A , 101 :14246 , 2004
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.
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

Title : The genome sequence of Bacillus anthracis Ames and comparison to closely related bacteria - Read_2003_Nature_423_81
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
Ref : Nature , 423 :81 , 2003
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.
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

Title : The complete genome sequence of the Arabidopsis and tomato pathogen Pseudomonas syringae pv. tomato DC3000 - Buell_2003_Proc.Natl.Acad.Sci.U.S.A_100_10181
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
Ref : Proc Natl Acad Sci U S A , 100 :10181 , 2003
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.
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

Title : Genome of Geobacter sulfurreducens: metal reduction in subsurface environments - Methe_2003_Science_302_1967
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
Ref : Science , 302 :1967 , 2003
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.
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

Title : Complete genome sequence of the oral pathogenic Bacterium porphyromonas gingivalis strain W83 - Nelson_2003_J.Bacteriol_185_5591
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
Ref : Journal of Bacteriology , 185 :5591 , 2003
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.
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

Title : Genome sequence of Chlamydophila caviae (Chlamydia psittaci GPIC): examining the role of niche-specific genes in the evolution of the Chlamydiaceae - Read_2003_Nucleic.Acids.Res_31_2134
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
Ref : Nucleic Acids Research , 31 :2134 , 2003
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.
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

Title : Genome sequence of the dissimilatory metal ion-reducing bacterium Shewanella oneidensis - Heidelberg_2002_Nat.Biotechnol_20_1118
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
Ref : Nat Biotechnol , 20 :1118 , 2002
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.
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

Title : The complete genome sequence of Chlorobium tepidum TLS, a photosynthetic, anaerobic, green-sulfur bacterium - Eisen_2002_Proc.Natl.Acad.Sci.U.S.A_99_9509
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
Ref : Proceedings of the National Academy of Sciences of the United States of America , 99 :9509 , 2002
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.
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

Title : Complete genome sequence of Caulobacter crescentus - Nierman_2001_Proc.Natl.Acad.Sci.U.S.A_98_4136
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
Ref : Proc Natl Acad Sci U S A , 98 :4136 , 2001
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.
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

Title : Complete genome sequence of a virulent isolate of Streptococcus pneumoniae - Tettelin_2001_Science_293_498
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
Ref : Science , 293 :498 , 2001
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.
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

Title : Complete genome sequence of Neisseria meningitidis serogroup B strain MC58 - Tettelin_2000_Science_287_1809
Author(s) : Tettelin H , Saunders NJ , Heidelberg J , Jeffries AC , Nelson KE , Eisen JA , Ketchum KA , Hood DW , Peden JF , Dodson RJ , Nelson WC , Gwinn ML , Deboy R , Peterson JD , Hickey EK , Haft DH , Salzberg SL , White O , Fleischmann RD , Dougherty BA , Mason T , Ciecko A , Parksey DS , Blair E , Cittone H , Clark EB , Cotton MD , Utterback TR , Khouri H , Qin H , Vamathevan J , Gill J , Scarlato V , Masignani V , Pizza M , Grandi G , Sun L , Smith HO , Fraser CM , Moxon ER , Rappuoli R , Venter JC
Ref : Science , 287 :1809 , 2000
Abstract : The 2,272,351-base pair genome of Neisseria meningitidis strain MC58 (serogroup B), a causative agent of meningitis and septicemia, contains 2158 predicted coding regions, 1158 (53.7%) of which were assigned a biological role. Three major islands of horizontal DNA transfer were identified; two of these contain genes encoding proteins involved in pathogenicity, and the third island contains coding sequences only for hypothetical proteins. Insights into the commensal and virulence behavior of N. meningitidis can be gleaned from the genome, in which sequences for structural proteins of the pilus are clustered and several coding regions unique to serogroup B capsular polysaccharide synthesis can be identified. Finally, N. meningitidis contains more genes that undergo phase variation than any pathogen studied to date, a mechanism that controls their expression and contributes to the evasion of the host immune system.
ESTHER : Tettelin_2000_Science_287_1809
PubMedSearch : Tettelin_2000_Science_287_1809
PubMedID: 10710307
Gene_locus related to this paper: neigo-pip , neima-metx , neimb-q9k0t9 , neime-ESD , neime-NMA2216 , neime-NMB0276 , neime-NMB0868 , neime-NMB1828 , neime-NMB1877

Title : DNA sequence of both chromosomes of the cholera pathogen Vibrio cholerae - Heidelberg_2000_Nature_406_477
Author(s) : Heidelberg JF , Eisen JA , Nelson WC , Clayton RA , Gwinn ML , Dodson RJ , Haft DH , Hickey EK , Peterson JD , Umayam L , Gill SR , Nelson KE , Read TD , Tettelin H , Richardson D , Ermolaeva MD , Vamathevan J , Bass S , Qin H , Dragoi I , Sellers P , McDonald L , Utterback T , Fleishmann RD , Nierman WC , White O , Salzberg SL , Smith HO , Colwell RR , Mekalanos JJ , Venter JC , Fraser CM
Ref : Nature , 406 :477 , 2000
Abstract : Here we determine the complete genomic sequence of the gram negative, gamma-Proteobacterium Vibrio cholerae El Tor N16961 to be 4,033,460 base pairs (bp). The genome consists of two circular chromosomes of 2,961,146 bp and 1,072,314 bp that together encode 3,885 open reading frames. The vast majority of recognizable genes for essential cell functions (such as DNA replication, transcription, translation and cell-wall biosynthesis) and pathogenicity (for example, toxins, surface antigens and adhesins) are located on the large chromosome. In contrast, the small chromosome contains a larger fraction (59%) of hypothetical genes compared with the large chromosome (42%), and also contains many more genes that appear to have origins other than the gamma-Proteobacteria. The small chromosome also carries a gene capture system (the integron island) and host 'addiction' genes that are typically found on plasmids; thus, the small chromosome may have originally been a megaplasmid that was captured by an ancestral Vibrio species. The V. cholerae genomic sequence provides a starting point for understanding how a free-living, environmental organism emerged to become a significant human bacterial pathogen.
ESTHER : Heidelberg_2000_Nature_406_477
PubMedSearch : Heidelberg_2000_Nature_406_477
PubMedID: 10952301
Gene_locus related to this paper: vibch-rtxAABH , vibch-lipas , vibch-VC0135 , vibch-VC0522 , vibch-VC1418 , vibch-VC1725 , vibch-VC1974 , vibch-VC1986 , vibch-VC2097 , vibch-VC2432 , vibch-VC2610 , vibch-VC2718 , vibch-VCA0063 , vibch-VCA0092 , vibch-VCA0490 , vibch-VCA0688 , vibch-VCA0754 , vibch-VCA0863 , vibch-y1892 , vibch-y2276

Title : Evidence for lateral gene transfer between Archaea and bacteria from genome sequence of Thermotoga maritima - Nelson_1999_Nature_399_323
Author(s) : Nelson KE , Clayton RA , Gill SR , Gwinn ML , Dodson RJ , Haft DH , Hickey EK , Peterson JD , Nelson WC , Ketchum KA , McDonald L , Utterback TR , Malek JA , Linher KD , Garrett MM , Stewart AM , Cotton MD , Pratt MS , Phillips CA , Richardson D , Heidelberg J , Sutton GG , Fleischmann RD , Eisen JA , White O , Salzberg SL , Smith HO , Venter JC , Fraser CM
Ref : Nature , 399 :323 , 1999
Abstract : The 1,860,725-base-pair genome of Thermotoga maritima MSB8 contains 1,877 predicted coding regions, 1,014 (54%) of which have functional assignments and 863 (46%) of which are of unknown function. Genome analysis reveals numerous pathways involved in degradation of sugars and plant polysaccharides, and 108 genes that have orthologues only in the genomes of other thermophilic Eubacteria and Archaea. Of the Eubacteria sequenced to date, T. maritima has the highest percentage (24%) of genes that are most similar to archaeal genes. Eighty-one archaeal-like genes are clustered in 15 regions of the T. maritima genome that range in size from 4 to 20 kilobases. Conservation of gene order between T. maritima and Archaea in many of the clustered regions suggests that lateral gene transfer may have occurred between thermophilic Eubacteria and Archaea.
ESTHER : Nelson_1999_Nature_399_323
PubMedSearch : Nelson_1999_Nature_399_323
PubMedID: 10360571
Gene_locus related to this paper: thema-ESTA , thema-q9x0d6 , thema-q9x042 , thema-TM0033 , thema-TM0053 , thema-TM0077 , thema-TM0336 , thema-TM1160 , thema-TM1350

Title : Genome sequence of the radioresistant bacterium Deinococcus radiodurans R1 - White_1999_Science_286_1571
Author(s) : White O , Eisen JA , Heidelberg JF , Hickey EK , Peterson JD , Dodson RJ , Haft DH , Gwinn ML , Nelson WC , Richardson DL , Moffat KS , Qin H , Jiang L , Pamphile W , Crosby M , Shen M , Vamathevan JJ , Lam P , McDonald L , Utterback T , Zalewski C , Makarova KS , Aravind L , Daly MJ , Minton KW , Fleischmann RD , Ketchum KA , Nelson KE , Salzberg S , Smith HO , Venter JC , Fraser CM
Ref : Science , 286 :1571 , 1999
Abstract : The complete genome sequence of the radiation-resistant bacterium Deinococcus radiodurans R1 is composed of two chromosomes (2,648,638 and 412,348 base pairs), a megaplasmid (177,466 base pairs), and a small plasmid (45,704 base pairs), yielding a total genome of 3,284, 156 base pairs. Multiple components distributed on the chromosomes and megaplasmid that contribute to the ability of D. radiodurans to survive under conditions of starvation, oxidative stress, and high amounts of DNA damage were identified. Deinococcus radiodurans represents an organism in which all systems for DNA repair, DNA damage export, desiccation and starvation recovery, and genetic redundancy are present in one cell.
ESTHER : White_1999_Science_286_1571
PubMedSearch : White_1999_Science_286_1571
PubMedID: 10567266
Gene_locus related to this paper: deira-aryla , deira-DR0165 , deira-DR0334 , deira-DR0553 , deira-DR0593 , deira-DR0654 , deira-DR0657 , deira-DR0779 , deira-DR0791 , deira-DR0945 , deira-DR0964 , deira-DR1053 , deira-DR1326 , deira-DR1351 , deira-DR1352 , deira-DR1403 , deira-DR1537 , deira-DR1915 , deira-DR1931 , deira-DR2078 , deira-DR2248 , deira-DR2478 , deira-DR2503 , deira-DR2506 , deira-DR2522 , deira-DR2549 , deira-DR2551 , deira-DRA0060 , deira-DRA0150 , deira-DRA0307 , deira-DRA0340 , deira-DRB0023 , deira-DRB0097 , deira-este1 , deira-este2 , deira-lip1 , deira-lip2 , deira-lipest , deira-metx