Tettelin H

References (34)

Title : Genomic analysis reveals the molecular basis for capsule loss in the group B Streptococcus population - Rosini_2015_PLoS.One_10_e0125985
Author(s) : Rosini R , Campisi E , De Chiara M , Tettelin H , Rinaudo D , Toniolo C , Metruccio M , Guidotti S , Sorensen UB , Kilian M , Ramirez M , Janulczyk R , Donati C , Grandi G , Margarit I
Ref : PLoS ONE , 10 :e0125985 , 2015
Abstract : The human and bovine bacterial pathogen Streptococcus agalactiae (Group B Streptococcus, GBS) expresses a thick polysaccharide capsule that constitutes a major virulence factor and vaccine target. GBS can be classified into ten distinct serotypes differing in the chemical composition of their capsular polysaccharide. However, non-typeable strains that do not react with anti-capsular sera are frequently isolated from colonized and infected humans and cattle. To gain a comprehensive insight into the molecular basis for the loss of capsule expression in GBS, a collection of well-characterized non-typeable strains was investigated by genome sequencing. Genome based phylogenetic analysis extended to a wide population of sequenced strains confirmed the recently observed high clonality among GBS lineages mainly containing human strains, and revealed a much higher degree of diversity in the bovine population. Remarkably, non-typeable strains were equally distributed in all lineages. A number of distinct mutations in the cps operon were identified that were apparently responsible for inactivation of capsule synthesis. The most frequent genetic alterations were point mutations leading to stop codons in the cps genes, and the main target was found to be cpsE encoding the portal glycosyl transferase of capsule biosynthesis. Complementation of strains carrying missense mutations in cpsE with a wild-type gene restored capsule expression allowing the identification of amino acid residues essential for enzyme activity.
ESTHER : Rosini_2015_PLoS.One_10_e0125985
PubMedSearch : Rosini_2015_PLoS.One_10_e0125985
PubMedID: 25946017
Gene_locus related to this paper: strag-a0a076z217 , strag-a0a0h1ywg1

Title : High-level relatedness among Mycobacterium abscessus subsp. massiliense strains from widely separated outbreaks - Tettelin_2014_Emerg.Infect.Dis_20_364
Author(s) : Tettelin H , Davidson RM , Agrawal S , Aitken ML , Shallom S , Hasan NA , Strong M , de Moura VC , De Groote MA , Duarte RS , Hine E , Parankush S , Su Q , Daugherty SC , Fraser CM , Brown-Elliott BA , Wallace RJ, Jr. , Holland SM , Sampaio EP , Olivier KN , Jackson M , Zelazny AM
Ref : Emerg Infect Dis , 20 :364 , 2014
Abstract : Three recently sequenced strains isolated from patients during an outbreak of Mycobacterium abscessus subsp. massiliense infections at a cystic fibrosis center in the United States were compared with 6 strains from an outbreak at a cystic fibrosis center in the United Kingdom and worldwide strains. Strains from the 2 cystic fibrosis outbreaks showed high-level relatedness with each other and major-level relatedness with strains that caused soft tissue infections during an epidemic in Brazil. We identified unique single-nucleotide polymorphisms in cystic fibrosis and soft tissue outbreak strains, separate single-nucleotide polymorphisms only in cystic fibrosis outbreak strains, and unique genomic traits for each subset of isolates. Our findings highlight the necessity of identifying M. abscessus to the subspecies level and screening all cystic fibrosis isolates for relatedness to these outbreak strains. We propose 2 diagnostic strategies that use partial sequencing of rpoB and secA1 genes and a multilocus sequence typing protocol.
ESTHER : Tettelin_2014_Emerg.Infect.Dis_20_364
PubMedSearch : Tettelin_2014_Emerg.Infect.Dis_20_364
PubMedID: 24565502
Gene_locus related to this paper: mycab-b1mch4 , mycab-b1mdu3 , mycab-b1mes2 , mycab-b1mes3 , mycab-b1mfj3 , mycab-b1mgd3 , mycab-b1mkl9 , mycab-r4v1a9

Title : Genomic insights into the emerging human pathogen Mycobacterium massiliense - Tettelin_2012_J.Bacteriol_194_5450
Author(s) : Tettelin H , Sampaio EP , Daugherty SC , Hine E , Riley DR , Sadzewicz L , Sengamalay N , Shefchek K , Su Q , Tallon LJ , Conville P , Olivier KN , Holland SM , Fraser CM , Zelazny AM
Ref : Journal of Bacteriology , 194 :5450 , 2012
Abstract : Mycobacterium massiliense (Mycobacterium abscessus group) is an emerging pathogen causing pulmonary disease and skin and soft tissue infections. We report the genome sequence of the type strain CCUG 48898.
ESTHER : Tettelin_2012_J.Bacteriol_194_5450
PubMedSearch : Tettelin_2012_J.Bacteriol_194_5450
PubMedID: 22965080
Gene_locus related to this paper: mycab-b1mdu3 , mycab-b1mes2 , mycab-b1mes3 , mycab-b1mfj3 , mycab-i9cu79 , mycab-i0pm15 , mycab-i0p5k2 , mycab-h0ig31 , mycab-h0iii8 , myca9-b1miq0 , mycab-r4v1a9

Title : Whole genome sequencing to investigate the emergence of clonal complex 23 Neisseria meningitidis serogroup Y disease in the United States - Krauland_2012_PLoS.One_7_e35699
Author(s) : Krauland MG , Dunning Hotopp JC , Riley DR , Daugherty SC , Marsh JW , Messonnier NE , Mayer LW , Tettelin H , Harrison LH
Ref : PLoS ONE , 7 :e35699 , 2012
Abstract : In the United States, serogroup Y, ST-23 clonal complex Neisseria meningitidis was responsible for an increase in meningococcal disease incidence during the 1990s. This increase was accompanied by antigenic shift of three outer membrane proteins, with a decrease in the population that predominated in the early 1990s as a different population emerged later in that decade. To understand factors that may have been responsible for the emergence of serogroup Y disease, we used whole genome pyrosequencing to investigate genetic differences between isolates from early and late N. meningitidis populations, obtained from meningococcal disease cases in Maryland in the 1990s. The genomes of isolates from the early and late populations were highly similar, with 1231 of 1776 shared genes exhibiting 100% amino acid identity and an average pi(N) = 0.0033 and average pi(S) = 0.0216. However, differences were found in predicted proteins that affect pilin structure and antigen profile and in predicted proteins involved in iron acquisition and uptake. The observed changes are consistent with acquisition of new alleles through horizontal gene transfer. Changes in antigen profile due to the genetic differences found in this study likely allowed the late population to emerge due to escape from population immunity. These findings may predict which antigenic factors are important in the cyclic epidemiology of meningococcal disease.
ESTHER : Krauland_2012_PLoS.One_7_e35699
PubMedSearch : Krauland_2012_PLoS.One_7_e35699
PubMedID: 22558202

Title : Neisseria meningitidis is structured in clades associated with restriction modification systems that modulate homologous recombination - Budroni_2011_Proc.Natl.Acad.Sci.U.S.A_108_4494
Author(s) : Budroni S , Siena E , Dunning Hotopp JC , Seib KL , Serruto D , Nofroni C , Comanducci M , Riley DR , Daugherty SC , Angiuoli SV , Covacci A , Pizza M , Rappuoli R , Moxon ER , Tettelin H , Medini D
Ref : Proc Natl Acad Sci U S A , 108 :4494 , 2011
Abstract : Molecular data on a limited number of chromosomal loci have shown that the population of Neisseria meningitidis (Nm), a deadly human pathogen, is structured in distinct lineages. Given that the Nm population undergoes substantial recombination, the mechanisms resulting in the evolution of these lineages, their persistence in time, and the implications for the pathogenicity of the bacterium are not yet completely understood. Based on whole-genome sequencing, we show that Nm is structured in phylogenetic clades. Through acquisition of specific genes and through insertions and rearrangements, each clade has acquired and remodeled specific genomic tracts, with the potential to impact on the commensal and virulence behavior of Nm. Despite this clear evidence of a structured population, we confirm high rates of detectable recombination throughout the whole Nm chromosome. However, gene conversion events were found to be longer within clades than between clades, suggesting a DNA cleavage mechanism associated with the phylogeny of the species. We identify 22 restriction modification systems, probably acquired by horizontal gene transfer from outside of the species/genus, whose distribution in the different strains coincides with the phylogenetic clade structure. We provide evidence that these clade-associated restriction modification systems generate a differential barrier to DNA exchange consistent with the observed population structure. These findings have general implications for the emergence of lineage structure and virulence in recombining bacterial populations, and they could provide an evolutionary framework for the population biology of a number of other bacterial species that show contradictory population structure and dynamics.
ESTHER : Budroni_2011_Proc.Natl.Acad.Sci.U.S.A_108_4494
PubMedSearch : Budroni_2011_Proc.Natl.Acad.Sci.U.S.A_108_4494
PubMedID: 21368196
Gene_locus related to this paper: neigo-pip , neima-metx , neime-ESD , neime-NMA2216 , neime-NMB0276 , neime-NMB1877

Title : Structure and dynamics of the pan-genome of Streptococcus pneumoniae and closely related species - Donati_2010_Genome.Biol_11_R107
Author(s) : Donati C , Hiller NL , Tettelin H , Muzzi A , Croucher NJ , Angiuoli SV , Oggioni M , Dunning Hotopp JC , Hu FZ , Riley DR , Covacci A , Mitchell TJ , Bentley SD , Kilian M , Ehrlich GD , Rappuoli R , Moxon ER , Masignani V
Ref : Genome Biol , 11 :R107 , 2010
Abstract : BACKGROUND: Streptococcus pneumoniae is one of the most important causes of microbial diseases in humans. The genomes of 44 diverse strains of S. pneumoniae were analyzed and compared with strains of non-pathogenic streptococci of the Mitis group.
RESULTS: Despite evidence of extensive recombination, the S. pneumoniae phylogenetic tree revealed six major lineages. With the exception of serotype 1, the tree correlated poorly with capsular serotype, geographical site of isolation and disease outcome. The distribution of dispensable genes--genes present in more than one strain but not in all strains--was consistent with phylogeny, although horizontal gene transfer events attenuated this correlation in the case of ancient lineages. Homologous recombination, involving short stretches of DNA, was the dominant evolutionary process of the core genome of S. pneumoniae. Genetic exchange occurred both within and across the borders of the species, and S. mitis was the main reservoir of genetic diversity of S. pneumoniae. The pan-genome size of S. pneumoniae increased logarithmically with the number of strains and linearly with the number of polymorphic sites of the sampled genomes, suggesting that acquired genes accumulate proportionately to the age of clones. Most genes associated with pathogenicity were shared by all S. pneumoniae strains, but were also present in S. mitis, S. oralis and S. infantis, indicating that these genes are not sufficient to determine virulence.
CONCLUSIONS: Genetic exchange with related species sharing the same ecological niche is the main mechanism of evolution of S. pneumoniae. The open pan-genome guarantees the species a quick and economical response to diverse environments.
ESTHER : Donati_2010_Genome.Biol_11_R107
PubMedSearch : Donati_2010_Genome.Biol_11_R107
PubMedID: 21034474

Title : Identification of protective and broadly conserved vaccine antigens from the genome of extraintestinal pathogenic Escherichia coli - Moriel_2010_Proc.Natl.Acad.Sci.U.S.A_107_9072
Author(s) : Moriel DG , Bertoldi I , Spagnuolo A , Marchi S , Rosini R , Nesta B , Pastorello I , Corea VA , Torricelli G , Cartocci E , Savino S , Scarselli M , Dobrindt U , Hacker J , Tettelin H , Tallon LJ , Sullivan S , Wieler LH , Ewers C , Pickard D , Dougan G , Fontana MR , Rappuoli R , Pizza M , Serino L
Ref : Proc Natl Acad Sci U S A , 107 :9072 , 2010
Abstract : Extraintestinal pathogenic Escherichia coli (ExPEC) are a common cause of disease in both mammals and birds. A vaccine to prevent such infections would be desirable given the increasing antibiotic resistance of these bacteria. We have determined the genome sequence of ExPEC IHE3034 (ST95) isolated from a case of neonatal meningitis and compared this to available genome sequences of other ExPEC strains and a few nonpathogenic E. coli. We found 19 genomic islands present in the genome of IHE3034, which are absent in the nonpathogenic E. coli isolates. By using subtractive reverse vaccinology we identified 230 antigens present in ExPEC but absent (or present with low similarity) in nonpathogenic strains. Nine antigens were protective in a mouse challenge model. Some of them were also present in other pathogenic non-ExPEC strains, suggesting that a broadly protective E. coli vaccine may be possible. The gene encoding the most protective antigen was detected in most of the E. coli isolates, highly conserved in sequence and found to be exported by a type II secretion system which seems to be nonfunctional in nonpathogenic strains.
ESTHER : Moriel_2010_Proc.Natl.Acad.Sci.U.S.A_107_9072
PubMedSearch : Moriel_2010_Proc.Natl.Acad.Sci.U.S.A_107_9072
PubMedID: 20439758
Gene_locus related to this paper: ecoli-Aes , ecoli-rutD , ecoli-bioh , ecoli-C0410 , ecoli-C2429 , ecoli-C2451 , ecoli-C4836 , ecoli-dlhh , ecoli-entf , ecoli-fes , ecoli-IROD , ecoli-IROE , ecoli-pldb , ecoli-ptrb , ecoli-yafa , ecoli-yaim , ecoli-ybff , ecoli-ycfp , ecoli-ycjy , ecoli-yeiG , ecoli-YFBB , ecoli-yghX , ecoli-yhet , ecoli-yjfp , ecoli-YNBC , ecoli-ypfh , ecoli-yqia , ecoli-Z1930 , ecoli-YfhR , ecout-q1r7l6 , yerpe-YBTT

Title : Pyrosequencing-based comparative genome analysis of the nosocomial pathogen Enterococcus faecium and identification of a large transferable pathogenicity island - van Schaik_2010_BMC.Genomics_11_239
Author(s) : van Schaik W , Top J , Riley DR , Boekhorst J , Vrijenhoek JE , Schapendonk CM , Hendrickx AP , Nijman IJ , Bonten MJ , Tettelin H , Willems RJ
Ref : BMC Genomics , 11 :239 , 2010
Abstract : BACKGROUND: The Gram-positive bacterium Enterococcus faecium is an important cause of nosocomial infections in immunocompromized patients.
RESULTS: We present a pyrosequencing-based comparative genome analysis of seven E. faecium strains that were isolated from various sources. In the genomes of clinical isolates several antibiotic resistance genes were identified, including the vanA transposon that confers resistance to vancomycin in two strains. A functional comparison between E. faecium and the related opportunistic pathogen E. faecalis based on differences in the presence of protein families, revealed divergence in plant carbohydrate metabolic pathways and oxidative stress defense mechanisms. The E. faecium pan-genome was estimated to be essentially unlimited in size, indicating that E. faecium can efficiently acquire and incorporate exogenous DNA in its gene pool. One of the most prominent sources of genomic diversity consists of bacteriophages that have integrated in the genome. The CRISPR-Cas system, which contributes to immunity against bacteriophage infection in prokaryotes, is not present in the sequenced strains. Three sequenced isolates carry the esp gene, which is involved in urinary tract infections and biofilm formation. The esp gene is located on a large pathogenicity island (PAI), which is between 64 and 104 kb in size. Conjugation experiments showed that the entire esp PAI can be transferred horizontally and inserts in a site-specific manner.
CONCLUSIONS: Genes involved in environmental persistence, colonization and virulence can easily be aquired by E. faecium. This will make the development of successful treatment strategies targeted against this organism a challenge for years to come.
ESTHER : van Schaik_2010_BMC.Genomics_11_239
PubMedSearch : van Schaik_2010_BMC.Genomics_11_239
PubMedID: 20398277
Gene_locus related to this paper: entfc-c2hcr4 , entfc-q3xwb2 , entfc-q3xwy1 , entfc-q3xzi8 , entfc-q3y367

Title : Acidithiobacillus ferrooxidans metabolism: from genome sequence to industrial applications - Valdes_2008_BMC.Genomics_9_597
Author(s) : Valdes J , Pedroso I , Quatrini R , Dodson RJ , Tettelin H , Blake R, 2nd , Eisen JA , Holmes DS
Ref : BMC Genomics , 9 :597 , 2008
Abstract : BACKGROUND: Acidithiobacillus ferrooxidans is a major participant in consortia of microorganisms used for the industrial recovery of copper (bioleaching or biomining). It is a chemolithoautrophic, gamma-proteobacterium using energy from the oxidation of iron- and sulfur-containing minerals for growth. It thrives at extremely low pH (pH 1-2) and fixes both carbon and nitrogen from the atmosphere. It solubilizes copper and other metals from rocks and plays an important role in nutrient and metal biogeochemical cycling in acid environments. The lack of a well-developed system for genetic manipulation has prevented thorough exploration of its physiology. Also, confusion has been caused by prior metabolic models constructed based upon the examination of multiple, and sometimes distantly related, strains of the microorganism. RESULTS: The genome of the type strain A. ferrooxidans ATCC 23270 was sequenced and annotated to identify general features and provide a framework for in silico metabolic reconstruction. Earlier models of iron and sulfur oxidation, biofilm formation, quorum sensing, inorganic ion uptake, and amino acid metabolism are confirmed and extended. Initial models are presented for central carbon metabolism, anaerobic metabolism (including sulfur reduction, hydrogen metabolism and nitrogen fixation), stress responses, DNA repair, and metal and toxic compound fluxes. CONCLUSION: Bioinformatics analysis provides a valuable platform for gene discovery and functional prediction that helps explain the activity of A. ferrooxidans in industrial bioleaching and its role as a primary producer in acidic environments. An analysis of the genome of the type strain provides a coherent view of its gene content and metabolic potential.
ESTHER : Valdes_2008_BMC.Genomics_9_597
PubMedSearch : Valdes_2008_BMC.Genomics_9_597
PubMedID: 19077236
Gene_locus related to this paper: acif2-b7j3y8 , acif2-b7j4u5 , acif2-b7j5z4 , acif2-b7j620 , acif2-metx

Title : Genome sequence of Avery's virulent serotype 2 strain D39 of Streptococcus pneumoniae and comparison with that of unencapsulated laboratory strain R6 - Lanie_2007_J.Bacteriol_189_38
Author(s) : Lanie JA , Ng WL , Kazmierczak KM , Andrzejewski TM , Davidsen TM , Wayne KJ , Tettelin H , Glass JI , Winkler ME
Ref : Journal of Bacteriology , 189 :38 , 2007
Abstract : Streptococcus pneumoniae (pneumococcus) is a leading human respiratory pathogen that causes a variety of serious mucosal and invasive diseases. D39 is an historically important serotype 2 strain that was used in experiments by Avery and coworkers to demonstrate that DNA is the genetic material. Although isolated nearly a century ago, D39 remains extremely virulent in murine infection models and is perhaps the strain used most frequently in current studies of pneumococcal pathogenesis. To date, the complete genome sequences have been reported for only two S. pneumoniae strains: TIGR4, a recent serotype 4 clinical isolate, and laboratory strain R6, an avirulent, unencapsulated derivative of strain D39. We report here the genome sequences and new annotation of two different isolates of strain D39 and the corrected sequence of strain R6. Comparisons of these three related sequences allowed deduction of the likely sequence of the D39 progenitor and mutations that arose in each isolate. Despite its numerous repeated sequences and IS elements, the serotype 2 genome has remained remarkably stable during cultivation, and one of the D39 isolates contains only five relatively minor mutations compared to the deduced D39 progenitor. In contrast, laboratory strain R6 contains 71 single-base-pair changes, six deletions, and four insertions and has lost the cryptic pDP1 plasmid compared to the D39 progenitor strain. Many of these mutations are in or affect the expression of genes that play important roles in regulation, metabolism, and virulence. The nature of the mutations that arose spontaneously in these three strains, the relative global transcription patterns determined by microarray analyses, and the implications of the D39 genome sequences to studies of pneumococcal physiology and pathogenesis are presented and discussed.
ESTHER : Lanie_2007_J.Bacteriol_189_38
PubMedSearch : Lanie_2007_J.Bacteriol_189_38
PubMedID: 17041037
Gene_locus related to this paper: strp2-q04l35 , strpj-b8zns7 , strpn-AXE1 , strpn-b2dz20 , strpn-pepx , strpn-SP0614 , strpn-SP1343

Title : Genome sequence and identification of candidate vaccine antigens from the animal pathogen Dichelobacter nodosus - Myers_2007_Nat.Biotechnol_25_569
Author(s) : Myers GS , Parker D , Al-Hasani K , Kennan RM , Seemann T , Ren Q , Badger JH , Selengut JD , DeBoy RT , Tettelin H , Boyce JD , McCarl VP , Han X , Nelson WC , Madupu R , Mohamoud Y , Holley T , Fedorova N , Khouri H , Bottomley SP , Whittington RJ , Adler B , Songer JG , Rood JI , Paulsen IT
Ref : Nat Biotechnol , 25 :569 , 2007
Abstract : Dichelobacter nodosus causes ovine footrot, a disease that leads to severe economic losses in the wool and meat industries. We sequenced its 1.4-Mb genome, the smallest known genome of an anaerobe. It differs markedly from small genomes of intracellular bacteria, retaining greater biosynthetic capabilities and lacking any evidence of extensive ongoing genome reduction. Comparative genomic microarray studies and bioinformatic analysis suggested that, despite its small size, almost 20% of the genome is derived from lateral gene transfer. Most of these regions seem to be associated with virulence. Metabolic reconstruction indicated unsuspected capabilities, including carbohydrate utilization, electron transfer and several aerobic pathways. Global transcriptional profiling and bioinformatic analysis enabled the prediction of virulence factors and cell surface proteins. Screening of these proteins against ovine antisera identified eight immunogenic proteins that are candidate antigens for a cross-protective vaccine.
ESTHER : Myers_2007_Nat.Biotechnol_25_569
PubMedSearch : Myers_2007_Nat.Biotechnol_25_569
PubMedID: 17468768
Gene_locus related to this paper: dicnv-a5evg0 , dicnv-a5ewn0 , dicnv-a5ewp3

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 : 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 : Phylogenomics of the reproductive parasite Wolbachia pipientis wMel: a streamlined genome overrun by mobile genetic elements - Wu_2004_PLoS.Biol_2_E69
Author(s) : Wu M , Sun LV , Vamathevan J , Riegler M , Deboy R , Brownlie JC , McGraw EA , Martin W , Esser C , Ahmadinejad N , Wiegand C , Madupu R , Beanan MJ , Brinkac LM , Daugherty SC , Durkin AS , Kolonay JF , Nelson WC , Mohamoud Y , Lee P , Berry K , Young MB , Utterback T , Weidman J , Nierman WC , Paulsen IT , Nelson KE , Tettelin H , O'Neill SL , Eisen JA
Ref : PLoS Biol , 2 :E69 , 2004
Abstract : The complete sequence of the 1,267,782 bp genome of Wolbachia pipientis wMel, an obligate intracellular bacteria of Drosophila melanogaster, has been determined. Wolbachia, which are found in a variety of invertebrate species, are of great interest due to their diverse interactions with different hosts, which range from many forms of reproductive parasitism to mutualistic symbioses. Analysis of the wMel genome, in particular phylogenomic comparisons with other intracellular bacteria, has revealed many insights into the biology and evolution of wMel and Wolbachia in general. For example, the wMel genome is unique among sequenced obligate intracellular species in both being highly streamlined and containing very high levels of repetitive DNA and mobile DNA elements. This observation, coupled with multiple evolutionary reconstructions, suggests that natural selection is somewhat inefficient in wMel, most likely owing to the occurrence of repeated population bottlenecks. Genome analysis predicts many metabolic differences with the closely related Rickettsia species, including the presence of intact glycolysis and purine synthesis, which may compensate for an inability to obtain ATP directly from its host, as Rickettsia can. Other discoveries include the apparent inability of wMel to synthesize lipopolysaccharide and the presence of the most genes encoding proteins with ankyrin repeat domains of any prokaryotic genome yet sequenced. Despite the ability of wMel to infect the germline of its host, we find no evidence for either recent lateral gene transfer between wMel and D. melanogaster or older transfers between Wolbachia and any host. Evolutionary analysis further supports the hypothesis that mitochondria share a common ancestor with the alpha-Proteobacteria, but shows little support for the grouping of mitochondria with species in the order Rickettsiales. With the availability of the complete genomes of both species and excellent genetic tools for the host, the wMel-D. melanogaster symbiosis is now an ideal system for studying the biology and evolution of Wolbachia infections.
ESTHER : Wu_2004_PLoS.Biol_2_E69
PubMedSearch : Wu_2004_PLoS.Biol_2_E69
PubMedID: 15024419
Gene_locus related to this paper: wolpm-q73gf0 , wolpm-q73gx7

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 : Genomic insights into methanotrophy: the complete genome sequence of Methylococcus capsulatus (Bath) - Ward_2004_PLoS.Biol_2_e303
Author(s) : Ward N , Larsen O , Sakwa J , Bruseth L , Khouri H , Durkin AS , Dimitrov G , Jiang L , Scanlan D , Kang KH , Lewis M , Nelson KE , Methe B , Wu M , Heidelberg JF , Paulsen IT , Fouts D , Ravel J , Tettelin H , Ren Q , Read T , DeBoy RT , Seshadri R , Salzberg SL , Jensen HB , Birkeland NK , Nelson WC , Dodson RJ , Grindhaug SH , Holt I , Eidhammer I , Jonasen I , Vanaken S , Utterback T , Feldblyum TV , Fraser CM , Lillehaug JR , Eisen JA
Ref : PLoS Biol , 2 :e303 , 2004
Abstract : Methanotrophs are ubiquitous bacteria that can use the greenhouse gas methane as a sole carbon and energy source for growth, thus playing major roles in global carbon cycles, and in particular, substantially reducing emissions of biologically generated methane to the atmosphere. Despite their importance, and in contrast to organisms that play roles in other major parts of the carbon cycle such as photosynthesis, no genome-level studies have been published on the biology of methanotrophs. We report the first complete genome sequence to our knowledge from an obligate methanotroph, Methylococcus capsulatus (Bath), obtained by the shotgun sequencing approach. Analysis revealed a 3.3-Mb genome highly specialized for a methanotrophic lifestyle, including redundant pathways predicted to be involved in methanotrophy and duplicated genes for essential enzymes such as the methane monooxygenases. We used phylogenomic analysis, gene order information, and comparative analysis with the partially sequenced methylotroph Methylobacterium extorquens to detect genes of unknown function likely to be involved in methanotrophy and methylotrophy. Genome analysis suggests the ability of M. capsulatus to scavenge copper (including a previously unreported nonribosomal peptide synthetase) and to use copper in regulation of methanotrophy, but the exact regulatory mechanisms remain unclear. One of the most surprising outcomes of the project is evidence suggesting the existence of previously unsuspected metabolic flexibility in M. capsulatus, including an ability to grow on sugars, oxidize chemolithotrophic hydrogen and sulfur, and live under reduced oxygen tension, all of which have implications for methanotroph ecology. The availability of the complete genome of M. capsulatus (Bath) deepens our understanding of methanotroph biology and its relationship to global carbon cycles. We have gained evidence for greater metabolic flexibility than was previously known, and for genetic components that may have biotechnological potential.
ESTHER : Ward_2004_PLoS.Biol_2_e303
PubMedSearch : Ward_2004_PLoS.Biol_2_e303
PubMedID: 15383840
Gene_locus related to this paper: metca-q60a38 , metca-q60bu6 , metca-q60cn0 , metca-q605j8 , metca-q606x9 , metca-q607f7 , metca-q607m2 , metca-q609v0

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 : 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 : Role of mobile DNA in the evolution of vancomycin-resistant Enterococcus faecalis - Paulsen_2003_Science_299_2071
Author(s) : Paulsen IT , Banerjei L , Myers GS , Nelson KE , Seshadri R , Read TD , Fouts DE , Eisen JA , Gill SR , Heidelberg JF , Tettelin H , Dodson RJ , Umayam L , Brinkac L , Beanan M , Daugherty S , DeBoy RT , Durkin S , Kolonay J , Madupu R , Nelson W , Vamathevan J , Tran B , Upton J , Hansen T , Shetty J , Khouri H , Utterback T , Radune D , Ketchum KA , Dougherty BA , Fraser CM
Ref : Science , 299 :2071 , 2003
Abstract : The complete genome sequence of Enterococcus faecalis V583, a vancomycin-resistant clinical isolate, revealed that more than a quarter of the genome consists of probable mobile or foreign DNA. One of the predicted mobile elements is a previously unknown vanB vancomycin-resistance conjugative transposon. Three plasmids were identified, including two pheromone-sensing conjugative plasmids, one encoding a previously undescribed pheromone inhibitor. The apparent propensity for the incorporation of mobile elements probably contributed to the rapid acquisition and dissemination of drug resistance in the enterococci.
ESTHER : Paulsen_2003_Science_299_2071
PubMedSearch : Paulsen_2003_Science_299_2071
PubMedID: 12663927
Gene_locus related to this paper: entfa-EF0101 , entfa-EF0274 , entfa-EF0381 , entfa-EF0449 , entfa-EF0667 , entfa-EF0786 , entfa-EF1028 , entfa-EF1236 , entfa-EF1505 , entfa-EF1536 , entfa-EF1670 , entfa-EF2618 , entfa-EF2728 , entfa-EF2792 , entfa-EF2963 , entfa-EF3191

Title : Complete genome sequence of the Q-fever pathogen Coxiella burnetii - Seshadri_2003_Proc.Natl.Acad.Sci.U.S.A_100_5455
Author(s) : Seshadri R , Paulsen IT , Eisen JA , Read TD , Nelson KE , Nelson WC , Ward NL , Tettelin H , Davidsen TM , Beanan MJ , DeBoy RT , Daugherty SC , Brinkac LM , Madupu R , Dodson RJ , Khouri HM , Lee KH , Carty HA , Scanlan D , Heinzen RA , Thompson HA , Samuel JE , Fraser CM , Heidelberg JF
Ref : Proc Natl Acad Sci U S A , 100 :5455 , 2003
Abstract : The 1,995,275-bp genome of Coxiella burnetii, Nine Mile phase I RSA493, a highly virulent zoonotic pathogen and category B bioterrorism agent, was sequenced by the random shotgun method. This bacterium is an obligate intracellular acidophile that is highly adapted for life within the eukaryotic phagolysosome. Genome analysis revealed many genes with potential roles in adhesion, invasion, intracellular trafficking, host-cell modulation, and detoxification. A previously uncharacterized 13-member family of ankyrin repeat-containing proteins is implicated in the pathogenesis of this organism. Although the lifestyle and parasitic strategies of C. burnetii resemble that of Rickettsiae and Chlamydiae, their genome architectures differ considerably in terms of presence of mobile elements, extent of genome reduction, metabolic capabilities, and transporter profiles. The presence of 83 pseudogenes displays an ongoing process of gene degradation. Unlike other obligate intracellular bacteria, 32 insertion sequences are found dispersed in the chromosome, indicating some plasticity in the C. burnetii genome. These analyses suggest that the obligate intracellular lifestyle of C. burnetii may be a relatively recent innovation.
ESTHER : Seshadri_2003_Proc.Natl.Acad.Sci.U.S.A_100_5455
PubMedSearch : Seshadri_2003_Proc.Natl.Acad.Sci.U.S.A_100_5455
PubMedID: 12704232
Gene_locus related to this paper: coxbu-BIOH , coxbu-CBU0752 , coxbu-CBU1119 , coxbu-CBU1225 , coxbu-CBU1529 , coxbu-CBU1769 , coxbu-CBU1975

Title : The Brucella suis genome reveals fundamental similarities between animal and plant pathogens and symbionts - Paulsen_2002_Proc.Natl.Acad.Sci.U.S.A_99_13148
Author(s) : Paulsen IT , Seshadri R , Nelson KE , Eisen JA , Heidelberg JF , Read TD , Dodson RJ , Umayam L , Brinkac LM , Beanan MJ , Daugherty SC , DeBoy RT , Durkin AS , Kolonay JF , Madupu R , Nelson WC , Ayodeji B , Kraul M , Shetty J , Malek J , Van Aken SE , Riedmuller S , Tettelin H , Gill SR , White O , Salzberg SL , Hoover DL , Lindler LE , Halling SM , Boyle SM , Fraser CM
Ref : Proc Natl Acad Sci U S A , 99 :13148 , 2002
Abstract : The 3.31-Mb genome sequence of the intracellular pathogen and potential bioterrorism agent, Brucella suis, was determined. Comparison of B. suis with Brucella melitensis has defined a finite set of differences that could be responsible for the differences in virulence and host preference between these organisms, and indicates that phage have played a significant role in their divergence. Analysis of the B. suis genome reveals transport and metabolic capabilities akin to soil/plant-associated bacteria. Extensive gene synteny between B. suis chromosome 1 and the genome of the plant symbiont Mesorhizobium loti emphasizes the similarity between this animal pathogen and plant pathogens and symbionts. A limited repertoire of genes homologous to known bacterial virulence factors were identified.
ESTHER : Paulsen_2002_Proc.Natl.Acad.Sci.U.S.A_99_13148
PubMedSearch : Paulsen_2002_Proc.Natl.Acad.Sci.U.S.A_99_13148
PubMedID: 12271122
Gene_locus related to this paper: brume-BMEI0552 , brume-BMEI0733 , brume-BMEI1044 , brume-BMEI1119 , brume-BMEI1365 , brume-BMEI1594 , brume-BMEI1608 , brume-BMEI1822 , brume-BMEI1884 , brume-BMEI1951 , brume-BMEI2011 , brume-BMEII0047 , brume-BMEII0681 , brume-BMEII0989 , brume-PCAD , brusu-BR0288 , brusu-BR1291 , brusu-BR1327 , brusu-BRA0989

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 and comparative genomic analysis of an emerging human pathogen, serotype V Streptococcus agalactiae - Tettelin_2002_Proc.Natl.Acad.Sci.U.S.A_99_12391
Author(s) : Tettelin H , Masignani V , Cieslewicz MJ , Eisen JA , Peterson S , Wessels MR , Paulsen IT , Nelson KE , Margarit I , Read TD , Madoff LC , Wolf AM , Beanan MJ , Brinkac LM , Daugherty SC , DeBoy RT , Durkin AS , Kolonay JF , Madupu R , Lewis MR , Radune D , Fedorova NB , Scanlan D , Khouri H , Mulligan S , Carty HA , Cline RT , Van Aken SE , Gill J , Scarselli M , Mora M , Iacobini ET , Brettoni C , Galli G , Mariani M , Vegni F , Maione D , Rinaudo D , Rappuoli R , Telford JL , Kasper DL , Grandi G , Fraser CM
Ref : Proc Natl Acad Sci U S A , 99 :12391 , 2002
Abstract : The 2,160,267 bp genome sequence of Streptococcus agalactiae, the leading cause of bacterial sepsis, pneumonia, and meningitis in neonates in the U.S. and Europe, is predicted to encode 2,175 genes. Genome comparisons among S. agalactiae, Streptococcus pneumoniae, Streptococcus pyogenes, and the other completely sequenced genomes identified genes specific to the streptococci and to S. agalactiae. These in silico analyses, combined with comparative genome hybridization experiments between the sequenced serotype V strain 2603 V/R and 19 S. agalactiae strains from several serotypes using whole-genome microarrays, revealed the genetic heterogeneity among S. agalactiae strains, even of the same serotype, and provided insights into the evolution of virulence mechanisms.
ESTHER : Tettelin_2002_Proc.Natl.Acad.Sci.U.S.A_99_12391
PubMedSearch : Tettelin_2002_Proc.Natl.Acad.Sci.U.S.A_99_12391
PubMedID: 12200547
Gene_locus related to this paper: strag-ESTA , strag-GBS0040 , strag-GBS1828 , strag-pepx , strag-SAG0108 , strag-SAG0246 , strag-SAG0383 , strag-SAG0521 , strag-SAG0679 , strag-SAG0680 , strag-SAG0681 , strag-SAG0785 , strag-SAG0912 , strag-SAG1040 , strag-SAG1562 , strag-SAG2132

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 : The malaria genome sequencing project: complete sequence of Plasmodium falciparum chromosome 2 - Gardner_1999_Parassitologia_41_69
Author(s) : Gardner MJ , Tettelin H , Carucci DJ , Cummings LM , Smith HO , Fraser CM , Venter JC , Hoffman SL
Ref : Parassitologia , 41 :69 , 1999
Abstract : An international consortium has been formed to sequence the entire genome of the human malaria parasite Plasmodium falciparum. We sequenced chromosome 2 of clone 3D7 using a shotgun sequencing strategy. Chromosome 2 is 947 kb in length, has a base composition of 80.2% A + T, and contains 210 predicted genes. In comparison to the Saccharomyces cerevisiae genome, chromosome 2 has a lower gene density, a greater proportion of genes containing introns, and nearly twice as many proteins containing predicted non-globular domains. A group of putative surface proteins was identified, rifins, which are encoded by a gene family comprising up to 7% of the protein-encoding gene in the genome. The rifins exhibit considerable sequence diversity and may play an important role in antigenic variation. Sixteen genes encoded on chromosome 2 showed signs of a plastid or mitochondrial origin, including several genes involved in fatty acid biosynthesis. Completion of the chromosome 2 sequence demonstrated that the A + T-rich genome of P. falciparum can be sequenced by the shotgun approach. Within 2-3 years, the sequence of almost all P. falciparum genes will have been determined, paving the way for genetic, biochemical, and immunological research aimed at developing new drugs and vaccines against malaria.
ESTHER : Gardner_1999_Parassitologia_41_69
PubMedSearch : Gardner_1999_Parassitologia_41_69
PubMedID: 10697835

Title : Chromosome 2 sequence of the human malaria parasite Plasmodium falciparum - Gardner_1998_Science_282_1126
Author(s) : Gardner MJ , Tettelin H , Carucci DJ , Cummings LM , Aravind L , Koonin EV , Shallom S , Mason T , Yu K , Fujii C , Pederson J , Shen K , Jing J , Aston C , Lai Z , Schwartz DC , Pertea M , Salzberg S , Zhou L , Sutton GG , Clayton R , White O , Smith HO , Fraser CM , Hoffman SL
Ref : Science , 282 :1126 , 1998
Abstract : Chromosome 2 of Plasmodium falciparum was sequenced; this sequence contains 947,103 base pairs and encodes 210 predicted genes. In comparison with the Saccharomyces cerevisiae genome, chromosome 2 has a lower gene density, introns are more frequent, and proteins are markedly enriched in nonglobular domains. A family of surface proteins, rifins, that may play a role in antigenic variation was identified. The complete sequencing of chromosome 2 has shown that sequencing of the A+T-rich P. falciparum genome is technically feasible.
ESTHER : Gardner_1998_Science_282_1126
PubMedSearch : Gardner_1998_Science_282_1126
PubMedID: 9804551

Title : The nucleotide sequence of Saccharomyces cerevisiae chromosome XV - Dujon_1997_Nature_387_98
Author(s) : Dujon B , Albermann K , Aldea M , Alexandraki D , Ansorge W , Arino J , Benes V , Bohn C , Bolotin-Fukuhara M , Bordonne R , Boyer J , Camasses A , Casamayor A , Casas C , Cheret G , Cziepluch C , Daignan-Fornier B , Dang DV , de Haan M , Delius H , Durand P , Fairhead C , Feldmann H , Gaillon L , Galisson F , Gamo FJ , Gancedo C , Goffeau A , Goulding SE , Grivell LA , Habbig B , Hand NJ , Hani J , Hattenhorst U , Hebling U , Hernando Y , Herrero E , Heumann K , Hiesel R , Hilger F , Hofmann B , Hollenberg CP , Hughes B , Jauniaux JC , Kalogeropoulos A , Katsoulou C , Kordes E , Lafuente MJ , Landt O , Louis EJ , Maarse AC , Madania A , Mannhaupt G , Marck C , Martin RP , Mewes HW , Michaux G , Paces V , Parle-McDermott AG , Pearson BM , Perrin A , Pettersson B , Poch O , Pohl TM , Poirey R , Portetelle D , Pujol A , Purnelle B , Ramezani Rad M , Rechmann S , Schwager C , Schweizer M , Sor F , Sterky F , Tarassov IA , Teodoru C , Tettelin H , Thierry A , Tobiasch E , Tzermia M , Uhlen M , Unseld M , Valens M , Vandenbol M , Vetter I , Vlcek C , Voet M , Volckaert G , Voss H , Wambutt R , Wedler H , Wiemann S , Winsor B , Wolfe KH , Zollner A , Zumstein E , Kleine K
Ref : Nature , 387 :98 , 1997
Abstract : Chromosome XV was one of the last two chromosomes of Saccharomyces cerevisiae to be discovered. It is the third-largest yeast chromosome after chromosomes XII and IV, and is very similar in size to chromosome VII. It alone represents 9% of the yeast genome (8% if ribosomal DNA is included). When systematic sequencing of chromosome XV was started, 93 genes or markers were identified, and most of them were mapped. However, very little else was known about chromosome XV which, in contrast to shorter chromosomes, had not been the object of comprehensive genetic or molecular analysis. It was therefore decided to start sequencing chromosome XV only in the third phase of the European Yeast Genome Sequencing Programme, after experience was gained on chromosomes III, XI and II. The sequence of chromosome XV has been determined from a set of partly overlapping cosmid clones derived from a unique yeast strain, and physically mapped at 3.3-kilobase resolution before sequencing. As well as numerous new open reading frames (ORFs) and genes encoding tRNA or small RNA molecules, the sequence of 1,091,283 base pairs confirms the high proportion of orphan genes and reveals a number of ancestral and successive duplications with other yeast chromosomes.
ESTHER : Dujon_1997_Nature_387_98
PubMedSearch : Dujon_1997_Nature_387_98
PubMedID: 9169874
Gene_locus related to this paper: yeast-FSH3 , yeast-yo059

Title : The nucleotide sequence of Saccharomyces cerevisiae chromosome XVI - Bussey_1997_Nature_387_103
Author(s) : Bussey H , Storms RK , Ahmed A , Albermann K , Allen E , Ansorge W , Araujo R , Aparicio A , Barrell B , Badcock K , Benes V , Botstein D , Bowman S , Bruckner M , Carpenter J , Cherry JM , Chung E , Churcher C , Coster F , Davis K , Davis RW , Dietrich FS , Delius H , DiPaolo T , Dubois E , Dusterhoft A , Duncan M , Floeth M , Fortin N , Friesen JD , Fritz C , Goffeau A , Hall J , Hebling U , Heumann K , Hilbert H , Hillier L , Hunicke-Smith S , Hyman R , Johnston M , Kalman S , Kleine K , Komp C , Kurdi O , Lashkari D , Lew H , Lin A , Lin D , Louis EJ , Marathe R , Messenguy F , Mewes HW , Mirtipati S , Moestl D , Muller-Auer S , Namath A , Nentwich U , Oefner P , Pearson D , Petel FX , Pohl TM , Purnelle B , Rajandream MA , Rechmann S , Rieger M , Riles L , Roberts D , Schafer M , Scharfe M , Scherens B , Schramm S , Schroder M , Sdicu AM , Tettelin H , Urrestarazu LA , Ushinsky S , Vierendeels F , Vissers S , Voss H , Walsh SV , Wambutt R , Wang Y , Wedler E , Wedler H , Winnett E , Zhong WW , Zollner A , Vo DH , Hani J
Ref : Nature , 387 :103 , 1997
Abstract : The nucleotide sequence of the 948,061 base pairs of chromosome XVI has been determined, completing the sequence of the yeast genome. Chromosome XVI was the last yeast chromosome identified, and some of the genes mapped early to it, such as GAL4, PEP4 and RAD1 (ref. 2) have played important roles in the development of yeast biology. The architecture of this final chromosome seems to be typical of the large yeast chromosomes, and shows large duplications with other yeast chromosomes. Chromosome XVI contains 487 potential protein-encoding genes, 17 tRNA genes and two small nuclear RNA genes; 27% of the genes have significant similarities to human gene products, and 48% are new and of unknown biological function. Systematic efforts to explore gene function have begun.
ESTHER : Bussey_1997_Nature_387_103
PubMedSearch : Bussey_1997_Nature_387_103
PubMedID: 9169875
Gene_locus related to this paper: yeast-MCFS1 , yeast-YPR147C

Title : The nucleotide sequence of Saccharomyces cerevisiae chromosome VII - Tettelin_1997_Nature_387_81
Author(s) : Tettelin H , Agostoni Carbone ML , Albermann K , Albers M , Arroyo J , Backes U , Barreiros T , Bertani I , Bjourson AJ , Bruckner M , Bruschi CV , Carignani G , Castagnoli L , Cerdan E , Clemente ML , Coblenz A , Coglievina M , Coissac E , Defoor E , Del Bino S , Delius H , Delneri D , de Wergifosse P , Dujon B , Kleine K , et al.
Ref : Nature , 387 :81 , 1997
Abstract : The complete nucleotide sequence of Saccharomyces cerevisiae chromosome VII has 572 predicted open reading frames (ORFs), of which 341 are new. No correlation was found between G+C content and gene density along the chromosome, and their variations are random. Of the ORFs, 17% show high similarity to human proteins. Almost half of the ORFs could be classified in functional categories, and there is a slight increase in the number of transcription (7.0%) and translation (5.2%) factors when compared with the complete S. cerevisiae genome. Accurate verification procedures demonstrate that there are less than two errors per 10,000 base pairs in the published sequence.
ESTHER : Tettelin_1997_Nature_387_81
PubMedSearch : Tettelin_1997_Nature_387_81
PubMedID: 9169869
Gene_locus related to this paper: yeast-ROG1 , yeast-SAY1

Title : Life with 6000 genes - Goffeau_1996_Science_274_563
Author(s) : Goffeau A , Barrell BG , Bussey H , Davis RW , Dujon B , Feldmann H , Galibert F , Hoheisel JD , Jacq C , Johnston M , Louis EJ , Mewes HW , Murakami Y , Philippsen P , Tettelin H , Oliver SG
Ref : Science , 274 :546 , 1996
Abstract : The genome of the yeast Saccharomyces cerevisiae has been completely sequenced through a worldwide collaboration. The sequence of 12,068 kilobases defines 5885 potential protein-encoding genes, approximately 140 genes specifying ribosomal RNA, 40 genes for small nuclear RNA molecules, and 275 transfer RNA genes. In addition, the complete sequence provides information about the higher order organization of yeast's 16 chromosomes and allows some insight into their evolutionary history. The genome shows a considerable amount of apparent genetic redundancy, and one of the major problems to be tackled during the next stage of the yeast genome project is to elucidate the biological functions of all of these genes.
ESTHER : Goffeau_1996_Science_274_563
PubMedSearch : Goffeau_1996_Science_274_563
PubMedID: 8849441
Gene_locus related to this paper: yeast-ATG15 , yeast-SAY1

Title : Complete DNA sequence of yeast chromosome XI - Dujon_1994_Nature_369_371
Author(s) : Dujon B , Alexandraki D , Andre B , Ansorge W , Baladron V , Ballesta JP , Banrevi A , Bolle PA , Bolotin-Fukuhara M , Bossier P , Bou G , Boyer J , Bultrago MJ , Cheret G , Colleaux L , Dalgnan-Fornler B , del Rey F , Dlon C , Domdey H , Dsterhoft A , Dsterhus S , Entlan KD , Erfle H , Esteban PF , Feldmann H , Fernandes L , Robo GM , Fritz C , Fukuhara H , Gabel C , Gaillon L , Carcia-Cantalejo JM , Garcia-Ramirez JJ , Gent NE , Ghazvini M , Goffeau A , Gonzalez A , Grothues D , Guerreiro P , Hegemann J , Hewitt N , Hilger F , Hollenberg CP , Horaitis O , Indge KJ , Jacquier A , James CM , Jauniaux C , Jimenez A , Keuchel H , Kirchrath L , Kleine K , Ktter P , Legrain P , Liebl S , Louis EJ , Maia e Silva A , Marck C , Monnier AL , Mostl D , Mller S , Obermaier B , Oliver SG , Pallier C , Pascolo S , Pfeiffer F , Philippsen P , Planta RJ , Pohl FM , Pohl TM , Pohlmann R , Portetelle D , Purnelle B , Puzos V , Ramezani Rad M , Rasmussen SW , Remacha M , Revuelta JL , Richard GF , Rieger M , Rodrigues-Pousada C , Rose M , Rupp T , Santos MA , Schwager C , Sensen C , Skala J , Soares H , Sor F , Stegemann J , Tettelin H , Thierry A , Tzermia M , Urrestarazu LA , van Dyck L , Van Vliet-Reedijk JC , Valens M , Vandenbo M , Vilela C , Vissers S , von Wettstein D , Voss H , Wiemann S , Xu G , Zimmermann J , Haasemann M , Becker I , Mewes HW
Ref : Nature , 369 :371 , 1994
Abstract : The complete DNA sequence of the yeast Saccharomyces cerevisiae chromosome XI has been determined. In addition to a compact arrangement of potential protein coding sequences, the 666,448-base-pair sequence has revealed general chromosome patterns; in particular, alternating regional variations in average base composition correlate with variations in local gene density along the chromosome. Significant discrepancies with the previously published genetic map demonstrate the need for using independent physical mapping criteria.
ESTHER : Dujon_1994_Nature_369_371
PubMedSearch : Dujon_1994_Nature_369_371
PubMedID: 8196765
Gene_locus related to this paper: yeast-mgll