Daugherty SC

References (33)

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 : Draft genome sequences of the diarrheagenic Escherichia coli collection - Hazen_2012_J.Bacteriol_194_3026
Author(s) : Hazen TH , Sahl JW , Redman JC , Morris CR , Daugherty SC , Chibucos MC , Sengamalay NA , Fraser-Liggett CM , Steinsland H , Whittam TS , Whittam B , Manning SD , Rasko DA
Ref : Journal of Bacteriology , 194 :3026 , 2012
Abstract : We report the draft genome sequences of the collection referred to as the Escherichia coli DECA collection, which was assembled to contain representative isolates of the 15 most common diarrheagenic clones in humans (http:\/\/shigatox.net/new/). These genomes represent a valuable resource to the community of researchers who examine these enteric pathogens.
ESTHER : Hazen_2012_J.Bacteriol_194_3026
PubMedSearch : Hazen_2012_J.Bacteriol_194_3026
PubMedID: 22582382
Gene_locus related to this paper: ecoli-d7xp23 , ecoli-fes , ecoli-MCMK , ecoli-yaim , ecoli-ybff , ecoli-ycfp , ecoli-YFBB , ecoli-yhet , ecoli-yiel , ecoli-ypt1 , ecoli-yqia , ecoli-Z1341 , ecoli-Z1930 , ecoli-YfhR

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 : An Enterotoxin-Bearing Pathogenicity Island in Staphylococcus epidermidis - Madhusoodanan_2011_J.Bacteriol_193_1854
Author(s) : Madhusoodanan J , Seo KS , Remortel B , Park JY , Hwang SY , Fox LK , Park YH , Deobald CF , Wang D , Liu S , Daugherty SC , Gill AL , Bohach GA , Gill SR
Ref : Journal of Bacteriology , 193 :1854 , 2011
Abstract : Cocolonization of human mucosal surfaces causes frequent encounters between various staphylococcal species, creating opportunities for the horizontal acquisition of mobile genetic elements. The majority of Staphylococcus aureus toxins and virulence factors are encoded on S. aureus pathogenicity islands (SaPIs). Horizontal movement of SaPIs between S. aureus strains plays a role in the evolution of virulent clinical isolates. Although there have been reports of the production of toxic shock syndrome toxin 1 (TSST-1), enterotoxin, and other superantigens by coagulase-negative staphylococci, no associated pathogenicity islands have been found in the genome of Staphylococcus epidermidis, a generally less virulent relative of S. aureus. We show here the first evidence of a composite S. epidermidis pathogenicity island (SePI), the product of multiple insertions in the genome of a clinical isolate. The taxonomic placement of S. epidermidis strain FRI909 was confirmed by a number of biochemical tests and multilocus sequence typing. The genome sequence of this strain was analyzed for other unique gene clusters and their locations. This pathogenicity island encodes and expresses staphylococcal enterotoxin C3 (SEC3) and staphylococcal enterotoxin-like toxin L (SElL), as confirmed by quantitative reverse transcription-PCR (qRT-PCR) and immunoblotting. We present here an initial characterization of this novel pathogenicity island, and we establish that it is stable, expresses enterotoxins, and is not obviously transmissible by phage transduction. We also describe the genome sequence, excision, replication, and packaging of a novel bacteriophage in S. epidermidis FRI909, as well as attempts to mobilize the SePI element by this phage.
ESTHER : Madhusoodanan_2011_J.Bacteriol_193_1854
PubMedSearch : Madhusoodanan_2011_J.Bacteriol_193_1854
PubMedID: 21317317
Gene_locus related to this paper: staep-SE0386 , staep-SE0389 , staep-SE0424 , staep-SE0564 , staep-SE0980 , staep-SE1436 , staep-SE1460 , staep-SE1510 , staep-SE1929 , staep-SERP2035 , staep-SE2328

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 : Secrets of soil survival revealed by the genome sequence of Arthrobacter aurescens TC1 - Mongodin_2006_PLoS.Genet_2_e214
Author(s) : Mongodin EF , Shapir N , Daugherty SC , DeBoy RT , Emerson JB , Shvartzbeyn A , Radune D , Vamathevan J , Riggs F , Grinberg V , Khouri H , Wackett LP , Nelson KE , Sadowsky MJ
Ref : PLoS Genet , 2 :e214 , 2006
Abstract : Arthrobacter sp. strains are among the most frequently isolated, indigenous, aerobic bacterial genera found in soils. Member of the genus are metabolically and ecologically diverse and have the ability to survive in environmentally harsh conditions for extended periods of time. The genome of Arthrobacter aurescens strain TC1, which was originally isolated from soil at an atrazine spill site, is composed of a single 4,597,686 basepair (bp) circular chromosome and two circular plasmids, pTC1 and pTC2, which are 408,237 bp and 300,725 bp, respectively. Over 66% of the 4,702 open reading frames (ORFs) present in the TC1 genome could be assigned a putative function, and 13.2% (623 genes) appear to be unique to this bacterium, suggesting niche specialization. The genome of TC1 is most similar to that of Tropheryma, Leifsonia, Streptomyces, and Corynebacterium glutamicum, and analyses suggest that A. aurescens TC1 has expanded its metabolic abilities by relying on the duplication of catabolic genes and by funneling metabolic intermediates generated by plasmid-borne genes to chromosomally encoded pathways. The data presented here suggest that Arthrobacter's environmental prevalence may be due to its ability to survive under stressful conditions induced by starvation, ionizing radiation, oxygen radicals, and toxic chemicals.
ESTHER : Mongodin_2006_PLoS.Genet_2_e214
PubMedSearch : Mongodin_2006_PLoS.Genet_2_e214
PubMedID: 17194220
Gene_locus related to this paper: artat-a1r1g1 , artat-a1r2c8 , artat-a1r3u0 , artat-a1r3x5 , artat-a1r4v1 , artat-a1r5d9 , artat-a1r6c9 , artat-a1r6v0 , artat-a1r6v1 , artat-a1r6y1 , artat-a1r7h1 , artat-a1r7q0 , artat-a1r7v1 , artat-a1r9g3 , artat-a1r9t7 , artat-a1r9u8 , artat-a1r171 , artat-a1r172 , artat-a1r173 , artat-a1r612 , artat-a1r682 , artat-a1ra89 , artat-a1ra98 , artat-a1ram7 , artat-a1rb20 , artat-a1rbd0 , artat-a1rbi2 , artat-a1rbl7 , artat-a1rbz2 , artat-a1r0x8 , artat-a1r1x6 , artat-a1r6f6

Title : Metabolic complementarity and genomics of the dual bacterial symbiosis of sharpshooters - Wu_2006_PLoS.Biol_4_e188
Author(s) : Wu D , Daugherty SC , Van Aken SE , Pai GH , Watkins KL , Khouri H , Tallon LJ , Zaborsky JM , Dunbar HE , Tran PL , Moran NA , Eisen JA
Ref : PLoS Biol , 4 :e188 , 2006
Abstract : Mutualistic intracellular symbiosis between bacteria and insects is a widespread phenomenon that has contributed to the global success of insects. The symbionts, by provisioning nutrients lacking from diets, allow various insects to occupy or dominate ecological niches that might otherwise be unavailable. One such insect is the glassy-winged sharpshooter (Homalodisca coagulata), which feeds on xylem fluid, a diet exceptionally poor in organic nutrients. Phylogenetic studies based on rRNA have shown two types of bacterial symbionts to be coevolving with sharpshooters: the gamma-proteobacterium Baumannia cicadellinicola and the Bacteroidetes species Sulcia muelleri. We report here the sequencing and analysis of the 686,192-base pair genome of B. cicadellinicola and approximately 150 kilobase pairs of the small genome of S. muelleri, both isolated from H. coagulata. Our study, which to our knowledge is the first genomic analysis of an obligate symbiosis involving multiple partners, suggests striking complementarity in the biosynthetic capabilities of the two symbionts: B. cicadellinicola devotes a substantial portion of its genome to the biosynthesis of vitamins and cofactors required by animals and lacks most amino acid biosynthetic pathways, whereas S. muelleri apparently produces most or all of the essential amino acids needed by its host. This finding, along with other results of our genome analysis, suggests the existence of metabolic codependency among the two unrelated endosymbionts and their insect host. This dual symbiosis provides a model case for studying correlated genome evolution and genome reduction involving multiple organisms in an intimate, obligate mutualistic relationship. In addition, our analysis provides insight for the first time into the differences in symbionts between insects (e.g., aphids) that feed on phloem versus those like H. coagulata that feed on xylem. Finally, the genomes of these two symbionts provide potential targets for controlling plant pathogens such as Xylella fastidiosa, a major agroeconomic problem, for which H. coagulata and other sharpshooters serve as vectors of transmission.
ESTHER : Wu_2006_PLoS.Biol_4_e188
PubMedSearch : Wu_2006_PLoS.Biol_4_e188
PubMedID: 16729848
Gene_locus related to this paper: bauch-q1lsz2

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 : Genome sequence of Synechococcus CC9311: Insights into adaptation to a coastal environment - Palenik_2006_Proc.Natl.Acad.Sci.U.S.A_103_13555
Author(s) : Palenik B , Ren Q , Dupont CL , Myers GS , Heidelberg JF , Badger JH , Madupu R , Nelson WC , Brinkac LM , Dodson RJ , Durkin AS , Daugherty SC , Sullivan SA , Khouri H , Mohamoud Y , Halpin R , Paulsen IT
Ref : Proc Natl Acad Sci U S A , 103 :13555 , 2006
Abstract : Coastal aquatic environments are typically more highly productive and dynamic than open ocean ones. Despite these differences, cyanobacteria from the genus Synechococcus are important primary producers in both types of ecosystems. We have found that the genome of a coastal cyanobacterium, Synechococcus sp. strain CC9311, has significant differences from an open ocean strain, Synechococcus sp. strain WH8102, and these are consistent with the differences between their respective environments. CC9311 has a greater capacity to sense and respond to changes in its (coastal) environment. It has a much larger capacity to transport, store, use, or export metals, especially iron and copper. In contrast, phosphate acquisition seems less important, consistent with the higher concentration of phosphate in coastal environments. CC9311 is predicted to have differences in its outer membrane lipopolysaccharide, and this may be characteristic of the speciation of some cyanobacterial groups. In addition, the types of potentially horizontally transferred genes are markedly different between the coastal and open ocean genomes and suggest a more prominent role for phages in horizontal gene transfer in oligotrophic environments.
ESTHER : Palenik_2006_Proc.Natl.Acad.Sci.U.S.A_103_13555
PubMedSearch : Palenik_2006_Proc.Natl.Acad.Sci.U.S.A_103_13555
PubMedID: 16938853
Gene_locus related to this paper: syns3-q0i8r7 , syns3-q0i9w2 , syns3-q0i996 , syns3-q0ia13 , syns3-q0ia55 , syns3-q0ib73 , syns3-q0ibm2 , syns3-q0ibp1 , syns3-q0iby1 , syns9-q3ax89 , syns3-q0ibv4

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 : Complete genome sequence of the plant commensal Pseudomonas fluorescens Pf-5 - Paulsen_2005_Nat.Biotechnol_23_873
Author(s) : Paulsen IT , Press CM , Ravel J , Kobayashi DY , Myers GS , Mavrodi DV , DeBoy RT , Seshadri R , Ren Q , Madupu R , Dodson RJ , Durkin AS , Brinkac LM , Daugherty SC , Sullivan SA , Rosovitz MJ , Gwinn ML , Zhou L , Schneider DJ , Cartinhour SW , Nelson WC , Weidman J , Watkins K , Tran K , Khouri H , Pierson EA , Pierson LS, 3rd , Thomashow LS , Loper JE
Ref : Nat Biotechnol , 23 :873 , 2005
Abstract : Pseudomonas fluorescens Pf-5 is a plant commensal bacterium that inhabits the rhizosphere and produces secondary metabolites that suppress soilborne plant pathogens. The complete sequence of the 7.1-Mb Pf-5 genome was determined. We analyzed repeat sequences to identify genomic islands that, together with other approaches, suggested P. fluorescens Pf-5's recent lateral acquisitions include six secondary metabolite gene clusters, seven phage regions and a mobile genomic island. We identified various features that contribute to its commensal lifestyle on plants, including broad catabolic and transport capabilities for utilizing plant-derived compounds, the apparent ability to use a diversity of iron siderophores, detoxification systems to protect from oxidative stress, and the lack of a type III secretion system and toxins found in related pathogens. In addition to six known secondary metabolites produced by P. fluorescens Pf-5, three novel secondary metabolite biosynthesis gene clusters were also identified that may contribute to the biocontrol properties of P. fluorescens Pf-5.
ESTHER : Paulsen_2005_Nat.Biotechnol_23_873
PubMedSearch : Paulsen_2005_Nat.Biotechnol_23_873
PubMedID: 15980861
Gene_locus related to this paper: psef5-metx , psef5-q4k3c9 , psef5-q4k4b4 , psef5-q4k4t4 , psef5-q4k4u7 , psef5-q4k4y2 , psef5-q4k5b5 , psef5-q4k5k6 , psef5-q4k5w4 , psef5-q4k6z9 , psef5-q4k7i6 , psef5-q4k7u9 , psef5-q4k8j2 , psef5-q4k9i3 , psef5-q4k458 , psef5-q4k713 , psef5-q4k717 , psef5-q4k873 , psef5-q4k906 , psef5-q4k982 , psef5-q4k989 , psef5-q4k993 , psef5-q4kax4 , psef5-q4kay8 , psef5-q4kaz0 , psef5-q4kaz4 , psef5-q4kb21 , psef5-q4kbd7 , psef5-q4kbs3 , psef5-q4kbs6 , psef5-q4kc18 , psef5-q4kc21 , psef5-q4kcd3 , psef5-q4kch8 , psef5-q4kcj3 , psef5-q4kck4 , psef5-q4kcn8 , psef5-q4kcq2 , psef5-q4kcx3 , psef5-q4kd54 , psef5-q4kda1 , psef5-q4kdb4 , psef5-q4ke18 , psef5-q4keh1 , psef5-q4kej0 , psef5-q4keq4 , psef5-q4kes9 , psef5-q4kf14 , psef5-q4kfj4 , psef5-q4kfw0 , psef5-q4kfw1 , psef5-q4kfx7 , psef5-q4kgg3 , psef5-q4kgj9 , psef5-q4kgs6 , psef5-q4kh30 , psef5-q4kha2 , psef5-q4khf1 , psef5-q4khl0 , psef5-q4khv5 , psef5-q4ki42 , psef5-q4kj24 , psef5-q4kj95 , psef5-q4kjk5 , psef5-q4kjk7 , psef5-q4kjm8 , psef5-q4kjt7 , psef5-q4kk20 , psef5-q4kk22 , psef5-q4kk59 , psef5-q4kkf7 , psefl-PLTG , psepf-PHAZ , psef5-q4kfd8

Title : The psychrophilic lifestyle as revealed by the genome sequence of Colwellia psychrerythraea 34H through genomic and proteomic analyses - Methe_2005_Proc.Natl.Acad.Sci.U.S.A_102_10913
Author(s) : Methe BA , Nelson KE , Deming JW , Momen B , Melamud E , Zhang X , Moult J , Madupu R , Nelson WC , Dodson RJ , Brinkac LM , Daugherty SC , Durkin AS , DeBoy RT , Kolonay JF , Sullivan SA , Zhou L , Davidsen TM , Wu M , Huston AL , Lewis M , Weaver B , Weidman JF , Khouri H , Utterback TR , Feldblyum TV , Fraser CM
Ref : Proc Natl Acad Sci U S A , 102 :10913 , 2005
Abstract : The completion of the 5,373,180-bp genome sequence of the marine psychrophilic bacterium Colwellia psychrerythraea 34H, a model for the study of life in permanently cold environments, reveals capabilities important to carbon and nutrient cycling, bioremediation, production of secondary metabolites, and cold-adapted enzymes. From a genomic perspective, cold adaptation is suggested in several broad categories involving changes to the cell membrane fluidity, uptake and synthesis of compounds conferring cryotolerance, and strategies to overcome temperature-dependent barriers to carbon uptake. Modeling of three-dimensional protein homology from bacteria representing a range of optimal growth temperatures suggests changes to proteome composition that may enhance enzyme effectiveness at low temperatures. Comparative genome analyses suggest that the psychrophilic lifestyle is most likely conferred not by a unique set of genes but by a collection of synergistic changes in overall genome content and amino acid composition.
ESTHER : Methe_2005_Proc.Natl.Acad.Sci.U.S.A_102_10913
PubMedSearch : Methe_2005_Proc.Natl.Acad.Sci.U.S.A_102_10913
PubMedID: 16043709
Gene_locus related to this paper: colp3-q47uc4 , colp3-q47uc7 , colp3-q47ut6 , colp3-q47ut7 , colp3-q47v81 , colp3-q47vk3 , colp3-q47vy9 , colp3-q47w94 , colp3-q47wj4 , colp3-q47wr2 , colp3-q47ws7 , colp3-q47ws9 , colp3-q47x08 , colp3-q47x48 , colp3-q47yd5 , colp3-q47ye2 , colp3-q47yq1 , colp3-q47yv1 , colp3-q47za7 , colp3-q47zp5 , colp3-q48ac9 , colp3-q48aj8 , colp3-q48aq9 , colp3-q480e1 , colp3-q481z4 , colp3-q482y8 , colp3-q484d8 , colp3-q484k3 , colp3-q485e4 , colp3-q485t4 , colp3-q486t5 , colp3-q487b7 , colp3-q487s5 , colp3-q488a3 , colp3-q488d2 , colp3-q488d8 , colp3-q488e7 , colp3-q488f8 , colp3-q488p2 , colp3-q489b1 , colp3-q489i6 , colp3-q47ya3

Title : Genome sequence of the PCE-dechlorinating bacterium Dehalococcoides ethenogenes - Seshadri_2005_Science_307_105
Author(s) : Seshadri R , Adrian L , Fouts DE , Eisen JA , Phillippy AM , Methe BA , Ward NL , Nelson WC , DeBoy RT , Khouri HM , Kolonay JF , Dodson RJ , Daugherty SC , Brinkac LM , Sullivan SA , Madupu R , Nelson KE , Kang KH , Impraim M , Tran K , Robinson JM , Forberger HA , Fraser CM , Zinder SH , Heidelberg JF
Ref : Science , 307 :105 , 2005
Abstract : Dehalococcoides ethenogenes is the only bacterium known to reductively dechlorinate the groundwater pollutants, tetrachloroethene (PCE) and trichloroethene, to ethene. Its 1,469,720-base pair chromosome contains large dynamic duplicated regions and integrated elements. Genes encoding 17 putative reductive dehalogenases, nearly all of which were adjacent to genes for transcription regulators, and five hydrogenase complexes were identified. These findings, plus a limited repertoire of other metabolic modes, indicate that D. ethenogenes is highly evolved to utilize halogenated organic compounds and H2. Diversification of reductive dehalogenase functions appears to have been mediated by recent genetic exchange and amplification. Genome analysis provides insights into the organism's complex nutrient requirements and suggests that an ancestor was a nitrogen-fixing autotroph.
ESTHER : Seshadri_2005_Science_307_105
PubMedSearch : Seshadri_2005_Science_307_105
PubMedID: 15637277
Gene_locus related to this paper: dehm1-q3z6q3 , dehm1-q3z6x9 , dehm1-q3z6z2 , dehm1-q3z8f3 , dehm1-q3za50

Title : Major structural differences and novel potential virulence mechanisms from the genomes of multiple campylobacter species - Fouts_2005_PLoS.Biol_3_e15
Author(s) : Fouts DE , Mongodin EF , Mandrell RE , Miller WG , Rasko DA , Ravel J , Brinkac LM , DeBoy RT , Parker CT , Daugherty SC , Dodson RJ , Durkin AS , Madupu R , Sullivan SA , Shetty JU , Ayodeji MA , Shvartsbeyn A , Schatz MC , Badger JH , Fraser CM , Nelson KE
Ref : PLoS Biol , 3 :e15 , 2005
Abstract : Sequencing and comparative genome analysis of four strains of Campylobacter including C. lari RM2100, C. upsaliensis RM3195, and C. coli RM2228 has revealed major structural differences that are associated with the insertion of phage- and plasmid-like genomic islands, as well as major variations in the lipooligosaccharide complex. Poly G tracts are longer, are greater in number, and show greater variability in C. upsaliensis than in the other species. Many genes involved in host colonization, including racR/S, cadF, cdt, ciaB, and flagellin genes, are conserved across the species, but variations that appear to be species specific are evident for a lipooligosaccharide locus, a capsular (extracellular) polysaccharide locus, and a novel Campylobacter putative licABCD virulence locus. The strains also vary in their metabolic profiles, as well as their resistance profiles to a range of antibiotics. It is evident that the newly identified hypothetical and conserved hypothetical proteins, as well as uncharacterized two-component regulatory systems and membrane proteins, may hold additional significant information on the major differences in virulence among the species, as well as the specificity of the strains for particular hosts.
ESTHER : Fouts_2005_PLoS.Biol_3_e15
PubMedSearch : Fouts_2005_PLoS.Biol_3_e15
PubMedID: 15660156
Gene_locus related to this paper: camje-CJ0796C , camjr-q5ht69 , camjr-q5ht95 , camjr-q5huc7 , camjr-q5hwg6 , camju-a3yll6

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 : 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 : 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 : 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 : 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 : 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