Genome sequence of Vibrio parahaemolyticus: a pathogenic mechanism distinct from that of V cholerae

Makino, Kozo; Oshima, Koichiro; Kurokawa, Ken; Yokoyama, Katsushi; Uda, Takayuki; Tagomori, Kenichi; Iijima, Yoshio; Najima, Masatomo; Nakano, Masayuki; Yamashita, Atsushi; Kubota, Yoshino; Kimura, Shigenobu; Yasunaga, Teruo; Honda, Takeshi; Shinagawa, Hideo; Hattori, Masahira; Iida, Tetsuya

doi:10.1016/s0140-6736(03)12659-1

Cited by 924 publications

(1,023 citation statements)

References 24 publications

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“…The attC sequences in the V. vulnificus genome can be recognized by a conserved 6-bp boundary sequence of TAAC-AA at the 5Ј-end and a partially complementary 6-bp boundary sequence of GC-GTTA at the 3Ј-end. This signature of SI is conserved between V. cholerae (Heidelberg et al 2000) and V. parahaemolyticus (Makino et al 2003), and it is consistent with the consensus of the two core sites (inverse core: RYYYAAC; core: GTTRRRY) for integrons (Stokes and Hall 1989;Collis et al 1998). A total of 188 attC sites were found in the V. vulnificus SI, and the entire SI region spans 138 kbp in the large chromosome (Fig.…”

Section: Vulnificus Super-integronsupporting

confidence: 81%

“…We selected strain YJ016 (Shao and Hor 2000), a biotype 1 hospital isolate from Taiwan, as a target for sequencing. Here we report the complete nucleotide sequence of the pathogenic V. vulnificus YJ016 genome and the comparative analysis of V. vulnificus with recently obtained genome sequences of V. cholerae (Heidelberg et al 2000) and V. parahaemolyticus (Makino et al 2003). We discovered a significant difference in chromosomal organization of the vibrio pathogens, and we identified several mechanisms underlying the dynamic evolution of the bacteria.…”

mentioning

confidence: 85%

“…As more sequence information becomes available for Vibrio species (Heidelberg et al 2000;Makino et al 2003), it is now possible to conduct comparative analysis at the wholegenome level to address the issue of how Vibrio species evolved. Compared with V. cholerae, the genome of V. vulnificus is at least one megabase bigger, although both share the same organization as two circular replicons.…”

Section: Comparative Analysis Of V Vulnificusmentioning

confidence: 99%

“…5). It has a genome size (5.2 Mb) close to that of V. vulnificus (5.3 Mb), and the V. parahaemolyticus SI is also located on the large chromosome (Makino et al 2003). However, the V. parahaemolyticus SI is entirely different from the V. vulnificus SI, suggesting that the SI of vibrio bacteria evolved rapidly.…”

Section: Genome Research 2583mentioning

confidence: 99%

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Comparative Genome Analysis of Vibrio vulnificus, a Marine Pathogen

et al. 2003

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The halophile Vibrio vulnificus is an etiologic agent of human mortality from seafood-borne infections. We applied whole-genome sequencing and comparative analysis to investigate the evolution of this pathogen. The genome of biotype 1 strain, V. vulnificus YJ016, was sequenced and includes two chromosomes of estimated 3377 kbp and 1857 kbp in size, and a plasmid of 48,508 bp. A super-integron (SI) was identified, and the SI region spans 139 kbp and contains 188 gene cassettes. In contrast to non-SI sequences, the captured gene cassettes are unique for any given Vibrio species and are highly variable among V. vulnificus strains. Multiple rearrangements were found when comparing the 5.3-Mbp V. vulnificus YJ016 genome and the 4.0-Mbp V. cholerae El Tor N16961 genome. The organization of gene clusters of capsular polysaccharide, iron metabolism, and RTX toxin showed distinct genetic features of V. vulnificus and V. cholerae. The content of the V. vulnificus genome contained gene duplications and evidence of horizontal transfer, allowing for genetic diversity and function in the marine environment. The genomic information obtained in this study can be applied to monitoring vibrio infections and identifying virulence genes in V. vulnificus.[Supplemental material is available online at www.genome.org and at http://genome.nhri.org.tw/vv/. The nucleotide sequence data from this study have been submitted to DDBJ/EMBL/GenBank under accession nos. BA000037, BA000038, and AP005352.]Vibrio vulnificus is an etiologic agent for severe human infection acquired through wounds or contaminated seafood. This organism is divided into three biotypes according to their different biochemical and biological properties (Linkous and Oliver 1999). Among them the biotype 1 strains are most frequently isolated from the clinical specimens. Opportunistic infection in susceptible individuals typically causes mortality within 24 to 48 h of the exposure. The bacterium is halophilic, and it is abundantly present in estuarine ecosystems throughout the world. Isolated incidents of V. vulnificus infection have been reported in the U.S.A., Europe, Korea, Taiwan (Park et al. 1991;Chuang et al. 1992;Dalsgaard et al. 1996;Hlady and Klontz 1996), and many other countries. According to CDC statistics, V. vulnificus is a major bacterial cause of mortality associated with food-borne diseases, and it results in the highest death rate of any causative agent (Todd 1989).V. vulnificus belongs to the ␥-group of Proteobacteria, and it shares morphological and biochemical characteristics with other human vibrio pathogens, including Vibrio cholerae and Vibrio parahaemolyticus. Bacteria of the Vibrionaceae family, which show a comma-shape microscopic appearance and a polar flagellum appendage, are mostly aquatic inhabitants that require NaCl for optimal growth. On the basis of clinical and epidemiology studies, diseases associated with V. vulnificus infection have been found to present in two patterns (Blake et al. 1979). In one, primary septicemia occurred in individ...

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Section: Vulnificus Super-integronsupporting

confidence: 81%

mentioning

confidence: 85%

Section: Comparative Analysis Of V Vulnificusmentioning

confidence: 99%

Section: Genome Research 2583mentioning

confidence: 99%

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Comparative Genome Analysis of Vibrio vulnificus, a Marine Pathogen

et al. 2003

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“…To identify those ORFs of E. coli MG1655 that are restricted to clades of different phylogenetic depths, we narrowed our analysis to the gene contents of sequenced enteric bacteria, currently the best represented bacterial group, including five strains of E. coli (Blattner et al 1997;Hayashi et al 2001;Perna et al 2001;Welch et al 2002;Wei et al 2003), two subspecies/serovars of S. enterica (McClelland et al 2001;Parkhill et al 2001a), two species of Buchnera (Shigenobu et al 2000;Tamas et al 2002), and two strains of Yersinia pestis (Parkhill et al 2001b;Deng et al 2002) as well as those of several other ␥-Proteobacteria, including Vibrio cholerae (Schoolnik and Yildiz 2000), Vibrio parahaemolyticus (Makino et al 2003), Haemophilus influenzae (Fleischmann et al 1995), Pasteurella multocida (May et al 2001), Pseudomonas aeruginosa (Stover et al 2000), Xylella fastidiosa (Simpson et al 2000), Xanthomonas campestris, and Xanthomonas citri (da Silva et al 2002). (Species are listed in order of increasing genetic distance to E.…”

Section: Methods Delimiting Orfans In Clades Of Different Phylogenetimentioning

confidence: 99%

Bacterial Genomes as New Gene Homes: The Genealogy of ORFans in E. coli

Daubin¹,

Ochman²

2004

Genome Res.

244

259

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Differences in gene repertoire among bacterial genomes are usually ascribed to gene loss or to lateral gene transfer from unrelated cellular organisms. However, most bacteria contain large numbers of ORFans, that is, annotated genes that are restricted to a particular genome and that possess no known homologs. The uniqueness of ORFans within a genome has precluded the use of a comparative approach to examine their function and evolution. However, by identifying sequences unique to monophyletic groups at increasing phylogenetic depths, we can make direct comparisons of the characteristics of ORFans of different ages in the Escherichia coli genome, and establish their functional status and evolutionary rates. Relative to the genes ancestral to γ-Proteobacteria and to those genes distributed sporadically in other prokaryotic species, ORFans in the E. coli lineage are short, A+T rich, and evolve quickly. Moreover, most encode functional proteins. Based on these features, ORFans are not attributable to errors in gene annotation, limitations of current databases, or to failure of methods for detecting homology. Rather, ORFans in the genomes of free-living microorganisms apparently derive from bacteriophage and occasionally become established by assuming roles in key cellular functions

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VibrioSpecies

2008

Medical Toxicology of Natural Substances

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Genome sequence of Vibrio parahaemolyticus: a pathogenic mechanism distinct from that of V cholerae

Cited by 924 publications

References 24 publications

Comparative Genome Analysis of Vibrio vulnificus, a Marine Pathogen

Comparative Genome Analysis of Vibrio vulnificus, a Marine Pathogen

Bacterial Genomes as New Gene Homes: The Genealogy of ORFans in E. coli

VibrioSpecies

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