Complete Genome Sequence of Enterohemorrhagic Eschelichia coli O157:H7 and Genomic Comparison with a Laboratory Strain K-12

Hayashi, Tetsuya; Makino, Kozo; Ohnishi, Makoto; Kurokawa, Ken; Ishii, Kazuo; Yokoyama, Katsushi; Han, Chang Gyun; Ohtsubo, Eiichi; Nakayama, Keisuke; Murata, Tetsuya; Tanaka, Masashi; Tobe, Toru; Iida, Tetsuya; Takami, Hideto; Honda, Takeshi; Sasakawa, Chihiro; Ogasawara, Nagahisa; Yasunaga, Teruo; Kuhara, Satoru; Shiba, Tadayoshi; Hattori, Masahira; Shinagawa, Hideo

doi:10.1093/dnares/8.1.11

Cited by 1,181 publications

(1,083 citation statements)

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“…Even the sequenced O157 genome contains 1.34 Mb of DNA that is not present in the K-12 genome and lacks 530 kb of DNA that is present in the K-12 genome (33). Similar indel-directed differences between the two sequenced O157 strains, EDL 933 and Sakai, can be observed (5,13,33). The probable existence of O157 in hypermutable states, due to defects in its methyl-directed mismatch repair system, may contribute to the large number of horizontal transfer events occurring in the genome, leading to genetic variation in the serotype and its strains (21,22,28).…”

Section: Discussionmentioning

confidence: 57%

Insertions, Deletions, and Single-Nucleotide Polymorphisms at Rare Restriction Enzyme Sites Enhance Discriminatory Power of Polymorphic Amplified Typing Sequences, a Novel Strain Typing System for Escherichia coli O157:H7

et al. 2004

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Polymorphic amplified typing sequences (PATS) for Escherichia coli O157:H7 (O157) was previously based on indels containing XbaI restriction enzyme sites occurring in O-island sequences of the O157 genome. This strain-typing system, referred to as XbaI-based PATS, typed every O157 isolate tested in a reproducible, rapid, straightforward, and easy-to-interpret manner and had technical advantages over pulsed-field gel electrophoresis (PFGE). However, the system was less discriminatory than PFGE and was unable to differentiate fully between unrelated isolates. To overcome this drawback, we enhanced PATS by using another infrequently cutting restriction enzyme, AvrII (also known as BlnI), to identify additional polymorphic regions that could increase the discriminatory ability of PATS typing. Referred to as AvrII-based PATS, the system identified seven new polymorphic regions in the O157 genome. Unlike XbaI, polymorphisms involving AvrII sites were caused by both indels and single-nucleotide polymorphisms occurring in O-island and backbone sequences of the O157 genome. AvrII-based PATS by itself provided poor discrimination of the O157 isolates tested. However, when primer pairs amplifying the seven polymorphic AvrII sites were combined with those amplifying the eight polymorphic XbaI sites (combined PATS), the discriminatory power of PATS was enhanced. Combined PATS matched related O157 isolates better than PFGE while differentiating between unrelated isolates. PATS typed every O157 isolate tested and directly targeted polymorphic sequences responsible for differences in the restriction digest patterns of O157 genomic DNA, utilizing PCR rather than relying on gel electrophoresis. This enabled PATS to resolve the ambiguity in PFGE typing, including that arising from the "more distantly related" and "untypeable" profiles.

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Section: Discussionmentioning

confidence: 57%

Insertions, Deletions, and Single-Nucleotide Polymorphisms at Rare Restriction Enzyme Sites Enhance Discriminatory Power of Polymorphic Amplified Typing Sequences, a Novel Strain Typing System for Escherichia coli O157:H7

et al. 2004

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“…It was recently suggested that the EHEC genome encodes a second TTSS that could mediate the secretion of the LEE-encoded effector protein EspB in an E. coli K-12 background (16). This would imply that the inability of EHEC LEE to confer pathogenic properties to E. coli K-12 might be due to the inefficiency of the LEE-encoded secretion apparatus.…”

Section: Discussionmentioning

confidence: 99%

“…The finding that mutation of neither espF nor cesF altered the TER phenotype of EHEC led us to examine the potential roles of the other EspF-like protein encoded by EHEC in more detail. In addition to the LEE-encoded EspF homolog, EHEC encodes two additional EspF-like sequences elsewhere on the chromosome (16,28). We have designated these genes U-espF and M-espF (the letter designations refer to the specific cryptic prophage sequences on the EHEC chromosome closest to the respective genes) (28).…”

Section: Fig 2 Ehec Redistributes Occludin In T84 Cells (A)mentioning

confidence: 99%

Comparative Analysis of EspF from Enteropathogenic and Enterohemorrhagic Escherichia coli in Alteration of Epithelial Barrier Function

et al. 2004

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Enteropathogenic Escherichia coli (EPEC) and enterohemorrhagic E. coli (EHEC) are related intestinal pathogens that harbor highly similar pathogenicity islands known as the locus of enterocyte effacement (LEE). Despite their genetic similarity, these two pathogens disrupt epithelial tight junction barrier function with distinct kinetics. EHEC-induced reduction in transepithelial electrical resistance (TER), a measure of barrier function disruption, is significantly slower and more modest in comparison to that induced by EPEC. The variation in bacterial adherence only partially accounted for these differences. The LEE-encoded effector protein EspF has been shown to be critical for EPEC-induced alterations in TER. EspF from both EPEC and EHEC is expressed and secreted upon growth in tissue culture medium. The mutation of EHEC cesF suggested that the optimal expression and secretion of EHEC EspF required its chaperone CesF, as has been shown for EPEC. In contrast to EPEC espF and cesF, mutation of the corresponding EHEC homologs did not dramatically alter the decrease in TER. These differences could possibly be explained by the presence of additional espF-like sequences (designated U-and M-espF, where the letter designations refer to the specific cryptic prophage sequences on the EHEC chromosome closest to the respective genes) in EHEC. Reverse transcription-PCR analyses revealed coordinate regulation of EHEC U-espF and the LEE-encoded espF, with enhanced expression in bacteria grown in Dulbecco-Vogt modified Eagle's medium compared to bacteria grown in Luria broth. Both EHEC espF and U-espF complemented an EPEC espF deletion strain for barrier function alteration. The overexpression of U-espF, but not espF, in wild-type EHEC potentiated the TER response. These studies reveal further similarities and differences in the pathogenesis of EPEC and EHEC.

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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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Complete Genome Sequence of Enterohemorrhagic Eschelichia coli O157:H7 and Genomic Comparison with a Laboratory Strain K-12

Cited by 1,181 publications

References 53 publications

Insertions, Deletions, and Single-Nucleotide Polymorphisms at Rare Restriction Enzyme Sites Enhance Discriminatory Power of Polymorphic Amplified Typing Sequences, a Novel Strain Typing System for Escherichia coli O157:H7

Insertions, Deletions, and Single-Nucleotide Polymorphisms at Rare Restriction Enzyme Sites Enhance Discriminatory Power of Polymorphic Amplified Typing Sequences, a Novel Strain Typing System for Escherichia coli O157:H7

Comparative Analysis of EspF from Enteropathogenic and Enterohemorrhagic Escherichia coli in Alteration of Epithelial Barrier Function

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

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