DNA Research

DNA Research 2001 8(1):11-22; doi:10.1093/dnares/8.1.11
© 2001 by Kazusa DNA Research Institute

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

Tetsuya Hayashi^1,*, Kozo Makino^2,*, Makoto Ohnishi¹, Ken Kurokawa³, Kazuo Ishii⁴, Katsushi Yokoyama², Chang-Gyun Han⁵, Eiichi Ohtsubo⁵, Keisuke Nakayama¹, Takahiro Murata⁶, Masashi Tanaka³, Toru Tobe⁷, Tetsuya Iida⁸, Hideto Takami⁹, Takeshi Honda⁸, Chihiro Sasakawa⁷, Naotake Ogasawara¹⁰, Teruo Yasunaga³, Satoru Kuhara¹¹, Tadayoshi Shiba⁴, Masahira Hattori^4,12 and Hideo Shinagawa²

¹Department of Microbiology, Miyazaki Medical College 5200 Kiyotake, Miyazaki 899-1692, Japan
²Department of Molecular Microbiology, Research Institute for Microbial Diseases, Osaka University 3-1 Yamadaoka, Suita, Osaka 565-0871, Japan
³Genome Information Research Center, Osaka University 3-1 Yamadaoka, Suita, Osaka 565-0871, Japan
⁴School of Science, Kitasato University 1-15-1 Kitasato,Sagamihara, Kanagawa 228-8555, Japan
⁵Institute of Molecular and Cellular Biosciences, University of Tokyo Bunkyo-ku, Tokyo 113, Japan
⁶Department of Bacteriology, Shinshu University School of Medicine 3-1-1 Asahi, Matsumoto, Nagano 390-8621, Japan
⁷Department of Microbiology and Immunology, Institute of Medical Science,University of Tokyo 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
⁸Department of Bacterial Infections, Research Institute for Microbial Diseases, Osaka University 3-1 Yamadaoka,Osaka 565-0871, Japan
⁹Deep-sea Microorganisms Research Group, Japan Marine Science and Technology Center 2-15 Natsushima, Yokosuka, Kanagawa 237-0061, Japan
¹⁰Graduate School of Biological Science,Nara Institute of Science and Technology 8916-5 Ikoma, Nara 630-0101, Japan
¹¹Graduate School of Genetic Resources Technology, Kyushu University 6-10-1 Hakozaki, Higashi-ku, Fukuoka 812-8581, Japan
¹²Genome Sequencing Team, Human Genome Research Group, RIKEN Genomic Sciences Center 1-7-22 Shuehiro-cho, Tsurumi-ku, Yokohama-city, Kanagawa, 230-0045 Japan

* Corresponding authors: T. Hayashi Tel. +1-985-85-0871, Fax. +81-985-6475, E-mail: thayash{at}fc.miyazaki-med.ac.jp K. Makino Tel. +81-6-6879-8318, Fax. +81-6-6879-8320, E-mail: makino{at}biken.osaka-u.ac.jp

Escherichia coli O157:H7 is a major food-borne infectious pathogen that causes diarrhea, hemorrhagic colitis, and hemolytic uremic syndrome. Here we report the complete chromosome sequence of an O157:H7 strain isolated from the Sakai outbreak, and the results of genomic comparison with a benign laboratory strain, K-12 MG1655. The chromosome is 5.5 Mb in size, 859 Kb larger than that of K-12. We identified a 4.1-Mb sequence highly conserved between the two strains, which may represent the fundamental backbone of the E. coli chromosome. The remaining 1.4-Mb sequence comprises of O157:H7-specific sequences, most of which are horizontally transferred foreign DNAs. The predominant roles of bacteriophages in the emergence of O157:H7 is evident by the presence of 24 prophages and prophage-like elements that occupy more than half of the O157:H7-specific sequences. The O157:H7 chromosome encodes 1632 proteins and 20 tRNAs that are not present in K-12. Among these, at least 131 proteins are assumed to have virulence-related functions. Genome-wide codon usage analysis suggested that the O157:H7-specific tRNAs are involved in the efficient expression of the strain-specific genes. A complete set of the genes specific to O157:H7 presented here sheds new insight into the pathogenicity and the physiology of O157:H7, and will open a way to fully understand the molecular mechanisms underlying the O157:H7 infection.

Key words: E. coli O157:H7; genome sequence; E. coli K-12; bacterial pathogenicity; evolution

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				P. Germon, D. Roche, S. Melo, S. Mignon-Grasteau, U. Dobrindt, J. Hacker, C. Schouler, and M. Moulin-Schouleur tDNA locus polymorphism and ecto-chromosomal DNA insertion hot-spots are related to the phylogenetic group of Escherichia coli strains Microbiology, March 1, 2007; 153(3): 826 - 837. [Abstract] [Full Text] [PDF]

				H. Ando, H. Abe, N. Sugimoto, and T. Tobe Maturation of functional type III secretion machinery by activation of anaerobic respiration in enterohaemorrhagic Escherichia coli Microbiology, February 1, 2007; 153(2): 464 - 473. [Abstract] [Full Text] [PDF]

				T. E. Besser, N. Shaikh, N. J. Holt, P. I. Tarr, M. E. Konkel, P. Malik-Kale, C. W. Walsh, T. S. Whittam, and J. L. Bono Greater Diversity of Shiga Toxin-Encoding Bacteriophage Insertion Sites among Escherichia coli O157:H7 Isolates from Cattle than in Those from Humans Appl. Envir. Microbiol., February 1, 2007; 73(3): 671 - 679. [Abstract] [Full Text] [PDF]

				L. Krause, A. C. McHardy, T. W. Nattkemper, A. Puhler, J. Stoye, and F. Meyer GISMO--gene identification using a support vector machine for ORF classification Nucleic Acids Res., January 28, 2007; 35(2): 540 - 549. [Abstract] [Full Text] [PDF]

				W. M. El-Sharoud and G. W. Niven The influence of ribosome modulation factor on the survival of stationary-phase Escherichia coli during acid stress Microbiology, January 1, 2007; 153(1): 247 - 253. [Abstract] [Full Text] [PDF]

				M. Steele, K. Ziebell, Y. Zhang, A. Benson, P. Konczy, R. Johnson, and V. Gannon Identification of Escherichia coli O157:H7 Genomic Regions Conserved in Strains with a Genotype Associated with Human Infection Appl. Envir. Microbiol., January 1, 2007; 73(1): 22 - 31. [Abstract] [Full Text] [PDF]

				Z. Ouyang and R. Isaacson Identification and Characterization of a Novel ABC Iron Transport System, fit, in Escherichia coli Infect. Immun., December 1, 2006; 74(12): 6949 - 6956. [Abstract] [Full Text] [PDF]

				S. D. Alcaine, Y. Soyer, L. D. Warnick, W.-L. Su, S. Sukhnanand, J. Richards, E. D. Fortes, P. McDonough, T. P. Root, N. B. Dumas, et al. Multilocus Sequence Typing Supports the Hypothesis that Cow- and Human-Associated Salmonella Isolates Represent Distinct and Overlapping Populations Appl. Envir. Microbiol., December 1, 2006; 72(12): 7575 - 7585. [Abstract] [Full Text] [PDF]

				H. Willenbrock, A. Petersen, C. Sekse, K. Kiil, Y. Wasteson, and D. W. Ussery Design of a Seven-Genome Escherichia coli Microarray for Comparative Genomic Profiling J. Bacteriol., November 15, 2006; 188(22): 7713 - 7721. [Abstract] [Full Text] [PDF]

				K. Shima, Y. Wu, N. Sugimoto, M. Asakura, K. Nishimura, and S. Yamasaki Comparison of a PCR-Restriction Fragment Length Polymorphism (PCR-RFLP) Assay to Pulsed-Field Gel Electrophoresis To Determine the Effect of Repeated Subculture and Prolonged Storage on RFLP Patterns of Shiga Toxin-Producing Escherichia coli O157:H7 J. Clin. Microbiol., November 1, 2006; 44(11): 3963 - 3968. [Abstract] [Full Text] [PDF]

				T. Tobe, S. A. Beatson, H. Taniguchi, H. Abe, C. M. Bailey, A. Fivian, R. Younis, S. Matthews, O. Marches, G. Frankel, et al. An extensive repertoire of type III secretion effectors in Escherichia coli O157 and the role of lambdoid phages in their dissemination PNAS, October 3, 2006; 103(40): 14941 - 14946. [Abstract] [Full Text] [PDF]

				J. E. Afset, G. Bruant, R. Brousseau, J. Harel, E. Anderssen, L. Bevanger, and K. Bergh Identification of Virulence Genes Linked with Diarrhea Due to Atypical Enteropathogenic Escherichia coli by DNA Microarray Analysis and PCR. J. Clin. Microbiol., October 1, 2006; 44(10): 3703 - 3711. [Abstract] [Full Text] [PDF]

				C. Putonti, Y. Luo, C. Katili, S. Chumakov, G. E. Fox, D. Graur, and Y. Fofanov A Computational Tool for the Genomic Identification of Regions of Unusual Compositional Properties and Its Utilization in the Detection of Horizontally Transferred Sequences Mol. Biol. Evol., October 1, 2006; 23(10): 1863 - 1868. [Abstract] [Full Text] [PDF]

				D. Terekhova, R. Iyer, G. P. Wormser, and I. Schwartz Comparative Genome Hybridization Reveals Substantial Variation among Clinical Isolates of Borrelia burgdorferi Sensu Stricto with Different Pathogenic Properties. J. Bacteriol., September 1, 2006; 188(17): 6124 - 6134. [Abstract] [Full Text] [PDF]

				X.-Z. Huang, M. P. Nikolich, and L. E. Lindler Current trends in plague research: from genomics to virulence. Clin. Med. Res., September 1, 2006; 4(3): 189 - 199. [Abstract] [Full Text] [PDF]

				E. Brzuszkiewicz, H. Bruggemann, H. Liesegang, M. Emmerth, T. Olschlager, G. Nagy, K. Albermann, C. Wagner, C. Buchrieser, L. Emody, et al. How to become a uropathogen: Comparative genomic analysis of extraintestinal pathogenic Escherichia coli strains PNAS, August 22, 2006; 103(34): 12879 - 12884. [Abstract] [Full Text] [PDF]

				I. T. Kudva, B. Krastins, H. Sheng, R. W. Griffin, D. A. Sarracino, P. I. Tarr, C. J. Hovde, S. B. Calderwood, and M. John Proteomics-based Expression Library Screening (PELS): A Novel Method for Rapidly Defining Microbial Immunoproteomes Mol. Cell. Proteomics, August 1, 2006; 5(8): 1514 - 1519. [Abstract] [Full Text] [PDF]

				Y. Xie, Y. Yao, V. Kolisnychenko, C.-H. Teng, and K. S. Kim HbiF Regulates Type 1 Fimbriation Independently of FimB and FimE Infect. Immun., July 1, 2006; 74(7): 4039 - 4047. [Abstract] [Full Text] [PDF]

				J. Xie, B. Foxman, L. Zhang, and C. F. Marrs Molecular Epidemiologic Identification of Escherichia coli Genes That Are Potentially Involved in Movement of the Organism from the Intestinal Tract to the Vagina and Bladder. J. Clin. Microbiol., July 1, 2006; 44(7): 2434 - 2441. [Abstract] [Full Text] [PDF]

				C. G. Moreira, K. Palmer, M. Whiteley, M. P. Sircili, L. R. Trabulsi, A. F. P. Castro, and V. Sperandio Bundle-Forming Pili and EspA Are Involved in Biofilm Formation by Enteropathogenic Escherichia coli J. Bacteriol., June 1, 2006; 188(11): 3952 - 3961. [Abstract] [Full Text] [PDF]

				M. Withers, L. Wernisch, and M. d. Reis Archaeology and evolution of transfer RNA genes in the Escherichia coli genome RNA, June 1, 2006; 12(6): 933 - 942. [Abstract] [Full Text] [PDF]

				W. Zhang, W. Qi, T. J. Albert, A. S. Motiwala, D. Alland, E. K. Hyytia-Trees, E. M. Ribot, P. I. Fields, T. S. Whittam, and B. Swaminathan Probing genomic diversity and evolution of Escherichia coli O157 by single nucleotide polymorphisms Genome Res., June 1, 2006; 16(6): 757 - 767. [Abstract] [Full Text] [PDF]

				L. A. Wilson and P. M. Sharp Enterobacterial Repetitive Intergenic Consensus (ERIC) Sequences in Escherichia coli: Evolution and Implications for ERIC-PCR Mol. Biol. Evol., June 1, 2006; 23(6): 1156 - 1168. [Abstract] [Full Text] [PDF]

				E. Loukiadis, M. Kerouredan, L. Beutin, E. Oswald, and H. Brugere Characterization of Shiga Toxin Gene (stx)-Positive and Intimin Gene (eae)-Positive Escherichia coli Isolates from Wastewater of Slaughterhouses in France. Appl. Envir. Microbiol., May 1, 2006; 72(5): 3245 - 3251. [Abstract] [Full Text] [PDF]

				M. Miura, J. Terajima, H. Izumiya, J. Mitobe, T. Komano, and H. Watanabe OspE2 of Shigella sonnei Is Required for the Maintenance of Cell Architecture of Bacterium-Infected Cells. Infect. Immun., May 1, 2006; 74(5): 2587 - 2595. [Abstract] [Full Text] [PDF]

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