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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