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Journal of Bacteriology, August 2002, p. 4601-4611, Vol. 184, No. 16
0021-9193/02/$04.00+0     DOI: 10.1128/JB.184.16.4601-4611.2002
Copyright © 2002, American Society for Microbiology. All Rights Reserved.

Genome Sequence of Yersinia pestis KIM{dagger}

Wen Deng,1 Valerie Burland,1 Guy Plunkett III,1 Adam Boutin,1 George F. Mayhew,1 Paul Liss,1 Nicole T. Perna,2,3 Debra J. Rose,1 Bob Mau,3 Shiguo Zhou,2,4 David C. Schwartz,1,2,4 Jaqueline D. Fetherston,5 Luther E. Lindler,6 Robert R. Brubaker,7 Gregory V. Plano,8 Susan C. Straley,5 Kathleen A. McDonough,9 Matthew L. Nilles,10 Jyl S. Matson,10 Frederick R. Blattner,1,2* and Robert D. Perry5

Laboratory of Genetics,1 Genome Center,2 Department of Animal Health and Biomedical Sciences,3 Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706,4 Department of Microbiology and Immunology, University of Kentucky, Lexington, Kentucky, 40536-0084,5 Department of Bacterial Diseases, Division of Communicable Diseases and Immunology, Walter Reed Army Institute of Research, Washington, District of Columbia 20307-5100,6 Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan 48824,7 Department of Microbiology and Immunology, University of Miami School of Medicine, Miami, Florida 33176,8 David Axelrod Institute, Wadsworth Center, Albany, New York 12201-2002,9 Department of Microbiology and Immunology, School of Medicine and Health Sciences, University of North Dakota, Grand Forks, North Dakota 58202-9037,10

Received 17 January 2002/ Accepted 14 May 2002

We present the complete genome sequence of Yersinia pestis KIM, the etiologic agent of bubonic and pneumonic plague. The strain KIM, biovar Mediaevalis, is associated with the second pandemic, including the Black Death. The 4.6-Mb genome encodes 4,198 open reading frames (ORFs). The origin, terminus, and most genes encoding DNA replication proteins are similar to those of Escherichia coli K-12. The KIM genome sequence was compared with that of Y. pestis CO92, biovar Orientalis, revealing homologous sequences but a remarkable amount of genome rearrangement for strains so closely related. The differences appear to result from multiple inversions of genome segments at insertion sequences, in a manner consistent with present knowledge of replication and recombination. There are few differences attributable to horizontal transfer. The KIM and E. coli K-12 genome proteins were also compared, exposing surprising amounts of locally colinear "backbone," or synteny, that is not discernible at the nucleotide level. Nearly 54% of KIM ORFs are significantly similar to K-12 proteins, with conserved housekeeping functions. However, a number of E. coli pathways and transport systems and at least one global regulator were not found, reflecting differences in lifestyle between them. In KIM-specific islands, new genes encode candidate pathogenicity proteins, including iron transport systems, putative adhesins, toxins, and fimbriae.

* Corresponding author. Mailing address: Laboratory of Genetics, 445 Henry Mall, University of Wisconsin—Madison, Madison, WI 53706. Phone: (608) 262-2534. Fax: (608) 263-7459. E-mail: fred{at}genome.wisc.edu.

{dagger} This is paper number 3594 from the Laboratory of Genetics.

Journal of Bacteriology, August 2002, p. 4601-4611, Vol. 184, No. 16
0021-9193/02/$04.00+0     DOI: 10.1128/JB.184.16.4601-4611.2002
Copyright © 2002, American Society for Microbiology. All Rights Reserved.



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