title: Genome sequence of Yersinia pestis KIM.
abstract: 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.
authors.affiliation: Laboratory of Genetics, University of Wisconsin, Madison, Wisconsin 53706, USA.
authors.forename: Wen
authors.initials: W
authors.lastname: Deng
authors.forename: Valerie
authors.initials: V
authors.lastname: Burland
authors.forename: Guy
authors.initials: G
authors.lastname: Plunkett
authors.forename: Adam
authors.initials: A
authors.lastname: Boutin
authors.forename: George F
authors.initials: GF
authors.lastname: Mayhew
authors.forename: Paul
authors.initials: P
authors.lastname: Liss
authors.forename: Nicole T
authors.initials: NT
authors.lastname: Perna
authors.forename: Debra J
authors.initials: DJ
authors.lastname: Rose
authors.forename: Bob
authors.initials: B
authors.lastname: Mau
authors.forename: Shiguo
authors.initials: S
authors.lastname: Zhou
authors.forename: David C
authors.initials: DC
authors.lastname: Schwartz
authors.forename: Jaqueline D
authors.initials: JD
authors.lastname: Fetherston
authors.forename: Luther E
authors.initials: LE
authors.lastname: Lindler
authors.forename: Robert R
authors.initials: RR
authors.lastname: Brubaker
authors.forename: Gregory V
authors.initials: GV
authors.lastname: Plano
authors.forename: Susan C
authors.initials: SC
authors.lastname: Straley
authors.forename: Kathleen A
authors.initials: KA
authors.lastname: McDonough
authors.forename: Matthew L
authors.initials: ML
authors.lastname: Nilles
authors.forename: Jyl S
authors.initials: JS
authors.lastname: Matson
authors.forename: Frederick R
authors.initials: FR
authors.lastname: Blattner
authors.forename: Robert D
authors.initials: RD
authors.lastname: Perry
mesh_terms: D001435:Bacteriophages; D001692:Biological Transport / Q000235:genetics; D012634:Bodily Secretions; D002633:Chemotaxis / Q000235:genetics; D004261:DNA Replication / Q000235:genetics; D004251:DNA Transposable Elements / Q000235:genetics; D004734:Energy Metabolism / Q000235:genetics; D004926:Escherichia coli / Q000235:genetics; D015964:Gene Expression Regulation, Bacterial; D020459:Genes, rRNA / Q000235:genetics; D016680:Genome, Bacterial; D009876:Operon / Q000235:genetics; D010957:Plasmids / Q000235:genetics; D014176:Protein Biosynthesis / Q000235:genetics; D012091:Repetitive Sequences, Nucleic Acid; D014774:Virulence; D015010:Yersinia pestis / Q000235:genetics* / Q000378:metabolism / Q000472:pathogenicity
chemical_list: D004251:DNA Transposable Elements