Genome sequence of Yersinia pestis KIM.
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.
Deng
Wen
W
Laboratory of Genetics, University of Wisconsin, Madison, Wisconsin 53706, USA.
Burland
Valerie
V
Plunkett
Guy
G
Boutin
Adam
A
Mayhew
George F
GF
Liss
Paul
P
Perna
Nicole T
NT
Rose
Debra J
DJ
Mau
Bob
B
Zhou
Shiguo
S
Schwartz
David C
DC
Fetherston
Jaqueline D
JD
Lindler
Luther E
LE
Brubaker
Robert R
RR
Plano
Gregory V
GV
Straley
Susan C
SC
McDonough
Kathleen A
KA
Nilles
Matthew L
ML
Matson
Jyl S
JS
Blattner
Frederick R
FR
Perry
Robert D
RD
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
D004251:DNA Transposable Elements