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.

Analysis of the aerobactin and ferric hydroxamate uptake systems of Yersinia pestis

“…In Y. pestis strains KIM10+, CO92, 91001, Angola, Antiqua and Nepal516, iucA has undergone a frameshift mutation (Deng et al, 2002;Parkhill et al, 2001;Song et al, 2004). The frameshift mutation in Y. pestis iucA1/iucA2 is the result of a single base deletion in the L179 codon.…”

“…The E. coli aerobactin biosynthetic operon consists of four genes, iucABCD, with the receptor encoded by a separate gene, iutA . In Y. pestis, iucA has undergone a frameshift, generating two separate open reading frames [iucA1 (y3380) and iucA2 (y3381) in strain KIM10+] (Deng et al, 2002). The remaining genes are intact and the proteins encoded share 67-74 % similarity with their E. coli counterparts (Fig.…”

Bacterial Genomes as New Gene Homes: The Genealogy of ORFans in E. coli

“…To identify those ORFs of E. coli MG1655 that are restricted to clades of different phylogenetic depths, we narrowed our analysis to the gene contents of sequenced enteric bacteria, currently the best represented bacterial group, including five strains of E. coli (Blattner et al 1997;Hayashi et al 2001;Perna et al 2001;Welch et al 2002;Wei et al 2003), two subspecies/serovars of S. enterica (McClelland et al 2001;Parkhill et al 2001a), two species of Buchnera (Shigenobu et al 2000;Tamas et al 2002), and two strains of Yersinia pestis (Parkhill et al 2001b;Deng et al 2002) as well as those of several other ␥-Proteobacteria, including Vibrio cholerae (Schoolnik and Yildiz 2000), Vibrio parahaemolyticus (Makino et al 2003), Haemophilus influenzae (Fleischmann et al 1995), Pasteurella multocida (May et al 2001), Pseudomonas aeruginosa (Stover et al 2000), Xylella fastidiosa (Simpson et al 2000), Xanthomonas campestris, and Xanthomonas citri (da Silva et al 2002). (Species are listed in order of increasing genetic distance to E.…”

Identification of critical amino acid residues in the plague biofilm Hms proteins

“…The 102 kb pgm locus in Y. pestis contains the highpathogenicity island (Ybt) and the hmsHFRS operon encoding four of the six hms genes required for biofilm formation and its regulation. Escherichia coli K-12 pgaABCD (formerly ycdSRQP) encode proteins with similarities (ranging from 34 to 83 %) to Hms proteins and are required for the synthesis of an EPS containing poly-b-1,6-N-acetyl-D-glucosamine (Blattner et al, 1997;Deng et al, 2002;Fetherston et al, 1992;Jones et al, 1999;Lillard et al, 1997;Wang et al, 2004). HmsH and HmsF are outer-membrane proteins while HmsS, HmsR, and HmsT are located in the inner membrane.…”