Related Experiment Videos
Genome sequence of Yersinia pestis KIM
Wen Deng1, Valerie Burland, Guy Plunkett
1Laboratory of Genetics, University of Wisconsin, Madison, Wisconsin 53706, USA.
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.
Insights
The complete genome sequence of Yersinia pestis KIM, responsible for plague, was determined. This analysis revealed significant genome rearrangement compared to related strains, highlighting differences in pathogenicity genes.
Area of Science:
- Genomics
- Microbiology
- Pathogen Evolution
Background:
- Yersinia pestis is the causative agent of plague, a devastating zoonotic disease.
- The KIM strain, biovar Mediaevalis, is historically significant, linked to the second pandemic, including the Black Death.
- Understanding the genomic basis of Y. pestis virulence is crucial for public health.
Purpose of the Study:
- To present the complete genome sequence of Yersinia pestis KIM.
- To compare the KIM genome with other Y. pestis strains and Escherichia coli K-12 to understand genomic evolution and identify virulence factors.
- To elucidate the genetic basis of Y. pestis pathogenicity.
Main Methods:
- Whole-genome sequencing of Yersinia pestis KIM.
- Comparative genomics analysis comparing KIM with Y. pestis CO92 and Escherichia coli K-12.
- Identification and characterization of open reading frames (ORFs) and genomic islands.
Main Results:
- The 4.6-Mb KIM genome contains 4,198 ORFs, sharing similarities in replication genes with E. coli K-12.
- Significant genome rearrangement, primarily inversions at insertion sequences, was observed between KIM and Y. pestis CO92.
- Comparative analysis revealed conserved "backbone" synteny with E. coli K-12, with approximately 54% shared protein similarity, but also identified KIM-specific genes encoding putative pathogenicity factors.
Conclusions:
- The Yersinia pestis KIM genome sequence provides a valuable resource for studying plague pathogenesis and evolution.
- Genome rearrangements play a significant role in the diversification of Y. pestis strains.
- KIM-specific genomic islands harbor novel genes contributing to the bacterium's virulence and adaptation.