Complete Genome Sequence Of Yersinia Pestis 91001, A Strain Avirulent To Human Being

Background: Yersinia pestis is the etiologic agent of bubonic and pneumonic plague, which has claimed numerous lives in human history. Here we report the complete genome sequence of Y. pestis 91001, a strain avirulent to human being which was isolated from a kind of rodent - Microtus brandtii. We also carried out comparative genomics and preliminary proteomics to read through the secrets of Y. pestis pathogenicity. Methods: We utilized "whole genome shotgun" approach to get the genome sequence of 91001. Based on the finished and annotated genome sequence of 91001, as well as previously published genome sequence of C092 and KIM, we performed detailed comparative genomics analysis on their chromosome and plasmids. For the important phenotypes - nitrate reduction and glycerol fermentation, we carried out large scale screening among 257 strains isolated in China to clarify the genetic mechanism of these two phenotypes.Results: The genome of 91001 consists of one chromosome and four plasmids. The pPCPl plasmid of 9,609 bp is almost identical to the counterparts from reference strains, and this plasmid possesses 10 CDS. Plasmid pCDl encodes a type III secretory apparatus, and there are 98 CDS in 70,159 bp range. Although the CDS are quite similar to reference plasmids, there are obvious rearrangements among them. Another plasmid is pMTl, and this 106,642 bp plasmid has slightly different architecture compared with reference ones. There is no mutation in virulent-related genes of pMTl, and pMTl of 91001 seems to retain more fragments of an ancestor plasmid. pCRY is a novel plasmid discovered in this work. It is 21,742 bp long and harbors a cryptic Type IV secretory system. pCRY seems to be able to replicate and partition independently. The length of chromosome from 91001 is 4,595,065 bp, and among the 4,037 predicted CDS, 141 are possible pseudogenes. There are many IS in the chromosome, and due to the rearrangments mediated by IS, the structure of 91001 chromosome shows dramatic differences compared with CO92 and KIM. According to the results of comparative genomics and experiments, we deduce the genetic mechanisms of nitrate reduction, glycerol fermentation, arabinose and milibiose utilization in 91001. The preliminary proteomics research uncovered 1193 proteins by different methods, which count for 28.7% of all the predicted CDS in 91001.Conclusion: According to the analysis of plasmids structure, pseudogenes distribution, nitrate reduction negative mechanism, gene comparason and chromosome architecture, we safely draw a conclusion that 91001 and other strain isolate from Microtus brandtii and Microtus qinghaii were evolved from ancestor Y. pestis in a different lineage. The large genome frgments deletions in 91001 chromosome and pseuogenes may contribute to its unqiue pathogenicity and host-specificity.