Application of DNA Microarrays to Study the Evolutionary Genomics of Yersinia pestis and Yersinia pseudotuberculosis

Abstract

Yersinia pestis, the causative agent of plague, diverged from Yersinia pseudotuberculosis, an enteric pathogen, an estimated 1500–20,000 years ago. Genetic characterization of these closely related organisms represents a useful model to study the rapid emergence of bacterial pathogens that threaten mankind. To this end, we undertook genome-wide DNA microarray analysis of 22 strains of Y. pestis and 10 strains of Y. pseudotuberculosis of diverse origin. Eleven Y. pestis DNA loci were deemed absent or highly divergent in all strains of Y. pseudotuberculosis. Four were regions of phage origin, whereas the other seven included genes encoding a vitamin B12 receptor and the insect toxin sepC. Sixteen differences were identified between Y. pestis strains, with biovar Antiqua and Mediaevalis strains showing most divergence from the arrayed CO92 Orientalis strain. Fifty-eight Y. pestis regions were specific to a limited number of Y. pseudotuberculosis strains, including the high pathogenicity island, three putative autotransporters, and several possible insecticidal toxins and hemolysins. The O-antigen gene cluster and one of two possible flagellar operons had high levels of divergence between Y. pseudotuberculosis strains. This study reports chromosomal differences between species, biovars, serotypes, and strains of Y. pestis and Y. pseudotuberculosis that may relate to the evolution of these species in their respective niches.

Yersinia pestis Biofilm in the Flea Vector and Its Role in the Transmission of Plague

“…Based on these analyses, it was estimated that Y. pestis diverged from its Y. pseudotuberculosis ancestor only within the last 10,000-20,000 years (Achtman et al 1999(Achtman et al , 2004. Further comparative genomics analyses confirmed a high degree of genomic identity between the two species (Chain et al 2004;Hinchliffe et al 2003;Zhou et al 2004). The close phylogenetic relationship of Y. pseudotuberculosis and Y. pestis implies that the change from a comparatively benign foodand water-borne enteric pathogen to a highly virulent, arthropod-borne systemic pathogen occurred quite recently in evolutionary terms and is based on relatively few genetic differences (Hinnebusch 1997;Lorange et al 2005).…”

Microevolution and history of the plague bacillus, Yersinia pestis

“…We infer that these molecular grouping represent distinct bacterial populations. Independent support for the existence of these populations also can be deduced from other molecular analyses, which have examined subsets of the diversity examined here (3)(4)(5)(6)(7)(8).…”

“…Based on a correlation between the current geographical sources of the biovars and the inferred sources of historical plague, Devignat (2) suggested that Antiqua caused Justinian's plague and Medievalis caused the Black Death. Each of the biovars seems to be distinct according to the genomic patterns of IS100 insertion elements, supernumerary DNA islands, or multilocus variable number of tandem repeat analysis (MLVA) (3)(4)(5)(6)(7)(8). However, direct evidence uniquely associating any of the biovars with historical plague is lacking.…”

“…Although multiple nonsynonymous polymorphisms were found here (Table 7), the frequency of nonsynonymous SNPs was only slightly higher than the frequency of SNPs within our pairwise genome comparisons. Similarly, only 14-16 genotypes were detected by whole gene microarrays (6,7). In contrast, MLVA might be particularly suitable for genotyping within a hierarchical approach because it distinguished 102 patterns among 104 isolates and correlated strongly with geographical source within 1.ORI (Fig.…”

Genomic comparison of Bradyrhizobium japonicum strains with different symbiotic nitrogen-fixing capabilities and other Bradyrhizobiaceae members

“…Comparative genomic hybridizations (CGHs) by DNA micro-and macroarrays have been employed to reveal the evolution and function of pathogenicity in genomic terms in organisms such as Escherichia coli (Dobrindt et al, 2003;Carter et al, 2008), Yersinia pestis (Hinchliffe et al, 2003), Yersinia pseudotuberculosis (Zhou et al, 2004), Xylella fastidiosa (Koide et al, 2004), Campylobacter jejuni (Pearson et al, 2003), Streptococcus agalactiae (Brochet et al, 2006) and Streptococcus pneumoniae (Obert et al, 2006). The results of these studies indicate that mobile genetic elements such as phages, transposons and GIs contribute to pathogenicity acquisition and environmental adaptation.…”