The 102-kilobase pgm locus of Yersinia pestis: sequence analysis and comparison of selected regions among different Yersinia pestis and Yersinia pseudotuberculosis strains

Abstract

We report the complete 119,443-bp sequence of the pgm locus from Yersinia pestis and its flanking regions. Sequence analysis confirms that the 102-kb unstable pgm locus is composed of two distinct parts: the pigmentation segment and a high-pathogenicity island (HPI) which carries virulence genes involved in iron acquisition (yersiniabactin biosynthetic gene cluster). Within the HPI, three genes coding for proteins related to phage proteins were uncovered. They are located at both extremities indicating that the entire HPI was acquired en bloc by phage-mediated horizontal transfer. We identified, within the pigmentation segment, two novel loci that may be involved in virulence: a fimbriae gene cluster and a locus probably encoding a two component regulatory system similar to the BvgAS regulatory system of Bordetella pertussis. Three genes containing frameshift mutations and two genes interrupted by insertion element insertion were found within this region. To investigate diversity among different Y. pestis and Yersinia pseudotuberculosis strains, the sequence of selected regions of the pgm locus and flanking regions were compared from 20 different Y. pestis and 10 Y. pseudotuberculosis strains. The results showed that the genes interrupted in Y. pestis are intact in Y. pseudotuberculosis. However, one of these mutations, in the bvgS homologue, is only present in Y. pestis strains of biovar Orientalis and not in those of the biovars Antiqua and Medievalis. The results obtained by analysis of variable positions in the sequence are in accordance with historical records, confirming that biovar Orientalis is the most recent lineage. Furthermore, sequence comparisons among 29 Yersinia strains suggest that Y. pestis is a recently emerged pathogen that is probably entering the initial phase of reductive evolution.

FIG. 1

Map of the pgm locus and flanking regions showing the position and orientation of known genes and CDSs. We used the following functional categories: related to virulence (red), phage-related functions (light blue), transport proteins (dark blue), regulatory proteins (purple), nitrogen and carbon metabolism (brown), miscellaneous (yellow), insertion elements (black), and proteins of unknown function (green). The thick lines below the gene map indicate flanking regions (gray), pigmentation segment (black), and HPI (blue). Numbers at the right end of the map indicate the scale in kilobases.

FIG. 2

Distribution of the base composition of the CDS within the 119-kb region sequenced. The DNA sequence was analyzed for the base composition by using GMP Tool Box (unpublished) with a window size of 1,000 bases and was shifted each time by 250 bp. Because of the difference in average size of the genes present on the HPI and the pigmentation segment, the G+C content was calculated only from the CDSs. Intergenic regions were not considered. The percentage of the G+C is indicated. The thick line below indicates the region defined as HPI and as pigmentation segment.