Diversity in a variable-number tandem repeat from Yersinia pestis

Abstract

We have identified a tetranucleotide repeat sequence, (CAAA)(N), in the genome of Yersinia pestis, the causative agent of plague. This variable-number tandem repeat (VNTR) region has nine alleles and great diversity (calculated as 1 minus the sum of the squared allele frequencies) (diversity value, 0.82) within a set of 35 diverse Y. pestis strains. In contrast, the nucleotide sequence of the lcrV (low-calcium-response) gene differed only slightly among these strains, having a haplotype diversity value of 0.17. Replicated cultures, phenotypic variants of particular strains, and extensively cultured replicates within strains did not differ in VNTR allele type. Thus, while a high mutation rate must contribute to the great diversity of this locus, alleles appear stable under routine laboratory culture conditions. The classic three plague biovars did not have single identifying alleles, although there were allelic biases within biovar categories. The antiqua biovar was the most diverse, with four alleles observed in 5 strains, while the orientalis and mediaevalis biovars exhibited five alleles in 21 strains and three alleles in 8 strains, respectively. The CAAA VNTR is located immediately adjacent to the transcriptional promoters for flanking open reading frames and may affect their activity. This VNTR marker may provide a high-resolution tool for epidemiological analyses of plague.

FIG. 1

Nucleotide sequence of the VNTR region. The CAAA repeat region that varies among Y. pestis strains is underlined. Orf-1 shows strong similarity to a gene encoding a 190-amino-acid hypothetical protein from E. coli. Orf-2 shows similarity to the B. subtilis gene tagO involved in teichoic acid synthesis. The putative ribosome binding sequence for Orf-1 (SD) is underlined. The PCR priming sequences are labeled and underlined.

FIG. 2

Gel image of different alleles in the CAAA repeat region. All samples except Y. enterocolitica produced an amplicon in reactions containing the PCR primers described in the text. Strains correspond to those listed in Table 1; Pest, Pestoides. Numbers at left are in base pairs.