Variation of the Mycobacterium tuberculosis PE_PGRS 33 gene among clinical isolates

Abstract

PE_PGRS 33, one of about 60 PE_PGRS genes in the Mycobacterium tuberculosis genome, encodes a surface-expressed protein that may be involved in the antigenic variation of M. tuberculosis strains and evasion of the host immune system. While genetic differences between the PE_PGRS 33 genes of H37Rv and CDC 1551 have been noted, genetic variation in this gene among clinical isolates has not been evaluated. In order to gain a better understanding of the genetic basis for the role of PE_PGRS in antigenic variation and evasion of the host immune system, we investigated the genetic diversity of the PE_PGRS 33 gene among 123 clinical M. tuberculosis isolates from a population-based study, using PCR and DNA sequencing. The 123 isolates belonged to principal genetic groups 1, 2, and 3 and had IS 6110 copy numbers ranging from 1 to 22. Eighty-four (68.3%) of the 123 isolates were found to have at least one sequence variation in the PE_PGRS 33 gene, relative to that of H37Rv. Twenty-five different sequence variations were observed and included three insertions (ranging from 9 to 87 bp), nine deletions (ranging from 1 to 273 bp), one insertion-and-deletion event, and 12 single-nucleotide polymorphisms (six synonymous and six nonsynonymous). Analysis of the relationships among the different PE_PGRS 33 gene sequence variations suggests that polymorphisms in the gene are shifting along evolutionary lineages. The observed genetic diversity of the PE_PGRS 33 gene supports its role in antigenic variation and can serve as a basis for future investigations of the function of the PE_PGRS 33 gene among clinical isolates.

FIG. 1.

Map of the positions of different sequence variations found in the M. tuberculosis PE_PGRS33 gene. Triangles represent insertions, brackets represent deletions, and lines extending from the PE_PGRS map represent SNPs. The asterisk represents a deletion of 1 bp. The sequence variations were designated A through Y and are described in Table 1.

FIG. 2.

Dendrogram showing the genetic relationships among the 23 different PE_PGRS33 alleles based on the analysis of deletions, insertions, and SNPs within the PE_PGRS33 gene that were found among the 123 clinical M. tuberculosis isolates. The sequence variations found among the 123 isolates were designated A through Y and are described in Table 1. For each of the 23 PE_PGRS33 alleles, the number and percentage of the 123 clinical M. tuberculosis isolates having the allele and the principal genetic group based on SNPs in the katG and gyrA genes (15) to which the isolates belong are indicated.