Sequence Diversity in the pe_pgrs Genes of Mycobacterium tuberculosis Is Independent of Human T Cell Recognition

ABSTRACTTheMycobacterium tuberculosisgenome includes the large family ofpe_pgrsgenes, whose functions are unknown. Because of precedents in other pathogens in which gene families showing high sequence variation are involved in antigenic variation, a similar role has been proposed for thepe_pgrsgenes. However, the impact of immune selection onpe_pgrsgenes has not been examined. Here, we sequenced 27pe_pgrsgenes in 94 clinical strains from five phylogenetic lineages of theM. tuberculosiscomplex (MTBC). We found thatpe_pgrsgenes were overall more diverse than the remainder of the MTBC genome, but individual members of the family varied widely in their nucleotide diversity and insertion/deletion (indel) content: some were more, and others were much less, diverse than the genome average. Individualpe_pgrsgenes also differed in the ratio of nonsynonymous to synonymous mutations, suggesting that different selection pressures act on individualpe_pgrsgenes. Using bioinformatic methods, we tested whether sequence diversity inpe_pgrsgenes might be selected by human T cell recognition, the major mechanism of adaptive immunity to MTBC. We found that the large majority of predicted human T cell epitopes were confined to the conserved PE domain and experimentally confirmed the antigenicity of this domain in tuberculosis patients. In contrast, despite being genetically diverse, the PGRS domains harbored few predicted T cell epitopes. These results indicate that human T cell recognition is not a significant force driving sequence diversity inpe_pgrsgenes, which is consistent with the previously reported conservation of human T cell epitopes in the MTBC.IMPORTANCERecognition ofMycobacterium tuberculosisantigens by T lymphocytes is known to be important for immune protection against tuberculosis, but it is unclear whether human T cell recognition drives antigenic variation inM. tuberculosis. We previously discovered that the known human T cell epitopes in theM. tuberculosiscomplex are highly conserved, but we hypothesized that undiscovered epitopes with naturally occurring sequence variants might exist. To test this hypothesis, we examined thepe_pgrsgenes, a large family of genes that has been proposed to function in immune evasion byM. tuberculosis. We found that thepe_pgrsgenes exhibit considerable sequence variation, but the regions containing T cell epitopes and the regions of variation are distinct. These findings confirm that the majority of human T cell epitopes ofM. tuberculosisare highly conserved and indicate that selection forces other than T cell recognition drive sequence variation in thepe_pgrsgenes.