Human T cell epitopes of Mycobacterium tuberculosis are evolutionarily hyperconserved

Abstract

Mycobacterium tuberculosis is an obligate human pathogen capable of persisting in individual hosts for decades. We sequenced the genomes of 21 strains representative of the global diversity and six major lineages of the M. tuberculosis complex (MTBC) at 40- to 90-fold coverage using Illumina next-generation DNA sequencing. We constructed a genome-wide phylogeny based on these genome sequences. Comparative analyses of the sequences showed, as expected, that essential genes in MTBC were more evolutionarily conserved than nonessential genes. Notably, however, most of the 491 experimentally confirmed human T cell epitopes showed little sequence variation and had a lower ratio of nonsynonymous to synonymous changes than seen in essential and nonessential genes. We confirmed these findings in an additional data set consisting of 16 antigens in 99 MTBC strains. These findings are consistent with strong purifying selection acting on these epitopes, implying that MTBC might benefit from recognition by human T cells.

Figure 1

Neighbour-joining phylogeny based on 9,037 variable common nucleotide positions across 21 human M. tuberculosis complex genome sequences. The tree is rooted with M. canettii, the closest known outgroup. Node support following 1,000 bootstrap replications is indicated. Branches are coloured according to the six main phylogeographic lineages of MTBC defined previously,-. Highly congruent topologies were obtained by Maximum likelihood and Bayesian inference (Supplementary Fig. 1).

Figure 2

Average gene-by-gene nucleotide diversity across three gene classes. Boxplot indicating median (horizontal line), interquartile range (box), and minimum and maximum values (whiskers).

Figure 3

Ratio of the rates of synonymous and non-synonymous substitutions (dN/dS) in various gene classes of MTBC. Overall dN/dS was calculated based on the number of non-redundant synonymous and non-synonymous changes after comparing each of the 21 MTBC genomes to the inferred most likely recent common ancestor of MTBC. This shows that essential genes are more conserved than non-essential genes, and that antigens are as conserved as essential genes. Figures for the epitope- and non-epitope regions refer to the calculations after excluding the three outlier antigens esxH, pstS1, and Rv1986.

Figure 4

Number of variable amino acid positions in 491 human T cell epitopes of MTBC. This demonstrates the remarkable lack of genetic variability among the regions of the genome that interact with the human immune system.