Copin Richard, Coscollá Mireia, Seiffert Salome N, Bothamley Graham, Sutherland Jayne, Mbayo Georgetta, Gagneux Sebastien, Ernst Joel D
mBio. 2014 Jan 14;5(1):e00960-13. doi: 10.1128/mBio.00960-13.
The Mycobacterium tuberculosis genome includes the large family of pe_pgrs genes, 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 the pe_pgrs genes. However, the impact of immune selection on pe_pgrs genes has not been examined. Here, we sequenced 27 pe_pgrs genes in 94 clinical strains from five phylogenetic lineages of the M. tuberculosis complex (MTBC). We found that pe_pgrs genes 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. Individual pe_pgrs genes also differed in the ratio of nonsynonymous to synonymous mutations, suggesting that different selection pressures act on individual pe_pgrs genes. Using bioinformatic methods, we tested whether sequence diversity in pe_pgrs genes 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 in pe_pgrs genes, which is consistent with the previously reported conservation of human T cell epitopes in the MTBC.
Recognition of Mycobacterium tuberculosis antigens 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 in M. tuberculosis. We previously discovered that the known human T cell epitopes in the M. tuberculosis complex are highly conserved, but we hypothesized that undiscovered epitopes with naturally occurring sequence variants might exist. To test this hypothesis, we examined the pe_pgrs genes, a large family of genes that has been proposed to function in immune evasion by M. tuberculosis. We found that the pe_pgrs genes 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 of M. tuberculosis are highly conserved and indicate that selection forces other than T cell recognition drive sequence variation in the pe_pgrs genes.
结核分枝杆菌基因组包含庞大的pe_pgrs基因家族，其功能尚不清楚。鉴于其他病原体中有先例表明，显示出高序列变异的基因家族参与抗原变异，因此有人提出pe_pgrs基因也有类似作用。然而，尚未研究免疫选择对pe_pgrs基因的影响。在此，我们对结核分枝杆菌复合群（MTBC）五个系统发育谱系的94株临床菌株中的27个pe_pgrs基因进行了测序。我们发现，pe_pgrs基因总体上比MTBC基因组的其余部分更多样化，但该家族的各个成员在核苷酸多样性和插入/缺失（indel）含量方面差异很大：有些比基因组平均水平更多样化，而另一些则远低于基因组平均水平。各个pe_pgrs基因在非同义突变与同义突变的比例上也存在差异，这表明不同的选择压力作用于各个pe_pgrs基因。我们使用生物信息学方法，测试了pe_pgrs基因中的序列多样性是否可能是由人类T细胞识别选择的，而人类T细胞识别是对MTBC适应性免疫的主要机制。我们发现，绝大多数预测的人类T细胞表位局限于保守的PE结构域，并通过实验证实了该结构域在结核病患者中的抗原性。相比之下，尽管PGRS结构域在遗传上具有多样性，但几乎没有预测的T细胞表位。这些结果表明，人类T细胞识别不是驱动pe_pgrs基因序列多样性的重要因素，这与先前报道的MTBC中人类T细胞表位的保守性一致。
已知T淋巴细胞对结核分枝杆菌抗原的识别对于抗结核免疫保护很重要，但尚不清楚人类T细胞识别是否驱动结核分枝杆菌的抗原变异。我们先前发现，结核分枝杆菌复合群中已知的人类T细胞表位高度保守，但我们推测可能存在具有天然序列变异的未发现表位。为了验证这一假设，我们研究了pe_pgrs基因，这是一个被认为在结核分枝杆菌免疫逃逸中起作用的庞大基因家族。我们发现，pe_pgrs基因表现出相当大的序列变异，但包含T细胞表位的区域和变异区域是不同的。这些发现证实了结核分枝杆菌的大多数人类T细胞表位高度保守，并表明除T细胞识别之外的选择力量驱动pe_pgrs基因的序列变异。
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