Data from: Evolution of smooth tubercle bacilli PE and PE_PGRS genes: evidence for a prominent role of recombination and imprint of positive selection

Background: PE and PE_PGRS are two mycobateria-restricted multigene families encoding membrane associated and secreted proteins that have expanded mainly in the pathogenic species, notably the Mycobacterium tuberculosis complex (MTBC). Several lines of evidence attribute to PE and PE_PGRS genes critical roles in mycobacterial pathogenicity. To get more insight into the nature of these genes, we sought to address their evolutionary trajectories in the group of smooth tubercle bacilli (STB), the putative ancestor of the clonal MTBC. Methodology/Principal Findings: By focussing on six polymorphic STB PE/PE_PGRS genes, we demonstrate significant incongruence among single gene genealogies and detect strong signals of recombination using various approaches. Coalescent-based estimation of population recombination and mutation rates (ρ and θ, respectively) indicates that the two mechanisms are of roughly equal importance in generating diversity (ρ/θ = 1.457), a finding in a marked contrast to house keeping genes (HKG) whose evolution is chiefly brought about by mutation (ρ/θ = 0.012). In comparison to HKG, we found 15 times higher mean rate of nonsynonymous substitutions, with strong evidence of positive selection acting on PE_PGRS62 (dN/dS = 1.42), a gene that has previously been shown to be essential for mycobacterial survival in macrophages and granulomas. Imprint of positive selection operating on specific amino acid residues or along branches of PE_PGRS62 phylogenetic tree was further demonstrated using maximum likelihood- and covarion-based approaches, respectively. Strikingly, PE_PGR62 proved highly conserved in present-day MTBC strains. Conclusions/Significance: Overall the data indicate that, in STB, PE/PE_PGRS genes have undergone a strong diversification process that is speeded up by recombination, with evidence of positive selection. The finding that positive selection involved an essential PE_PGRS gene whose sequence appears to be driven to fixation in present-day MTBC strains lends further support to the critical role of PE/PE_PGRS genes in the evolution of mycobacterial pathogenicity.

背景：PE家族与PE_PGRS家族是两类仅在分枝杆菌中存在的多基因家族，编码膜结合与分泌型蛋白，主要在致病性分枝杆菌中发生扩增，尤以结核分枝杆菌复合群（Mycobacterium tuberculosis complex, MTBC）为甚。多项研究证据表明，PE与PE_PGRS基因在分枝杆菌的致病性中发挥关键作用。为深入解析这类基因的本质，本研究旨在探究其在克隆性MTBC的推定祖先——光滑结核分枝杆菌（smooth tubercle bacilli, STB）类群中的演化轨迹。
研究方法与主要发现：本研究聚焦6个具有多态性的STB PE/PE_PGRS基因，发现单基因谱系树间存在显著的不一致性，并通过多种方法检测到强烈的重组信号。基于溯祖理论的群体重组率与突变率（分别记为ρ与θ）估算结果显示，这两种机制在产生基因多样性方面的作用大致相当（ρ/θ=1.457），这与主要依靠突变驱动演化的持家基因（house keeping genes, HKG）形成鲜明对比（后者ρ/θ=0.012）。与持家基因相比，PE/PE_PGRS基因的非同义替换平均速率高出15倍，且有充分证据表明正选择作用于PE_PGRS62基因（非同义替换率/同义替换率（dN/dS）=1.42），该基因此前被证实对分枝杆菌在巨噬细胞与肉芽肿中的存活至关重要。研究进一步分别通过最大似然法与基于共变演化模型（covarion）的分析方法，证实了正选择在PE_PGRS62系统发育树的特定氨基酸残基或分支上的作用印记。值得注意的是，PE_PGRS62在现今的MTBC菌株中呈现高度保守性。
结论与意义：综合来看，研究数据表明，在光滑结核分枝杆菌中，PE/PE_PGRS基因经历了由重组加速的强烈多样化过程，且存在正选择作用的证据。本研究发现正选择作用于一个必需PE_PGRS基因，且该基因的序列在现今MTBC菌株中呈现固定化趋势，这一发现进一步支持了PE/PE_PGRS基因在分枝杆菌致病性演化中的关键作用。