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与PE_PGRS是两类分枝杆菌（mycobacteria）限制性多基因家族，编码膜结合蛋白与分泌蛋白，主要在致病菌类群中发生扩增，尤以结核分枝杆菌复合群（Mycobacterium tuberculosis complex, MTBC）为著。多项研究证据表明，PE与PE_PGRS基因在分枝杆菌致病过程中发挥关键作用。为深入解析此类基因的本质，本研究旨在探究其在光滑结核杆菌（smooth tubercle bacilli, STB）——克隆性MTBC的推定祖先类群——中的演化轨迹。
研究方法与主要结果：本研究聚焦6个具有多态性的STB来源PE/PE_PGRS基因，证实单基因谱系树间存在显著不一致性，并通过多种方法检测到强烈的重组信号。基于溯祖理论（coalescent theory）的种群重组率与突变率（分别记为ρ与θ）估算结果显示，这两种机制在产生遗传多样性方面的作用大致相当（ρ/θ=1.457），这一结果与主要依靠突变驱动演化的持家基因（house keeping genes, HKG，ρ/θ=0.012）形成鲜明对比。与持家基因相比，本研究发现非同义替换的平均速率高出15倍，同时获得了PE_PGRS62基因受正向选择（positive selection）作用的有力证据（dN/dS=1.42）；该基因此前已被证实对分枝杆菌在巨噬细胞（macrophage）与肉芽肿（granuloma）中的存活至关重要。分别借助最大似然法（maximum likelihood）与基于共变密码子模型（covarion model）的分析方法，进一步证实了PE_PGRS62系统发育树的特定氨基酸残基或分支上存在正向选择印记。值得注意的是，PE_PGRS62在当代MTBC菌株中呈现高度保守性。
结论与意义：综合来看，数据表明在STB中，PE/PE_PGRS基因经历了由重组加速的强烈多样化进程，且存在正向选择作用的证据。此次研究发现，受正向选择作用的是一个必需PE_PGRS基因，其序列在当代MTBC菌株中似乎已被推向固定，这一发现进一步佐证了PE/PE_PGRS基因在分枝杆菌致病能力演化过程中的关键作用。