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.

研究背景：PE与PE_PGRS是两类分枝杆菌专属的多基因家族，编码膜结合蛋白与分泌蛋白，其扩增主要集中于致病菌类群，尤以结核分枝杆菌复合群（Mycobacterium tuberculosis complex, MTBC）最为显著。多项研究证据表明，PE及PE_PGRS基因在分枝杆菌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光滑型结核杆菌（smooth tubercle bacilli, STB）——克隆性MTBC的推定祖先类群——中的演化轨迹。

材料与方法/主要结果：本研究聚焦于6个具有多态性的STB PE/PE_PGRS基因，证实单基因谱系间存在显著的拓扑不一致性，并通过多种分析方法检测到强烈的重组信号。基于溯祖理论的群体重组率（ρ）与突变率（θ）估算结果显示，二者在产生基因多样性方面的作用大致相当（ρ/θ=1.457），这一发现与持家基因（house keeping genes, HKG）的演化模式形成鲜明反差：持家基因的演化主要由突变驱动（ρ/θ=0.012）。与持家基因相比，本研究中PE/PE_PGRS基因的非同义替换平均速率高出15倍，且有充分证据显示正选择作用于PE_PGRS62基因（dN/dS=1.42）——该基因此前已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。我们进一步分别采用最大似然法与协变分子模型法，证实正选择印记分别作用于PE_PGRS62系统发育树的特定氨基酸残基与分支。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，本研究数据表明，在STB类群中，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。本次研究发现，正选择靶向了一个在当代MTBC菌株中序列趋于固定的关键PE_PGRS基因，这一结果进一步支持了PE/PE_PGRS基因在分枝杆菌致病性演化过程中的核心作用。