Tracing the evolution of RNA structure in ribosomes

The elucidation of ribosomal structure has shown that the function of ribosomes is fundamentally confined to dynamic interactions established between the RNA components of the ribosomal ensemble. These findings now enable a detailed analysis of the evolution of ribosomal RNA (rRNA) structure. The origin and diversification of rRNA was studied here using phylogenetic tools directly at the structural level. A rooted universal tree was reconstructed from the combined secondary structures of large (LSU) and small (SSU) subunit rRNA using cladistic methods and considerations in statistical mechanics. The evolution of the complete repertoire of structural ribosomal characters was formally traced lineage-by-lineage in the tree, showing a tendency towards molecular simplification and a homogeneous reduction of ribosomal structural change with time. Character tracing revealed patterns of evolution in inter-subunit bridge contacts and tRNA-binding sites that were consistent with the proposed coupling of tRNA translocation and subunit movement. These patterns support the concerted evolution of tRNA-binding sites in the two subunits and the ancestral nature and common origin of certain structural ribosomal features, such as the peptidyl (P) site, the functional relay of the penultimate stem helix of SSU rRNA, and other structures participating in ribosomal dynamics. Overall results provide a rare insight into the evolution of ribosomal structure.

核糖体结构的解析表明，核糖体的功能本质上局限于核糖体复合体（ribosomal ensemble）的RNA组分之间建立的动态相互作用。如今，这些发现为核糖体RNA（ribosomal RNA, rRNA）结构的进化研究提供了细致分析的可行路径。本研究直接在结构层面借助系统发育工具（phylogenetic tools），探究了rRNA的起源与多样化进程。基于大亚基（Large Subunit Unit, LSU）和小亚基（Small Subunit Unit, SSU）rRNA的联合二级结构（secondary structures），结合分支分类学方法（cladistic methods）与统计力学（statistical mechanics）相关考量，研究人员重建了一棵有根的通用生命树。本研究正式沿树内各谱系，追踪了整套核糖体结构性状的进化历程，结果显示出分子简化的趋势，且随着时间推移，核糖体结构的变化呈现均匀减弱的特征。性状追踪揭示了亚基间桥接接触位点与tRNA结合位点的进化模式，该模式与此前提出的tRNA易位与亚基移动的耦合假说相符。上述结果支持两个亚基的tRNA结合位点协同进化，以及部分核糖体结构特征的祖先性与共同起源，例如肽酰（P）位点（peptidyl (P) site）、小亚基rRNA倒数第二茎螺旋的功能中继链，以及其他参与核糖体动态过程的结构。整体研究结果为核糖体结构的进化历程提供了难得的科学洞见。