Evolutionary Patterns in the Sequence and Structure of Transfer RNA: A Window into Early Translation and the Genetic Code

Transfer RNA (tRNA) molecules play vital roles during protein synthesis. Their acceptor arms are aminoacylated with specific amino acid residues while their anticodons delimit codon specificity. The history of these two functions has been generally linked in evolutionary studies of the genetic code. However, these functions could have been differentially recruited as evolutionary signatures were left embedded in tRNA molecules. Here we built phylogenies derived from the sequence and structure of tRNA, we forced taxa into monophyletic groups using constraint analyses, tested competing evolutionary hypotheses, and generated timelines of amino acid charging and codon discovery. Charging of Sec, Tyr, Ser and Leu appeared ancient, while specificities related to Asn, Met, and Arg were derived. The timelines also uncovered an early role of the second and then first codon bases, identified codons for Ala and Pro as the most ancient, and revealed important evolutionary take-overs related to the loss of the long variable arm in tRNA. The lack of correlation between ancestries of amino acid charging and encoding indicated that the separate discoveries of these functions reflected independent histories of recruitment. These histories were probably curbed by co-options and important take-overs during early diversification of the living world.

转运RNA（Transfer RNA, tRNA）分子在蛋白质合成过程中发挥着至关重要的作用。其受体臂（acceptor arms）会与特定氨基酸残基发生氨酰化修饰，而反密码子（anticodons）则决定了密码子识别特异性（codon specificity）。长期以来，在遗传密码（genetic code）的进化研究中，这两种功能的演化历史通常被绑定在一起。然而，随着进化标记（evolutionary signatures）嵌入tRNA分子之中，这两类功能在演化过程中可能被差异化招募。

本研究基于tRNA的序列与结构构建了系统发育树（phylogenies），通过约束分析（constraint analyses）将类群限定为单系群（monophyletic groups），检验了竞争性进化假说（competing evolutionary hypotheses），并绘制了氨酰化（amino acid charging）与密码子发现（codon discovery）的演化时间线。结果显示，硒代半胱氨酸（Sec）、酪氨酸（Tyr）、丝氨酸（Ser）与亮氨酸（Leu）的氨酰化过程起源较早，而与天冬酰胺（Asn）、甲硫氨酸（Met）、精氨酸（Arg）相关的密码子识别特异性则起源较晚。该时间线还揭示了密码子第二位碱基较早发挥作用、随后第一位碱基参与其中的演化模式，确定丙氨酸（Ala）与脯氨酸（Pro）对应的密码子为最古老的密码子，并揭示了与tRNA长可变臂（long variable arm）丢失相关的重要演化替代事件。

氨酰化与密码子编码的祖先起源之间缺乏相关性，这表明这两类功能的独立发现反映了二者各自独立的招募历史。这些演化历程大概率在生命世界的早期多样化（early diversification of the living world）进程中，通过共征用（co-options）与关键的功能替代事件（take-overs）得到了塑造与整合。