Table_10_Genome-Wide Analysis Reveals Ancestral Lack of Seventeen Different tRNAs and Clade-Specific Loss of tRNA-CNNs in Archaea.XLSX

Transfer RNA (tRNA) is a category of RNAs that specifically decode messenger RNAs (mRNAs) into proteins by recognizing a set of 61 codons commonly adopted by different life domains. The composition and abundance of tRNAs play critical roles in shaping codon usage and pairing bias, which subsequently modulate mRNA translation efficiency and accuracy. Over the past few decades, effort has been concentrated on evaluating the specificity and redundancy of different tRNA families. However, the mechanism and processes underlying tRNA evolution have only rarely been investigated. In this study, by surveying tRNA genes in 167 completely sequenced genomes, we systematically investigated the composition and evolution of tRNAs in Archaea from a phylogenetic perspective. Our data revealed that archaeal genomes are compact in both tRNA types and copy number. Generally, no more than 44 different types of tRNA are present in archaeal genomes to decode the 61 canonical codons, and most of them have only one gene copy per genome. Among them, tRNA-Met was significantly overrepresented, with an average of three copies per genome. In contrast, the tRNA-UAU and 16 tRNAs with A-starting anticodons (tRNA-ANNs) were rarely detected in all archaeal genomes. The conspicuous absence of these tRNAs across the archaeal phylogeny suggests they might have not been evolved in the common ancestor of Archaea, rather than have lost independently from different clades. Furthermore, widespread absence of tRNA-CNNs in the Methanococcales and Methanobacteriales genomes indicates convergent loss of these tRNAs in the two clades. This clade-specific tRNA loss may be attributing to the reductive evolution of their genomes. Our data suggest that the current tRNA profiles in Archaea are contributed not only by the ancestral tRNA composition, but also by differential maintenance and loss of redundant tRNAs.

转运RNA（tRNA）是一类RNA，其特定功能为解码信使RNA（mRNA）并将其转化为蛋白质，这一过程通过识别不同生命领域普遍采用的61种密码子集来完成。tRNA的组成与丰度对于塑造密码子使用和配对偏差起着至关重要的作用，进而调节mRNA的翻译效率和准确性。在过去几十年中，研究重点集中于评估不同tRNA家族的特异性和冗余性。然而，关于tRNA进化的机制和过程却鲜有深入研究。在本研究中，通过对167个完全测序的基因组中的tRNA基因进行调研，我们从系统发育的角度对古菌中的tRNA组成与进化进行了全面探究。我们的数据揭示，古菌基因组在tRNA类型及拷贝数上均较为紧凑。通常情况下，古菌基因组中不超过44种不同的tRNA类型即可解码61种标准密码子，且大多数情况下每个基因组中只含有一个基因拷贝。其中，tRNA-Met的丰度显著较高，每个基因组平均拥有三个拷贝。相比之下，tRNA-UAU以及所有古菌基因组中均未检测到的16种以A开头的反密码子（tRNA-ANNs）则极为罕见。这些tRNA在古菌系统发育中的显著缺失表明，它们可能并未在古菌的共同祖先中进化，而是独立于不同分支中逐渐丧失。此外，甲烷球菌目和甲烷杆菌目基因组中广泛缺失tRNA-CNNs的现象表明，这两个分支中可能发生了这些tRNA的趋同丧失。这种分支特异性的tRNA丧失可能与它们基因组简约化进化有关。我们的数据表明，当前古菌中的tRNA特征不仅由祖先tRNA组成所贡献，还受到冗余tRNA的维持和丧失差异的影响。