Table_1_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.

转移RNA（tRNA）是一类特定的RNA，其功能在于识别不同生命领域普遍采用的61种密码子，并将信使RNA（mRNA）解码成蛋白质。tRNA的组成和丰度在塑造密码子使用和配对偏差中发挥着至关重要的作用，这些偏差进而调节mRNA的翻译效率和准确性。在过去几十年中，研究主要集中在评估不同tRNA家族的特异性和冗余度上。然而，tRNA进化的机制和过程却鲜有研究。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tRNA的组成和进化进行了深入探究。我们的数据揭示了古菌基因组在tRNA类型和拷贝数上均表现出紧凑性。通常情况下，古菌基因组中不超过44种不同的tRNA类型用于解码61种标准密码子，并且大多数情况下，每个基因组中只存在一个基因拷贝。其中，tRNA-Met在基因组中的丰度显著，平均每个基因组有3个拷贝。相比之下，tRNA-UAU以及所有古菌基因组中均难以检测到的16种以A起始的反密码子tRNA（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，它们可能并非在古菌的共同祖先中进化，而是从不同的分支中独立丧失。此外，甲烷球菌目和甲烷杆菌目基因组中广泛缺失tRNA-CNNs，这表明这两个分支中这些tRNA的丧失可能是趋同性的。这种特定分支的tRNA丧失可能归因于其基因组的简约进化。我们的数据表明，古菌中当前的tRNA谱不仅源于祖先tRNA的组成，还受到冗余tRNA差异维护和丧失的影响。