Evolution of initiator tRNAs and selection of methionine as the initiating amino acid
Evolution of initiator tRNAs and selection of methionine as the initiating amino acid
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DOI：
10.1080/15476286.2016.1195943
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发表时间：
2016-01-01
期刊：
影响因子：
4.1
通讯作者：
Varshney, Umesh
中科院分区：
文献类型：
--
作者：
Bhattacharyya, Souvik;Varshney, Umesh
转移RNA（tRNA）在塑造生物分子进化中起着重要作用。起始tRNA（tRNA（i））是一类特殊的tRNA，它携带甲硫氨酸（或其衍生物甲酰基甲硫氨酸）进入核糖体，启动一个耗能巨大但受高度调控的蛋白质合成过程。tRNA（i）的进化过程和选择甲硫氨酸作为通用起始氨基酸仍然是一个谜。我们使用全序列、tRNA的受体-TC臂（“微螺旋”）和反密码子-二氢尿苷臂区域构建了系统发育树，这些区域来自158个物种，属于所有3个生命领域。所有的树木都清晰地组合成三个生命领域。使用大量物种的所有tRNA数据生成的大型树未能揭示主要的进化事件和可能是tRNA祖先的可能的延伸体tRNA序列的身份（i）。因此，我们使用微螺旋或物种特异性tRNA的整个序列构建了树，并对50种真细菌物种进行了重复分析。我们鉴定了tRNA（Pro）、tRNA（Glu）或tRNA（Thr）（但令人惊讶的是，没有延伸tRNA（Met））可能是tRNA（i）的祖先。然后，我们确定了影响选择甲硫氨酸作为起始氨基酸的因素。在所有氨基酸中，蛋氨酸的合成代谢成本最高，其出现的总频率在生命的3个领域中几乎保持不变。我们的相关性分析表明，它的高代谢成本是独立的侧链的许多理化性质。我们的研究结果表明，选择甲硫氨酸作为起始氨基酸可能是一个碳代谢进化的结果，它在调节翻译起始中起着重要作用。
Transfer RNAs (tRNAs) have been important in shaping biomolecular evolution. Initiator tRNAs (tRNA(i)), a special class of tRNAs, carry methionine (or its derivative, formyl-methionine) to ribosomes to start an enormously energy consuming but a highly regulated process of protein synthesis. The processes of tRNA(i) evolution, and selection of methionine as the universal initiating amino acid remain an enigmatic problem. We constructed phylogenetic trees using the whole sequence, the acceptor-TC arm ('minihelix'), and the anticodon-dihydrouridine arm regions of tRNA(i) from 158 species belonging to all 3 domains of life. All the trees distinctly assembled into 3 domains of life. Large trees, generated using data for all the tRNAs of a vast number of species, fail to reveal the major evolutionary events and identity of the probable elongator tRNA sequences that could be ancestor of tRNA(i). Therefore, we constructed trees using the minihelix or the whole sequence of species specific tRNAs, and iterated our analysis on 50 eubacterial species. We identified tRNA(Pro), tRNA(Glu), or tRNA(Thr) (but surprisingly not elongator tRNA(Met)) as probable ancestors of tRNA(i). We then determined the factors imposing selection of methionine as the initiating amino acid. Overall frequency of occurrence of methionine, whose metabolic cost of synthesis is the highest among all amino acids, remains almost unchanged across the 3 domains of life. Our correlation analysis shows that its high metabolic cost is independent of many physicochemical properties of the side chain. Our results indicate that selection of methionine, as the initiating amino acid was possibly a consequence of the evolution of one-carbon metabolism, which plays an important role in regulating translation initiation.