Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Japan.
Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Japan Faculty of Environment and Information Studies, Keio University, Fujisawa, Japan.
Mol Biol Evol. 2016 Feb;33(2):530-40. doi: 10.1093/molbev/msv253. Epub 2015 Nov 5.
Transfer RNA (tRNA) is essential for the translation of genetic information into proteins, and understanding its molecular evolution is important if we are to understand the genetic code. In general, long variable-arm (V-arm) structures form in tRNA(Leu), tRNA(Ser), and bacterial and organellar tRNA(Tyr). However, as we have previously reported, noncanonical V-arms occur in nematode tRNA(Gly) and tRNA(Ile), and potentially affect translational fidelity. Here, we comprehensively analyzed 69 eukaryotic genome sequences and examined the evolutionary divergence of the V-arm-containing tRNAs. In total, 253 V-arm-containing tRNAs, with neither leucine nor serine anticodons, were identified in organisms ranging from nematodes to fungi, plants, and vertebrates. We defined them as "noncanonical V-arm-containing tRNAs" (nov-tRNAs). Moreover, 2,415 nov-tRNA-like sequences lacking some of the conserved features of tRNAs were also identified, largely in vertebrate genomes. These nov-tRNA/nov-tRNA-like sequences can be categorized into three types, based on differences in their possible evolutionary origins. The type A nov-tRNAs in nematodes probably evolved not only from tRNA(Leu) but also from tRNA(Ser) and other isotypes on several independent occasions. The type B nov-tRNAs are dispersed abundantly throughout vertebrate genomes, and seem to have originated from retrotransposable elements. The type C nov-tRNAs may have been acquired from plant chloroplasts or from bacteria through horizontal transfer. Our findings provide unexpected insight into the evolution of the tRNA molecule, which was diverse and occurred independently in nematodes, vertebrates, and plants.
转移 RNA（tRNA）对于将遗传信息翻译成蛋白质至关重要，如果我们要理解遗传密码，那么了解其分子进化就很重要。一般来说，长的可变臂（V 臂）结构会在 tRNA（Leu）、tRNA（Ser）以及细菌和细胞器 tRNA（Tyr）中形成。然而，正如我们之前所报道的，非典型的 V 臂会出现在线虫 tRNA（Gly）和 tRNA（Ile）中，并可能影响翻译的准确性。在这里，我们全面分析了 69 个真核生物基因组序列，并研究了含有 V 臂的 tRNA 的进化分歧。总共在从线虫到真菌、植物和脊椎动物的生物体中鉴定出 253 个含有 V 臂且不含亮氨酸或丝氨酸反密码子的 tRNA。我们将其定义为“非典型 V 臂含有 tRNA”（nov-tRNA）。此外，还鉴定出 2415 个缺少一些 tRNA 保守特征的 nov-tRNA 样序列，这些序列主要存在于脊椎动物基因组中。这些 nov-tRNA/nov-tRNA 样序列可以根据其可能的进化起源的差异分为三种类型。线虫中的 A 型 nov-tRNA 可能不仅从 tRNA（Leu），而且从 tRNA（Ser）和其他几个独立的类型进化而来。B 型 nov-tRNA 广泛分散在脊椎动物基因组中，似乎起源于反转录转座元件。C 型 nov-tRNA 可能是从植物叶绿体或通过水平转移从细菌中获得的。我们的发现为 tRNA 分子的进化提供了意想不到的见解，这种进化在线虫、脊椎动物和植物中是多样化的，并且是独立发生的。
