Sequence Evidence in the Archaeal Genomes that tRNAs Emerged Through the Combination of Ancestral Genes as 5′ and 3′ tRNA Halves
Sequence Evidence in the Archaeal Genomes that tRNAs Emerged Through the Combination of Ancestral Genes as 5′ and 3′ tRNA Halves
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DOI：
10.1371/journal.pone.0001622
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发表时间：
2008-02-20
期刊：
影响因子：
3.7
通讯作者：
Kanai, Akio
中科院分区：
文献类型：
--
作者：
Fujishima, Kosuke;Sugahara, Junichi;Kanai, Akio
在古细菌寄生虫马纳米古菌中发现了分离的5'和3'半转移RNA（tRNA）分子，即所谓的分裂tRNA，这让我们想知道祖先的tRNA是由1个还是2个基因编码的。我们进行了全面的系统发育分析的tRNA在45个古菌物种，探讨三种类型的tRNA（非内含子，内含子和分裂）之间的关系。我们将1953个成熟的tRNA序列分为22个簇。所有分裂的tRNA都显示出与具有相同反密码子的其他tRNA的系统发育关系。我们还通过人工分离7种原始古生菌的tRNA序列的反密码子来模拟分裂的tRNA，并分析了5'和3' tRNA半部分的序列相似性和多样性。网络分析揭示了5'端和3'端tRNA序列的特征和拓扑结构的差异：5'端tRNA序列相似性大于80%，可分为6个不同的组; 39个tRNA序列相似性大于88%，可分为9个不同的组，说明2个tRNA序列的进化背景不同。此外，5'和3'半的组合对应于密码子表中氨基酸的变化。我们不仅在tRNA（iMet）、tRNA（Thr）、tRNA（Ile）、tRNA（Gly）、tRNA（Gln）、tRNA（Glu）、tRNA（Asp）、tRNA（Lys）、tRNA（Arg）和tRNA（Leu）中发现了普遍保守的5 '-3' tRNA半体组合，而且在tRNA（Pro）、tRNA（Ala）和tRNA（Trp）中发现了门特异性组合。我们的研究结果支持了tRNA是通过单独基因的组合而出现的这一观点，并解释了古细菌tRNA进化过程中出现的序列多样性。
The discovery of separate 5' and 3' halves of transfer RNA (tRNA) molecules-so-called split tRNA-in the archaeal parasite Nanoarchaeum equitans made us wonder whether ancestral tRNA was encoded on 1 or 2 genes. We performed a comprehensive phylogenetic analysis of tRNAs in 45 archaeal species to explore the relationship between the three types of tRNAs (nonintronic, intronic and split). We classified 1953 mature tRNA sequences into 22 clusters. All split tRNAs have shown phylogenetic relationships with other tRNAs possessing the same anticodon. We also mimicked split tRNA by artificially separating the tRNA sequences of 7 primitive archaeal species at the anticodon and analyzed the sequence similarity and diversity of the 5' and 3' tRNA halves. Network analysis revealed specific characteristics of and topological differences between the 5' and 3' tRNA halves: the 5' half sequences were categorized into 6 distinct groups with asequence similarity of >80%, while the 39 half sequences were categorized into 9 groups with a higher sequence similarity of >88%, suggesting different evolutionary backgrounds of the 2 halves. Furthermore, the combinations of 5' and 3' halves corresponded with the variation of amino acids in the codon table. We found not only universally conserved combinations of 5'-3' tRNA halves in tRNA(iMet), tRNA(Thr), tRNA(Ile), tRNA(Gly), tRNA(Gln), tRNA(Glu), tRNA(Asp), tRNA(Lys), tRNA(Arg) and tRNA(Leu) but also phylum-specific combinations in tRNA(Pro), tRNA(Ala), and tRNA(Trp). Our results support the idea that tRNA emerged through the combination of separate genes and explain the sequence diversity that arose during archaeal tRNA evolution.