Sequence evidence in the archaeal genomes that tRNAs emerged through the combination of ancestral genes as 5′ and 3′ tRNA halves

Kosuke Fujishima, Junichi Sugahara, Masaru Tomita, Akio Kanai

研究成果: Article査読

39 被引用数 (Scopus)

抄録

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 archaal 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 a sequence similarity of > 80%, while the 3′ 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 coresponded with the variation of amino acids in the codon table. We found not only universally conserved combinations of 5′-3′ tRNA halves in tRNS Imet, tRNA Thr, tRNAIle, tRNAGly, tRNAGin, tRNAGlu, tRNAAsp, tRNALys, tRNA Arg and tRNA but also phylum-specific combinations in tRNAPro, tRNAAla, and tRNATrp. 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.

本文言語English
論文番号e1622
ジャーナルPloS one
3
2
DOI
出版ステータスPublished - 2008 2 20

ASJC Scopus subject areas

  • 生化学、遺伝学、分子生物学(全般)
  • 農業および生物科学(全般)
  • 一般

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