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

Research output: Contribution to journalArticle

37 Citations (Scopus)

Abstract

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.

Original languageEnglish
Article numbere1622
JournalPLoS One
Volume3
Issue number2
DOIs
Publication statusPublished - 2008 Feb 20

Fingerprint

Archaeal Genome
transfer RNA
Transfer RNA
Genes
genome
genes
Anticodon
Nanoarchaeota
RNA, Transfer, Gly
RNA, Transfer, Thr
Archaeal RNA
RNA, Transfer, Arg
RNA, Transfer, Pro
RNA, Transfer, Asp
RNA, Transfer, Ala
RNA, Transfer, Glu
RNA, Transfer, Ile
RNA, Transfer, Lys
nucleotide sequences

ASJC Scopus subject areas

  • Agricultural and Biological Sciences(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Medicine(all)

Cite this

Sequence evidence in the archaeal genomes that tRNAs emerged through the combination of ancestral genes as 5′ and 3′ tRNA halves. / Fujishima, Kosuke; Sugahara, Junichi; Tomita, Masaru; Kanai, Akio.

In: PLoS One, Vol. 3, No. 2, e1622, 20.02.2008.

Research output: Contribution to journalArticle

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