Cargando…

Sequence Evidence in the Archaeal Genomes that tRNAs Emerged Through the Combination of Ancestral Genes as 5′ and 3′ tRNA Halves

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 exp...

Descripción completa

Detalles Bibliográficos
Autores principales: Fujishima, Kosuke, Sugahara, Junichi, Tomita, Masaru, Kanai, Akio
Formato: Texto
Lenguaje:English
Publicado: Public Library of Science 2008
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2237900/
https://www.ncbi.nlm.nih.gov/pubmed/18286179
http://dx.doi.org/10.1371/journal.pone.0001622
_version_ 1782150415019671552
author Fujishima, Kosuke
Sugahara, Junichi
Tomita, Masaru
Kanai, Akio
author_facet Fujishima, Kosuke
Sugahara, Junichi
Tomita, Masaru
Kanai, Akio
author_sort Fujishima, Kosuke
collection PubMed
description 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 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 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.
format Text
id pubmed-2237900
institution National Center for Biotechnology Information
language English
publishDate 2008
publisher Public Library of Science
record_format MEDLINE/PubMed
spelling pubmed-22379002008-02-20 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 PLoS One Research Article 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 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 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. Public Library of Science 2008-02-20 /pmc/articles/PMC2237900/ /pubmed/18286179 http://dx.doi.org/10.1371/journal.pone.0001622 Text en Fujishima et al. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
spellingShingle Research Article
Fujishima, Kosuke
Sugahara, Junichi
Tomita, Masaru
Kanai, Akio
Sequence Evidence in the Archaeal Genomes that tRNAs Emerged Through the Combination of Ancestral Genes as 5′ and 3′ tRNA Halves
title Sequence Evidence in the Archaeal Genomes that tRNAs Emerged Through the Combination of Ancestral Genes as 5′ and 3′ tRNA Halves
title_full Sequence Evidence in the Archaeal Genomes that tRNAs Emerged Through the Combination of Ancestral Genes as 5′ and 3′ tRNA Halves
title_fullStr Sequence Evidence in the Archaeal Genomes that tRNAs Emerged Through the Combination of Ancestral Genes as 5′ and 3′ tRNA Halves
title_full_unstemmed Sequence Evidence in the Archaeal Genomes that tRNAs Emerged Through the Combination of Ancestral Genes as 5′ and 3′ tRNA Halves
title_short Sequence Evidence in the Archaeal Genomes that tRNAs Emerged Through the Combination of Ancestral Genes as 5′ and 3′ tRNA Halves
title_sort sequence evidence in the archaeal genomes that trnas emerged through the combination of ancestral genes as 5′ and 3′ trna halves
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2237900/
https://www.ncbi.nlm.nih.gov/pubmed/18286179
http://dx.doi.org/10.1371/journal.pone.0001622
work_keys_str_mv AT fujishimakosuke sequenceevidenceinthearchaealgenomesthattrnasemergedthroughthecombinationofancestralgenesas5and3trnahalves
AT sugaharajunichi sequenceevidenceinthearchaealgenomesthattrnasemergedthroughthecombinationofancestralgenesas5and3trnahalves
AT tomitamasaru sequenceevidenceinthearchaealgenomesthattrnasemergedthroughthecombinationofancestralgenesas5and3trnahalves
AT kanaiakio sequenceevidenceinthearchaealgenomesthattrnasemergedthroughthecombinationofancestralgenesas5and3trnahalves