ArticlePloS one2008
Sequence evidence in the archaeal genomes that tRNAs emerged through the combination of ancestral genes as 5' and 3' tRNA halves.
Article in PloS one, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed.
- Traces of a Primitive RNA Ring in Current Genomes.Biology · 2025Article
- Article
- tRNA diversification among uncultured archeon clones.Bioinformation · 2018Article
- Intercompartmental Piecewise Gene Transfer.Genes · 2017Review
- Evolutionary Analysis of HIV-1 Pol Proteins Reveals Representative Residues for Viral Subtype Differentiation.Frontiers in microbiology · 2017Article
- Disrupted tRNA Genes and tRNA Fragments: A Perspective on tRNA Gene Evolution.Life (Basel, Switzerland) · 2015Review
- tRNA gene diversity in the three domains of life.Frontiers in genetics · 2014Review
- Handling tRNA introns, archaeal way and eukaryotic way.Frontiers in genetics · 2014Review
- Circularly permuted tRNA genes: their expression and implications for their physiological relevance and development.Frontiers in genetics · 2014Review
- Identification and functional characterization of tRNA-derived RNA fragments (tRFs) in respiratory syncytial virus infection.Molecular therapy : the journal of the American Society of Gene Therapy · 2013Article
- Does the genetic code have a eukaryotic origin?Genomics, proteomics & bioinformatics · 2013Article
- The RNA world hypothesis: the worst theory of the early evolution of life (except for all the others)(a).Biology direct · 2012Article
- Mapping hidden potential identity elements by computing the average discriminating power of individual tRNA positions.DNA research : an international journal for rapid publication of reports on genes and genomes · 2012Article
- Genomic heterogeneity in a natural archaeal population suggests a model of tRNA gene disruption.PloS one · 2012Article
- A model of proto-anti-codon RNA enzymes requiring L-amino acid homochirality.Journal of molecular evolution · 2011Article
- Coadaptation of isoacceptor tRNA genes and codon usage bias for translation efficiency in Aedes aegypti and Anopheles gambiae.Insect molecular biology · 2011Article
- The last universal common ancestor (LUCA) and the ancestors of archaea and bacteria were progenotes.Journal of molecular evolution · 2011Article
- Genomic organization of eukaryotic tRNAs.BMC genomics · 2010Article
- Transfer RNA processing in archaea: unusual pathways and enzymes.FEBS letters · 2010Review
- Disrupted tRNA gene diversity and possible evolutionary scenarios.Journal of molecular evolution · 2009Article
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4 authors.
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No grant is acknowledged in the PubMed record.
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 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.
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