ArticlePLoS computational biology2008
Evolutionary patterns in the sequence and structure of transfer RNA: early origins of archaea and viruses.
Article in PLoS computational biology, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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Who cites it
29 citing papers in PubMed, 45 citations in OpenAlex.
- Reassessing viral origins and evolutionary placement in the tree of life.Antonie van Leeuwenhoek · 2026Review
- Tracing the Origin and Evolution of the Secondary Structure of RNA.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Menzerath-Altmann's Law of Syntax in RNA Accretion History.Life (Basel, Switzerland) · 2021Article
- Descent of Bacteria and Eukarya From an Archaeal Root of Life.Evolutionary bioinformatics online · 2020Article
- Theoretical minimal RNA rings designed according to coding constraints mimic deamination gradients.Die Naturwissenschaften · 2019Article
- Rooting Phylogenies and the Tree of Life While Minimizing Ad Hoc and Auxiliary Assumptions.Evolutionary bioinformatics online · 2018Review
- Evolution of initiator tRNAs and selection of methionine as the initiating amino acid.RNA biology · 2016Article
- Coevolution Theory of the Genetic Code at Age Forty: Pathway to Translation and Synthetic Life.Life (Basel, Switzerland) · 2016Article
- A Comprehensive tRNA Genomic Survey Unravels the Evolutionary History of tRNA Arrays in Prokaryotes.Genome biology and evolution · 2015Article
- A tree of cellular life inferred from a genomic census of molecular functions.Journal of molecular evolution · 2014Article
- RNA sociology: group behavioral motifs of RNA consortia.Life (Basel, Switzerland) · 2014Review
- Pragmatic turn in biology: From biological molecules to genetic content operators.World journal of biological chemistry · 2014Review
- Archaea: the first domain of diversified life.Archaea (Vancouver, B.C.) · 2014Review
- Global patterns of protein domain gain and loss in superkingdoms.PLoS computational biology · 2014Article
- A phylogenomic census of molecular functions identifies modern thermophilic archaea as the most ancient form of cellular life.Archaea (Vancouver, B.C.) · 2014Article
- Rethinking quasispecies theory: From fittest type to cooperative consortia.World journal of biological chemistry · 2013Review
- Comparative analysis of proteomes and functionomes provides insights into origins of cellular diversification.Archaea (Vancouver, B.C.) · 2013Article
- Structural phylogenomics retrodicts the origin of the genetic code and uncovers the evolutionary impact of protein flexibility.PloS one · 2013Article
- The RNA world hypothesis: the worst theory of the early evolution of life (except for all the others)(a).Biology direct · 2012Article
- The evolutionary history of protein fold families and proteomes confirms that the archaeal ancestor is more ancient than the ancestors of other superkingdoms.BMC evolutionary biology · 2012Article
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Transfer RNAs (tRNAs) are ancient molecules that are central to translation. Since they probably carry evolutionary signatures that were left behind when the living world diversified, we reconstructed phylogenies directly from the sequence and structure of tRNA using well-established phylogenetic methods. The trees placed tRNAs with long variable arms charging Sec, Tyr, Ser, and Leu consistently at the base of the rooted phylogenies, but failed to reveal groupings that would indicate clear evolutionary links to organismal origin or molecular functions. In order to uncover evolutionary patterns in the trees, we forced tRNAs into monophyletic groups using constraint analyses to generate timelines of organismal diversification and test competing evolutionary hypotheses. Remarkably, organismal timelines showed Archaea was the most ancestral superkingdom, followed by viruses, then superkingdoms Eukarya and Bacteria, in that order, supporting conclusions from recent phylogenomic studies of protein architecture. Strikingly, constraint analyses showed that the origin of viruses was not only ancient, but was linked to Archaea. Our findings have important implications. They support the notion that the archaeal lineage was very ancient, resulted in the first organismal divide, and predated diversification of tRNA function and specificity. Results are also consistent with the concept that viruses contributed to the development of the DNA replication machinery during the early diversification of the living world.
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