ArticlePloS one2008
Evolutionary patterns in the sequence and structure of transfer RNA: a window into early translation and the genetic code.
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 18 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
18 citing papers in PubMed, 36 citations in OpenAlex.
- Tracing the Origin and Evolution of the Secondary Structure of RNA.Methods in molecular biology (Clifton, N.J.) · 2026Article
- The Role of Mutations, Addition of Amino Acids, and Exchange of Genetic Information in the Coevolution of Primitive Coding Systems.International journal of molecular sciences · 2025Article
- Menzerath-Altmann's Law of Syntax in RNA Accretion History.Life (Basel, Switzerland) · 2021Article
- Theoretical minimal RNA rings designed according to coding constraints mimic deamination gradients.Die Naturwissenschaften · 2019Article
- Coding of Class I and II Aminoacyl-tRNA Synthetases.Advances in experimental medicine and biology · 2017Review
- Piecemeal Buildup of the Genetic Code, Ribosomes, and Genomes from Primordial tRNA Building Blocks.Life (Basel, Switzerland) · 2016Article
- Evolution of initiator tRNAs and selection of methionine as the initiating amino acid.RNA biology · 2016Article
- Computing the origin and evolution of the ribosome from its structure - Uncovering processes of macromolecular accretion benefiting synthetic biology.Computational and structural biotechnology journal · 2015Review
- Extensive tRNA gene changes in synthetic Brassica napus.Journal of molecular evolution · 2014Article
- The natural history of transfer RNA and its interactions with the ribosome.Frontiers in genetics · 2014Article
- Comparative analysis of barophily-related amino acid content in protein domains of Pyrococcus abyssi and Pyrococcus furiosus.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 phylogenomic roots of modern biochemistry: origins of proteins, cofactors and protein biosynthesis.Journal of molecular evolution · 2012Article
- Proteome evolution and the metabolic origins of translation and cellular life.Journal of molecular evolution · 2011Article
- The ancient history of the structure of ribonuclease P and the early origins of Archaea.BMC bioinformatics · 2010Article
- The evolutionary history of the structure of 5S ribosomal RNA.Journal of molecular evolution · 2009Article
- A gripping tale of ribosomal frameshifting: extragenic suppressors of frameshift mutations spotlight P-site realignment.Microbiology and molecular biology reviews : MMBR · 2009Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Transfer RNA (tRNA) molecules play vital roles during protein synthesis. Their acceptor arms are aminoacylated with specific amino acid residues while their anticodons delimit codon specificity. The history of these two functions has been generally linked in evolutionary studies of the genetic code. However, these functions could have been differentially recruited as evolutionary signatures were left embedded in tRNA molecules. Here we built phylogenies derived from the sequence and structure of tRNA, we forced taxa into monophyletic groups using constraint analyses, tested competing evolutionary hypotheses, and generated timelines of amino acid charging and codon discovery. Charging of Sec, Tyr, Ser and Leu appeared ancient, while specificities related to Asn, Met, and Arg were derived. The timelines also uncovered an early role of the second and then first codon bases, identified codons for Ala and Pro as the most ancient, and revealed important evolutionary take-overs related to the loss of the long variable arm in tRNA. The lack of correlation between ancestries of amino acid charging and encoding indicated that the separate discoveries of these functions reflected independent histories of recruitment. These histories were probably curbed by co-options and important take-overs during early diversification of the living world.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.