ArticleeLife2021
A computational screen for alternative genetic codes in over 250,000 genomes.
Article in eLife, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 41 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.
The trial behind it
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
41 citing papers in PubMed, 63 citations in OpenAlex.
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- Glutamine codon-driven translational readthrough reveals context-dependent stop codon decoding fidelity.bioRxiv : the preprint server for biology · 2026Article
- Frequent occurrence and predicted functions of tRNAs with 4-base-pair anticodon stems in bacteria: extended superwobble hypothesis.Nucleic acids research · 2026Article
- Biocontrol potential and molecular basis of predation in a marine raptorial ciliate.The ISME journal · 2026Article
- VIRE: a metagenome-derived, planetary-scale virome resource with environmental context.Nucleic acids research · 2026Article
- Cell-supporting cytoskeletons and phagocytic acquisition of compatible solutes emerge as common strategies for high-salt adaptation in different ciliates.Science China. Life sciences · 2025Article
- Methanogenic archaea encoding Pyrrolysine maintain ambiguous amber codon usage.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Evaluating computational tools for protein-coding sequence detection: Are they up to the task?RNA (New York, N.Y.) · 2025Article
- Interpreting ribosome dynamics during mRNA translation.The Journal of biological chemistry · 2025Review
- 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
- Genetic Code-Locking Confers Stable Virus Resistance to a Recoded Organism.Biochemistry · 2025Article
- Lineage-specific expansions of polinton-like viruses in photosynthetic cryptophytes.Microbiome · 2025Article
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- Review
- Evolution of the Genetic Code in the Ascoideales (CUG-Ser2) Yeast Clade: The Ancestral tRNA-Leu(CAG) Gene Is Retained in Most Saccharomycopsis Species but Is Nonessential and Not Used for Translation.Genome biology and evolution · 2024Article
- Robust genetic codes enhance protein evolvability.PLoS biology · 2024Article
- Genomic factors shape carbon and nitrogen metabolic niche breadth across Saccharomycotina yeasts.Science (New York, N.Y.) · 2024Article
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 2 institutions in 1 country.
Funding
Abstract
The genetic code has been proposed to be a 'frozen accident,' but the discovery of alternative genetic codes over the past four decades has shown that it can evolve to some degree. Since most examples were found anecdotally, it is difficult to draw general conclusions about the evolutionary trajectories of codon reassignment and why some codons are affected more frequently. To fill in the diversity of genetic codes, we developed Codetta, a computational method to predict the amino acid decoding of each codon from nucleotide sequence data. We surveyed the genetic code usage of over 250,000 bacterial and archaeal genome sequences in GenBank and discovered five new reassignments of arginine codons (AGG, CGA, and CGG), representing the first sense codon changes in bacteria. In a clade of uncultivated Bacilli, the reassignment of AGG to become the dominant methionine codon likely evolved by a change in the amino acid charging of an arginine tRNA. The reassignments of CGA and/or CGG were found in genomes with low GC content, an evolutionary force that likely helped drive these codons to low frequency and enable their reassignment.
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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 Socratic graph.