ArticleBiology direct2012
Stop codons in bacteria are not selectively equivalent.
Article in Biology direct, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed, 42 citations in OpenAlex.
- Genetic constraints on protein loop evolution: out-of-frame stop codons limitFrontiers in molecular biosciences · 2026Article
- Pyrrolysine Aminoacyl-tRNA Synthetase as a Tool for Expanding the Genetic Code.International journal of molecular sciences · 2025Review
- StORF-Reporter: finding genes between genes.Nucleic acids research · 2023Article
- Evolution of termination codons of proteins and the TAG-TGA paradox.Scientific reports · 2023Article
- CRISPR-Cas-Guided Mutagenesis of Chromosome and Virulence Plasmid in Shigella flexneri by Cytosine Base Editing.mSystems · 2023Article
- Comparative Mitogenome Analysis of Gerbils and the Mitogenome Phylogeny of Gerbillinae (Rodentia: Muridae).Biochemical genetics · 2022Article
- Stop Codon Usage as a Window into Genome Evolution: Mutation, Selection, Biased Gene Conversion and the TAG Paradox.Genome biology and evolution · 2022Article
- Why Is the UAG (Amber) Stop Codon Almost Absent in Highly Expressed Bacterial Genes?Life (Basel, Switzerland) · 2022Article
- Variation in Release Factor Abundance Is Not Needed to Explain Trends in Bacterial Stop Codon Usage.Molecular biology and evolution · 2022Article
- Intergenic ORFs as elementary structural modules of de novo gene birth and protein evolution.Genome research · 2021Article
- ReScribe: An Unrestrained Tool Combining Multiplex Recombineering and Minimal-PAM ScCas9 for Genome RecodingACS synthetic biology · 2021Article
- Collateral Toxicity Limits the Evolution of Bacterial Release Factor 2 toward Total Omnipotence.Molecular biology and evolution · 2020Article
- In eubacteria, unlike eukaryotes, there is no evidence for selection favouring fail-safe 3' additional stop codons.PLoS genetics · 2019Article
- Purifying and positive selection in the evolution of stop codons.Scientific reports · 2018Article
- Refining the Ambush Hypothesis: Evidence That GC- and AT-Rich Bacteria Employ Different Frameshift Defence Strategies.Genome biology and evolution · 2018Article
- Selection on start codons in prokaryotes and potential compensatory nucleotide substitutions.Scientific reports · 2017Article
- Genomic analysis of methanogenic archaea reveals a shift towards energy conservation.BMC genomics · 2017Article
- ATGC database and ATGC-COGs: an updated resource for micro- and macro-evolutionary studies of prokaryotic genomes and protein family annotation.Nucleic acids research · 2017Article
- Coevolution between Stop Codon Usage and Release Factors in Bacterial Species.Molecular biology and evolution · 2016Article
- Comprehensive analysis of stop codon usage in bacteria and its correlation with release factor abundance.The Journal of biological chemistry · 2014Article
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 2 countries.
Funding
Abstract
backgroundThe evolution and genomic stop codon frequencies have not been rigorously studied with the exception of coding of non-canonical amino acids. Here we study the rate of evolution and frequency distribution of stop codons in bacterial genomes.
resultsWe show that in bacteria stop codons evolve slower than synonymous sites, suggesting the action of weak negative selection. However, the frequency of stop codons relative to genomic nucleotide content indicated that this selection regime is not straightforward. The frequency of TAA and TGA stop codons is GC-content dependent, with TAA decreasing and TGA increasing with GC-content, while TAG frequency is independent of GC-content. Applying a formal, analytical model to these data we found that the relationship between stop codon frequencies and nucleotide content cannot be explained by mutational biases or selection on nucleotide content. However, with weak nucleotide content-dependent selection on TAG, -0.5 < Nes < 1.5, the model fits all of the data and recapitulates the relationship between TAG and nucleotide content. For biologically plausible rates of mutations we show that, in bacteria, TAG stop codon is universally associated with lower fitness, with TAA being the optimal for G-content < 16% while for G-content > 16% TGA has a higher fitness than TAG.
conclusionsOur data indicate that TAG codon is universally suboptimal in the bacterial lineage, such that TAA is likely to be the preferred stop codon for low GC content while the TGA is the preferred stop codon for high GC content. The optimization of stop codon usage may therefore be useful in genome engineering or gene expression optimization applications.
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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.