ArticleMolecular biology and evolution2016
Coevolution between Stop Codon Usage and Release Factors in Bacterial Species.
Article in Molecular biology and evolution, 2016. 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, 46 citations in OpenAlex.
- Compensatory evolution facilitates loss of prfB autoregulation in Pseudomonas fluorescens SBW25.Molecular biology and evolution · 2026Article
- Glutamine codon-driven translational readthrough reveals context-dependent stop codon decoding fidelity.bioRxiv : the preprint server for biology · 2026Article
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- Comparative Genomics Insights Into the Evolutionary Disparities Between Nitroplast-Evolved Ecotype UCYN-A2 and Its Closest Relative UCYN-A1.Ecology and evolution · 2025Article
- Genomic AT Bias Coupled with Amino Acid Metabolism Modulates Codon Usage.Journal of molecular evolution · 2025Article
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- Differential Selection for Translation Efficiency Shapes Translation Machineries in Bacterial Species.Microorganisms · 2024Article
- Fluorescent reporters give new insights into antibiotics-induced nonsense and frameshift mistranslation.Scientific reports · 2024Article
- Stop Codon Usage as a Window into Genome Evolution: Mutation, Selection, Biased Gene Conversion and the TAG Paradox.Genome biology and evolution · 2022Article
- Overview of tRNA Modifications in Chloroplasts.Microorganisms · 2022Article
- Variation in Release Factor Abundance Is Not Needed to Explain Trends in Bacterial Stop Codon Usage.Molecular biology and evolution · 2022Article
- Physiological and muscle tissue responses inFrontiers in physiology · 2022Article
- Detailed Dissection and Critical Evaluation of the Pfizer/BioNTech and Moderna mRNA Vaccines.Vaccines · 2021Article
- Spurious regulatory connections dictate the expression-fitness landscape of translation factors.Molecular systems biology · 2021Article
- Effective Population Size Predicts Local Rates but Not Local Mitigation of Read-through Errors.Molecular biology and evolution · 2021Article
- In eubacteria, unlike eukaryotes, there is no evidence for selection favouring fail-safe 3' additional stop codons.PLoS genetics · 2019Article
- Understanding the Genetic Code.Journal of bacteriology · 2019Review
- Translation Control ofInternational journal of molecular sciences · 2019Review
- 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
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Three stop codons in bacteria represent different translation termination signals, and their usage is expected to depend on their differences in translation termination efficiency, mutation bias, and relative abundance of release factors (RF1 decoding UAA and UAG, and RF2 decoding UAA and UGA). In 14 bacterial species (covering Proteobacteria, Firmicutes, Cyanobacteria, Actinobacteria and Spirochetes) with cellular RF1 and RF2 quantified, UAA is consistently over-represented in highly expressed genes (HEGs) relative to lowly expressed genes (LEGs), whereas UGA usage is the opposite even in species where RF2 is far more abundant than RF1. UGA usage relative to UAG increases significantly with PRF2 [=RF2/(RF1 + RF2)] as expected from adaptation between stop codons and their decoders. PRF2 is > 0.5 over a wide range of AT content (measured by PAT3 as the proportion of AT at third codon sites), but decreases rapidly toward zero at the high range of PAT3 This explains why bacterial lineages with high PAT3 often have UGA reassigned because of low RF2. There is no indication that UAG is a minor stop codon in bacteria as claimed in a recent publication. The claim is invalid because of the failure to apply the two key criteria in identifying a minor codon: (1) it is least preferred by HEGs (or most preferred by LEGs) and (2) it corresponds to the least abundant decoder. Our results suggest a more plausible explanation for why UAA usage increases, and UGA usage decreases, with PAT3, but UAG usage remains low over the entire PAT3 range.
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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.