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Cited by 46RNA and protein synthesis mechanismsEvolution and Genetic DynamicsGenomics and Phylogenetic Studies

Coevolution between Stop Codon Usage and Release Factors in Bacterial Species

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Wei, Yulong, Wang, Juan, Xia, Xuhua·2016·Molecular Biology and Evolution
DOI 10.1093/molbev/msw107PMC PMC4989110
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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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  • Highly expressed genes in diverse bacterial species strongly prefer UAA codons even in strongly GC-rich genomes with an overwhelming majority of stop codons being UGA.

    “Highly expressed genes in diverse bacterial species strongly prefer UAA codons even in strongly GC-rich genomes with an overwhelming majority of stop codons being UGA [74,75].”

    From Detailed Dissection and Critical Evaluation of the Pfizer/BioNTech and Moderna mRNA Vaccines (2021) · cites this paper as [74]

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Cited by

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Authors
Wei, Y., Wang, J., & Xia, X.
Affiliations
University of Ottawa (CA)
Corresponding author
Xia, Xuhua
ORCID
Venue
Molecular Biology and Evolution
Publisher
Oxford University Press (OUP)
Published
2016-06-13
Volume
33
Issue
9
Pages
2357-2367
ISSN
  • 0737-4038 (ISSN-L)
  • 1537-1719
DOI
10.1093/molbev/msw107
PMC
PMC4989110
OpenAlex
W2429224016
Cited by
46
References
4
Citations by year
2026: 4 · 2025: 5 · 2024: 2 · 2023: 1 · 2022: 6 · 2021: 3 · 2020: 3 · 2019: 7 · 2018: 10 · 2017: 3 · 2016: 2
FWCI
3.13
Type
journal article
Language
en
Open access
Licence
cc-by
Locations
  • Molecular Biology and Evolution (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • HighWire Press Open Archive (submittedVersion)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Evolution and Genetic Dynamics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
Keywords
release factors, RF1, RF2, unnatural amino acids, UAG, UGA, coevolution, translation termination, highly expressed genes, lowly expressed genes, codon usage bias, A+T content, codon reassignment
MeSH terms
Bacteria, Escherichia coli, Biological Evolution, Models, Molecular, Mutation, Peptide Chain Termination, Translational, Peptide Termination Factors, Ribosomes, Protein Biosynthesis, Codon, Terminator, Evolution, Molecular, Escherichia coli Proteins

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