Synonymous codon usage in Drosophila melanogaster: Natural selection and translational accuracy
Open accessAbstract
I present evidence that natural selection biases synonymous codon usage to enhance the accuracy of protein synthesis in Drosophila melanogaster. Since the fitness cost of a translational misincorporation will depend on how the amino acid substitution affects protein function, selection for translational accuracy predicts an association between codon usage in DNA and functional constraint at the protein level. The frequency of preferred codons is significantly higher at codons conserved for amino acids than at nonconserved codons in 38 genes compared between D. melanogaster and Drosophila virilis or Drosophila pseudoobscura (Z = 5.93, P < 10(-6)). Preferred codon usage is also significantly higher in putative zinc-finger and homeodomain regions than in the rest of 28 D. melanogaster transcription factor encoding genes (Z = 8.38, P < 10(-6)). Mutational alternatives (within-gene differences in mutation rates, amino acid changes altering codon preference states, and doublet mutations at adjacent bases) do not appear to explain this association between synonymous codon usage and amino acid constraint.
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The codon optimization in the previous section suffers from the lack of consideration for translation accuracy.
“The codon optimization in the previous section suffers from the lack of consideration for translation accuracy [36,37].”
From Detailed Dissection and Critical Evaluation of the Pfizer/BioNTech and Moderna mRNA Vaccines (2021) · cites this paper as [37]
Akashi found greater codon adaptation in conserved amino acid sites than in variable amino acid sites.
“He found greater codon adaptation in conserved amino acid sites than in variable amino acid sites.”
From Detailed Dissection and Critical Evaluation of the Pfizer/BioNTech and Moderna mRNA Vaccines (2021) · cites this paper as [37]
The difference between conserved and variable sites has resulted from selection for accuracy.
“This is consistent with his inference that the difference between the conserved and variable sites has resulted from selection for accuracy.”
From Detailed Dissection and Critical Evaluation of the Pfizer/BioNTech and Moderna mRNA Vaccines (2021) · cites this paper as [37]
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- Authors
- Akashi, H.
- Affiliations
- University of Chicago (US)
- Corresponding author
- Akashi, H
- ORCID
- Akashi, H
- Venue
- Genetics
- Publisher
- Oxford University Press (OUP)
- Published
- 1994-03-01
- Volume
- 136
- Issue
- 3
- Pages
- 927-935
- ISSN
- 0016-6731 (ISSN-L)
- 1943-2631
- OpenAlex
- W2147126179
- Cited by
- 742
- References
- 1
- Citations by year
- 2026: 20 · 2025: 15 · 2024: 23 · 2023: 12 · 2022: 24 · 2021: 22 · 2020: 19 · 2019: 19 · 2018: 39 · 2017: 26 · 2016: 32 · 2015: 27 · 2014: 50 · 2013: 31 · 2012: 36
- FWCI
- 3.36
- Type
- journal article
- Language
- en
- Open access
- green
- europepmc.org
- Licence
- academic.oup.com/journals/pages/open_access/funder_policies/chorus/standard_publication_model (vor)
- Locations
- Genetics (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed (publishedVersion)
- 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
- synonymous codon usage, Drosophila melanogaster, translational accuracy, natural selection, amino acid conservation, zinc finger proteins, homeodomain transcription factor, transcription factors, mutational bias, Drosophila virilis, Drosophila pseudoobscura
- MeSH terms
- Animals, Base Sequence, Codon, Drosophila, Drosophila melanogaster, Selection, Genetic, Species Specificity, Transcription Factors, Protein Biosynthesis, Genes, Insect
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