ArticleG3 (Bethesda, Md.)2017
The Impact of Selection at the Amino Acid Level on the Usage of Synonymous Codons.
Article in G3 (Bethesda, Md.), 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- Temporal and gene-specific dynamics of codon usage evolution in SARS-CoV-2 genomes.BMC genomics · 2026Article
- Evolutionary dynamics of the calcium/cation antiporter superfamily in Brassicaceae: codon usage, selection pressure, andFrontiers in plant science · 2025Article
- Amino acid sequence encodes protein abundance shaped by protein stability at reduced synthesis cost.Protein science : a publication of the Protein Society · 2025Article
- The Quest for Immunity: Exploring Human Herpesviruses as Vaccine Vectors.International journal of molecular sciences · 2023Review
- The Influence of the Selection at the Amino Acid Level on Synonymous Codon Usage from the Viewpoint of Alternative Genetic Codes.International journal of molecular sciences · 2023Article
- No evidence for widespread positive selection on double substitutions within codons in primates and yeasts.Frontiers in genetics · 2022Article
- Natural Selection Plays an Important Role in Shaping the Codon Usage of Structural Genes of the Viruses Belonging to theViruses · 2020Article
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- Presyncodon, a Web Server for Gene Design with the Evolutionary Information of the Expression Hosts.International journal of molecular sciences · 2018Article
- New Insight into Parrots' Mitogenomes Indicates That Their Ancestor Contained a Duplicated Region.Molecular biology and evolution · 2018Article
- Differences in Codon Usage Bias between Photosynthesis-Related Genes and Genetic System-Related Genes of Chloroplast Genomes in Cultivated and Wild Solanum Species.International journal of molecular sciences · 2018Article
- Base composition is the primary factor responsible for the variation of amino acid usage in zebra finch (Taeniopygia guttata).PloS one · 2018Article
- Genetic Code Optimization for Cotranslational Protein Folding: Codon Directional Asymmetry Correlates with Antiparallel Betasheets, tRNA Synthetase Classes.Computational and structural biotechnology journal · 2017Article
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
There are two main forces that affect usage of synonymous codons: directional mutational pressure and selection. The effectiveness of protein translation is usually considered as the main selectional factor. However, biased codon usage can also be a byproduct of a general selection at the amino acid level interacting with nucleotide replacements. To evaluate the validity and strength of such an effect, we superimposed >3.5 billion unrestricted mutational processes on the selection of nonsynonymous substitutions based on the differences in physicochemical properties of the coded amino acids. Using a modified evolutionary optimization algorithm, we determined the conditions in which the effect on the relative codon usage is maximized. We found that the effect is enhanced by mutational processes generating more adenine and thymine than guanine and cytosine, as well as more purines than pyrimidines. Interestingly, this effect is observed only under an unrestricted model of nucleotide substitution, and disappears when the mutational process is time-reversible. Comparison of the simulation results with data for real protein coding sequences indicates that the impact of selection at the amino acid level on synonymous codon usage cannot be neglected. Furthermore, it can considerably interfere, especially in AT-rich genomes, with other selections on codon usage,
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