ArticleG3 (Bethesda, Md.)2015
GC-Content of Synonymous Codons Profoundly Influences Amino Acid Usage.
Article in G3 (Bethesda, Md.), 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
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Who cites it
34 citing papers in PubMed.
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- Strategies of Environmental Adaptation in the Haloarchaeal GeneraMicroorganisms · 2025Article
- Expanding the synthetic biology toolbox of Cupriavidus necator for establishing fatty acid production.Journal of industrial microbiology & biotechnology · 2024Article
- Strong Purifying Selection in Haploid Tissue-Specific Genes of Scots Pine Supports the Masking Theory.Molecular biology and evolution · 2023Article
- Telomeric retrotransposons show propensity to form G-quadruplexes in various eukaryotic species.Mobile DNA · 2023Article
- Low Complexity Regions in Proteins and DNA are Poorly Correlated.Molecular biology and evolution · 2023Article
- 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
- Revealing the Host-Dependent Nature of an Engineered Genetic Inverter in Concordance with Physiology.Biodesign research · 2023Article
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- Comparison of compositional constraints: Nuclear genome vs plasmid genome of Pseudomonas syringae pv. tomato DC3000.Journal of biosciences · 2022Article
- The Mutational Robustness of the Genetic Code and Codon Usage in Environmental Context: A Non-Extremophilic Preference?Life (Basel, Switzerland) · 2021Article
- Phylogenetic analysis of mutational robustness based on codon usage supports that the standard genetic code does not prefer extreme environments.Scientific reports · 2021Article
- Homopeptide and homocodon levels across fungi are coupled to GC/AT-bias and intrinsic disorder, with unique behaviours for some amino acids.Scientific reports · 2021Article
- Inferring the number and position of changes in selective regime in a non-equilibrium mutation-selection framework.BMC ecology and evolution · 2021Article
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- Aerobactin Seems To Be a Promising Marker Compared With Unstable RmpA2 for the Identification of Hypervirulent Carbapenem-ResistantFrontiers in cellular and infection microbiology · 2021Article
Corrections and comments
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Amino acids typically are encoded by multiple synonymous codons that are not used with the same frequency. Codon usage bias has drawn considerable attention, and several explanations have been offered, including variation in GC-content between species. Focusing on a simple parameter-combined GC proportion of all the synonymous codons for a particular amino acid, termed GCsyn-we try to deepen our understanding of the relationship between GC-content and amino acid/codon usage in more details. We analyzed 65 widely distributed representative species and found a close association between GCsyn, GC-content, and amino acids usage. The overall usages of the four amino acids with the greatest GCsyn and the five amino acids with the lowest GCsyn both vary with the regional GC-content, whereas the usage of the remaining 11 amino acids with intermediate GCsyn is less variable. More interesting, we discovered that codon usage frequencies are nearly constant in regions with similar GC-content. We further quantified the effects of regional GC-content variation (low to high) on amino acid usage and found that GC-content determines the usage variation of amino acids, especially those with extremely high GCsyn, which accounts for 76.7% of the changed GC-content for those regions. Our results suggest that GCsyn correlates with GC-content and has impact on codon/amino acid usage. These findings suggest a novel approach to understanding the role of codon and amino acid usage in shaping genomic architecture and evolutionary patterns of organisms.
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