ArticlePloS one2013
Amino acid usage is asymmetrically biased in AT- and GC-rich microbial genomes.
Article in PloS one, 2013. 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, 33 citations in OpenAlex.
- Extended sequence context shapes mutational bias inProceedings of the National Academy of Sciences of the United States of America · 2026Article
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- Functional Assessment of Orphan Proteins in theMicroorganisms · 2026Article
- Phylogenomic analyses indicate the archaeal superphylum DPANN originated from free-living euryarchaeal-like ancestors.Nature microbiology · 2025Article
- Genomic AT Bias Coupled with Amino Acid Metabolism Modulates Codon Usage.Journal of molecular evolution · 2025Article
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- Living in trinity of extremes: Genomic and proteomic signatures of halophilic, thermophilic, and pH adaptation.Current research in structural biology · 2024Article
- Shifts in mutation spectra enhance access to beneficial mutations.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
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- Selection for Cheaper Amino Acids Drives Nucleotide Usage at the Start of Translation in Eukaryotic Genes.Genomics, proteomics & bioinformatics · 2021Article
- Comparative Genomics Provides Insights into the Genetic Diversity and Evolution of the DPANN Superphylum.mSystems · 2021Article
- Aerobic prokaryotes do not have higher GC contents than anaerobic prokaryotes, but obligate aerobic prokaryotes have.BMC evolutionary biology · 2019Article
- Amino acid compositions contribute to the proteins' evolution under the influence of their abundances and genomic GC content.Scientific reports · 2018Article
- Article
- The GC Content as a Main Factor Shaping the Amino Acid Usage During Bacterial Evolution Process.Frontiers in microbiology · 2018Article
- NullSeq: A Tool for Generating Random Coding Sequences with Desired Amino Acid and GC Contents.PLoS computational biology · 2016Article
- Genome-Wide Analysis of the Synonymous Codon Usage Patterns in Riemerella anatipestifer.International journal of molecular sciences · 2016Article
- (Meta)genomic insights into the pathogenome of Cellulosimicrobium cellulans.Scientific reports · 2016Article
- Energy efficiency trade-offs drive nucleotide usage in transcribed regions.Nature communications · 2016Article
- GC-Content of Synonymous Codons Profoundly Influences Amino Acid Usage.G3 (Bethesda, Md.) · 2015Article
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Authors and funding
5 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
introductionGenomic base composition ranges from less than 25% AT to more than 85% AT in prokaryotes. Since only a small fraction of prokaryotic genomes is not protein coding even a minor change in genomic base composition will induce profound protein changes. We examined how amino acid and codon frequencies were distributed in over 2000 microbial genomes and how these distributions were affected by base compositional changes. In addition, we wanted to know how genome-wide amino acid usage was biased in the different genomes and how changes to base composition and mutations affected this bias. To carry this out, we used a Generalized Additive Mixed-effects Model (GAMM) to explore non-linear associations and strong data dependences in closely related microbes; principal component analysis (PCA) was used to examine genomic amino acid- and codon frequencies, while the concept of relative entropy was used to analyze genomic mutation rates.
resultsWe found that genomic amino acid frequencies carried a stronger phylogenetic signal than codon frequencies, but that this signal was weak compared to that of genomic %AT. Further, in contrast to codon usage bias (CUB), amino acid usage bias (AAUB) was differently distributed in AT- and GC-rich genomes in the sense that AT-rich genomes did not prefer specific amino acids over others to the same extent as GC-rich genomes. AAUB was also associated with relative entropy; genomes with low AAUB contained more random mutations as a consequence of relaxed purifying selection than genomes with higher AAUB.
conclusionGenomic base composition has a substantial effect on both amino acid- and codon frequencies in bacterial genomes. While phylogeny influenced amino acid usage more in GC-rich genomes, AT-content was driving amino acid usage in AT-rich genomes. We found the GAMM model to be an excellent tool to analyze the genomic data used in this study.
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