ArticleNucleic acids research2012
Codon usage bias in prokaryotic pyrimidine-ending codons is associated with the degeneracy of the encoded amino acids.
Article in Nucleic acids research, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed, 29 citations in OpenAlex.
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- Translational Selection for Speed Is Not Sufficient to Explain Variation in Bacterial Codon Usage Bias.Genome biology and evolution · 2018Article
- Discrepancy among the synonymous codons with respect to their selection as optimal codon in bacteria.DNA research : an international journal for rapid publication of reports on genes and genomes · 2016Article
- An integrated, structure- and energy-based view of the genetic code.Nucleic acids research · 2016Review
- Comparative analysis of codon usage bias in Crenarchaea and Euryarchaea genome reveals differential preference of synonymous codons to encode highly expressed ribosomal and RNA polymerase proteins.Journal of genetics · 2016Article
- Distinctive Genome Reduction Rates Revealed by Genomic Analyses of Two Coxiella-Like Endosymbionts in Ticks.Genome biology and evolution · 2015Article
- System analysis of synonymous codon usage biases in archaeal virus genomes.Journal of theoretical biology · 2014Article
- Auxiliary tRNAs: large-scale analysis of tRNA genes reveals patterns of tRNA repertoire dynamics.Nucleic acids research · 2014Article
- Selection on GGU and CGU codons in the high expression genes in bacteria.Journal of molecular evolution · 2014Article
- Synonymous codon bias and functional constraint on GC3-related DNA backbone dynamics in the prokaryotic nucleoid.Nucleic acids research · 2014Article
- Comparative Genomics of Trypanosomatid Pathogens using Codon Usage Bias.Bioinformation · 2013Article
- scnRCA: a novel method to detect consistent patterns of translational selection in mutationally-biased genomes.PloS one · 2013Article
Corrections and comments
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Synonymous codons are unevenly distributed among genes, a phenomenon termed codon usage bias. Understanding the patterns of codon bias and the forces shaping them is a major step towards elucidating the adaptive advantage codon choice can confer at the level of individual genes and organisms. Here, we perform a large-scale analysis to assess codon usage bias pattern of pyrimidine-ending codons in highly expressed genes in prokaryotes. We find a bias pattern linked to the degeneracy of the encoded amino acid. Specifically, we show that codon-pairs that encode two- and three-fold degenerate amino acids are biased towards the C-ending codon while codons encoding four-fold degenerate amino acids are biased towards the U-ending codon. This codon usage pattern is widespread in prokaryotes, and its strength is correlated with translational selection both within and between organisms. We show that this bias is associated with an improved correspondence with the tRNA pool, avoidance of mis-incorporation errors during translation and moderate stability of codon-anticodon interaction, all consistent with more efficient translation.
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