codon usage bias

Edge evidence

• codon usage bias regulates translation RO:0002211

  Biased codon usage tunes elongation rate via tRNA availability.

  • DOI:10.1038/nrg2899 Plotkin & Kudla review how synonymous codon bias modulates translation.
• codon usage bias associated with gene expression level biolink:associated_with

  Codon bias is strongest in highly expressed genes.

  • DOI:10.1146/annurev.genet.42.110807.091442 Hershberg & Petrov review translational selection on codon bias correlating with expression level.
• gene expression level strengthens selection for codon usage bias

  Selection on synonymous codons scales with protein production; highly expressed genes show stronger codon preferences.

  • DOI:10.1146/annurev.genet.42.110807.091442 Hershberg & Petrov: codon bias correlates most strongly with gene expression level.
  • DOI:10.32942/x2802v Cope et al.: codon-specific selection scales with per-gene protein production rate (ROC-SEMPPR).
• tRNA abundance influences codon usage bias

  Synonymous codons decoded by more abundant tRNAs tend to be more adapted and often preferred.

  • DOI:10.1038/nrg2899 Plotkin & Kudla define tAI from relative tRNA gene copy numbers; the more abundant the decoding tRNA, the more adapted the codon.
• 5' mRNA secondary structure inhibits translation initiation RO:0002212

  Start-region RNA folding can limit ribosome access and dominate expression effects of synonymous codons.

  • DOI:10.1038/nrg2899 Plotkin & Kudla: 5' structure generally disadvantageous; GFP expression in E. coli strongly inhibited when 5' folding energy below ~-10 kcal/mol (RBS/SD/start-codon occlusion).
• translation initiation part of translation biolink:part_of

  Initiation is the first stage of translation.

  • DOI:10.1038/nrg2899 Plotkin & Kudla discuss translation initiation as a major mechanism linking 5' sequence features to expression.