title: Codon usage bias in prokaryotic pyrimidine-ending codons is associated with the degeneracy of the encoded amino acids.
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.
authors.affiliation: Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 91120, Israel.
authors.forename: Naama
authors.initials: N
authors.lastname: Wald
authors.forename: Maya
authors.initials: M
authors.lastname: Alroy
authors.forename: Maya
authors.initials: M
authors.lastname: Botzman
authors.forename: Hanah
authors.initials: H
authors.lastname: Margalit
mesh_terms: D000596:Amino Acids / Q000378:metabolism; D000926:Anticodon / Q000737:chemistry; D001105:Archaea / Q000235:genetics*; D001419:Bacteria / Q000235:genetics*; D001482:Base Composition; D003062:Codon / Q000737:chemistry*; D003596:Cytosine / Q000032:analysis; D015870:Gene Expression; D005815:Genetic Code; D014176:Protein Biosynthesis; D012343:RNA, Transfer / Q000235:genetics; D014498:Uracil / Q000032:analysis
chemical_list: D000596:Amino Acids; D000926:Anticodon; D003062:Codon; D014498:Uracil; D003596:Cytosine; D012343:RNA, Transfer