Codon usage bias in prokaryotic pyrimidine-ending codons is associated with the degeneracy of the encoded amino acids.

Nucleic Acids Research
Naama WaldHanah Margalit

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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Citations

Dec 18, 2013·Gene·Siddhartha Sankar SatapathySuvendra Kumar Ray
Nov 26, 2013·Journal of Molecular Evolution·Siddhartha Sankar SatapathySuvendra Kumar Ray
Apr 2, 2014·Journal of Theoretical Biology·Sen Li, Jie Yang
Jul 19, 2016·DNA Research : an International Journal for Rapid Publication of Reports on Genes and Genomes·Siddhartha Sankar SatapathySuvendra Kumar Ray
Jul 28, 2016·Nucleic Acids Research·Henri Grosjean, Eric Westhof
Feb 1, 2018·Genome Biology and Evolution·Saurabh Mahajan, Deepa Agashe

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