Codon Usage

Abstract

Genetic codes have degeneracy; that is, most amino acids (18 out of 20 in the universal genetic code) are encoded by more than one codon. Codons encoding the same amino acid are called synonymous codons. In both prokaryotic and eukaryotic genes, the synonymous codons are not used with equal frequencies.

Keywords: synonymous codon; translational selection; mutation bias; tRNA abundance; gene expression

Figure 1.

Codon usage bias in different organisms. (a, e) Escherichia coli, (b, f) Saccharomyces cerevisiae, (c, g) Drosophila melanogaster and (d, h) Homo sapiens. Codon usage bias is measured by the ‘effective number of codons’ (Nc). ‘G+C%’ is the G+C content at third codon positions. The sources for the sequence data are given in Table . The average Nc for each organism is 47.3 for E. coli, 50.6 for S. cerevisiae, 49.2 for D. melanogaster and 48.7 for H. sapiens. Arrowheads indicate the average Nc for ribosomal protein genes (including predicted genes) with more than 100 codons. The number of ribosomal protein genes included (and the average Nc) for each organism is 39 (36.3) for E. coli, 102 (29.9) for S. cerevisiae and 94 (39.3) for D. melanogaster.

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References

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Further Reading

Akashi H (1994) Synonymous codon usage in Drosophila melanogaster: natural selection and translational accuracy. Genetics 136: 927–935.

Akashi H (2001) Gene expression and molecular evolution. Current Opinion in Genetics and Development 11: 660–666.

Eyre‐Walker A (1999) Evidence of selection on silent site base composition in mammals: potential implications for the evolution of isochores and junk DNA. Genetics 152: 675–683.

Powell JR and Moriyama EN (1997) Evolution of codon usage bias in Drosophila. Proceedings of the National Academy of Sciences of the United States of America 94: 7784–7790.

Urrutia AO and Hurst LD (2001) Codon usage bias covaries with expression breadth and the rate of synonymous evolution in humans, but this is not evidence for selection. Genetics 159: 1191–1199.

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How to Cite close
Moriyama, Etsuko N(Jul 2006) Codon Usage. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1038/npg.els.0005102]