Etsuko N Moriyama, University of Nebraska, Lincoln, Nebraska, USA
Published online: July 2006
DOI: 10.1038/npg.els.0005102
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
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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’ (N
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| References | |
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| Moriyama EN and Powell JR (1997) Codon usage bias and tRNA abundance in Drosophila. Journal of Molecular Evolution 45: 514–523. | |
| Moriyama EN and Powell JR (1998) Gene length and codon usage bias in Drosophila melanogaster, Saccharomyces cerevisiae and Escherichia coli. Nucleic Acids Research 26: 3188–3193. | |
| ePath National Center for Biotechnology Information. [ftp://ncbi.nlm. nih.gov/refseq/] [ftp://ncbi.nlm.nih.gov/genbank/genomes/D_melanogaster/Scaffolds/LARGE/]. | |
| Sharp PM and Li W-H (1987a) The codon adaptation index – a measure of directional synonymous codon usage bias, and its potential applications. Nucleic Acids Research 15: 1281–1295. | |
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| Shields DC, Sharp PM, Higgins DG and Wright F (1988) ‘Silent’ sites in Drosophila genes are not neutral: evidence of selection among synonymous codons. Molecular Biology and Evolution 5: 704–716. | |
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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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