Nucleic Acids Res. 1988 Sep 12;16(17):8207-11.
Codon usage patterns in Escherichia coli, Bacillus subtilis, Saccharomyces cerevisiae, Schizosaccharomyces pombe, Drosophila melanogaster and Homo sapiens; a review of the considerable within-species diversity.
Sharp PM 1 , Cowe E , Higgins DG , Shields DC , Wolfe KH , Wright F .
Author information
- 1 Department of Genetics, Trinity College, Dublin, Ireland.
Abstract
The genetic code is degenerate, but alternative synonymous codons are generally not used with equal frequency.
Since the pioneering work of Grantham's group it has been apparent that
genes from one species often share similarities in codon frequency; under the "genome hypothesis" there is a species-specific pattern to codon usage. However, it has become clear that in most species there are also considerable differences among genes.
Multivariate analyses have revealed that in each species so far
examined there is a single major trend in codon usage among genes,
usually from highly biased to more nearly even usage of synonymous
codons.
Thus, to represent the codon usage pattern of an organism it is not
sufficient to sum over all genes as this conceals the underlying
heterogeneity. Rather, it is necessary to describe the trend among genes seen in that species.
We illustrate these trends for six species where codon usage has been
examined in detail, by presenting the pooled codon usage for the 10% of
genes at either end of the major trend.
Closely-related organisms have similar patterns of codon usage, and so
the six species in Table 1 are representative of wider groups.
For example, with respect to codon usage, Salmonella typhimurium
closely resembles E. coli, while all mammalian species so far examined
(principally mouse, rat and cow) largely resemble humans.
- PMID:
- 3138659
- PMCID:
- PMC338553
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