Sharp P M, Cowe E, Higgins D G, Shields D C, Wolfe K H, Wright F
Department of Genetics, Trinity College, Dublin, Ireland.
Nucleic Acids Res. 1988 Sep 12;16(17):8207-11. doi: 10.1093/nar/16.17.8207.
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.
遗传密码是简并的，但替代同义密码子的使用频率通常并不相等。自格兰瑟姆团队的开创性工作以来，很明显一个物种的基因在密码子频率上常常具有相似性；在“基因组假说”下，存在物种特异性的密码子使用模式。然而，现在已经清楚的是，在大多数物种中，基因之间也存在相当大的差异。多变量分析表明，在目前所研究的每个物种中，基因之间的密码子使用存在单一的主要趋势，通常是从高度偏向使用同义密码子到使用更为接近均匀的同义密码子。因此，要表示一个生物体的密码子使用模式，对所有基因进行求和是不够的，因为这会掩盖潜在的异质性。相反，有必要描述该物种中基因之间的趋势。我们通过展示主要趋势两端10%的基因的合并密码子使用情况，来说明六个已详细研究密码子使用的物种的这些趋势。亲缘关系密切的生物体具有相似的密码子使用模式，因此表1中的六个物种代表了更广泛的类群。例如，就密码子使用而言，鼠伤寒沙门氏菌与大肠杆菌非常相似，而目前所研究的所有哺乳动物物种（主要是小鼠、大鼠和牛）在很大程度上与人类相似。
