Smith N G, Eyre-Walker A
Centre for the Study of Evolution and School of Biological Sciences, University of Sussex, Brighton, BN1 9QG, UK.
J Mol Evol. 2001 Sep;53(3):225-36. doi: 10.1007/s002390010212.
Natural selection favors certain synonymous codons which aid translation in Escherichia coli, yet codons not favored by translational selection persist. We use the frequency distributions of synonymous polymorphisms to test three hypotheses for the existence of translationally sub-optimal codons: (1) selection is a relatively weak force, so there is a balance between mutation, selection, and drift; (2) at some sites there is no selection on codon usage, so some synonymous sites are unaffected by translational selection; and (3) translationally sub-optimal codons are favored by alternative selection pressures at certain synonymous sites. We find that when all the data is considered, model 1 is supported and both models 2 and 3 are rejected as sole explanations for the existence of translationally sub-optimal codons. However, we find evidence in favor of both models 2 and 3 when the data is partitioned between groups of amino acids and between regions of the genes. Thus, all three mechanisms appear to contribute to the existence of translationally sub-optimal codons in E. coli.
自然选择青睐某些有助于大肠杆菌翻译的同义密码子，但未受翻译选择青睐的密码子依然存在。我们使用同义多态性的频率分布来检验关于翻译次优密码子存在的三个假说：（1）选择是一种相对较弱的力量，因此在突变、选择和漂变之间存在平衡；（2）在某些位点对密码子使用没有选择，因此一些同义位点不受翻译选择的影响；（3）翻译次优密码子在某些同义位点受到其他选择压力的青睐。我们发现，当考虑所有数据时，模型1得到支持，而模型2和模型3作为翻译次优密码子存在的唯一解释被拒绝。然而，当数据按氨基酸组和基因区域划分时，我们发现支持模型2和模型3的证据。因此，所有这三种机制似乎都促成了大肠杆菌中翻译次优密码子的存在。
