Shields D C
Department of Genetics, Trinity College, Dublin, Ireland.
J Mol Evol. 1990 Aug;31(2):71-80. doi: 10.1007/BF02109476.
A model of synonymous codon usage is developed in which the most frequent codons are selectively advantageous because of their coadaptation with tRNA abundances. Random drift opposes the progress of this coevolution by pushing codon frequencies in the direction of the frequency that would result from mutation in the absence of selection. It is predicted that, within a certain range, an increased mutation bias away from an advantageous codon has little influence on its usage in highly expressed genes. However, a subsequent small increase in mutation bias over a critical range leads to a large reduction in the frequency of the codon. The switch in preference from one synonym to another is a sharp transition, with no stable intermediate state in which neither codon is advantageous. Codon usage patterns were compared among three related bacterial species of differing genomic G & C contents, Escherichia coli, Serratia marcescens, and Proteus vulgaris. It was found that although changes in mutation biases do not always result in switches in codon preferences, some switches have occurred in the direction of species-specific mutation biases. Fluctuating mutation biases may therefore be the main cause of differences between species in their codon preferences.
建立了一种同义密码子使用模型，其中最常用的密码子由于与tRNA丰度的共同适应而具有选择优势。随机漂变通过将密码子频率推向在无选择情况下由突变产生的频率方向，来对抗这种共同进化的进程。据预测，在一定范围内，远离优势密码子的突变偏向增加对其在高表达基因中的使用影响很小。然而，在临界范围之上随后的突变偏向小幅增加会导致该密码子的频率大幅降低。从一个同义密码子到另一个同义密码子的偏好转变是一个急剧的转变，不存在两个密码子都无优势的稳定中间状态。比较了基因组G&C含量不同的三种相关细菌物种（大肠杆菌、粘质沙雷氏菌和普通变形杆菌）之间的密码子使用模式。发现虽然突变偏向的变化并不总是导致密码子偏好的转变，但有些转变已朝着物种特异性突变偏向的方向发生。因此，波动的突变偏向可能是物种间密码子偏好差异的主要原因。
