Morton B R, So B G
Department of Biological Sciences, Barnard College, Columbia University, 3009 Broadway, New York, NY 10027, USA.
J Mol Evol. 2000 Feb;50(2):184-93. doi: 10.1007/s002399910020.
Highly expressed plastid genes display codon adaptation, which is defined as a bias toward a set of codons which are complementary to abundant tRNAs. This type of adaptation is similar to what is observed in highly expressed Escherichia coli genes and is probably the result of selection to increase translation efficiency. In the current work, the codon adaptation of plastid genes is studied with regard to three specific features that have been observed in E. coli and which may influence translation efficiency. These features are (1) a relatively low codon adaptation at the 5' end of highly expressed genes, (2) an influence of neighboring codons on codon usage at a particular site (codon context), and (3) a correlation between the level of codon adaptation of a gene and its amino acid content. All three features are found in plastid genes. First, highly expressed plastid genes have a noticeable decrease in codon adaptation over the first 10-20 codons. Second, for the twofold degenerate NNY codon groups, highly expressed genes have an overall bias toward the NNC codon, but this is not observed when the 3' neighboring base is a G. At these sites highly expressed genes are biased toward NNT instead of NNC. Third, plastid genes that have higher codon adaptations also tend to have an increased usage of amino acids with a high G + C content at the first two codon positions and GNN codons in particular. The correlation between codon adaptation and amino acid content exists separately for both cytosolic and membrane proteins and is not related to any obvious functional property. It is suggested that at certain sites selection discriminates between nonsynonymous codons based on translational, not functional, differences, with the result that the amino acid sequence of highly expressed proteins is partially influenced by selection for increased translation efficiency.
高表达的质体基因呈现密码子适应性，这被定义为对一组与丰富的转运RNA互补的密码子的偏好。这种适应性类型与在高表达的大肠杆菌基因中观察到的情况相似，可能是为提高翻译效率而进行选择的结果。在当前的研究中，针对在大肠杆菌中观察到的、可能影响翻译效率的三个特定特征，对质体基因的密码子适应性进行了研究。这些特征是：（1）高表达基因5'端相对较低的密码子适应性；（2）相邻密码子对特定位点密码子使用的影响（密码子上下文）；（3）基因的密码子适应性水平与其氨基酸含量之间的相关性。在质体基因中发现了所有这三个特征。首先，高表达的质体基因在最初的10 - 20个密码子中密码子适应性有明显下降。其次，对于双重简并的NNY密码子组，高表达基因总体上偏向于NNC密码子，但当3'相邻碱基为G时则未观察到这种情况。在这些位点，高表达基因偏向于NNT而非NNC。第三，具有较高密码子适应性的质体基因在前两个密码子位置也倾向于增加具有高G + C含量的氨基酸的使用，特别是GNN密码子。密码子适应性与氨基酸含量之间的相关性在胞质蛋白和膜蛋白中分别存在，且与任何明显的功能特性无关。有人提出，在某些位点，选择是基于翻译而非功能差异来区分非同义密码子的，结果是高表达蛋白的氨基酸序列部分受到提高翻译效率的选择的影响。
