Moriyama E N, Powell J R
Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520-8106, USA.
J Mol Evol. 1997 Nov;45(5):514-23. doi: 10.1007/pl00006256.
Codon usage bias of 1,117 Drosophila melanogaster genes, as well as fewer D. pseudoobscura and D. virilis genes, was examined from the perspective of relative abundance of isoaccepting tRNAs and their changes during development. We found that each amino acid contributes about equally and highly significantly to overall codon usage bias, with the exception of Asp which had very low contribution to overall bias. Asp was also the only amino acid that did not show a clear preference for one of its synonymous codons. Synonymous codon usage in Drosophila was consistent with "optimal" codons deduced from the isoaccepting tRNA availability. Interestingly, amino acids whose major isoaccepting tRNAs change during development did not show as strong bias as those with developmentally unchanged tRNA pools. Asp is the only amino acid for which the major isoaccepting tRNAs change between larval and adult stages. We conclude that synonymous codon usage in Drosophila is well explained by tRNA availability and is probably influenced by developmental changes in relative abundance.
从同功tRNA的相对丰度及其在发育过程中的变化角度，研究了1117个黑腹果蝇基因以及较少的拟暗果蝇和 virilis果蝇基因的密码子使用偏好。我们发现，除了天冬氨酸对总体密码子使用偏好贡献非常低外，每种氨基酸对总体密码子使用偏好的贡献大致相同且高度显著。天冬氨酸也是唯一对其同义密码子之一没有明显偏好的氨基酸。果蝇中的同义密码子使用与从同功tRNA可用性推导的“最优”密码子一致。有趣的是，其主要同功tRNA在发育过程中发生变化的氨基酸，与tRNA库在发育过程中不变的氨基酸相比，没有表现出那么强烈的偏好。天冬氨酸是唯一主要同功tRNA在幼虫和成虫阶段之间发生变化的氨基酸。我们得出结论，果蝇中的同义密码子使用可以通过tRNA可用性得到很好的解释，并且可能受到相对丰度发育变化的影响。
