Ring Karen Lee, Cavalcanti Andre R O
Biology Department, Pomona College, Claremont, California, USA.
Mol Biol Evol. 2008 Jan;25(1):179-86. doi: 10.1093/molbev/msm237. Epub 2007 Nov 1.
Tetrahymena thermophila and Paramecium tetraurelia are ciliates that reassign TAA and TAG from stop codons to glutamine codons. Because of the lack of full genome sequences, few studies have concentrated on analyzing the effects of codon reassignment in protein evolution. We used the recently sequenced genome of these species to analyze the patterns of amino acid substitution in ciliates that reassign the code. We show that, as expected, the codon reassignment has a large impact on amino acid substitutions in closely related proteins; however, contrary to expectations, these effects also hold for very diverged proteins. Previous studies have used amino acid substitution data to calculate the minimization of the genetic code; our results show that because of the lasting influence of the code in the patterns of substitution, such studies are tautological. These different substitution patterns might affect alignment of ciliate proteins, as alignment programs use scoring matrices based on substitution patterns of organisms that use the standard code. We also show that glutamine is used more frequently in ciliates than in other species, as often as expected based on the presence of the 2 new reassigned codons, indicating that the frequencies of amino acids in proteomes is mostly determined by neutral processes based on their number of codons.
嗜热四膜虫和四尾草履虫是纤毛虫，它们将TAA和TAG从终止密码子重新分配为谷氨酰胺密码子。由于缺乏完整的基因组序列，很少有研究专注于分析密码子重新分配在蛋白质进化中的影响。我们利用这些物种最近测序的基因组来分析重新分配密码子的纤毛虫中氨基酸替换的模式。我们发现，正如预期的那样，密码子重新分配对密切相关蛋白质中的氨基酸替换有很大影响；然而，与预期相反，这些影响在差异很大的蛋白质中也存在。以前的研究利用氨基酸替换数据来计算遗传密码的最小化；我们的结果表明，由于密码在替换模式中的持久影响，这类研究是同义反复的。这些不同的替换模式可能会影响纤毛虫蛋白质的比对，因为比对程序使用基于使用标准密码的生物体替换模式的评分矩阵。我们还表明，谷氨酰胺在纤毛虫中的使用频率高于其他物种，这与基于两个新重新分配密码子的存在所预期的频率一样，表明蛋白质组中氨基酸的频率大多由基于其密码子数量的中性过程决定。
