Xia X
Museum of Natural Science, Louisiana State University, Baton Rouge 70803, USA.
Genetics. 1996 Nov;144(3):1309-20. doi: 10.1093/genetics/144.3.1309.
The rate of protein synthesis depends on both the rate of initiation of translation and the rate of elongation of the peptide chain. The rate of initiation depends on the encountering rate between ribosomes and mRNA; this rate in turn depends on the concentration of ribosomes and mRNA. Thus, patterns of codon usage that increase transcriptional efficiency should increase mRNA concentration, which in turn would increase the initiation rate and the rate of protein synthesis. An optimality model of the transcriptional process is presented with the prediction that the most frequently used ribonucleotide at the third codon sites in mRNA molecules should be the same as the most abundant ribonucleotide at the third codon sites in mRNA molecules should be the same as the most abundant ribonucleotide in the cellular matrix where mRNA is transcribed. This prediction is supported by four kinds of evidence. First, A-ending codons are the most frequently used synonymous codons in mitochondria, where ATP is much more abundant than that of the three other ribonucleotides. Second, A-ending codons are more frequently used in mitochondrial genes than in nuclear genes. Third, protein genes from organisms with a high metabolic rate use more A-ending codons and have higher A content in their introns than those from organisms with a low metabolic rate.
蛋白质合成的速率取决于翻译起始速率和肽链延伸速率。起始速率取决于核糖体与mRNA的相遇速率；而该速率又取决于核糖体和mRNA的浓度。因此，提高转录效率的密码子使用模式应会增加mRNA浓度，进而提高起始速率和蛋白质合成速率。本文提出了一个转录过程的最优性模型，预测mRNA分子中第三个密码子位点最常使用的核糖核苷酸应与mRNA分子转录所在细胞基质中最丰富的核糖核苷酸相同。这一预测得到了四类证据的支持。第一，以A结尾的密码子是线粒体中最常使用的同义密码子，在线粒体中ATP比其他三种核糖核苷酸丰富得多。第二，线粒体基因中以A结尾的密码子比核基因中更常被使用。第三，与低代谢率生物相比，高代谢率生物的蛋白质基因使用更多以A结尾的密码子，且其内含子中的A含量更高。
