Alvarez F, Robello C, Vignali M
Departamento de Genética, Facultad de Medicina, Montevideo, Uruguay.
Mol Biol Evol. 1994 Sep;11(5):790-802. doi: 10.1093/oxfordjournals.molbev.a040159.
In this study we analyze and compare the trends in codon usage in five representative species of kinetoplastid protozoans (Crithidia fasciculata, Leishmania donovani, L. major, Trypanosoma cruzi and T. brucei), with the purpose of investigating the processes underlying these trends. A principal component analysis shows that the G+C content at the third codon position represents the main source of codon-usage variation, both within species (among genes) and among species. The non-Trypanosoma species exhibit narrow distributions in codon usage, while both Trypanosoma species present large within-species heterogeneity. The three non-Trypanosoma species have very similar codon-usage preferences. These codon preferences are also shared by the highly expressed genes of T. cruzi and to a lesser degree by those of T. brucei. This leads to the conclusion that the codon preferences shared by these species are the ancestral ones in the kinetoplastids. On the other hand, the study of noncoding sequences shows that Trypanosoma species exhibit mutational biases toward A + T richness, while the non-Trypanosoma species present mutational pressure in the opposite direction. These data taken together allow us to infer the origin of the different codon-usage distributions observed in the five species studied. In C. fasciculata and Leishmania, both mutational biases and (translational) selection pull toward G + C richness, resulting in a narrow distribution. In Trypanosoma species the mutational pressure toward A + T richness produced a shift in their genomes that differentially affected coding and noncoding sequences. The effect of these pressures on the third codon position of genes seems to have been inversely proportional to the level of gene expression.
在本研究中，我们分析并比较了五种代表性动基体原生动物（fasiculata克氏锥虫、杜氏利什曼原虫、硕大利什曼原虫、克氏锥虫和布氏锥虫）的密码子使用趋势，目的是研究这些趋势背后的过程。主成分分析表明，第三密码子位置的G+C含量代表了物种内（基因间）和物种间密码子使用变异的主要来源。非锥虫物种的密码子使用分布较窄，而两种锥虫物种在物种内均表现出较大的异质性。三种非锥虫物种具有非常相似的密码子使用偏好。这些密码子偏好也为克氏锥虫的高表达基因所共有，布氏锥虫的高表达基因在较小程度上也有这些偏好。由此得出结论，这些物种共有的密码子偏好是动基体中的祖先偏好。另一方面，对非编码序列的研究表明，锥虫物种表现出向富含A+T的突变偏向，而非锥虫物种则呈现相反方向的突变压力。综合这些数据，我们可以推断在所研究的五个物种中观察到的不同密码子使用分布的起源。在fasiculata克氏锥虫和利什曼原虫中，突变偏向和（翻译）选择都倾向于富含G+C，导致分布较窄。在锥虫物种中，向富含A+T的突变压力导致其基因组发生变化，对编码和非编码序列产生了不同的影响。这些压力对基因第三密码子位置的影响似乎与基因表达水平成反比。
