Ardell D H
Department of Biological Sciences, Stanford University, CA 94305, USA.
J Mol Evol. 1998 Jul;47(1):1-13. doi: 10.1007/pl00006356.
Distances between amino acids were derived from the polar requirement measure of amino acid polarity and Benner and co-workers' (1994) 74-100 PAM matrix. These distances were used to examine the average effects of amino acid substitutions due to single-base errors in the standard genetic code and equally degenerate randomized variants of the standard code. Second-position transitions conserved all distances on average, an order of magnitude more than did second-position transversions. In contrast, first-position transitions and transversions were about equally conservative. In comparison with randomized codes, second-position transitions in the standard code significantly conserved mean square differences in polar requirement and mean Benner matrix-based distances, but mean absolute value differences in polar requirement were not significantly conserved. The discrepancy suggests that these commonly used distance measures may be insufficient for strict hypothesis testing without more information. The translational consequences of single-base errors were then examined in different codon contexts, and similarities between these contexts explored with a hierarchical cluster analysis. In one cluster of codon contexts corresponding to the RNY and GNR codons, second-position transversions between C and G and transitions between C and U were most conservative of both polar requirement and the matrix-based distance. In another cluster of codon contexts, second-position transitions between A and G were most conservative. Despite the claims of previous authors to the contrary, it is shown theoretically that the standard code may have been shaped by position-invariant forces such as mutation and base content. These forces may have left heterogeneous signatures in the code because of differences in translational fidelity by codon position. A scenario for the origin of the code is presented wherein selection for error minimization could have occurred multiple times in disjoint parts of the code through a phyletic process of competition between lineages. This process permits error minimization without the disruption of previously useful messages, and does not predict that the code is optimally error-minimizing with respect to modern error. Instead, the code may be a record of genetic process and patterns of mutation before the radiation of modern organisms and organelles.
氨基酸之间的距离源自氨基酸极性的极性需求度量以及本纳及其同事(1994年)的74 - 100 PAM矩阵。这些距离用于研究标准遗传密码中由于单碱基错误导致的氨基酸替换的平均效应,以及标准密码同等简并的随机变体。第二位的转换平均保留了所有距离,比第二位的颠换多一个数量级。相比之下,第一位的转换和颠换的保守程度大致相同。与随机密码相比,标准密码中的第二位转换在极性需求的均方差差异和基于本纳矩阵的平均距离方面显著保守,但极性需求的平均绝对值差异并未显著保守。这种差异表明,在没有更多信息的情况下,这些常用的距离度量可能不足以进行严格的假设检验。然后在不同的密码子背景下研究了单碱基错误的翻译后果,并通过层次聚类分析探索了这些背景之间的相似性。在一组对应于RNY和GNR密码子的密码子背景中,C和G之间的第二位颠换以及C和U之间的转换在极性需求和基于矩阵的距离方面最为保守。在另一组密码子背景中,A和G之间的第二位转换最为保守。尽管先前的作者有相反的说法,但从理论上表明,标准密码可能是由诸如突变和碱基含量等位置不变的力量塑造的。由于密码子位置的翻译保真度不同,这些力量可能在密码中留下了异质的特征。提出了一种密码起源的设想,其中通过谱系间竞争的系统发育过程,在密码的不连续部分可能多次发生了使错误最小化的选择。这个过程允许在不破坏先前有用信息的情况下使错误最小化,并且并不预测该密码相对于现代错误是最优的错误最小化。相反,该密码可能是现代生物体和细胞器辐射之前遗传过程和突变模式的记录。