Wnętrzak Małgorzata, Błażej Paweł, Mackiewicz Paweł
Faculty of Biotechnology, University of Wrocław, ul. Fryderyka Joliot-Curie 14a, 50-383 Wrocław, Poland.
Biosystems. 2019 Jul;181:44-50. doi: 10.1016/j.biosystems.2019.04.012. Epub 2019 Apr 28.
The distinct structure and universality of the standard genetic code (SGC) have fascinated the scientists ever since the first amino acid assignments were discovered. There are several hypotheses trying to explain the origin and evolution of this code. One of them postulates that the SGC evolved to minimize harmful effects of amino acid replacements in proteins, caused by mutations and translational errors. Many investigations concerning this hypothesis have already been carried out, but they were focused mainly on the consequences of single-point mutations. Therefore, we decided to check the influence of other types of mutations, i.e. insertions and deletions, on the robustness to amino acid replacements of the SGC. Such mutations cause shifts in the reading frame during the translation process which result in more harmful consequences in coded proteins than in the case of single-point mutations. We applied a multi-objective optimization algorithm to find the best and the worst genetic codes, regarding their robustness to both single-point and frameshift mutations, for various amino acid properties. Then we compared the features of the found codes with the properties of the standard genetic code. The results show that the SGC is not fully optimized for minimizing the effects of frameshift mutations but it is, nevertheless, much closer to the best solutions than to the worst ones. It implies that a certain tendency to minimize the costs of amino acids replacements resulting from various kinds of mutations is present in the standard genetic code.
自首次发现氨基酸分配以来,标准遗传密码(SGC)独特的结构和通用性一直吸引着科学家们。有几种假说试图解释这种密码的起源和进化。其中一种假说假定,SGC的进化是为了将由突变和翻译错误导致的蛋白质中氨基酸替换的有害影响降至最低。关于这一假说已经进行了许多研究,但它们主要集中在单点突变的后果上。因此,我们决定研究其他类型的突变,即插入和缺失,对SGC氨基酸替换稳健性的影响。此类突变在翻译过程中会导致阅读框移位,与单点突变相比,这会在编码蛋白质中造成更有害的后果。我们应用了一种多目标优化算法,针对各种氨基酸特性,找出在对单点突变和移码突变的稳健性方面最佳和最差的遗传密码。然后我们将所发现密码的特征与标准遗传密码的特性进行了比较。结果表明,SGC在将移码突变的影响降至最低方面并未得到充分优化,但尽管如此,它与最佳解决方案的接近程度远高于最差解决方案。这意味着标准遗传密码中存在某种将各类突变导致的氨基酸替换成本降至最低的趋势。