Department of Genomics, University of Wrocław, ul. Joliot-Curie 14a, Wrocław, 50-383, Poland.
BMC Bioinformatics. 2019 Mar 6;20(1):114. doi: 10.1186/s12859-019-2661-4.
The standard genetic code is a recipe for assigning unambiguously 21 labels, i.e. amino acids and stop translation signal, to 64 codons. However, at early stages of the translational machinery development, the codons did not have to be read unambiguously and the early genetic codes could have contained some ambiguous assignments of codons to amino acids. Therefore, the goal of this work was to obtain the genetic code structures which could have evolved assuming different types of inaccuracy of the translational machinery starting from unambiguous assignments of codons to amino acids.
We developed a theoretical model assuming that the level of uncertainty of codon assignments can gradually decrease during the simulations. Since it is postulated that the standard code has evolved to be robust against point mutations and mistranslations, we developed three simulation scenarios assuming that such errors can influence one, two or three codon positions. The simulated codes were selected using the evolutionary algorithm methodology to decrease coding ambiguity and increase their robustness against mistranslation.
The results indicate that the typical codon block structure of the genetic code could have evolved to decrease the ambiguity of amino acid to codon assignments and to increase the fidelity of reading the genetic information. However, the robustness to errors was not the decisive factor that influenced the genetic code evolution because it is possible to find theoretical codes that minimize the reading errors better than the standard genetic code.
标准遗传密码是一个将 21 个标签（即氨基酸和停止翻译信号）明确分配给 64 个密码子的配方。然而，在翻译机制发展的早期阶段，密码子不必被明确读取，早期的遗传密码可能包含一些密码子与氨基酸的模糊分配。因此，这项工作的目的是从明确分配密码子到氨基酸开始，获得假设翻译机制存在不同类型不准确性的遗传密码结构。
我们开发了一个理论模型，假设在模拟过程中，密码子分配的不确定性水平可以逐渐降低。由于假设标准密码已经进化到能够抵抗点突变和误译，我们开发了三种模拟场景，假设这些错误可以影响一个、两个或三个密码子位置。模拟代码是使用进化算法方法选择的，以降低编码模糊性并提高其对误译的鲁棒性。
结果表明，遗传密码的典型密码子块结构可能已经进化，以降低氨基酸到密码子分配的模糊性，并提高读取遗传信息的保真度。然而，错误的鲁棒性并不是影响遗传密码进化的决定性因素，因为有可能找到比标准遗传密码更好地最小化读取错误的理论代码。
