Department of Bioinformatics and Genomics, Faculty of Biotechnology, University of Wrocław, ul. Joliot-Curie 14a, Wrocław, Poland.
Department of Bioinformatics and Genomics, Faculty of Biotechnology, University of Wrocław, ul. Joliot-Curie 14a, Wrocław, Poland.
Biosystems. 2021 Dec;210:104528. doi: 10.1016/j.biosystems.2021.104528. Epub 2021 Sep 4.
It is assumed that at the early stage of cell evolution its translation machinery was characterized by high noise, i.e. ambiguous assignment of codons to amino acids in the genetic code, which initially encoded only few amino acids. Next, during its evolution new amino acids were added to this code. Taking into account this facts, we investigated theoretical models of genetic code's structure, which evolved from a set of ambiguous codons assignments into a coding system with a low level of uncertainty. We considered three types of translational inaccuracies assuming a different number of fixed codon positions. We applied a modified version of evolutionary algorithm for finding the genetic codes that the most effectively reduced the initial uncertainty in the assignment of codons to encoded labels, i.e. amino acids and a stop translation signal. We examined codes with the number of labels from four to 22. Our results indicated that the quality of genetic code structure is strongly dependent on the number of encoded labels as well as the type of translational mechanism. The more strict assignments of codon to the labels was preferred by the codes encoding more number of labels. The results showed that a smaller degeneracy of codes evolved from a more tolerant coding with the stepwise addition of coded amino acids to the genetic code. The distribution of codon groups in the standard genetic code corresponds well to the translation model assuming two fixed codon positions, whereas the six-codon groups can be relics form previous stages of evolution when the code characterized by a greater uncertainty.
据推测，在细胞进化的早期阶段，其翻译机制的特点是高噪音，即遗传密码中密码子与氨基酸的分配模糊，遗传密码最初只编码少数几种氨基酸。接下来，在进化过程中，新的氨基酸被添加到这个密码子中。考虑到这些事实，我们研究了遗传密码结构的理论模型，这些模型从一组模糊的密码子分配演变成了一个具有低不确定性水平的编码系统。我们考虑了三种类型的翻译不准确情况，假设固定的密码子位置数量不同。我们应用了一种改进的进化算法版本，用于寻找最有效地降低密码子到编码标签（即氨基酸和停止翻译信号）分配初始不确定性的遗传密码。我们研究了标签数量从 4 到 22 的代码。我们的结果表明，遗传密码结构的质量强烈依赖于编码标签的数量以及翻译机制的类型。对于编码更多标签的代码，密码子与标签的分配更加严格。结果表明，随着编码氨基酸的逐步添加，代码的简并度逐渐降低，从而进化出了更严格的编码。标准遗传密码中的密码子组分布与假设存在两个固定密码子位置的翻译模型非常吻合，而六个密码子组可能是遗传密码在具有更大不确定性的早期阶段进化的遗迹。
