Abstract
The standard genetic code (SGC) is a set of rules according to which 64 codons are assigned to 20 canonical amino acids and stop coding signal. As a consequence, the SGC is redundant because there is a greater number of codons than the number of encoded labels. This redundancy implies the existence of codons that encode the same genetic information. The size and organization of such synonymous codon blocks are important characteristics of the SGC structure whose evolution is still unclear. Therefore, we studied possible evolutionary mechanisms of the codon block structure. We conducted computer simulations assuming that coding systems at early stages of the SGC evolution were sets of ambiguous codon assignments with high entropy. We included three types of reading systems characterized by different inaccuracy and pattern of codon recognition. In contrast to the previous study, we allowed for evolution of the reading systems and their competition. The simulations performed under minimization of translational errors and reduction of coding ambiguity produced the coding system resistant to these errors. The reading system similar to that present in the SGC dominated the others very quickly. The survived system was also characterized by low entropy and possessed properties similar to that in the SGC. Our simulation show that the unambiguous SGC could emerged from a code with a lower level of ambiguity and the number of tRNAs increased during the evolution.
Highlights
The structure and properties of the standard genetic (SGC) code have intrigued scientists since the first ascriptions of codons to amino acids were discovered in the sixties of the last century [1,2]
The results presented in in the previous paragraph indicate that the M1 reading system was the most preferred, which suggests that codon blocks induced by this rule should be present in the structure of the genetic codes selected after simulations
In this paper, we investigated a potential emergence of genetic codes from a set of highly ambiguous codon assignments to the codes characterized by an unequivocal assignment of codons to encoded labels
Summary
The structure and properties of the standard genetic (SGC) code have intrigued scientists since the first ascriptions of codons to amino acids were discovered in the sixties of the last century [1,2]. Many hypotheses concerning the origin and evolution of SGC have been proposed (see for review: [3,4,5,6,7,8]) It is still unclear which factors played a decisive role in the process of the genetic code emergence and evolution. In order to explain this fact, Crick proposed the wobble rule, which refers to interactions between the first base in a tRNA anticodon and the third base of translated codon in a transcript (mRNA) This rule assumes that the base pairing between these two RNAs does not have to follow Watson–Crick base pair rules, i.e., cytosine–guanine and adenine–uracil, but that other interactions are possible, i.e., guanine–uracil, hypoxanthine–uracil, hypoxanthine–adenine and hypoxanthine–cytosine. Additional experiments revealed that other modified bases can pair with the typical ones [11]
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