Models of genetic code structure evolution with variable number of coded labels

Pawlak, Konrad; Wnętrzak, Małgorzata; Mackiewicz, Dorota; Mackiewicz, Paweł; Błażej, Paweł

doi:10.1016/j.biosystems.2021.104528

Cited by 2 publications

(7 citation statements)

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“…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. A similar problem was discussed in our previous papers [13,14], where we showed that the structure of genetic codes similar to that in the SGC could evolve under error minimization restrictions and the stepwise addition of amino acids to the genetic code. However, in the previous studies, the method of reading genetic information and its degeneracy, or more precisely, the way of recognizing not only a codon but also its codon neighborhood encoding the same label, was fixed and unchanged from the start of genetic code evolution.…”

Section: Discussionmentioning

confidence: 59%

“…This approach has been used in our previous works [13,14], where we studied the process of genetic code evolution from a set of ambiguous codon assignments characterized by a large value of entropy to nearly unambiguous coding systems. However, it was assumed that the type of reading system was fixed during the whole simulation run.…”

Section: Representation Of Genetic Codesmentioning

confidence: 99%

“…The results based on these simulations showed that the structure of the SGC would emerge from highly ambiguous coding systems under relatively simple criteria, i.e., the reduction of translational noise and a stepwise addition of amino acids into the code [13,14]. The codon block structure observed in the best surviving code was characterized by low translational noise as well as a high robustness against point mutations.…”

Section: Introductionmentioning

confidence: 99%

“…This assumption appears to be a good starting point for further investigations of the SGC evolution. It was proposed that these codes evolved together from a set of ambiguous codon assignments towards a coding system with a low level of ambiguity to reduce an initial high translational noise [5,[12][13][14]. During the genetic code evolution, amino acids were gradually added to the code, which was profitable because it increased the diversity of synthesized proteins [6,[15][16][17].…”

Section: Introductionmentioning

confidence: 99%

“…These assumptions were included in a simulation model to show the origin of coding system structure [13,14]. This model assumed that every code was a set of rules, described by selected random variables, according to which 64 codons were assigned to specific genetic information, i.e., labels.…”

Section: Introductionmentioning

confidence: 99%

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Model of Genetic Code Structure Evolution under Various Types of Codon Reading

Błażej

Pawlak

Mackiewicz

et al. 2022

IJMS

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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.

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Section: Discussionmentioning

confidence: 59%

Section: Representation Of Genetic Codesmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%