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

Abstract

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.

Keywords: Amino acid; Codon; Genetic code.