Abstract
The standard genetic code (SGC) is a mapping between the 64 possible arrangements of the four RNA nucleotides (C, A, U, G) into triplets or codons, where 61 codons are assigned to a specific amino acid and the other three are stop codons for terminating protein synthesis. Aminoacyl-tRNA synthetases (aaRSs) are responsible for implementing the SGC by specifically amino-acylating only its cognate transfer RNA (tRNA), thereby linking an amino acid with its corresponding anticodon triplets. tRNAs molecules bind each codon with its anticodon. To understand the meaning of symmetrical/asymmetrical properties of the SGC, we designed synthetic genetic codes with known symmetries and with the same degeneracy of the SGC. We determined their impact on the substitution rates for each amino acid under a neutral model of protein evolution. We prove that the phenotypic graphs of the SGC for codons and anticodons for all the possible arrangements of nucleotides are asymmetric and the amino acids do not form orbits. In the symmetrical synthetic codes, the amino acids are grouped according to their codonicity, this is the number of triplets encoding a given amino acid. Both the SGC and symmetrical synthetic codes exhibit a probability of occurrence of the amino acids proportional to their degeneracy. Unlike the SGC, the synthetic codes display a constant probability of occurrence of the amino acid according to their codonicity. The asymmetry of the phenotypic graphs of codons and anticodons of the SGC, has important implications on the evolutionary processes of proteins.
Highlights
The decipherment of the standard genetic code (SGC) is a landmark achievement in biological sciences [1,2]
Protein synthesis is the outcome of a complex translation system that involves ribozymes, ribosomal proteins, aminoacyl-tRNA synthetases, elongation and termination factors, and three kinds of RNA molecules, to wit, messenger RNA, ribosomal RNA, and transfer RNA
Each of the three possible arrangements of the nucleotides in the square yields different orderings of the codon triplets in the hypercube [33]; a fourth arrangement of the nucleotides is given by the square with its two diagonals, representing a scenario where all possible nucleotide changes are within reach in one step mutation
Summary
The decipherment of the standard genetic code (SGC) is a landmark achievement in biological sciences [1,2]. Different models for the evolution of the genetic code have been proposed based on different properties of the amino acids and the triplets [13]. Anticodons beginning with purines (R) are always of only one kind for one amino acid; this is usually G, sometimes a modified purine This remarkable wobbling property permits that two or more neighboring codon triplets share a common anticodon. The implication of the asymmetry becomes apparent: the occurrence of each amino acid in protein evolution is independent of the presence/absence of the remaining 19 amino acids This means that the process of molecular evolution applied to proteins sequences becomes free and independent from the strict rules dictated by the SGC due to the selected asymmetry—or lack of symmetry—of the graph of codons and anticodons. The asymmetry of the anticodon code is disassociated with the deterministic character of the SGC
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