The Standard Genetic Code and its relation to mutational pressure: robustness and equilibrium criteria

ABSTRACT

Under the assumption of even point mutation pressure on the DNA strand, rates for transitions from one amino acid into another were assessed. Nearly 25por ciento of all mutations were silent. About 48por ciento of the mutations from a given amino acid stream either into the same amino acid or into an amino acid of the same class. These results suggest a great stability of the Standard Genetic Code respect to mutation load. Concepts from chemical equilibrium theory are applicable into this case provided that mutation rate constants are given. It was obtained that unequal synonymic codon usage may lead to changes in the equilibrium concentrations. Data from real biological species showed that several amino acids are close to the respective equilibrium concentration. However in all the cases the concentration of leucine nearly doubled its equilibrium concentration, whereas for the stop command (Term) it was about 10 times lower. The overall distance from equilibrium for a set of species suggests that eukaryotes are closer to equilibrium than prokaryotes, and the HIV virus was closest to equilibrium among 15 species. We obtained that contemporary species are closer to the equilibrium than the Last Universal Common Ancestor (LUCA) was. Similarly, non-preserved regions in proteins are closer to equilibrium than the preserved ones. We suggest that this approach can be useful for exploring some aspects of biological evolution in the framework of Standard Genetic Code properties(AU)