Properties of the Genetic Code under Directional, Asymmetric Mutational Pressure

Abstract

We have used the Monte Carlo method for simulating the evolution of protein coding sequences from the Borrelia burgdorferi genome under the directional mutational pressure, described by the nucleotide substitution matrix experimentally found for this genome. Since the mutational pressure is asymmetric - different for each of the two DNA strands, and the coding sequences are also asymmetric, the mutagenic effect depends on the topology of the coding sequence on the chromosome. While the direct effect of the directional mutational pressure on the codon usage is predictable, the effect on the amino-acid composition depends on the degeneracy of the genetic code, initial composition of the protein sequence and codon usage. Assuming additional degeneracy of information connected with the structure of amino-acids, we have found that the best strategy for the evolution of some genes in the B. burgdorferi genome is to change the mutational pressure by inversions, which corresponds to changing the substitution matrix to the mirror one. It mimics the behavior of a stock market player who can gain by investing only in two stock sets even if during that time both sets have lost.