Simulation of Prokaryotic Genome Evolution Subjected to Mutational Pressures Associated with DNA Replication

Abstract

Each of two differently replicated DNA strands (leading and lagging) is subjected to the distinct mutational pressure associated with its synthesis. To simulate the influence of these pressures on the gene and genome evolution we worked out a computer model in which protein coding sequences were mutated according to the direct pressure (of the strand on which they were located), the reverse pressure (of the opposite strand), and the changing pressure (when the latter pressures were applied alternately). Simulated genomes were eliminated by the occurrence of stop codons in the gene sequences and the loss of their coding properties. The selection against stop codons appeared more deleterious than for coding signal. The leading strand pressure eliminated more genes because of the coding signal loss whereas the lagging strand pressure generated more stop codons. Generally, the reverse and changing pressures destroyed the coding signal weaker than the direct pressure. © Springer-Verlag Berlin Heidelberg 2013.