Simulation of Bacterial Genome Evolution under Replicational Mutational Pressures

Directional mutational pressure associated with replication is one of the most significant forces shaping structure of bacterial genomes and influencing the evolution of their genes. Here we introduced the model of bacterial genome evolution including two mutational pressures acting in differently replicated DNA strands (leading and lagging). The simulations were performed on the population of protein coding genes of the Borrelia burgdorferi genome. The simulated genomes were eliminated by selection because of: (i) stop codon occurrence in their gene sequences and (ii) the loss of their coding signal which was calculated according to the algorithm for recognition of protein coding sequences. The stop codon selection appeared much stronger than the one based on the coding signal and led to elimination of more genomes from the population. The genes were subjected both to the direct mutational pressure, characteristic to the strand on which they are coded and to the reverse pressure, typical of the opposite strand. Generally, the elimination of genomes because of stop codons occurrence was the most frequent for the reverse pressure whereas the coding signal selection eliminated genome most often for the direct pressure. The leading strand mutational pressure is more destructive for coding signal whereas the the lagging strand pressure generates more stop codons in gene sequences.