Selection Pressure in Alternative Reading Frames

Overlapping genes are two protein-coding sequences sharing a significant part of the same DNA locus in different reading frames. Although in recent times an increasing number of examples have been found in bacteria the underlying mechanisms of their evolution are unknown. In this work we explore how selective pressure in a protein-coding sequence influences its overlapping genes in alternative reading frames. We model evolution using a time-continuous Markov process and derive the corresponding model for the remaining frames to quantify selection pressure and genetic noise. Our findings lead to the presumption that, once information is embedded in the reverse reading frame −2 (relative to the mother gene in +1) purifying selection in the protein-coding reading frame automatically protects the sequences in both frames. We also found that this coincides with the fact that the genetic noise measured using the conditional entropy is minimal in frame −2 under selection in the coding frame.