Selection pressure in alternative reading frames.

Katharina Mir,Steffen Schober,Bryan A White

doi:10.1371/journal.pone.0108768

Abstract

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.

Highlights

Overlapping genes are protein coding genes sharing the same DNA locus in different reading frames
Until lately most authors denied the existence of overlapping genes in bacterial genomes, bacterial genome annotation programs excluded overlapping candidates in alternative reading frames deliberately [2,3,4,5]
We apply the conditional entropy introduced in Eq (2) to answer the question how long the information which amino acid was transmitted is conserved in the different reading frames

Summary

Introduction

Overlapping genes are protein coding genes sharing the same DNA locus in different reading frames. As DNA consists of two strands and each amino acid is encoded by non-overlapping triplets (codons), up to six reading frames are possible at a given locus. Until lately most authors denied the existence of overlapping genes in bacterial genomes, bacterial genome annotation programs excluded overlapping candidates in alternative reading frames deliberately [2,3,4,5]. This paper is concerned with the question how selection pressure in the protein-coding frame influences alternative reading frames. Is it possible to protect by selection two protein-coding sequences simultaneously? Is it possible to protect by selection two protein-coding sequences simultaneously? We explore this question using a stochastic model for the evolution of the protein-coding reading frame and predict the consequent behaviour in the alternative reading frames

Methods

Results

Discussion

Conclusion