The Evolutionary Impact of Functional RNA Secondary Structures within Protein-Coding Regions in Yeast

Abstract

In recent years, the importance of functional RNAs in biological processes has been repeatedly demonstrated. Furthermore, a number of studies have indicated that the number and biological significance of functional RNAs has been underestimated. Here we focus on the impact of functional RNAs on the evolutionary rate of protein-coding genes. We used computational methods to predict a set of novel functional RNA secondary structures in the yeast genome. We found that the presence of predicted functional RNAs within coding regions causes a decrease in both synonymous and nonsynonymous evolutionary rates of the corresponding protein. We studied yeast genomes because abundant functional data is available for Saccharomyces cerevisiae, a common model genetic organism. Furthermore, the set of yeast duplicate genes produced by an ancient whole genome duplication provides a useful model for studying the evolution of gene function in yeast, and results from duplicate gene analysis also demonstrate that the duplicate gene with a greater number of coding functional RNAs also tends to have a relatively slower rate of protein evolution. Moreover, we discovered that genes with a significant portion of functional RNAs within their coding regions tend to be associated with either protein biosynthesis or transport.