Level of Gene Expression Is a Major Determinant of Protein Evolution in the Viral Order Mononegavirales

Abstract

Although the rate at which proteins change is a key parameter in molecular evolution, its determinants are poorly understood in viruses. A variety of factors, including gene length, codon usage bias, protein abundance, protein function, and gene expression level, have been shown to affect the rate of protein evolution in a diverse array of organisms. However, the role of these factors in viral evolution has yet to be addressed. The polar 3'-5' stepwise attenuation of transcription in the Mononegavirales, a group of single-strand negative-sense RNA viruses, provides a unique system to explore the determinants of protein evolution in viruses. We analyzed the relative importance of a variety of factors in shaping patterns of sequence variation in full-length genomes from 13 Mononegavirales species. Our analysis suggests that the level of gene expression, and by extension the relative genomic position of each gene, is a key determinant of the protein evolution in these viruses. This appears to be the consequence of selection for translational robustness, but not for translational accuracy, in highly expressed genes. The small genome size and number of proteins encoded by these viruses allowed us to identify other protein-specific factors that may also play a role in virus evolution, such as host-virus interactions and functional constraints. Finally, we explored the evolutionary pressures acting on noncoding regions in Mononegavirales genomes and observed that, despite being less constrained than coding regions, their evolutionary rates are also associated with genomic position.