Functional and Structural Determinants of Long- and Short-Term Evolution of Herpesvirus Proteins

Understanding the factors that shape viral protein evolution is a central question in evolutionary virology. However, these determinants are poorly characterized for the majority of viruses, because functional data is scarce and because most viruses encode few proteins, limiting comparisons between them. Here, we focus on the Orthoherpesviridae family whose related viruses, including human-infecting herpesviruses, allow evolutionary investigation at different timescales. We employ different models to estimate evolutionary rates of numerous herpesvirus proteins and residues, and assess their relationship to a set of structural, cellular and functional characteristics. Core genes whose orthologs are found in distant genera, evolve at similar rates within genera, despite their evolutionary distance and their differences in viral replication and environments. This likely stems from constraints imposed to maintain the structural fold across viruses, and is corroborated by the finding that fold complexity is a major determinant of evolutionary rates. Focusing on the evolution of specific protein regions, we show that surface and disordered regions are enriched with positively selected residues. However, motifs embedded in disordered regions, important for binding host proteins, have conserved occurrences across viruses. Additionally, viral proteins predicted to form biomolecular condensates often evolve slowly despite having high disordered content. In summary, our analyses reveal short- and long-term evolutionary constraints of herpesvirus proteins. These include constraints imposed by the protein structural fold and by elements within disordered regions important for host-virus interactions. These constraints are relevant when considering potential pathways of virus evolvability and for developing new antiviral treatments.