Comparative Genomics of Viral Genomes and Identification of Three Novel Viroporin-Like Superfamilies

Abstract

Introduction: Viroporins are small multifunctional proteins that modify cellular membranes facilitating processes such as viral nucleic acid entry and the release of virions from infected cells. We are interested in studying the evolutionary relationships among these proteins, in particular their organization into families and superfamilies.

Methods: We applied a variety of computational strategies to perform comparative genomics analyses of 120 viral genomes, using the phylogenetic profile method. This allowed the identification of 12 families, organized into four functionally related groups. Additionally, we compiled a list of 40 families from the Transporter Classification Database (TCDB) with viroporin-like attributes (i.e., length ≤300 aas, similar topologies, and/or documented viroporin activities). We then used TCDB as a reference to search for evidence of homology among families. Our well-established bioinformatic pipeline for inference of homology included (1) sequence similarity, (2) compatibility of topology and hydropathy profiles, (3) similarity of family-based HMM profiles, (4) shared motifs, and (5) conserved domains.

Results: We were able to infer homology among 15 families, four of which (Vpu-C, p10 viroporin/GDU1, FAST, and R-FAST) expanded the established Influenza A/B Virus M2 Protein (M2) superfamily. The other families constituted three novel superfamilies: viroporin-1, consisting of three families (RVP10, NS3, and NSP4); viroporin-2, composed of two functionally linked families (SARS-VP and M-protein); and viroporin-3 composed of 3 functionally related families (viroporin E, IBV-E, and PRRSV).

Conclusion: The application of comparative genomics and remote homology identification strategies allowed the classification of homologous and functionally related viroporin-like families into superfamilies. These results will be useful in future functional, mechanistic, and evolutionary studies of viroporins.

Keywords: Bioinformatics; Comparative genomics; Homology; Superfamily; Viroporin.