Phylogenetic prediction of nucleation complexes and their roles in capsid assembly

Infectious diseases are among the leading causes of death, especially in developing countries. Novel insights into viral life cycles can be exploited for antiviral therapies. One such opportunity is packaging signal mediated assembly of viral capsids, in which multiple dispersed sequence/structure motifs in the genome, called packaging signals (PSs), regulate capsid formation. I have developed a novel phylogenetic method to group viruses by their PS distributions. This method is specifically designed to identify PSs that are in similar positions in extended families of viruses, thus identifying candidates within the PS distribution that may have specific functions. We exemplify this for two viral families: Hepadnaviridae and Leviviridae. After identification of the PS motif in hepatitis B virus (HBV), the method was applied to different sets of HBV sequences. The distribution pattern of PSs highlighted small groups of highly conserved PSs. Weinvestigated their roles in formation of the nucleation complex, and identified a pair that formed into PSs on the same short fragment and may have a double functional role. Using this focus on function, PSs were predicted in related avian and mammalian HBV strains. Application to Leviviridae required an extension to include a secondary structure context. This identified six PSs conserved across MS2, BZ13, and Qβ. I developed a computational model of virus assembly in order to test their roles in nucleation and demonstrated that three of these PSs play crucial roles in nucleation of assembly. Studying PS-mediated assembly through phylogeny has thus led to an increased understanding of the essential nucleation of this process in two unrelated viruses.