UC Riverside

Viruses are intracellular parasites that can invade the cells of all known organisms. All viruses contain two components: a DNA or RNA genome and the capsid. Although the essential role of a viral capsid is to protect its genome, it must also release its genome for replication. To meet these two contesting requirements, viral capsids undergo a dynamic and reversible reorganization of biologically relevant surface peptides critical for their infectivity. Plant RNA viruses in the family Bromoviridae have a single-strand, positive-sense RNA genome divided among three genomic RNAs. These RNAs and subgenomic RNA get packaged into three homogeneous or four heterogeneous virion particles. In bromoviruses, the three virions, each carrying unique RNA species, have been physically inseparable by known separation techniques due to their particle homogeneity. Therefore, whether essential structural dynamism existed in these morphologically indistinguishable virions which could be of biological importance was unknown. Chapter 1 of this dissertation focused on investigating the stability and capsid dynamics of the three virions of brome mosaic virus (BMV), the type species of the genus Bromovirus, assembled autonomously in Nicotiana benthamiana using a robust agroinfiltration strategy. As the three virion types in BMV are identical in their morphology and electrophoretic mobility patterns, the use of a thermal denaturation assay and limited proteolysis followed by peptide mass mapping with MALDI-TOF enabled us to identify qualitative differences in capsid dynamics of three virions in BMV. Chapter 2 focused on understanding the comparative capsid dynamics among the three virions of BMV and cowpea chlorotic mottle virus (CCMV), a member of the family Bromoviridae that shares an identical genome organization and packaging scheme as BMV. Chapter 3 analyzed the relative dynamics of BMV and CCMV capsids assembled in the presence of heterologous replicase. Chapter 4 investigated the biological significance of co-packaging of a genetically redundant subgenomic RNA4 in BMV. Chapter 5 characterized Virus-like Particles (VLPs) assembled from the Gag protein of human immunodeficiency virus (HIV-1) in N. benthamiana. Finally, Chapter 6 attempted to silence the NbSKP1 gene in N. benthamiana using virus-induced gene silencing (VIGS) and studied the following effect on cucumber mosaic virus-Q strain accumulation.