Viruses as self-packing nano-containers

Shedding light on the conformational dynamics of viral RNAs during genome encapsidation

Dr. Alex Borodavka - Astbury Centre for Structural Molecular Biology, University of Leeds

RNA viruses are ubiquitous pathogens that infect organisms from every kingdom of life. Despite significant progress in structural biology, mechanisms of RNA virus genome packaging and assembly remain poorly understood. We have developed fluorescence correlation spectroscopy based assembly assays to monitor the conformations of viral genomes during assembly of simple ssRNA viruses. We have shown than interactions of RNA with cognate coat protein (CP) in two model viruses, cause a rapid collapse of their genomic RNAs during early stages of assembly. The collapse is caused by CP binding at multiple sites on the RNA, and is facilitated by additional protein-protein contacts. The specificity in RNA-CP interactions observed at low concentrations reflects the packaging selectivity in these viruses usually seen in vivo. RNA compaction by CP and cation-induced RNA condensation are distinct processes, implying that cognate RNA-CP contacts are required for assembly nucleation at low concentrations while charge neutralisation may work at higher concentrations in rather non-specific manner.
A different class of RNA viruses with segmented dsRNA genomes, including reoviruses and rotaviruses, possess segmented genomes, comprising 10-12 distinct double-stranded RNA molecules that are packaged into each virion. There is no plausible model explaining the highly efficient mechanism of this molecular process. Non-structural proteins encoded by these viruses are required for segment assortment in these viruses. Biophysical characterisation of conformational dynamics of large viral RNAs reveals fundamental mechanisms underpinning genome packaging and assembly in simple RNA viruses, as well as highlighting the role(s) of a non-structural RNA-binding protein in more complex dsRNA viruses.