The impact of local assembly rules on RNA packaging in a T=1 satellite plant virus

The vast majority of viruses consist of a nucleic acid surrounded by a protective icosahedral protein shell called the capsid. During viral infection of a host cell, the timing and efficiency of the assembly process is important for ensuring the production of infectious new progeny virus particles. In the class of single-stranded RNA (ssRNA) viruses, the assembly of the capsid takes place in tandem with packaging of the ssRNA genome in a highly cooperative co-assembly process. In simple ssRNA viruses such as the bacteriophage MS2 and small RNA plant viruses such as STNV, this cooperative process results from multiple interactions between the protein shell and sites in the RNA genome which have been termed packaging signals. Using a stochastic assembly algorithm which includes cooperative interactions between the protein shell and packaging signals in the RNA genome, we demonstrate that highly efficient assembly of STNV capsids arises from a set of simple local rules. Altering the local assembly rules results in different nucleation scenarios with varying assembly efficiencies, which in some cases depend strongly on interactions with RNA packaging signals. Our results provide a potential simple explanation based on local assembly rules for the ability of some ssRNA viruses to spontaneously assemble around charged polymers and other non-viral RNAs in vitro. Author Summary Assembly in single-stranded RNA plant viruses takes place via a highly cooperative process in which capsid proteins co-assemble around ssRNA. In the small satellite plant virus STNV, small hairpins present in the genome, termed packaging signals, bind to capsid proteins during assembly and allow for efficient formation of the capsid shell. Although these hairpins have been visualised in X-ray crystallography, the local rules of their interaction with the capsid proteins and how they ensure an efficient assembly process is somewhat unknown. Here we test several assembly scenarios involving different local rules for the protein-protein and RNA-protein interactions and find that assembly efficiency is highly dependent on the local assembly rules. Interestingly, while certain local assembly rules are consistent with a packaging signal mediated assembly model, some local rules predict reasonable assembly efficiency independent of packaging signal distribution. This may explain the ability to package charged polymer materials in some plant viruses.