Project co-supervised by Prof. Peter Stockley at Leeds and Prof. Reidun Twarock at University of York, as part of the White Rose network "Structural and Mechanistic Biology at the RNA/Ligand Interface"
Novelty and timeliness
We have recently discovered a previously unsuspected feature of the assembly of single-stranded RNA
viruses. Using single molecule fluorescence techniques (Borodavka et al, PNAS, 109, 15769) we have been
able to show that there is genome specificity in the self-assembly of viral capsids in vitro at the low
(nanomolar) concentration present inside cells. This both reflects what emerges from in vivo assembly
reactions and explains why previous in vitro studies came to the opposite conclusions. At the much higher
concentrations traditionally used for reassembly the sequence-specificity is lost and the assembly reactions
become very error prone (Dykeman et al. Phys Rev E, 87, 022717). The specificity is a consequence of
multiple viral coat protein (CP) interactions with short, dispersed RNA sequences/motifs within the cognate
genomes we term Packaging Signals (PSs). The CP-PS interactions are potential anti-viral targets and the
Universities of York & Leeds have filed a patent to exploit these discoveries. It is now vital to investigate how
widely PSs occur and what their role(s) in assembly are.
The student will join the group at a point where we have developed RNA footprinting to detect the presence of RNA PS-coat protein contacts within infectious virions. These studies need to be expanded to see if similar PSs exist in more complex virions with multipartite genomes, e.g. influenza virus. The student will use advanced biophysical techniques, such as single-molecule fluoresence, to determine how such sites contribute positively to virion assembly. We have established in monopartite ssRNA viruses that PS-binding ligands can inhibit assembly and the student will be invokved in extending these studies.
4. These data will be incorporated into the mathematical modelling of ssRNA viral evolution being
carried out in York.
More information about the Stockley lab: http://www.fbs.leeds.ac.uk/staff/profile.php?un=gen6pgs
More information about the Twarock lab: http://www.york.ac.uk/biology/research/biochemistry-biophysics/reidun-twarock/#profile
Borodavka,A.,Tuma, R. & Stockley, P. G. (2012) Evidence that Viral RNAs have Evolved for Efficient, Two-stage Packaging. PNAS, 109, 15769-15774.
Patel N, White SJ, Thompson RF, Bingham R, Weiß EU, Maskell DP, Zlotnick A, Dykeman E, Tuma R, Twarock R, Ranson NA, Stockley PG. (2017) HBV RNA pre-genome encodes specific motifs that mediate interactions with the viral core protein that promote nucleocapsid assembly. Nat Microbiol. 2:17098.
Twarock, R. & Stockley, P.G. (2019) RNA-mediated Virus Assembly: Mechanisms and Consequences for Viral Evolution and Therapy Ann. Rev. Biophys, 48, 495-514.