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Defining a novel assembly pathway in ssRNA viruses using X-ray footprinting.

  • Full or part time
  • Application Deadline
    Applications accepted all year round
  • Competition Funded PhD Project (European/UK Students Only)
    Competition Funded PhD Project (European/UK Students Only)

Project Description

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:
More information about the Twarock lab:

Funding Notes

Awards are available after 1 October 2019;
The awards are available for new research students undertaking full-time research study leading to the degree of PhD. Students who are already registered for PhD research study are excluded from this competition;
The award will cover academic fees at the UK rate and a maintenance grant (~£14k);

How to apply:
View Website


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.

How good is research at University of Leeds in Biological Sciences?

FTE Category A staff submitted: 60.90

Research output data provided by the Research Excellence Framework (REF)

Click here to see the results for all UK universities

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