Gaining control over host ribosomes is arguably the most important event during RNA virus infection, and regulation of viral gene expression occurs mostly at the level of translation. −1 Programmed ribosomal frameshifting (PRF) is a viral translational control strategy in which elongating ribosomes ‘slip’ into the −1 reading frame when they encounter a structured ‘stimulatory element’ in the viral RNA that is difficult to unwind – often a stem-loop or pseudoknot [1]. PRF usually occurs at a fixed efficiency, thereby specifying the relative abundance of proteins encoded in the two reading frames. However, in some cases PRF efficiency is variable, and is determined by levels of a specific stimulatory protein. In cardioviruses, −1 PRF only occurs when the viral 2A protein recognises its cognate RNA element [2,3,4]. In arteriviruses, −2 PRF is stimulated by a complex between viral protein nsp1β, host poly(C) binding protein, and a C-rich stretch in the RNA [5,6].
Stimulatory elements present an intriguing paradox – they must be stable enough to present a blockade to the elongating ribosome, yet also dynamic enough to allow remodelling and unwinding as translation continues. Recent studies suggest that they may adopt several conformations, and that protein components (e.g. 2A, nsp1β) also bind to the ribosome itself [2]. Furthermore, several host anti-viral proteins have recently been identified (e.g. Shiftless) that bind to and modulate the stability of these elements [7]. However, a lack of structural data on these important complexes has hampered our understanding.
There are several model stimulatory elements available to work on. You will purify RNA-protein complexes and determine their structures by X-ray crystallography and cryo-EM, thus defining the "rules" governing the molecular interaction. You will also characterise the stability and conformational dynamics of these elements in solution by using cutting edge single-molecule approaches (e.g. FRET to study conformational changes, optical tweezers to measure resistance to unwinding) and examine how host anti-viral proteins affect these properties. You will also have the opportunity to investigate interactions between stimulatory elements and mammalian ribosomes.
You will join a vibrant, diverse and highly supportive training environment with the combined expertise of two supervisors – protein-RNA biochemistry and structural biology (Hill lab, https://www.york.ac.uk/biology/our-staff/chris-hill/) and single-molecule biophysics and advanced fluorescent imaging (Leake lab, https://www.york.ac.uk/physics/research/physics-of-life). You will also benefit from rapid access to state-of the art X-ray crystallography and cryo-EM infrastructure at the York Structural Biology Laboratory (https://www.york.ac.uk/chemistry/research/ysbl/facilities/eleanor-and-guy-dodson-building), and the molecular interactions laboratory at the Biology Technology Facility. No previous experience in these techniques is necessary and you will receive a thorough experimental training. Candidates from under-represented groups are particularly encouraged to apply.
Benefits of being in the DiMeN DTP:
This project is part of the Discovery Medicine North Doctoral Training Partnership (DiMeN DTP), a diverse community of PhD students across the North of England researching the major health problems facing the world today. Our partner institutions (Universities of Leeds, Liverpool, Newcastle, York and Sheffield) are internationally recognised as centres of research excellence and can offer you access to state-of the-art facilities to deliver high impact research.
We are very proud of our student-centred ethos and committed to supporting you throughout your PhD. As part of the DTP, we offer bespoke training in key skills sought after in early career researchers, as well as opportunities to broaden your career horizons in a range of non-academic sectors.
Being funded by the MRC means you can access additional funding for research placements, international training opportunities or internships in science policy, science communication and beyond. See how our current DiMeN students have benefited from this funding here: http://www.dimen.org.uk/overview/student-profiles/flexible-supplement-awards
Further information on the programme and how to apply can be found on our website:
http://www.dimen.org.uk/how-to-apply/application-overview
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