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  White Rose BBSRC DTP: Defining the mechanism of enteroviral cis-replicative elements using structural, biophysical and virological approaches

   White Rose BBSRC Doctoral Training Partnership

  Dr Chris Hill, Dr C G Baumann, Dr Trevor Sweeney, Dr S Quinn  Sunday, January 07, 2024  Funded PhD Project (Students Worldwide)

About the Project

Enteroviruses (e.g. poliovirus, enterovirus 71, rhinovirus) comprise a diverse group of human and animal pathogens, which together are estimated to cause over one billion infections annually. Once inside the host cell, their positive-sense, single-stranded RNA genomes must be replicated by first synthesizing a negative-sense strand followed by a new positive-sense RNA molecule. The primer for RNA synthesis is the uridylated form of VPg, a small viral protein.

The enterovirus genome is highly structured, and several conserved RNA structures are essential regulators of genome synthesis. A “cloverleaf” structure at the 5′ end of RNA binds to both host poly(rC)-binding protein 2 (PCBP2) and the viral 3CD protein – a precursor form of the mature 3C (protease) and 3D (polymerase) proteins. The cis-replicative element “cre”, required for VPg uridylation by 3D, binds to both 3CD and 3C proteins. However, our understanding of this network of interactions has been hampered by the lack of high-resolution three-dimensional structures.

You will study the structural and mechanistic basis of cloverleaf/PCBP2/3CD and cre/3C/3CD complex assembly. This will involve the reconstitution of RNA-protein complexes in vitro, purification of complexes, sample optimization, cryo-EM data collection and processing. You will also study protein-protein and protein-RNA-interactions using a variety of single-molecule biophysical techniques to probe RNA conformational dynamics and the kinetics of complex assembly. Key findings will be further explored in virus-infected cells, in collaboration with the Sweeney group (Pirbright Institute). You will join an interdisciplinary, diverse and highly supportive training environment with the combined expertise of four supervisors: structural biology and RNA biochemistry (Hill group), advanced single-molecule imaging (Baumann and Quinn groups) and enterovirus molecular biology (Sweeney group). You will also benefit from access to state-of the art cryo-EM infrastructure at YSBL, and the Molecular Interactions laboratory in the Bioscience Technology Facility. Candidates from under-represented groups are particularly encouraged to apply.

About the DTP

This studentship is offered as part of the White Rose BBSRC Doctoral Training Partnership (DTP) in Mechanistic Biology, which brings together the research of the world-class molecular and cellular bioscience centres at the White Rose universities of Leeds, Sheffield and York.

Our mission is to train excellent bio-scientists who understand how living systems work and can innovate to address global challenges, such as the impact of climate change, a healthier old age, sustainable food production, land use and energy production.

What is on offer?

This is a core studentship for entry in October 2024.  

Join us and you will receive a 4-year, funded PhD programme of research and skills training, with cross-disciplinary supervision, plus a structured programme of cohort-wide training and networking events. A highlight is the annual symposium, which is planned and delivered by students.

A unique part of your training will be the Professional Internships for PhD Students (PIPS), where you will spend three months at a host organisation of your choosing, gaining experience of work in a professional environment, and acquiring transferable skills that will be beneficial in your future career.

How to apply – Expression of Interest

Students may apply for up to three projects anywhere in the Doctoral Training Partnership (DTP).  Applications will be to the DTP centrally, using an online Expression of Interest (EoI). The EoI will include:

§ CV information; not submitted separately

§ Equality, Diversity and Inclusion (EDI) data

§ Names of two referees

Deadline for EoIs is midnight Sunday 7th January 2024.

Submit EoIs using this link:

Shortlisted candidates will be required to make formal applications to the Graduate School at each institution, supplying the necessary paperwork.

Interviews will be held either Friday 2nd and Monday 5th to Friday 9th February, or Monday 19th to Friday 23rd and Monday 26th February 2024, in-person at Leeds, Sheffield and York, with a panel representing all 3 Universities. Shortlisted candidates will be notified of a specific time/date to attend. If you have applied for more than one project and are selected for interview, you will be interviewed only once. 


Biological Sciences (4)

Funding Notes

Appointed candidates will be fully funded for 4 years:
 Tax-free annual stipend at the UKRI rate. The rate for starters in 2023/24 was £18,622. (Rates for 2024/25 starters are not yet available).
 UKRI tuition fees – These are paid directly to the host institution.
 A Research Training and Support Grant
 An allowance for Fieldwork/Conference/Travel
 A Professional Internship for PhD Students (PIPS) allowance
Not all projects will be funded; the DTP will appoint a limited number of candidates via a competitive process.


• Helena-Bueno K, Ekemezie CL, Brown CR, Baslé A, Blaza JN, Hill CH*, Melnikov SV*. (2022) A bacterial ribosome hibernation factor with evolutionary connections to eukaryotic protein synthesis. bioRxiv .11.24.517861; doi: (under revision at Nature)
• Hill CH†*, Pekarek L†, Napthine S†, Kibe A, Firth AE, Graham SC*, Caliskan N*, Brierley I*. (2021) Structural and molecular basis for Cardiovirus 2A protein as a viral gene expression switch. Nature Communications. Dec 9;12(1):7166. doi: 10.1038/s41467-021-27400-7.
• Hill CH*†, Cook GM†, Napthine S†, Kibe A, Brown K, Caliskan N, Firth AE*, Graham SC*, Brierley I*. (2021) Investigating molecular mechanisms of 2A-stimulated ribosomal pausing and frameshifting in Theilovirus. Nucleic Acids Research. Nov 18;49(20):11938-11958. doi: 10.1093/nar/gkab969.
• Hill CH, Borekaite V, Kumar A, Casañal A, Kubik P, Degliesposti G, Maslen S, Mariani A, von Loeffelholz O, Girbig M, Skehel M, Passmore LA (2019). Activation of the endonuclease that defines mRNA 3′-ends requires incorporation into an 8-subunit core cleavage and polyadenylation factor complex. Molecular Cell 73(6):1217-1231.e11, PMID: 30737185
(† equal contribution, *corresponding author)
• Fung, H.K.H, Grimes, S., Huet, A., Duda, R.L., Chechik, M., Gault, J., Robinson, C.V., Hendrix, R.W., Jardine, P.J., Conway, J.F., Baumann*, C.G. and Antson*, A.A. (2022) Structural basis of DNA packaging by a ring-type ATPase from an archetypal viral system. Nucleic Acids Research. 50: 8719-8732.
• Haworth, A.S., Hodges, S.L., Capatina, A.L., Isom, L.L., Baumann, C.G. and Brackenbury*, W.J. (2022) Subcellular dynamics and functional activity of the cleaved intracellular domain of the Na+ channel β1 subunit. Journal of Biological Chemistry. 298: 102174.
• Pitruzzello, G., Baumann, C.G., Johnson, S. and Krauss*, T.F. (2022) Single-cell motility rapidly quantifying heteroresistance in populations of Escherichia coli and Salmonella typhimurium. Small Science 2100123.
• Whelan, F., Lafita, A., Gilburt, J., Degut, C., Griffiths, S.C., Jenkins, H.T., St. John, A.N., Paci, E., Moir, J.W.B., Plevin, M.J., Baumann, C.G., Bateman*, A. and Potts*, J.R. (2021) Periscope proteins are variable-length regulators of bacterial cell surface interactions. PNAS 118: e2101349118.
(*corresponding author)
• Sweeney TR*, Dhote V, Guca E, Hellen CUT, Hashem Y, Pestova TV. (2021) Functional role and ribosomal position of the unique N-terminal region of DHX29, a factor required for initiation on structured mammalian mRNAs. Nucleic Acids Research 49(22):12955-12969
• Mears HV and Sweeney TR*. (2020) Mouse Ifit1b is a cap1-RNA binding protein which inhibits mouse coronavirus translation and is regulated by complexing with Ifit1c. Journal of Biological Chemistry 295(51):17781-17801.
• Fajardo T, Jr, Sanford TJ, Mears HV, Jasper A, Storrie S, Mansur DS, and Sweeney TR*. (2020) The flavivirus polymerase NS5 regulates translation of viral genomic RNA. Nucleic Acids Research 48(9):5081-5093.
• Sanford TJ, Mears HV, Fajardo T, Jr, Locker N, Sweeney TR*. (2019) Circularization of flavivirus genomic RNA inhibits de novo translation initiation. Nucleic Acids Research 47(18):9789-9802.
(*corresponding author)
• Dresser L, Graham SP, Miller LM, Schaefer C, Conteduca D, Johnson S, Leake MC, Quinn SD*. (2022) Tween-20 Induces the Structural Remodeling of Single Lipid Vesicles. Journal of Physical Chemistry Letters. Jun 9;13(23):5341-5350. doi: 10.1021/acs.jpclett.2c00704.
• Srinivasan S, Regmi R, Lin X, Dreyer CA, Chen X, Quinn SD, He W, Coleman MA, Carraway KL 3rd, Zhang B, Schlau-Cohen GS. (2022) Ligand-induced transmembrane conformational coupling in monomeric EGFR. Nature Communications. Jul 6;13(1):3709. doi: 10.1038/s41467-022-31299-z.
• Dresser L, Hunter P, Yendybayeva F, Hargreaves AL, Howard JAL, Evans GJO, Leake MC, Quinn SD*. (2021) Amyloid-β oligomerization monitored by single-molecule stepwise photobleaching. Methods. Sep;193:80-95. doi: 10.1016/j.ymeth.2020.06.007.
• Juan-Colás J, Dresser L, Morris K, Lagadou H, Ward RH, Burns A, Tear S, Johnson S, Leake MC, Quinn SD* (2020) The Mechanism of Vesicle Solubilization by the Detergent Sodium Dodecyl Sulfate. Langmuir 36 (39), 11499-11507. DOI: 10.1021/acs.langmuir.0c01810
(*corresponding author)