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MRC DiMeN Doctoral Training Partnership: Mass-spectrometry analysis and live cell/zebrafish imaging to discover the function of novel post-translational modifications occurring in hypoxia signalling

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  • Full or part time
    Dr V See
    Prof C Eyers
    Dr P Elks
    Prof S Rocha
  • Application Deadline
    No more applications being accepted
  • Competition Funded PhD Project (European/UK Students Only)
    Competition Funded PhD Project (European/UK Students Only)

Project Description

To survive, multicellular organism need to sense and respond to changes in oxygen level. Episodes of low oxygen (hypoxia) occur during many physiological processes and also in pathological circumstances such as stroke, ageing and cancer. Hypoxia inducible factor (HIF) is the main transcription factor involved in the adaptation to hypoxia and it is therefore crucial to understand how HIF is regulated by both the available oxygen levels and other signalling cues experienced by the cells. We have initiated an un-biased mass spectrometry (MS)-based proteomic analysis of HIF family member post-translational modifications (PTMs), identifying numerous novel PTMs. We now seek to define their function, by studying site conservation and the functional effect of the PTM on HIF activity. Remarkably, one novel phosphorylation site in human HIF-1α is absent in fish, which constitutes an ancient evolutionary mutation in species constantly exposed to low oxygen environments.

The aim of the project is to establish the role and function of the newly discovered HIF PTMs in cells and in vivo using model organisms (zebrafish). This project builds on recent discoveries of HIF PTMs by the labs of C Eyers and V See. These PTMs are predicted to regulate HIF stability or activity. Understanding the function of these modifications is timely as it could contribute to the quest for therapeutic regulators of HIF function, a current focus of pharmaceutical industry.

Experimental approach: A combination of peptide and protein-based Mass Spectrometry analysis will be used to understand how these novel HIF PTMs occur in combination (at the level of the intact protein). Native ion mobility-MS, together with other biochemical strategies will be used to assess the PTMs’ impact on protein conformation, stability, and protein/DNA binding interactions. The consequence of the PTMs on HIF subcellular localisation, diffusion, binding interaction and transcription activity will be investigated by live cell imaging, using mutants of HIF fused to fluorescent tags. To fully characterise the function of some of the HIF mutants in vivo, zebrafish lines will be generated (collaboration with the University of Sheffield). The student will therefore be working both at the forefront of protein modifications analysis and live cell imaging, using cell lines and zebrafish models.
More information on the primary supervisor lab can be found here: http://pcwww.liv.ac.uk/~violaine/

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 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 can be found on our website:
http://www.dimen.org.uk/

Funding Notes

Funding notes
Studentships are fully funded by the Medical Research Council (MRC) for 3.5yrs
Includes:
Stipend at national UKRI standard rate
Tuition fees
Research training and support grant (RTSG)
Travel allowance
Studentships commence: 1st October 2019.

To qualify, you must be a UK or EU citizen who has been resident in the UK/EU for 3 years prior to commencement. Applicants must have obtained, or be about to obtain, at least a 2.1 honours degree (or equivalent) in a relevant subject. All applications are scored blindly based on merit. Please read additional guidance here: https://goo.gl/8YfJf8
Good luck.

References

Taylor, S. E., Bagnall, J., Mason, D., Levy, R., Fernig, D. G., & See, V. (2016). Differential sub-nuclear distribution of hypoxia-inducible factors (HIF)-1 and-2 alpha impacts on their stability and mobility. OPEN BIOLOGY, 6(9). doi:10.1098/rsob.160195

Bagnall, J., Leedale, J., Taylor, S. E., Spiller, D. G., White, M. R. H., Sharkey, K. J., . . . See, V. (2014). Tight Control of Hypoxia-inducible Factor-alpha Transient Dynamics Is Essential for Cell Survival in Hypoxia. JOURNAL OF BIOLOGICAL CHEMISTRY, 289(9), 5549-5564. doi:10.1074/jbc.M113.500405

Vonderach, Matthias, Byrne, Dominic P, Barran, Perdita E, Eyers, Patrick A and Eyers, Claire E (2018). DNA Binding and Phosphorylation Regulate the Core Structure of the NF-κB p50 Transcription Factor. Journal of the American Society for Mass Spectrometry. doi:10.1007/s13361-018-1984-0



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