Linking the unfolded protein response to oxygen sensing - A phosphoproteomic approach to identify novel substrates of the ER kinase PERK

Background

The aging process is characterised by tissue decline and the onset of age-associated diseases. It is not, however, immutable, and can be modulated by manipulating the cell signalling pathways perturbed as cells and organisms age. A key characteristic of aging is the progressive accumulation of damaged/unfolded proteins in the endoplasmic reticulum (ER) leading to activation of the unfolded protein response (UPR). The UPR is the collective name for a number of cell signalling pathways that act in concert to restore normal cellular function by halting protein synthesis, clearing misfolded proteins and increasing the production of molecular chaperones. PERK, an ER-resident protein kinase, is critical to the UPR and acts to stall global protein synthesis. However inappropriate PERK activity is associated with the pathology of several age-related disorders including degenerative neurological diseases and cancer. Despite this key role for PERK very few direct substrates have been identified. 

Project Description and Experimental Approach

We have identified a new role for PERK as a regulator of the hypoxia-inducible factor (HIF)-dependent response to low oxygen – another key signalling pathway disrupted in human diseases¹. In this project you will define how the UPR, and PERK specifically, communicates with the HIF-dependent response to low oxygen. Initially, you will identify new PERK-dependent phosphorylation events by performing phosphoproteomic mass-spectrometry experiments². You will then determine the functional outcome of deleting/ mutating candidate PERK substrates on both the UPR and HIF signalling using state of the art CRISPR/Cas9-mediated genome editing techniques and relevant kinase assays. Completion of these experiments will lead to a greater understanding of how these signalling pathways communicate and contribute to the aging process.

Training and Environment

This Liverpool-based studentship provides an opportunity to use cutting edge mass-spectrometry coupled with genome editing techniques to dissect the function of important stress-responsive pathways. The placement in Newcastle University will provide excellent training in validating kinase-substrate relationships. The depth of expertise at both institutions and the world class facilities available, will provide an excellent training environment and give you a highly sought-after skill set to enhance your future career prospects.

Please contact Dr Niall Kenneth (niall.kenneth@liverpool.ac.uk) for more details and informal enquires.

1. Ivanova et al. PERK/eIF2α signaling inhibits HIF-induced gene expression during the unfolded protein response via YB1-dependent regulation of HIF1α translation. NAR. 46,(2018).

2. Hardman et al. Strong anion exchange‐mediated phosphoproteomics reveals extensive human non‐canonical phosphorylation. EMBO J. (2019)

HOW TO APPLY

Applications should be made by emailing bbsrcdtp@liverpool.ac.uk with a CV and a covering letter, including whatever additional information you feel is pertinent to your application; you may wish to indicate, for example, why you are particularly interested in the selected project/s and at the selected University. Applications not meeting these criteria will be rejected. We will also require electronic copies of your degree certificates and transcripts.

In addition to the CV and covering letter, please email a completed copy of the NLD BBSRC DTP Studentship Application Details Form (Word

document) to bbsrcdtp@liverpool.ac.uk, noting the additional details that are required for your application which are listed in this form. A blank copy of this form can be found at: https://www.nld-dtp.org.uk/how-apply.