Project details:
Bacterial pathogens, such as Klebsiella pneumoniae and Legionella pneumophila, residing inside host immune cells such as macrophages, must subvert host cell defences in order to avoid destruction. The mechanisms by which bacteria can ’rewire’ host cell functions are generally poorly understood but may frequently involve secretion of effector virulence factor proteins from the bacteria into the host cell that interfere with cellular processes. The identification of host proteins and protein complexes targeted by effector proteins necessary for infection can provide insights into their underlying molecular mechanisms, and potentially even single out pharmacological intervention targets in the host cell (’host directed therapy’)
1. We propose to develop and apply advanced methodology in quantitative mass spectrometry.
2–4. To characterize: (i) pathogen-host protein-protein interactions by affinity purification of bacterial effector proteins from macrophages and mass spectrometry analysis, (ii) global changes of protein complexes in response to macrophage infection with bacterial pathogens, (iii) global changes in host protein abundance or post translational modification state (phosphorylation, ubiquitination) in response to macrophage infection with bacterial pathogens.
We will assemble these data into an integrated map of host cell rewiring and assess the functional consequences of removing key host cell proteins (by knockdown/out, chemical inhibition) on infection assays.
This project will be supervised by Dr Ben Collins (Queen’s University School of Biological Sciences), Professor Jose Bengoechea and Dr Gunnar Neels Schroeder (Queen’s University School of Medicine, Dentistry and Biomedical Sciences).
All applications MUST be submitted through
https://dap.qub.ac.uk/portal/user/u_login.php.
Specific skills/experience required by applicants:
No specific skills are required; however, interests/experience in the following areas is desirable:
- Mass spectrometry-based proteomics
- Cellular microbiology
- Computational biology
All applicants must meet the academic entry requirements:
https://www.qub.ac.uk/courses/postgraduate-research/biological-sciences-phd.html#entry
Funding Notes
Only UK and EU students are eligible to apply. Before applying, it is strongly recommended that you read the full information on eligibility criteria available from DfE: View Website.
Please note in particular that not all successful applicants may be eligible to receive a full studentship (i.e. fees and stipend) - please read in detail the Residency and Citizenship requirements in the document linked to above.
References
1.Nicod, C., Banaei-Esfahani, A. & Collins, B. C. Elucidation of host–pathogen protein–protein interactions to uncover mechanisms of host cell rewiring. Curr. Opin. Microbiol.39, 7–15 (2017).
2.Hülsmann, J. et al.AP-SWATH Reveals Direct Involvement of VCP/p97 in Integrated Stress Response Signaling Through Facilitating CReP/PPP1R15B Degradation. Mol. Cell. Proteomics17, 1295–1307 (2018).
3.Heusel, M. et al.Complex‐centric proteome profiling by SEC‐SWATH‐MS. Mol. Syst. Biol.15, e8438 (2019).
4.Meier, F. et al.Parallel accumulation –serial fragmentation combined with data-independent acquisition (diaPASEF): Bottom-up proteomics with near optimal ion usage. bioRxiv656207 (2019) doi:10.1101/656207.
