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EASTBIO Understanding the role of RNA in regulating metabolic enzymes in multi-drug resistant Staphylococcus aureus


School of Biological Sciences

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Dr S Granneman , Mr Iain McNae No more applications being accepted Competition Funded PhD Project (Students Worldwide)

About the Project

Introduction:
S. aureus is one of the most successful human and livestock pathogens and a common cause of skin infections and respiratory diseases that can be life threatening. S. aureus is such an effective pathogen because it can very rapidly adapt to environmental insults, such as alteration in host temperature and attack by the immune system. This enables it not only to survive in hostile conditions, but also to persist within the host. To achieve such rapid adaptation, S. aureus remodels its transcriptome within minutes of stress imposition. Transcription factors were thought to be mainly responsible for directing this process, however, post-transcriptional regulators, such as RNA-binding proteins (RBPs), are now recognized as key players in controlling adaptive responses by modulating mRNA translation and/or degradation rates. Although several RBPs have been discovered in S. aureus and shown to be important for pathogenicity, the majority have unknown functions. This underscores the need for a thorough characterization of these molecules.

The project:
Although RBPs are believed to play a fundamental role in regulating gene expression during host adaptive responses, it remains unclear which RBPs are the key players in this process and how they control rapid gene expression remodelling. Using novel proteomic approaches (Asencio et al., 2018; Urdaneta et al., 2018), we have recently uncovered RNA-binding domains for a large number of novel S. aureus RBPs, including many metabolic enzymes (metRBPs).

Our current working model is that S. aureus metRBPs function as novel post-transcriptional regulators that directly alter gene expression in response to changes in nutrient availability.

To test this hypothesis, the student will be given the opportunity to learn a wide array of techniques to functionally characterize several novel metabolic RBPs that are linked to antibiotic resistance and/or host survival.

The goals of this project are to understand
(1) how RNA-binding contributes to the activity of the metRBPs.
(2) what RNAs these metRBPs bind in vivo (van Nues et al., 2017).
(3) how important this RNA-binding activity is for surviving the host environment.

Techniques that the student will be using include (but are not limited to): production of recombinant proteins in our Protein Production Facility (EPPF), testing interaction with RNA using EMSA and related biochemical approaches, crystallizing proteins bound to RNA, genetic manipulation of S. aureus using CRISPR, in silico modelling of protein-RNA interactions, programming using Python and R and cross-linking and immunoprecipitation assays (CRAC; van Nues et al., 2017). Thus, the project provides a fantastic learning environment for students that wish to develop skills in these areas.

The School of Biological Sciences is committed to Equality & Diversity: https://www.ed.ac.uk/biology/equality-and-diversity

How to Apply:
The “Institution Website” button will take you to our Online Application checklist. Complete each step and download the checklist which will provide a list of funding options and guide you through the application process.



Funding Notes

This 4 year PhD project is part of a competition funded by EASTBIO BBSRC Doctoral Training Partnership http://www.eastscotbiodtp.ac.uk/how-apply-0. This opportunity is open to UK and International students and provides funding to cover stipend and UK level tuition fees. The fee difference will be covered by the University of Edinburgh for successful international applicants. Please refer to UKRI website (https://www.ukri.org/our-work/developing-people-and-skills/find-studentships-and-doctoral-training/get-a-studentship-to-fund-your-doctorate/) and Annex B of the UKRI Training Grant Terms and Conditions (https://www.ukri.org/wp-content/uploads/2020/10/UKRI-291020-guidance-to-training-grant-terms-and-conditions.pdf) for full eligibility criteria.


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