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Investigating the ubiquitin network in exercising human skeletal muscle

Principal Supervisor: Dr Yu-Chiang Lai

Secondary Supervisor(s): Prof Gareth Wallis

University of Registration: University of Birmingham

BBSRC Research Themes:

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Deadline: 4 January, 2024


Project Outline

We all knew that being physically active is beneficial for health, but until now we still do not have a clear understanding of what is happening deep in the body, or how the molecular communication changes that bring health. Since protein ubiquitylation is one of the key post-translational modifications affecting all most all biological function, our lab has focused on understanding how exercise improves muscle health and disease by researching protein ubiquitylation and ubiquitin signalling events. There are considerable research interests on ubiquitin-modifying enzymes (e.g. MuRF1, Atrogin1 and USP19) in muscle atrophy. However, information about which ubiqtuin E3 ligases/DUBs (deubiquitylases) account for the beneficial effects of exercise and what are their molecular partners and functions remains unclear. This PhD project will aim to fill the knowledge gaps by investigating the potential candidates that have been identified from our previous “Omic” databases (e.g. from ubiquitylome, phosphoproteome and RNAseq)

We have identified a list of DUBs, whose gene and/or protein expressions were changed in exercised human skeletal muscle. More interestingly, many of the potential targets were also occurring opposite changes in their protein/gene expression in aged skeletal muscle and/or disease-associated cardiomyocytes. To better understand their translational and functional roles, the student will first verify their gene and protein expression and study their localisation in exercised human skeletal muscles (Objective 1). The student will also aim to test whether genetic manipulation of these enzymes can alter the beneficial effects of exercise in myoblasts/cardiomyocytes and rodent tissues (Objective 2 and 3). Findings are expected to create new research avenues and accelerate the discovery of pharmaceutical targets for improving metabolic health and anti-ageing.

Our lab has been developing and collating a range of highly effective experimental tools for gaining mechanistic insights on the role of ubiquitin-modifying enzymes. For example, we established an E2 library screening platform and an effective workflow of the state-of the-art CRISPR/Cas9 technology for generating gene knockout and knock-in cells, which is crucial for this project. We also plan to use proteomic-based approaches, through collaboration with Dr Rahul Samant (Babraham Institute, Cambridge) to validate the candidate protein’s functional outputs and pathways in mouse or human muscle.

References

  1. Nishimura Y, Musa I, Holm L, Lai YC. (2021) Recent advances in measuring and understanding the regulation of exercise-mediated protein degradation in skeletal muscle. Am J Physiol Cell Physiol 321(2): C276-C287.
  2. Lord S, Lai YC. (2022) Exercise mediates ubiquitin signalling in human skeletal muscle. FASEB Bioadv. 4(6):402-407

Techniques

  • Molecular cloning, gene transfection, and CRISPR/Cas9 knock out/in technology.
  • Protein expression, purification, characterisation, and chemical modification.
  • Biochemical and enzymatic assays
  • Scientific data analysis and bioinformatics