Defining the Role of Ubiquitin System in Skeletal Muscle Atrophy

Muscle atrophy is a systematic shift of the balance between protein synthesis and degradation toward a catabolic state. While muscle protein synthesis is primarily dependent on activation of the phosphoinositide 3-kinase-Akt (also known as PKB) and mammalian target of rapamycin (mTOR) pathways, the molecular mechanisms controlling muscle protein degradation are less well defined. An important breakthrough in the field was the use of microarray technology identifying more than a hundred atrophy-related genes, termed ‘atrogenes’. Among the identified genes most were associated with the ubiquitin proteasome and lysosome autophagy pathways, suggesting that these ubiquitin-mediated protein/organelle degradation processes are central to the atrophy response.

Objectives and Methods: This project aims to understand how ubiquitin systems regulate muscle protein degradation under physiological and pathological conditions. The first aim is to elucidate how MURF1 and MAFbx, two E3 ligases highly associated muscle protein degradation, contribute to muscle atrophy. The student will apply affinity-mediated proteomics to identify downstream substrates and regulatory interactors. In parallel, we will deploy quantitative proteomics establishing MuRF1 and MAFbx specific ubiquitylome database, a publishable resource for elucidating targets of the ubiquitin signalling under atrophy process. All potential substrates identified in these studies will then be validated in mouse models of muscle atrophy.
The second aim will be to identify novel E3 ligases and downstream effectors of ubiquitylation during muscle atrophy. In collaboration with Dr Satpal Virdee (University of Dundee) we are establishing activity-based proteomic platforms that will allow us to identify active E3 ligases, deubiquitylase, and ubiquitin binding proteins in cell/tissue lysates. The project will adopt this platform to identify specific E3 ligases and ubiquitin interacting proteins in lysate from genetic mouse models of muscle atrophy or glucocorticoid treated mice.

This project tackles the scientific questions by applying a range of state-of-the-art techniques, including molecular, cellular and chemical biology, biochemistry, mass spectrometry and animal experimentation. Dr. Lai will oversee all biochemical, molecular & cell biological studies whilst animal physiological studies will be performed with the Lavery group in the Institute of Metabolism and Systems Research, College of Medical and Dental Sciences. Ubiquitin analysis will be performed in collaboration with the MRC Protein Phosphorylation & Ubiquitylation Unit, School of Life Science, University of Dundee. Thus the project will be based on strong collaborative and multidisciplinary foundations. The student will also benefit immensely from internal and external collaborations, including clinicians at the Queen Elizabeth Hospital.