Proteome Organisation & Dynamics

The functional state of a cell is ultimately defined by the state of its proteome, i.e. abundance, localisation, turnover and mobility of all proteins and their organisation in complexes and organelles. Numerous cellular systems contribute to proteome homeostasis through prevention, detection and removal of abnormal proteins. These quality control systems operate throughout the protein life cycle, from synthesis to degradation. Hence the definition of abnormal protein is very broad, including mutated, misfolded, mislocalised and damaged molecules.

Selective protein degradation by the ubiquitin-proteasome system (UPS) plays a key role in proteome abundance and quality control, whereby a cascade of ubiquitin-activating (E1), ubiquitin-conjugating (E2) and ubiquitin-protein ligase (E3) enzymes marks proteins with polyubiquitin chains of varying linkages for degradation at the proteasome. When degradation is not possible, the impact of abnormal proteins can be mitigated through their asymmetric partitioning during cell division. Despite the activity of such systems, proteome homeostasis declines with ageing and in numerous diseases, including some cancers and late-onset neurodegenerative disorders, resulting in accumulation of abnormal proteins and loss of cell functionality. Thus, understanding the mechanisms of protein quality control is not only important from the point of view of basic research but can also contribute to elucidating causes of diseases at the molecular level.

Figure showing analysis of protein dynamics with tandem fluorescent protein timers
Figure 1. Analysis of protein dynamics with tandem fluorescent protein timers (tFTs). (a) A tFT is a fusion of two conventional fluorescent proteins: sfGFP (green) and mCherry (red). Due to different maturation kinetics of mCherry (slow) and sfGFP (fast), the mCherry/sfGFP ratio is a measure of protein age and can be used to follow trafficking, inheritance and degradation of tFT-tagged proteins. (b) Analysis of protein inheritance with tFTs. During yeast cell division, old molecules of the Hxt1 glucose transporter stay at the plasma membrane in the mother cell, whereas the bud receives freshly produced Hxt1 molecules. (c) Analysis of protein degradation with tFTs. Fluorescence measurements of yeast colonies expressing tFT-tagged proteins.

We employ a multidisciplinary approach to dissect mechanisms of protein quality control in yeast and human cells through a combination of molecular and cell biology techniques, biochemistry, computational biology and development of genomic and proteomic approaches (Figure 1) that allow us to follow proteome dynamics down to single cell level. Through systematic characterisation of selective protein degradation machinery and patterns of protein turnover/inheritance, we aim:

  • to identify quality control mechanisms for different types of abnormal proteins (e.g. our recent work revealed a quality control pathway for proteins mislocalised to the inner nuclear membrane, Figure 2)
  • to understand how abnormal proteins are recognised in the cell
  • to examine the roles of protein quality systems in healthy cells, to investigate their contributions to disease progression and ageing, and to ultimately explore their potential as targets for therapeutic interventions
Figure showing a pathway of protein quality control at the inner nuclear membrane mediated by Asi ubiquitin ligase
Figure 2. A pathway of protein quality control at the inner nuclear membrane (INM) is mediated by the Asi ubiquitin ligase. This pathway appears to have a dual function: to control the abundance of specific INM-resident proteins, resembling classical endoplasmic reticulum-associated protein degradation (ERAD) pathways, and to maintain the identity of the INM, by identifying and targeting for degradation proteins that mislocalise to the INM.

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