PRO-CLEAR · Mechanisms for the selective clearance of chemically damaged proteins in mammalian cells
Horizon 2020 — Marie Skłodowska-Curie Actions
- Duration
- 2021-09-01 → 2023-08-31
- EU contribution
- €191,149
- Participants
- 1
- Scheme
- MSCA-IF
Lines connect the coordinator with its partners.
Results in brief
Mechanisms for the selective clearance of chemically damaged proteins in mammalian cells
This project addresses the fundamental question of how cells identify and selectively remove individual damaged proteins. Degradation of damaged proteins is essential for the survival of all cells. Impaired protein turnover can lead to diverse disorders such as neurodegeneration. In human cells, a system of quality control factors can surveil the proteome for damage. For example, misfolded proteins can be recognized and selectively degraded to prevent the build-up of toxic aggregates throughout life and in response to stress. In addition, proteins can experience any of several hundred chemical modifications throughout their life-cycle. How cells monitor the proteome for these types of modifications and potential signs of damage remains poorly understood. In this project, we aimed to identify chemical modifications that can act as marks of protein damage, to induce their selective removal. More specifically, we asked: How can we measure the impact of individual protein modifications on protein turnover? Which known forms of chemical damage could serve as triggers of selective protein degradation in human cells? What is the underlying cellular machinery and how can it recognize chemically damaged proteins at the molecular level? And lastly, how does this chemical protein surveillance contribute to maintaining an intact proteome under physiological conditions and proteotoxic stress. This project was designed to test the long-standing hypothesis that chemical protein modifications could provide a generic signal, that allows human cells to broadly survey the proteome for damage. In addition to its contribution to our fundamental understanding of cell homeostasis, these questions are central to understanding the mechanisms at play when protein homeostasis is perturbed, for example during ageing or neurodegeneration. In addition, the machinery that mediates selective protein degradation can be reprogrammed to target other proteins in a cell by pharmacological means. For example, the class of IMiD drugs mimics a chemical modification recognized by the ubiquitin ligase CUL4/CRBN and redirects its activity towards therapeutically relevant proteins, such as IKZF1. This mechanism underlies the action of the drug thalidomide, which has been highly successful in the treatment of multiple myeloma. Identifying other such chemical protein surveillance factors could therefore also open up avenues for designing new targeted protein therapeutics in future projects.
Data: CORDIS, © European Union
Project objective
Cellular homeostasis and survival critically depend on the ability to remove misfolded and damaged proteins. In cells, proteins are continuously exposed to reactive metabolites which introduce modifications such as oxidation, carbonylation, glycation or carbamylation. Such non-enzymatic post-translational modifications (nePTM) can irreversibly block critical interaction surfaces or reactive sites and thus pose a constant threat to proteome integrity. In line with this view, levels of nePTM are increased in diseased and aged tissues. In contrast, nePTM-bearing proteins are selectively degraded in healthy cells, suggesting the existence of a so far unknown pathway that recognizes and eliminates nePTM-bearing proteins.In this project, I will study the impact of nePTMs on protein turnover and explore the underlying molecular mechanisms. More specifically, I plan to (I) establish a reporter assay to monitor the degradation of proteins displaying individual amino acid modifications in human cells. This will allow to test effects of common nePTMs and to identify the precise chemical adducts that induce protein clearance. Aim (II) is to uncover the cellular machinery that mediates nePTM-triggered protein degradation. To this end, I will perform a genome-wide CRISPR screen for genes required to eliminate a fluorescent model substrate. Aim (III) of the project is to understand the mechanisms underlying the recognition and clearance of nePTMs. I will therefore characterize one newly identified mediator of nePTM-clearance in detail and test its ability to bind, degrade or modify nePTM-bearing proteins and will study the impact of its knockout on the turnover of endogenous proteins.Together these experiments promise to uncover a novel pathway for the quality control of chemically damaged proteins which will form the basis for understanding its role in physiology and human disease.
Original text from CORDIS.
Participants
- EIDGENOESSISCHE TECHNISCHE HOCHSCHULE ZUERICH · ZuerichCoordinatorSwitzerland
Links
Data: CORDIS, © European Union