Rewiring of the UPS network upon REDOX stress

• Applicant: Dr. Ilaria Piazza
• Subject Area: Biochemistry
• Term: since 2024
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 535634027

The targeted degradation of proteins is essential for cellular function and fitness in all organisms. Damaged proteins must be recognized and removed to prevent collateral damage, while numerous signaling pathways rely on the specific degradation of proteins. In eukaryotes, the two major systems for protein degradation are the ubiquitin-proteasome system (UPS) and autophagy. Perturbations in either proteolytic pathway can lead to severe pathological conditions including cancer and neurodegeneration. In the UPS, protein substrates are tagged with a poly-ubiquitin mark, directing them to the proteasome where they are unfolded and degraded. Compared to this case-by-case degradation device, autophagy delivers substrates in bulk to a proteolytic organelle, the lysosome. As for the UPS, many proteins targeted by autophagy are marked with ubiquitin. In this SFB, we will address the molecular mechanisms of how proteins destined for degradation are channeled between the UPS and autophagy, focusing on protein degradation in the cytoplasm, the nucleus and other organelles. In addition to addressing the crosstalk between the two major proteolytic pathways, we will investigate how small molecules can be used to chemically reprogram the distinct degradation systems. In fact, the controlled targeted proteolysis of proteins has huge potential in medical research, bearing a great promise to develop, for example, novel anti-cancer drugs. In this sub-project we will investigate how small molecule metals can reprogram the UPS system enabling targeted proteolysis upon REDOX stress responses using proteomics. We will identify and characterize new metal-mediated molecular glues in the proteome through three aims. 1) We will systematically assess whether zinc metal ions are present at protein-protein interaction interfaces of E3 ligases and their protein substrates. 2) We will analyze if cellular redox states are regulating interactions between E3 ligases and substrates through interfaces bridged by zinc ions. 3) We will address if alternative metal-mediated molecular glues (e.g.: through copper, iron, manganese) occur in eukaryotes under reductive stress in different organelles: nucleus, mitochondria, cytosol. Since this SFB features an exceptional team combining expertise in the UPS and autophagy, new candidate interactions discovered with proteomics will be further characterized using a variety of approaches from structural biology to molecular medicine available in this collaborative center. Our consortium will reveal fundamental principles underlying the targeted degradation of proteins and uncover mechanisms of, and crosstalk between, the major cellular proteolytic systems, as well as how they can be reprogrammed by small molecules.

• DFG Programme: Research Grants
• International Connection: Austria
• Cooperation Partner: Professor Sascha Martens, Ph.D.