Munich Cluster for Systems Neurology (SyNergy)

Project description:

Ubiquitination is key for protein homeostasis and molecular signaling in cells. Given that methods to map ubiquitin E3 ligase-substrate pairs are complex and resource intensive, we have recently developed a Ubiquitin (Ub)-specific proximity and orientation dependent (Ub-POD) labeling technique for E3 ligase-substrate pairs directly in cells (Mukhopadhyay et al. 2024; Mukhopadhyay et al. 2025). Having established a simple, scalable tool for the dissection of ubiquitin ligase substrates, we sought to tackle another challenging implication of the ubiquitin system and focus on the fact that cellular processes and pathways are often organized at the surface of cellular compartments where also regulation through ubiquitination occurs. Prominent examples are the cellular response to endolysosome membrane damage and inflammatory signaling. However, often the identity of ubiquitination targets and the molecular consequence of ubiquitination is only poorly understood. This project will develop Ub-POD into a technique that allows to ear mark local pools of ubiquitin at specific cellular locations with the ultimate goal to map local ubiquitinome dynamics of membranous and membrane-less compartments in cells. Our work will lead to a versatile method for probing compartment-specific ubiquitin signatures in health and disease states and has the capacity to create novel insight into ubiquitin and organelle biology with possible implications for AD, PD and ALS-FTD.