Coordinating ribosome biogenesis and nucleolar protein quality control by SUMO signaling

• Applicant: Professor Dr. Stefan Müller
• Subject Area: Cell Biology ; Biochemistry
• Term: since 2025
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 571860567

The nucleolus is a membrane-less molecular condensate, best characterized for its role in orchestrating rRNA transcription and initial steps of ribosome biogenesis. There is growing evidence that, in addition to its function in ribosome biogenesis, the nucleolus functions in protein quality control under proteotoxic stress. It has been shown that transient nucleolar sequestration of misfolded proteins or orphaned ribosomal proteins (r-proteins) shields them from aggregation. However, it remains largely unexplored how both functions are interconnected and coordinated. Based on our published and preliminary work we follow the idea that the ubiquitin-like SUMO system integrates ribosome biogenesis and nucleolar proteome homeostasis to safeguard cellular proteostasis. Ribosome biogenesis relies on a balanced supply of ribosomal proteins and rRNA molecules, which are assembled in a coordinated stepwise manner with the help of several hundred so-called trans-acting factors. We have demonstrated that distinct trans-acting factors involved in early ribosome maturation undergo reversible post-translational modification with SUMO. We further revealed that removal of SUMO from these factors by the nucleolar SUMO deconjugases SENP3 and SENP5 is required for proper 40S and 60S ribosome formation. Based on the observation that SENP3 activity is lost in response to proteotoxic stress we propose that nucleolar SENPs act as stress sensors whose inactivation halts ribosome biogenesis to protect cells from generating mis-assembled ribosomes under proteotoxic stress. Stress-induced inhibition of ribosome assembly will also result in the accumulation of orphaned aggregation-prone r-proteins that are toxic to cells if left unchecked. Our data demonstrate that depletion of SENP3/5 not only enhances SUMOylation of trans-acting factors, but also induces modification of r-proteins. We follow the hypothesis that enhanced SUMOylation contributes to nucleolar sequestration of orphaned r-proteins preventing their aggregation by keeping them in a soluble state or by feeding them into the ubiquitin-proteasome system. In support of this idea, we found that SUMOylation primes r-proteins for ubiquitylation by the SUMO-targeted ubiquitin ligase RNF111. Based on these findings, we follow the idea that nucleolar SUMO isopeptidases and the SUMO-targeted ubiquitin ligase RNF111 display critical functions in coordinating ribosome biogenesis with nucleolar protein quality. Our major objectives are: 1) Defining the SUMO-regulated composition of early pre-ribosomes; 2) Profiling the landscape of the SUMO signaling machinery on ribosome maturation; 3) Dissecting nucleolar SUMO signaling in quality control of orphaned r-proteins; 4) Explore the role of SUMO signaling in nucleolar sequestration and clearance of defective ribosomal products. We anticipate that our planned work will provide unprecedented insight in nucleolar protein quality control pathways.

• DFG Programme: Research Grants