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Cdc48 cofactor Shp1 regulates signal-induced SCFMet30 disassembly

Significance Ubiquitylation affects many important cellular processes and has been linked to a number of human diseases. It has become a synonym for protein degradation, but ubiquitylation also has important nonproteolytic signaling functions. Understanding the molecular concepts that govern ubiquitin signaling is of great importance for development of diagnostics and therapeutics. The cadmium-induced inactivation of the SCFMet30 ubiquitin ligase via the disassembly of the multisubunit ligase complex illustrates an example for nonproteolytic signaling pathways. Dissociation is triggered by autoubiquitylation of the F-box protein Met30, which is the recruiting signal for the highly conserved AAA-ATPase Cdc48/p97. Here we show that the UBX cofactor Shp1/p47 is important for this ubiquitin-dependent active remodeling of a multiprotein complex in response to a specific environmental signal. Organisms can adapt to a broad spectrum of sudden and dramatic changes in their environment. These abrupt changes are often perceived as stress and trigger responses that facilitate survival and eventual adaptation. The ubiquitin–proteasome system (UPS) is involved in most cellular processes. Unsurprisingly, components of the UPS also play crucial roles during various stress response programs. The budding yeast SCFMet30 complex is an essential cullin-RING ubiquitin ligase that connects metabolic and heavy metal stress to cell cycle regulation. Cadmium exposure results in the active dissociation of the F-box protein Met30 from the core ligase, leading to SCFMet30 inactivation. Consequently, SCFMet30 substrate ubiquitylation is blocked and triggers a downstream cascade to activate a specific transcriptional stress response program. Signal-induced dissociation is initiated by autoubiquitylation of Met30 and serves as a recruitment signal for the AAA-ATPase Cdc48/p97, which actively disassembles the complex. Here we show that the UBX cofactor Shp1/p47 is an additional key element for SCFMet30 disassembly during heavy metal stress. Although the cofactor can directly interact with the ATPase, Cdc48 and Shp1 are recruited independently to SCFMet30 during cadmium stress. An intact UBX domain is crucial for effective SCFMet30 disassembly, and a concentration threshold of Shp1 recruited to SCFMet30 needs to be exceeded to initiate Met30 dissociation. The latter is likely related to Shp1-mediated control of Cdc48 ATPase activity. This study identifies Shp1 as the crucial Cdc48 cofactor for signal-induced selective disassembly of a multisubunit protein complex to modulate activity.