Signal-induced disassembly of the SCF ubiquitin ligase complex by Cdc48/p97.

A large group of E3 ubiquitin ligases is formed by the multisubunit SCF complex, whose core complex (Rbx1/Cul1-Cdc53/Skp1) binds one of many substrate recruiting F-box proteins to form an array of SCF ligases with diverse substrate specificities. It has long been thought that ubiquitylation by SCF ligases is regulated at the level of substrate binding. Here we describe an alternative mechanism of SCF regulation by active dissociation of the F-box subunit. We show that cadmium stress induces selective recruitment of the AAA(+) ATPase Cdc48/p97 to catalyze dissociation of the F-box subunit from the yeast SCF(Met30) ligase to block substrate ubiquitylation and trigger downstream events. Our results not only provide an additional layer of ubiquitin ligase regulation but also suggest that targeted, signal-dependent dissociation of multisubunit enzyme complexes is an important mechanism in control of enzyme function.

Ubiquitin and transcription: The SCF/Met4 pathway, a (protein-) complex issue.

Ubiquitylation has emerged as an omnipresent factor at all levels of transcriptional regulation. A recent study that describes the yeast transcriptional activator Met4 as a functional component of the very same ubiquitin ligase that regulates its own activity highlights the close relation between transcription and the ubiquitin proteasome system.

A transcriptional activator is part of an SCF ubiquitin ligase to control degradation of its cofactors.

Multisubunit protein complexes pose a challenge to the coordinated regulation of individual components. We show how the yeast transactivating factor Met4 functions as a component of the SCF(Met30) ubiquitin ligase to synchronize its own activity with cofactor assembly. Cells maintain Met4 in a dormant state by a regulatory ubiquitin chain assembled by SCF(Met30). Nutritional and heavy-metal stress block Met4 ubiquitylation resulting in Met4 activation, which induces a stress-response program including cell-cycle arrest. Met4 relies on assembly with various cofactors for promoter binding. We report here that the stability of these DNA-binding cofactors is regulated by SCF(Met30). Remarkably, the transcriptional activator Met4 functions as a substrate-specificity factor in the context of SCF(Met30/Met4) to coordinate cofactor degradation with its own activity status. Our results establish an additional layer for substrate recruitment by SCF ubiquitin ligases and provide conceptual insight into coordinated regulation of protein complexes.

Chemical genetics screen for enhancers of rapamycin identifies a specific inhibitor of an SCF family E3 ubiquitin ligase.

The target of rapamycin (TOR) plays a central role in eukaryotic cell growth control. With prevalent hyperactivation of the mammalian TOR (mTOR) pathway in human cancers, strategies to enhance TOR pathway inhibition are needed. We used a yeast-based screen to identify small-molecule enhancers of rapamycin (SMERs) and discovered an inhibitor (SMER3) of the Skp1-Cullin-F-box (SCF)(Met30) ubiquitin ligase, a member of the SCF E3-ligase family, which regulates diverse cellular processes including transcription, cell-cycle control and immune response. We show here that SMER3 inhibits SCF(Met30) in vivo and in vitro, but not the closely related SCF(Cdc4). Furthermore, we demonstrate that SMER3 diminishes binding of the F-box subunit Met30 to the SCF core complex in vivo and show evidence for SMER3 directly binding to Met30. Our results show that there is no fundamental barrier to obtaining specific inhibitors to modulate function of individual SCF complexes.

A dominant suppressor mutation of the met30 cell cycle defect suggests regulation of the Saccharomyces cerevisiae Met4-Cbf1 transcription complex by Met32.

Met30 is the substrate recognition subunit of the essential ubiquitin ligase SCF(Met30). The essential function of Met30 is the inactivation of the Saccharomyces cerevisiae transcription factor Met4, because fully activated Met4 induces a cell cycle arrest. Met4 regulates expression of genes involved in the sulfur assimilation pathway and coordinates the transcriptional program and cell cycle progression in response to cadmium and arsenic stress. Met4 lacks DNA binding activity and requires either Cbf1 or one of the two homologous proteins Met31 and Met32 for promoter association. Accordingly, met4 mutants, cbf1 mutants, and met31 met32 double mutants are methionine auxotroph. We isolated a truncated version of Met32 (Met32(Delta145-192)) as a dominant suppressor of the cell cycle defect of met30 mutants. Expression of Met32(Delta145-192) significantly reduced induction of Met4-regulated genes. Interestingly, both Cbf1- and Met31/32-dependent genes were affected by Met32(Delta145-192). Mechanistically, Met32(Delta145-192) prevented recruitment of Met4 to both Cbf1 and Met31/32-dependent promoters. We further demonstrated that Met32 is part of the Cbf1-Met4 complex bound to Cbf1-recruiting promoter elements and that Met31/32 are required for formation of a stable Met4-Cbf1 transcription complex. These results suggest a regulatory role of Met32 as part of the Cbf1-Met4 complex and provide molecular insight into coordination of cell cycle response and modulation of gene expression programs.

The yeast ubiquitin ligase SCFMet30: connecting environmental and intracellular conditions to cell division.

Ubiquitination regulates a host of cellular processes and is well known for its role in progression through the cell division cycle. In budding yeast, cadmium and arsenic stress, the availability of sulfur containing amino acids, and the intracellular concentration of S-adenosylmethionine are linked to cell cycle regulation through the ubiquitin ligase SCFMet30. Regulation is achieved by ubiquitination of the transcription factor Met4. Met4 activity is controlled by a regulatory K48-linked ubiquitin chain that is synthesized by Cdc34/SCFMet30. A ubiquitin-interacting-motif (UIM) present in Met4 prevents degradation of ubiquitinated Met4 allowing the ubiquitin chain to function as a reversible switch of Met4 activity. Here we discuss mechanisms of Met4 and SCFMet30 regulation in response to intracellular and environmental conditions, and describe the integration of these signals with cell cycle control.

Proteolysis-independent regulation of the transcription factor Met4 by a single Lys 48-linked ubiquitin chain.

The ubiquitin ligase SCF(Met30) is required for cell cycle progression in budding yeast. The critical function of SCF(Met30) is inactivation of the transcriptional activator Met4. Here we show that a single ubiquitin chain is attached to Met4 through lysine at position 163. Inhibition of Met4 ubiquitination by mutating lysine to arginine at this position constitutively activates, but does not stabilize, Met4. This supports a proteolysis-independent role of Cdc34-SCF(Met30)-catalysed Met4 ubiquitination. Surprisingly, the ubiquitin chain attached to Met4 is linked through Lys 48 in ubiquitin, a ubiquitin chain structure that is usually required for substrate targeting to the 26S proteasome. These results suggest that Lys 48-linked ubiquitin chains can have a regulatory role independent of proteolysis.