Brenda A. Schulman

The discovery and characterization of the ubiquitin system was founded on classical enzymology approaches that established fundamental principles of protein ubiquitylation. Cullin-RING ligases (CRLs) represent the largest class of human ubiquitin ligases, yet detailed enzymology of these multi-subunit assemblies has lagged behind other systems such as nucleic acid polymerases. Here, we employed pre-steady state kinetics and global data fitting using KinTek Explorer to systematically investigate the kinetic parameters controlling CRL-dependent ubiquitin transfer. Using a well-characterized in vitro reconstituted system exploring CUL2-dependent CRLs, we modeled substrate priming, showing that the system is highly amenable to global fitting of kinetic data. The results show that product dissociation from the CRL is significantly slower than substrate dissociation, explaining previously reported slow steady-state ubiquitylation rates. Extending this framework to poly-ubiquitin chain formation revealed catalytic efficiencies 15–42-fold greater than substrate priming. Comparative analysis of CUL1-dependent and CUL2-dependent systems showed remarkably similar kinetic parameters, including the K _m of ubiquitin-carrying enzyme for CRLs, despite differences in substrate receptor and enzyme architecture. We further examined drug-induced neo-substrate ubiquitylation using the pomalidomide-CRBN-SALL4 system, revealing atypical kinetics characterized by rapid ubiquitin transfer paired with an elevated K _m , ultimately yielding catalytic efficiencies comparable to natural substrates. The findings establish pre-steady state kinetics and global data fitting as powerful enzymological tools for dissecting CRL-dependent ubiquitylation across different CRL families and substrate contexts, with important implications for understanding both physiological ubiquitylation and therapeutic targeted protein degradation strategies.

T-cell exhaustion limits durable antitumor responses and remains a barrier to adoptive cell therapies (ACT) in solid tumors. To identify regulators of T-cell persistence, we performed genome-wide CRISPR knockout screens in primary human CD8+ T cells expressing an NY-ESO-1–specific T-cell receptor and subjected them to repeat tumor cell rechallenges. These screens revealed an enrichment of single-guide RNAs targeting components of cullin–RING E3 ubiquitin ligases, particularly cullin-5–RING E3 ligase (CRL5) assemblies comprising CUL5, RNF7, and ARIH2. Disruption of CRL5 genes in T cells preserved cytotoxic activity and enhanced cytokine production while sustaining effector-associated transcriptional programs and suppressing exhaustion-related signatures. Pharmacologic inhibition of cullin neddylation with the NEDD8-activating enzyme inhibitor MLN4924 recapitulated CRL5 loss and enhanced T-cell effector function in vitro. In a human melanoma xenograft model, ACT with CRL5-deficient T cells improved tumor control. Together, these findings identify CRL5 as a negative regulator of T-cell fitness and a potential therapeutic target to enhance ACT durability in solid tumors. Significance: The CRL5 complex negatively regulates CD8+ T-cell persistence during chronic antigen stimulation, identifying CRL5 disruption as a potential strategy to sustain T-cell effector function and improve ACT. See related commentary by Hanina and Maus, p. XX . See related article by Bachl et al., p. XX .

The GID/CTLH family of E3 ubiquitin ligases employs several substrate receptor subunits that recruit distinct degrons, but the substrate recognition mechanisms of the CTLH ^MKLN1 assembly have largely remained elusive. Here, we reconstitute CTLH ^MKLN1 -dependent ubiquitylation of three biochemically distinct substrates – MKLN1 itself, ZMYND19, and FAM72A-recruited UNG2, and determine cryo-EM structures of each substrate bound to MKLN1. The structures reveal how MKLN1’s discoidin and Kelch β-propeller domains engage substrates through multivalent contacts. MKLN1 recruits itself through discoidin-Kelch interactions between MKLN1 dimers, forming an assembly that competes with other substrates. ZMYND19 and FAM72A each bind to MKLN1 through loops engaging the discoidin trench domain while their C-terminal Arg residues engage the MKLN1 Kelch central channel, identifying MKLN1 as an Arg/C-degron receptor. The acetylated N-terminus of UNG2 is positioned within a Y-shaped tunnel of FAM72A, defining an adaptor-mediated Ac/N-degron recognition mechanism. Thus, our data reveal how combinatorial deployment of MKLN1 discoidin and Kelch domains enable a single receptor subunit to recognize a diverse substrate repertoire, adding to a complex picture of degron recognition across the GID/CTLH family.

Proteasome regulatory particles determine cellular protein degradation capacities. Yet specific ubiquitin-independent degradation targets of individual proteasome regulatory particles, and physiological roles of such pathways remain largely elusive. Here, through a chemical biology-driven approach, we identify a covalent small molecule that selectively targets a conformationally dynamic pocket in the non-catalytic proteasome regulator PSME4 and modulates tumor cell proteasome targets. Using this chemical probe together with orthogonal genetic perturbations, we show that blocking or reducing PSME4 stabilizes STAT1, restores interferon-associated transcription, enhances antigen presentation, and disrupts IL-6/STAT3 signaling, collectively reprogramming tumor inflammation and suppressing tumor growth in vivo . These findings define a PSME4-STAT1-STAT3 axis that couples proteasomal degradation to antigen presentation and cytokine signaling and provide a framework for pharmacologically targeting non-catalytic proteasome regulators to reprogram tumor immunity. More broadly, our findings reveal that proteasome composition can actively govern the balance between immunostimulatory and immunosuppressive signaling programs.

Most eukaryotic membrane proteins are inserted into the membrane at the endoplasmic reticulum (ER). This essential process relies on molecular quality control machineries to prevent mistargeting and incorrect structure formation. Here, we show that the ER membrane protein complex (EMC) forms an evolutionarily conserved supercomplex with the P5A-ATPase Spf1/ATP13A1. Biochemical, structural and cellular analyses demonstrate that the EMC and Spf1 associate in a stoichiometric manner and retain their individual catalytic activities, the transmembrane domain (TMD) insertase function of the EMC and the TMD dislocase activity of Spf1. Our cryo-electron microscopy structures show that the EMC insertase cavity and the Spf1 dislocase cleft are positioned in close proximity within the membrane and reveal that the ATPase cycle of Spf1 remodels the interface between the two machineries and alters cytoplasmic accessibility of both substrate-binding cavities. Together, our study provides structural insights into how membrane protein insertion and extraction machineries can be spatially coordinated at the ER membrane, suggesting that functionally distinct proteostasis factors can assemble into hubs to support membrane protein biogenesis and quality control.

The GID/CTLH family of E3 ubiquitin ligases employs several substrate receptor subunits that recruit distinct degrons, but the substrate recognition mechanism of the CTLHMKLN1 assembly has largely remained elusive. Here, we reconstitute CTLHMKLN1-dependent ubiquitylation of three biochemically distinct substrates - MKLN1 itself, ZMYND19, and FAM72A-recruited UNG2, and determine cryo-EM structures of each substrate bound to MKLN1. The structures reveal how MKLN1's discoidin and Kelch β-propeller domains engage substrates through multivalent contacts. MKLN1 recruits itself through discoidin - Kelch interactions between MKLN1 dimers, forming an assembly that competes with other substrates. ZMYND19 and FAM72A each bind to MKLN1 through loops engaging the discoidin trench domain while their C-terminal Arg residues engage the MKLN1 Kelch central channel, identifying MKLN1 as an Arg/C-degron receptor. The acetylated N-terminus of UNG2 is positioned within a Y-shaped tunnel of FAM72A, defining an adaptor-mediated Ac/N-degron recognition mechanism. Thus, our data reveal how combinatorial deployment of MKLN1 discoidin and Kelch domains enable a single receptor subunit to recognize a diverse substrate repertoire, adding to a complex picture of degron recognition across the GID/CTLH family.

FBXO7 and PI31 variants are linked to rare Parkinsonian syndromes, implicating their dysfunction in neurodegeneration. We define how both engage each other and regulate the proteasome 20S core particle (CP). In cells, each can associate independently with the proteasome, with multiple domains in FBXO7 contributing. Utilizing cryo-EM we visualized how FBXO7’s C-terminal domain engages multiple subunits within the CP interior, blocking the β5 peptidase activity. In contrast, we visualized PI31 engagement of all three catalytic sites within the 20S CP, revealing the previously unknown structural basis for β1 inhibition. Furthermore, we establish how disease-associated variants impact both FBXO7 and PI31 function, including disruption of proteasome inhibition and SKP1–FBXO7–PI31 complex assembly. These results establish an unexpected function for FBXO7, providing a mechanistic basis for investigation of its role in proteasome regulation in Parkinson’s disease.

Cellular responses to amino acid fluctuations often hinge on ubiquitin-mediated control of metabolic enzymes, yet the underlying E3 ligase pathways remain poorly defined. Using quantitative proteomics and active cullin-RING ligase (CRL) profiling, we identify LRRC58 as a cysteine-responsive substrate receptor whose stability increases sharply under cysteine starvation. Proteomics reveals an inverse relationship between LRRC58 and the metabolic enzyme cysteine dioxygenase 1 (CDO1), suggesting a cysteine-linked regulatory axis. Biochemical reconstitution and cryo-EM structures show that LRRC58 forms an active CUL2- or CUL5-based CRL that selectively positions CDO1 for ubiquitylation at Lys8. Disease mutant versions of CDO1 mapping to the LRRC58 interface and impaired for the endogenous ubiquitylation pathway were degraded through orthogonal targeting by a VHL-based degrader. Together, our proteomics-guided discovery pipeline, cellular stability studies, and structural analyses uncover a metabolically-tuned LRRC58-CDO1 pathway that links cysteine availability to selective proteasomal turnover, reveals principles of metabolite-regulated CRL activity, and showcases mechanisms distinguishing endogenous and targeted protein degradation.