Cullin-RING E3 Ubiquitin Ligases Research Articles

A multistage Plasmodium CRL4WIG1 ubiquitin ligase is critical for the formation of functional microtubule organization centers in microgametocytes.

Malaria is a mosquito-borne infectious disease caused by unicellular eukaryotic parasites of the Plasmodium genus. Protein ubiquitination by E3 ligases is a critical post-translational modification required for various cellular processes during the lifecycle of Plasmodium parasites. However, little is known about the repertoire and function of these enzymes in Plasmodium. Here, we show that Plasmodium expresses a conserved cullin RING E3 ligase (CRL) complex that is functionally related to CRL4 in other eukaryotes. In P. falciparum asexual blood stages, a cullin-4 scaffold interacts with the RING protein RBX1, the adaptor protein DDB1, and a set of putative receptor proteins that may determine substrate specificity for ubiquitination. These receptor proteins contain WD40-repeat domains and include WD-repeat protein important for gametogenesis 1 (WIG1). This CRL4-related complex is also expressed in P. berghei gametocytes, with WIG1 being the only putative receptor detected in both the schizont and gametocyte stages. WIG1 disruption leads to a complete block in microgamete formation. Proteomic analyses indicate that WIG1 disruption alters proteostasis of ciliary proteins and components of the DNA replication machinery during gametocytogenesis. Further analysis by ultrastructure expansion microscopy (U-ExM) indicates that WIG1-dependent depletion of ciliary proteins is associated with impaired the formation of the microtubule organization centers that coordinate mitosis with axoneme formation and altered DNA replication during microgametogenesis. This work identifies a CRL4-related ubiquitin ligase in Plasmodium that is critical for the formation of microgametes by regulating proteostasis of ciliary and DNA replication proteins.IMPORTANCEPlasmodium parasites undergo fascinating lifecycles with multiple developmental steps, converting into morphologically distinct forms in both their mammalian and mosquito hosts. Protein ubiquitination by ubiquitin ligases emerges as an important post-translational modification required to control multiple developmental stages in Plasmodium. Here, we identify a cullin RING E3 ubiquitin ligase (CRL) complex expressed in the replicating asexual blood stages and in the gametocyte stages that mediate transmission to the mosquito. WIG1, a putative substrate recognition protein of this ligase complex, is essential for the maturation of microgametocytes into microgametes upon ingestion by a mosquito. More specifically, WIG1 is required for proteostasis of ciliary proteins and components of the DNA replication machinery during gametocytogenesis. This requirement is linked to DNA replication and microtubule organization center formation, both critical to the development of flagellated microgametes.

Allosteric degraders induce CRL5 ASB8 mediated degradation of XPO1.

The nuclear export receptor Exportin 1 (XPO1/CRM1) is often overexpressed in cancer cells resulting in aberrant localization of many cancer-related protein cargoes. The XPO1 inhibitor and cancer drug selinexor (KPT-330), and its analog KPT-185, block XPO1-cargo binding thereby restoring cargo localization. Selinexor binding induces cullin-RING E3 ubiquitin ligase (CRL) substrate receptor ASB8-mediated XPO1 degradation. Here we reveal the mechanism of inhibitor-XPO1 engagement by CRL5ASB8. Cryogenic electron microscopy (cryo-EM) structures show ASB8 binding to a large surface of selinexor/KPT-185-XPO1 that includes a three-dimensional degron unique to the drug-bound exportin. The structure explains weak XPO1-ASB8 binding in the absence of selinexor/KPT-185 that is unproductive for proteasomal degradation, and the substantial affinity increase upon selinexor/KPT-185 conjugation, which results in CRL5 ASB8 -mediated XPO1 ubiquitination. In contrast to previously characterized small molecule degraders, which all act as molecular glues, selinexor/KPT-185 binds extensively to XPO1 but hardly contacts ASB8. Instead, selinexor/KPT-185 binds XPO1 and stabilizes a unique conformation of the NES/inhibitor-binding groove that binds ASB8. Selinexor/KPT-185 is an allosteric degrader. We have explained how drug-induced protein degradation is mediated by a CRL5 system through an allosteric rather than a molecular glue mechanism, expanding the modes of targeted protein degradation beyond the well-known molecular glues of CRL4.

RBX1-CRLs Promote Perinatal Heart Development by Regulating Hippo-YAP Signaling

Background: During development, the heart is the first organ to form, ensuring the pumping of blood through the body. Defects in cardiac morphogenesis can lead to congenital heart diseases (CHD) or predispose the heart to cardiomyopathies in adult life. The molecular mechanisms underlying this process remain incompletely understood. Cullin-RING E3 ubiquitin ligases (CRLs) are multi-subunit complexes critical to maintaining protein homeostasis by targeting diverse protein substrates for ubiquitination and subsequent degradation. In CRLs, RBX1 serves as the catalytic subunit that promotes the transfer of ubiquitin to the target protein. Germline ablation of RBX1 in worms, flies, and mice caused embryonic lethality. Deletion of RBX1 in zebrafish resulted in cardiac malformation and dysfunction, which was rescued by endothelial, but not myocardial, RBX1 overexpression. However, the cardiomyocyte-autonomous role of RBX1 in the heart in vertebrates is unknown. Therefore, we hypothesize that cardiomyocyte RBX1 is indispensable for cardiac development. Methods and Results: We generated a cardiomyocyte-specific RBX1 knockout (RBX1CKO) mouse model via αMHCCre. RBX1-deficient mouse embryos were initially morphologically indistinguishable from the littermate controls at E14.5, but began to show peripheral edema and hemorrhage at E16.5, and eventually died around E18.5. Histological analysis of RBX1CKO hearts revealed severe myocardial hypoplasia and bi-ventricular non-compaction by E14.5. Bulk RNA sequencing and proteomic analyses of RBX1CKO hearts identified perturbations in glycolytic to oxidative transition and dysregulation of sarcomeric proteins. EdU incorporation assay showed a significant reduction in cardiomyocyte proliferation in E14.5 RBX1-deficient hearts, accompanied by the impaired nuclear translocation of YAP, a co-transcriptional factor essential for cardiomyocyte proliferation and maturation. Mechanistically, RBX1 deficiency destabilized multiple CRLs and resulted in the accumulation of Hippo kinases and adaptor proteins such as SAV1, LATS1/2, and MOB1, leading to the elevated phosphorylation and inactivation of YAP. We further demonstrated that loss of RBX1 inhibited the degradation of the Hippo adaptor MOB1, likely due to suppressed ubiquitination. Conclusion: Our study identifies RBX1 as an essential regulator of ventricular maturation and found that RBX1-mediated proteolysis of Hippo kinases serves as a critical checkpoint to ensure YAP activation and, hence, cardiomyocyte proliferation and maturation during cardiac development. AHA Predoctoral Fellowship, American Heart Association, 23PRE1012641. This is the full abstract presented at the American Physiology Summit 2024 meeting and is only available in HTML format. There are no additional versions or additional content available for this abstract. Physiology was not involved in the peer review process.

Regulation of NKCC2 Ubiquitination by baSubstrate Recognition Adaptor FBXL13 in Thick Ascending Limbs

NaCl reabsorption by the thick ascending limb (TAL) is mediated by the Na/K/2Cl cotransporter (NKCC2). Nitric Oxide and atrial natriuretic peptide decrease NaCl absorption in the TAL by increasing the second messenger cyclic guanosine monophosphate (cGMP). We recently showed that NKCC2 is constitutively ubiquitinated, and cGMP enhances the rate of ubiquitination. The cGMP-dependent increase in NKCC2 ubiquitination is mediated by the CRL (Cullin-Ring-E3 ubiquitin Ligase) complex, which is the largest family of E3 ubiquitin ligase in mammals. By using a targeted proteomics approach, we identified a substrate recognition adaptor F-Box leucine-rich repeat 13 (FBXL13) that bind the NH2-terminus portion of NKCC2. FBXL13 is expressed in rats TALs and co-immunoprecipitates with NKCC2. Therefore, we hypothesized that the substrate recognition adaptor FBXL13 mediates NKCC2 ubiquitination. To test our hypothesis, we generated a global FBXL13 knockout mice by crossing FBXL13-Flox with a global Cre mice. We confirmed the deletion of FBXL13 in tail by PCR and in TALs by Western blot. First, we studied whether deletion of FBXL13 affects total NKCC2 expression. For this, TALs from FBXL13-Flox and FBXL13-KO mice were lysed, and equal amount of protein resolved by SDS-PAGE and detected by Western blot. We found that total NKCC2 expression in FBXL13-KO mice is increased by 73% (FBXL13-Flox: 100% vs. FBXL13-KO mice: 173 ± 37%, p<0.05). These data suggest that NKCC2 has been accumulated and not degraded. We tested whether FBXL13 mediates the cGMP-dependent increase on NKCC2 ubiquitination. TALs from FBXL13-Flox control mice and FBXL13-KO mice were incubated at 37°C during proteasome inhibition with MG132 and treated with vehicle or db-cGMP 500μM. Ubiquitinated proteins were pulled down and NKCC2 measured by Western blot. We found that cGMP increased NKCC2 ubiquitination by 24 ± 10% in FBXL13-Flox mice, whereas this effect was completely absent in FBXL13-KO mice (-14 ± 12%, p<0.05). These data suggest that FBXL13 mediates the cGMP-dependent increase in NKCC2 ubiquitination in native TALs. Finally, we study the role of FBXL13 on renal function by measuring bumetanide-induced natriuresis. Bumetanide is a loop diuretic that specifically inhibits NKCC2. We observed that the FBXL13-KO mice has higher bumetanide-induced Na+ excretion (Flox: 88.8 ± 6.6 μmol Na+ vs. FBXL13-KO: 124.0 ± 14.6 μmol Na+, p<0.05). These data are in alignment with the results previous since higher bumetanide-induced natriuresis response would result with higher NKCC2 expression. We conclude that the cGMP-dependent increase in NKCC2 ubiquitination is mediated by the novel substrate recognition adaptor FBXL13. To our knowledge, this is the first evidence showing a substrate recognition adaptor FBXL13 that interacts with NKCC2 in native TALs. NIH - 1K01DK123192. This is the full abstract presented at the American Physiology Summit 2024 meeting and is only available in HTML format. There are no additional versions or additional content available for this abstract. Physiology was not involved in the peer review process.

Plasmodium falciparum contains functional SCF and CRL4 ubiquitin E3 ligases, and CRL4 is critical for cell division and membrane integrity.

Protein ubiquitination is essential for cellular homeostasis and regulation of several processes, including cell division and genome integrity. Ubiquitin E3 ligases determine substrate specificity for ubiquitination, and Cullin-RING E3 ubiquitin ligases (CRLs) make the largest group among the ubiquitin E3 ligases. Although conserved and most studied in model eukaryotes, CRLs remain underappreciated in Plasmodium and related parasites. To investigate the CRLs of human malaria parasite Plasmodium falciparum, we generated parasites expressing tagged P. falciparum cullin-1 (PfCullin-1), cullin-2 (PfCullin-2), Rbx1 (PfRbx1) and Skp1 (PfSkp1). PfCullin-1 and PfCullin-2 were predominantly expressed in erythrocytic trophozoite and schizont stages, with nucleocytoplasmic localization and chromatin association, suggesting their roles in different cellular compartments and DNA-associated processes. Immunoprecipitation, in vitro protein-protein interaction, and ubiquitination assay confirmed the presence of a functional Skp1-Cullin-1-Fbox (PfSCF) complex, comprising of PfCullin-1, PfRbx1, PfSkp1, PfFBXO1, and calcyclin binding protein. Immunoprecipitation, sequence analysis, and ubiquitination assay indicated that PfCullin-2 forms a functional human CRL4-like complex (PfCRL4), consisting of PfRbx1, cleavage and polyadenylation specificity factor subunit_A and WD40 repeat proteins. PfCullin-2 knock-down at the protein level, which would hinder PfCRL4 assembly, significantly decreased asexual and sexual erythrocytic stage development. The protein levels of several pathways, including protein translation and folding, lipid biosynthesis and transport, DNA replication, and protein degradation were significantly altered upon PfCullin-2 depletion, which likely reflects association of PfCRL4 with multiple pathways. PfCullin-2-depleted schizonts had poorly delimited merozoites and internal membraned structures, suggesting a role of PfCRL4 in maintaining membrane integrity. PfCullin-2-depleted parasites had a significantly lower number of nuclei/parasite than the normal parasites, indicating a crucial role of PfCRL4 in cell division. We demonstrate the presence of functional CRLs in P. falciparum, with crucial roles for PfCRL4 in cell division and maintaining membrane integrity.

Genome-Wide Identification and Analysis of APC E3 Ubiquitin Ligase Genes Family in Triticum aestivum.

E3 ubiquitin ligases play a pivotal role in ubiquitination, a crucial post-translational modification process. Anaphase-promoting complex (APC), a large cullin-RING E3 ubiquitin ligase, regulates the unidirectional progression of the cell cycle by ubiquitinating specific target proteins and triggering plant immune responses. Several E3 ubiquitin ligases have been identified owing to advancements in sequencing and annotation of the wheat genome. However, the types and functions of APC E3 ubiquitin ligases in wheat have not been reported. This study identified 14 members of the APC gene family in the wheat genome and divided them into three subgroups (CCS52B, CCS52A, and CDC20) to better understand their functions. Promoter sequence analysis revealed the presence of several cis-acting elements related to hormone and stress responses in the APC E3 ubiquitin ligases in wheat. All identified APC E3 ubiquitin ligase family members were highly expressed in the leaves, and the expression of most genes was induced by the application of methyl jasmonate (MeJA). In addition, the APC gene family in wheat may play a role in plant defense mechanisms. This study comprehensively analyzes APC genes in wheat, laying the groundwork for future research on the function of APC genes in response to viral infections and expanding our understanding of wheat immunity mechanisms.

Structural insights into the ubiquitylation strategy of the oligomeric CRL2FEM1B E3 ubiquitin ligase

Cullin-RING E3 ubiquitin ligase (CRL) family members play critical roles in numerous biological processes and diseases including cancer and Alzheimer’s disease. Oligomerization of CRLs has been reported to be crucial for the regulation of their activities. However, the structural basis for its regulation and mechanism of its oligomerization are not fully known. Here, we present cryo-EM structures of oligomeric CRL2FEM1B in its unneddylated state, neddylated state in complex with BEX2 as well as neddylated state in complex with FNIP1/FLCN. These structures reveal that asymmetric dimerization of N8-CRL2FEM1B is critical for the ubiquitylation of BEX2 while FNIP1/FLCN is ubiquitylated by monomeric CRL2FEM1B. Our data present an example of the asymmetric homo-dimerization of CRL. Taken together, this study sheds light on the ubiquitylation strategy of oligomeric CRL2FEM1B according to substrates with different scales.

Monoubiquitination empowers ubiquitin chain elongation

Ubiquitination often generates lysine 48-linked polyubiquitin chains that signal proteolytic destruction of the protein target. A significant subset of ubiquitination proceeds by a priming/extending mechanism, in which a substrate is first mono-ubiquitinated with a priming E2 conjugating enzyme or a set of E3 ARIH/E2 enzymes specific for priming. This is then followed by ubiquitin chain extension catalyzed by an E2 enzyme capable of elongation. This report provides further insights into the priming/extending mechanism. We employed reconstituted ubiquitination systems of substrates CK1α and β-catenin by Cullin-RING E3 ubiquitin ligases (CRLs) CRL4CRBN and CRL1βTrCP, respectively, in the presence of priming E2 UbcH5c and elongating E2 Cdc34b. We have established a new “Apyrase chase” strategy that uncouples priming from chain elongation, which allows accurate measurement of the decay rates of the ubiquitinated substrate with a defined chain length. Our work has revealed highly robust turnover of mono-ubiquitinated β-catenin that empowers efficient polyubiquitination. The results of competition experiments suggest that the interactions between the ubiquitinated β-catenin and CRL1βTrCP are highly dynamic. Moreover, ubiquitination of the ubiquitin-modified β-catenin appeared more resistant to inhibition by competitors than the unmodified substrate, suggesting tighter binding with CRL1βTrCP. These findings support a role for conjugated ubiquitin in enhancing interactions with E3.

Exploiting the Cullin E3 Ligase Adaptor Protein SKP1 for Targeted Protein Degradation.

Targeted protein degradation with proteolysis targeting chimeras (PROTACs) is a powerful therapeutic modality for eliminating disease-causing proteins through targeted ubiquitination and proteasome-mediated degradation. Most PROTACs have exploited substrate receptors of Cullin-RING E3 ubiquitin ligases such as cereblon and VHL. Whether core, shared, and essential components of the Cullin-RING E3 ubiquitin ligase complex can be used for PROTAC applications remains less explored. Here, we discovered a cysteine-reactive covalent recruiter EN884 against the SKP1 adapter protein of the SKP1-CUL1-F-box containing the SCF complex. We further showed that this recruiter can be used in PROTAC applications to degrade neo-substrate proteins such as BRD4 and the androgen receptor in a SKP1- and proteasome-dependent manner. Our studies demonstrate that core and essential adapter proteins within the Cullin-RING E3 ubiquitin ligase complex can be exploited for targeted protein degradation applications and that covalent chemoproteomic strategies can enable recruiter discovery against these targets.

CRL4b Inhibition Ameliorates Experimental Autoimmune Encephalomyelitis Progression.

Multiple sclerosis, and its murine model experimental autoimmune encephalomyelitis (EAE), is a neurodegenerative autoimmune disease of the CNS characterized by T cell influx and demyelination. Similar to other autoimmune diseases, therapies can alleviate symptoms but often come with side effects, necessitating the exploration of new treatments. We recently demonstrated that the Cullin-RING E3 ubiquitin ligase 4b (CRL4b) aided in maintaining genome stability in proliferating T cells. In this study, we examined whether CRL4b was required for T cells to expand and drive EAE. Mice lacking Cul4b (Cullin 4b) in T cells had reduced EAE symptoms and decreased inflammation during the peak of the disease. Significantly fewer CD4+ and CD8+ T cells were found in the CNS, particularly among the CD4+ T cell population producing IL-17A, IFN-γ, GM-CSF, and TNF-α. Additionally, Cul4b-deficient CD4+ T cells cultured invitro with their wild-type counterparts were less likely to expand and differentiate into IL-17A- or IFN-γ-producing effector cells. When wild-type CD4+ T cells were activated invitro in the presence of the recently developed CRL4 inhibitor KH-4-43, they exhibited increased apoptosis and DNA damage. Treatment of mice with KH-4-43 following EAE induction resulted in stabilized clinical scores and significantly reduced numbers of T cells and innate immune cells in the CNS compared with control mice. Furthermore, KH-4-43 treatment resulted in elevated expression of p21 and cyclin E2 in T cells. These studies support that therapeutic inhibition of CRL4 and/or CRL4-related pathways could be used to treat autoimmune disease.

Targeted Protein Degradation through Recruitment of the CUL4 Complex Adaptor Protein DDB1.

Targeted protein degradation has arisen as a powerful therapeutic modality for eliminating proteins. Thus far, most heterobifunctional proteolysis targeting chimeras (PROTACs) have utilized recruiters against substrate receptors of Cullin RING E3 ubiquitin ligases, such as cereblon and VHL. However, previous studies have surprisingly uncovered molecular glue degraders that exploit a CUL4 adaptor protein DDB1 to degrade neosubstrate proteins. Here, we sought to investigate whether DDB1 recruiters can be discovered that can be exploited for PROTAC applications. We utilized activity-based protein profiling and cysteine chemoproteomic screening to identify a covalent recruiter that targets C173 on DDB1 and exploited this recruiter to develop PROTACs against BRD4 and androgen receptor (AR). We demonstrated that the BRD4 PROTAC results in selective degradation of the short BRD4 isoform over the long isoform in a proteasome, NEDDylation, and DDB1-dependent manner. We also demonstrated degradation of AR with the AR PROTAC in prostate cancer cells. Our study demonstrated that covalent chemoproteomic approaches can be used to discover recruiters against Cullin RING adapter proteins and that these recruiters can be used for PROTAC applications to degrade neo-substrates.

Cullin5 drives experimental asthma exacerbations by modulating alveolar macrophage antiviral immunity

Asthma exacerbations caused by respiratory viral infections are a serious global health problem. Impaired antiviral immunity is thought to contribute to the pathogenesis, but the underlying mechanisms remain understudied. Here using mouse models we find that Cullin5 (CUL5), a key component of Cullin-RING E3 ubiquitin ligase 5, is upregulated and associated with increased neutrophil count and influenza-induced exacerbations of house dust mite-induced asthma. By contrast, CUL5 deficiency mitigates neutrophilic lung inflammation and asthma exacerbations by augmenting IFN-β production. Mechanistically, following thymic stromal lymphopoietin stimulation, CUL5 interacts with O-GlcNAc transferase (OGT) and induces Lys48-linked polyubiquitination of OGT, blocking the effect of OGT on mitochondrial antiviral-signaling protein O-GlcNAcylation and RIG-I signaling activation. Our results thus suggest that, in mouse models, pre-existing allergic injury induces CUL5 expression, impairing antiviral immunity and promoting neutrophilic inflammation for asthma exacerbations. Targeting of the CUL5/IFN-β signaling axis may thereby serve as a possible therapy for treating asthma exacerbations.

CRL2APPBP2-mediated TSPYL2 degradation counteracts human mesenchymal stem cell senescence.

Cullin-RING E3 ubiquitin ligases (CRLs), the largest family of multi-subunit E3 ubiquitin ligases in eukaryotic cells, represent core cellular machinery for executing protein degradation and maintaining proteostasis. Here, we asked what roles Cullin proteins play in human mesenchymal stem cell (hMSC) homeostasis and senescence. To this end, we conducted a comparative aging phenotype analysis by individually knocking down Cullin members in three senescence models: replicative senescent hMSCs, Hutchinson-Gilford Progeria Syndrome hMSCs, and Werner syndrome hMSCs. Among all family members, we found that CUL2 deficiency rendered hMSCs the most susceptible to senescence. To investigate CUL2-specific underlying mechanisms, we then applied CRISPR/Cas9-mediated gene editing technology to generate CUL2-deficient human embryonic stem cells (hESCs). When we differentiated these into hMSCs, we found that CUL2 deletion markedly accelerates hMSC senescence. Importantly, we identified that CUL2 targets and promotes ubiquitin proteasome-mediated degradation of TSPYL2 (a known negative regulator of proliferation) through the substrate receptor protein APPBP2, which in turn down-regulates one of the canonical aging marker-P21waf1/cip1, and thereby delays senescence. Our work provides important insights into how CRL2APPBP2-mediated TSPYL2 degradation counteracts hMSC senescence, providing a molecular basis for directing intervention strategies against aging and aging-related diseases.

Molecular basis for C-degron recognition by CRL2APPBP2 ubiquitin ligase

E3 ubiquitin ligases determine the specificity of eukaryotic protein degradation by selective binding to destabilizing protein motifs, termed degrons, in substrates for ubiquitin-mediated proteolysis. The exposed C-terminal residues of proteins can act as C-degrons that are recognized by distinct substrate receptors (SRs) as part of dedicated cullin-RING E3 ubiquitin ligase (CRL) complexes. APPBP2, an SR of Cullin 2-RING ligase (CRL2), has been shown to recognize R-x-x-G/C-degron; however, the molecular mechanism of recognition remains elusive. By solving several cryogenic electron microscopy structures of active CRL2APPBP2 bound with different R-x-x-G/C-degrons, we unveiled the molecular mechanisms underlying the assembly of the CRL2APPBP2 dimer and tetramer, as well as C-degron recognition. The structural study, complemented by binding experiments and cell-based assays, demonstrates that APPBP2 specifically recognizes the R-x-x-G/C-degron via a bipartite mechanism; arginine and glycine, which play critical roles in C-degron recognition, accommodate distinct pockets that are spaced by two residues. In addition, the binding pocket is deep enough to enable the interaction of APPBP2 with the motif placed at or up to three residues upstream of the C-end. Overall, our study not only provides structural insight into CRL2APPBP2-mediated protein turnover but also serves as the basis for future structure-based chemical probe design.

Unlocking DCAFs To Catalyze Degrader Development: An Arena for Innovative Approaches.

Chemically induced proximity-based targeted protein degradation (TPD) has become a prominent paradigm in drug discovery. With the clinical benefit demonstrated by certain small-molecule protein degraders that target the cullin-RING E3 ubiquitin ligases (CRLs), the field has proactively strategized to tackle anticipated drug resistance by harnessing additional E3 ubiquitin ligases to enrich the arsenal of this therapeutic approach. Here, we endeavor to explore the collaborative efforts involved in unlocking a broad range of CRL4DCAF for degrader drug development. Throughout the discussion, we also highlight how both conventional and innovative approaches in drug discovery can be taken to realize this objective. Moving ahead, we expect a greater allocation of resources in TPD to pursue these high-hanging fruits.

The Highs and Lows of FBXW7: New Insights into Substrate Affinity in Disease and Development.

FBXW7 is a critical regulator of cell cycle, cell signaling, and development. A highly conserved F-box protein and component of the SKP1-Cullin-F-box (SCF) complex, FBXW7 functions as a recognition subunit within a Cullin-RING E3 ubiquitin ligase responsible for ubiquitinating substrate proteins and targeting them for proteasome-mediated degradation. In human cells, FBXW7 promotes degradation of a large number of substrate proteins, including many that impact disease, such as NOTCH1, Cyclin E, MYC, and BRAF. A central focus for investigation has been to understand the molecular mechanisms that allow the exquisite substrate specificity exhibited by FBXW7. Recent work has produced a clearer understanding of how FBXW7 physically interacts with both high-affinity and low-affinity substrates. We review new findings that provide insights into the consequences of "hotspot" missense mutations of FBXW7 that are found in human cancers. Finally, we discuss how the FBXW7-substrate interaction, and the kinases responsible for substrate phosphorylation, contribute to patterned protein degradation in C. elegans development.

Deficiency of Cullin 3, a Protein Encoded by a Schizophrenia and Autism Risk Gene, Impairs Behaviors by Enhancing the Excitability of Ventral Tegmental Area (VTA) DA Neurons.

The dopaminergic neuromodulator system is fundamental to brain functions. Abnormal dopamine (DA) pathway is implicated in psychiatric disorders, including schizophrenia (SZ) and autism spectrum disorder (ASD). Mutations in Cullin 3 (CUL3), a core component of the Cullin-RING ubiquitin E3 ligase complex, have been associated with SZ and ASD. However, little is known about the function and mechanism of CUL3 in the DA system. Here, we show that CUL3 is critical for the function of DA neurons and DA-relevant behaviors in male mice. CUL3-deficient mice exhibited hyperactive locomotion, deficits in working memory and sensorimotor gating, and increased sensitivity to psychostimulants. In addition, enhanced DA signaling and elevated excitability of the VTA DA neurons were observed in CUL3-deficient animals. Behavioral impairments were attenuated by dopamine D2 receptor antagonist haloperidol and chemogenetic inhibition of DA neurons. Furthermore, we identified HCN2, a hyperpolarization-activated and cyclic nucleotide-gated channel, as a potential target of CUL3 in DA neurons. Our study indicates that CUL3 controls DA neuronal activity by maintaining ion channel homeostasis and provides insight into the role of CUL3 in the pathogenesis of psychiatric disorders.SIGNIFICANCE STATEMENT This study provides evidence that Cullin 3 (CUL3), a core component of the Cullin-RING ubiquitin E3 ligase complex that has been associated with autism spectrum disorder and schizophrenia, controls the excitability of dopamine (DA) neurons in mice. Its DA-specific heterozygous deficiency increased spontaneous locomotion, impaired working memory and sensorimotor gating, and elevated response to psychostimulants. We showed that CUL3 deficiency increased the excitability of VTA DA neurons, and inhibiting D2 receptor or DA neuronal activity attenuated behavioral deficits of CUL3-deficient mice. We found HCN2, a hyperpolarization-activated channel, as a target of CUL3 in DA neurons. Our findings reveal CUL3's role in DA neurons and offer insights into the pathogenic mechanisms of autism spectrum disorder and schizophrenia.

The CUL4B‐based E3 ubiquitin ligase regulates mitosis and brain development by recruiting phospho‐specific DCAFs

The paralogs CUL4A and CUL4B assemble cullin‐RING E3 ubiquitin ligase (CRL) complexes regulating multiple chromatin‐associated cellular functions. Although they are structurally similar, we found that the unique N‐terminal extension of CUL4B is heavily phosphorylated during mitosis, and the phosphorylation pattern is perturbed in the CUL4B‐P50L mutation causing X‐linked intellectual disability (XLID). Phenotypic characterization and mutational analysis revealed that CUL4B phosphorylation is required for efficient progression through mitosis, controlling spindle positioning and cortical tension. While CUL4B phosphorylation triggers chromatin exclusion, it promotes binding to actin regulators and to two previously unrecognized CUL4B‐specific substrate receptors (DCAFs), LIS1 and WDR1. Indeed, co‐immunoprecipitation experiments and biochemical analysis revealed that LIS1 and WDR1 interact with DDB1, and their binding is enhanced by the phosphorylated N‐terminal domain of CUL4B. Finally, a human forebrain organoid model demonstrated that CUL4B is required to develop stable ventricular structures that correlate with onset of forebrain differentiation. Together, our study uncovers previously unrecognized DCAFs relevant for mitosis and brain development that specifically bind CUL4B, but not the CUL4B‐P50L patient mutant, by a phosphorylation‐dependent mechanism.

Omaveloxolone (SkyclarysTM) for patients with Friedreich’s ataxia

STRUCTURE: Omaveloxolone {N-[(4aS,6aR,6bS,8aR,12aS,14aR,14bS)-11-cyano-2,2,6a,6b, 9,9,12a-heptamethyl-10,14-dioxo-1,2,3,4,4a,5,6,6a,6b,7,8,8a,9,10,12a,14,14a,14b-octa-decahydropicen-4a-yl]-2,2-difluoropropanamide} is a semisynthetic triterpenoid based on the natural product oleanolic acid. It contains a highly reactive cyanoenone functionality, which binds covalently and reversibly by Michael addition to cysteines in proteins, such as the cysteine-based sensor protein Kelch-like ECH-associated protein 1 (KEAP1). The molecular formula of omaveloxolone is C33H44F2N2O3 and its molecular weight is 554.7 g/mol. MECHANISM OF ACTION: The pathophysiology of Friedreich’s ataxia is associated with an expansion of GAA repeats in the first intron of FXN encoding the small mitochondrial protein frataxin (FXN), which has a role in mitochondrial homeostasis and iron metabolism. FXN deficiency leads to impaired mitochondrial function and increased production of reactive oxygen species (ROS) (1), in turn causing inflammation with further ROS production, creating a vicious cycle that ultimately results in cellular dysfunction (2). Omaveloxolone is an inducer of a network of endogenous cytoprotective proteins regulated by transcription factor nuclear factor-erythroid 2 p45-related factor 2 (NRF2), the master regulator of cellular redox homeostasis. At basal state, the levels of NRF2 are low due to its continuous proteasomal degradation (3) mediated by KEAP1, a substrate adapter of a Cullin-RING E3 ubiquitin ligase. Omaveloxolone (pink circle), via its cyanoenone functionality, binds to sensor cysteines (primarily C151) in KEAP1 and inactivates it (4). As a result, the newly synthesized NRF2 accumulates, forms a heterodimer with a small musculoaponeurotic fibrosarcoma (sMAF) protein, and induces transcription of its target genes by binding to the antioxidant response element (ARE) sequences in their regulatory regions. The NRF2-transcriptional network encompasses an array of broadly cytoprotective proteins (5), including those responsible for the biosynthesis of glutathione (GSH). Collectively, the NRF2 transcriptional targets counteract oxidative and inflammatory stress, and support proteostasis, mitochondrial function, and bioenergetics. Omaveloxolone also inhibits inflammation, in part via NRF2 (which inhibits transcription of proinflammatory genes) and, in part, due to its potential to bind to cysteines in proteins involved in inflammatory cascades (e.g., IKKβ, shown in beige). Omaveloxolone (also known as RTA-408); brand name is SKYCLARYS. Omaveloxolone is the first and only FDA-approved drug for patients with Friedreich’s ataxia. Omaveloxolone has received Orphan Drug, Fast Track, and Rare Pediatric Disease Designations from the FDA, and Orphan Drug Designation for the treatment of Friedreich’s ataxia from the European Commission. It is currently not approved outside of the USA. SKYCLARYS™ is approved in the USA by the FDA and is indicated for the treatment of Friedreich’s ataxia in adults and adolescents aged 16 years and older. The recommended dosage is 150 mg to be taken orally daily. Reata Pharmaceuticals. Headache (37%), nausea (33%), diarrhea (20%), abdominal pain (29%), fatigue (24%), musculoskeletal pain (20%), vomiting (16%), oropharyngeal pain (18%), influenza (16%), muscle spasms (14%), back pain (13%), decreased appetite (12%), rash (10%). The most common laboratory abnormalities (occurring in 37% of patients) are elevated aspartate/alanine transaminases. In clinical trials, most effects diminished or stopped after 12 weeks of treatment. 2014–2020: Phase 1 trials (NCT02029716, NCT03664453, NCT04008186) 2014–present: Phase 2 trials (NCT02255435, NCT02029729, NCT02142959, NCT02128113, NCT03902002, NCT02255422) February 2023: FDA approval for SKYCLARYS™ (omaveloxolone). We thank the Medical Research Council (MR/W023806/1 and MR/T014644/1), the Biotechnology and Biological Sciences Research Council and GlaxoSmithKline (BB/T508111/1, BB/X00029X/1, and BB/T017546/1), Tenovus Scotland (T19/30 and T22/08), Reata Pharmaceuticals, and Medical Research Scotland (PHD-50477-2021) for supporting our research and the COST Action CA20121, supported by the European Cooperation in Science and Technology (www.cost.eu) (https://benbedphar.org/about-benbedphar/). A.T. D.-K. is a member of the Scientific Advisory Board of Evgen Pharma and collaborates with GlaxoSmithKline and Reata Pharmaceuticals. S.D.N. has no interests to declare.

Ubiquitination of NKCC2 by the cullin-RING E3 ubiquitin ligase family in the thick ascending limb of the loop of Henle.

The Na+/K+/2Cl- cotransporter (NKCC2) in the thick ascending limb of the loop of Henle (TAL) mediates NaCl reabsorption. cGMP, the second messenger of nitric oxide and atrial natriuretic peptide, inhibits NKCC2 activity by stimulating NKCC2 ubiquitination and decreasing surface NKCC2 levels. Among the E3 ubiquitin ligase families, the cullin-RING E3 ubiquitin ligase (CRL) family is the largest. Cullins are molecular scaffold proteins that recruit multiple subunits to form the CRL complex. We hypothesized that a CRL complex mediates the cGMP-dependent increase in NKCC2 ubiquitination in TALs. Cullin-1, cullin-2, cullin-3, cullin-4A, and cullin-5 were expressed at the protein level, whereas the other members of the cullin family were expressed at the mRNA level, in rat TALs. CRL complex activity is regulated by neuronal precursor cell-expressed developmentally downregulated protein 8 (Nedd8) to cullins, a process called neddylation. Inhibition of cullin neddylation blunted the cGMP-dependent increase in ubiquitinated NKCC2 while increasing the expression of cullin-1 by threefold, but this effect was not seen with other cullins. CRL complex activity is also regulated by cullin-associated Nedd8-dissociated 1 (CAND1). CAND1 binds to cullins and promotes the exchange of substrate-recognition proteins to target different proteins for ubiquitination. CAND1 inhibition exacerbated the cGMP-dependent increase in NKCC2 ubiquitination and decreased surface NKCC2 expression. Finally, cGMP increased neddylation of cullins. We conclude that the cGMP-dependent increase in NKCC2 ubiquitination is mediated by a CRL complex. To the best of our knowledge, this is the first evidence that a CRL complex mediates NKCC2 ubiquitination in native TALs.NEW & NOTEWORTHY The Na+/K+/2Cl- cotransporter (NKCC2) reabsorbs NaCl by the thick ascending limb. Nitric oxide and atrial natriuretic peptide decrease NaCl reabsorption in thick ascending limbs by increasing the second messenger cGMP. The present findings indicate that cGMP increases NKCC2 ubiquitination via a cullin-RING ligase complex and regulates in part surface NKCC2 levels. Identifying the E3 ubiquitin ligases that regulate NKCC2 expression and activity may provide new targets for the development of specific loop diuretics.