Mahogunin Ring Finger-1 (MGRN1) E3 Ubiquitin Ligase Inhibits Signaling from Melanocortin Receptor by Competition with G��s

Mahogunin ring finger-1 (MGRN1) is a RING domain-containing ubiquitin ligase mutated in mahoganoid, a mouse mutation causing coat color darkening, congenital heart defects, high embryonic lethality, and spongiform neurodegeneration. The melanocortin hormones regulate pigmentation, cortisol production, food intake, and body weight by signaling through five G protein-coupled receptors positively coupled to the cAMP pathway (MC1R–MC5R). Genetic analysis has shown that mouse Mgrn1 is an accessory protein for melanocortin signaling that may inhibit MC1R and MC4R by unknown mechanisms. These melanocortin receptors (MCRs) regulate pigmentation and body weight, respectively. We show that human melanoma cells express 4 MGRN1 isoforms differing in the C-terminal exon 17 and in usage of exon 12. This exon contains nuclear localization signals. MGRN1 isoforms decreased MC1R and MC4R signaling to cAMP, without effect on β₂-adrenergic receptor. Inhibition was independent on receptor plasma membrane expression, ubiquitylation, internalization, or stability and occurred upstream of Gα_s binding to/activation of adenylyl cyclase. MGRN1 co-immunoprecipitated with MCRs, suggesting a physical interaction of the proteins. Significantly, overexpression of Gα_s abolished the inhibitory effect of MGRN1 and decreased co-immunoprecipitation with MCRs, suggesting competition between MGRN1 and Gα_s for binding to MCRs. Although all MGRN1s were located in the cytosol in the absence of MCRs, exon 12-containing isoforms accumulated in the nuclei upon co-expression with the receptors. Therefore, MGRN1 inhibits MCR signaling by a new mechanism involving displacement of Gα_s, thus accounting for key features of the mahoganoid phenotype. Moreover, MGRN1 might provide a novel pathway for melanocortin signaling from the cell surface to the nucleus.     

Identification of Integrin α3 as a New Substrate of the Adenovirus E4orf6/E1B 55-Kilodalton E3 Ubiquitin Ligase Complex

The human adenovirus E4orf6 and E1B55K proteins promote viral replication by targeting several cellular proteins for degradation. The E4orf6 product has been shown by our group and others to form an E3 ubiquitin ligase complex that contains elongins B and C and cullin family member Cul5. E1B55K associates with this complex, where it is believed to function primarily to introduce bound substrates for degradation via proteasomes. In addition to p53, its first known substrate, the E4orf6/E1B 55-kDa complex (E4orf6/E1B55K) was shown to promote the degradation of Mre11 and DNA ligase IV; however, additional substrates are believed to exist. This notion is strengthened by the fact that none of these substrates seems likely to be associated with additional functions shown to be mediated by the E4orf6-associated E3 ubiquitin ligase complex, including export of late viral mRNAs and blockage of export of the bulk cellular mRNAs from the nucleus. In an attempt to identify new E4orf6/E1B55K substrates, we undertook a proteomic screen using human p53-null, non-small-cell lung carcinoma H1299 cells expressing either E4orf6 protein alone or in combination with E1B55K through infection by appropriate adenovirus vectors. One cellular protein that appeared to be degraded by E1B55K in combination with the E4orf6 protein was a species of molecular mass ∼130 kDa that was identified as the integrin α3 subunit (i.e., very late activation antigen 3 alpha subunit). Preliminary analyses suggested that degradation of α3 may play a role in promoting release and spread of progeny virions.Viruses are well known to promote replication by inhibiting or enhancing endogenous cellular machinery or, in some cases, by reprogramming key cellular pathways. Human adenoviruses have developed effective ways to modulate the immune response, apoptosis, double-strand break repair, mRNA export, and translation to optimize virus replication and the spreading of progeny virions. The expression of adenovirus E1A proteins stabilizes p53 and induces apoptosis (8, 33); however, this effect is reversed in infected cells by the action of two early products: the E1B 55-kDa (E1B55K) and E4orf6 proteins (35, 36). We and others have shown that these proteins act through the formation of an E3 ubiquitin ligase complex analogous to the SCF and VBC complexes but which contains, in addition to elongins B and C and the RING protein Rbx1, the cullin family member Cul5 (18, 41, 43). This E4orf6-mediated E3 ligase complex blocks p53-induced apoptosis (35, 36) by promoting the ubiquitination of p53, followed by its degradation by proteasomes (41, 43). E4orf6 protein mediates the assembly of the complex by its interaction with elongin C through its three BC boxes (11, 41, 43). E1B55K, which appears to associate with the E4orf6 protein only when present in the ligase complex (4), is thought to function as a substrate recognition factor that brings substrates to the complex because, although both E4orf6 and E1B55K bind p53 independently, interaction of E1B55K with p53 is essential for the efficient degradation of p53 (41, 48). In addition to protecting infected cells from early lysis via p53-induced apoptosis, the E4orf6/E1B55K ligase complex performs other functions essential for virus replication. Two other substrates of the complex have been identified: a member of the MRN DNA repair complex, Mre11, and the central component of the nonhomologous end-joining DNA repair system, DNA ligase IV (2, 56). Degradation of both of these proteins prevents viral genome concatenation, which interferes with the packaging of viral DNA into virions (2, 56). E1B55K binds to p53, Mre11, and DNA ligase IV and has been demonstrated to colocalize with p53 and Mre11 in perinuclear cytoplasmic bodies termed aggresomes (1, 2, 32). More recently, we and others have obtained results that suggest that the E4orf6-associated E3 ligase complex regulates viral and cellular mRNA export (5, 66). The Cul5-based ligase activity was shown to be essential for selective viral mRNA export and the block of cellular mRNA export from the nucleus (66), thus contributing to the shutoff of cellular protein synthesis initiated by L4-100K (20). The actual substrates of the complex responsible for regulating mRNA export are currently unknown.As discussed in detail below, our efforts to identify substrates of the E4orf6/E1B55K complex led us to consider a member of the integrin family as a potential substrate. Integrins are members of a family of surface receptors that function in several ways through the formation of cell-extracellular matrices and cell-cell interactions (reviewed in references 21, 26, and 63). Integrins are typically composed of two transmembrane glycoproteins forming heterodimers of α and β subunits each of approximately 80 to 150 kDa. There are at least 18 α subunits and 8 β subunits in mammals that can dimerize in limited combinations to form more than 20 functionally distinct integrins with different ligand specificities. Integrin heterodimers function as transmembrane receptors that link external factors to intracellular signaling pathways. In addition to roles in cell adhesion, these communication events are implicated in a large range of cellular processes, including proliferation, differentiation, translation, migration, and apoptosis. Some of these processes depend on the intracellular trafficking pathways of the integrins (reviewed in references 9, 24, 40, and 44), including the long-loop recycling pathway in which integrins present in clathrin-coated endosomes move first to the perinuclear recycling center, where some accumulate, including the β1 integrin subunit (31), before returning to the plasma membrane. The integrin α3β1 is a member of the β1 integrin subfamily in which the α3 subunit (VLA-3a) is coupled to the β1 subunit to form the very late activation antigen (VLA-3 or CD49c) (21, 59, 60). α3β1 is expressed in a wide range of tissues in which it binds a variety of extracellular matrix substrates, including fibronectin, collagen, thrombospondin 1, and laminins 1, 5, 8, 10, and 11 (13). These associations allow the integrin α3β1 to fill its primary role in cell adhesion. α3β1 also participates in intercellular adhesion through several protein-protein interactions (10, 27, 53, 55, 58), making it a major contributor in the regulation of cellular adhesion.Human adenovirus type 5 (Ad5) particles interact with cell surface receptors to facilitate internalization into target cells. In the high-affinity interacting model (reviewed in reference 29), the viral fiber knob polypeptide binds the coxsackie adenovirus receptor (CAR) protein on the surface of cells as the primary cell binding event (primary receptor). The penton base polypeptide then binds a cell surface integrin (secondary receptor), leading to entry of the capsid into the cell by a process termed receptor-mediated endocytosis or clathrin-mediated endocytosis. Several types of integrins have been identified as being used by Ad5 to mediate virus internalization: αMβ1, αMβ2, αVβ1, αVβ3, αVβ5, and α5β1 (22, 30, 49, 65). Salone et al. have shown that α3β1 serves as an alternative cellular receptor for adenovirus serotype 5 (49). It promotes entry of the virus into cells, transduction of DNA, and mediates adenovirus infection in both CAR-positive and CAR-negative cell lines. Thus, in addition to functions related to cell adhesion, integrin α3β1 plays an important role in the adenovirus infection cycle.To identify new targets for degradation by the E4orf6/E1B55K ubiquitin ligase, we used a proteomic screen covering most cellular proteins to look for any polypeptide that exhibited a significant decrease in amount following the coexpression from appropriate adenovirus vectors of the E4orf6 protein and E1B55K. This screen revealed several interesting candidates, including integrin α3, a species of 130 kDa that also was found to be reduced in wild-type (wt) virus infection. The degradation of α3 was seen to be dependent on the Cul5-based ligase complex driven by E4orf6 and E1B55K. We also found evidence that the E4orf6/E1B55K ligase complex appears to be involved in cell detachment from the extracellular matrix, a function that could play a role in virus spread.     

BioID-based Identification of Skp Cullin F-box (SCF)β-TrCP1/2 E3 Ligase Substrates

The identification of ubiquitin E3 ligase substrates has been challenging, due in part to low-affinity, transient interactions, the rapid degradation of targets and the inability to identify proteins from poorly soluble cellular compartments. SCF^β-TrCP1 and SCF^β-TrCP2 are well-studied ubiquitin E3 ligases that target substrates for proteasomal degradation, and play important roles in Wnt, Hippo, and NFκB signaling. Combining 26S proteasome inhibitor (MG132) treatment with proximity-dependent biotin labeling (BioID) and semiquantitative mass spectrometry, here we identify SCF^β-TrCP1/2 interacting partners. Based on their enrichment in the presence of MG132, our data identify over 50 new putative SCF^β-TrCP1/2 substrates. We validate 12 of these new substrates and reveal previously unsuspected roles for β-TrCP in the maintenance of nuclear membrane integrity, processing (P)-body turnover and translational control. Together, our data suggest that β-TrCP is an important hub in the cellular stress response. The technique presented here represents a complementary approach to more standard IP-MS methods and should be broadly applicable for the identification of substrates for many ubiquitin E3 ligases.More than 600 putative ubiquitin E3 ligases are encoded in the human genome (1, 2). Although a number of these proteins are known to play critical roles in human health (1–4), the specific biological functions—and substrates—of most E3s remain poorly characterized. The identification of E3 substrates has been difficult in part because: (1) ligase - substrate interactions are often of low affinity (generally in the high nm to microMolar (μM) range) and/or of a transient nature; (2) many substrates are subjected to rapid proteasomal degradation and are therefore not available for detection; (3) the human ubiquitome is extremely complex, and; (4) many substrate proteins are localized to poorly soluble cellular compartments, making their isolation and identification by standard immunoprecipitation (IP)-based techniques extremely challenging (1–4).Methods such as protein chip (5) and yeast two-hybrid screening (6) have been used to identify a limited number of E3-substrate interactions. However, these methods are not conducted in live mammalian cells, and may not be generally applicable for the identification of substrates of the hundreds of unique multi-protein E3 complexes (e.g. SCF, APC, VHL, etc.) or the identification of E3-substrate interactions that are dependent on specific types of post-translational modifications. Several putative inhibitors of apoptosis substrates were identified using the recently described NEDDylator technique (7), in which the E2 protein UBC12 (UBE2M) is fused to the E3 ligase of interest, allowing for the conjugation of the ubiquitin-like protein NEDD8 to substrates. Global protein stability profiling (8) and quantitative mass spectrometry methods (9) have also been used successfully to identify E3 targets. However, because of their cost and/or complexity, and the challenges posed by the extremely large size of the human ubiquitome, these methods have not been widely adopted to date.Proximity-based biotinylation, or BioID¹ (10), is a new method developed for the characterization of protein-protein interactions in living cells. Briefly, a protein of interest is fused in-frame with an E. coli biotin conjugating enzyme mutant (BirA R118G, or BirA*). The BirA* moiety can efficiently activate biotin, but exhibits a reduced affinity for the activated molecule (11); biotinoyl-AMP thus simply diffuses away from BirA* and reacts with nearby amine groups - including those present on lysine residues in neighboring polypeptides. Following cell lysis, biotinylated proteins can be affinity purified using streptavidin and identified using mass spectrometry (Fig. 1A). Since interactors are covalently modified with biotin, robust lysis conditions can be used to solubilize polypeptides localized to poorly soluble cellular compartments (10, 12–16). Moreover, since this method does not require that protein-protein interactions be maintained post-lysis, weak and/or transient interactors may also be identified. We reasoned that BioID may be exploited to capture ubiquitin E3 ligase substrates and tested this notion here.Open in a separate windowFig. 1.BioID can be used to identify ubiquitin E3 ligase substrates. A, An N-terminal tag consisting of the FLAG epitope and the mutant E. coli biotin conjugating protein BirA R118G (BirA*) was fused to the N terminus of the human F-box proteins β-TrCP1 and β-TrCP2. The BirA* protein converts biotin (black hexagon) to biotinoyl-AMP (yellow hexagon). The mutant BirA protein exhibits a reduced affinity for the activated biotin molecule; biotinoyl-AMP thus diffuses away and reacts with free amine groups on lysine residues in nearby polypeptides, including e.g. the bait protein itself, other SCF complex components (CUL1, SKP1), SCF substrates (S) and substrate binding partners (A, B). In the presence of the 26S proteasome inhibitor MG132, β-TrCP substrates are stabilized. Following cell lysis under stringent buffer conditions, biotinylated proteins are affinity purified using streptavidin coupled to Sepharose beads. Streptavidin-bound proteins are washed and subjected to trypsin proteolysis, and the liberated peptides are identified using tandem mass spectrometry. B, Expression of FLAGBirA*-β-TrCP1/2 leads to biotinylation of endogenous proteins. 293 T-REx cells expressing FLAGBirA*-β-TrCP1 or FLAGBirA*-β-TrCP2 were treated with tetracycline (1 μg/ml) to induce protein expression, and with biotin (50 μm) to enable proximity-dependent polypeptide labeling. Whole cell lysates were subjected to SDS-PAGE and immunoblotted with an anti-FLAG antibody (top panel) or streptavidin-HRP (horseradish peroxidase; bottom panel). C, β-TrCP1/2 interactors displaying a substrate profile. Proteins identified in the BioID analysis with a ProteinProphet score ≥0.85 (corresponding to ≤1% FDR), a SAINT score ≥0.75, and a spectral count ratio (+MG132/untreated) log₂ >1. Circles, polypeptides identified in β-TrCP1 BioID; squares, proteins identified in β-TrCP2 BioID. Previously identified β-TrCP interactors are highlighted in blue. Proteins demonstrated in this study to be stabilized following β-TrCP1/2 knockdown (see Fig. 2 and Supplemental Fig. 2) are highlighted in green. D, Overlap of FLAG IP-MS and BioID substrate candidates. Diagram highlighting the overlap between BioID hits displaying a substrate profile (pink), FLAG IP-MS hits displaying a substrate profile (yellow), and previously reported β-TrCP interactors (blue). E, Functional categories of FLAG IP-MS and BioID substrate candidates. Numbers of previously reported β-TrCP interactors within each category are indicated in blue and numbers of new substrate candidates in each category indicated in red.The human beta transducin repeat-containing polypeptides β-TrCP1 (FBXW1) and β-TrCP2 (FBXW11) are evolutionarily conserved paralogous F-box proteins sharing >80% amino acid sequence identity and >90% homology, and act as substrate recognition components of SCF (Skp1-Cullin-F-box) complexes (17). A number of β-TrCP substrates have been well documented, implicating these ligases in numerous biological functions, including regulation of the NFκB, Hippo, Wnt and Hedgehog signaling pathways (18–21). Some β-TrCP targets harbor the sequence DSGX(n)S or variants thereof. Phosphorylation of this sequence is required for SCF^β-TrCP1/2 binding and thus regulates the half-life of these “phosphodegron”-containing proteins (21, 22). However, other bona fide SCF^β-TrCP1/2 substrates contain highly degenerate or non-canonical degrons, which are thought to mediate constitutive turnover (21). A single, simple linear sequence motif that could predict β-TrCP binding has thus not been defined.Here we demonstrate that BioID performed on cells treated with the proteasome inhibitor MG132 can recover many of the previously characterized substrates and stable interactors of β-TrCP1/2. Using semi-quantitative mass spectrometry, we identify and validate a number of new substrates, linking these well-studied E3 ligases to several new biological functions. The method used here is simple, scalable, and should be broadly applicable for the identification of substrates for many other E3s.     

Quantitative Proteomics of Human Fibroblasts with I1061T Mutation in Niemann–Pick C1 (NPC1) Protein Provides Insights into the Disease Pathogenesis

Niemann-Pick type C (NPC) disease is a fatal neurodegenerative disorder characterized by the accumulation of unesterified cholesterol in the late endosomal/lysosomal compartments. Mutations in the NPC1 protein are implicated in 95% of patients with NPC disease. The most prevalent mutation is the missense mutation I1061T that occurs in ∼15–20% of the disease alleles. In our study, an isobaric labeling-based quantitative analysis of proteome of NPC1^I1061T primary fibroblasts when compared with wild-type cells identified 281 differentially expressed proteins based on stringent data analysis criteria. Gene ontology enrichment analysis revealed that these proteins play important roles in diverse cellular processes such as protein maturation, energy metabolism, metabolism of reactive oxygen species, antioxidant activity, steroid metabolism, lipid localization, and apoptosis. The relative expression level of a subset of differentially expressed proteins (TOR4A, DHCR24, CLGN, SOD2, CHORDC1, HSPB7, and GAA) was independently and successfully substantiated by Western blotting. We observed that treating NPC1^I1061T cells with four classes of seven different compounds that are potential NPC drugs increased the expression level of SOD2 and DHCR24. We have also shown an abnormal accumulation of glycogen in NPC1^I1061T fibroblasts possibly triggered by defective processing of lysosomal alpha-glucosidase. Our study provides a starting point for future more focused investigations to better understand the mechanisms by which the reported dysregulated proteins triggers the pathological cascade in NPC, and furthermore, their effect upon therapeutic interventions.Niemann-Pick type C (NPC)¹ disease is a rare autosomal recessive neurodegenerative disorder in which the transport of cholesterol and glycosphingolipids from late endosomal/lysosomal (LE/Ly) compartments to plasma membrane or endoplasmic reticulum (ER) is impaired. The trafficking defect leads to an excessive accumulation of these lipids in the LE/Ly compartments (1). The disease is often diagnosed in early childhood, and as it progresses there is a gradual loss of Purkinje cells in the cerebellum leading to ataxia, dysarthria, vertical supranuclear gaze palsy, and decline of neurological functions (2). NPC disease occurs with an estimated frequency of 1 in 120,000 to 150,000 live births (1). Currently, there is no cure for NPC disease, and available therapeutic efforts are focused on symptom treatment.Approximately 95% of NPC cases are caused by mutations in the NPC1 gene, whereas the remaining 5% are because of mutations in the NPC2 gene (3). NPC1 is a large glycoprotein of 140–170 kDa with 13 transmembrane domains that resides primarily on the limiting membrane of LE/Ly compartments. At steady state, NPC1 is synthesized in the ER and targeted to the LE/Ly compartments where it mediates cholesterol transport via unknown mechanisms. To date over 254 disease-causing mutations, including both missense and nonsense mutations, have been reported on the various domains of NPC1 (4). Among these mutations, I1061T occurs in the luminal side of NPC1 protein and accounts for ∼15–20% of the disease-causing alleles in NPC patients (5). NPC1^I1061T protein is synthesized but fails to advance in the secretory pathway because of its recognition as a misfolded protein by the ER quality control machinery and is consequently targeted for proteasomal degradation (5). Interestingly, if the NPC1^I1061T mutant protein escapes from the ER quality control, it can properly localize to the late endosome and is functional in maintaining cellular cholesterol homeostasis (5). Because NPC1 containing the I1061T mutation is the most common mutation, detailed exploration of the proteome of NPC1^I1061T cells and its comparison to wild-type will further enhance our insight into its molecular mechanisms. Moreover a better understanding of the pathophysiology of the NPC disease from such studies will facilitate implementation of effective therapeutic strategies.Mass spectrometry-based proteomics has emerged as a preferred method for in-depth characterization and quantification of the protein components of biological systems (6). Furthermore, isobaric labeling is a powerful tool for quantitative proteomics studies, which enables concurrent identification and multiplexed quantification of proteins in different samples using tandem mass spectrometry (MS/MS) (7). To identify proteins with relevance to NPC pathogenesis because of I1061T mutation, we have used an amine-reactive six-plex tandem mass tags (TMT) isobaric reagent to differentially label and perform a proteomics comparison of primary fibroblasts derived from healthy and I1061T-mutant individuals. Three biological replicates of NPC1^I1061T and NPC1^WT cells were labeled with different isotopic variant of the TMT 6-plex tag, combined, and analyzed by the multidimensional protein identification technology (MudPIT) technique (8). After filtering MS/MS spectra with low reporter ion intensities from 4308 nonredundant identified proteins, a total of 3553 distinct proteins were quantified. Further data analysis enabled characterization of 281 differentially expressed proteins (DEPs) that were statistically significant (False discovery rate (FDR) = 5%). We assessed our TMT results by validating the expression level of seven proteins by Western blotting. From a therapeutic perspective, we monitored the expression of two DEPs, SOD2 and DHCR24, in the NPC1^I1061T fibroblasts upon treatment with potential NPC drugs: β-cycodextrins (MβCD and HPCD) (9), histone deacetylase inhibitors (HDACIs, such as CI-994, SAHA, and VPA) (10), antioxidant N-acetyl cysteine (NAC), and an oxysterol derivative pharmacological chaperone, mo56HC (11). We have also examined the cellular glycogen levels in NPC1^WT and NPC1^I1061T fibroblasts by staining with periodic acid-Schiff reagents.     

Meta-Analysis Reveals the Association of Common Variants in the Uncoupling Protein (UCP) 1–3 Genes with Body Mass Index Variability

Background

The relationship between uncoupling protein (UCP) 1–3 polymorphisms and susceptibility to obesity has been investigated in several genetic studies. However, the impact of these polymorphisms on obesity is still under debate, with contradictory results being reported. Until this date, no meta-analysis evaluated the association of UCP polymorphisms with body mass index (BMI) variability. Thus, this paper describe a meta-analysis conducted to evaluate if the -3826A/G (UCP1); -866G/A, Ala55Val and Ins/Del (UCP2) and -55C/T (UCP3) polymorphisms are associated with BMI changes.

Methods

A literature search was run to identify all studies that investigated associations between UCP1-3 polymorphisms and BMI. Weighted mean differences (WMD) were calculated for different inheritance models.

Results

Fifty-six studies were eligible for inclusion in the meta-analysis. Meta-analysis results showed that UCP2 55Val/Val genotype was associated with increased BMI in Europeans [Random Effect Model (REM) WMD 0.81, 95% CI 0.20, 1.41]. Moreover, the UCP2 Ins allele and UCP3-55T/T genotype were associated with increased BMI in Asians [REM WMD 0.46, 95% CI 0.09, 0.83 and Fixed Effect Model (FEM) WMD 1.63, 95% CI 0.25, 3.01]. However, a decreased BMI mean was observed for the UCP2-866 A allele in Europeans under a dominant model of inheritance (REM WMD −0.18, 95% CI −0.35, −0.01). There was no significant association of the UCP1-3826A/G polymorphism with BMI mean differences.

Conclusions

The meta-analysis detected a significant association between the UCP2-866G/A, Ins/Del, Ala55Val and UCP3-55C/T polymorphisms and BMI mean differences.     

Protein Inhibitor of Activated STAT 1 (PIAS1) Is Identified as the SUMO E3 Ligase of CCAAT/Enhancer-Binding Protein β (C/EBPβ) during Adipogenesis

It is well recognized that PIAS1, a SUMO (small ubiquitin-like modifier) E3 ligase, modulates such cellular processes as cell proliferation, DNA damage responses, and inflammation responses. Recent studies have shown that PIAS1 also plays a part in cell differentiation. However, the role of PIAS1 in adipocyte differentiation remains unknown. CCAAT/enhancer-binding protein β (C/EBPβ), a major regulator of adipogenesis, is a target of SUMOylation, but the E3 ligase responsible for the SUMOylation of C/EBPβ has not been identified. The present study showed that PIAS1 functions as a SUMO E3 ligase of C/EBPβ to regulate adipogenesis. PIAS1 expression was significantly and transiently induced on day 4 of 3T3-L1 adipocyte differentiation, when C/EBPβ began to decline. PIAS1 was found to interact with C/EBPβ through the SAP (scaffold attachment factor A/B/acinus/PIAS) domain and SUMOylate it, leading to increased ubiquitination and degradation of C/EBPβ. C/EBPβ became more stable when PIAS1 was silenced by RNA interference (RNAi). Moreover, adipogenesis was inhibited by overexpression of wild-type PIAS1 and promoted by knockdown of PIAS1. The mutational study indicated that the catalytic activity of SUMO E3 ligase was required for PIAS1 to restrain adipogenesis. Importantly, the inhibitory effect of PIAS1 overexpression on adipogenesis was rescued by overexpressed C/EBPβ. Thus, PIAS1 could play a dynamic role in adipogenesis by promoting the SUMOylation of C/EBPβ.     

Proteasomal Degradation of Eukaryotic Elongation Factor-2 Kinase (EF2K) Is Regulated by cAMP-PKA Signaling and the SCFβTRCP Ubiquitin E3 Ligase

Protein translation and degradation are critical for proper protein homeostasis, yet it remains unclear how these processes are dynamically regulated, or how they may directly balance or synergize with each other. An important translational control mechanism is the Ca²⁺/calmodulin-dependent phosphorylation of eukaryotic elongation factor-2 (eEF-2) by eukaryotic elongation factor-2 kinase (EF2K), which inhibits elongation of nascent polypeptide chains during translation. We previously described a reduction of EF2K activity in PC12 cells treated with NGF or forskolin. Here, we show that both forskolin- and IGF-1-mediated reductions of EF2K activity in PC12 cells are due to decreased EF2K protein levels, and this is attenuated by application of the proteasome inhibitor, MG132. We further demonstrate that proteasome-mediated degradation of EF2K occurs in response to A2A-type adenosine receptor stimulation, and that activation of protein kinase A (PKA) or phospho-mimetic mutation of the previously characterized PKA site, Ser-499, were sufficient to induce EF2K turnover in PC12 cells. A similar EF2K degradation mechanism was observed in primary neurons and HEK cells. Expression of a dominant-negative form of Cul1 in HEK cells demonstrated that EF2K levels are regulated by an SCF-type ubiquitin E3 ligase. Specifically, EF2K binds to the F-box proteins, βTRCP1 and βTRCP2, and βTRCP regulates EF2K levels and polyubiquitylation. We propose that the proteasomal degradation of EF2K provides a mechanistic link between activity-dependent protein synthesis and degradation.     

WW Domain Containing E3 Ubiquitin Protein Ligase 1 (WWP1) Negatively Regulates TLR4-Mediated TNF-α and IL-6 Production by Proteasomal Degradation of TNF Receptor Associated Factor 6 (TRAF6)

Background

Toll-like receptors (TLRs) play a pivotal role in the defense against invading pathogens by detecting pathogen-associated molecular patterns (PAMPs). TLR4 recognizes lipopolysaccharides (LPS) in the cell walls of Gram-negative bacteria, resulting in the induction and secretion of proinflammatory cytokines such as TNF-α and IL-6. The WW domain containing E3 ubiquitin protein ligase 1 (WWP1) regulates a variety of cellular biological processes. Here, we investigated whether WWP1 acts as an E3 ubiquitin ligase in TLR-mediated inflammation.

Methodology/Results

Knocking down WWP1 enhanced the TNF-α and IL-6 production induced by LPS, and over-expression of WWP1 inhibited the TNF-α and IL-6 production induced by LPS, but not by TNF-α. WWP1 also inhibited the IκB-α, NF-κB, and MAPK activation stimulated by LPS. Additionally, WWP1 could degrade TRAF6, but not IRAK1, in the proteasome pathway, and knocking down WWP1 reduced the LPS-induced K48-linked, but not K63-linked, polyubiquitination of endogenous TRAF6.

Conclusions/Significance

We identified WWP1 as an important negative regulator of TLR4-mediated TNF-α and IL-6 production. We also showed that WWP1 functions as an E3 ligase when cells are stimulated with LPS by binding to TRAF6 and promoting K48-linked polyubiquitination. This results in the proteasomal degradation of TRAF6.     

Quantitative Proteomics Reveals Protein–Protein Interactions with Fibroblast Growth Factor 12 as a Component of the Voltage-Gated Sodium Channel 1.2 (Nav1.2) Macromolecular Complex in Mammalian Brain

Voltage-gated sodium channels (Nav1.1–Nav1.9) are responsible for the initiation and propagation of action potentials in neurons, controlling firing patterns, synaptic transmission and plasticity of the brain circuit. Yet, it is the protein–protein interactions of the macromolecular complex that exert diverse modulatory actions on the channel, dictating its ultimate functional outcome. Despite the fundamental role of Nav channels in the brain, information on its proteome is still lacking. Here we used affinity purification from crude membrane extracts of whole brain followed by quantitative high-resolution mass spectrometry to resolve the identity of Nav1.2 protein interactors. Of the identified putative protein interactors, fibroblast growth factor 12 (FGF12), a member of the nonsecreted intracellular FGF family, exhibited 30-fold enrichment in Nav1.2 purifications compared with other identified proteins. Using confocal microscopy, we visualized native FGF12 in the brain tissue and confirmed that FGF12 forms a complex with Nav1.2 channels at the axonal initial segment, the subcellular specialized domain of neurons required for action potential initiation. Co-immunoprecipitation studies in a heterologous expression system validate Nav1.2 and FGF12 as interactors, whereas patch-clamp electrophysiology reveals that FGF12 acts synergistically with CaMKII, a known kinase regulator of Nav channels, to modulate Nav1.2-encoded currents. In the presence of CaMKII inhibitors we found that FGF12 produces a bidirectional shift in the voltage-dependence of activation (more depolarized) and the steady-state inactivation (more hyperpolarized) of Nav1.2, increasing the channel availability. Although providing the first characterization of the Nav1.2 CNS proteome, we identify FGF12 as a new functionally relevant interactor. Our studies will provide invaluable information to parse out the molecular determinant underlying neuronal excitability and plasticity, and extending the relevance of iFGFs signaling in the normal and diseased brain.Voltage-gated sodium channels (Nav)¹ are transmembrane proteins consisting of a pore-forming α subunit (Nav1.1-Nav1.9) and one or more accessory β-subunits (β₁–β₄) (1–3). Predominately clustered at the axonal initial segment (AIS), the α subunit alone is necessary and sufficient for channel assembly and the initiation and propagation of action potentials following membrane depolarization (4). Although the α subunit is functional on its own, it is the transient and stable protein–protein interactions that modulate subcellular trafficking, compartmentalization, functional expression, and fine-tune the channel biophysical properties (5–9). Thus, the Nav channel and the protein constituents that comprise the protein–protein interaction network are all part of a macromolecular complex that modulates the spatiotemporal dynamics of neuronal input and output playing a critical role in synaptic transmission, signal integration, and neuronal plasticity. Perturbations in this protein–protein interaction network can lead to deficits in neuronal excitability, and eventually neurodegeneration and cell death (10–15).Given the relevance of these interactions for the native channel activity and its overall role in controlling brain circuits, it is increasingly important to uncover these associations. Antibody-based affinity purification (AP) combined with mass spectrometry (MS) is widely used for the enrichment and analysis of target proteins and constituents of their protein–protein interactions as it can be performed at near physiological conditions and preserves post-translational modifications relevant to protein complex organization (16–19). Differential mass spectrometry provides an unbiased method for the efficient, MS-based measurement of relative protein fold changes across multiple complex biological samples. This technology has been successfully applied to a number of ion channels (20–26), but—to the best of our knowledge—not to the study of any member of the Nav channel family. Using a target-directed AP approach combined with quantitative MS, we identified proteins constituting the putative interactome of Nav1.2, one of three dominant Nav channel isoforms in the mammalian brain, from native tissue (1, 2, 4, 8). Among these putative interactors, the fibroblast growth factor 12 (FGF12), a member of the intracellular FGF family (5, 13, 14), stood out as one of the most abundant coprecipitating proteins with ∼30-fold enrichment over other interactors. With a combination of confocal microscopy in brain tissue, reconstitution of the interactor in a heterologous systems and electrophysiological assays, we provide validation for FGF12 as a bona fide relevant component of the Nav1.2 proteome and a modulator of Nav1.2-encoded currents. Altogether, the identified channel/protein interaction between FGF12 and Nav1.2 provides new insights for structural and functional interpretation of neuronal excitability, synaptic transmission, and plasticity in the normal and diseased brain.     

The MID1 E3 Ligase Catalyzes the Polyubiquitination of Alpha4 (α4), a Regulatory Subunit of Protein Phosphatase 2A (PP2A): NOVEL INSIGHTS INTO MID1-MEDIATED REGULATION of PP2A*

Alpha4 (α4) is a key regulator of protein phosphatase 2A (PP2A) and mTOR in steps essential for cell-cycle progression. α4 forms a complex with PP2A and MID1, a microtubule-associated ubiquitin E3 ligase that facilitates MID1-dependent regulation of PP2A and the dephosphorylation of MID1 by PP2A. Ectopic overexpression of α4 is associated with hepatocellular carcinomas, breast cancer, and invasive adenocarcinomas. Here, we provide data suggesting that α4 is regulated by ubiquitin-dependent degradation mediated by MID1. In cells stably expressing a dominant-negative form of MID1, significantly elevated levels of α4 were observed. Treatment of cells with the specific proteasome inhibitor, lactacystin, resulted in a 3-fold increase in α4 in control cells and a similar level in mutant cells. Using in vitro assays, individual MID1 E3 domains facilitated monoubiquitination of α4, whereas full-length MID1 as well as RING-Bbox1 and RING-Bbox1-Bbox2 constructs catalyzed its polyubiquitination. In a novel non-biased functional screen, we identified a leucine to glutamine substitution at position 146 within Bbox1 that abolished MID1-α4 interaction and the subsequent polyubiquitination of α4, indicating that direct binding to Bbox1 was necessary for the polyubiquitination of α4. The mutant had little impact on the RING E3 ligase functionality of MID1. Mass spectrometry data confirmed Western blot analysis that ubiquitination of α4 occurs only within the last 105 amino acids. These novel findings identify a new role for MID1 and a mechanism of regulation of α4 that is likely to impact the stability and activity level of PP2Ac.     

Photoaffinity labeling of the TF1-ATPase from the thermophilic bacterium PS3 with 3′-O-(4-benzoyl)benzoyl ADP

(1) 3′-O-(4-Benzoyl)benzoyl ADP (BzADP) was used as a photoaffinity label for covalent binding of adenine nucleotide analogs to the nucleotide binding site(s) of the thermophilic bacterium PS3 ATPase (TF₁). (2) As with the CF₁-ATPase (Bar-Zvi, D. and Shavit, N. (1984) Biochim. Biophys. Acta 765, 340–356) noncovalently bound BzADP is a reversible inhibitor of the TF₁-ATPase. BzADP changes the kinetics of ATP hydrolysis from noncooperative to cooperative in the same way as ADP does, but, in contrast to the effect on the CF₁-ATPase, it has no effect on the V_max. In the absence of Mg²⁺ 1 mol BzADP binds noncovalently to TF₁, while with Mg²⁺ 3 mol are bound. (3) Photoactivation of BzADP results in the covalent binding of the analog to the nucleotide binding site(s) on TF₁ and correlates with the inactivation of the ATPase. Complete inactivation of the TF₁-ATPase occurs after covalent binding of 2 mol BzADP / mol TF₁. Photoinactivation of TF₁ by BzADP is prevented if excess of either ADP or ATP is present during irradiation. (4) Analysis by polyacrylamide gel electrophoresis in the presence of sodium dodecyl sulfate of the Bz[³H]ADP-labeled TF₁-ATPase shows that all the radioactivity is incorporated into the β subunit.     

Structure of LNX1:Ubc13 ~ Ubiquitin Complex Reveals the Role of Additional Motifs for the E3 Ligase Activity of LNX1

LNX1 (ligand of numb protein-X1) is a RING and PDZ domain-containing E3 ubiquitin ligase that ubiquitinates human c-Src kinase. Here, we report the identification and structure of the ubiquitination domain of LNX1, the identification of Ubc13/Ube2V2 as a functional E2 in vitro, and the structural and functional studies of the Ubc13~Ub intermediate in complex with the ubiquitination domain of LNX1. The RING domain of LNX1 is embedded between two zinc-finger motifs (Zn-RING-Zn), both of which are crucial for its ubiquitination activity. In the heterodimeric complex, the ubiquitin of one monomer shares more buried surface area with LNX1 of the other monomer and these interactions are unique and essential for catalysis. This study reveals how the LNX1 RING domain is structurally and mechanistically dependent on other motifs for its E3 ligase activity, and describes how dimeric LNX1 recruits ubiquitin-loaded Ubc13 for Ub transfer via E3 ligase-mediated catalysis.