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Conserved L464 in p97 D1-D2 linker is critical for p97 cofactor regulated ATPase activity. Biochem J 2021; 478:3185-3204. [PMID: 34405853 DOI: 10.1042/bcj20210288] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 08/10/2021] [Accepted: 08/18/2021] [Indexed: 11/17/2022]
Abstract
p97 protein is a highly conserved, abundant, functionally diverse, structurally dynamic homohexameric AAA enzyme-containing N, D1, and D2 domains. A truncated p97 protein containing the N and D1 domains and the D1-D2 linker (ND1L) exhibits 79% of wild-type (WT) ATPase activity whereas the ND1 domain alone without the linker only has 2% of WT activity. To investigate the relationship between the D1-D2 linker and the D1 domain, we produced p97 ND1L mutants and demonstrated that this 22-residue linker region is essential for D1 ATPase activity. The conserved amino acid leucine 464 (L464) is critical for regulating D1 and D2 ATPase activity by p97 cofactors p37, p47, and Npl4-Ufd1 (NU). Changing leucine to alanine, proline, or glutamate increased the maximum rate of ATP turnover (kcat) of p47-regulated ATPase activities for these mutants, but not for WT. p37 and p47 increased the kcat of the proline substituted linker, suggesting that they induced linker conformations facilitating ATP hydrolysis. NU inhibited D1 ATPase activities of WT and mutant ND1L proteins, but activated D2 ATPase activity of full-length p97. To further understand the mutant mechanism, we used single-particle cryo-EM to visualize the full-length p97L464P and revealed the conformational change of the D1-D2 linker, resulting in a movement of the helix-turn-helix motif (543-569). Taken together with the biochemical and structural results we conclude that the linker helps maintain D1 in a competent conformation and relays the communication to/from the N-domain to the D1 and D2 ATPase domains, which are ∼50 Å away.
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2
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Kwon D, Kim SM, Correia MA. Cytochrome P450 endoplasmic reticulum-associated degradation (ERAD): therapeutic and pathophysiological implications. Acta Pharm Sin B 2020; 10:42-60. [PMID: 31993306 PMCID: PMC6976991 DOI: 10.1016/j.apsb.2019.11.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 10/30/2019] [Accepted: 10/31/2019] [Indexed: 02/07/2023] Open
Abstract
The hepatic endoplasmic reticulum (ER)-anchored cytochromes P450 (P450s) are mixed-function oxidases engaged in the biotransformation of physiologically relevant endobiotics as well as of myriad xenobiotics of therapeutic and environmental relevance. P450 ER-content and hence function is regulated by their coordinated hemoprotein syntheses and proteolytic turnover. Such P450 proteolytic turnover occurs through a process known as ER-associated degradation (ERAD) that involves ubiquitin-dependent proteasomal degradation (UPD) and/or autophagic-lysosomal degradation (ALD). Herein, on the basis of available literature reports and our own recent findings of in vitro as well as in vivo experimental studies, we discuss the therapeutic and pathophysiological implications of altered P450 ERAD and its plausible clinical relevance. We specifically (i) describe the P450 ERAD-machinery and how it may be repurposed for the generation of antigenic P450 peptides involved in P450 autoantibody pathogenesis in drug-induced acute hypersensitivity reactions and liver injury, or viral hepatitis; (ii) discuss the relevance of accelerated or disrupted P450-ERAD to the pharmacological and/or toxicological effects of clinically relevant P450 drug substrates; and (iii) detail the pathophysiological consequences of disrupted P450 ERAD, contributing to non-alcoholic fatty liver disease (NAFLD)/non-alcoholic steatohepatitis (NASH) under certain synergistic cellular conditions.
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Key Words
- 3MA, 3-methyladenine
- AAA, ATPases associated with various cellular activities
- ACC1, acetyl-CoA carboxylase 1
- ACC2, acetyl-CoA carboxylase 2
- ACHE, acetylcholinesterase
- ACOX1, acyl-CoA oxidase 1
- ALD, autophagic-lysosomal degradation
- AMPK1
- AP-1, activator protein 1
- ASK1, apoptosis signal-regulating kinase
- ATF2, activating transcription factor 2
- AdipoR1, gene of adiponectin receptor 1
- Atg14, autophagy-related 14
- CBZ, carbamazepine
- CHIP E3 ubiquitin ligase
- CHIP, carboxy-terminus of Hsc70-interacting protein
- Cytochromes P450
- Endoplasmic reticulum-associated degradation
- FOXO, forkhead box O
- Fas, fatty acid synthase
- GAPDH, glyceraldehyde 3-phosphate dehydrogenase
- INH, isoniazid
- IRS1, insulin receptor substrate 1
- Il-1β, interleukin 1 β
- Il-6, interleukin 6
- Insig1, insulin-induced gene 1
- JNK1
- Lpl, lipoprotein lipase
- Mcp1, chemokine (C–C motif) ligand 1
- Non-alcoholic fatty liver disease
- Non-alcoholic steatohepatitis
- Pgc1, peroxisome proliferator-activated receptor coactivator 1
- SREBP1c, sterol regulatory element binding transcription factor 1c
- Scd1, stearoyl-coenzyme A desaturase
- Tnf, tumor necrosis factor
- UPD, ubiquitin (Ub)-dependent proteasomal degradation
- Ub, ubiquitin
- gp78/AMFR E3 ubiquitin ligase
- gp78/AMFR, autocrine motility factor receptor
- shRNAi, shRNA interference
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Abstract
p97 is an essential hexameric AAA+ ATPase involved in a wide range of cellular processes. Mutations in the enzyme are implicated in the etiology of an autosomal dominant neurological disease in which patients are heterozygous with respect to p97 alleles, containing one copy each of WT and disease-causing mutant genes, so that, in vivo, p97 molecules can be heterogeneous in subunit composition. Studies of p97 have, however, focused on homohexameric constructs, where protomers are either entirely WT or contain a disease-causing mutation, showing that for WT p97, the N-terminal domain (NTD) of each subunit can exist in either a down (ADP) or up (ATP) conformation. NMR studies establish that, in the ADP-bound state, the up/down NTD equilibrium shifts progressively toward the up conformation as a function of disease mutant severity. To understand NTD functional dynamics in biologically relevant p97 heterohexamers comprising both WT and disease-causing mutant subunits, we performed a methyl-transverse relaxation optimized spectroscopy (TROSY) NMR study on a series of constructs in which only one of the protomer types is NMR-labeled. Our results show positive cooperativity of NTD up/down equilibria between neighboring protomers, allowing us to define interprotomer pathways that mediate the allosteric communication between subunits. Notably, the perturbed up/down NTD equilibrium in mutant subunits is partially restored by neighboring WT protomers, as is the two-pronged binding of the UBXD1 adaptor that is affected in disease. This work highlights the plasticity of p97 and how subtle perturbations to its free-energy landscape lead to significant changes in NTD conformation and adaptor binding.
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Wright FA, Bonzerato CG, Sliter DA, Wojcikiewicz RJH. The erlin2 T65I mutation inhibits erlin1/2 complex-mediated inositol 1,4,5-trisphosphate receptor ubiquitination and phosphatidylinositol 3-phosphate binding. J Biol Chem 2018; 293:15706-15714. [PMID: 30135210 DOI: 10.1074/jbc.ra118.004547] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 07/19/2018] [Indexed: 12/11/2022] Open
Abstract
The erlin1/2 complex is a ∼2-MDa endoplasmic reticulum membrane-located ensemble of the ∼40-kDa type II membrane proteins erlin1 and erlin2. The best defined function of this complex is to mediate the ubiquitination of activated inositol 1,4,5-trisphosphate receptors (IP3Rs) and their subsequent degradation. However, it remains unclear how mutations of the erlin1/2 complex affect its cellular function and cause cellular dysfunction and diseases such as hereditary spastic paraplegia. Here, we used gene editing to ablate erlin1 or erlin2 expression to better define their individual roles in the cell and examined the functional effects of a spastic paraplegia-linked mutation to erlin2 (threonine to isoleucine at position 65; T65I). Our results revealed that erlin2 is the dominant player in mediating the interaction between the erlin1/2 complex and IP3Rs and that the T65I mutation dramatically inhibits this interaction and the ability of the erlin1/2 complex to promote IP3R ubiquitination and degradation. Remarkably, we also discovered that the erlin1/2 complex specifically binds to phosphatidylinositol 3-phosphate, that erlin2 binds this phospholipid much more strongly than does erlin1, that the binding is inhibited by T65I mutation of erlin2, and that multiple determinants within the erlin2 polypeptide comprise the phosphatidylinositol 3-phosphate-binding site. Overall, these results indicate that erlin2 is the primary mediator of the cellular roles of the erlin1/2 complex and that disease-linked mutations of erlin2 can affect both IP3R processing and lipid binding.
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Affiliation(s)
- Forrest A Wright
- From the Department of Pharmacology, State University of New York (SUNY) Upstate Medical University, Syracuse, New York 13210 and
| | - Caden G Bonzerato
- From the Department of Pharmacology, State University of New York (SUNY) Upstate Medical University, Syracuse, New York 13210 and
| | - Danielle A Sliter
- Biochemistry Section, Surgical Neurology Branch, NINDS, National Institutes of Health, Bethesda, Maryland 20892
| | - Richard J H Wojcikiewicz
- From the Department of Pharmacology, State University of New York (SUNY) Upstate Medical University, Syracuse, New York 13210 and
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Proteomic Characterization of Armillaria mellea Reveals Oxidative Stress Response Mechanisms and Altered Secondary Metabolism Profiles. Microorganisms 2017; 5:microorganisms5030060. [PMID: 28926970 PMCID: PMC5620651 DOI: 10.3390/microorganisms5030060] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Revised: 09/08/2017] [Accepted: 09/13/2017] [Indexed: 12/22/2022] Open
Abstract
Armillaria mellea is a major plant pathogen. Yet, the strategies the organism uses to infect susceptible species, degrade lignocellulose and other plant material and protect itself against plant defences and its own glycodegradative arsenal are largely unknown. Here, we use a combination of gel and MS-based proteomics to profile A. mellea under conditions of oxidative stress and changes in growth matrix. 2-DE and LC-MS/MS were used to investigate the response of A. mellea to H2O2 and menadione/FeCl3 exposure, respectively. Several proteins were detected with altered abundance in response to H2O2, but not menadione/FeCl3 (i.e., valosin-containing protein), indicating distinct responses to these different forms of oxidative stress. One protein, cobalamin-independent methionine synthase, demonstrated a common response in both conditions, which may be a marker for a more general stress response mechanism. Further changes to the A. mellea proteome were investigated using MS-based proteomics, which identified changes to putative secondary metabolism (SM) enzymes upon growth in agar compared to liquid cultures. Metabolomic analyses revealed distinct profiles, highlighting the effect of growth matrix on SM production. This establishes robust methods by which to utilize comparative proteomics to characterize this important phytopathogen.
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A conserved inter-domain communication mechanism regulates the ATPase activity of the AAA-protein Drg1. Sci Rep 2017; 7:44751. [PMID: 28303975 PMCID: PMC5356007 DOI: 10.1038/srep44751] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Accepted: 02/13/2017] [Indexed: 11/14/2022] Open
Abstract
AAA-ATPases fulfil essential roles in different cellular pathways and often act in form of hexameric complexes. Interaction with pathway-specific substrate and adaptor proteins recruits them to their targets and modulates their catalytic activity. This substrate dependent regulation of ATP hydrolysis in the AAA-domains is mediated by a non-catalytic N-terminal domain. The exact mechanisms that transmit the signal from the N-domain and coordinate the individual AAA-domains in the hexameric complex are still the topic of intensive research. Here, we present the characterization of a novel mutant variant of the eukaryotic AAA-ATPase Drg1 that shows dysregulation of ATPase activity and altered interaction with Rlp24, its substrate in ribosome biogenesis. This defective regulation is the consequence of amino acid exchanges at the interface between the regulatory N-domain and the adjacent D1 AAA-domain. The effects caused by these mutations strongly resemble those of pathological mutations of the AAA-ATPase p97 which cause the hereditary proteinopathy IBMPFD (inclusion body myopathy associated with Paget’s disease of the bone and frontotemporal dementia). Our results therefore suggest well conserved mechanisms of regulation between structurally, but not functionally related members of the AAA-family.
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Kim SM, Wang Y, Nabavi N, Liu Y, Correia MA. Hepatic cytochromes P450: structural degrons and barcodes, posttranslational modifications and cellular adapters in the ERAD-endgame. Drug Metab Rev 2016; 48:405-33. [PMID: 27320797 DOI: 10.1080/03602532.2016.1195403] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The endoplasmic reticulum (ER)-anchored hepatic cytochromes P450 (P450s) are enzymes that metabolize endo- and xenobiotics i.e. drugs, carcinogens, toxins, natural and chemical products. These agents modulate liver P450 content through increased synthesis or reduction via inactivation and/or proteolytic degradation, resulting in clinically significant drug-drug interactions. P450 proteolytic degradation occurs via ER-associated degradation (ERAD) involving either of two distinct routes: Ubiquitin (Ub)-dependent 26S proteasomal degradation (ERAD/UPD) or autophagic lysosomal degradation (ERAD/ALD). CYP3A4, the major human liver/intestinal P450, and the fast-turnover CYP2E1 species are degraded via ERAD/UPD entailing multisite protein phosphorylation and subsequent ubiquitination by gp78 and CHIP E3 Ub-ligases. We are gaining insight into the nature of the structural determinants involved in CYP3A4 and CYP2E1 molecular recognition in ERAD/UPD [i.e. K48-linked polyUb chains and linear and/or "conformational" phosphodegrons consisting either of consecutive sequences on surface loops and/or disordered regions, or structurally-assembled surface clusters of negatively charged acidic (Asp/Glu) and phosphorylated (Ser/Thr) residues, within or vicinal to which, Lys-residues are targeted for ubiquitination]. Structural inspection of select human liver P450s reveals that such linear or conformational phosphodegrons may indeed be a common P450-ERAD/UPD feature. By contrast, although many P450s such as the slow-turnover CYP2E1 species and rat liver CYP2B1 and CYP2C11 are degraded via ERAD/ALD, little is known about the mechanism of their ALD-targeting. On the basis of our current knowledge of ALD-substrate targeting, we propose a tripartite conjunction of K63-linked Ub-chains, P450 structural "LIR" motifs and selective cellular "cargo receptors" as plausible P450-ALD determinants.
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Affiliation(s)
- Sung-Mi Kim
- a Department of Cellular & Molecular Pharmacology , University of California San Francisco , San Francisco , CA , USA
| | - YongQiang Wang
- a Department of Cellular & Molecular Pharmacology , University of California San Francisco , San Francisco , CA , USA
| | - Noushin Nabavi
- a Department of Cellular & Molecular Pharmacology , University of California San Francisco , San Francisco , CA , USA
| | - Yi Liu
- a Department of Cellular & Molecular Pharmacology , University of California San Francisco , San Francisco , CA , USA
| | - Maria Almira Correia
- a Department of Cellular & Molecular Pharmacology , University of California San Francisco , San Francisco , CA , USA ;,b Department of Pharmaceutical Chemistry , University of California San Francisco , San Francisco , CA , USA ;,c Department of Bioengineering and Therapeutic Sciences , University of California San Francisco , San Francisco , CA , USA ;,d The Liver Center, University of California San Francisco , San Francisco , CA , USA
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Mountassif D, Fabre L, Zaid Y, Halawani D, Rouiller I. Cryo-EM of the pathogenic VCP variant R155P reveals long-range conformational changes in the D2 ATPase ring. Biochem Biophys Res Commun 2015; 468:636-41. [PMID: 26549226 DOI: 10.1016/j.bbrc.2015.11.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Accepted: 11/02/2015] [Indexed: 11/25/2022]
Abstract
Single amino acid mutations in valosin containing protein (VCP/p97), a highly conserved member of the ATPases associated with diverse cellular activities (AAA) family of ATPases has been linked to a severe degenerative disease affecting brain, muscle and bone tissue. Previous studies have demonstrated the role of VCP mutations in altering the ATPase activity of the D2 ring; however the structural consequences of these mutations remain unclear. In this study, we report the three-dimensional (3D) map of the pathogenic VCP variant, R155P, as revealed by single-particle Cryo-Electron Microscopy (EM) analysis at 14 Å resolution. We show that the N-terminal R155P mutation induces a large structural reorganisation of the D2 ATPase ring. Results from docking studies using crystal structure data of available wild-type VCP in the EM density maps indicate that the major difference is localized at the interface between two protomers within the D2 ring. Consistent with a conformational change, the VCP R155P variant shifted the isoelectric point of the protein and reduced its interaction with its well-characterized cofactor, nuclear protein localization-4 (Npl4). Together, our results demonstrate that a single amino acid substitution in the N-terminal domain can relay long-range conformational changes to the distal D2 ATPase ring. Our results provide the first structural clues of how VCP mutations may influence the activity and function of the D2 ATPase ring.
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Affiliation(s)
- Driss Mountassif
- Department of Anatomy and Cell Biology, McGill University, Groupe de recherche axé sur la structure des protéines (GRASP), Groupe d'Étude des Proteines Membranaires (GÉPROM), 3640 University Street, Montreal H3A 0C7, Canada
| | - Lucien Fabre
- Department of Anatomy and Cell Biology, McGill University, Groupe de recherche axé sur la structure des protéines (GRASP), Groupe d'Étude des Proteines Membranaires (GÉPROM), 3640 University Street, Montreal H3A 0C7, Canada
| | - Younes Zaid
- Department of Anatomy and Cell Biology, McGill University, Groupe de recherche axé sur la structure des protéines (GRASP), Groupe d'Étude des Proteines Membranaires (GÉPROM), 3640 University Street, Montreal H3A 0C7, Canada; Current address: Laboratory of Thrombosis and Hemostasis, Montreal Heart Institute, Montreal, Quebec, Canada
| | - Dalia Halawani
- Department of Anatomy and Cell Biology, McGill University, Groupe de recherche axé sur la structure des protéines (GRASP), Groupe d'Étude des Proteines Membranaires (GÉPROM), 3640 University Street, Montreal H3A 0C7, Canada; Current address: Department of Cell Biology, Lerner Research Institute, 9500 Euclid Avenue NC10, Cleveland, OH 44195, USA
| | - Isabelle Rouiller
- Department of Anatomy and Cell Biology, McGill University, Groupe de recherche axé sur la structure des protéines (GRASP), Groupe d'Étude des Proteines Membranaires (GÉPROM), 3640 University Street, Montreal H3A 0C7, Canada.
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Chapman E, Maksim N, de la Cruz F, La Clair JJ. Inhibitors of the AAA+ chaperone p97. Molecules 2015; 20:3027-49. [PMID: 25685910 PMCID: PMC4576884 DOI: 10.3390/molecules20023027] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2014] [Accepted: 02/03/2015] [Indexed: 12/22/2022] Open
Abstract
It is remarkable that a pathway as ubiquitous as protein quality control can be targeted to treat cancer. Bortezomib, an inhibitor of the proteasome, was first approved by the US Food and Drug Administration (FDA) more than 10 years ago to treat refractory myeloma and later extended to lymphoma. Its use has increased the survival rate of myeloma patients by as much as three years. This success was followed with the recent accelerated approval of the natural product derived proteasome inhibitor carfilzomib (Kyprolis®), which is used to treat patients with bortezomib-resistant multiple myeloma. The success of these two drugs has validated protein quality control as a viable target to fight select cancers, but begs the question why are proteasome inhibitors limited to lymphoma and myeloma? More recently, these limitations have encouraged the search for additional targets within the protein quality control system that might offer heightened cancer cell specificity, enhanced clinical utility, a lower rate of resistance, reduced toxicity, and mitigated side effects. One promising target is p97, an ATPase associated with various cellular activities (AAA+) chaperone. p97 figures prominently in protein quality control as well as serving a variety of other cellular functions associated with cancer. More than a decade ago, it was determined that up-regulation of p97 in many forms of cancer correlates with a poor clinical outcome. Since these initial discoveries, a mechanistic explanation for this observation has been partially illuminated, but details are lacking. Understandably, given this clinical correlation, myriad roles within the cell, and its importance in protein quality control, p97 has emerged as a potential therapeutic target. This review provides an overview of efforts towards the discovery of small molecule inhibitors of p97, offering a synopsis of efforts that parallel the excellent reviews that currently exist on p97 structure, function, and physiology.
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Affiliation(s)
- Eli Chapman
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Arizona, Tucson, AZ 85721-0207, USA.
| | - Nick Maksim
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Arizona, Tucson, AZ 85721-0207, USA.
| | - Fabian de la Cruz
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Arizona, Tucson, AZ 85721-0207, USA.
| | - James J La Clair
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Arizona, Tucson, AZ 85721-0207, USA.
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Meyer H, Weihl CC. The VCP/p97 system at a glance: connecting cellular function to disease pathogenesis. J Cell Sci 2014; 127:3877-83. [PMID: 25146396 DOI: 10.1242/jcs.093831] [Citation(s) in RCA: 285] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The ATPase valosin-containing protein (VCP)/p97 has emerged as a central and important element of the ubiquitin system. Together with a network of cofactors, it regulates an ever-expanding range of processes that stretch into almost every aspect of cellular physiology. Its main role in proteostasis and key functions in signaling pathways are of relevance to degenerative diseases and genomic stability. In this Cell Science at a Glance and the accompanying poster, we give a brief overview of this complex system. In addition, we discuss the pathogenic basis for VCP/p97-associated diseases and then highlight in more detail new exciting links to the translational stress response and RNA biology that further underscore the significance of the VCP/p97 system.
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Affiliation(s)
- Hemmo Meyer
- Centre for Medical Biotechnology, Faculty of Biology, University of Duisburg-Essen, 45117 Essen, Germany
| | - Conrad C Weihl
- Department of Neurology and Hope Center for Neurological Disorders, Washington University School of Medicine, St Louis, MO 63110, USA
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Chan NC, den Besten W, Sweredoski MJ, Hess S, Deshaies RJ, Chan DC. Degradation of the deubiquitinating enzyme USP33 is mediated by p97 and the ubiquitin ligase HERC2. J Biol Chem 2014; 289:19789-98. [PMID: 24855649 DOI: 10.1074/jbc.m114.569392] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Because the deubiquitinating enzyme USP33 is involved in several important cellular processes (β-adrenergic receptor recycling, centrosome amplification, RalB signaling, and cancer cell migration), its levels must be carefully regulated. Using quantitative mass spectrometry, we found that the intracellular level of USP33 is highly sensitive to the activity of p97. Knockdown or chemical inhibition of p97 causes robust accumulation of USP33 due to inhibition of its degradation. The p97 adaptor complex involved in this function is the Ufd1-Npl4 heterodimer. Furthermore, we identified HERC2, a HECT domain-containing E3 ligase, as being responsible for polyubiquitination of USP33. Inhibition of p97 causes accumulation of polyubiquitinated USP33, suggesting that p97 is required for postubiquitination processing. Thus, our study has identified several key molecules that control USP33 degradation within the ubiquitin-proteasome system.
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Affiliation(s)
- Nickie C Chan
- From the Division of Biology and Biological Engineering, the Howard Hughes Medical Institute, and
| | | | - Michael J Sweredoski
- From the Division of Biology and Biological Engineering, the Proteome Exploration Laboratory/Beckman Institute, California Institute of Technology, Pasadena, California 91125
| | - Sonja Hess
- From the Division of Biology and Biological Engineering, the Proteome Exploration Laboratory/Beckman Institute, California Institute of Technology, Pasadena, California 91125
| | - Raymond J Deshaies
- From the Division of Biology and Biological Engineering, the Howard Hughes Medical Institute, and
| | - David C Chan
- From the Division of Biology and Biological Engineering, the Howard Hughes Medical Institute, and
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Wang Y, Wan B, Zhou J, Li R, Yu L. BRSK2 is a valosin-containing protein (VCP)-interacting protein that affects VCP functioning in endoplasmic reticulum-associated degradation. Biotechnol Lett 2013; 35:1983-9. [PMID: 23907667 DOI: 10.1007/s10529-013-1295-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2013] [Accepted: 07/01/2013] [Indexed: 11/29/2022]
Abstract
Endoplasmic reticulum-associated protein degradation (ERAD) removes improperly-folded proteins from the ER membrane into the cytosol where they undergo proteasomal degradation. Valosin-containing protein (VCP)/p97 mediates in the extraction of ERAD substrates from the ER. BRSK2 (also known as SAD-A), a serine/threonine kinase of the AMP-activated protein kinase family affected VCP/p97 activity in ERAD. In addition, BRSK2 interacted with VCP/p97 via three of the four functional domains of VCP/p97. Immunofluorescence demonstrated that BRSK2 and VCP/p97 were co-localized and also that knockdown of endogenous BRSK2 induced increased levels of CD3δ, a substrate in ERAD for VCP/p97. Thus, BRSK2 might affect the activity of VCP/p97 in ERAD.
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Affiliation(s)
- Yingli Wang
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, 220 Handan Road, Shanghai, People's Republic of China,
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VCP is essential for mitochondrial quality control by PINK1/Parkin and this function is impaired by VCP mutations. Neuron 2013; 78:65-80. [PMID: 23498974 DOI: 10.1016/j.neuron.2013.02.029] [Citation(s) in RCA: 173] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/19/2013] [Indexed: 12/12/2022]
Abstract
Mutations in VCP cause multisystem degeneration impacting the nervous system, muscle, and/or bone. Patients may present with ALS, Parkinsonism, frontotemporal dementia, myopathy, Paget's disease, or a combination of these. The disease mechanism is unknown. We developed a Drosophila model of VCP mutation-dependent degeneration. The phenotype is reminiscent of PINK1 and parkin mutants, including a pronounced mitochondrial defect. Indeed, VCP interacts genetically with the PINK1/parkin pathway in vivo. Paradoxically, VCP complements PINK1 deficiency but not parkin deficiency. The basis of this paradox is resolved by mechanistic studies in vitro showing that VCP recruitment to damaged mitochondria requires Parkin-mediated ubiquitination of mitochondrial targets. VCP recruitment coincides temporally with mitochondrial fission, and VCP is required for proteasome-dependent degradation of Mitofusins in vitro and in vivo. Further, VCP and its adaptor Npl4/Ufd1 are required for clearance of damaged mitochondria via the PINK1/Parkin pathway, and this is impaired by pathogenic mutations in VCP.
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Kappel L, Loibl M, Zisser G, Klein I, Fruhmann G, Gruber C, Unterweger S, Rechberger G, Pertschy B, Bergler H. Rlp24 activates the AAA-ATPase Drg1 to initiate cytoplasmic pre-60S maturation. ACTA ACUST UNITED AC 2013. [PMID: 23185031 PMCID: PMC3514788 DOI: 10.1083/jcb.201205021] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Formation of eukaryotic ribosomes is driven by energy-consuming enzymes. The AAA-ATPase Drg1 is essential for the release of several shuttling proteins from cytoplasmic pre-60S particles and the loading of late joining proteins. However, its exact role in ribosome biogenesis has been unknown. Here we show that the shuttling protein Rlp24 recruited Drg1 to pre-60S particles and stimulated its ATPase activity. ATP hydrolysis in the second AAA domain of Drg1 was required to release shuttling proteins. In vitro, Drg1 specifically and exclusively extracted Rlp24 from purified pre-60S particles. Rlp24 release required ATP and was promoted by the interaction of Drg1 with the nucleoporin Nup116. Subsequent ATP hydrolysis in the first AAA domain dissociated Drg1 from Rlp24, liberating both proteins for consecutive cycles of activity. Our results show that release of Rlp24 by Drg1 defines a key event in large subunit formation that is a prerequisite for progression of cytoplasmic pre-60S maturation.
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Affiliation(s)
- Lisa Kappel
- Institut für Molekulare Biowissenschaften, Karl-Franzens Universität Graz, A-8010 Graz, Austria
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15
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Chia WS, Chia DX, Rao F, Bar Nun S, Geifman Shochat S. ATP binding to p97/VCP D1 domain regulates selective recruitment of adaptors to its proximal N-domain. PLoS One 2012; 7:e50490. [PMID: 23226521 PMCID: PMC3513293 DOI: 10.1371/journal.pone.0050490] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2012] [Accepted: 10/23/2012] [Indexed: 11/18/2022] Open
Abstract
p97/Valosin-containing protein (VCP) is a member of the AAA-ATPase family involved in many cellular processes including cell division, intracellular trafficking and extraction of misfolded proteins in endoplasmic reticulum-associated degradation (ERAD). It is a homohexamer with each subunit containing two tandem D1 and D2 ATPase domains and N- and C-terminal regions that function as adaptor protein binding domains. p97/VCP is directed to its many different functional pathways by associating with various adaptor proteins. The regulation of the recruitment of the adaptor proteins remains unclear. Two adaptor proteins, Ufd1/Npl4 and p47, which bind exclusively to the p97/VCP N-domain and direct p97/VCP to either ERAD-related processes or homotypic fusion of Golgi fragments, were studied here. Surface plasmon resonance biosensor-based assays allowed the study of binding kinetics in real time. In competition experiments, it was observed that in the presence of ATP, Ufd1/Npl4 was able to compete more effectively with p47 for binding to p97/VCP. By using non-hydrolysable ATP analogues and the hexameric truncated p97/N-D1 fragment, it was shown that binding rather than hydrolysis of ATP to the proximal D1 domain strengthened the Ufd1/Npl4 association with the N-domain, thus regulating the recruitment of either Ufd1/Npl4 or p47. This novel role of ATP and an assigned function to the D1 AAA-ATPase domain link the multiple functions of p97/VCP to the metabolic status of the cell.
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Affiliation(s)
- Wei Sheng Chia
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Diana Xueqi Chia
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Feng Rao
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Shoshana Bar Nun
- Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Susana Geifman Shochat
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
- * E-mail:
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16
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Finley D, Ulrich HD, Sommer T, Kaiser P. The ubiquitin-proteasome system of Saccharomyces cerevisiae. Genetics 2012; 192:319-60. [PMID: 23028185 PMCID: PMC3454868 DOI: 10.1534/genetics.112.140467] [Citation(s) in RCA: 301] [Impact Index Per Article: 25.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2012] [Accepted: 07/28/2012] [Indexed: 12/14/2022] Open
Abstract
Protein modifications provide cells with exquisite temporal and spatial control of protein function. Ubiquitin is among the most important modifiers, serving both to target hundreds of proteins for rapid degradation by the proteasome, and as a dynamic signaling agent that regulates the function of covalently bound proteins. The diverse effects of ubiquitylation reflect the assembly of structurally distinct ubiquitin chains on target proteins. The resulting ubiquitin code is interpreted by an extensive family of ubiquitin receptors. Here we review the components of this regulatory network and its effects throughout the cell.
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Affiliation(s)
- Daniel Finley
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115
| | - Helle D. Ulrich
- Cancer Research UK London Research Institute, Clare Hall Laboratories, South Mimms, EN6 3LD, United Kingdom
| | - Thomas Sommer
- Max-Delbrück Center for Molecular Medicine, 13125 Berlin, Germany
| | - Peter Kaiser
- Department of Biological Chemistry, University of California, Irvine, California 92697
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17
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Kamiya Y, Uekusa Y, Sumiyoshi A, Sasakawa H, Hirao T, Suzuki T, Kato K. NMR characterization of the interaction between the PUB domain of peptide:N-glycanase and ubiquitin-like domain of HR23. FEBS Lett 2012; 586:1141-6. [PMID: 22575648 DOI: 10.1016/j.febslet.2012.03.027] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2012] [Accepted: 03/09/2012] [Indexed: 01/09/2023]
Abstract
PUB domains are identified in several proteins functioning in the ubiquitin (Ub)-proteasome system and considered as p97-binding modules. To address the further functional roles of these domains, we herein characterized the interactions of the PUB domain of peptide:N-glycanase (PNGase) with Ub and Ub-like domain (UBL) of the proteasome shuttle factor HR23. NMR data indicated that PNGase-PUB exerts an acceptor preferentially for HR23-UBL, electrostatically interacting with the UBL surface employed for binding to other Ub/UBL motifs. Our findings imply that PNGase-PUB serves not only as p97-binding module but also as a possible activator of HR23 in endoplasmic reticulum-associated degradation mechanisms.
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Affiliation(s)
- Yukiko Kamiya
- Okazaki Institute for Integrative Bioscience, National Institutes of Natural Sciences, Okazaki, Aichi, Japan
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18
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Distinct conformations of the protein complex p97-Ufd1-Npl4 revealed by electron cryomicroscopy. Proc Natl Acad Sci U S A 2012; 109:1098-103. [PMID: 22232657 DOI: 10.1073/pnas.1114341109] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
p97 is a key regulator of numerous cellular pathways and associates with ubiquitin-binding adaptors to remodel ubiquitin-modified substrate proteins. How adaptor binding to p97 is coordinated and how adaptors contribute to substrate remodeling is unclear. Here we present the 3D electron cryomicroscopy reconstructions of the major Ufd1-Npl4 adaptor in complex with p97. Our reconstructions show that p97-Ufd1-Npl4 is highly dynamic and that Ufd1-Npl4 assumes distinct positions relative to the p97 ring upon addition of nucleotide. Our results suggest a model for substrate remodeling by p97 and also explains how p97-Ufd1-Npl4 could form other complexes in a hierarchical model of p97-cofactor assembly.
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19
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Kloppsteck P, Ewens CA, Förster A, Zhang X, Freemont PS. Regulation of p97 in the ubiquitin–proteasome system by the UBX protein-family. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2012; 1823:125-9. [DOI: 10.1016/j.bbamcr.2011.09.006] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2011] [Revised: 09/02/2011] [Accepted: 09/07/2011] [Indexed: 01/27/2023]
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20
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Molecular motor proteins and amyotrophic lateral sclerosis. Int J Mol Sci 2011; 12:9057-82. [PMID: 22272119 PMCID: PMC3257116 DOI: 10.3390/ijms12129057] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2011] [Revised: 11/28/2011] [Accepted: 11/30/2011] [Indexed: 12/11/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disorder affecting motor neurons in the brain, brainstem and spinal cord, which is characterized by motor dysfunction, muscle dystrophy and progressive paralysis. Both inherited and sporadic forms of ALS share common pathological features, however, the initial trigger of neurodegeneration remains unknown. Motor neurons are uniquely targeted by ubiquitously expressed proteins in ALS but the reason for this selectively vulnerability is unclear. However motor neurons have unique characteristics such as very long axons, large cell bodies and high energetic metabolism, therefore placing high demands on cellular transport processes. Defects in cellular trafficking are now widely reported in ALS, including dysfunction to the molecular motors dynein and kinesin. Abnormalities to dynein in particular are linked to ALS, and defects in dynein-mediated axonal transport processes have been reported as one of the earliest pathologies in transgenic SOD1 mice. Furthermore, dynein is very highly expressed in neurons and neurons are particularly sensitive to dynein dysfunction. Hence, unravelling cellular transport processes mediated by molecular motor proteins may help shed light on motor neuron loss in ALS.
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Abstract
Inclusion body myopathy with Paget disease of the bone and frontotemporal dementia (IBMPFD) is a multisystem degenerative disorder caused by mutations in the valosin-containing protein (VCP) gene. How missense mutations in this abundant, ubiquitously expressed, multifunctional protein lead to the degeneration of disparate tissues is unclear. VCP participates in diverse cellular functions by associating with an expanding collection of substrates and cofactors that dictate its functionality. In this issue of the JCI, Wang and colleagues have further expanded the VCP interactome by identifying neurofibromin-1 (NF1) as a novel VCP interactor in the CNS. IBMPFD-associated mutations disrupt binding of VCP to NF1, resulting in reduced synaptogenesis. Thus, aberrant interactions between VCP and NF1 may explain the dementia phenotype and cognitive delay observed in patients with IBMPFD and neurofibromatosis type 1.
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Affiliation(s)
- Conrad C Weihl
- Department of Neurology, Washington University School of Medicine, Saint Louis, Missouri 63110, USA.
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22
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Crystal structure of human FAF1 UBX domain reveals a novel FcisP touch-turn motif in p97/VCP-binding region. Biochem Biophys Res Commun 2011; 407:531-4. [PMID: 21414298 DOI: 10.1016/j.bbrc.2011.03.052] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2011] [Accepted: 03/11/2011] [Indexed: 11/24/2022]
Abstract
UBX domain is a general p97/VCP-binding module found in an increasing number of proteins including FAF1, p47, SAKS1 and UBXD7. FAF1, a multi-functional tumor suppressor protein, binds to the N domain of p97/VCP through its C-terminal UBX domain and thereby inhibits the proteasomal protein degradation in which p97/VCP acts as a co-chaperone. Here we report the crystal structure of human FAF1 UBX domain at 2.9Å resolution. It reveals that the conserved FP sequence in the p97/VCP-binding region adopts a rarely observed cis-Pro touch-turn structure. We call it an FcisP touch-turn motif and suggest that it is the conserved structural element of the UBX domain. Four FAF1 UBX molecules in an asymmetric unit of the crystal show two different conformations of the FcisP touch-turn motif. The phenyl ring of F(619) in the motif stacks partly over cis-Pro(620) in one conformation, whereas it is swung out from cis-P(620), in the other conformation, and forms hydrophobic contacts with the residues of the neighboring molecule. In addition, the entire FcisP touch-turn motif is pulled out in the second conformation by about 2Å in comparison to the first conformation. Those conformational differences observed in the p97/VCP-binding motif caused by the interaction with neighboring molecules presumably represent the conformational change of the UBX domain on its binding to the N domain of p97/VCP.
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23
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Kumsta C, Thamsen M, Jakob U. Effects of oxidative stress on behavior, physiology, and the redox thiol proteome of Caenorhabditis elegans. Antioxid Redox Signal 2011; 14:1023-37. [PMID: 20649472 PMCID: PMC3052275 DOI: 10.1089/ars.2010.3203] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Accumulation of reactive oxygen species has been implicated in various diseases and aging. However, the precise physiological effects of accumulating oxidants are still largely undefined. Here, we applied a short-term peroxide stress treatment to young Caenorhabditis elegans and measured behavioral, physiological, and cellular consequences. We discovered that exposure to peroxide stress causes a number of immediate changes, including loss in mobility, decreased growth rate, and decreased cellular adenosine triphosphate levels. Many of these alterations, which are highly reminiscent of changes in aging animals, are reversible, suggesting the presence of effective antioxidant systems in young C. elegans. One of these antioxidant systems involves the highly abundant protein peroxiredoxin 2 (PRDX-2), whose gene deletion causes phenotypes symptomatic of chronic peroxide stress and shortens lifespan. Applying the quantitative redox proteomic technique OxICAT to oxidatively stressed wild-type and prdx-2 deletion worms, we identified oxidation-sensitive cysteines in 40 different proteins, including proteins involved in mobility and feeding (e.g., MYO-2 and LET-75), protein translation and homeostasis (e.g., elongation factor 1 [EFT-1] and heat shock protein 1), and adenosine triphosphate regeneration (e.g., nucleoside diphosphate kinase). The oxidative modification of some of these redox-sensitive cysteines may contribute to the physiological and behavioral changes observed in oxidatively stressed animals.
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Affiliation(s)
- Caroline Kumsta
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109, USA
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24
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Acharya P, Liao M, Engel JC, Correia MA. Liver cytochrome P450 3A endoplasmic reticulum-associated degradation: a major role for the p97 AAA ATPase in cytochrome P450 3A extraction into the cytosol. J Biol Chem 2010; 286:3815-28. [PMID: 21107009 DOI: 10.1074/jbc.m110.186981] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The CYP3A subfamily of hepatic cytochromes P450, being engaged in the metabolism and clearance of >50% of clinically relevant drugs, can significantly influence therapeutics and drug-drug interactions. Our characterization of CYP3A degradation has indicated that CYPs 3A incur ubiquitin-dependent proteasomal degradation (UPD) in an endoplasmic reticulum (ER)-associated degradation (ERAD) process. Cytochromes P450 are monotopic hemoproteins N-terminally anchored to the ER membrane with their protein bulk readily accessible to the cytosolic proteasome. Given this topology, it was unclear whether they would require the AAA-ATPase p97 chaperone complex that retrotranslocates/dislocates ubiquitinated ER-integral and luminal proteins into the cytosol for proteasomal delivery. To assess the in vivo relevance of this p97-CYP3A association, we used lentiviral shRNAs to silence p97 (80% mRNA and 90% protein knockdown relative to controls) in sandwich-cultured rat hepatocytes. This extensive hepatic p97 knockdown remarkably had no effect on cellular morphology, ER stress, and/or apoptosis, despite the well recognized strategic p97 roles in multiple important cellular processes. However, such hepatic p97 knockdown almost completely abrogated CYP3A extraction into the cytosol, resulting in a significant accumulation of parent and ubiquitinated CYP3A species that were firmly ER-tethered. Little detectable CYP3A accumulated in the cytosol, even after concomitant inhibition of proteasomal degradation, thereby documenting a major role of p97 in CYP3A extraction and delivery to the 26 S proteasome during its UPD/ERAD. Intriguingly, the accumulated parent CYP3A was functionally active, indicating that p97 can regulate physiological CYP3A content and thus influence its clinically relevant function.
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Affiliation(s)
- Poulomi Acharya
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California 94158-2517, USA
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25
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Manno A, Noguchi M, Fukushi J, Motohashi Y, Kakizuka A. Enhanced ATPase activities as a primary defect of mutant valosin-containing proteins that cause inclusion body myopathy associated with Paget disease of bone and frontotemporal dementia. Genes Cells 2010; 15:911-22. [PMID: 20604808 DOI: 10.1111/j.1365-2443.2010.01428.x] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Valosin-containing protein (VCP) has been shown to colocalize with abnormal protein aggregates, such as nuclear inclusions of Huntington disease and Machado-Joseph disease, Lewy bodies in Parkinson disease. Several mis-sense mutations in the human VCP gene have been identified in patients suffering inclusion body myopathy associated with Paget disease of bone and frontotemporal dementia (IBMPFD). Recently, we have shown that VCP possesses both aggregate-forming and aggregate-clearing activities. Here, we showed that in cells treated with proteasome inhibitors VCP first appeared as several small aggregates throughout the cells; and then, these small aggregates gathered together into a single big aggregate. Subcellular localization and ATPase activity of VCP clearly influenced the localization of the aggregates. Furthermore, all tested IBMPFD-causing mutant VCPs, possessed elevated ATPase activities and enhanced aggregate-forming activities in cultured cells. In Drosophila, these mutants and VCP(T761E), a super active VCP, did not appear to spontaneously induce eye degeneration, but worsened the phenotype when co-expressed with polyglutamines. Unexpectedly, these VCPs did not apparently change sizes and the amounts of polyglutamine aggregates in Drosophila eyes. Elevated ATPase activities, thus, may be a hidden primary defect causing IBMPFD pathological phenotypes, which would be revealed when abnormal proteins are accumulated, as typically observed in aging.
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Affiliation(s)
- Atsushi Manno
- Laboratory of Functional Biology, Kyoto University Graduate School of Biostudies, Kyoto 606-8501, Japan
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26
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Tai HC, Besche H, Goldberg AL, Schuman EM. Characterization of the Brain 26S Proteasome and its Interacting Proteins. Front Mol Neurosci 2010; 3. [PMID: 20717473 PMCID: PMC2901091 DOI: 10.3389/fnmol.2010.00012] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2009] [Accepted: 04/21/2010] [Indexed: 11/30/2022] Open
Abstract
Proteasome-mediated proteolysis is important for synaptic plasticity, neuronal development, protein quality control, and many other processes in neurons. To define proteasome composition in brain, we affinity purified 26S proteasomes from cytosolic and synaptic compartments of the rat cortex. Using tandem mass spectrometry, we identified the standard 26S subunits and a set of 28 proteasome-interacting proteins that associated substoichiometrically and may serve as regulators or cofactors. This set differed from those in other tissues and we also found several proteins that associated only with either the cytosolic or the synaptic proteasome. The latter included the ubiquitin-binding factor TAX1BP1 and synaptic vesicle protein SNAP-25. Native gel electrophoresis revealed a higher proportion of doubly-capped 26S proteasome (19S-20S-19S) in the cortex than in the liver or kidney. To investigate the interplay between proteasome regulation and synaptic plasticity, we exposed cultured neurons to glutamate receptor agonist NMDA. Within 4 h, this agent caused a prolonged decrease in the activity of the ubiquitin-proteasome system as shown by disassembly of 26S proteasomes, decrease in ubiquitin-protein conjugates, and dissociation of the ubiquitin ligases UBE3A (E6-AP) and HUWE1 from the proteasome. Surprisingly, the regulatory 19S particles were rapidly degraded by proteasomal, not lysosomal degradation, and the dissociated E3 enzymes also degraded. Thus the content of proteasomes and their set of associated proteins can be altered by neuronal activity, in a manner likely to influence synaptic plasticity and learning.
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Affiliation(s)
- Hwan-Ching Tai
- Division of Chemistry and Chemical Engineering, California Institute of Technology Pasadena, CA, USA
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27
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Ju JS, Weihl CC. Inclusion body myopathy, Paget's disease of the bone and fronto-temporal dementia: a disorder of autophagy. Hum Mol Genet 2010; 19:R38-45. [PMID: 20410287 DOI: 10.1093/hmg/ddq157] [Citation(s) in RCA: 103] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Inclusion body myopathy associated with Paget's disease of the bone and fronto-temporal dementia (IBMPFD) is a progressive autosomal dominant disorder caused by mutations in p97/VCP (valosin-containing protein). p97/VCP is a member of the AAA+ (ATPase associated with a variety of activities) protein family and participates in multiple cellular processes. One particularly important role for p97/VCP is facilitating intracellular protein degradation. p97/VCP has traditionally been thought to mediate the ubiquitin-proteasome degradation of proteins; however, recent studies challenge this dogma. p97/VCP clearly participates in the degradation of aggregate-prone proteins, a process principally mediated by autophagy. In addition, IBMPFD mutations in p97/VCP lead to accumulation of autophagic structures in patient and transgenic animal tissue. This is likely due to a defect in p97/VCP-mediated autophagosome maturation. The following review will discuss the evidence for p97/VCP in autophagy and how a disruption in this process contributes to IBMPFD pathogenesis.
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Affiliation(s)
- Jeong-Sun Ju
- Department of Neurology, Washington University School of Medicine, Saint Louis, MO 63110, USA
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28
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Lim PJ, Danner R, Liang J, Doong H, Harman C, Srinivasan D, Rothenberg C, Wang H, Ye Y, Fang S, Monteiro MJ. Ubiquilin and p97/VCP bind erasin, forming a complex involved in ERAD. J Cell Biol 2009; 187:201-17. [PMID: 19822669 PMCID: PMC2768832 DOI: 10.1083/jcb.200903024] [Citation(s) in RCA: 119] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2009] [Accepted: 09/23/2009] [Indexed: 01/17/2023] Open
Abstract
Unwanted proteins in the endoplasmic reticulum (ER) are exported into the cytoplasm and degraded by the proteasome through the ER-associated protein degradation pathway (ERAD). Disturbances in ERAD are linked to ER stress, which has been implicated in the pathogenesis of several human diseases. However, the composition and organization of ERAD complexes in human cells is still poorly understood. In this paper, we describe a trimeric complex that we propose functions in ERAD. Knockdown of erasin, a platform for p97/VCP and ubiquilin binding, or knockdown of ubiquilin in human cells slowed degradation of two classical ERAD substrates. In Caenorhabditis elegans, ubiquilin and erasin are ER stress-response genes that are regulated by the ire-1 branch of the unfolded protein response pathway. Loss of ubiquilin or erasin resulted in activation of ER stress, increased accumulation of polyubiquitinated proteins, and shortened lifespan in worms. Our results strongly support a role for this complex in ERAD and in the regulation of ER stress.
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Affiliation(s)
- Precious J. Lim
- Medical Biotechnology Center, University of Maryland Biotechnology Institute, Baltimore, MD 21201
| | - Rebecca Danner
- Medical Biotechnology Center, University of Maryland Biotechnology Institute, Baltimore, MD 21201
| | - Jing Liang
- Medical Biotechnology Center, University of Maryland Biotechnology Institute, Baltimore, MD 21201
| | - Howard Doong
- Medical Biotechnology Center, University of Maryland Biotechnology Institute, Baltimore, MD 21201
| | - Christine Harman
- Medical Biotechnology Center, University of Maryland Biotechnology Institute, Baltimore, MD 21201
| | - Deepa Srinivasan
- Medical Biotechnology Center, University of Maryland Biotechnology Institute, Baltimore, MD 21201
| | - Cara Rothenberg
- Medical Biotechnology Center, University of Maryland Biotechnology Institute, Baltimore, MD 21201
| | - Hongmin Wang
- Medical Biotechnology Center, University of Maryland Biotechnology Institute, Baltimore, MD 21201
| | - Yihong Ye
- National Institute of Diabetes and Digestive and Kidney Disease, National Institutes of Health, Bethesda, MD 20892
| | - Shengyun Fang
- Medical Biotechnology Center, University of Maryland Biotechnology Institute, Baltimore, MD 21201
| | - Mervyn J. Monteiro
- Medical Biotechnology Center, University of Maryland Biotechnology Institute, Baltimore, MD 21201
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29
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Cayli S, Klug J, Chapiro J, Fröhlich S, Krasteva G, Orel L, Meinhardt A. COP9 signalosome interacts ATP-dependently with p97/valosin-containing protein (VCP) and controls the ubiquitination status of proteins bound to p97/VCP. J Biol Chem 2009; 284:34944-53. [PMID: 19826004 DOI: 10.1074/jbc.m109.037952] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Ubiquitinated proteins can alternatively be delivered directly to the proteasome or via p97/VCP (valosin-containing protein). Whereas the proteasome degrades ubiquitinated proteins, the homohexameric ATPase p97/VCP seems to control the ubiquitination status of recruited substrates. The COP9 signalosome (CSN) is also involved in the ubiquitin/proteasome system (UPS) as exemplified by regulating the neddylation of ubiquitin E3 ligases. Here, we show that p97/VCP colocalizes and directly interacts with subunit 5 of the CSN (CSN5) in vivo and is associated with the entire CSN complex in an ATP-dependent manner. Furthermore, we provide evidence that the CSN and in particular the isopeptidase activity of its subunit CSN5 as well as the associated deubiquitinase USP15 are required for proper processing of polyubiquitinated substrates bound to p97/VCP. Moreover, we show that in addition to NEDD8, CSN5 binds to oligoubiquitin chains in vitro. Therefore, CSN and p97/VCP could form an ATP-dependent complex that resembles the 19 S proteasome regulatory particle and serves as a key mediator between ubiquitination and degradation pathways.
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Affiliation(s)
- Sevil Cayli
- Unit of Reproductive Biology, Department of Anatomy and Cell Biology, Justus-Liebig-University, 35385 Giessen, Germany
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30
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Weihl CC, Pestronk A, Kimonis VE. Valosin-containing protein disease: inclusion body myopathy with Paget's disease of the bone and fronto-temporal dementia. Neuromuscul Disord 2009; 19:308-15. [PMID: 19380227 DOI: 10.1016/j.nmd.2009.01.009] [Citation(s) in RCA: 182] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2008] [Revised: 12/15/2008] [Accepted: 01/18/2009] [Indexed: 01/18/2023]
Abstract
Mutations in valosin-containing protein (VCP) cause inclusion body myopathy (IBM) associated with Paget's disease of the bone (PDB) and fronto-temporal dementia (FTD) or IBMPFD. Although IBMPFD is a multisystem disorder, muscle weakness is the presenting symptom in greater than half of patients and an isolated symptom in 30%. Patients with the full spectrum of the disease make up only 12% of those affected; therefore it is important to consider and recognize IBMPFD in a neuromuscular clinic. The current review describes the skeletal muscle phenotype and common muscle histochemical features in IBMPFD. In addition to myopathic features; vacuolar changes and tubulofilamentous inclusions are found in a subset of patients. The most consistent findings are VCP, ubiquitin and TAR DNA-binding protein 43 (TDP-43) positive inclusions. VCP is a ubiquitously expressed multifunctional protein that is a member of the AAA+ (ATPase associated with various activities) protein family. It has been implicated in multiple cellular functions ranging from organelle biogenesis to protein degradation. Although the role of VCP in skeletal muscle is currently unknown, it is clear that VCP mutations lead to the accumulation of ubiquitinated inclusions and protein aggregates in patient tissue, transgenic animals and in vitro systems. We suggest that IBMPFD is novel type of protein surplus myopathy. Instead of accumulating a poorly degraded and aggregated mutant protein as seen in some myofibrillar and nemaline myopathies, VCP mutations disrupt its normal role in protein homeostasis resulting in the accumulation of ubiquitinated and aggregated proteins that are deleterious to skeletal muscle.
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Affiliation(s)
- Conrad C Weihl
- Department of Neurology, Washington University School of Medicine, Saint Louis, MO 63110, USA.
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31
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Morreale G, Conforti L, Coadwell J, Wilbrey AL, Coleman MP. Evolutionary divergence of valosin-containing protein/cell division cycle protein 48 binding interactions among endoplasmic reticulum-associated degradation proteins. FEBS J 2009; 276:1208-20. [PMID: 19175675 DOI: 10.1111/j.1742-4658.2008.06858.x] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Endoplasmic reticulum (ER)-associated degradation (ERAD) is a cell-autonomous process that eliminates large quantities of misfolded, newly synthesized protein, and is thus essential for the survival of any basic eukaryotic cell. Accordingly, the proteins involved and their interaction partners are well conserved from yeast to mammals, and Saccharomyces cerevisiae is widely used as a model system with which to investigate this fundamental cellular process. For example, valosin-containing protein (VCP) and its yeast homologue cell division cycle protein 48 (Cdc48p), which help to direct polyubiquitinated proteins for proteasome-mediated degradation, interact with an equivalent group of ubiquitin ligases in mouse and in S. cerevisiae. A conserved structural motif for cofactor binding would therefore be expected. We report a VCP-binding motif (VBM) shared by mammalian ubiquitin ligase E4b (Ube4b)-ubiquitin fusion degradation protein 2a (Ufd2a), hydroxymethylglutaryl reductase degradation protein 1 (Hrd1)-synoviolin and ataxin 3, and a related sequence in M(r) 78,000 glycoprotein-Amfr with slightly different binding properties, and show that Ube4b and Hrd1 compete for binding to the N-terminal domain of VCP. Each of these proteins is involved in ERAD, but none has an S. cerevisiae homologue containing the VBM. Some other invertebrate model organisms also lack the VBM in one or more of these proteins, in contrast to vertebrates, where the VBM is widely conserved. Thus, consistent with their importance in ERAD, evolution has developed at least two ways to bring these proteins together with VCP-Cdc48p. However, the differing molecular architecture of VCP-Cdc48p complexes indicates a key point of divergence in the molecular details of ERAD mechanisms.
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Affiliation(s)
- Giacomo Morreale
- Laboratory of Molecular Signalling, The Babraham Institute, Cambridge, UK.
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32
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Humphreys D, Hume PJ, Koronakis V. The Salmonella effector SptP dephosphorylates host AAA+ ATPase VCP to promote development of its intracellular replicative niche. Cell Host Microbe 2009; 5:225-33. [PMID: 19286132 PMCID: PMC2724103 DOI: 10.1016/j.chom.2009.01.010] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2008] [Revised: 11/14/2008] [Accepted: 01/20/2009] [Indexed: 11/24/2022]
Abstract
Virulence effectors delivered into intestinal epithelial cells by Salmonella trigger actin remodeling to direct pathogen internalization and intracellular replication in Salmonella-containing vacuoles (SCVs). One such effector, SptP, functions early during pathogen entry to deactivate Rho GTPases and reverse pathogen-induced cytoskeletal changes following uptake. SptP also harbors a C-terminal protein tyrosine phosphatase (PTPase) domain with no clear host substrates. Investigating SptP's longevity in infected cells, we uncover a late function of SptP, showing that it associates with SCVs, and its PTPase activity increases pathogen replication. Direct SptP binding and specific dephosphorylation of the AAA+ ATPase valosin-containing protein (VCP/p97), a facilitator of cellular membrane fusion and protein degradation, enhanced pathogen replication in SCVs. VCP and its adaptors p47 and Ufd1 were necessary for generating Salmonella-induced filaments on SCVs, a membrane fusion event characteristic of the pathogen replicative phase. Thus, Salmonella regulates the biogenesis of an intracellular niche through SptP-mediated dephosphorylation of VCP.
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Affiliation(s)
- Daniel Humphreys
- Cambridge University Department of Pathology, Tennis Court Road, Cambridge CB2 1QP, UK
| | - Peter J. Hume
- Cambridge University Department of Pathology, Tennis Court Road, Cambridge CB2 1QP, UK
| | - Vassilis Koronakis
- Cambridge University Department of Pathology, Tennis Court Road, Cambridge CB2 1QP, UK
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33
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Rubin BR, Bogan JS. Intracellular retention and insulin-stimulated mobilization of GLUT4 glucose transporters. VITAMINS AND HORMONES 2009; 80:155-92. [PMID: 19251038 DOI: 10.1016/s0083-6729(08)00607-9] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
GLUT4 glucose transporters are expressed nearly exclusively in adipose and muscle cells, where they cycle to and from the plasma membrane. In cells not stimulated with insulin, GLUT4 is targeted to specialized GLUT4 storage vesicles (GSVs), which sequester it away from the cell surface. Insulin acts within minutes to mobilize these vesicles, translocating GLUT4 to the plasma membrane to enhance glucose uptake. The mechanisms controlling GSV sequestration and mobilization are poorly understood. An insulin-regulated aminopeptidase that cotraffics with GLUT4, IRAP, is required for basal GSV retention and insulin-stimulated mobilization. TUG and Ubc9 bind GLUT4, and likely retain GSVs within unstimulated cells. These proteins may be components of a retention receptor, which sequesters GLUT4 and IRAP away from recycling vesicles. Insulin may then act on this protein complex to liberate GLUT4 and IRAP, discharging GSVs into a recycling pathway for fusion at the cell surface. How GSVs are anchored intracellularly, and how insulin mobilizes these vesicles, are the important topics for ongoing research. Regulation of GLUT4 trafficking is tissue-specific, perhaps in part because the formation of GSVs requires cell type-specific expression of sortilin. Proteins controlling GSV retention and mobilization can then be more widely expressed. Indeed, GLUT4 likely participates in a general mechanism by which the cell surface delivery of various membrane proteins can be controlled by extracellular stimuli. Finally, it is not known if defects in the formation or intracellular retention of GSVs contribute to human insulin resistance, or play a role in the pathogenesis of type 2 diabetes.
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Affiliation(s)
- Bradley R Rubin
- Department of Internal Medicine, Yale School of Medicine, New Haven, CT 06520-8020, USA
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34
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Tai HC, Schuman EM. Ubiquitin, the proteasome and protein degradation in neuronal function and dysfunction. Nat Rev Neurosci 2008; 9:826-38. [PMID: 18931696 DOI: 10.1038/nrn2499] [Citation(s) in RCA: 357] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Eukaryotic protein degradation by the proteasome and the lysosome is a dynamic and complex process in which ubiquitin has a key regulatory role. The distinctive morphology of the postmitotic neuron creates unique challenges for protein degradation systems with respect to cell-surface protein turnover and substrate delivery to proteolytic machineries that are required for both synaptic plasticity and self-renewal. Moreover, the discovery of ubiquitin-positive protein aggregates in a wide spectrum of neurodegenerative diseases underlines the importance and vulnerability of the degradative system in neurons. In this article, we discuss the molecular mechanism of protein degradation in the neuron with respect to both its function and its dysfunction.
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Affiliation(s)
- Hwan-Ching Tai
- Division of Chemistry of Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
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35
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Park S, Rancour DM, Bednarek SY. In planta analysis of the cell cycle-dependent localization of AtCDC48A and its critical roles in cell division, expansion, and differentiation. PLANT PHYSIOLOGY 2008; 148:246-58. [PMID: 18660433 PMCID: PMC2528134 DOI: 10.1104/pp.108.121897] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2008] [Accepted: 07/14/2008] [Indexed: 05/18/2023]
Abstract
CDC48/p97 is a conserved homohexameric AAA-ATPase chaperone required for a variety of cellular processes but whose role in the development of a multicellular model system has not been examined. Here, we have used reverse genetics, visualization of a functional Arabidopsis (Arabidopsis thaliana) CDC48 fluorescent fusion protein, and morphological analysis to examine the subcellular distribution and requirements for AtCDC48A in planta. Homozygous Atcdc48A T-DNA insertion mutants arrest during seedling development, exhibiting decreased cell expansion and displaying pleiotropic defects in pollen and embryo development. Atcdc48A insertion alleles show significantly reduced male transmission efficiency due to defects in pollen tube growth. Yellow fluorescent protein-AtCDC48A, a fusion protein that functionally complements the insertion mutant defects, localizes in the nucleus and cytoplasm and is recruited to the division mid-zone during cytokinesis. The pattern of nuclear localization differs according to the stage of the cell cycle and differentiation state. Inducible expression of an Atcdc48A Walker A ATPase mutant in planta results in cytokinesis abnormalities, aberrant cell divisions, and root trichoblast differentiation defects apparent in excessive root hair emergence. At the biochemical level, our data suggest that the endogenous steady-state protein level of AtCDC48A is dependent upon the presence of ATPase-active AtCDC48A. These results demonstrate that CDC48A/p97 is critical for cytokinesis, cell expansion, and differentiation in plants.
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Affiliation(s)
- Sookhee Park
- Department of Biochemistry , University of Wisconsin, Madison, Wisconsin 53706, USA
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36
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Braun RJ, Zischka H. Mechanisms of Cdc48/VCP-mediated cell death — from yeast apoptosis to human disease. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2008; 1783:1418-35. [DOI: 10.1016/j.bbamcr.2008.01.015] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2007] [Accepted: 01/16/2008] [Indexed: 10/22/2022]
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37
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Roda O, Chiva C, Espuña G, Gabius HJ, Real FX, Navarro P, Andreu D. A proteomic approach to the identification of new tPA receptors in pancreatic cancer cells. Proteomics 2008; 6 Suppl 1:S36-41. [PMID: 16544279 DOI: 10.1002/pmic.200500376] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
We have developed a strategy to identify putative tissue-type plasminogen activator (tPA)receptors present in pancreatic cancer cells by affinity capture with tPA-Sepharose followed by 2-DE and MALDI-MS PMF. Proteins pulled down from either total lysates or raft membrane fractions were characterized and compared with those from a total lysate of an endothelial cell line (HUVEC) to identify pancreas-restricted tPA receptors. A total of 31 proteins were found by this approach, including annexin A2, already described as a tPA receptor in pancreas and endothelial cells, other proteins acting as tPA receptors (i.e., enolase, cytokeratins 8 and 18) in other tissues, and additional proteins not previously identified as candidate tPA receptors. Confirmation of the results was performed for some of these proteins using immunoblotting. These studies are the basis for further functional analyses on the role of these proteins in the biological effects of tPA.
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Affiliation(s)
- Oriol Roda
- Department of Experimental and Health Sciences, Pompeu Fabra University, Barcelona, Spain
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38
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Briggs LC, Baldwin GS, Miyata N, Kondo H, Zhang X, Freemont PS. Analysis of nucleotide binding to P97 reveals the properties of a tandem AAA hexameric ATPase. J Biol Chem 2008; 283:13745-52. [PMID: 18332143 PMCID: PMC2376215 DOI: 10.1074/jbc.m709632200] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
p97, an essential chaperone in endoplasmic reticulum-associated degradation and organelle biogenesis, contains two AAA domains (D1 and D2) and assembles as a stable hexamer. We present a quantitative analysis of nucleotide binding to both D1 and D2 domains of p97, the first detailed study of nucleotide binding to both AAA domains for this type of AAA+ ATPase. We report that adenosine 5′-O-(thiotriphosphate) (ATPγS) binds with similar affinity to D1 and D2, but ADP binds with higher affinity to D1 than D2, offering an explanation for the higher ATPase activity in D2. Stoichiometric measurements suggest that although both ADP and ATPγS can saturate all 6 nucleotide binding sites in D1, only 3–4 of the 6 D2 sites can bind ATPγS simultaneously. ATPγS binding triggers a downstream cooperative conformational change of at least three monomers, which involves conserved arginine fingers and is necessary for ATP hydrolysis.
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Affiliation(s)
- Louise C Briggs
- Division of Molecular Biosciences, Imperial College London, South Kensington, London SW7 2AZ, United Kingdom
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39
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Abstract
The AAA (ATPase associated with various cellular activities) p97 [also known as VCP (valosin-containing protein)] participates in numerous biological activities and is an essential component of the ubiquitin signalling pathway. A plethora of adaptors have been reported for p97, and increasing evidence is suggesting that it is through adaptor binding that p97 is diverted into different cellular pathways. Studying the interaction between p97 and its adaptors is therefore crucial to our understanding of the physiological roles of the protein. The interactions between p97 and the PUB [PNGase (peptide N-glycosidase)/ubiquitin-associated] domain of PNGase, the UBX (ubiquitin regulatory X) domain of p47, and the UBD (ubiquitin D) domain of Npl4 have been structurally characterized. UBX and UBD are structural homologues that share similar p97-binding modes; it is plausible that other proteins that contain a UBX/UBX-like domain also interact with p97 via similar mechanisms. In addition, several short p97-interacting motifs, such as VBM (VCP-binding motif), VIM (VCP-interacting motif) and SHP, have been identified recently and are also shared between p97 adaptors, hinting that proteins possessing the same p97-binding motif might also share common p97-binding mechanisms. In this review, we aim to summarize our current knowledge on adaptor binding to p97.
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40
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Hozumi A, Padma P, Toda T, Ide H, Inaba K. Molecular characterization of axonemal proteins and signaling molecules responsible for chemoattractant-induced sperm activation inCiona intestinalis. ACTA ACUST UNITED AC 2008; 65:249-67. [DOI: 10.1002/cm.20258] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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41
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Isaacson RL, Simpson PJ, Liu M, Cota E, Zhang X, Freemont P, Matthews S. A new labeling method for methyl transverse relaxation-optimized spectroscopy NMR spectra of alanine residues. J Am Chem Soc 2007; 129:15428-9. [PMID: 18041839 DOI: 10.1021/ja0761784] [Citation(s) in RCA: 92] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Rivka L Isaacson
- Division of Molecular Biosciences, Faculty of Natural Sciences, Imperial College London, South Kensington, London, UK
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42
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Guinto JB, Ritson GP, Taylor JP, Forman MS. Valosin-containing protein and the pathogenesis of frontotemporal dementia associated with inclusion body myopathy. Acta Neuropathol 2007; 114:55-61. [PMID: 17457594 DOI: 10.1007/s00401-007-0224-7] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2007] [Revised: 03/29/2007] [Accepted: 04/04/2007] [Indexed: 12/12/2022]
Abstract
Frontotemporal dementia with inclusion body myopathy and Paget's disease of bone (IBMPFD) is a rare, autosomal dominant disorder caused by mutations in the gene valosin-containing protein (VCP). The CNS pathology is characterized by a novel pattern of ubiquitin pathology distinct from sporadic and familial frontotemporal lobar degeneration with ubiquitin-positive inclusions without VCP mutations. Yet, the ubiquitin-positive inclusions in IBMPFD also stain for TAR DNA binding protein, a feature that links this rare disease with the pathology associated with the majority of sporadic FTD as well as disease resulting from different genetic alterations. VCP, a member of the AAA-ATPase gene family, associates with a plethora of protein adaptors to perform a variety of cellular processes including Golgi assembly/disassembly and regulation of the ubiquitin-proteasome system. However, the mechanism whereby mutations in VCP lead to CNS, muscle, and bone disease is largely unknown. In this report, we review current literature on IBMPFD, focusing on the pathology of the disease and the biology of VCP with respect to IBMPFD.
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Affiliation(s)
- Jake B Guinto
- Department of Pathology and Laboratory Medicine, University of Pennsylvania School of Medicine, 422 Curie Blvd., 605B Stellar-Chance Building, Philadelphia, PA, 19104-6140, USA
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43
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Zhao G, Zhou X, Wang L, Li G, Schindelin H, Lennarz WJ. Studies on peptide:N-glycanase-p97 interaction suggest that p97 phosphorylation modulates endoplasmic reticulum-associated degradation. Proc Natl Acad Sci U S A 2007; 104:8785-90. [PMID: 17496150 PMCID: PMC1885580 DOI: 10.1073/pnas.0702966104] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
During endoplasmic reticulum-associated degradation, the multifunctional AAA ATPase p97 is part of a protein degradation complex. p97 associates via its N-terminal domain with various cofactors to recruit ubiquitinated substrates. It also interacts with alternative substrate-processing cofactors, such as Ufd2, Ufd3, and peptide:N-glycanase (PNGase) in higher eukaryotes. These cofactors determine different fates of the substrates and they all bind outside of the N-terminal domain of p97. Here, we describe a cofactor-binding motif of p97 contained within the last 10 amino acid residues of the C terminus, which is both necessary and sufficient to mediate interactions of p97 with PNGase and Ufd3. The crystal structure of the N-terminal domain of PNGase in complex with this motif provides detailed insight into the interaction between p97 and its substrate-processing cofactors. Phosphorylation of p97's highly conserved penultimate tyrosine residue, which is the main phosphorylation site during T cell receptor stimulation, completely blocks binding of either PNGase or Ufd3 to p97. This observation suggests that phosphorylation of this residue modulates endoplasmic reticulum-associated protein degradation activity by discharging substrate-processing cofactors.
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Affiliation(s)
- Gang Zhao
- *Center for Structural Biology, Stony Brook University, Stony Brook, NY 11794-5115
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794-5215; and
| | - Xiaoke Zhou
- *Center for Structural Biology, Stony Brook University, Stony Brook, NY 11794-5115
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794-5215; and
| | - Liqun Wang
- *Center for Structural Biology, Stony Brook University, Stony Brook, NY 11794-5115
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794-5215; and
| | - Guangtao Li
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794-5215; and
| | - Hermann Schindelin
- *Center for Structural Biology, Stony Brook University, Stony Brook, NY 11794-5115
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794-5215; and
- Rudolf Virchow Center for Experimental Biomedicine and Institute of Structural Biology, University of Würzburg, Versbacher Strasse 9, 97078 Würzburg, Germany
- To whom correspondence may be addressed. E-mail: or
| | - William J. Lennarz
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794-5215; and
- To whom correspondence may be addressed. E-mail: or
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44
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Isaacson RL, Pye VE, Simpson P, Meyer HH, Zhang X, Freemont PS, Matthews S. Detailed structural insights into the p97-Npl4-Ufd1 interface. J Biol Chem 2007; 282:21361-9. [PMID: 17491009 DOI: 10.1074/jbc.m610069200] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The AAA ATPase, p97, achieves its versatility through binding to a wide range of cofactor proteins that adapt it to different cellular functions. The heterodimer UN (comprising Ufd1 and Npl4) is an adaptor complex that recruits p97 for numerous tasks, many of which involve the ubiquitin pathway. Insights into the structural specificity of p97 for its UN adaptor are currently negligible. Here, we present the solution structure of the Npl4 "ubiquitin-like" domain (UBD), which adopts a beta-grasp fold with a 3(10) helical insert. Moreover we performed a chemical shift perturbation analysis of its binding surface with the p97 N domain. We assigned the backbone amides of the p97 N domain and probed both its reciprocal binding surface with Npl4 UBD and its interaction with the p97-binding region of Ufd1. NMR data recorded on a 400-kDa full-length UN-hexamer p97 complex reveals an identical mode of interaction. We calculated a structural model for the p97 N-Npl4 UBD complex, and a comparison with the p97-p47 adaptor complex reveals subtle differences in p97 adaptor recognition and specificity.
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Affiliation(s)
- Rivka L Isaacson
- Division of Molecular Biosciences, Imperial College London, Biochemistry Building, South Kensington, London SW7 2AZ, United Kingdom
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45
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McConnell E, Lass A, Wójcik C. Ufd1-Npl4 is a negative regulator of cholera toxin retrotranslocation. Biochem Biophys Res Commun 2007; 355:1087-90. [PMID: 17331469 DOI: 10.1016/j.bbrc.2007.02.077] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2007] [Accepted: 02/16/2007] [Indexed: 11/30/2022]
Abstract
The A1 chain of the cholera toxin (CT) undergoes retrotranslocation to the cytosol across the endoplasmic reticulum (ER) membrane by hijacking ER-associated degradation (ERAD). In the cytosol the CT A1 chain stimulates adenylyl cyclase. The VCP(Ufd1-Npl4) complex mediates retrotranslocation of emerging ER proteins. While one group reported that VCP is required for CT retrotranslocation, another group concluded the opposite. We show that VCP is dispensable for CT retrotranslocation, however RNAi of either Ufd1 or Npl4 induces an increase in adenylyl cyclase activity induced by CT. RNAi of VCP, Ufd1 or Npl4 did not affect adenylyl cyclase activity induced by forskolin. These findings are coherent with our previous report showing that depletion of Ufd1-Npl4 accelerates ERAD of reporter substrates. To integrate contradictory results we propose a new model, where Ufd1-Npl4 is a negative regulator of retrotranslocation, delaying the retrotranslocation of ERAD substrates independently of its association with VCP.
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Affiliation(s)
- Elizabeth McConnell
- Department of Anatomy and Cell Biology, Indiana University School of Medicine, 8600 University Blvd., Evansville, IN 47712, USA
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46
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Latterich M. p97 adaptor choice regulates organelle biogenesis. Dev Cell 2007; 11:755-7. [PMID: 17141151 DOI: 10.1016/j.devcel.2006.11.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
The AAA protein p97 requires adaptor-like cofactors for its numerous cellular functions. In this issue of Developmental Cell, Uchiyama et al. (2006) identify p37 as a p97 adaptor that is required constitutively for ER and Golgi membrane fusion, analogous to the mitotic membrane fusion role of the adaptor p47. Their study suggests that related p97 adaptors involved in similar cellular pathways can be subject to differential regulation.
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Affiliation(s)
- Martin Latterich
- Department of Anatomy and Cell Biology, McGill University, 3640 University Street, Montreal, Quebec, H3A 2B2, Canada
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47
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Pye VE, Beuron F, Keetch CA, McKeown C, Robinson CV, Meyer HH, Zhang X, Freemont PS. Structural insights into the p97-Ufd1-Npl4 complex. Proc Natl Acad Sci U S A 2007; 104:467-72. [PMID: 17202270 PMCID: PMC1761865 DOI: 10.1073/pnas.0603408104] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
p97/VCP (Cdc48 in yeast) is an essential and abundant member of the AAA+ family of ATPases and is involved in a number of diverse cellular pathways through interactions with different adaptor proteins. The two most characterized adaptors for p97 are p47 and the Ufd1 (ubiquitin fusion degradation 1)-Npl4 (nuclear protein localization 4) complex. p47 directs p97 to membrane fusion events and has been shown to be involved in protein degradation. The Ufd1-Npl4 complex directs p97 to an essential role in endoplasmic reticulum-associated degradation and an important role in mitotic spindle disassembly postmitosis. Here we describe the structural features of the Ufd1-Npl4 complex and its interaction with p97 with the aid of EM and other biophysical techniques. The Ufd1-Npl4 heterodimer has an elongated bilobed structure that is approximately 80 x 30 A in dimension. One Ufd1-Npl4 heterodimer is shown to interact with one p97 hexamer to form the p97-Ufd1-Npl4 complex. The Ufd1-Npl4 heterodimer emanates from one region on the periphery of the N-D1 plane of the p97 hexamer. Intriguingly, the p97-p47 and the p97-Ufd1-Npl4 complexes are significantly different in stoichiometry, symmetry, and quaternary arrangement, reflecting their specific actions and their ability to interact with additional cofactors that cooperate with p97 in diverse cellular pathways.
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Affiliation(s)
- Valerie E. Pye
- *Division of Molecular Biosciences, Faculty of Natural Sciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - Fabienne Beuron
- *Division of Molecular Biosciences, Faculty of Natural Sciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - Catherine A. Keetch
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, United Kingdom; and
| | - Ciaran McKeown
- *Division of Molecular Biosciences, Faculty of Natural Sciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - Carol V. Robinson
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, United Kingdom; and
| | - Hemmo H. Meyer
- Institute of Biochemistry, Eidgenössiche Technische Hochschule Zurich, 8093 Zurich, Switzerland
| | - Xiaodong Zhang
- *Division of Molecular Biosciences, Faculty of Natural Sciences, Imperial College London, London SW7 2AZ, United Kingdom
- To whom correspondence may be addressed. E-mail:
or
| | - Paul S. Freemont
- *Division of Molecular Biosciences, Faculty of Natural Sciences, Imperial College London, London SW7 2AZ, United Kingdom
- To whom correspondence may be addressed. E-mail:
or
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48
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Ballar P, Shen Y, Yang H, Fang S. The Role of a Novel p97/Valosin-containing Protein-interacting Motif of gp78 in Endoplasmic Reticulum-associated Degradation. J Biol Chem 2006; 281:35359-68. [PMID: 16987818 DOI: 10.1074/jbc.m603355200] [Citation(s) in RCA: 109] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Improperly folded proteins in the endoplasmic reticulum (ER) are eliminated via ER-associated degradation, a process that dislocates misfolded proteins from the ER membrane into the cytosol, where they undergo proteasomal degradation. Dislocation requires a subclass of ubiquitin ligases that includes gp78 in addition to the AAA ATPase p97/VCP and its cofactor, the Ufd1-Npl4 dimer. We have previously reported that gp78 interacts directly with p97/VCP. Here, we identify a novel p97/VCP-interacting motif (VIM) within gp78 that mediates this interaction. We demonstrate that the VIM of gp78 recruits p97/VCP to the ER, but has no effect on Ufd1 localization. We also show that gp78 VIM interacts with the ND1 domain of p97/VCP that was shown previously to be the binding site for Ufd1. To evaluate the role of Ufd1 in gp78-p97/VCP-mediated degradation of CD3delta, a known substrate of gp78, RNA interference was used to silence the expression of Ufd1 and p97/VCP. Inhibition of p97/VCP, but not Ufd1, stabilized CD3delta in cells that overexpress gp78. However, both p97/VCP and Ufd1 appear to be required for CD3delta degradation in cells expressing physiological levels of gp78. These results raise the possibility that Ufd1 and gp78 may bind p97/VCP in a mutually exclusive manner and suggest that gp78 might act in a Ufd1-independent degradation pathway for misfolded ER proteins, which operates in parallel with the previously established p97/VCP-Ufd1-Npl4-mediated mechanism.
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Affiliation(s)
- Petek Ballar
- Medical Biotechnology Center, University of Maryland Biotechnology Institute, Baltimore, Maryland 21201, USA
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Liang J, Yin C, Doong H, Fang S, Peterhoff C, Nixon RA, Monteiro MJ. Characterization of erasin (UBXD2): a new ER protein that promotes ER-associated protein degradation. J Cell Sci 2006; 119:4011-24. [PMID: 16968747 DOI: 10.1242/jcs.03163] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Ubiquitin regulator-X (UBX) is a discrete protein domain that binds p97/valosin-containing protein (VCP), a molecular chaperone involved in diverse cell processes, including endoplasmic-reticulum-associated protein degradation (ERAD). Here we characterize a human UBX-containing protein, UBXD2, that is highly conserved in mammals, which we have renamed erasin. Biochemical fractionation, immunofluorescence and electron microscopy, and protease protection experiments suggest that erasin is an integral membrane protein of the endoplasmic reticulum and nuclear envelope with both its N- and C-termini facing the cytoplasm or nucleoplasm. Localization of GFP-tagged deletion derivatives of erasin in HeLa cells revealed that a single 21-amino-acid sequence located near the C-terminus is necessary and sufficient for localization of erasin to the endoplasmic reticulum. Immunoprecipitation and GST-pulldown experiments confirmed that erasin binds p97/VCP via its UBX domain. Additional immunoprecipitation assays indicated that erasin exists in a complex with other p97/VCP-associated factors involved in ERAD. Overexpression of erasin enhanced the degradation of the ERAD substrate CD3δ, whereas siRNA-mediated reduction of erasin expression almost completely blocked ERAD. Erasin protein levels were increased by endoplasmic reticulum stress. Immunohistochemical staining of brain tissue from patients with Alzheimer's disease and control subjects revealed that erasin accumulates preferentially in neurons undergoing neurofibrillary degeneration in Alzheimer's disease. These results suggest that erasin may be involved in ERAD and in Alzheimer's disease.
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Affiliation(s)
- Jing Liang
- Graduate Program in Molecular Medicine, and Institute for Neurodegenerative Diseases, University of Maryland Biotechnology Institute, 725 West Lombard Street, Baltimore, MD 21201, USA
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Wójcik C, Rowicka M, Kudlicki A, Nowis D, McConnell E, Kujawa M, DeMartino GN. Valosin-containing protein (p97) is a regulator of endoplasmic reticulum stress and of the degradation of N-end rule and ubiquitin-fusion degradation pathway substrates in mammalian cells. Mol Biol Cell 2006; 17:4606-18. [PMID: 16914519 PMCID: PMC1635394 DOI: 10.1091/mbc.e06-05-0432] [Citation(s) in RCA: 148] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Valosin-containing protein (VCP; p97; cdc48 in yeast) is a hexameric ATPase of the AAA family (ATPases with multiple cellular activities) involved in multiple cellular functions, including degradation of proteins by the ubiquitin (Ub)-proteasome system (UPS). We examined the consequences of the reduction of VCP levels after RNA interference (RNAi) of VCP. A new stringent method of microarray analysis demonstrated that only four transcripts were nonspecifically affected by RNAi, whereas approximately 30 transcripts were affected in response to reduced VCP levels in a sequence-independent manner. These transcripts encoded proteins involved in endoplasmic reticulum (ER) stress, apoptosis, and amino acid starvation. RNAi of VCP promoted the unfolded protein response, without eliciting a cytosolic stress response. RNAi of VCP inhibited the degradation of R-GFP (green fluorescent protein) and Ub-(G76V)-GFP, two cytoplasmic reporter proteins degraded by the UPS, and of alpha chain of the T-cell receptor, an established substrate of the ER-associated degradation (ERAD) pathway. Surprisingly, RNAi of VCP had no detectable effect on the degradation of two other ERAD substrates, alpha1-antitrypsin and deltaCD3. These results indicate that VCP is required for maintenance of normal ER structure and function and mediates the degradation of some proteins via the UPS, but is dispensable for the UPS-dependent degradation of some ERAD substrates.
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Affiliation(s)
- Cezary Wójcik
- *Department of Anatomy and Cell Biology, Indiana University School of Medicine, Evansville, IN 47712
- Departments of Physiology and
| | - Maga Rowicka
- Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390; and
| | - Andrzej Kudlicki
- Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390; and
| | - Dominika Nowis
- *Department of Anatomy and Cell Biology, Indiana University School of Medicine, Evansville, IN 47712
| | - Elizabeth McConnell
- *Department of Anatomy and Cell Biology, Indiana University School of Medicine, Evansville, IN 47712
| | - Marek Kujawa
- Department of Histology and Embryology, Medical University of Warsaw, 02-004 Warsaw, Poland
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