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Nandi P, DeVore K, Wang F, Li S, Walker JD, Truong TT, LaPorte MG, Wipf P, Schlager H, McCleerey J, Paquette W, Columbres RCA, Gan T, Poh YP, Fromme P, Flint AJ, Wolf M, Huryn DM, Chou TF, Chiu PL. Mechanism of allosteric inhibition of human p97/VCP ATPase and its disease mutant by triazole inhibitors. Commun Chem 2024; 7:177. [PMID: 39122922 PMCID: PMC11316111 DOI: 10.1038/s42004-024-01267-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2024] [Accepted: 08/01/2024] [Indexed: 08/12/2024] Open
Abstract
Human p97 ATPase is crucial in various cellular processes, making it a target for inhibitors to treat cancers, neurological, and infectious diseases. Triazole allosteric p97 inhibitors have been demonstrated to match the efficacy of CB-5083, an ATP-competitive inhibitor, in cellular models. However, the mechanism is not well understood. This study systematically investigates the structures of new triazole inhibitors bound to both wild-type and disease mutant forms of p97 and measures their effects on function. These inhibitors bind at the interface of the D1 and D2 domains of each p97 subunit, shifting surrounding helices and altering the loop structures near the C-terminal α2 G helix to modulate domain-domain communications. A key structural moiety of the inhibitor affects the rotameric conformations of interacting side chains, indirectly modulating the N-terminal domain conformation in p97 R155H mutant. The differential effects of inhibitor binding to wild-type and mutant p97 provide insights into drug design with enhanced specificity, particularly for oncology applications.
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Affiliation(s)
- Purbasha Nandi
- School of Molecular Sciences, Arizona State University, Tempe, AZ, USA
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ, USA
- Biology Department, Brookhaven National Laboratory, Upton, NY, USA
| | - Kira DeVore
- School of Molecular Sciences, Arizona State University, Tempe, AZ, USA
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ, USA
| | - Feng Wang
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Shan Li
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Joel D Walker
- University of Pittsburgh Chemical Diversity Center, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, USA
| | - Thanh Tung Truong
- University of Pittsburgh Chemical Diversity Center, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, USA
- Faculty of Pharmacy, Phenikaa University, Hanoi, Vietnam
| | - Matthew G LaPorte
- University of Pittsburgh Chemical Diversity Center, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, USA
| | - Peter Wipf
- University of Pittsburgh Chemical Diversity Center, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, USA
| | | | - John McCleerey
- Curia Global, Albany, NY, USA
- Graduate School of Arts and Sciences, Boston University, Boston, MA, USA
| | | | - Rod Carlo A Columbres
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
- Center for Cancer Research, National Cancer Institute, National Institute of Health, Bethesda, MD, USA
| | - Taiping Gan
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Yu-Ping Poh
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ, USA
- Biodesign Center for Mechanism of Evolution, Arizona State University, Tempe, AZ, USA
| | - Petra Fromme
- School of Molecular Sciences, Arizona State University, Tempe, AZ, USA
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ, USA
| | - Andrew J Flint
- Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | | | - Donna M Huryn
- University of Pittsburgh Chemical Diversity Center, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Pharmaceutical Sciences, University of Pittsburgh School of Pharmacy, Pittsburgh, PA, USA
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA, USA
| | - Tsui-Fen Chou
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
- Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA, USA.
| | - Po-Lin Chiu
- School of Molecular Sciences, Arizona State University, Tempe, AZ, USA.
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ, USA.
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2
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Maduka AO, Manohar S, Foster MW, Silva GM. Localized K63 ubiquitin signaling is regulated by VCP/p97 during oxidative stress. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.20.598218. [PMID: 38948861 PMCID: PMC11213022 DOI: 10.1101/2024.06.20.598218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
Under stress conditions, cells reprogram their molecular machineries to mitigate damage and promote survival. Ubiquitin signaling is globally increased during oxidative stress, controlling protein fate and supporting stress defenses at several subcellular compartments. However, the rules driving subcellular ubiquitin localization to promote these concerted response mechanisms remain understudied. Here, we show that K63-linked ubiquitin chains, known to promote proteasome-independent pathways, accumulate primarily in non-cytosolic compartments during oxidative stress induced by sodium arsenite in mammalian cells. Our subcellular ubiquitin proteomic analyses of non-cytosolic compartments expanded 10-fold the pool of proteins known to be ubiquitinated during arsenite stress (2,046) and revealed their involvement in pathways related to immune signaling and translation control. Moreover, subcellular proteome analyses revealed proteins that are recruited to non-cytosolic compartments under stress, including a significant enrichment of helper ubiquitin-binding adaptors of the ATPase VCP that processes ubiquitinated substrates for downstream signaling. We further show that VCP recruitment to non-cytosolic compartments under arsenite stress occurs in a ubiquitin-dependent manner mediated by its adaptor NPLOC4. Additionally, we show that VCP and NPLOC4 activities are critical to sustain low levels of non-cytosolic K63-linked ubiquitin chains, supporting a cyclical model of ubiquitin conjugation and removal that is disrupted by cellular exposure to reactive oxygen species. This work deepens our understanding of the role of localized ubiquitin and VCP signaling in the basic mechanisms of stress response and highlights new pathways and molecular players that are essential to reshape the composition and function of the human subcellular proteome under dynamic environments.
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Affiliation(s)
| | - Sandhya Manohar
- Institute for Biochemistry, Department of Biology, ETH Zürich, 8093 Zürich, Switzerland
| | - Matthew W. Foster
- Proteomics and Metabolomics Core Facility, Duke University, Durham, NC, 27708, USA
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3
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Jones NH, Liu Q, Urnavicius L, Dahan NE, Vostal LE, Kapoor TM. Allosteric activation of VCP, an AAA unfoldase, by small molecule mimicry. Proc Natl Acad Sci U S A 2024; 121:e2316892121. [PMID: 38833472 PMCID: PMC11181084 DOI: 10.1073/pnas.2316892121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Accepted: 04/17/2024] [Indexed: 06/06/2024] Open
Abstract
The loss of function of AAA (ATPases associated with diverse cellular activities) mechanoenzymes has been linked to diseases, and small molecules that activate these proteins can be powerful tools to probe mechanisms and test therapeutic hypotheses. Unlike chemical inhibitors that can bind a single conformational state to block enzyme function, activator binding must be permissive to different conformational states needed for mechanochemistry. However, we do not know how AAA proteins can be activated by small molecules. Here, we focus on valosin-containing protein (VCP)/p97, an AAA unfoldase whose loss of function has been linked to protein aggregation-based disorders, to identify druggable sites for chemical activators. We identified VCP ATPase Activator 1 (VAA1), a compound that dose-dependently stimulates VCP ATPase activity up to ~threefold. Our cryo-EM studies resulted in structures (ranging from ~2.9 to 3.7 Å-resolution) of VCP in apo and ADP-bound states and revealed that VAA1 binds an allosteric pocket near the C-terminus in both states. Engineered mutations in the VAA1-binding site confer resistance to VAA1, and furthermore, modulate VCP activity. Mutation of a phenylalanine residue in the VCP C-terminal tail that can occupy the VAA1 binding site also stimulates ATPase activity, suggesting that VAA1 acts by mimicking this interaction. Together, our findings uncover a druggable allosteric site and a mechanism of enzyme regulation that can be tuned through small molecule mimicry.
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Affiliation(s)
- Natalie H. Jones
- Laboratory of Chemistry and Cell Biology, The Rockefeller University, New York, NY10065
- Tri-Institutional PhD Program in Chemical Biology, New York, NY10065
| | - Qiwen Liu
- Laboratory of Chemistry and Cell Biology, The Rockefeller University, New York, NY10065
| | - Linas Urnavicius
- Laboratory of Chemistry and Cell Biology, The Rockefeller University, New York, NY10065
| | - Noa E. Dahan
- Laboratory of Chemistry and Cell Biology, The Rockefeller University, New York, NY10065
- The David Rockefeller Graduate Program in Bioscience, The Rockefeller University, New York, NY10065
| | - Lauren E. Vostal
- Laboratory of Chemistry and Cell Biology, The Rockefeller University, New York, NY10065
- Tri-Institutional PhD Program in Chemical Biology, New York, NY10065
| | - Tarun M. Kapoor
- Laboratory of Chemistry and Cell Biology, The Rockefeller University, New York, NY10065
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4
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Batra S, Vaquer-Alicea JI, Valdez C, Taylor SP, Manon VA, Vega AR, Kashmer OM, Kolay S, Lemoff A, Cairns NJ, White CL, Diamond MI. VCP regulates early tau seed amplification via specific cofactors. RESEARCH SQUARE 2024:rs.3.rs-4307848. [PMID: 38826306 PMCID: PMC11142303 DOI: 10.21203/rs.3.rs-4307848/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
Background Neurodegenerative tauopathies may progress based on seeding by pathological tau assemblies, whereby an aggregate is released from one cell, gains entry to an adjacent or connected cell, and serves as a specific template for its own replication in the cytoplasm. In vitro seeding reactions typically take days, yet seeding into the complex cytoplasmic milieu happens within hours, implicating a machinery with unknown players that controls this process in the acute phase. Methods We used proximity labeling to identify factors that control seed amplification within 5h of seed exposure. We fused split-APEX2 to the C-terminus of tau repeat domain (RD) to reconstitute peroxidase activity 5h after seeded intracellular tau aggregation. Valosin containing protein (VCP/p97) was the top hit. VCP harbors dominant mutations that underlie two neurodegenerative diseases, multisystem proteinopathy and vacuolar tauopathy, but its mechanistic role is unclear. We used immortalized cells and human neurons to study the effects of VCP on tau seeding. We exposed cells to fibrils or brain homogenates in cell culture media and measured effects on uptake and induction of intracellular tau aggregation following various genetic and chemical manipulations of VCP. Results VCP knockdown reduced tau seeding. Chemical inhibitors had opposing effects on aggregation in HEK293T tau biosensor cells and human neurons alike: ML-240 increased seeding efficiency, whereas NMS-873 decreased it. The inhibitors were effective only when administered within 8h of seed exposure, indicating a role for VCP early in seed processing. We screened 30 VCP co-factors in HEK293T biosensor cells by genetic knockout or knockdown. Reduction of ATXN3, NSFL1C, UBE4B, NGLY1, and OTUB1 decreased tau seeding, as did NPLOC4, which also uniquely increased soluble tau levels. By contrast, reduction of FAF2 increased tau seeding. Conclusions Divergent effects on tau seeding of chemical inhibitors and cofactor reduction indicate that VCP regulates this process. This is consistent with a dedicated cytoplasmic processing complex based on VCP that directs seeds acutely towards degradation vs. amplification.
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Affiliation(s)
- Sushobhna Batra
- UT Southwestern: The University of Texas Southwestern Medical Center
| | | | - Clarissa Valdez
- UT Southwestern: The University of Texas Southwestern Medical Center
| | - Skyler P Taylor
- UT Southwestern: The University of Texas Southwestern Medical Center
| | - Victor A Manon
- UT Southwestern: The University of Texas Southwestern Medical Center
| | - Anthony R Vega
- UT Southwestern: The University of Texas Southwestern Medical Center
| | - Omar M Kashmer
- UT Southwestern: The University of Texas Southwestern Medical Center
| | - Sourav Kolay
- UT Southwestern: The University of Texas Southwestern Medical Center
| | - Andrew Lemoff
- UT Southwestern: The University of Texas Southwestern Medical Center
| | - Nigel J Cairns
- University of Exeter Faculty of Health and Life Sciences
| | - Charles L White
- UT Southwestern: The University of Texas Southwestern Medical Center
| | - Marc I Diamond
- UT Southwestern: The University of Texas Southwestern Medical Center
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5
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Ahlstedt BA, Ganji R, Mukkavalli S, Paulo JA, Gygi SP, Raman M. UBXN1 maintains ER proteostasis and represses UPR activation by modulating translation. EMBO Rep 2024; 25:672-703. [PMID: 38177917 PMCID: PMC10897191 DOI: 10.1038/s44319-023-00027-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 11/24/2023] [Accepted: 11/30/2023] [Indexed: 01/06/2024] Open
Abstract
ER protein homeostasis (proteostasis) is essential for proper folding and maturation of proteins in the secretory pathway. Loss of ER proteostasis can lead to the accumulation of misfolded or aberrant proteins in the ER and triggers the unfolded protein response (UPR). In this study, we find that the p97 adaptor UBXN1 is an important negative regulator of the UPR. Loss of UBXN1 sensitizes cells to ER stress and activates the UPR. This leads to widespread upregulation of the ER stress transcriptional program. Using comparative, quantitative proteomics we show that deletion of UBXN1 results in a significant enrichment of proteins involved in ER-quality control processes including those involved in protein folding and import. Notably, we find that loss of UBXN1 does not perturb p97-dependent ER-associated degradation (ERAD). Our studies indicate that loss of UBXN1 increases translation in both resting and ER-stressed cells. Surprisingly, this process is independent of p97 function. Taken together, our studies have identified a new role for UBXN1 in repressing translation and maintaining ER proteostasis in a p97 independent manner.
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Affiliation(s)
- Brittany A Ahlstedt
- Department of Developmental Molecular and Chemical Biology, Tufts University School of Medicine, Boston, MA, USA
- ALPCA diagnostics, Salem, NH, USA
| | - Rakesh Ganji
- Department of Developmental Molecular and Chemical Biology, Tufts University School of Medicine, Boston, MA, USA
| | - Sirisha Mukkavalli
- Department of Developmental Molecular and Chemical Biology, Tufts University School of Medicine, Boston, MA, USA
- Dana Farber Cancer Research Institute, Boston, MA, USA
| | - Joao A Paulo
- Department of Cell Biology Harvard Medical School, Boston, MA, USA
| | - Steve P Gygi
- Department of Cell Biology Harvard Medical School, Boston, MA, USA
| | - Malavika Raman
- Department of Developmental Molecular and Chemical Biology, Tufts University School of Medicine, Boston, MA, USA.
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Li H, Ji Z, Paulo JA, Gygi SP, Rapoport TA. Bidirectional substrate shuttling between the 26S proteasome and the Cdc48 ATPase promotes protein degradation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.20.572403. [PMID: 38187576 PMCID: PMC10769200 DOI: 10.1101/2023.12.20.572403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Most eukaryotic proteins are degraded by the 26S proteasome after modification with a polyubiquitin chain. Substrates lacking unstructured segments cannot be degraded directly and require prior unfolding by the Cdc48 ATPase (p97 or VCP in mammals) in complex with its ubiquitin-binding partner Ufd1-Npl4 (UN). Here, we use purified yeast components to reconstitute Cdc48-dependent degradation of well-folded model substrates by the proteasome. We show that a minimal system consists of the 26S proteasome, the Cdc48-UN ATPase complex, the proteasome cofactor Rad23, and the Cdc48 cofactors Ubx5 and Shp1. Rad23 and Ubx5 stimulate polyubiquitin binding to the 26S proteasome and the Cdc48-UN complex, respectively, allowing these machines to compete for substrates before and after their unfolding. Shp1 stimulates protein unfolding by the Cdc48-UN complex, rather than substrate recruitment. In vivo experiments confirm that many proteins undergo bidirectional substrate shuttling between the 26S proteasome and Cdc48 ATPase before being degraded.
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7
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Jones NH, Liu Q, Urnavicius L, Dahan NE, Vostal LE, Kapoor TM. Allosteric activation of VCP, a AAA unfoldase, by small molecule mimicry. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.02.560478. [PMID: 37873168 PMCID: PMC10592943 DOI: 10.1101/2023.10.02.560478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
The loss of function of AAA (ATPases associated with diverse cellular activities) mechanoenzymes has been linked to diseases, and small molecules that activate these proteins can be powerful tools to probe mechanisms and test therapeutic hypotheses. Unlike chemical inhibitors that can bind a single conformational state to block enzyme activity, activator binding must be permissive to different conformational states needed for enzyme function. However, we do not know how AAA proteins can be activated by small molecules. Here, we focus on valosin-containing protein (VCP)/p97, a AAA unfoldase whose loss of function has been linked to protein aggregation-based disorders, to identify druggable sites for chemical activators. We identified VCP Activator 1 (VA1), a compound that dose-dependently stimulates VCP ATPase activity up to ∼3-fold. Our cryo-EM studies resulted in structures (∼2.9-3.5 Å-resolution) of VCP in apo and ADP-bound states, and revealed VA1 binding an allosteric pocket near the C-terminus in both states. Engineered mutations in the VA1 binding site confer resistance to VA1, and furthermore, modulate VCP activity to a similar level as VA1-mediated activation. The VA1 binding site can alternatively be occupied by a phenylalanine residue in the VCP C-terminal tail, a motif that is post-translationally modified and interacts with cofactors. Together, our findings uncover a druggable allosteric site and a mechanism of enzyme regulation that can be tuned through small molecule mimicry. Significance The loss of function of valosin-containing protein (VCP/p97), a mechanoenzyme from the AAA superfamily that hydrolyzes ATP and uses the released energy to extract or unfold substrate proteins, is linked to protein aggregation-based disorders. However, druggable allosteric sites to activate VCP, or any AAA mechanoenzyme, have not been identified. Here, we report cryo-EM structures of VCP in two states in complex with VA1, a compound we identified that dose-dependently stimulates VCP's ATP hydrolysis activity. The VA1 binding site can also be occupied by a phenylalanine residue in the VCP C-terminal tail, suggesting that VA1 acts through mimicry of this interaction. Our study reveals a druggable allosteric site and a mechanism of enzyme regulation.
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Batra S, Vaquer-Alicea J, Manon VA, Kashmer OM, Lemoff A, Cairns NJ, White CL, Diamond MI. VCP increases or decreases tau seeding using specific cofactors. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.30.555637. [PMID: 37693404 PMCID: PMC10491269 DOI: 10.1101/2023.08.30.555637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
Background Neurodegenerative tauopathies may progress based on seeding by pathological tau assemblies, whereby an aggregate is released from one cell, gains entry to an adjacent or connected cell, and serves as a specific template for its own replication in the cytoplasm. In vitro seeding reactions typically take days, yet seeding into the complex cytoplasmic milieu can happen within hours. A cellular machinery might regulate this process, but potential players are unknown. Methods We used proximity labeling to identify factors that control seed amplification. We fused split-APEX2 to the C-terminus of tau repeat domain (RD) to reconstitute peroxidase activity upon seeded intracellular tau aggregation. We identified valosin containing protein (VCP/p97) 5h after seeding. Mutations in VCP underlie two neurodegenerative diseases, multisystem proteinopathy and vacuolar tauopathy, but its mechanistic role is unclear. We utilized tau biosensors, a cellular model for tau aggregation, to study the effects of VCP on tau seeding. Results VCP knockdown reduced tau seeding. However, distinct chemical inhibitors of VCP and the proteasome had opposing effects on aggregation, but only when given <8h of seed exposure. ML-240 increased seeding efficiency ~40x, whereas NMS-873 decreased seeding efficiency by 50%, and MG132 increased seeding ~10x. We screened VCP co-factors in HEK293 biosensor cells by genetic knockout or knockdown. Reduction of ATXN3, NSFL1C, UBE4B, NGLY1, and OTUB1 decreased tau seeding, as did NPLOC4, which also uniquely increased soluble tau levels. Reduction of FAF2 and UBXN6 increased tau seeding. Conclusions VCP uses distinct cofactors to determine seed replication efficiency, consistent with a dedicated cytoplasmic processing complex that directs seeds towards dissolution vs. amplification.
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Affiliation(s)
- Sushobhna Batra
- Center for Alzheimer's and Neurodegenerative Diseases, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX
| | - Jaime Vaquer-Alicea
- Center for Alzheimer's and Neurodegenerative Diseases, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX
| | - Victor A Manon
- Center for Alzheimer's and Neurodegenerative Diseases, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX
| | - Omar M Kashmer
- Center for Alzheimer's and Neurodegenerative Diseases, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX
| | - Andrew Lemoff
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX
| | - Nigel J Cairns
- Department of Clinical and Biological Sciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
| | - Charles L White
- Department of Pathology, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX
| | - Marc I Diamond
- Center for Alzheimer's and Neurodegenerative Diseases, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX
- Department of Neurology, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX
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Chu S, Xie X, Payan C, Stochaj U. Valosin containing protein (VCP): initiator, modifier, and potential drug target for neurodegenerative diseases. Mol Neurodegener 2023; 18:52. [PMID: 37545006 PMCID: PMC10405438 DOI: 10.1186/s13024-023-00639-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 06/27/2023] [Indexed: 08/08/2023] Open
Abstract
The AAA+ ATPase valosin containing protein (VCP) is essential for cell and organ homeostasis, especially in cells of the nervous system. As part of a large network, VCP collaborates with many cofactors to ensure proteostasis under normal, stress, and disease conditions. A large number of mutations have revealed the importance of VCP for human health. In particular, VCP facilitates the dismantling of protein aggregates and the removal of dysfunctional organelles. These are critical events to prevent malfunction of the brain and other parts of the nervous system. In line with this idea, VCP mutants are linked to the onset and progression of neurodegeneration and other diseases. The intricate molecular mechanisms that connect VCP mutations to distinct brain pathologies continue to be uncovered. Emerging evidence supports the model that VCP controls cellular functions on multiple levels and in a cell type specific fashion. Accordingly, VCP mutants derail cellular homeostasis through several mechanisms that can instigate disease. Our review focuses on the association between VCP malfunction and neurodegeneration. We discuss the latest insights in the field, emphasize open questions, and speculate on the potential of VCP as a drug target for some of the most devastating forms of neurodegeneration.
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Affiliation(s)
- Siwei Chu
- Department of Physiology, McGill University, Montreal, HG3 1Y6, Canada
| | - Xinyi Xie
- Department of Physiology, McGill University, Montreal, HG3 1Y6, Canada
| | - Carla Payan
- Department of Physiology, McGill University, Montreal, HG3 1Y6, Canada
| | - Ursula Stochaj
- Department of Physiology, McGill University, Montreal, HG3 1Y6, Canada.
- Quantitative Life Sciences Program, McGill University, Montreal, Canada.
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10
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Common Markers and Small Molecule Inhibitors in Golgi Studies. Methods Mol Biol 2022; 2557:453-493. [PMID: 36512231 PMCID: PMC10178357 DOI: 10.1007/978-1-0716-2639-9_27] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
In this chapter, we provide a detailed guide for the application of commonly used small molecules to study Golgi structure and function in vitro. Furthermore, we have curated a concise, validated list of endomembrane markers typically used in downstream assays to examine the consequent effect on the Golgi via microscopy and western blot after drug treatment. This chapter will be useful for researchers beginning their foray into the field of intracellular trafficking and Golgi biology.
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11
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Wang F, Li S, Wang TY, Lopez GA, Antoshechkin I, Chou TF. P97/VCP ATPase inhibitors can rescue p97 mutation-linked motor neuron degeneration. Brain Commun 2022; 4:fcac176. [PMID: 35865348 PMCID: PMC9294923 DOI: 10.1093/braincomms/fcac176] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 05/11/2022] [Accepted: 07/06/2022] [Indexed: 12/12/2022] Open
Abstract
Mutations in p97/VCP cause two motor neuron diseases: inclusion body myopathy associated with Paget disease of bone and frontotemporal dementia and familial amyotrophic lateral sclerosis. How p97 mutations lead to motor neuron degeneration is, however, unknown. Here we used patient-derived induced pluripotent stem cells to generate p97 mutant motor neurons. We reduced the genetic background variation by comparing mutant motor neurons to its isogenic wild type lines. Proteomic analysis reveals that p97R155H/+ motor neurons upregulate several cell cycle proteins at Day 14, but this effect diminishes by Day 20. Molecular changes linked to delayed cell cycle exit are observed in p97 mutant motor neurons. We also find that two p97 inhibitors, CB-5083 and NMS-873, restore some dysregulated protein levels. In addition, two p97 inhibitors and a food and drug administration-approved cyclin-dependent kinase 4/6 inhibitor, Abemaciclib, can rescue motor neuron death. Overall, we successfully used iPSC-derived motor neurons, identified dysregulated proteome and transcriptome and showed that p97 inhibitors rescue phenotypes in this disease model.
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Affiliation(s)
- F Wang
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - S Li
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - T Y Wang
- Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA 91125, USA
| | - G A Lopez
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - I Antoshechkin
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - T F Chou
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
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12
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Compounds activating VCP D1 ATPase enhance both autophagic and proteasomal neurotoxic protein clearance. Nat Commun 2022; 13:4146. [PMID: 35842429 PMCID: PMC9288506 DOI: 10.1038/s41467-022-31905-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 07/08/2022] [Indexed: 01/04/2023] Open
Abstract
Enhancing the removal of aggregate-prone toxic proteins is a rational therapeutic strategy for a number of neurodegenerative diseases, especially Huntington's disease and various spinocerebellar ataxias. Ideally, such approaches should preferentially clear the mutant/misfolded species, while having minimal impact on the stability of wild-type/normally-folded proteins. Furthermore, activation of both ubiquitin-proteasome and autophagy-lysosome routes may be advantageous, as this would allow effective clearance of both monomeric and oligomeric species, the latter which are inaccessible to the proteasome. Here we find that compounds that activate the D1 ATPase activity of VCP/p97 fulfill these requirements. Such effects are seen with small molecule VCP activators like SMER28, which activate autophagosome biogenesis by enhancing interactions of PI3K complex components to increase PI(3)P production, and also accelerate VCP-dependent proteasomal clearance of such substrates. Thus, this mode of VCP activation may be a very attractive target for many neurodegenerative diseases.
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13
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Scarian E, Fiamingo G, Diamanti L, Palmieri I, Gagliardi S, Pansarasa O. The Role of VCP Mutations in the Spectrum of Amyotrophic Lateral Sclerosis-Frontotemporal Dementia. Front Neurol 2022; 13:841394. [PMID: 35273561 PMCID: PMC8902152 DOI: 10.3389/fneur.2022.841394] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 01/28/2022] [Indexed: 01/02/2023] Open
Abstract
Amyotrophic Lateral Sclerosis (ALS) and Frontotemporal Dementia (FTD) are two neurological diseases which, respectively, and primarily affect motor neurons and frontotemporal lobes. Although they can lead to different signs and symptoms, it is now evident that these two pathologies form a continuum and that hallmarks of both diseases can be present within the same person in the so-called ALS-FTD spectrum. Many studies have focused on the genetic overlap of these pathologies and it is now clear that different genes, such as C9orf72, TARDBP, SQSTM1, FUS, and p97/VCP can be mutated in both the diseases. VCP was one of the first genes associated with both FTD and ALS representing an early example of gene overlapping. VCP belongs to the type II AAA (ATPases Associated with diverse cellular activities) family and is involved in ubiquitinated proteins degradation, autophagy, lysosomal clearance and mitochondrial quality control. Since its numerous roles, mutations in this gene lead to different pathological features, first and foremost TDP-43 mislocalization. This review aims to outline recent findings on VCP roles and on how its mutations are linked to the neuropathology of ALS and FTD.
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Affiliation(s)
- Eveljn Scarian
- Department of Brain and Behavioral Sciences, University of Pavia, Pavia, Italy.,Cellular Models and Neuroepigenetics Unit, IRCCS Mondino Foundation, Pavia, Italy
| | - Giuseppe Fiamingo
- Department of Brain and Behavioral Sciences, University of Pavia, Pavia, Italy
| | - Luca Diamanti
- Neuroncology Unit, IRCCS Mondino Foundation, Pavia, Italy
| | - Ilaria Palmieri
- Department of Molecular Medicine, University of Pavia, Pavia, Italy.,Neurogenetics Research Center, IRCCS Mondino Foundation, Pavia, Italy
| | - Stella Gagliardi
- Molecular Biology and Transcriptomics Unit, IRCCS Mondino Foundation, Pavia, Italy
| | - Orietta Pansarasa
- Cellular Models and Neuroepigenetics Unit, IRCCS Mondino Foundation, Pavia, Italy
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14
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Bourbouli M, Paraskevas GP, Rentzos M, Mathioudakis L, Zouvelou V, Bougea A, Tychalas A, Kimiskidis VK, Constantinides V, Zafeiris S, Tzagournissakis M, Papadimas G, Karadima G, Koutsis G, Kroupis C, Kartanou C, Kapaki E, Zaganas I. Genotyping and Plasma/Cerebrospinal Fluid Profiling of a Cohort of Frontotemporal Dementia-Amyotrophic Lateral Sclerosis Patients. Brain Sci 2021; 11:brainsci11091239. [PMID: 34573259 PMCID: PMC8472580 DOI: 10.3390/brainsci11091239] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2021] [Revised: 09/05/2021] [Accepted: 09/14/2021] [Indexed: 11/16/2022] Open
Abstract
Frontotemporal dementia (FTD) and amyotrophic lateral sclerosis (ALS) are part of the same pathophysiological spectrum and have common genetic and cerebrospinal fluid (CSF) biomarkers. Our aim here was to identify causative gene variants in a cohort of Greek patients with FTD, ALS and FTD-ALS, to measure levels of CSF biomarkers and to investigate genotype-phenotype/CSF biomarker associations. In this cohort of 130 patients (56 FTD, 58 ALS and 16 FTD-ALS), we performed C9orf72 hexanucleotide repeat expansion analysis, whole exome sequencing and measurement of “classical” (Aβ42, total tau and phospho-tau) and novel (TDP-43) CSF biomarkers and plasma progranulin. Through these analyses, we identified 14 patients with C9orf72 repeat expansion and 11 patients with causative variants in other genes (three in TARDBP, three in GRN, three in VCP, one in FUS, one in SOD1). In ALS patients, we found that levels of phospho-tau were lower in C9orf72 repeat expansion and MAPT c.855C>T (p.Asp285Asp) carriers compared to non-carriers. Additionally, carriers of rare C9orf72 and APP variants had lower levels of total tau and Aβ42, respectively. Plasma progranulin levels were decreased in patients carrying GRN pathogenic variants. This study expands the genotypic and phenotypic spectrum of FTD/ALS and offers insights in possible genotypic/CSF biomarker associations.
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Affiliation(s)
- Mara Bourbouli
- Neurogenetics Laboratory, Neurology Department, Medical School, University of Crete, 71003 Heraklion, Greece; (M.B.); (L.M.); (S.Z.); (M.T.)
- 1st Department of Neurology, School of Medicine, National and Kapodistrian University of Athens, Eginition Hospital, 11528 Athens, Greece; (G.P.P.); (M.R.); (V.Z.); (A.B.); (V.C.); (G.P.); (G.K.); (G.K.); (C.K.); (E.K.)
| | - George P. Paraskevas
- 1st Department of Neurology, School of Medicine, National and Kapodistrian University of Athens, Eginition Hospital, 11528 Athens, Greece; (G.P.P.); (M.R.); (V.Z.); (A.B.); (V.C.); (G.P.); (G.K.); (G.K.); (C.K.); (E.K.)
- 2nd Department of Neurology, School of Medicine, National and Kapodistrian University of Athens, Attikon University General Hospital, 12462 Athens, Greece
| | - Mihail Rentzos
- 1st Department of Neurology, School of Medicine, National and Kapodistrian University of Athens, Eginition Hospital, 11528 Athens, Greece; (G.P.P.); (M.R.); (V.Z.); (A.B.); (V.C.); (G.P.); (G.K.); (G.K.); (C.K.); (E.K.)
| | - Lambros Mathioudakis
- Neurogenetics Laboratory, Neurology Department, Medical School, University of Crete, 71003 Heraklion, Greece; (M.B.); (L.M.); (S.Z.); (M.T.)
| | - Vasiliki Zouvelou
- 1st Department of Neurology, School of Medicine, National and Kapodistrian University of Athens, Eginition Hospital, 11528 Athens, Greece; (G.P.P.); (M.R.); (V.Z.); (A.B.); (V.C.); (G.P.); (G.K.); (G.K.); (C.K.); (E.K.)
| | - Anastasia Bougea
- 1st Department of Neurology, School of Medicine, National and Kapodistrian University of Athens, Eginition Hospital, 11528 Athens, Greece; (G.P.P.); (M.R.); (V.Z.); (A.B.); (V.C.); (G.P.); (G.K.); (G.K.); (C.K.); (E.K.)
| | - Athanasios Tychalas
- Department of Neurology, Papageorgiou General Hospital, 56403 Thessaloniki, Greece;
| | - Vasilios K. Kimiskidis
- 1st Department of Neurology, AHEPA Hospital, Aristotle University of Thessaloniki, 54621 Thessaloniki, Greece;
| | - Vasilios Constantinides
- 1st Department of Neurology, School of Medicine, National and Kapodistrian University of Athens, Eginition Hospital, 11528 Athens, Greece; (G.P.P.); (M.R.); (V.Z.); (A.B.); (V.C.); (G.P.); (G.K.); (G.K.); (C.K.); (E.K.)
| | - Spiros Zafeiris
- Neurogenetics Laboratory, Neurology Department, Medical School, University of Crete, 71003 Heraklion, Greece; (M.B.); (L.M.); (S.Z.); (M.T.)
| | - Minas Tzagournissakis
- Neurogenetics Laboratory, Neurology Department, Medical School, University of Crete, 71003 Heraklion, Greece; (M.B.); (L.M.); (S.Z.); (M.T.)
| | - Georgios Papadimas
- 1st Department of Neurology, School of Medicine, National and Kapodistrian University of Athens, Eginition Hospital, 11528 Athens, Greece; (G.P.P.); (M.R.); (V.Z.); (A.B.); (V.C.); (G.P.); (G.K.); (G.K.); (C.K.); (E.K.)
| | - Georgia Karadima
- 1st Department of Neurology, School of Medicine, National and Kapodistrian University of Athens, Eginition Hospital, 11528 Athens, Greece; (G.P.P.); (M.R.); (V.Z.); (A.B.); (V.C.); (G.P.); (G.K.); (G.K.); (C.K.); (E.K.)
| | - Georgios Koutsis
- 1st Department of Neurology, School of Medicine, National and Kapodistrian University of Athens, Eginition Hospital, 11528 Athens, Greece; (G.P.P.); (M.R.); (V.Z.); (A.B.); (V.C.); (G.P.); (G.K.); (G.K.); (C.K.); (E.K.)
| | - Christos Kroupis
- Department of Clinical Biochemistry, Attikon University General Hospital, Medical School, National and Kapodistrian University of Athens, 12462 Athens, Greece;
| | - Chrisoula Kartanou
- 1st Department of Neurology, School of Medicine, National and Kapodistrian University of Athens, Eginition Hospital, 11528 Athens, Greece; (G.P.P.); (M.R.); (V.Z.); (A.B.); (V.C.); (G.P.); (G.K.); (G.K.); (C.K.); (E.K.)
| | - Elisabeth Kapaki
- 1st Department of Neurology, School of Medicine, National and Kapodistrian University of Athens, Eginition Hospital, 11528 Athens, Greece; (G.P.P.); (M.R.); (V.Z.); (A.B.); (V.C.); (G.P.); (G.K.); (G.K.); (C.K.); (E.K.)
| | - Ioannis Zaganas
- Neurogenetics Laboratory, Neurology Department, Medical School, University of Crete, 71003 Heraklion, Greece; (M.B.); (L.M.); (S.Z.); (M.T.)
- Correspondence: ; Tel.: +30-2810-394643
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15
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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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16
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AAA+ ATPase p97/VCP mutants and inhibitor binding disrupt inter-domain coupling and subsequent allosteric activation. J Biol Chem 2021; 297:101187. [PMID: 34520757 PMCID: PMC8517850 DOI: 10.1016/j.jbc.2021.101187] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 08/31/2021] [Accepted: 09/02/2021] [Indexed: 11/19/2022] Open
Abstract
The human AAA+ ATPase p97, also known as valosin-containing protein, a potential target for cancer therapeutics, plays a vital role in the clearing of misfolded proteins. p97 dysfunction is also known to play a crucial role in several neurodegenerative disorders, such as MultiSystem Proteinopathy 1 (MSP-1) and Familial Amyotrophic Lateral Sclerosis (ALS). However, the structural basis of its role in such diseases remains elusive. Here, we present cryo-EM structural analyses of four disease mutants p97R155H, p97R191Q, p97A232E, p97D592N, as well as p97E470D, implicated in resistance to the drug CB-5083, a potent p97 inhibitor. Our cryo-EM structures demonstrate that these mutations affect nucleotide-driven allosteric activation across the three principal p97 domains (N, D1, and D2) by predominantly interfering with either (1) the coupling between the D1 and N-terminal domains (p97R155H and p97R191Q), (2) the interprotomer interactions (p97A232E), or (3) the coupling between D1 and D2 nucleotide domains (p97D592N, p97E470D). We also show that binding of the competitive inhibitor, CB-5083, to the D2 domain prevents conformational changes similar to those seen for mutations that affect coupling between the D1 and D2 domains. Our studies enable tracing of the path of allosteric activation across p97 and establish a common mechanistic link between active site inhibition and defects in allosteric activation by disease-causing mutations and have potential implications for the design of novel allosteric compounds that can modulate p97 function.
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17
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Nandi P, Li S, Columbres RCA, Wang F, Williams DR, Poh YP, Chou TF, Chiu PL. Structural and Functional Analysis of Disease-Linked p97 ATPase Mutant Complexes. Int J Mol Sci 2021; 22:ijms22158079. [PMID: 34360842 PMCID: PMC8347982 DOI: 10.3390/ijms22158079] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 07/22/2021] [Accepted: 07/25/2021] [Indexed: 01/14/2023] Open
Abstract
IBMPFD/ALS is a genetic disorder caused by a single amino acid mutation on the p97 ATPase, promoting ATPase activity and cofactor dysregulation. The disease mechanism underlying p97 ATPase malfunction remains unclear. To understand how the mutation alters the ATPase regulation, we assembled a full-length p97R155H with its p47 cofactor and first visualized their structures using single-particle cryo-EM. More than one-third of the population was the dodecameric form. Nucleotide presence dissociates the dodecamer into two hexamers for its highly elevated function. The N-domains of the p97R155H mutant all show up configurations in ADP- or ATPγS-bound states. Our functional and structural analyses showed that the p47 binding is likely to impact the p97R155H ATPase activities via changing the conformations of arginine fingers. These functional and structural analyses underline the ATPase dysregulation with the miscommunication between the functional modules of the p97R155H.
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Affiliation(s)
- Purbasha Nandi
- Biodesign Center for Applied Structural Discovery, School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, USA;
| | - Shan Li
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; (S.L.); (R.C.A.C.); (F.W.); (Y.-P.P.)
| | - Rod Carlo A. Columbres
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; (S.L.); (R.C.A.C.); (F.W.); (Y.-P.P.)
| | - Feng Wang
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; (S.L.); (R.C.A.C.); (F.W.); (Y.-P.P.)
| | | | - Yu-Ping Poh
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; (S.L.); (R.C.A.C.); (F.W.); (Y.-P.P.)
| | - Tsui-Fen Chou
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; (S.L.); (R.C.A.C.); (F.W.); (Y.-P.P.)
- Correspondence: (T.-F.C.); (P.-L.C.)
| | - Po-Lin Chiu
- Biodesign Center for Applied Structural Discovery, School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, USA;
- Correspondence: (T.-F.C.); (P.-L.C.)
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18
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Creekmore BC, Chang YW, Lee EB. The Cryo-EM Effect: Structural Biology of Neurodegenerative Disease Proteostasis Factors. J Neuropathol Exp Neurol 2021; 80:494-513. [PMID: 33860329 PMCID: PMC8177850 DOI: 10.1093/jnen/nlab029] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Neurodegenerative diseases are characterized by the accumulation of misfolded proteins. This protein aggregation suggests that abnormal proteostasis contributes to aging-related neurodegeneration. A better fundamental understanding of proteins that regulate proteostasis may provide insight into the pathophysiology of neurodegenerative disease and may perhaps reveal novel therapeutic opportunities. The 26S proteasome is the key effector of the ubiquitin-proteasome system responsible for degrading polyubiquitinated proteins. However, additional factors, such as valosin-containing protein (VCP/p97/Cdc48) and C9orf72, play a role in regulation and trafficking of substrates through the normal proteostasis systems of a cell. Nonhuman AAA+ ATPases, such as the disaggregase Hsp104, also provide insights into the biochemical processes that regulate protein aggregation. X-ray crystallography and cryo-electron microscopy (cryo-EM) structures not bound to substrate have provided meaningful information about the 26S proteasome, VCP, and Hsp104. However, recent cryo-EM structures bound to substrate have provided new information about the function and mechanism of these proteostasis factors. Cryo-EM and cryo-electron tomography data combined with biochemical data have also increased the understanding of C9orf72 and its role in maintaining proteostasis. These structural insights provide a foundation for understanding proteostasis mechanisms with near-atomic resolution upon which insights can be gleaned regarding the pathophysiology of neurodegenerative diseases.
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Affiliation(s)
- Benjamin C Creekmore
- From the Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Graduate Program in Biochemistry and Molecular Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Translational Neuropathology Research Laboratory, Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Yi-Wei Chang
- From the Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Edward B Lee
- Translational Neuropathology Research Laboratory, Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
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19
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Zhu C, Rogers A, Asleh K, Won J, Gao D, Leung S, Li S, Vij KR, Zhu J, Held JM, You Z, Nielsen TO, Shao J. Phospho-Ser 784-VCP Is Required for DNA Damage Response and Is Associated with Poor Prognosis of Chemotherapy-Treated Breast Cancer. Cell Rep 2021; 31:107745. [PMID: 32521270 PMCID: PMC7282751 DOI: 10.1016/j.celrep.2020.107745] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 05/01/2020] [Accepted: 05/18/2020] [Indexed: 12/15/2022] Open
Abstract
Spatiotemporal protein reorganization at DNA damage sites induced by genotoxic chemotherapies is crucial for DNA damage response (DDR), which influences treatment response by directing cancer cell fate. This process is orchestrated by valosin-containing protein (VCP), an AAA+ ATPase that extracts polyubiquinated chromatin proteins and facilitates their turnover. However, because of the essential and pleiotropic effects of VCP in global proteostasis, it remains challenging practically to understand and target its DDR-specific functions. We describe a DNA-damage-induced phosphorylation event (Ser784), which selectively enhances chromatin-associated protein degradation mediated by VCP and is required for DNA repair, signaling, and cell survival. These functional effects of Ser784 phosphorylation on DDR correlate with a decrease in VCP association with chromatin, cofactors NPL4/UFD1, and polyubiquitinated substrates. Clinically, high phospho-Ser784-VCP levels are significantly associated with poor outcome among chemotherapy-treated breast cancer patients. Thus, Ser784 phosphorylation is a DDR-specific enhancer of VCP function and a potential predictive biomarker for chemotherapy treatments.
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Affiliation(s)
- Cuige Zhu
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Anna Rogers
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Karama Asleh
- Department of Pathology, University of British Columbia, Vancouver, BC V5Z 1M9, Canada
| | - Jennifer Won
- Department of Pathology, University of British Columbia, Vancouver, BC V5Z 1M9, Canada
| | - Dongxia Gao
- Department of Pathology, University of British Columbia, Vancouver, BC V5Z 1M9, Canada
| | - Samuel Leung
- Department of Pathology, University of British Columbia, Vancouver, BC V5Z 1M9, Canada
| | - Shan Li
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Kiran R Vij
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Jian Zhu
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Jason M Held
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA; Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Anesthesiology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Zhongsheng You
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Torsten O Nielsen
- Department of Pathology, University of British Columbia, Vancouver, BC V5Z 1M9, Canada
| | - Jieya Shao
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA; Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO 63110, USA.
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20
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Mukkavalli S, Klickstein JA, Ortiz B, Juo P, Raman M. The p97-UBXN1 complex regulates aggresome formation. J Cell Sci 2021; 134:237808. [PMID: 33712450 DOI: 10.1242/jcs.254201] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 03/03/2021] [Indexed: 11/20/2022] Open
Abstract
The recognition and disposal of misfolded proteins is essential for the maintenance of cellular homeostasis. Perturbations in the pathways that promote degradation of aberrant proteins contribute to a variety of protein aggregation disorders broadly termed proteinopathies. The AAA-ATPase p97 (also known as VCP), in combination with adaptor proteins, functions to identify ubiquitylated proteins and target them for degradation by the proteasome or through autophagy. Mutations in p97 cause multi-system proteinopathies; however, the precise defects underlying these disorders are unclear. Here, we systematically investigate the role of p97 and its adaptors in the process of formation of aggresomes, membrane-less structures containing ubiquitylated proteins that arise upon proteasome inhibition. We demonstrate that p97 mediates aggresome formation and clearance, and identify a novel role for the adaptor UBXN1 in the process of aggresome formation. UBXN1 is recruited to aggresomes, and UBXN1-knockout cells are unable to form aggresomes. Loss of p97-UBXN1 results in increased Huntingtin polyQ inclusion bodies both in mammalian cells and in a C. elegans model of Huntington's disease. Together, our results identify evolutionarily conserved roles for p97-UBXN1 in the disposal of protein aggregates.
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Affiliation(s)
- Sirisha Mukkavalli
- Department of Developmental Molecular and Chemical Biology, Tufts University School of Medicine, Boston, MA 02111, USA
| | - Jacob Aaron Klickstein
- Department of Developmental Molecular and Chemical Biology, Tufts University School of Medicine, Boston, MA 02111, USA
| | - Betty Ortiz
- Department of Developmental Molecular and Chemical Biology, Tufts University School of Medicine, Boston, MA 02111, USA
| | - Peter Juo
- Department of Developmental Molecular and Chemical Biology, Tufts University School of Medicine, Boston, MA 02111, USA
| | - Malavika Raman
- Department of Developmental Molecular and Chemical Biology, Tufts University School of Medicine, Boston, MA 02111, USA
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21
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Moon SL, Morisaki T, Stasevich TJ, Parker R. Coupling of translation quality control and mRNA targeting to stress granules. J Cell Biol 2021; 219:151851. [PMID: 32520986 PMCID: PMC7401812 DOI: 10.1083/jcb.202004120] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 05/05/2020] [Accepted: 05/06/2020] [Indexed: 02/07/2023] Open
Abstract
Stress granules are dynamic assemblies of proteins and nontranslating RNAs that form when translation is inhibited in response to diverse stresses. Defects in ubiquitin–proteasome system factors including valosin-containing protein (VCP) and the proteasome impact the kinetics of stress granule induction and dissolution as well as being implicated in neuropathogenesis. However, the impacts of dysregulated proteostasis on mRNA regulation and stress granules are not well understood. Using single mRNA imaging, we discovered ribosomes stall on some mRNAs during arsenite stress, and the release of transcripts from stalled ribosomes for their partitioning into stress granules requires the activities of VCP, components of the ribosome-associated quality control (RQC) complex, and the proteasome. This is an unexpected contribution of the RQC system in releasing mRNAs from translation under stress, thus identifying a new type of stress-activated RQC (saRQC) distinct from canonical RQC pathways in mRNA substrates, cellular context, and mRNA fate.
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Affiliation(s)
- Stephanie L Moon
- Department of Human Genetics, University of Michigan, Ann Arbor, MI.,Center for RNA Biomedicine, University of Michigan, Ann Arbor, MI
| | - Tatsuya Morisaki
- Department of Biochemistry, Colorado State University, Fort Collins, CO
| | - Timothy J Stasevich
- Department of Biochemistry, Colorado State University, Fort Collins, CO.,World Research Hub Initiative, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
| | - Roy Parker
- Department of Biochemistry, University of Colorado, Boulder, CO.,Howard Hughes Medical Institute, Chevy Chase, MD
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22
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Alderson TR, Kay LE. NMR spectroscopy captures the essential role of dynamics in regulating biomolecular function. Cell 2021; 184:577-595. [PMID: 33545034 DOI: 10.1016/j.cell.2020.12.034] [Citation(s) in RCA: 97] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 12/09/2020] [Accepted: 12/21/2020] [Indexed: 01/02/2023]
Abstract
Biomolecules are in constant motion. To understand how they function, and why malfunctions can cause disease, it is necessary to describe their three-dimensional structures in terms of dynamic conformational ensembles. Here, we demonstrate how nuclear magnetic resonance (NMR) spectroscopy provides an essential, dynamic view of structural biology that captures biomolecular motions at atomic resolution. We focus on examples that emphasize the diversity of biomolecules and biochemical applications that are amenable to NMR, such as elucidating functional dynamics in large molecular machines, characterizing transient conformations implicated in the onset of disease, and obtaining atomic-level descriptions of intrinsically disordered regions that make weak interactions involved in liquid-liquid phase separation. Finally, we discuss the pivotal role that NMR has played in driving forward our understanding of the biomolecular dynamics-function paradigm.
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Affiliation(s)
- T Reid Alderson
- Department of Biochemistry, The University of Toronto, Toronto, ON M5S 1A8, Canada; Department of Molecular Genetics, The University of Toronto, Toronto, ON M5S 1A8, Canada; Department of Chemistry, The University of Toronto, Toronto, ON M5S A18, Canada.
| | - Lewis E Kay
- Department of Biochemistry, The University of Toronto, Toronto, ON M5S 1A8, Canada; Department of Molecular Genetics, The University of Toronto, Toronto, ON M5S 1A8, Canada; Department of Chemistry, The University of Toronto, Toronto, ON M5S A18, Canada; Program in Molecular Medicine, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada.
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23
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Emerging role of VCP/p97 in cardiovascular diseases: novel insights and therapeutic opportunities. Biochem Soc Trans 2021; 49:485-494. [PMID: 33439255 PMCID: PMC7925001 DOI: 10.1042/bst20200981] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 11/22/2020] [Accepted: 11/25/2020] [Indexed: 12/22/2022]
Abstract
Valosin-containing protein (VCP/p97) is a member of the conserved type II AAA+ (ATPases associated with diverse cellular activities) family of proteins with multiple biological functions, especially in protein homeostasis. Mutations in VCP/p97 are reportedly related to unique autosomal dominant diseases, which may worsen cardiac function. Although the structure of VCP/p97 has been clearly characterized, with reports of high abundance in the heart, research focusing on the molecular mechanisms underpinning the roles of VCP/p97 in the cardiovascular system has been recently undertaken over the past decades. Recent studies have shown that VCP/p97 deficiency affects myocardial fibers and induces heart failure, while overexpression of VCP/p97 eliminates ischemia/reperfusion injury and relieves pathological cardiac hypertrophy caused by cardiac pressure overload, which is related to changes in the mitochondria and calcium overload. However, certain studies have drawn opposing conclusions, including the mitigation of ischemia/reperfusion injury via inhibition of VCP/p97 ATPase activity. Nevertheless, these emerging studies shed light on the role of VCP/p97 and its therapeutic potential in cardiovascular diseases. In other words, VCP/p97 may be involved in the development of cardiovascular disease, and is anticipated to be a new therapeutic target. This review summarizes current findings regarding VCP/p97 in the cardiovascular system for the first time, and discusses the role of VCP/p97 in cardiovascular disease.
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24
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Cdc48/Shp1 participates in dissociation of protein complexes to regulate their activity. Curr Genet 2021; 67:263-265. [PMID: 33388824 DOI: 10.1007/s00294-020-01136-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 11/17/2020] [Accepted: 11/19/2020] [Indexed: 10/22/2022]
Abstract
The AAA-ATPase p97/Cdc48 is one of the most abundant proteins in eukaryotes, and owing to its multiple functions, is considered the swiss army knife of cells. Recent findings demonstrate that p97/Cdc48 and its cofactor p47/Shp1 control the heavy metal stress response by active, signal-triggered disassembly of a multisubunit ubiquitin ligase. Here we review this pathway and describe recently achieved mechanistic insight into the role of p47/Shp1 in this process.
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25
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Huang TN, Shih YT, Lin SC, Hsueh YP. Social behaviors and contextual memory of Vcp mutant mice are sensitive to nutrition and can be ameliorated by amino acid supplementation. iScience 2020; 24:101949. [PMID: 33437936 PMCID: PMC7786123 DOI: 10.1016/j.isci.2020.101949] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 11/01/2020] [Accepted: 12/11/2020] [Indexed: 02/06/2023] Open
Abstract
Both genetic variations and nutritional deficiency are associated with autism spectrum disorders and other neurological disorders. However, it is less clear whether or how nutritional deficiency and genetic variations influence each other under pathogenic conditions. "Valosin-containing protein" (VCP, also known as p97) is associated with multiple neurological disorders and regulates dendritic spine formation by controlling endoplasmic reticulum formation and protein synthesis efficiency. Increased protein synthesis ameliorates the dendritic spine defects of Vcp-deficient neurons. Therefore, we investigated if Vcp-deficient mice are sensitive to nutritional conditions. Here, we show that social interaction and contextual memory of Vcp-deficient mice are indeed influenced by different dietary protein levels. Moreover, leucine supplementation ameliorates the behavioral deficits and dendritic spine density of Vcp-deficient mice, strengthening evidence for the role of protein synthesis in VCP function. Our study illustrates that genetic variation and nutrient factors cross-talk to influence neuronal and behavioral phenotypes.
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Affiliation(s)
- Tzyy-Nan Huang
- Institute of Molecular Biology, Academia Sinica, 128, Academia Road, Section 2, Taipei 11529, Taiwan, Republic of China
| | - Yu-Tzu Shih
- Institute of Molecular Biology, Academia Sinica, 128, Academia Road, Section 2, Taipei 11529, Taiwan, Republic of China
| | - Si-Cih Lin
- Institute of Molecular Biology, Academia Sinica, 128, Academia Road, Section 2, Taipei 11529, Taiwan, Republic of China
| | - Yi-Ping Hsueh
- Institute of Molecular Biology, Academia Sinica, 128, Academia Road, Section 2, Taipei 11529, Taiwan, Republic of China
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26
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Kracht M, van den Boom J, Seiler J, Kröning A, Kaschani F, Kaiser M, Meyer H. Protein Phosphatase-1 Complex Disassembly by p97 is Initiated through Multivalent Recognition of Catalytic and Regulatory Subunits by the p97 SEP-domain Adapters. J Mol Biol 2020; 432:6061-6074. [PMID: 33058883 DOI: 10.1016/j.jmb.2020.10.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 10/02/2020] [Accepted: 10/02/2020] [Indexed: 12/19/2022]
Abstract
The AAA-ATPase VCP/p97 cooperates with the SEP-domain adapters p37, UBXN2A and p47 in stripping inhibitor-3 (I3) from protein phosphatase-1 (PP1) for activation. In contrast to p97-mediated degradative processes, PP1 complex disassembly is ubiquitin-independent. It is therefore unclear how selective targeting is achieved. Using biochemical reconstitution and crosslink mass spectrometry, we show here that SEP-domain adapters use a multivalent substrate recognition strategy. An N-terminal sequence element predicted to form a helix, together with the SEP-domain, binds and engages the direct target I3 in the central pore of p97 for unfolding, while its partner PP1 is held by a linker between SHP box and UBX domain locked onto the peripheral N-domain of p97. Although the I3-binding element is functional in p47, p47 in vitro requires a transplant of the PP1-binding linker from p37 for activity stressing that both sites are essential to control specificity. Of note, unfolding is then governed by an inhibitory segment in the N-terminal region of p47, suggesting a regulatory function. Together, this study reveals how p97 adapters engage a protein complex for ubiquitin-independent disassembly while ensuring selectivity for one subunit.
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Affiliation(s)
- Matthias Kracht
- Centre for Medical Biotechnology, Faculty of Biology, University of Duisburg-Essen, 45117 Essen, Germany
| | - Johannes van den Boom
- Centre for Medical Biotechnology, Faculty of Biology, University of Duisburg-Essen, 45117 Essen, Germany
| | - Jonas Seiler
- Centre for Medical Biotechnology, Faculty of Biology, University of Duisburg-Essen, 45117 Essen, Germany
| | - Alexander Kröning
- Centre for Medical Biotechnology, Faculty of Biology, University of Duisburg-Essen, 45117 Essen, Germany
| | - Farnusch Kaschani
- Chemical Biology and Analytics Core Facility, Centre for Medical Biotechnology, Faculty of Biology, University of Duisburg-Essen, 45117 Essen, Germany
| | - Markus Kaiser
- Chemical Biology and Analytics Core Facility, Centre for Medical Biotechnology, Faculty of Biology, University of Duisburg-Essen, 45117 Essen, Germany
| | - Hemmo Meyer
- Centre for Medical Biotechnology, Faculty of Biology, University of Duisburg-Essen, 45117 Essen, Germany.
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An intrinsically disordered motif regulates the interaction between the p47 adaptor and the p97 AAA+ ATPase. Proc Natl Acad Sci U S A 2020; 117:26226-26236. [PMID: 33028677 DOI: 10.1073/pnas.2013920117] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
VCP/p97, an enzyme critical to proteostasis, is regulated through interactions with protein adaptors targeting it to specific cellular tasks. One such adaptor, p47, forms a complex with p97 to direct lipid membrane remodeling. Here, we use NMR and other biophysical methods to study the structural dynamics of p47 and p47-p97 complexes. Disordered regions in p47 are shown to be critical in directing intra-p47 and p47-p97 interactions via a pair of previously unidentified linear motifs. One of these, an SHP domain, regulates p47 binding to p97 in a manner that depends on the nucleotide state of p97. NMR and electron cryomicroscopy data have been used as restraints in molecular dynamics trajectories to develop structural ensembles for p47-p97 complexes in adenosine diphosphate (ADP)- and adenosine triphosphate (ATP)-bound conformations, highlighting differences in interactions in the two states. Our study establishes the importance of intrinsically disordered regions in p47 for the formation of functional p47-p97 complexes.
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28
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Lauinger L, Flick K, Yen JL, Mathur R, Kaiser P. Cdc48 cofactor Shp1 regulates signal-induced SCF Met30 disassembly. Proc Natl Acad Sci U S A 2020; 117:21319-21327. [PMID: 32817489 PMCID: PMC7474596 DOI: 10.1073/pnas.1922891117] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Organisms can adapt to a broad spectrum of sudden and dramatic changes in their environment. These abrupt changes are often perceived as stress and trigger responses that facilitate survival and eventual adaptation. The ubiquitin-proteasome system (UPS) is involved in most cellular processes. Unsurprisingly, components of the UPS also play crucial roles during various stress response programs. The budding yeast SCFMet30 complex is an essential cullin-RING ubiquitin ligase that connects metabolic and heavy metal stress to cell cycle regulation. Cadmium exposure results in the active dissociation of the F-box protein Met30 from the core ligase, leading to SCFMet30 inactivation. Consequently, SCFMet30 substrate ubiquitylation is blocked and triggers a downstream cascade to activate a specific transcriptional stress response program. Signal-induced dissociation is initiated by autoubiquitylation of Met30 and serves as a recruitment signal for the AAA-ATPase Cdc48/p97, which actively disassembles the complex. Here we show that the UBX cofactor Shp1/p47 is an additional key element for SCFMet30 disassembly during heavy metal stress. Although the cofactor can directly interact with the ATPase, Cdc48 and Shp1 are recruited independently to SCFMet30 during cadmium stress. An intact UBX domain is crucial for effective SCFMet30 disassembly, and a concentration threshold of Shp1 recruited to SCFMet30 needs to be exceeded to initiate Met30 dissociation. The latter is likely related to Shp1-mediated control of Cdc48 ATPase activity. This study identifies Shp1 as the crucial Cdc48 cofactor for signal-induced selective disassembly of a multisubunit protein complex to modulate activity.
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Affiliation(s)
- Linda Lauinger
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, CA 92697-1700
| | - Karin Flick
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, CA 92697-1700
| | - James L Yen
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, CA 92697-1700
| | - Radhika Mathur
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, CA 92697-1700
| | - Peter Kaiser
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, CA 92697-1700
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29
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Rydzek S, Shein M, Bielytskyi P, Schütz AK. Observation of a Transient Reaction Intermediate Illuminates the Mechanochemical Cycle of the AAA-ATPase p97. J Am Chem Soc 2020; 142:14472-14480. [DOI: 10.1021/jacs.0c03180] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Simon Rydzek
- Bavarian NMR Center, Department of Chemistry, Technical University of Munich, 85748 Garching, Germany
| | - Mikhail Shein
- Bavarian NMR Center, Department of Chemistry, Technical University of Munich, 85748 Garching, Germany
| | - Pavlo Bielytskyi
- Bavarian NMR Center, Department of Chemistry, Technical University of Munich, 85748 Garching, Germany
| | - Anne K. Schütz
- Bavarian NMR Center, Department of Chemistry, Technical University of Munich, 85748 Garching, Germany
- Institute of Structural Biology, Helmholtz Zentrum München, 85764 Neuherberg, Germany
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30
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Bolus H, Crocker K, Boekhoff-Falk G, Chtarbanova S. Modeling Neurodegenerative Disorders in Drosophila melanogaster. Int J Mol Sci 2020; 21:E3055. [PMID: 32357532 PMCID: PMC7246467 DOI: 10.3390/ijms21093055] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 04/14/2020] [Accepted: 04/21/2020] [Indexed: 12/12/2022] Open
Abstract
Drosophila melanogaster provides a powerful genetic model system in which to investigate the molecular mechanisms underlying neurodegenerative diseases. In this review, we discuss recent progress in Drosophila modeling Alzheimer's Disease, Parkinson's Disease, Amyotrophic Lateral Sclerosis (ALS), Huntington's Disease, Ataxia Telangiectasia, and neurodegeneration related to mitochondrial dysfunction or traumatic brain injury. We close by discussing recent progress using Drosophila models of neural regeneration and how these are likely to provide critical insights into future treatments for neurodegenerative disorders.
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Affiliation(s)
- Harris Bolus
- Department of Biological Sciences, University of Alabama, Tuscaloosa, AL 35487, USA;
| | - Kassi Crocker
- Genetics Graduate Training Program, School of Medicine and Public Health, University of Wisconsin–Madison, Madison, WI 53705, USA;
- Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin–Madison, Madison, WI 53705, USA
| | - Grace Boekhoff-Falk
- Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin–Madison, Madison, WI 53705, USA
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31
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Sui X, Pan M, Li YM. Insights into the Design of p97-targeting Small Molecules from Structural Studies on p97 Functional Mechanism. Curr Med Chem 2020; 27:298-316. [PMID: 31584361 DOI: 10.2174/0929867326666191004162411] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 08/24/2019] [Accepted: 08/27/2019] [Indexed: 12/14/2022]
Abstract
p97, also known as valosin-containing protein or CDC48, is a member of the AAA+ protein family that is highly conserved in eukaryotes. It binds to various cofactors in the body to perform its protein-unfolding function and participates in DNA repair, degradation of subcellular membrane proteins, and protein quality control pathways, among other processes. Its malfunction can lead to many diseases, such as inclusion body myopathy, associated with Paget's disease of bone and/or frontotemporal dementia, amyotrophic lateral sclerosis disease, and others. In recent years, many small-molecule inhibitors have been deployed against p97, including bis (diethyldithiocarbamate)- copper and CB-5083, which entered the first phase of clinical tests but failed. One bottleneck in the design of p97 drugs is that its molecular mechanism remains unclear. This paper summarizes recent studies on the molecular mechanisms of p97, which may lead to insight into how the next generation of small molecules targeting p97 can be designed.
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Affiliation(s)
- Xin Sui
- Department of Chemistry, Tsinghua University, Beijing 100086, China
| | - Man Pan
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois 60637, United States
| | - Yi-Ming Li
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, Anhui 230009, China
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32
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Abstract
p97 belongs to the functional diverse superfamily of AAA+ (ATPases Associated with diverse cellular Activities) ATPases and is characterized by an N-terminal regulatory domain and two stacked hexameric ATPase domains forming a central protein conducting channel. p97 is highly versatile and has key functions in maintaining protein homeostasis including protein quality control mechanisms like the ubiquitin proteasome system (UPS) and autophagy to disassemble polyubiquitylated proteins from chromatin, membranes, macromolecular protein complexes and aggregates which are either degraded by the proteasome or recycled. p97 can use energy derived from ATP hydrolysis to catalyze substrate unfolding and threading through its central channel. The function of p97 in a large variety of different cellular contexts is reflected by its simultaneous association with different cofactors, which are involved in substrate recognition and processing, thus leading to the formation of transient multi-protein complexes. Dysregulation in protein homeostasis and proteotoxic stress are often involved in the development of cancer and neurological diseases and targeting the UPS including p97 in cancer is a well-established pharmacological strategy. In this chapter we will describe structural and functional aspects of the p97 interactome in regulating diverse cellular processes and will discuss the role of p97 in targeted cancer therapy.
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33
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Shaping the Nascent Ribosome: AAA-ATPases in Eukaryotic Ribosome Biogenesis. Biomolecules 2019; 9:biom9110715. [PMID: 31703473 PMCID: PMC6920918 DOI: 10.3390/biom9110715] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Revised: 11/04/2019] [Accepted: 11/05/2019] [Indexed: 02/08/2023] Open
Abstract
AAA-ATPases are molecular engines evolutionarily optimized for the remodeling of proteins and macromolecular assemblies. Three AAA-ATPases are currently known to be involved in the remodeling of the eukaryotic ribosome, a megadalton range ribonucleoprotein complex responsible for the translation of mRNAs into proteins. The correct assembly of the ribosome is performed by a plethora of additional and transiently acting pre-ribosome maturation factors that act in a timely and spatially orchestrated manner. Minimal disorder of the assembly cascade prohibits the formation of functional ribosomes and results in defects in proliferation and growth. Rix7, Rea1, and Drg1, which are well conserved across eukaryotes, are involved in different maturation steps of pre-60S ribosomal particles. These AAA-ATPases provide energy for the efficient removal of specific assembly factors from pre-60S particles after they have fulfilled their function in the maturation cascade. Recent structural and functional insights have provided the first glimpse into the molecular mechanism of target recognition and remodeling by Rix7, Rea1, and Drg1. Here we summarize current knowledge on the AAA-ATPases involved in eukaryotic ribosome biogenesis. We highlight the latest insights into their mechanism of mechano-chemical complex remodeling driven by advanced cryo-EM structures and the use of highly specific AAA inhibitors.
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34
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Blythe EE, Gates SN, Deshaies RJ, Martin A. Multisystem Proteinopathy Mutations in VCP/p97 Increase NPLOC4·UFD1L Binding and Substrate Processing. Structure 2019; 27:1820-1829.e4. [PMID: 31623962 DOI: 10.1016/j.str.2019.09.011] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 08/19/2019] [Accepted: 09/20/2019] [Indexed: 11/25/2022]
Abstract
Valosin-containing protein (VCP)/p97 is an essential ATP-dependent protein unfoldase. Dominant mutations in p97 cause multisystem proteinopathy (MSP), a disease affecting the brain, muscle, and bone. Despite the identification of numerous pathways that are perturbed in MSP, the molecular-level defects of these p97 mutants are not completely understood. Here, we use biochemistry and cryoelectron microscopy to explore the effects of MSP mutations on the unfoldase activity of p97 in complex with its substrate adaptor NPLOC4⋅UFD1L (UN). We show that all seven analyzed MSP mutants unfold substrates faster. Mutant homo- and heterohexamers exhibit tighter UN binding and faster substrate processing. Our structural studies suggest that the increased UN affinity originates from a decoupling of p97's nucleotide state and the positioning of its N-terminal domains. Together, our data support a gain-of-function model for p97-UN-dependent processes in MSP and underscore the importance of N-terminal domain movements for adaptor recruitment and substrate processing by p97.
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Affiliation(s)
- Emily E Blythe
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; Department of Molecular & Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Stephanie N Gates
- Department of Molecular & Cell Biology, University of California, Berkeley, CA 94720, USA; Howard Hughes Medical Institute, University of California, Berkeley, CA 94720, USA; California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Raymond J Deshaies
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; Amgen Research, Thousand Oaks, CA 91320, USA
| | - Andreas Martin
- Department of Molecular & Cell Biology, University of California, Berkeley, CA 94720, USA; Howard Hughes Medical Institute, University of California, Berkeley, CA 94720, USA; California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA.
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35
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Jerath NU. Resolving a Multi-Generational Neuromuscular Mystery in a Family Presenting with a Variable Scapuloperoneal Syndrome in a c.464G>A, p.Arg155His VCP Mutation. Case Rep Genet 2019; 2019:2403024. [PMID: 31687228 PMCID: PMC6803746 DOI: 10.1155/2019/2403024] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 07/26/2019] [Accepted: 08/31/2019] [Indexed: 01/01/2023] Open
Abstract
Valosin containing protein (VCP) mutations have been reported to present with a high degree of variability and can be present in patients even if they may have an initial normal work up. A 55-year-old woman was labeled as "normal" and "pain medication seeking" after an unrevealing work up of clinical, laboratory, electrodiagnostic, radiographic, pathologic, and genetic testing. She continued to present with chronic neck pain, and had variable features of scapuloperoneal atrophy, which was also seen in her family. The patient and her family were found to have a known pathogenic c.464G>A, p.Arg155His (R155H) mutation in the VCP gene. Despite traditional thinking of attempting to localize neurological syndromes, VCP mutations are difficult to localize as they can present with significant clinical heterogeneity including a scapuloperoneal syndrome with variable neuropathic and myopathic features.
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Affiliation(s)
- Nivedita U. Jerath
- AdventHealth Orlando, Neuromuscular Division, 1573 West Fairbanks, Winter Park, FL 32789, USA
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36
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Abstract
In this issue of Molecular Cell, Weith et al. (2018) demonstrate that p97, together with a SEP adaptor, can catalyze ordered subunit exchange to facilitate the biogenesis of protein phosphatase-1 (PP1) holoenzyme, establishing a novel ubiquitin-independent "segregase" function for this versatile ATPase.
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Affiliation(s)
- Lihui Wang
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yihong Ye
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
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37
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Zhong M, Lee GM, Sijbesma E, Ottmann C, Arkin MR. Modulating protein-protein interaction networks in protein homeostasis. Curr Opin Chem Biol 2019; 50:55-65. [PMID: 30913483 DOI: 10.1016/j.cbpa.2019.02.012] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Revised: 02/06/2019] [Accepted: 02/09/2019] [Indexed: 12/12/2022]
Abstract
Protein-protein interactions (PPIs) occur in complex networks. These networks are highly dependent on cellular context and can be extensively altered in disease states such as cancer and viral infection. In recent years, there has been significant progress in developing inhibitors that target individual PPIs either orthosterically (at the interface) or allosterically. These molecules can now be used as tools to dissect PPI networks. Here, we review recent examples that highlight the use of small molecules and engineered proteins to probe PPIs within the complex networks that regulate protein homeostasis. Researchers have discovered multiple mechanisms to modulate PPIs involved in host/viral interactions, deubiquitinases, the ATPase p97/VCP, and HSP70 chaperones. However, few studies have evaluated the effect of such modulators on the target's network or have compared the biological implications of different modulation strategies. Such studies will have an important impact on next generation therapeutics.
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Affiliation(s)
- Mengqi Zhong
- Department of Pharmaceutical Chemistry and the Small Molecule Discovery Center, University of California, San Francisco, CA, USA
| | - Gregory M Lee
- Department of Pharmaceutical Chemistry and the Small Molecule Discovery Center, University of California, San Francisco, CA, USA
| | - Eline Sijbesma
- Department of Biomedical Engineering, Laboratory of Chemical Biology, and Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Christian Ottmann
- Department of Biomedical Engineering, Laboratory of Chemical Biology, and Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Michelle R Arkin
- Department of Pharmaceutical Chemistry and the Small Molecule Discovery Center, University of California, San Francisco, CA, USA.
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38
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Milone M, Liewluck T. The unfolding spectrum of inherited distal myopathies. Muscle Nerve 2018; 59:283-294. [PMID: 30171629 DOI: 10.1002/mus.26332] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Revised: 08/26/2018] [Accepted: 08/28/2018] [Indexed: 12/30/2022]
Abstract
Distal myopathies are a group of rare muscle diseases characterized by distal weakness at onset. Although acquired myopathies can occasionally present with distal weakness, the majority of distal myopathies have a genetic etiology. Their age of onset varies from early-childhood to late-adulthood while the predominant muscle weakness can affect calf, ankle dorsiflexor, or distal upper limb muscles. A spectrum of muscle pathological changes, varying from nonspecific myopathic changes to rimmed vacuoles to myofibrillar pathology to nuclei centralization, have been noted. Likewise, the underlying molecular defect is heterogeneous. In addition, there is emerging evidence that distal myopathies can result from defective proteins encoded by genes causative of neurogenic disorders, be manifestation of multisystem proteinopathies or the result of the altered interplay between different genes. In this review, we provide an overview on the clinical, electrophysiological, pathological, and molecular aspects of distal myopathies, focusing on the most recent developments in the field. Muscle Nerve 59:283-294, 2019.
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Affiliation(s)
| | - Teerin Liewluck
- Department of Neurology, Mayo Clinic, Rochester, Minnesota, USA
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39
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Wei Y, Toth JI, Blanco GA, Bobkov AA, Petroski MD. Adapted ATPase domain communication overcomes the cytotoxicity of p97 inhibitors. J Biol Chem 2018; 293:20169-20180. [PMID: 30381397 DOI: 10.1074/jbc.ra118.004301] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 10/10/2018] [Indexed: 12/15/2022] Open
Abstract
The AAA+ ATPase p97 regulates ubiquitin-dependent protein homeostasis and has been pursued as a cancer drug target. The ATP-competitive inhibitor CB-5083 and allosteric inhibitor NMS-873 are the most advanced p97 inhibitors described to date. Previous studies have reported that their cytotoxicity can be readily overcome and involves single p97 mutations in the linker between the D1 and D2 ATPase domains and within D2. We report here that the proline 472 to leucine (P472L) mutation, in the D1-D2 linker and identified in CB-5083-resistant cells, desensitizes p97 to both inhibitor classes. This mutation does not disrupt the distinct D2-binding sites of the inhibitors. Instead, P472L changes ATPase domain communication within the p97 hexamer. P472L enhances cooperative D2 ATP binding and hydrolysis. This mechanism alters the function of the D1-D2 linker in the control of D2 activity involving the ATP-bound state of D1. Although increased D2 activity is sufficient to desensitize the P472L mutant to NMS-873, the mutant's desensitization to CB-5083 also requires D1 ATPase domain function. Our study highlights the remarkable adaptability of p97 ATPase domain communication that enables escape from mechanistically distinct classes of cytotoxic p97 inhibitors.
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Affiliation(s)
- Yang Wei
- From the NCI-designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California 92037
| | - Julia I Toth
- From the NCI-designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California 92037
| | - Gabrielle A Blanco
- From the NCI-designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California 92037
| | - Andrey A Bobkov
- From the NCI-designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California 92037
| | - Matthew D Petroski
- From the NCI-designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California 92037.
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40
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Yi L, Kaler SG. Interaction between the AAA ATPase p97/VCP and a concealed UBX domain in the copper transporter ATP7A is associated with motor neuron degeneration. J Biol Chem 2018; 293:7606-7617. [PMID: 29599289 DOI: 10.1074/jbc.ra117.000686] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2017] [Revised: 03/09/2018] [Indexed: 11/06/2022] Open
Abstract
The copper-transporting ATPase ATP7A contains eight transmembrane domains and is required for normal human copper homeostasis. Mutations in the ATP7A gene may lead to infantile-onset cerebral degeneration (Menkes disease); occipital horn syndrome (OHS), a related but much milder illness; or an adult-onset isolated distal motor neuropathy. The ATP7A missense mutation T994I is located in the sixth transmembrane domain of ATP7A, represents one of the variants associated with the latter phenotype, and is associated with an abnormal interaction with p97/valosin-containing protein (VCP), a hexameric AAA ATPase (ATPase associated with diverse cellular activities) with multiple biological functions. In this study, we further characterized this interaction and discovered a concealed UBX domain in the third lumenal loop of ATP7A, between its fifth and sixth transmembrane domains. We show that the T994I substitution results in conformational exposure of the UBX domain, which then binds the N-terminal domain of p97/VCP. We also show that this abnormal interaction occurs at or near the cell plasma membrane. The UBX domain has a conserved hydrophobic FP (Phe-Pro) motif, and substitution with di-alanine abrogated the interaction and restored the proper intracellular localization of ATP7A in the trans-Golgi network. Using protein MS, we identified potential coordinating components of the ATP7AT994I-p97 complex, including NSFL1 cofactor (NSF1C or p47) that may be relevant to the pathophysiology and clinical effects associated with ATP7AT994I Our study represents the first report of p97/VCP binding to a UBX domain that is not normally exposed, resulting in an aberrant protein-protein interaction leading to motor neuron degeneration.
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Affiliation(s)
- Ling Yi
- From the Section on Translational Neuroscience, Molecular Medicine Branch, Eunice Kennedy Shriver NICHD, National Institutes of Health, Bethesda, Maryland 20892-3754
| | - Stephen G Kaler
- From the Section on Translational Neuroscience, Molecular Medicine Branch, Eunice Kennedy Shriver NICHD, National Institutes of Health, Bethesda, Maryland 20892-3754
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41
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Pöhler R, Krahn JH, van den Boom J, Dobrynin G, Kaschani F, Eggenweiler HM, Zenke FT, Kaiser M, Meyer H. A Non-Competitive Inhibitor of VCP/p97 and VPS4 Reveals Conserved Allosteric Circuits in Type I and II AAA ATPases. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201711429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Robert Pöhler
- Molecular Biology I, Centre for Medical Biotechnology; University of Duisburg-Essen; 45117 Essen Germany
| | - Jan H. Krahn
- Chemical Biology, Centre for Medical Biotechnology; University of Duisburg-Essen; 45117 Essen Germany
| | - Johannes van den Boom
- Molecular Biology I, Centre for Medical Biotechnology; University of Duisburg-Essen; 45117 Essen Germany
| | - Grzegorz Dobrynin
- Molecular Biology I, Centre for Medical Biotechnology; University of Duisburg-Essen; 45117 Essen Germany
| | - Farnusch Kaschani
- Chemical Biology, Centre for Medical Biotechnology; University of Duisburg-Essen; 45117 Essen Germany
| | - Hans-Michael Eggenweiler
- Medicinal Chemistry DA and Translational Innovation Platform Oncology, Global R&D, Healthcare; Merck KGaA; Frankfurter Str. 250 64293 Darmstadt Germany
| | - Frank T. Zenke
- Medicinal Chemistry DA and Translational Innovation Platform Oncology, Global R&D, Healthcare; Merck KGaA; Frankfurter Str. 250 64293 Darmstadt Germany
| | - Markus Kaiser
- Chemical Biology, Centre for Medical Biotechnology; University of Duisburg-Essen; 45117 Essen Germany
| | - Hemmo Meyer
- Molecular Biology I, Centre for Medical Biotechnology; University of Duisburg-Essen; 45117 Essen Germany
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42
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Pöhler R, Krahn JH, van den Boom J, Dobrynin G, Kaschani F, Eggenweiler HM, Zenke FT, Kaiser M, Meyer H. A Non-Competitive Inhibitor of VCP/p97 and VPS4 Reveals Conserved Allosteric Circuits in Type I and II AAA ATPases. Angew Chem Int Ed Engl 2018; 57:1576-1580. [PMID: 29271116 DOI: 10.1002/anie.201711429] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Revised: 12/15/2017] [Indexed: 01/16/2023]
Abstract
AAA ATPases have pivotal functions in diverse cellular processes essential for survival and proliferation. Revealing strategies for chemical inhibition of this class of enzymes is therefore of great interest for the development of novel chemotherapies or chemical tools. Here, we characterize the compound MSC1094308 as a reversible, allosteric inhibitor of the type II AAA ATPase human ubiquitin-directed unfoldase (VCP)/p97 and the type I AAA ATPase VPS4B. Subsequent proteomic, genetic and biochemical studies indicate that MSC1094308 binds to a previously characterized drugable hotspot of p97, thereby inhibiting the D2 ATPase activity. Our results furthermore indicate that a similar allosteric site exists in VPS4B, suggesting conserved allosteric circuits and drugable sites in both type I and II AAA ATPases. Our results may thus guide future chemical tool and drug discovery efforts for the biomedically relevant AAA ATPases.
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Affiliation(s)
- Robert Pöhler
- Molecular Biology I, Centre for Medical Biotechnology, University of Duisburg-Essen, 45117, Essen, Germany
| | - Jan H Krahn
- Chemical Biology, Centre for Medical Biotechnology, University of Duisburg-Essen, 45117, Essen, Germany
| | - Johannes van den Boom
- Molecular Biology I, Centre for Medical Biotechnology, University of Duisburg-Essen, 45117, Essen, Germany
| | - Grzegorz Dobrynin
- Molecular Biology I, Centre for Medical Biotechnology, University of Duisburg-Essen, 45117, Essen, Germany
| | - Farnusch Kaschani
- Chemical Biology, Centre for Medical Biotechnology, University of Duisburg-Essen, 45117, Essen, Germany
| | - Hans-Michael Eggenweiler
- Medicinal Chemistry DA and Translational Innovation Platform Oncology, Global R&D, Healthcare, Merck KGaA, Frankfurter Str. 250, 64293, Darmstadt, Germany
| | - Frank T Zenke
- Medicinal Chemistry DA and Translational Innovation Platform Oncology, Global R&D, Healthcare, Merck KGaA, Frankfurter Str. 250, 64293, Darmstadt, Germany
| | - Markus Kaiser
- Chemical Biology, Centre for Medical Biotechnology, University of Duisburg-Essen, 45117, Essen, Germany
| | - Hemmo Meyer
- Molecular Biology I, Centre for Medical Biotechnology, University of Duisburg-Essen, 45117, Essen, Germany
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43
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Tang WK, Zhang T, Ye Y, Xia D. Structural basis for nucleotide-modulated p97 association with the ER membrane. Cell Discov 2017; 3:17045. [PMID: 29238611 PMCID: PMC5725882 DOI: 10.1038/celldisc.2017.45] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Accepted: 11/01/2017] [Indexed: 01/26/2023] Open
Abstract
Association of the cytosolic AAA (ATPases associated with various cellular activities) protein p97 to membranes is essential for various cellular processes including endoplasmic reticulum (ER)-associated degradation. The p97 consists of two ATPase domains and an N domain that interacts with numerous cofactors. The N domain of p97 is known to undergo a large nucleotide-dependent conformation switch, but its physiological relevance is unclear. Here we show p97 is recruited to canine ER membranes predominantly by interacting with VCP-interacting membrane protein (VIMP), an ER-resident protein. We found that the recruitment is modulated through a nucleotide-dependent conformation switch of the N domain in wild-type p97, but this modulation is absent in pathogenic mutants. We demonstrate the molecular mechanism of the modulation by a series of structures of p97, VIMP and their complexes and suggest a physiological role of the nucleotide-dependent N domain conformation switch. The lack of modulation in pathogenic mutants is caused by changes in interactions between the N and D1 domain, as demonstrated by multiple intermediate positions adopted by N domains of mutant p97. Our findings suggest the nucleotide-modulated membrane association may also have a role in other p97-dependent processes.
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Affiliation(s)
- Wai Kwan Tang
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Ting Zhang
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Disease, National Institutes of Health, Bethesda, MD, USA
| | - Yihong Ye
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Disease, National Institutes of Health, Bethesda, MD, USA
| | - Di Xia
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
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44
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Huang S, Wang Y. Golgi structure formation, function, and post-translational modifications in mammalian cells. F1000Res 2017; 6:2050. [PMID: 29225785 PMCID: PMC5710388 DOI: 10.12688/f1000research.11900.1] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/20/2017] [Indexed: 01/04/2023] Open
Abstract
The Golgi apparatus is a central membrane organelle for trafficking and post-translational modifications of proteins and lipids in cells. In mammalian cells, it is organized in the form of stacks of tightly aligned flattened cisternae, and dozens of stacks are often linked laterally into a ribbon-like structure located in the perinuclear region of the cell. Proper Golgi functionality requires an intact architecture, yet Golgi structure is dynamically regulated during the cell cycle and under disease conditions. In this review, we summarize our current understanding of the relationship between Golgi structure formation, function, and regulation, with focus on how post-translational modifications including phosphorylation and ubiquitination regulate Golgi structure and on how Golgi unstacking affects its functions, in particular, protein trafficking, glycosylation, and sorting in mammalian cells.
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Affiliation(s)
- Shijiao Huang
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Yanzhuang Wang
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
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45
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VCP/p97-Mediated Unfolding as a Principle in Protein Homeostasis and Signaling. Mol Cell 2017; 69:182-194. [PMID: 29153394 DOI: 10.1016/j.molcel.2017.10.028] [Citation(s) in RCA: 267] [Impact Index Per Article: 38.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Revised: 10/06/2017] [Accepted: 10/20/2017] [Indexed: 01/14/2023]
Abstract
The AAA+-type ATPase p97 governs an ever-expanding number of cellular processes reaching from degradation of damaged proteins and organelles to key signaling events and chromatin regulation with thousands of client proteins. With its relevance for cellular homeostasis and genome stability, it is linked to muscular and neuronal degeneration and, conversely, constitutes an attractive anti-cancer drug target. Its molecular function is ATP-driven protein unfolding, which is directed by ubiquitin and assisted by a host of cofactor proteins. This activity underlies p97's diverse ability to pull proteins out of membranes, unfold proteins for proteasomal degradation, or segregate proteins from partners for downstream activity. Recent advances in structural analysis and biochemical reconstitution have underscored this notion, resolved detailed molecular motions within the p97 hexamer, and suggested substrate threading through the central channel of the p97 hexamer as the driving mechanism. We will discuss the mechanisms and open questions in the context of the diverse cellular activities.
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46
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Her NG, Toth JI, Ma CT, Wei Y, Motamedchaboki K, Sergienko E, Petroski MD. p97 Composition Changes Caused by Allosteric Inhibition Are Suppressed by an On-Target Mechanism that Increases the Enzyme's ATPase Activity. Cell Chem Biol 2017; 23:517-28. [PMID: 27105284 DOI: 10.1016/j.chembiol.2016.03.012] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Revised: 02/23/2016] [Accepted: 03/16/2016] [Indexed: 11/27/2022]
Abstract
The AAA ATPase p97/VCP regulates protein homeostasis using a diverse repertoire of cofactors to fulfill its biological functions. Here we use the allosteric p97 inhibitor NMS-873 to analyze its effects on enzyme composition and the ability of cells to adapt to its cytotoxicity. We found that p97 inhibition changes steady state cofactor-p97 composition, leading to the enrichment of a subset of its cofactors and polyubiquitin bound to p97. We isolated cells specifically insensitive to NMS-873 and identified a new mutation (A530T) in p97. A530T is sufficient to overcome the cytotoxicity of NMS-873 and alleviates p97 composition changes caused by the molecule but not other p97 inhibitors. This mutation does not affect NMS-873 binding but increases p97 catalytic efficiency through altered ATP and ADP binding. Collectively, these findings identify cofactor-p97 interactions sensitive to p97 inhibition and reveal a new on-target mechanism to suppress the cytotoxicity of NMS-873.
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Affiliation(s)
- Nam-Gu Her
- Tumor Initiation and Maintenance Program, NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Julia I Toth
- Tumor Initiation and Maintenance Program, NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Chen-Ting Ma
- Conrad Prebys Center for Chemical Genomics, NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Yang Wei
- Tumor Initiation and Maintenance Program, NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Khatereh Motamedchaboki
- Tumor Initiation and Maintenance Program, NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Eduard Sergienko
- Conrad Prebys Center for Chemical Genomics, NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Matthew D Petroski
- Tumor Initiation and Maintenance Program, NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA.
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47
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Zhou N, Ma B, Stoll S, Hays TT, Qiu H. The valosin-containing protein is a novel repressor of cardiomyocyte hypertrophy induced by pressure overload. Aging Cell 2017; 16:1168-1179. [PMID: 28799247 PMCID: PMC5595673 DOI: 10.1111/acel.12653] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/01/2017] [Indexed: 12/22/2022] Open
Abstract
Hypertension‐induced left ventricular hypertrophy (LVH) is an independent risk factor for heart failure. Regression of LVH has emerged as a major goal in the treatment of hypertensive patients. Here, we tested our hypothesis that the valosin‐containing protein (VCP), an ATPase associate protein, is a novel repressor of cardiomyocyte hypertrophy under the pressure overload stress. Left ventricular hypertrophy (LVH) was determined by echocardiography in 4‐month male spontaneously hypertensive rats (SHRs) vs. age‐matched normotensive Wistar Kyoto (WKY) rats. VCP expression was found to be significantly downregulated in the left ventricle (LV) tissues from SHRs vs. WKY rats. Pressure overload was induced by transverse aortic constriction (TAC) in wild‐type (WT) mice. At the end of 2 weeks, mice with TAC developed significant LVH whereas the cardiac function remained unchanged. A significant reduction of VCP at both the mRNA and protein levels in hypertrophic LV tissue was found in TAC WT mice compared to sham controls. Valosin‐containing protein VCP expression was also observed to be time‐ and dose‐dependently reduced in vitro in isolated neonatal rat cardiomyocytes upon the treatment of angiotensin II. Conversely, transgenic (TG) mice with cardiac‐specific overexpression of VCP showed a significant repression in TAC‐induced LVH vs. litter‐matched WT controls upon 2‐week TAC. TAC‐induced activation of the mechanistic target of rapamycin complex 1 (mTORC1) signaling observed in WT mice LVs was also significantly blunted in VCP TG mice. In conclusion, VCP acts as a novel repressor that is able to prevent cardiomyocyte hypertrophy from pressure overload by modulating the mTORC1 signaling pathway.
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Affiliation(s)
- Ning Zhou
- Division of Cardiology; Department of Internal Medicine; Tongji Hospital; Tongji Medical College; Huazhong University of Science and Technology; Wuhan China
- Division of Physiology; Department of Basic Sciences; School of Medicine; Loma Linda University; Loma Linda CA USA
| | - Ben Ma
- Division of Physiology; Department of Basic Sciences; School of Medicine; Loma Linda University; Loma Linda CA USA
| | - Shaunrick Stoll
- Division of Physiology; Department of Basic Sciences; School of Medicine; Loma Linda University; Loma Linda CA USA
| | - Tristan T. Hays
- Division of Physiology; Department of Basic Sciences; School of Medicine; Loma Linda University; Loma Linda CA USA
| | - Hongyu Qiu
- Division of Physiology; Department of Basic Sciences; School of Medicine; Loma Linda University; Loma Linda CA USA
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48
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Rao MV, Williams DR, Cocklin S, Loll PJ. Interaction between the AAA + ATPase p97 and its cofactor ataxin3 in health and disease: Nucleotide-induced conformational changes regulate cofactor binding. J Biol Chem 2017; 292:18392-18407. [PMID: 28939772 DOI: 10.1074/jbc.m117.806281] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Revised: 09/16/2017] [Indexed: 12/29/2022] Open
Abstract
p97 is an essential ATPase associated with various cellular activities (AAA+) that functions as a segregase in diverse cellular processes, including the maintenance of proteostasis. p97 interacts with different cofactors that target it to distinct pathways; an important example is the deubiquitinase ataxin3, which collaborates with p97 in endoplasmic reticulum-associated degradation. However, the molecular details of this interaction have been unclear. Here, we characterized the binding of ataxin3 to p97, showing that ataxin3 binds with low-micromolar affinity to both wild-type p97 and mutants linked to degenerative disorders known as multisystem proteinopathy 1 (MSP1); we further showed that the stoichiometry of binding is one ataxin3 molecule per p97 hexamer. We mapped the binding determinants on each protein, demonstrating that ataxin3's p97/VCP-binding motif interacts with the inter-lobe cleft in the N-domain of p97. We also probed the nucleotide dependence of this interaction, confirming that ataxin3 and p97 associate in the presence of ATP and in the absence of nucleotide, but not in the presence of ADP. Our experiments suggest that an ADP-driven downward movement of the p97 N-terminal domain dislodges ataxin3 by inducing a steric clash between the D1-domain and ataxin3's C terminus. In contrast, MSP1 mutants of p97 bind ataxin3 irrespective of their nucleotide state, indicating a failure by these mutants to translate ADP binding into a movement of the N-terminal domain. Our model provides a mechanistic explanation for how nucleotides regulate the p97-ataxin3 interaction and why atypical cofactor binding is observed with MSP1 mutants.
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Affiliation(s)
- Maya V Rao
- From the Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, Pennsylvania 19102 and
| | - Dewight R Williams
- the LeRoy Eyring Center for Solid State Science, Arizona State University, Tempe, Arizona 85287
| | - Simon Cocklin
- From the Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, Pennsylvania 19102 and
| | - Patrick J Loll
- From the Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, Pennsylvania 19102 and
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49
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Burr R, Ribbens D, Raychaudhuri S, Stewart EV, Ho J, Espenshade PJ. Dsc E3 ligase localization to the Golgi requires the ATPase Cdc48 and cofactor Ufd1 for activation of sterol regulatory element-binding protein in fission yeast. J Biol Chem 2017; 292:16333-16350. [PMID: 28821619 DOI: 10.1074/jbc.m117.802025] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Revised: 08/08/2017] [Indexed: 11/06/2022] Open
Abstract
Sterol regulatory element-binding proteins (SREBPs) in the fission yeast Schizosaccharomyces pombe regulate lipid homeostasis and the hypoxic response under conditions of low sterol or oxygen availability. SREBPs are cleaved in the Golgi through the combined action of the Dsc E3 ligase complex, the rhomboid protease Rbd2, and the essential ATPases associated with diverse cellular activities (AAA+) ATPase Cdc48. The soluble SREBP N-terminal transcription factor domain is then released into the cytosol to enter the nucleus and regulate gene expression. Previously, we reported that Cdc48 binding to Rbd2 is required for Rbd2-mediated SREBP cleavage. Here, using affinity chromatography and mass spectrometry experiments, we identified Cdc48-binding proteins in S. pombe, generating a list of many previously unknown potential Cdc48-binding partners. We show that the established Cdc48 cofactor Ufd1 is required for SREBP cleavage but does not interact with the Cdc48-Rbd2 complex. Cdc48-Ufd1 is instead required at a step prior to Rbd2 function, during Golgi localization of the Dsc E3 ligase complex. Together, these findings demonstrate that two distinct Cdc48 complexes, Cdc48-Ufd1 and Cdc48-Rbd2, are required for SREBP activation and low-oxygen adaptation in S. pombe.
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Affiliation(s)
- Risa Burr
- From the Department of Cell Biology, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205
| | - Diedre Ribbens
- From the Department of Cell Biology, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205
| | - Sumana Raychaudhuri
- From the Department of Cell Biology, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205
| | - Emerson V Stewart
- From the Department of Cell Biology, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205
| | - Jason Ho
- From the Department of Cell Biology, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205
| | - Peter J Espenshade
- From the Department of Cell Biology, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205
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50
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The AAA+ ATPase p97, a cellular multitool. Biochem J 2017; 474:2953-2976. [PMID: 28819009 PMCID: PMC5559722 DOI: 10.1042/bcj20160783] [Citation(s) in RCA: 100] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Revised: 07/17/2017] [Accepted: 07/21/2017] [Indexed: 12/17/2022]
Abstract
The AAA+ (ATPases associated with diverse cellular activities) ATPase p97 is essential to a wide range of cellular functions, including endoplasmic reticulum-associated degradation, membrane fusion, NF-κB (nuclear factor kappa-light-chain-enhancer of activated B cells) activation and chromatin-associated processes, which are regulated by ubiquitination. p97 acts downstream from ubiquitin signaling events and utilizes the energy from ATP hydrolysis to extract its substrate proteins from cellular structures or multiprotein complexes. A multitude of p97 cofactors have evolved which are essential to p97 function. Ubiquitin-interacting domains and p97-binding domains combine to form bi-functional cofactors, whose complexes with p97 enable the enzyme to interact with a wide range of ubiquitinated substrates. A set of mutations in p97 have been shown to cause the multisystem proteinopathy inclusion body myopathy associated with Paget's disease of bone and frontotemporal dementia. In addition, p97 inhibition has been identified as a promising approach to provoke proteotoxic stress in tumors. In this review, we will describe the cellular processes governed by p97, how the cofactors interact with both p97 and its ubiquitinated substrates, p97 enzymology and the current status in developing p97 inhibitors for cancer therapy.
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