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Nobre CR, de Souza Paço M, de Almeida Duarte LF, Dos Santos Barbosa Ortega A, Moreno BB, de Camargo TFT, Parreira LM, da Costa Souza I, Monferrán MV, Wunderlin DA, Fernandes MN, Pereira CDS. Systemic effects of settleable atmospheric particulate matter (SePM) on swamp ghost crab Ucides cordatus. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 938:173295. [PMID: 38782293 DOI: 10.1016/j.scitotenv.2024.173295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Revised: 05/13/2024] [Accepted: 05/14/2024] [Indexed: 05/25/2024]
Abstract
Metallurgical activities are a significant source of settleable atmospheric particulate matter (SePM). The material is exposed to wind action, leading to its deposition throughout terrestrial and aquatic ecosystems, thus promoting contamination by metals and metalloids. However, knowledge of the impacts on biota is scarce. In aquatic coastal zones, evaluating hemolymph in invertebrates makes it possible to have insights into the pre-pathogenic effects and health status of organisms. Our study aimed to evaluate bioaccumulation and the sublethal effects of SePM on the mangrove crab Ucides cordatus by assessing biomarkers of cito-genotoxicity in the hemolymph. Organisms underwent a 30-day experiment with four treatments: control; 0.01 g.L-1, 0.1 g.L-1, 1 g.L-1 of SePM, with hemolymph sampled at 2, 7, 15, and 30 days of exposure to assess lipid peroxidation (LPO), DNA damage (strand break), cholinesterase (ChE) and lysosomal membrane stability (LMS). The results revealed metals' bioaccumulation in soft tissues (Al, Fe+, Fe++, Cu, Zr, Nb) and dose-time-dependent responses for LPO, DNA strand break, ChE, and LMS. Significant correlation was found between LPO and Cu (tissue), reduced LMS and Al and Fe (tissue), and Cu, Zn, Ag, and Bi in water. Hemolymph was related to the toxicokinetic and toxicodynamic of metals and metalloids from SePM in Ucides cordatus. New toxicological evidence was obtained to shed light on the impacts of SePM on the ecological status of coastal zones.
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Affiliation(s)
- Caio Rodrigues Nobre
- Department of Marine Sciences, Federal University of São Paulo, Baixada Santista Campus, 168 Maria Máximo Street, 11030-100 Santos, São Paulo, Brazil.
| | - Marina de Souza Paço
- Department of Marine Sciences, Federal University of São Paulo, Baixada Santista Campus, 168 Maria Máximo Street, 11030-100 Santos, São Paulo, Brazil
| | - Luis Felipe de Almeida Duarte
- Santa Cecília University: Post Graduate Program in Environmental Science and Technology, 277 Oswaldo Cruz Street, 11045-907 Boqueirão, Santos, São Paulo, Brazil
| | - Andressa Dos Santos Barbosa Ortega
- Institute of Biosciences, São Paulo State University "Júlio de Mesquita Filho", Litoral Paulista Campus, Infante Dom Henrique Square, s/n - Parque Bitaru, 11330-900 São Vicente, São Paulo, Brazil
| | - Beatriz Barbosa Moreno
- Department of Marine Sciences, Federal University of São Paulo, Baixada Santista Campus, 168 Maria Máximo Street, 11030-100 Santos, São Paulo, Brazil
| | - Thiago Felicíssimo Turíbio de Camargo
- Department of Marine Sciences, Federal University of São Paulo, Baixada Santista Campus, 168 Maria Máximo Street, 11030-100 Santos, São Paulo, Brazil
| | - Leticia Malvestio Parreira
- Department of Marine Sciences, Federal University of São Paulo, Baixada Santista Campus, 168 Maria Máximo Street, 11030-100 Santos, São Paulo, Brazil
| | - Iara da Costa Souza
- Department of Physiological Sciences, Federal University of São Carlos (DCF/UFSCar), Washington Luiz Highway, Km 235, 13565-905 São Carlos, São Paulo, Brazil
| | - Magdalena Victoria Monferrán
- ICYTAC: Institute of Food Science and Technology, Córdoba National University, CONICET, Faculty of Chemical Sciences, University City, 5000 Córdoba, Argentina
| | - Daniel Alberto Wunderlin
- ICYTAC: Institute of Food Science and Technology, Córdoba National University, CONICET, Faculty of Chemical Sciences, University City, 5000 Córdoba, Argentina
| | - Marisa Narciso Fernandes
- Department of Physiological Sciences, Federal University of São Carlos (DCF/UFSCar), Washington Luiz Highway, Km 235, 13565-905 São Carlos, São Paulo, Brazil
| | - Camilo Dias Seabra Pereira
- Department of Marine Sciences, Federal University of São Paulo, Baixada Santista Campus, 168 Maria Máximo Street, 11030-100 Santos, São Paulo, Brazil; Santa Cecília University: Post Graduate Program in Environmental Science and Technology, 277 Oswaldo Cruz Street, 11045-907 Boqueirão, Santos, São Paulo, Brazil
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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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3
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Pontifex CS, Zaman M, Fanganiello RD, Shutt TE, Pfeffer G. Valosin-Containing Protein (VCP): A Review of Its Diverse Molecular Functions and Clinical Phenotypes. Int J Mol Sci 2024; 25:5633. [PMID: 38891822 PMCID: PMC11172259 DOI: 10.3390/ijms25115633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 05/20/2024] [Accepted: 05/20/2024] [Indexed: 06/21/2024] Open
Abstract
In this review we examine the functionally diverse ATPase associated with various cellular activities (AAA-ATPase), valosin-containing protein (VCP/p97), its molecular functions, the mutational landscape of VCP and the phenotypic manifestation of VCP disease. VCP is crucial to a multitude of cellular functions including protein quality control, endoplasmic reticulum-associated degradation (ERAD), autophagy, mitophagy, lysophagy, stress granule formation and clearance, DNA replication and mitosis, DNA damage response including nucleotide excision repair, ATM- and ATR-mediated damage response, homologous repair and non-homologous end joining. VCP variants cause multisystem proteinopathy, and pathology can arise in several tissue types such as skeletal muscle, bone, brain, motor neurons, sensory neurons and possibly cardiac muscle, with the disease course being challenging to predict.
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Affiliation(s)
- Carly S. Pontifex
- Hotchkiss Brain Institute, Department of Clinical Neurosciences, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 1N4, Canada; (C.S.P.); (M.Z.); (T.E.S.)
| | - Mashiat Zaman
- Hotchkiss Brain Institute, Department of Clinical Neurosciences, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 1N4, Canada; (C.S.P.); (M.Z.); (T.E.S.)
- Alberta Child Health Research Institute, Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 1N4, Canada
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, AB T2N 1N4, Canada
| | | | - Timothy E. Shutt
- Hotchkiss Brain Institute, Department of Clinical Neurosciences, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 1N4, Canada; (C.S.P.); (M.Z.); (T.E.S.)
- Alberta Child Health Research Institute, Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 1N4, Canada
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Gerald Pfeffer
- Hotchkiss Brain Institute, Department of Clinical Neurosciences, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 1N4, Canada; (C.S.P.); (M.Z.); (T.E.S.)
- Alberta Child Health Research Institute, Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 1N4, Canada
- Heritage Medical Research Building 155, 3330 Hospital Dr NW, Calgary, AB T2N 4N1, Canada
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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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Shmara A, Perez-Rosendahl M, Murphy K, Kwon A, Smith C, Kimonis V. A clinicopathologic study of malignancy in VCP-associated multisystem proteinopathy. Orphanet J Rare Dis 2022; 17:272. [PMID: 35841038 PMCID: PMC9287862 DOI: 10.1186/s13023-022-02403-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 06/26/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Valosin containing protein (VCP) is an important protein with many vital functions mostly related to the ubiquitin-proteasome system that provides protein quality control. VCP-associated inclusion body myopathy with Paget disease of bone and frontotemporal dementia, also termed VCP disease and multisystem proteinopathy (MSP 1), is an autosomal dominant disorder caused by monoallelic variants in the VCP gene on human chromosome 9. VCP has also been strongly involved in cancer, with over-activity of VCP found in several cancers such as prostate, pancreatic, endometrial, esophageal cancers and osteosarcoma. Since MSP1 is caused by gain of function variants in the VCP gene, we hypothesized our patients would show increased risk for developing malignancies. We describe cases of 3 rare malignancies and 4 common cancers from a retrospective dataset. RESULTS Upon surveying 106 families with confirmed VCP variants, we found a higher rate of rare tumors including malignant peripheral nerve sheath tumor, anaplastic pleomorphic xanthoastrocytoma and thymoma. Some of these subjects developed cancer before displaying other classic VCP disease manifestations. We also present cases of common cancers; however, we did not find an increased rate compared to the general population. This could be related to the early mortality associated with this disease, since most patients die in their 50-60 s due to respiratory failure or cardiomyopathy which is earlier than the age at which most cancers appear. CONCLUSION This is the first study that expands the phenotype of VCP disease to potentially include rare cancers and highlights the importance of further investigation of the role of VCP in cancer development. The results of this study in VCP disease patients suggest that patients may be at an increased risk for rare tumors. A larger study will determine if patients with VCP disease develop cancer at a higher rate than the general population. If that is the case, they should be followed up more frequently and screened for recurrence and metastasis of their cancer.
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Affiliation(s)
- Alyaa Shmara
- Division of Genetic and Genomic Medicine, Department of Pediatrics, University of California-Irvine, Lab and FEDEX: Hewitt Hall, Rm 2038, Health Sciences Rd., Irvine, CA, 92697, USA
| | | | - Kady Murphy
- Division of Genetic and Genomic Medicine, Department of Pediatrics, University of California-Irvine, Lab and FEDEX: Hewitt Hall, Rm 2038, Health Sciences Rd., Irvine, CA, 92697, USA
| | - Ashley Kwon
- Division of Genetic and Genomic Medicine, Department of Pediatrics, University of California-Irvine, Lab and FEDEX: Hewitt Hall, Rm 2038, Health Sciences Rd., Irvine, CA, 92697, USA
| | - Charles Smith
- Department of Neurology and Sanders-Brown Center On Aging, University of Kentucky, Lexington, KY, USA
| | - Virginia Kimonis
- Division of Genetic and Genomic Medicine, Department of Pediatrics, University of California-Irvine, Lab and FEDEX: Hewitt Hall, Rm 2038, Health Sciences Rd., Irvine, CA, 92697, USA.
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Phospho-Ser 784-VCP Drives Resistance of Pancreatic Ductal Adenocarcinoma to Genotoxic Chemotherapies and Predicts the Chemo-Sensitizing Effect of VCP Inhibitor. Cancers (Basel) 2021; 13:cancers13205076. [PMID: 34680224 PMCID: PMC8534018 DOI: 10.3390/cancers13205076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 10/05/2021] [Accepted: 10/07/2021] [Indexed: 11/17/2022] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) patients have a dismal prognosis due in large part to chemotherapy resistance. However, a small subset containing defects in the DNA damage response (DDR) pathways are chemotherapy-sensitive. Identifying intrinsic and therapeutically inducible DDR defects can improve precision and efficacy of chemotherapies for PDAC. DNA repair requires dynamic reorganization of chromatin-associated proteins, which is orchestrated by the AAA+ ATPase VCP. We recently discovered that the DDR function of VCP is selectively activated by Ser784 phosphorylation. In this paper, we show that pSer784-VCP but not total VCP levels in primary PDAC tumors negatively correlate with patient survival. In PDAC cell lines, different pSer784-VCP levels are induced by genotoxic chemotherapy agents and positively correlate with genome stability and cell survival. Causal effects of pSer784-VCP on DNA repair and cell survival were confirmed using VCP knockdown and functional rescue. Importantly, DNA damage-induced pSer784-VCP rather than total VCP levels in PDAC cell lines predict their chemotherapy response and chemo-sensitizing ability of selective VCP inhibitor NMS-873. Therefore, pSer784-VCP drives genotoxic chemotherapy resistance of PDAC, and can potentially be used as a predictive biomarker as well as a sensitizing target to enhance the chemotherapy response of PDAC.
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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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Mishra S, Dunkerly-Eyring BL, Keceli G, Ranek MJ. Phosphorylation Modifications Regulating Cardiac Protein Quality Control Mechanisms. Front Physiol 2020; 11:593585. [PMID: 33281625 PMCID: PMC7689282 DOI: 10.3389/fphys.2020.593585] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 09/28/2020] [Indexed: 12/12/2022] Open
Abstract
Many forms of cardiac disease, including heart failure, present with inadequate protein quality control (PQC). Pathological conditions often involve impaired removal of terminally misfolded proteins. This results in the formation of large protein aggregates, which further reduce cellular viability and cardiac function. Cardiomyocytes have an intricately collaborative PQC system to minimize cellular proteotoxicity. Increased expression of chaperones or enhanced clearance of misfolded proteins either by the proteasome or lysosome has been demonstrated to attenuate disease pathogenesis, whereas reduced PQC exacerbates pathogenesis. Recent studies have revealed that phosphorylation of key proteins has a potent regulatory role, both promoting and hindering the PQC machinery. This review highlights the recent advances in phosphorylations regulating PQC, the impact in cardiac pathology, and the therapeutic opportunities presented by harnessing these modifications.
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Affiliation(s)
- Sumita Mishra
- Division of Cardiology, Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Brittany L Dunkerly-Eyring
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University, Baltimore, MD, United States
| | - Gizem Keceli
- Division of Cardiology, Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Mark J Ranek
- Division of Cardiology, Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, MD, United States
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Abstract
Valosin-containing protein (VCP) is essential for proteostasis during many cellular processes. However, it remains uncertain how its diverse functions are selectively regulated. We recently showed that DNA damage-induced Ser784 phosphorylation specifically increases VCP function for the DNA damage response and significantly influences the survival of chemotherapy-treated breast cancer patients.
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Affiliation(s)
- Jieya Shao
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA.,Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA
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10
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Shi X, Zhu K, Ye Z, Yue J. VCP/p97 targets the nuclear export and degradation of p27 Kip1 during G1 to S phase transition. FASEB J 2020; 34:5193-5207. [PMID: 32067276 DOI: 10.1096/fj.201901506r] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 01/13/2020] [Accepted: 02/02/2020] [Indexed: 12/17/2022]
Abstract
One of the critical regulatory mechanisms for cell cycle progression is the timely degradation of CDK inhibitors, including p21Cip1 and p27Kip1 . VCP/p97, an AAA-ATPase, is reported to be overexpressed in many types of cancers. Here, we found that treatment of MCF-7 human breast cancer cells with DBeQ, a VCP inhibitor, or VCP knockdown in MCF-7 cells arrested cells at G1 phase, accompanied with the blockage of both p21 and p27 degradation. Whereas, double knockdown of p21 and p27 in MCF-7 cells rendered cells refractory to DBeQ-induced G1 arrest. Moreover, inhibition or knockdown of VCP or UFD1, one of VCP's co-factors, in MCF-7, NIH3T3, or HEK293T cells blocked the nuclear export of p27 during earlier G1 phase after mitogen stimulation. We also identified the nuclear localization sequence (NLS) of VCP, and found that adding back wild-type VCP, not the NLS-deleted VCP mutant, restored the nuclear export and degradation of p27 in VCP knockout MCF-7 cells. Importantly, we found that VCP inhibition sensitized breast cancer cells to the treatment of several anticancer therapeutics both in vitro and in vivo. Taken together, our study not only uncovers the mechanisms underlying VCP-mediated cell proliferation control but also provides potential therapeutic option for cancer treatment.
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Affiliation(s)
- Xianli Shi
- City University of Hong Kong Shenzhen Research Institute, Shenzhen, China.,Department of Biomedical Sciences, City University of Hong Kong, Hong Kong, China
| | - Kaiyuan Zhu
- City University of Hong Kong Shenzhen Research Institute, Shenzhen, China.,Department of Biomedical Sciences, City University of Hong Kong, Hong Kong, China
| | - Zuodong Ye
- City University of Hong Kong Shenzhen Research Institute, Shenzhen, China.,Department of Biomedical Sciences, City University of Hong Kong, Hong Kong, China
| | - Jianbo Yue
- City University of Hong Kong Shenzhen Research Institute, Shenzhen, China.,Department of Biomedical Sciences, City University of Hong Kong, Hong Kong, China
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Singh AN, Oehler J, Torrecilla I, Kilgas S, Li S, Vaz B, Guérillon C, Fielden J, Hernandez‐Carralero E, Cabrera E, Tullis IDC, Meerang M, Barber PR, Freire R, Parsons J, Vojnovic B, Kiltie AE, Mailand N, Ramadan K. The p97-Ataxin 3 complex regulates homeostasis of the DNA damage response E3 ubiquitin ligase RNF8. EMBO J 2019; 38:e102361. [PMID: 31613024 PMCID: PMC6826192 DOI: 10.15252/embj.2019102361] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 09/16/2019] [Accepted: 09/19/2019] [Indexed: 12/31/2022] Open
Abstract
The E3 ubiquitin ligase RNF8 (RING finger protein 8) is a pivotal enzyme for DNA repair. However, RNF8 hyper-accumulation is tumour-promoting and positively correlates with genome instability, cancer cell invasion, metastasis and poor patient prognosis. Very little is known about the mechanisms regulating RNF8 homeostasis to preserve genome stability. Here, we identify the cellular machinery, composed of the p97/VCP ubiquitin-dependent unfoldase/segregase and the Ataxin 3 (ATX3) deubiquitinase, which together form a physical and functional complex with RNF8 to regulate its proteasome-dependent homeostasis under physiological conditions. Under genotoxic stress, when RNF8 is rapidly recruited to sites of DNA lesions, the p97-ATX3 machinery stimulates the extraction of RNF8 from chromatin to balance DNA repair pathway choice and promote cell survival after ionising radiation (IR). Inactivation of the p97-ATX3 complex affects the non-homologous end joining DNA repair pathway and hypersensitises human cancer cells to IR. We propose that the p97-ATX3 complex is the essential machinery for regulation of RNF8 homeostasis under both physiological and genotoxic conditions and that targeting ATX3 may be a promising strategy to radio-sensitise BRCA-deficient cancers.
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Affiliation(s)
- Abhay Narayan Singh
- Department of OncologyCancer Research UK/Medical Research Council Oxford Institute for Radiation OncologyUniversity of OxfordOxfordUK
| | - Judith Oehler
- Department of OncologyCancer Research UK/Medical Research Council Oxford Institute for Radiation OncologyUniversity of OxfordOxfordUK
- Present address:
Department of BiochemistryUniversity of OxfordOxfordUK
| | - Ignacio Torrecilla
- Department of OncologyCancer Research UK/Medical Research Council Oxford Institute for Radiation OncologyUniversity of OxfordOxfordUK
| | - Susan Kilgas
- Department of OncologyCancer Research UK/Medical Research Council Oxford Institute for Radiation OncologyUniversity of OxfordOxfordUK
| | - Shudong Li
- Department of OncologyCancer Research UK/Medical Research Council Oxford Institute for Radiation OncologyUniversity of OxfordOxfordUK
| | - Bruno Vaz
- Department of OncologyCancer Research UK/Medical Research Council Oxford Institute for Radiation OncologyUniversity of OxfordOxfordUK
| | - Claire Guérillon
- Novo Nordisk Foundation Center for Protein ResearchUniversity of CopenhagenCopenhagenDenmark
| | - John Fielden
- Department of OncologyCancer Research UK/Medical Research Council Oxford Institute for Radiation OncologyUniversity of OxfordOxfordUK
| | - Esperanza Hernandez‐Carralero
- Unidad de InvestigaciónHospital Universitario de CanariasLa LagunaSpain
- Instituto de Tecnologías BiomédicasUniversidad de La LagunaLa LagunaSpain
| | - Elisa Cabrera
- Unidad de InvestigaciónHospital Universitario de CanariasLa LagunaSpain
- Instituto de Tecnologías BiomédicasUniversidad de La LagunaLa LagunaSpain
| | - Iain DC Tullis
- Department of OncologyCancer Research UK/Medical Research Council Oxford Institute for Radiation OncologyUniversity of OxfordOxfordUK
| | - Mayura Meerang
- Institute of Pharmacology and Toxicology‐Vetsuisse FacultyUniversity of ZurichZurichSwitzerland
- Present address:
Department of Thoracic SurgeryUniversity Hospital ZurichZurichSwitzerland
| | - Paul R Barber
- Department of OncologyCancer Research UK/Medical Research Council Oxford Institute for Radiation OncologyUniversity of OxfordOxfordUK
| | - Raimundo Freire
- Unidad de InvestigaciónHospital Universitario de CanariasLa LagunaSpain
- Instituto de Tecnologías BiomédicasUniversidad de La LagunaLa LagunaSpain
- Universidad Fernando Pessoa CanariasSanta Maria de GuiaSpain
| | - Jason Parsons
- Department of Molecular and Clinical Cancer MedicineCancer Research CentreUniversity of LiverpoolLiverpoolUK
| | - Borivoj Vojnovic
- Department of OncologyCancer Research UK/Medical Research Council Oxford Institute for Radiation OncologyUniversity of OxfordOxfordUK
| | - Anne E Kiltie
- Department of OncologyCancer Research UK/Medical Research Council Oxford Institute for Radiation OncologyUniversity of OxfordOxfordUK
| | - Niels Mailand
- Novo Nordisk Foundation Center for Protein ResearchUniversity of CopenhagenCopenhagenDenmark
| | - Kristijan Ramadan
- Department of OncologyCancer Research UK/Medical Research Council Oxford Institute for Radiation OncologyUniversity of OxfordOxfordUK
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12
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Long XH, Zhou YF, Lan M, Huang SH, Li Liu Z, Shu Y. Valosin-containing protein promotes metastasis of osteosarcoma through autophagy induction and anoikis inhibition via the ERK/NF-κβ/beclin-1 signaling pathway. Oncol Lett 2019; 18:3823-3829. [PMID: 31516594 DOI: 10.3892/ol.2019.10716] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 06/07/2019] [Indexed: 12/19/2022] Open
Abstract
Valosin-containing protein (VCP) promotes the development of metastasis in osteosarcoma (OS) via the PI3K/Akt signaling pathway. However, inhibition of the PI3K/Akt pathway does not completely reverse VCP-mediated invasion and migration of OS, suggesting that VCP-mediated OS invasion and migration involves additional mechanisms. In the present study, a positive correlation between the expression of VCP and cell autophagy was observed among OS tissues. Inhibiting VCP may decrease the survival of malignant cells; however, an autophagy stimulator may compensate for VCP inhibition and promote malignant cell survival. Altering the level of autophagy did not affect cell invasiveness or migration. ERK, NF-κβ and beclin-1 protein expression levels were markedly decreased following VCP inhibition. These findings indicated that VCP may induce autophagy and enhance anoikis resistance without affecting cell invasiveness or migration. Via anoikis resistance, VCP may promote metastasis in OS. Therefore, targeting of the ERK/NF-κβ/beclin-1 signaling pathway may be an effective therapeutic strategy for the management of OS.
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Affiliation(s)
- Xin Hua Long
- Department of Emergency Surgery, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, P.R. China
| | - Yun Fei Zhou
- Department of Orthopedics, The First People's Hospital of Foshan, Foshan, Guangdong 528000, P.R. China
| | - Min Lan
- Department of Emergency Surgery, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, P.R. China
| | - Shan Hu Huang
- Department of Orthopedics, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, P.R. China
| | - Zhi Li Liu
- Department of Orthopedics, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, P.R. China
| | - Yong Shu
- Department of Orthopedics, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, P.R. China
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13
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Madigan VJ, Yuziuk JA, Chiarella AM, Tyson TO, Meganck RM, Elmore ZC, Tse LV, Hathaway NA, Asokan A. Ring finger protein 121 is a potent regulator of adeno-associated viral genome transcription. PLoS Pathog 2019; 15:e1007988. [PMID: 31386698 PMCID: PMC6697353 DOI: 10.1371/journal.ppat.1007988] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 08/16/2019] [Accepted: 07/17/2019] [Indexed: 12/12/2022] Open
Abstract
Adeno-associated viruses (AAV) are Dependoparvoviruses that have shown promise as recombinant vectors for gene therapy. While infectious pathways of AAV are well studied, gaps remain in our understanding of host factors affecting vector genome expression. Here, we map the role of ring finger protein 121 (RNF121), an E3 ubiquitin ligase, as a key regulator of AAV genome transcription. CRISPR-mediated knockout of RNF121 (RNF121 KO) in different cells markedly decreased AAV transduction regardless of capsid serotype or vector dose. Recombinant AAV transduction is partially rescued by overexpressing RNF121, but not by co-infection with helper Adenovirus. Major steps in the AAV infectious pathway including cell surface binding, cellular uptake, nuclear entry, capsid uncoating and second strand synthesis are unaffected. While gene expression from transfected plasmids or AAV genomes is unaffected, mRNA synthesis from AAV capsid-associated genomes is markedly decreased in RNF121 KO cells. These observations were attributed to transcriptional arrest as corroborated by RNAPol-ChIP and mRNA half-life measurements. Although AAV capsid proteins do not appear to be direct substrates of RNF121, the catalytic domain of the E3 ligase appears essential. Inhibition of ubiquitin-proteasome pathways revealed that blocking Valosin Containing Protein (VCP/p97), which targets substrates to the proteasome, can selectively and completely restore AAV-mediated transgene expression in RNF121 KO cells. Expanding on this finding, transcriptomic and proteomic analysis revealed that the catalytic subunit of DNA PK (DNAPK-Cs), a known activator of VCP, is upregulated in RNF121 KO cells and that the DNA damage machinery is enriched at sites of stalled AAV genome transcription. We postulate that a network of RNF121, VCP and DNA damage response elements function together to regulate transcriptional silencing and/or activation of AAV vector genomes. Recombinant AAV vectors are at the forefront of clinical gene therapy. There is a need to better understand the mechanisms dictating AAV transduction in the host. Here, we identify a network of host proteins involving RNF121, p97 and the DNA damage machinery as potent factors regulating AAV genome transcription. Our study sheds light on an understudied aspect of AAV biology with implications for gene therapy.
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Affiliation(s)
- Victoria J. Madigan
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States of America
- Gene Therapy Center, the University of North Carolina at Chapel Hill, Chapel Hill, NC, United States of America
- Department of Surgery, Duke University School of Medicine, Durham, NC, United States of America
| | - Julianne A. Yuziuk
- Gene Therapy Center, the University of North Carolina at Chapel Hill, Chapel Hill, NC, United States of America
| | - Anna M. Chiarella
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States of America
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, Chapel Hill, NC, United States of America
| | - Tyne O. Tyson
- Department of Surgery, Duke University School of Medicine, Durham, NC, United States of America
| | - Rita M. Meganck
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States of America
- Gene Therapy Center, the University of North Carolina at Chapel Hill, Chapel Hill, NC, United States of America
- Department of Surgery, Duke University School of Medicine, Durham, NC, United States of America
| | - Zachary C. Elmore
- Department of Surgery, Duke University School of Medicine, Durham, NC, United States of America
- Department of Molecular Genetics & Microbiology, Duke University School of Medicine, Durham, NC, United States of America
| | - Longping V. Tse
- Gene Therapy Center, the University of North Carolina at Chapel Hill, Chapel Hill, NC, United States of America
| | - Nathaniel A. Hathaway
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, Chapel Hill, NC, United States of America
| | - Aravind Asokan
- Department of Surgery, Duke University School of Medicine, Durham, NC, United States of America
- Department of Molecular Genetics & Microbiology, Duke University School of Medicine, Durham, NC, United States of America
- * E-mail:
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14
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Torrecilla I, Oehler J, Ramadan K. The role of ubiquitin-dependent segregase p97 (VCP or Cdc48) in chromatin dynamics after DNA double strand breaks. Philos Trans R Soc Lond B Biol Sci 2018; 372:rstb.2016.0282. [PMID: 28847819 PMCID: PMC5577460 DOI: 10.1098/rstb.2016.0282] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/24/2017] [Indexed: 12/27/2022] Open
Abstract
DNA double strand breaks (DSBs) are the most cytotoxic DNA lesions and, if not repaired, lead to chromosomal rearrangement, genomic instability and cell death. Cells have evolved a complex network of DNA repair and signalling molecules which promptly detect and repair DSBs, commonly known as the DNA damage response (DDR). The DDR is orchestrated by various post-translational modifications such as phosphorylation, methylation, ubiquitination or SUMOylation. As DSBs are located in complex chromatin structures, the repair of DSBs is engineered at two levels: (i) at sites of broken DNA and (ii) at chromatin structures that surround DNA lesions. Thus, DNA repair and chromatin remodelling machineries must work together to efficiently repair DSBs. Here, we summarize the current knowledge of the ubiquitin-dependent molecular unfoldase/segregase p97 (VCP in vertebrates and Cdc48 in worms and lower eukaryotes) in DSB repair. We identify p97 as an essential factor that regulates DSB repair. p97-dependent extraction of ubiquitinated substrates mediates spatio-temporal protein turnover at and around the sites of DSBs, thus orchestrating chromatin remodelling and DSB repair. As p97 is a druggable target, p97 inhibition in the context of DDR has great potential for cancer therapy, as shown for other DDR components such as PARP, ATR and CHK1.This article is part of the themed issue 'Chromatin modifiers and remodellers in DNA repair and signalling'.
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Affiliation(s)
- Ignacio Torrecilla
- Cancer Research UK and Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Judith Oehler
- Cancer Research UK and Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Kristijan Ramadan
- Cancer Research UK and Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Roosevelt Drive, Oxford OX3 7DQ, UK
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15
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Biau J, Chautard E, De Koning L, Court F, Pereira B, Verrelle P, Dutreix M. Predictive biomarkers of resistance to hypofractionated radiotherapy in high grade glioma. Radiat Oncol 2017; 12:123. [PMID: 28754127 PMCID: PMC5534104 DOI: 10.1186/s13014-017-0858-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 07/20/2017] [Indexed: 02/05/2023] Open
Abstract
Background Radiotherapy plays a major role in the management of high grade glioma. However, the radioresistance of glioma cells limits its efficiency and drives recurrence inside the irradiated tumor volume leading to poor outcome for patients. Stereotactic hypofractionated radiotherapy is one option for recurrent high grade gliomas. Optimization of hypofractionated radiotherapy with new radiosensitizing agents requires the identification of robust druggable targets involved in radioresistance. Methods We generated 11 xenografted glioma models: 6 were derived from cell lines (1 WHO grade III and 5 grade IV) and 5 were patient derived xenografts (2 WHO grade III and 3 grade IV). Xenografts were treated by hypofractionated radiotherapy (6x5Gy). We searched for 89 biomarkers of radioresistance (39 total proteins, 26 phosphoproteins and 24 ratios of phosphoproteins on total proteins) using Reverse Phase Protein Array. Results Both type of xenografted models showed equivalent spectrum of sensitivity and profile of response to hypofractionated radiotherapy. We report that Phospho-EGFR/EGFR, Phospho-Chk1/Chk1 and VCP were associated to resistance to hypofractionated radiotherapy. Conclusions Several compounds targeting EGFR or CHK1 are already in clinical use and combining them with stereotactic hypofractionated radiotherapy for recurrent high grade gliomas might be of particular interest. Electronic supplementary material The online version of this article (doi:10.1186/s13014-017-0858-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Julian Biau
- Institut Curie, PSL Research University, Centre de Recherche, 91400, Orsay, France. .,Institut Curie, PSL Research University, Centre de Recherche, 75248, Paris, France. .,UMR3347, CNRS, 91400, Orsay, France. .,U1021, INSERM, 91400, Orsay, France. .,Université Paris Sud, 91400, Orsay, France. .,Université Clermont Auvergne, INSERM, U1240 IMoST, F-63000, Clermont Ferrand, France. .,Radiotherapy Department, Université Clermont Auvergne, Centre Jean Perrin, 58 rue Montalembert, 63011, Clermont-Ferrand, France.
| | - Emmanuel Chautard
- Université Clermont Auvergne, INSERM, U1240 IMoST, F-63000, Clermont Ferrand, France.,Radiotherapy Department, Université Clermont Auvergne, Centre Jean Perrin, 58 rue Montalembert, 63011, Clermont-Ferrand, France
| | - Leanne De Koning
- Department of Translational Research, RPPA platform, Institut Curie, PSL Research University, 75248, Paris cedex05, France
| | - Frank Court
- Université Clermont Auvergne, CNRS UMR 6293, INSERM U1103, GReD Laboratory, 63000, Clermont-Ferrand, France
| | - Bruno Pereira
- Biostatistics Department, DRCI, Clermont-Ferrand Hospital, 63003, Clermont-Ferrand, France
| | - Pierre Verrelle
- Institut Curie, PSL Research University, Centre de Recherche, 91400, Orsay, France.,Institut Curie, PSL Research University, Centre de Recherche, 75248, Paris, France.,Radiotherapy Department, Université Clermont Auvergne, Centre Jean Perrin, 58 rue Montalembert, 63011, Clermont-Ferrand, France.,U1196, INSERM, 91400, Orsay, France.,UMR9187, CNRS, 91400, Orsay, France
| | - Marie Dutreix
- Institut Curie, PSL Research University, Centre de Recherche, 91400, Orsay, France.,Institut Curie, PSL Research University, Centre de Recherche, 75248, Paris, France.,UMR3347, CNRS, 91400, Orsay, France.,U1021, INSERM, 91400, Orsay, France.,Université Paris Sud, 91400, Orsay, France
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16
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Hänzelmann P, Schindelin H. The Interplay of Cofactor Interactions and Post-translational Modifications in the Regulation of the AAA+ ATPase p97. Front Mol Biosci 2017; 4:21. [PMID: 28451587 PMCID: PMC5389986 DOI: 10.3389/fmolb.2017.00021] [Citation(s) in RCA: 95] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 03/24/2017] [Indexed: 12/18/2022] Open
Abstract
The hexameric type II AAA ATPase (ATPase associated with various activities) p97 (also referred to as VCP, Cdc48, and Ter94) is critically involved in a variety of cellular activities including pathways such as DNA replication and repair which both involve chromatin remodeling, and is a key player in various protein quality control pathways mediated by the ubiquitin proteasome system as well as autophagy. Correspondingly, p97 has been linked to various pathophysiological states including cancer, neurodegeneration, and premature aging. p97 encompasses an N-terminal domain, two highly conserved ATPase domains and an unstructured C-terminal tail. This enzyme hydrolyzes ATP and utilizes the resulting energy to extract or disassemble protein targets modified with ubiquitin from stable protein assemblies, chromatin and membranes. p97 participates in highly diverse cellular processes and hence its activity is tightly controlled. This is achieved by multiple regulatory cofactors, which either associate with the N-terminal domain or interact with the extreme C-terminus via distinct binding elements and target p97 to specific cellular pathways, sometimes requiring the simultaneous association with more than one cofactor. Most cofactors are recruited to p97 through conserved binding motifs/domains and assist in substrate recognition or processing by providing additional molecular properties. A tight control of p97 cofactor specificity and diversity as well as the assembly of higher-order p97-cofactor complexes is accomplished by various regulatory mechanisms, which include bipartite binding, binding site competition, changes in oligomeric assemblies, and nucleotide-induced conformational changes. Furthermore, post-translational modifications (PTMs) like acetylation, palmitoylation, phosphorylation, SUMOylation, and ubiquitylation of p97 have been reported which further modulate its diverse molecular activities. In this review, we will describe the molecular basis of p97-cofactor specificity/diversity and will discuss how PTMs can modulate p97-cofactor interactions and affect the physiological and patho-physiological functions of p97.
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Affiliation(s)
- Petra Hänzelmann
- Rudolf Virchow Center for Experimental Biomedicine, University of WürzburgWürzburg, Germany
| | - Hermann Schindelin
- Rudolf Virchow Center for Experimental Biomedicine, University of WürzburgWürzburg, Germany
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17
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Franz A, Ackermann L, Hoppe T. Ring of Change: CDC48/p97 Drives Protein Dynamics at Chromatin. Front Genet 2016; 7:73. [PMID: 27200082 PMCID: PMC4853748 DOI: 10.3389/fgene.2016.00073] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Accepted: 04/16/2016] [Indexed: 12/31/2022] Open
Abstract
The dynamic composition of proteins associated with nuclear DNA is a fundamental property of chromosome biology. In the chromatin compartment dedicated protein complexes govern the accurate synthesis and repair of the genomic information and define the state of DNA compaction in vital cellular processes such as chromosome segregation or transcription. Unscheduled or faulty association of protein complexes with DNA has detrimental consequences on genome integrity. Consequently, the association of protein complexes with DNA is remarkably dynamic and can respond rapidly to cellular signaling events, which requires tight spatiotemporal control. In this context, the ring-like AAA+ ATPase CDC48/p97 emerges as a key regulator of protein complexes that are marked with ubiquitin or SUMO. Mechanistically, CDC48/p97 functions as a segregase facilitating the extraction of substrate proteins from the chromatin. As such, CDC48/p97 drives molecular reactions either by directed disassembly or rearrangement of chromatin-bound protein complexes. The importance of this mechanism is reflected by human pathologies linked to p97 mutations, including neurodegenerative disorders, oncogenesis, and premature aging. This review focuses on the recent insights into molecular mechanisms that determine CDC48/p97 function in the chromatin environment, which is particularly relevant for cancer and aging research.
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Affiliation(s)
- André Franz
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, Institute for Genetics, University of Cologne Cologne, Germany
| | - Leena Ackermann
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, Institute for Genetics, University of Cologne Cologne, Germany
| | - Thorsten Hoppe
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, Institute for Genetics, University of Cologne Cologne, Germany
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18
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Trusch F, Kowski K, Bravo-Rodriguez K, Beuck C, Sowislok A, Wettig B, Matena A, Sanchez-Garcia E, Meyer H, Schrader T, Bayer P. Molecular tweezers target a protein–protein interface and thereby modulate complex formation. Chem Commun (Camb) 2016; 52:14141-14144. [DOI: 10.1039/c6cc08039a] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Supramolecular binders select few residues on a protein surface and by their unique complexation mode disrupt a critical protein–protein interaction.
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19
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Kotula E, Faigle W, Berthault N, Dingli F, Loew D, Sun JS, Dutreix M, Quanz M. DNA-PK target identification reveals novel links between DNA repair signaling and cytoskeletal regulation. PLoS One 2013; 8:e80313. [PMID: 24282534 PMCID: PMC3840018 DOI: 10.1371/journal.pone.0080313] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2013] [Accepted: 10/01/2013] [Indexed: 11/19/2022] Open
Abstract
The DNA-dependent protein kinase (DNA-PK) may function as a key signaling kinase in various cellular pathways other than DNA repair. Using a two-dimensional gel electrophoresis approach and stable DNA double-strand break-mimicking molecules (Dbait32Hc) to activate DNA-PK in the nucleus and cytoplasm, we identified 26 proteins that were highly phosphorylated following DNA-PK activation. Most of these proteins are involved in protein stability and degradation, cell signaling and the cytoskeleton. We investigated the relationship between DNA-PK and the cytoskeleton and found that the intermediate filament (IF) vimentin was a target of DNA-PK in vitro and in cells. Vimentin was phosphorylated at Ser459, by DNA-PK, in cells transfected with Dbait32Hc. We produced specific antibodies and showed that Ser459-P-vimentin was mostly located at cell protrusions. In migratory cells, the vimentin phosphorylation induced by Dbait32Hc was associated with a lower cellular adhesion and migration capacity. Thus, this approach led to the identification of downstream cytoplasmic targets of DNA-PK and revealed a connection between DNA damage signaling and the cytoskeleton.
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Affiliation(s)
- Ewa Kotula
- Institut Curie, Centre National de Recherche Scientifique (CNRS) UMR3347, Institut National de la Santé et de Recherche Médicale (INSERM) U1021, Université Paris-Sud 11, Centre Universitaire, Orsay, France
- DNA Therapeutics, Evry, France
| | - Wolfgang Faigle
- Institut Curie, Centre de Recherche, Laboratory of Proteomic Mass Spectrometry, Paris, France
- University Hospital Zürich, Department of Clinical Neuroimmunology and MS Research, Paris, France
| | - Nathalie Berthault
- Institut Curie, Centre National de Recherche Scientifique (CNRS) UMR3347, Institut National de la Santé et de Recherche Médicale (INSERM) U1021, Université Paris-Sud 11, Centre Universitaire, Orsay, France
| | - Florent Dingli
- Institut Curie, Centre de Recherche, Laboratory of Proteomic Mass Spectrometry, Paris, France
| | - Damarys Loew
- Institut Curie, Centre de Recherche, Laboratory of Proteomic Mass Spectrometry, Paris, France
| | - Jian-Sheng Sun
- DNA Therapeutics, Evry, France
- Muséum National d’Histoire Naturelle, USM503, Paris, France
| | - Marie Dutreix
- Institut Curie, Centre National de Recherche Scientifique (CNRS) UMR3347, Institut National de la Santé et de Recherche Médicale (INSERM) U1021, Université Paris-Sud 11, Centre Universitaire, Orsay, France
- * E-mail:
| | - Maria Quanz
- Institut Curie, Centre National de Recherche Scientifique (CNRS) UMR3347, Institut National de la Santé et de Recherche Médicale (INSERM) U1021, Université Paris-Sud 11, Centre Universitaire, Orsay, France
- DNA Therapeutics, Evry, France
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20
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Eletr ZM, Yin L, Wilkinson KD. BAP1 is phosphorylated at serine 592 in S-phase following DNA damage. FEBS Lett 2013; 587:3906-11. [PMID: 24211834 DOI: 10.1016/j.febslet.2013.10.035] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2013] [Revised: 10/16/2013] [Accepted: 10/24/2013] [Indexed: 11/29/2022]
Abstract
The human BAP1 deubiquitinating enzyme is a chromatin-bound transcriptional regulator and tumor suppressor. BAP1 functions in suppressing cell proliferation, yet its role in the DNA damage response pathway is less understood. In this study we characterized DNA damage-induced phosphorylation of BAP1 at serine 592 (pS592) and the cellular outcomes of this modification. In contrast to the majority of BAP1, pS592-BAP1 is predominantly dissociated from chromatin. Our findings support a model whereby stress induced phosphorylation functions to displace BAP1 from specific promoters. We hypothesize that this regulates the transcription of a subset of genes involved in the response to DNA damage.
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Affiliation(s)
- Ziad M Eletr
- Department of Biochemistry, Emory University, Atlanta, GA 30322, USA
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21
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Yang FC, Lin YH, Chen WH, Huang JY, Chang HY, Su SH, Wang HT, Chiang CY, Hsu PH, Tsai MD, Tan BCM, Lee SC. Interaction between salt-inducible kinase 2 (SIK2) and p97/valosin-containing protein (VCP) regulates endoplasmic reticulum (ER)-associated protein degradation in mammalian cells. J Biol Chem 2013; 288:33861-33872. [PMID: 24129571 DOI: 10.1074/jbc.m113.492199] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Salt-inducible kinase 2 (SIK2) is an important regulator of cAMP response element-binding protein-mediated gene expression in various cell types and is the only AMP-activated protein kinase family member known to interact with the p97/valosin-containing protein (VCP) ATPase. Previously, we have demonstrated that SIK2 can regulate autophagy when proteasomal function is compromised. Here we report that physical and functional interactions between SIK2 and p97/VCP underlie the regulation of endoplasmic reticulum (ER)-associated protein degradation (ERAD). SIK2 co-localizes with p97/VCP in the ER membrane and stimulates its ATPase activity through direct phosphorylation. Although the expression of wild-type recombinant SIK2 accelerated the degradation and removal of ERAD substrates, the kinase-deficient variant conversely had no effect. Furthermore, down-regulation of endogenous SIK2 or mutation of the SIK2 target site on p97/VCP led to impaired degradation of ERAD substrates and disruption of ER homeostasis. Collectively, these findings highlight a mechanism by which the interplay between SIK2 and p97/VCP contributes to the regulation of ERAD in mammalian cells.
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Affiliation(s)
- Fu-Chia Yang
- Institute of Molecular Medicine, National Taiwan University, Taipei 100, Taiwan
| | - Ya-Huei Lin
- Institute of Molecular Medicine, National Taiwan University, Taipei 100, Taiwan
| | - Wei-Hao Chen
- Institute of Molecular Medicine, National Taiwan University, Taipei 100, Taiwan
| | - Jing-Yi Huang
- Institute of Molecular Medicine, National Taiwan University, Taipei 100, Taiwan
| | - Hsin-Yun Chang
- Institute of Molecular Medicine, National Taiwan University, Taipei 100, Taiwan
| | - Su-Hui Su
- Institute of Molecular Medicine, National Taiwan University, Taipei 100, Taiwan
| | - Hsiao-Ting Wang
- Institute of Molecular Medicine, National Taiwan University, Taipei 100, Taiwan
| | - Chun-Yi Chiang
- Institute of Molecular Medicine, National Taiwan University, Taipei 100, Taiwan
| | - Pang-Hung Hsu
- Genomics Research Center, Academia Sinica, Taipei 11529, Taiwan
| | - Ming-Daw Tsai
- Genomics Research Center, Academia Sinica, Taipei 11529, Taiwan; Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan
| | | | - Sheng-Chung Lee
- Institute of Molecular Medicine, National Taiwan University, Taipei 100, Taiwan; Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan; Institute of Clinical Medicine, National Taiwan University, Taipei 100, Taiwan.
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22
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Cdc48: a swiss army knife of cell biology. JOURNAL OF AMINO ACIDS 2013; 2013:183421. [PMID: 24167726 PMCID: PMC3791797 DOI: 10.1155/2013/183421] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2013] [Revised: 07/29/2013] [Accepted: 08/12/2013] [Indexed: 12/13/2022]
Abstract
Cdc48 (also called VCP and p97) is an abundant protein that plays essential regulatory functions in a broad array of cellular processes. Working with various cofactors, Cdc48 utilizes its ATPase activity to promote the assembly and disassembly of protein complexes. Here, we review key biological functions and regulation of Cdc48 in ubiquitin-related events. Given the broad employment of Cdc48 in cell biology and its intimate ties to human diseases (e.g., amyotrophic lateral sclerosis), studies of Cdc48 will bring significant insights into the mechanism and function of ubiquitin in health and diseases.
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Jiang N, Shen Y, Fei X, Sheng K, Sun P, Qiu Y, Larner J, Cao L, Kong X, Mi J. Valosin-containing protein regulates the proteasome-mediated degradation of DNA-PKcs in glioma cells. Cell Death Dis 2013; 4:e647. [PMID: 23722536 PMCID: PMC3674378 DOI: 10.1038/cddis.2013.171] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
DNA-dependent protein kinase (DNA-PK) has an important role in the repair of DNA damage and regulates the radiation sensitivity of glioblastoma cells. The VCP (valosine-containing protein), a chaperone protein that regulates ubiquitin-dependent protein degradation, is phosphorylated by DNA-PK and recruited to DNA double-strand break sites to regulate DNA damage repair. However, it is not clear whether VCP is involved in DNA-PKcs (DNA-PK catalytic subunit) degradation or whether it regulates the radiosensitivity of glioblastoma. Our data demonstrated that DNA-PKcs was ubiquitinated and bound to VCP. VCP knockdown resulted in the accumulation of the DNA-PKcs protein in glioblastoma cells, and the proteasome inhibitor MG132 synergised this increase. As expected, this increase promoted the efficiency of DNA repair in several glioblastoma cell lines; in turn, this enhanced activity decreased the radiation sensitivity and prolonged the survival fraction of glioblastoma cells in vitro. Moreover, the VCP knockdown in glioblastoma cells reduced the survival time of the xenografted mice with radiation treatment relative to the control xenografted glioblastoma mice. In addition, the VCP protein was also downregulated in ∼25% of GBM tissues from patients (WHO, grade IV astrocytoma), and the VCP protein level was correlated with patient survival (R2=0.5222, P<0.05). These findings demonstrated that VCP regulates DNA-PKcs degradation and increases the sensitivity of GBM cells to radiation.
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Affiliation(s)
- N Jiang
- Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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24
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Vaz B, Halder S, Ramadan K. Role of p97/VCP (Cdc48) in genome stability. Front Genet 2013; 4:60. [PMID: 23641252 PMCID: PMC3639377 DOI: 10.3389/fgene.2013.00060] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2013] [Accepted: 04/05/2013] [Indexed: 11/13/2022] Open
Abstract
Ubiquitin-dependent molecular chaperone p97, also known as valosin-containing protein (VCP) or Cdc48, is an AAA ATPase involved in protein turnover and degradation. p97 converts its own ATPase hydrolysis into remodeling activity on a myriad of ubiquitinated substrates from different cellular locations and pathways. In this way, p97 mediates extraction of targeted protein from cellular compartments or protein complexes. p97-dependent protein extraction from various cellular environments maintains cellular protein homeostasis. In recent years, p97-dependent protein extraction from chromatin has emerged as an essential evolutionarily conserved process for maintaining genome stability. Inactivation of p97 segregase activity leads to accumulation of ubiquitinated substrates on chromatin, consequently leading to protein-induced chromatin stress (PICHROS). PICHROS directly and negatively affects multiple DNA metabolic processes, including replication, damage responses, mitosis, and transcription, leading to genotoxic stress and genome instability. By summarizing and critically evaluating recent data on p97 function in various chromatin-associated protein degradation processes, we propose establishing p97 as a genome caretaker.
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Affiliation(s)
- Bruno Vaz
- Institute of Pharmacology and Toxicology, University Zürich-Vetsuisse Zürich, Switzerland ; Gray Institute for Radiation Oncology and Biology, Department of Oncology, University of Oxford Oxford, UK
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25
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Stone HR, Morris JR. DNA damage emergency: cellular garbage disposal to the rescue? Oncogene 2013; 33:805-13. [PMID: 23503465 DOI: 10.1038/onc.2013.60] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2012] [Revised: 12/18/2012] [Accepted: 12/22/2012] [Indexed: 12/19/2022]
Abstract
The proteasome is a cellular machine found in the cytosol, nucleus and on chromatin that performs much of the proteolysis in eukaryotic cells. Recent reports show it is enriched at sites of double-stranded DNA breaks (DSBs) in mammalian cells. What is it doing there? This review will address three possibilities suggested by recent reports: in degrading proteins after their ubiquitination at and eviction from chromatin; as a deubiquitinase, specific to the antagonism of ubiquitin conjugates generated as part of the signalling of a DSB; and as a functional component of DNA repair mechanism itself. These findings add complexity to the proteasome as a potential therapeutic target in cancer treatment.
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Affiliation(s)
- H R Stone
- School of Cancer Sciences, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham, UK
| | - J R Morris
- School of Cancer Sciences, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham, UK
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26
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Han B, Zhang L, Feng M, Fang Y, Li J. An Integrated Proteomics Reveals Pathological Mechanism of Honeybee (Apis cerena) Sacbrood Disease. J Proteome Res 2013; 12:1881-97. [DOI: 10.1021/pr301226d] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Bin Han
- Institute of Apicultural Research/Key Laboratory of
Pollinating Insect Biology, Ministry of Agriculture, Chinese Academy of Agricultural Science, Beijing, China
| | - Lan Zhang
- Institute of Apicultural Research/Key Laboratory of
Pollinating Insect Biology, Ministry of Agriculture, Chinese Academy of Agricultural Science, Beijing, China
| | - Mao Feng
- Institute of Apicultural Research/Key Laboratory of
Pollinating Insect Biology, Ministry of Agriculture, Chinese Academy of Agricultural Science, Beijing, China
| | - Yu Fang
- Institute of Apicultural Research/Key Laboratory of
Pollinating Insect Biology, Ministry of Agriculture, Chinese Academy of Agricultural Science, Beijing, China
| | - Jianke Li
- Institute of Apicultural Research/Key Laboratory of
Pollinating Insect Biology, Ministry of Agriculture, Chinese Academy of Agricultural Science, Beijing, China
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Cloutier P, Coulombe B. Regulation of molecular chaperones through post-translational modifications: decrypting the chaperone code. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2013; 1829:443-54. [PMID: 23459247 DOI: 10.1016/j.bbagrm.2013.02.010] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2012] [Revised: 02/15/2013] [Accepted: 02/19/2013] [Indexed: 12/30/2022]
Abstract
Molecular chaperones and their associated cofactors form a group of highly specialized proteins that orchestrate the folding and unfolding of other proteins and the assembly and disassembly of protein complexes. Chaperones are found in all cell types and organisms, and their activity must be tightly regulated to maintain normal cell function. Indeed, deregulation of protein folding and protein complex assembly is the cause of various human diseases. Here, we present the results of an extensive review of the literature revealing that the post-translational modification (PTM) of chaperones has been selected during evolution as an efficient mean to regulate the activity and specificity of these key proteins. Because the addition and reciprocal removal of chemical groups can be triggered very rapidly, this mechanism provides an efficient switch to precisely regulate the activity of chaperones on specific substrates. The large number of PTMs detected in chaperones suggests that a combinatory code is at play to regulate function, activity, localization, and substrate specificity for this group of biologically important proteins. This review surveys the core information currently available as a starting point toward the more ambitious endeavor of deciphering the "chaperone code".
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VCP gene variation predicts outcome of advanced non-small-cell lung cancer platinum-based chemotherapy. Tumour Biol 2013; 34:953-61. [PMID: 23412975 DOI: 10.1007/s13277-012-0631-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2012] [Accepted: 12/11/2012] [Indexed: 01/24/2023] Open
Abstract
Valosin-containing protein (VCP), or p97, is a member of the ATP-binding protein family, and is involved in numerous cellular events, such as, protein degradation, membrane fusion, and chaperone activity. VCP has been demonstrated playing a critical role in non-small-cell lung cancer (NSCLC) pathogenesis and progression recently. We investigated the association between VCP polymorphisms and clinical outcome in advanced NSCLC patients undergoing platinum-based chemotherapy. We recruited 663 Chinese advanced NSCLC patients who were treated with platinum-based regimens, and using their clinical data, we assessed the efficacy and side effects of their treatment. Three tag-single nucleotide polymorphisms (SNPs) of VCP were genotyped. SNP rs2074549 showed a significant association with severe neutropenia. Its G/G genotype increased the risk of grade 3 or 4 neutropenia compared with wild-type homozygotes A/A (P = .001, odds ratio = 2.975). Haplotype association analysis revealed that CGA was associated with the increased incidence of severe neutropenia (P = .041, odds ratio = 1.439). However, no significant relationship was found between the presence of VCP polymorphisms and treatment efficacy when objective response, progression-free survival, and overall survival (OS) were evaluated. Our study is the first to provide evidence that VCP polymorphisms are associated with a severe chemotherapy-related adverse outcome in platinum-treated advanced NSCLC patients.
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29
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Cloutier P, Lavallée-Adam M, Faubert D, Blanchette M, Coulombe B. A newly uncovered group of distantly related lysine methyltransferases preferentially interact with molecular chaperones to regulate their activity. PLoS Genet 2013; 9:e1003210. [PMID: 23349634 PMCID: PMC3547847 DOI: 10.1371/journal.pgen.1003210] [Citation(s) in RCA: 122] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2012] [Accepted: 11/14/2012] [Indexed: 01/01/2023] Open
Abstract
Methylation is a post-translational modification that can affect numerous features of proteins, notably cellular localization, turnover, activity, and molecular interactions. Recent genome-wide analyses have considerably extended the list of human genes encoding putative methyltransferases. Studies on protein methyltransferases have revealed that the regulatory function of methylation is not limited to epigenetics, with many non-histone substrates now being discovered. We present here our findings on a novel family of distantly related putative methyltransferases. Affinity purification coupled to mass spectrometry shows a marked preference for these proteins to associate with various chaperones. Based on the spectral data, we were able to identify methylation sites in substrates, notably trimethylation of K135 of KIN/Kin17, K561 of HSPA8/Hsc70 as well as corresponding lysine residues in other Hsp70 isoforms, and K315 of VCP/p97. All modification sites were subsequently confirmed in vitro. In the case of VCP, methylation by METTL21D was stimulated by the addition of the UBX cofactor ASPSCR1, which we show directly interacts with the methyltransferase. This stimulatory effect was lost when we used VCP mutants (R155H, R159G, and R191Q) known to cause Inclusion Body Myopathy with Paget's disease of bone and Fronto-temporal Dementia (IBMPFD) and/or familial Amyotrophic Lateral Sclerosis (ALS). Lysine 315 falls in proximity to the Walker B motif of VCP's first ATPase/D1 domain. Our results indicate that methylation of this site negatively impacts its ATPase activity. Overall, this report uncovers a new role for protein methylation as a regulatory pathway for molecular chaperones and defines a novel regulatory mechanism for the chaperone VCP, whose deregulation is causative of degenerative neuromuscular diseases. Methylation, or transfer of a single or multiple methyl groups (CH3), is one of many post-translational modifications that occur on proteins. Such modifications can, in turn, affect numerous aspects of a protein, notably cellular localization, turnover, activity, and molecular interactions. In addition to post-translational modifications, the structural organization of a protein or protein complex can also have a significant impact on its function and stability. A group of factors known as “molecular chaperones” aid newly synthesized proteins in reaching their native conformation or alternating between physiologically relevant states. We present here a new family of factors that promote methylation of chaperones and show that, at least in one case, this modification translates into a modulation in the activity of the substrate chaperone. Our results not only characterize the function of previously unknown gene products, uncover a new role for protein methylation as a regulatory pathway for chaperones, and define a novel regulatory mechanism for the chaperone VCP, whose deregulation is causative of neuromuscular diseases, but also suggest the existence of a post-translational modification code that regulates molecular chaperones. Further decrypting this “chaperone code” will help understanding how the functional organization of the proteome is orchestrated.
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Affiliation(s)
- Philippe Cloutier
- Institut de Recherches Cliniques de Montréal (IRCM), Montréal, Québec, Canada
| | - Mathieu Lavallée-Adam
- McGill Centre for Bioinformatics and School of Computer Science, McGill University, Montréal, Québec, Canada
| | - Denis Faubert
- Institut de Recherches Cliniques de Montréal (IRCM), Montréal, Québec, Canada
| | - Mathieu Blanchette
- McGill Centre for Bioinformatics and School of Computer Science, McGill University, Montréal, Québec, Canada
| | - Benoit Coulombe
- Institut de Recherches Cliniques de Montréal (IRCM), Montréal, Québec, Canada
- Department of Biochemistry, Université de Montréal, Montréal, Québec, Canada
- * E-mail:
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30
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Abstract
The recent development of mammalian target of rapamycin (mTOR) kinase domain inhibitors and genetic dissection of rapamycin-sensitive and -insensitive mTOR protein complexes (mTORC1 and mTORC2) have revealed that phosphorylation of the mTOR substrate 4E-BP1 on amino acids Thr37 and/or Thr46 represents a rapamycin-insensitive activity of mTORC1. Despite numerous previous reports utilizing serine (Ser)-to-alanine (Ala) and threonine (Thr)-to-Ala phosphorylation site mutants of 4E-BP1 to assess which post-translational modification(s) directly regulate binding to eIF4E, an ambiguous understanding persists. This manuscript demonstrates that the initial, rapamycin-insensitive phosphorylation event at Thr46 is sufficient to prevent eIF4E:4E-BP1 binding. This finding is relevant, particularly as mTOR kinase domain inhibitors continue to be assessed for clinical efficacy, since it clarifies a difference between the action of these second-generation mTOR inhibitors and those of rapamycin analogues.
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Affiliation(s)
- Mark Livingstone
- Biochemistry and McGill Cancer Centre, McGill University, Montreal, Canada ; Cytokine Signalling Unit, Institut Pasteur, Paris, France
| | - Michael Bidinosti
- Biochemistry and McGill Cancer Centre, McGill University, Montreal, Canada
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31
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Ishikawa H, Yasui K, Oketa Y, Suzuki M, Ono S. Increased expression of valosin-containing protein in the skin of patients with amyotrophic lateral sclerosis. J Clin Neurosci 2012; 19:522-6. [DOI: 10.1016/j.jocn.2011.05.044] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2011] [Revised: 04/22/2011] [Accepted: 05/08/2011] [Indexed: 10/14/2022]
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32
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Emerging functions of the VCP/p97 AAA-ATPase in the ubiquitin system. Nat Cell Biol 2012; 14:117-23. [PMID: 22298039 DOI: 10.1038/ncb2407] [Citation(s) in RCA: 630] [Impact Index Per Article: 52.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The ATP-driven chaperone valosin-containing protein (VCP)/p97 governs critical steps in ubiquitin-dependent protein quality control and intracellular signalling pathways. It cooperates with diverse partner proteins to help process ubiquitin-labelled proteins for recycling or degradation by the proteasome in many cellular contexts. Recent studies have uncovered unexpected cellular functions for p97 in autophagy, endosomal sorting and regulating protein degradation at the outer mitochondrial membrane, and elucidated a role for p97 in key chromatin-associated processes. These findings extend the functional relevance of p97 to lysosomal degradation and reveal a surprising dual role in protecting cells from protein stress and ensuring genome stability during proliferation.
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33
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The ubiquitin-selective segregase VCP/p97 orchestrates the response to DNA double-strand breaks. Nat Cell Biol 2011; 13:1376-82. [PMID: 22020440 DOI: 10.1038/ncb2367] [Citation(s) in RCA: 206] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2011] [Accepted: 09/23/2011] [Indexed: 12/12/2022]
Abstract
Unrepaired DNA double-strand breaks (DSBs) cause genetic instability that leads to malignant transformation or cell death. Cells respond to DSBs with the ordered recruitment of signalling and repair proteins to the site of lesion. Protein modification with ubiquitin is crucial for the signalling cascade, but how ubiquitylation coordinates the dynamic assembly of these complexes is poorly understood. Here, we show that the human ubiquitin-selective protein segregase p97 (also known as VCP; valosin-containing protein) cooperates with the ubiquitin ligase RNF8 to orchestrate assembly of signalling complexes and efficient DSB repair after exposure to ionizing radiation. p97 is recruited to DNA lesions by its ubiquitin adaptor UFD1-NPL4 and Lys-48-linked ubiquitin (K48-Ub) chains, whose formation is regulated by RNF8. p97 subsequently removes K48-Ub conjugates from sites of DNA damage to orchestrate proper association of 53BP1, BRCA1 and RAD51, three factors critical for DNA repair and genome surveillance mechanisms. Impairment of p97 activity decreases the level of DSB repair and cell survival after exposure to ionizing radiation. These findings identify the p97-UFD1-NPL4 complex as an essential factor in ubiquitin-governed DNA-damage response, highlighting its importance in guarding genome stability.
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34
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Koike M, Fukushi J, Ichinohe Y, Higashimae N, Fujishiro M, Sasaki C, Yamaguchi M, Uchihara T, Yagishita S, Ohizumi H, Hori S, Kakizuka A. Valosin-containing protein (VCP) in novel feedback machinery between abnormal protein accumulation and transcriptional suppression. J Biol Chem 2010; 285:21736-49. [PMID: 20410307 DOI: 10.1074/jbc.m109.099283] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Abnormal protein accumulation is often observed in human neurodegenerative disorders such as polyglutamine diseases and Parkinson disease. Genetic and biochemical analyses indicate that valosin-containing protein (VCP) is a crucial molecule in the pathogenesis of human neurodegenerative disorders. We report here that VCP was specifically modified in neuronal cells with abnormal protein accumulation; this modification caused the translocation of VCP into the nucleus. Modification-mimic forms of VCP induced transcriptional suppression with deacetylation of core histones, leading to cell atrophy and the decrease of de novo protein synthesis. Preventing VCP nuclear translocation in polyglutamine-expressing neuronal cells and Drosophila eyes mitigated neurite retraction and eye degenerations, respectively, concomitant with the recovery of core histone acetylation. This represents a novel feedback mechanism that regulates abnormal protein levels in the cytoplasm during physiological processes, as well as in pathological conditions such as abnormal protein accumulation in neurodegenerations.
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Affiliation(s)
- Masaaki Koike
- Laboratory of Functional Biology, Kyoto University Graduate School of Biostudies & Solution Oriented Research for Science and Technology, Kyoto 606-8501, Japan
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35
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Ewens CA, Kloppsteck P, Förster A, Zhang X, Freemont PS. Structural and functional implications of phosphorylation and acetylation in the regulation of the AAA+ protein p97. Biochem Cell Biol 2010; 88:41-8. [PMID: 20130678 DOI: 10.1139/o09-128] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
p97, also known as VCP (valosin-containing protein), is a hexameric AAA+ ATPase that participates in a variety of cellular processes. It is believed that p97 mediates these processes through the binding of various adaptor proteins. Many factors govern adaptor binding and the regulatory mechanisms are not yet well understood. Sites of phosphorylation and acetylation on p97 have been identified and such post-translational modifications may be involved in regulating p97 function. Phosphorylation and, to a lesser extent, acetylation of p97 have been shown to modify its properties - for example, by modulating adaptor binding and directing subcellular localization. These modifications have been implicated in a number of p97-mediated processes, including misfolded protein degradation, membrane fusion, and transcription factor activation. This review describes the known phosphorylation and acetylation sites on p97 and discusses their possible structural and functional implications.
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Affiliation(s)
- Caroline A Ewens
- Division of Molecular Biosciences, Centre for Structural Biology, Faculty of Natural Sciences, Imperial College London, London SW7 2AZ, United Kingdom
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36
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Livingstone M, Larsson O, Sukarieh R, Pelletier J, Sonenberg N. A chemical genetic screen for mTOR pathway inhibitors based on 4E-BP-dependent nuclear accumulation of eIF4E. ACTA ACUST UNITED AC 2010; 16:1240-9. [PMID: 20064434 DOI: 10.1016/j.chembiol.2009.11.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2009] [Revised: 10/20/2009] [Accepted: 11/13/2009] [Indexed: 12/31/2022]
Abstract
The signal transduction pathway wherein mTOR regulates cellular growth and proliferation is an active target for drug discovery. The search for new mTOR inhibitors has recently yielded a handful of promising compounds that hold therapeutic potential. This search has been limited by the lack of a high-throughput assay to monitor the phosphorylation of a direct rapamycin-sensitive mTOR substrate in cells. Here we describe a novel cell-based chemical genetic screen useful for efficiently monitoring mTOR signaling to 4E-BPs in response to stimuli. The screen is based on the nuclear accumulation of eIF4E, which occurs in a 4E-BP-dependent manner specifically upon inhibition of mTOR signaling. Using this assay in a small-scale screen, we have identified several compounds not previously known to inhibit mTOR signaling, demonstrating that this method can be adapted to larger screens.
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Affiliation(s)
- Mark Livingstone
- Department of Biochemistry and McGill Cancer Centre, McGill University, Montreal, QC H3A 1A3, Canada
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37
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Mori-Konya C, Kato N, Maeda R, Yasuda K, Higashimae N, Noguchi M, Koike M, Kimura Y, Ohizumi H, Hori S, Kakizuka A. p97/valosin-containing protein (VCP) is highly modulated by phosphorylation and acetylation. Genes Cells 2009; 14:483-97. [PMID: 19335618 DOI: 10.1111/j.1365-2443.2009.01286.x] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
p97/valosin-containing protein (VCP) is a member of the AAA family proteins, which plays various important roles in cells by using its ATPase activity. But mechanism of regulating its ATPase activity is mostly unknown. We report here that VCP is highly modified throughout the protein via acetylation and phosphorylation. In addition to six previously identified phosphorylation sites, we identified at least 14 serines, 14 threonines, 6 tyrosines and 22 lysines as potential modification sites. Interestingly, these sites included Lys251 and Lys524, which are very critical for the ATP binding in Walker A motif of D1 and D2 domains, respectively. It is notable that 16 sites are in the N-terminal region and 16 sites are clustered in D2alpha domain (from Pro646 to Gly765). Indeed, amino acid substitution of Lys696 and Thr761 profoundly affect VCP ATPase activities. From these results, we propose that D2alpha domain acts as a VCP ATPase Regulatory domain or "VAR domain". VCP modifications including those in this VAR domain may endorse adaptive and multiple functions to VCP in different cell conditions such as in the cell cycle and with abnormal protein accumulation.
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Affiliation(s)
- Chiho Mori-Konya
- The Laboratory of Functional Biology, Kyoto University Graduate School of Biostudies and Solution Oriented Research for Science and Technology (JST), Kyoto 606-8501, Japan
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38
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New ATPase regulators--p97 goes to the PUB. Int J Biochem Cell Biol 2009; 41:2380-8. [PMID: 19497384 DOI: 10.1016/j.biocel.2009.05.017] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2009] [Revised: 05/26/2009] [Accepted: 05/26/2009] [Indexed: 01/10/2023]
Abstract
The conserved eukaryotic AAA-type ATPase complex, known as p97 or VCP in mammals and Cdc48 in yeast, is involved in a number of cellular pathways, including fusion of homotypic membranes, protein degradation, and activation of membrane-bound transcription factors. Most likely, p97 is directed to this broad spectrum of cellular functions through its binding to specific cofactors. More than 20 different p97 cofactors have been described to date and our understanding of their cellular functions is rapidly expanding. Common to these proteins is their intimate connection with the ubiquitin system. Recently, a small, conserved family of proteins, containing PUB domains, was found to function as p97 adaptors. Intriguingly, their association with p97 is regulated by tyrosine phosphorylation, suggesting that they act as a relay between signalling pathways and p97 functions. Here we give an overview of the currently known PUB-domain proteins and other p97-interacting proteins.
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39
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Gitcho MA, Strider J, Carter D, Taylor-Reinwald L, Forman MS, Goate AM, Cairns NJ. VCP mutations causing frontotemporal lobar degeneration disrupt localization of TDP-43 and induce cell death. J Biol Chem 2009; 284:12384-98. [PMID: 19237541 PMCID: PMC2673306 DOI: 10.1074/jbc.m900992200] [Citation(s) in RCA: 91] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2009] [Indexed: 11/06/2022] Open
Abstract
Frontotemporal lobar degeneration (FTLD) with inclusion body myopathy and Paget disease of bone is a rare, autosomal dominant disorder caused by mutations in the VCP (valosin-containing protein) gene. The disease is characterized neuropathologically by frontal and temporal lobar atrophy, neuron loss and gliosis, and ubiquitin-positive inclusions (FTLD-U), which are distinct from those seen in other sporadic and familial FTLD-U entities. The major component of the ubiquitinated inclusions of FTLD with VCP mutation is TDP-43 (TAR DNA-binding protein of 43 kDa). TDP-43 proteinopathy links sporadic amyotrophic lateral sclerosis, sporadic FTLD-U, and most familial forms of FTLD-U. Understanding the relationship between individual gene defects and pathologic TDP-43 will facilitate the characterization of the mechanisms leading to neurodegeneration. Using cell culture models, we have investigated the role of mutant VCP in intracellular trafficking, proteasomal function, and cell death and demonstrate that mutations in the VCP gene 1) alter localization of TDP-43 between the nucleus and cytosol, 2) decrease proteasome activity, 3) induce endoplasmic reticulum stress, 4) increase markers of apoptosis, and 5) impair cell viability. These results suggest that VCP mutation-induced neurodegeneration is mediated by several mechanisms.
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Affiliation(s)
- Michael A Gitcho
- Alzheimer's Disease Research Center and the Department of Neurology, Washington University School of Medicine, St. Louis, Missouri 63110, USA
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40
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Li G, Zhao G, Schindelin H, Lennarz WJ. Tyrosine phosphorylation of ATPase p97 regulates its activity during ERAD. Biochem Biophys Res Commun 2008; 375:247-51. [PMID: 18706391 DOI: 10.1016/j.bbrc.2008.08.018] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2008] [Accepted: 08/02/2008] [Indexed: 12/01/2022]
Abstract
In eukaryotic cells, the endoplasmic reticulum-associated degradation (ERAD) pathway is essential for the disposal of misfolded proteins. Recently, we demonstrated the existence of a higher order complex consisting of the ER bound E3 ligase gp78, p97, PNGase, and HR23B in mammals. This complex may serve to facilitate the routing of misfolded glycoproteins out of the ER to the cytosol where they are degraded by the proteasome. In this complex, p97 functions as an organizer to mediate the interactions with gp78 and the deglycosylating enzyme PNGase. A novel protein-binding motif of mouse p97 was identified that consists of its last 10 amino acid residues; this motif is sufficient to mediate the interaction of p97 with PNGase and Ufd3. Phosphorylation of p97's highly conserved penultimate tyrosine residue, completely blocks binding of both PNGase and Ufd3 to mp97. We have found that c-Src kinase directly and selectively phosphorylated the penultimate tyrosine of p97 in vitro, and that overexpression of c-Src significantly increased the phosphorylation level of p97 in cells and caused accumulation of the ERAD substrate TCRalpha-GFP, as well as ubiquitin-conjugated substrates. These results suggest a role for p97 phosphorylation in the degradation of misfolded glycoproteins.
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Affiliation(s)
- Guangtao Li
- Department of Biochemistry and Cell Biology, 450 Life Science Building, Stony Brook University, Stony Brook, NY 11794-5215, USA
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Madsen L, Andersen KM, Prag S, Moos T, Semple CA, Seeger M, Hartmann-Petersen R. Ubxd1 is a novel co-factor of the human p97 ATPase. Int J Biochem Cell Biol 2008; 40:2927-42. [PMID: 18656546 DOI: 10.1016/j.biocel.2008.06.008] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2008] [Revised: 06/24/2008] [Accepted: 06/25/2008] [Indexed: 11/30/2022]
Abstract
The AAA ATPase complex known as p97 or VCP in mammals and Cdc48 in yeast is connected to a multitude of cellular pathways, including membrane fusion, protein folding, protein degradation and activation of membrane-bound transcription factors. The mechanism by which p97 participates in such a broad spectrum of cellular functions appears to be via recruiting certain specific co-factors. Here we isolate and characterize the human protein Ubxd1, a novel co-factor of p97. We show that Ubxd1 is a stable protein that localizes to the cytoplasm and nucleus and is highly enriched in centrosomes. In mice Ubxd1 is widely expressed, but especially abundant in brain. Curiously, Ubxd1 does not associate with p97 via its UBX domain, but via its PUB domain which binds the extreme C-terminus of p97. Phosphorylation of the penultimate tyrosine residue in p97 completely abolishes Ubxd1 interaction. Ternary complexes of Ubxd1, p47, and p97 were detected in vitro. Inhibition of Ubxd1 expression by siRNA did not affect the degradation of bulk protein or a model substrate of the ERAD pathway, indicating that Ubxd1 directs p97 activity to specialized functions in vivo.
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Affiliation(s)
- Louise Madsen
- Department of Biology, University of Copenhagen, Universitetsparken 13, DK-2100 Copenhagen Ø, Denmark
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The differentiation/retrodifferentiation program of human U937 leukemia cells is accompanied by changes of VCP/p97. BMC Cell Biol 2008; 9:12. [PMID: 18279508 PMCID: PMC2277395 DOI: 10.1186/1471-2121-9-12] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2007] [Accepted: 02/15/2008] [Indexed: 12/04/2022] Open
Abstract
Background Retrodifferentiation and regained proliferative capacity of growth-arrested human leukemic cells after monocyte-like differentiation requires proteolytic activities together with distinct regulatory factors. The AAA ATPase valosin-containing protein (VCP/p97) contributes to protein degradation and cell cycle regulation, respectively, and it was of interest to study a possible role of VCP/p97 during this myelomonocytic differentiation and retrodifferentiation. Results Separation of autonomously proliferating human U937 myeloid leukemia cells by centrifugal elutriation demonstrated unaltered VCP/p97 expression levels throughout distinct phases of the cell cycle. However, phorbol ester-induced G0/G1 cell cycle arrest in differentiating human U937 leukemia cells was associated with a significantly increased protein and mRNA amount of this AAA ATPase. These elevated VCP/p97 levels progressively decreased again when growth-arrested U937 cells entered a retrodifferentiation program and returned to the tumorigenic phenotype. Whereas VCP/p97 was observed predominantly in the cytosol of U937 tumor and retrodifferentiated cells, a significant nuclear accumulation appeared during differentiation and G0/G1 growth arrest. Analysis of subcellular compartments by immunoprecipitations and 2D Western blots substantiated these findings and revealed furthermore a tyrosine-specific phosphorylation of VCP/p97 in the cytosolic but not in the nuclear fractions. These altered tyrosine phosphorylation levels, according to distinct subcellular distributions, indicated a possible functional involvement of VCP/p97 in the leukemic differentiation process. Indeed, a down-modulation of VCP/p97 protein by siRNA revealed a reduced expression of differentiation-associated genes in subsequent DNA microarray analysis. Moreover, DNA-binding and proliferation-associated genes, which are down-regulated during differentiation of the leukemic cells, demonstrated elevated levels in the VCP/p97 siRNA transfectants. Conclusion The findings demonstrated that monocytic differentiation and G0/G1 growth arrest in human U937 leukemia cells was accompanied by an increase in VCP/p97 expression and a distinct subcellular distribution to be reverted during retrodifferentiation. Together with a down-modulation of VCP/p97 by siRNA, these results suggested an association of this AAA ATPase in the differentiation/retrodifferentiation program.
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Abstract
To ensure survival in the face of genomic insult, cells have evolved complex mechanisms to respond to DNA damage, termed the DNA damage checkpoint. The serine/threonine kinases ataxia telangiectasia-mutated (ATM) and ATM and Rad3-related (ATR) activate checkpoint signaling by phosphorylating substrate proteins at SQ/TQ motifs. Although some ATM/ATR substrates (Chk1, p53) have been identified, the lack of a more complete list of substrates limits current understanding of checkpoint pathways. Here, we use immunoaffinity phosphopeptide isolation coupled with mass spectrometry to identify 570 sites phosphorylated in UV-damaged cells, 498 of which are previously undescribed. Semiquantitative analysis yielded 24 known and 192 previously uncharacterized sites differentially phosphorylated upon UV damage, some of which were confirmed by SILAC, Western blotting, and immunoprecipitation/Western blotting. ATR-specific phosphorylation was investigated by using a Seckel syndrome (ATR mutant) cell line. Together, these results provide a rich resource for further deciphering ATM/ATR signaling and the pathways mediating the DNA damage response.
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Genetic and proteomic analyses of a proteasome-activating nucleotidase A mutant of the haloarchaeon Haloferax volcanii. J Bacteriol 2007; 190:193-205. [PMID: 17965165 DOI: 10.1128/jb.01196-07] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The halophilic archaeon Haloferax volcanii encodes two related proteasome-activating nucleotidase proteins, PanA and PanB, with PanA levels predominant during all phases of growth. In this study, an isogenic panA mutant strain of H. volcanii was generated. The growth rate and cell yield of this mutant strain were lower than those of its parent and plasmid-complemented derivatives. In addition, a consistent and discernible 2.1-fold increase in the number of phosphorylated proteins was detected when the panA gene was disrupted, based on phosphospecific fluorescent staining of proteins separated by 2-dimensional gel electrophoresis. Subsequent enrichment of phosphoproteins by immobilized metal ion and metal oxide affinity chromatography (in parallel and sequentially) followed by tandem mass spectrometry was employed to identify key differences in the proteomes of these strains as well as to add to the restricted numbers of known phosphoproteins within the Archaea. In total, 625 proteins (approximately 15% of the deduced proteome) and 9 phosphosites were identified by these approaches, and 31% (195) of the proteins were identified by multiple phosphoanalytical methods. In agreement with the phosphostaining results, the number of identified proteins that were reproducibly exclusive or notably more abundant in one strain was nearly twofold greater for the panA mutant than for the parental strain. Enriched proteins exclusive to or more abundant in the panA mutant (versus the wild type) included cell division (FtsZ, Cdc48), dihydroxyacetone kinase-linked phosphoenolpyruvate phosphotransferase system (EI, DhaK), and oxidoreductase homologs. Differences in transcriptional regulation and signal transduction proteins were also observed, including those differences (e.g., OsmC and BolA) which suggest that proteasome deficiency caused an up-regulation of stress responses (e.g., OsmC versus BolA). Consistent with this, components of the Fe-S cluster assembly, protein-folding, DNA binding and repair, oxidative and osmotic stress, phosphorus assimilation, and polyphosphate synthesis systems were enriched and identified as unique to the panA mutant. The cumulative proteomic data not only furthered our understanding of the archaeal proteasome system but also facilitated the assembly of the first subproteome map of H. volcanii.
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Mu JJ, Wang Y, Luo H, Leng M, Zhang J, Yang T, Besusso D, Jung SY, Qin J. A Proteomic Analysis of Ataxia Telangiectasia-mutated (ATM)/ATM-Rad3-related (ATR) Substrates Identifies the Ubiquitin-Proteasome System as a Regulator for DNA Damage Checkpoints. J Biol Chem 2007; 282:17330-4. [PMID: 17478428 DOI: 10.1074/jbc.c700079200] [Citation(s) in RCA: 135] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
ATM (ataxia telangiectasia-mutated) and ATR (ATM-Rad3-related) are proximal checkpoint kinases that regulate DNA damage response (DDR). Identification and characterization of ATM/ATR substrates hold the keys for the understanding of DDR. Few techniques are available to identify protein kinase substrates. Here, we screened for potential ATM/ATR substrates using phospho-specific antibodies against known ATM/ATR substrates. We identified proteins cross-reacting to phospho-specific antibodies in response to DNA damage by mass spectrometry. We validated a subset of the candidate substrates to be phosphorylated in an ATM/ATR-dependent manner in vivo. Combining with a functional checkpoint screen, we identified proteins that belong to the ubiquitin-proteasome system (UPS) to be required in mammalian DNA damage checkpoint control, particularly the G(1) cell cycle checkpoint, thus revealing protein ubiquitylation as an important regulatory mechanism downstream of ATM/ATR activation for checkpoint control.
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Affiliation(s)
- Jung-Jung Mu
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
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Zhao G, Zhou X, Wang L, Li G, Schindelin H, Lennarz WJ. Studies on peptide:N-glycanase-p97 interaction suggest that p97 phosphorylation modulates endoplasmic reticulum-associated degradation. Proc Natl Acad Sci U S A 2007; 104:8785-90. [PMID: 17496150 PMCID: PMC1885580 DOI: 10.1073/pnas.0702966104] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
During endoplasmic reticulum-associated degradation, the multifunctional AAA ATPase p97 is part of a protein degradation complex. p97 associates via its N-terminal domain with various cofactors to recruit ubiquitinated substrates. It also interacts with alternative substrate-processing cofactors, such as Ufd2, Ufd3, and peptide:N-glycanase (PNGase) in higher eukaryotes. These cofactors determine different fates of the substrates and they all bind outside of the N-terminal domain of p97. Here, we describe a cofactor-binding motif of p97 contained within the last 10 amino acid residues of the C terminus, which is both necessary and sufficient to mediate interactions of p97 with PNGase and Ufd3. The crystal structure of the N-terminal domain of PNGase in complex with this motif provides detailed insight into the interaction between p97 and its substrate-processing cofactors. Phosphorylation of p97's highly conserved penultimate tyrosine residue, which is the main phosphorylation site during T cell receptor stimulation, completely blocks binding of either PNGase or Ufd3 to p97. This observation suggests that phosphorylation of this residue modulates endoplasmic reticulum-associated protein degradation activity by discharging substrate-processing cofactors.
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Affiliation(s)
- Gang Zhao
- *Center for Structural Biology, Stony Brook University, Stony Brook, NY 11794-5115
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794-5215; and
| | - Xiaoke Zhou
- *Center for Structural Biology, Stony Brook University, Stony Brook, NY 11794-5115
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794-5215; and
| | - Liqun Wang
- *Center for Structural Biology, Stony Brook University, Stony Brook, NY 11794-5115
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794-5215; and
| | - Guangtao Li
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794-5215; and
| | - Hermann Schindelin
- *Center for Structural Biology, Stony Brook University, Stony Brook, NY 11794-5115
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794-5215; and
- Rudolf Virchow Center for Experimental Biomedicine and Institute of Structural Biology, University of Würzburg, Versbacher Strasse 9, 97078 Würzburg, Germany
- To whom correspondence may be addressed. E-mail: or
| | - William J. Lennarz
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794-5215; and
- To whom correspondence may be addressed. E-mail: or
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Sung FL, Pang RTK, Ma BBY, Lee MML, Chow SM, Poon TCW, Chan ATC. Pharmacoproteomics study of cetuximab in nasopharyngeal carcinoma. J Proteome Res 2007; 5:3260-7. [PMID: 17137327 DOI: 10.1021/pr050452g] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Epidermal growth factor receptor (EGFR) is usually overexpressed in nasopharyngeal carcinoma (NPC). Our recent in vitro study has demonstrated that cetuximab (an antibody drug against EGFR) inhibits the growth of NPC cell lines, HK1 and HONE-1. The present study investigates the effect of cetuximab on protein expressions of NPC cell lines. NPC cells were cultured in the absence or presence of cetuximab at the IC50 concentrations (3 nM for HK1 and 0.3 nM for HONE-1) for 48 h, and total cell lysates were extracted. The cell lysates were then subjected to two-dimensional polyacrylamide gel electrophoresis (2D PAGE), and the 2D gel images were compared to discover the protein changes caused by cetuximab treatment. The common differentially expressed proteins in NPC cell lines were identified by peptide mass fingerprinting. We found that heat shock protein gp96 was down-regulated, while alpha-enolase, tumor suppressor protein maspin, and p97 valosin containing protein were up-regulated after cetuximab treatment. Reverse-transcription polymerase chain reaction (RT-PCR) analysis confirmed that the changes in protein levels of gp96, maspin, and p97 coincided with mRNA levels, indicating that these proteins were regulated at transcriptional levels. Up-regulation of gp96 has been observed in various cancers and reported to have tumor protective effects. P97 is a multifunctional AAA (ATPase associated with a variety of activities) protein and is involved in numerous cellular activities including membrane transport, protein folding, protein degradation, and cell division. Maspin has been shown to increase apoptosis, and block the growth, invasion, and metastatic properties of many tumors. The comparative tumor suppression effects of cetuximab and maspin suggest that cetuximab might exert its antitumor effects partly by up-regulation of maspin expression. The study also indicates that proteomic analysis is a promising approach to elucidate the functional mechanisms of anticancer drugs. Pharmacoproteomic study may also help to identify clinical responders for drug treatment and provide insight for new drug development.
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Affiliation(s)
- Fion L Sung
- Hong Kong Cancer Institute, Department of Clinical Oncology, The Sir Y K Pao Center for Cancer, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, People's Republic of China
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Shi Y, Dodson GE, Mukhopadhyay PS, Shanware NP, Trinh AT, Tibbetts RS. Identification of carboxyl-terminal MCM3 phosphorylation sites using polyreactive phosphospecific antibodies. J Biol Chem 2007; 282:9236-43. [PMID: 17244605 DOI: 10.1074/jbc.m609256200] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The functionally related ATM (ataxia telangiectasia-mutated) and ATR (ATM-Rad3-related) protein kinases are critical regulators of DNA damage responses in mammalian cells. ATM and ATR share highly overlapping substrate specificities and show a strong preference for the phosphorylation of Ser or Thr residues followed by Gln. In this report we used a polyreactive phosphospecific antibody (alpha-pDSQ) that recognizes a subset of phosphorylated Asp-Ser-Gln sequences to purify candidate ATM/ATR substrates. This led to the identification of phosphorylation sites in the carboxyl terminus of the minichromosome maintenance protein 3 (MCM3), a component of the hexameric MCM DNA helicase. We show that the alpha-DSQ antibody recognizes tandem DSQ phosphorylation sites (Ser-725 and Ser-732) in the carboxyl terminus of murine MCM3 (mMCM3) and that ATM phosphorylates both sites in vitro. ATM phosphorylated the carboxyl termini of mMCM3 and human MCM3 in vivo and the phosphorylated form of MCM3 retained association with the canonical MCM complex. Although DNA damage did not affect steady-state levels of chromatin-bound MCM3, the ATM-phosphorylated form of MCM3 was preferentially localized to the soluble, nucleoplasmic fraction. This finding suggests that the carboxyl terminus of chromatin-loaded MCM3 may be sequestered from ATM-dependent checkpoint signals. Finally, we show that ATM and ATR jointly contribute to UV light-induced MCM3 phosphorylation, but that ATM is the predominant UV-activated MCM3 kinase in vivo. The carboxyl-terminal ATM phosphorylation sites are conserved in vertebrate MCM3 orthologs suggesting that this motif may serve important regulatory functions in response to DNA damage. Our findings also suggest that DSQ motifs are common phosphoacceptor motifs for ATM family kinases.
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Affiliation(s)
- Yuling Shi
- Department of Pharmacology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin 53706, USA
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Jentsch S, Rumpf S. Cdc48 (p97): a "molecular gearbox" in the ubiquitin pathway? Trends Biochem Sci 2006; 32:6-11. [PMID: 17142044 DOI: 10.1016/j.tibs.2006.11.005] [Citation(s) in RCA: 239] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2006] [Revised: 11/07/2006] [Accepted: 11/23/2006] [Indexed: 10/23/2022]
Abstract
Cdc48 (p97), a conserved chaperone-like ATPase of eukaryotic cells, has attracted attention recently because of its wide range of cellular functions. Cdc48 is intimately linked to the ubiquitin pathway because its primary action is to segregate ubiquitinated substrates from unmodified partners. This 'segregase' activity is crucial for certain proteasomal degradation pathways and for some nonproteolytic functions of ubiquitin. Cdc48 associates not only with different 'substrate-recruiting cofactors' but also with distinct 'substrate-processing cofactors'. The latter proteins control the degree of ubiquitination of bound substrates by shifting the polyubiquitination reaction into 'forward', 'neutral' or 'reverse'. We discuss how Cdc48 might use this 'gearbox activity' to control protein fate and propose a similar mode of action for the 19S cap of the proteasome.
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Affiliation(s)
- Stefan Jentsch
- Department of Molecular Cell Biology, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany.
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50
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Mimnaugh EG, Xu W, Vos M, Yuan X, Neckers L. Endoplasmic Reticulum Vacuolization and Valosin-Containing Protein Relocalization Result from Simultaneous Hsp90 Inhibition by Geldanamycin and Proteasome Inhibition by Velcade. Mol Cancer Res 2006; 4:667-81. [PMID: 16966435 DOI: 10.1158/1541-7786.mcr-06-0019] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Geldanamycin and Velcade, new anticancer drugs with novel mechanisms of action, are currently undergoing extensive clinical trials. Geldanamycin interrupts Hsp90 chaperone activity and causes down-regulation of its many client proteins by the ubiquitin-proteasome pathway; Velcade is a specific proteasome inhibitor. Misfolded Hsp90 clients within the endoplasmic reticulum (ER) lumen are cleared by ER--associated protein degradation, a sequential process requiring valosin-containing protein (VCP)-dependent retrotranslocation followed by ubiquitination and proteasomal proteolysis. Cotreatment of cells with geldanamycin and Velcade prevents destruction of destabilized, ubiquitinated Hsp90 client proteins, causing them to accumulate. Here, we report that misfolded protein accumulation within the ER resulting from geldanamycin and Velcade exposure overwhelms the ability of the VCP--centered machine to maintain the ER secretory pathway, causing the ER to distend into conspicuous vacuoles. Overexpression of dominant-negative VCP or the "small VCP--interacting protein" exactly recapitulated the vacuolated phenotype provoked by the drugs, associating loss of VCP function with ER vacuolization. In cells transfected with a VCP--enhanced yellow fluorescent protein fluorescent construct, geldanamycin plus Velcade treatment redistributed VCP--enhanced yellow fluorescent protein from the cytoplasm and ER into perinuclear aggresomes. In further support of the view that compromise of VCP function is responsible for ER vacuolization, small interfering RNA interference of VCP expression induced ER vacuolization that was markedly increased by Velcade. VCP knockdown by small interfering RNA eventually deconstructed both the ER and Golgi and interdicted protein trafficking through the secretory pathway to the plasma membrane. Thus, simultaneous geldanamycin and Velcade treatment has far-reaching secondary cytotoxic consequences that likely contribute to the cytotoxic activity of this anticancer drug combination.
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Affiliation(s)
- Edward G Mimnaugh
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, NIH, 9000 Rockville Pike, Building 10, Room 1-5940, Bethesda, MD 20892-1107, USA
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