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Sharma A, Dhavale DD, Kotzbauer PT, Weihl CC. VCP Inhibition Augments NLRP3 Inflammasome Activation. Inflammation 2024:10.1007/s10753-024-02013-6. [PMID: 38563877 DOI: 10.1007/s10753-024-02013-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 03/20/2024] [Accepted: 03/25/2024] [Indexed: 04/04/2024]
Abstract
Lysosomal membrane permeabilization caused either via phagocytosis of particulates or the uptake of protein aggregates can trigger the activation of NLRP3 inflammasome- an intense inflammatory response that drives the release of the pro-inflammatory cytokine IL-1β by regulating the activity of CASPASE 1. The maintenance of lysosomal homeostasis and lysosomal membrane integrity is facilitated by the AAA+ ATPase, VCP/p97 (VCP). However, the relationship between VCP and NLRP3 inflammasome activity remains unexplored. Here, we demonstrate that the VCP inhibitors, DBeQ and ML240 elicit the activation of NLRP3 inflammasome in bone marrow-derived macrophages (BMDMs) when used as activation stimuli. Moreover, genetic inhibition of VCP or VCP chemical inhibition enhances lysosomal membrane damage and augments LLoME-associated NLRP3 inflammasome activation in BMDMs. Similarly, VCP inactivation also augments NLRP3 inflammasome activation mediated by aggregated alpha-synuclein fibrils and lysosomal damage. These data suggest that VCP is a participant in the complex regulation of NLRP3 inflammasome activation.
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Affiliation(s)
- Ankita Sharma
- Department of Neurology, Hope Center for Neurological Diseases, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Dhruva D Dhavale
- Department of Neurology, Hope Center for Neurological Diseases, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Paul T Kotzbauer
- Department of Neurology, Hope Center for Neurological Diseases, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Conrad C Weihl
- Department of Neurology, Hope Center for Neurological Diseases, Washington University School of Medicine, St. Louis, MO, 63110, USA.
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2
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Hao J, Yu J, Yorek MS, Yu CL, Pope RM, Chimenti MS, Xiong Y, Klingelhutz A, Jabbari A, Li B. Keratinocyte FABP5-VCP complex mediates recruitment of neutrophils in psoriasis. Cell Rep 2023; 42:113449. [PMID: 37967009 PMCID: PMC10729729 DOI: 10.1016/j.celrep.2023.113449] [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: 04/28/2023] [Revised: 10/03/2023] [Accepted: 11/01/2023] [Indexed: 11/17/2023] Open
Abstract
One of the hallmarks of intractable psoriasis is neutrophil infiltration in skin lesions. However, detailed molecular mechanisms of neutrophil chemotaxis and activation remain unclear. Here, we demonstrate a significant upregulation of epidermal fatty acid binding protein (E-FABP, FABP5) in the skin of human psoriasis and psoriatic mouse models. Genetic deletion of FABP5 in mice by global knockout and keratinocyte conditional (Krt6a-Cre) knockout, but not myeloid cell conditional (LysM-Cre) knockout, attenuates psoriatic symptoms. Immunophenotypic analysis shows that FABP5 deficiency specifically reduces skin recruitment of Ly6G+ neutrophils. Mechanistically, activated keratinocytes produce chemokines and cytokines that trigger neutrophil chemotaxis and activation in an FABP5-dependent manner. Proteomic analysis further identifies that FABP5 interacts with valosin-containing protein (VCP), a key player in NF-κB signaling activation. Silencing of FABP5, VCP, or both inhibits NF-κB/neutrophil chemotaxis signaling. Collectively, these data demonstrate dysregulated FABP5 as a molecular mechanism promoting NF-κB signaling and neutrophil infiltration in psoriasis pathogenesis.
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Affiliation(s)
- Jiaqing Hao
- Department of Pathology, University of Iowa, Iowa City, IA, USA
| | - Jianyu Yu
- Department of Pathology, University of Iowa, Iowa City, IA, USA
| | - Matthew S Yorek
- Department of Pathology, University of Iowa, Iowa City, IA, USA
| | - Chi-Li Yu
- Proteomics Facility, University of Iowa, Iowa City, IA, USA
| | | | - Michael S Chimenti
- Iowa Institute of Human Genetics, University of Iowa, Iowa City, IA, USA
| | - Yiqin Xiong
- Department of Pathology, University of Iowa, Iowa City, IA, USA
| | - Aloysius Klingelhutz
- Department of Microbiology and Immunology, University of Iowa, Iowa City, IA, USA
| | - Ali Jabbari
- Department of Dermatology, University of Iowa, Iowa City, IA, USA; Iowa City VA Medical Center, Iowa City, IA, USA
| | - Bing Li
- Department of Pathology, University of Iowa, Iowa City, IA, USA.
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3
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Tsioras K, Smith KC, Edassery SL, Garjani M, Li Y, Williams C, McKenna ED, Guo W, Wilen AP, Hark TJ, Marklund SL, Ostrow LW, Gilthorpe JD, Ichida JK, Kalb RG, Savas JN, Kiskinis E. Analysis of proteome-wide degradation dynamics in ALS SOD1 iPSC-derived patient neurons reveals disrupted VCP homeostasis. Cell Rep 2023; 42:113160. [PMID: 37776851 PMCID: PMC10785776 DOI: 10.1016/j.celrep.2023.113160] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 07/18/2023] [Accepted: 09/06/2023] [Indexed: 10/02/2023] Open
Abstract
Mutations in SOD1 cause amyotrophic lateral sclerosis (ALS) through gain-of-function effects, yet the mechanisms by which misfolded mutant SOD1 (mutSOD1) protein impairs human motor neurons (MNs) remain unclear. Here, we use induced-pluripotent-stem-cell-derived MNs coupled to metabolic stable isotope labeling and mass spectrometry to investigate proteome-wide degradation dynamics. We find several proteins, including the ALS-causal valosin-containing protein (VCP), which predominantly acts in proteasome degradation and autophagy, that degrade slower in mutSOD1 relative to isogenic control MNs. The interactome of VCP is altered in mutSOD1 MNs in vitro, while VCP selectively accumulates in the affected motor cortex of ALS-SOD1 patients. Overexpression of VCP rescues mutSOD1 toxicity in MNs in vitro and in a C. elegans model in vivo, in part due to its ability to modulate the degradation of insoluble mutSOD1. Our results demonstrate that VCP contributes to mutSOD1-dependent degeneration, link two distinct ALS-causal genes, and highlight selective protein degradation impairment in ALS pathophysiology.
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Affiliation(s)
- Konstantinos Tsioras
- The Ken & Ruth Davee Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Kevin C Smith
- The Ken & Ruth Davee Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Seby L Edassery
- The Ken & Ruth Davee Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Mehraveh Garjani
- The Ken & Ruth Davee Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Yichen Li
- Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, Zilkha Neurogenetic Institute, University of Southern California, Keck School of Medicine, Los Angeles, CA 90033, USA
| | - Chloe Williams
- Department of Integrative Medical Biology, Umeå University, 90187 Umeå, Sweden
| | - Elizabeth D McKenna
- The Ken & Ruth Davee Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Wenxuan Guo
- Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, Zilkha Neurogenetic Institute, University of Southern California, Keck School of Medicine, Los Angeles, CA 90033, USA
| | - Anika P Wilen
- The Ken & Ruth Davee Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Timothy J Hark
- The Ken & Ruth Davee Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Stefan L Marklund
- Department of Medical Biosciences, Clinical Chemistry, Umeå University, 90187 Umeå, Sweden
| | - Lyle W Ostrow
- Department of Neurology, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, USA
| | | | - Justin K Ichida
- Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, Zilkha Neurogenetic Institute, University of Southern California, Keck School of Medicine, Los Angeles, CA 90033, USA
| | - Robert G Kalb
- The Ken & Ruth Davee Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Jeffrey N Savas
- The Ken & Ruth Davee Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Evangelos Kiskinis
- The Ken & Ruth Davee Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA; Simpson Querrey Institute, Northwestern University, Chicago, IL 60611, USA; Department of Neuroscience, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA.
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4
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Lin L, Yu H, Li L, Yang W, Chen X, Gong Y, Lei Q, Li Z, Zhou Z, Dai L, Zhang H, Hu H. TRIM55 promotes noncanonical NF-κB signaling and B cell-mediated immune responses by coordinating p100 ubiquitination and processing. Sci Signal 2023; 16:eabn5410. [PMID: 37816088 DOI: 10.1126/scisignal.abn5410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 09/20/2023] [Indexed: 10/12/2023]
Abstract
The ubiquitination-dependent processing of NF-κB2 (also known as p100) is a critical step in the activation of the noncanonical NF-κB pathway. We investigated the molecular mechanisms regulating this process and showed that TRIM55 was the E3 ubiquitin ligase that mediated the ubiquitination of p100 and coordinated its processing. TRIM55 deficiency impaired noncanonical NF-κB activation and B cell function. Mice with a B cell-specific Trim55 deficiency exhibited reduced germinal center formation and antibody production. These mice showed less severe symptoms than those of control mice upon the induction of a systemic lupus-like disease, suggesting B cell-intrinsic functions of TRIM55 in humoral immune responses and autoimmunity. Mechanistically, the ubiquitination of p100 mediated by TRIM55 was crucial for p100 processing by VCP, an ATPase that mediates ubiquitin-dependent protein degradation by the proteasome. Furthermore, we found that TRIM55 facilitated the interaction between TRIM21 and VCP as well as TRIM21-mediated K63-ubiquitination of VCP, both of which were indispensable for the formation of the VCP-UFD1-NPL4 complex and p100 processing. Together, our results reveal a mechanism by which TRIM55 fine-tunes p100 processing and regulates B cell-dependent immune responses in vivo, highlighting TRIM55 as a potential therapeutic target for lupus-like disease.
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Affiliation(s)
- Liangbin Lin
- Center for Immunology and Hematology, Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Hui Yu
- Center for Immunology and Hematology, Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Li Li
- Center for Immunology and Hematology, Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Wenyong Yang
- Center for Immunology and Hematology, Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Xueying Chen
- Center for Immunology and Hematology, Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Yanqiu Gong
- Department of General Practice, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Qingqiang Lei
- Center for Immunology and Hematology, Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Zhonghan Li
- School of Life Science, Sichuan University, Chengdu 610041, China
| | - Zhaocai Zhou
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, 2005 Songhua Road, Shanghai 200438, China
- Department of Medical Ultrasound, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200092, China
| | - Lunzhi Dai
- Department of General Practice, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Huiyuan Zhang
- Center for Immunology and Hematology, Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Hongbo Hu
- Center for Immunology and Hematology, Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
- Chongqing International Institute for Immunology, Chongqing 401338, China
- Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
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5
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Re Cecconi AD, Barone M, Gaspari S, Tortarolo M, Bendotti C, Porcu L, Terribile G, Piccirillo R. The p97-Nploc4 ATPase complex plays a role in muscle atrophy during cancer and amyotrophic lateral sclerosis. J Cachexia Sarcopenia Muscle 2022; 13:2225-2241. [PMID: 35611892 PMCID: PMC9397562 DOI: 10.1002/jcsm.13011] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 03/21/2022] [Accepted: 04/25/2022] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND The p97 complex participates in the degradation of muscle proteins during atrophy upon fasting or denervation interacting with different protein adaptors. We investigated whether and how it might also be involved in muscle wasting in cancer, where loss of appetite occurs, or amyotrophic lateral sclerosis (ALS), where motoneuron death causes muscle denervation and fatal paralysis. METHODS As cancer cachexia models, we used mice bearing colon adenocarcinoma C26, human renal carcinoma RXF393, or Lewis lung carcinoma, with breast cancer 4T1-injected mice as controls. As ALS models, we employed 129/SvHsd mice carrying the mutation G93A in human SOD1. The expression of p97 and its adaptors was analysed in their muscles by quantitative real-time polymerase chain reaction (qPCR) and western blot. We electroporated plasmids into muscles or treated mice with disulfiram (DSF) to test the effects of inhibiting p97 and nuclear protein localization protein 4 (Nploc4), one of its adaptors, on atrophy. RESULTS The mRNA levels of p97 were induced by 1.5-fold to 2-fold in tibialis anterior (TA) of all the cachectic models but not in the non-cachectic 4T1 tumour-bearing mice (P ≤ 0.05). Similarly, p97 was high both in mRNA and protein in TA from 17-week-old SOD1G93A mice (P ≤ 0.01). Electroporation of a shRNA for murine p97 into mouse muscle reduced the fibre atrophy caused by C26 (P = 0.0003) or ALS (P ≤ 0.01). When we interrogated a microarray, we had previously generated for the expression of p97 adaptors, we found Derl1, Herpud1, Nploc4, Rnf31, and Hsp90ab1 induced in cachectic TA from C26-mice (Fold change > 1.2, adjusted P ≤ 0.05). By qPCR, we validated their inductions in TA of cachectic and ALS models and selected Nploc4 as the one also induced at the protein level by 1.5-fold (P ≤ 0.01). Electroporation of a CRISPR/Cas9 vector against Nploc4 into muscle reduced the fibre atrophy caused by C26 (P = 0.01) or ALS (P ≤ 0.0001). Because DSF uncouples p97 from Nploc4, we treated atrophying myotubes with DSF, and found accumulated mono and polyubiquitinated proteins and reduced degradation of long-lived proteins by 35% (P ≤ 0.0001), including actin (P ≤ 0.05). DSF halves Nploc4 in the soluble muscle fraction (P ≤ 0.001) and given to C26-bearing mice limited the body and muscle weight loss (P ≤ 0.05), with no effect on tumour growth. CONCLUSIONS Overall, cancer cachexia and ALS seem to display similar mechanisms of muscle wasting at least at the catabolic level. The p97-Nploc4 complex appears to have a crucial role in muscle atrophy during these disorders and disrupting this complex might serve as a novel drug strategy.
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Affiliation(s)
- Andrea David Re Cecconi
- Department of NeurosciencesMario Negri Institute for Pharmacological Research IRCCSMilanItaly
| | - Mara Barone
- Department of NeurosciencesMario Negri Institute for Pharmacological Research IRCCSMilanItaly
| | - Simona Gaspari
- Department of NeurosciencesMario Negri Institute for Pharmacological Research IRCCSMilanItaly
| | - Massimo Tortarolo
- Department of NeurosciencesMario Negri Institute for Pharmacological Research IRCCSMilanItaly
| | - Caterina Bendotti
- Department of NeurosciencesMario Negri Institute for Pharmacological Research IRCCSMilanItaly
| | - Luca Porcu
- Department of OncologyMario Negri Institute for Pharmacological Research IRCCSMilanItaly
| | - Giulia Terribile
- Department of NeurosciencesMario Negri Institute for Pharmacological Research IRCCSMilanItaly
| | - Rosanna Piccirillo
- Department of NeurosciencesMario Negri Institute for Pharmacological Research IRCCSMilanItaly
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6
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Barter MJ, Butcher A, Wang H, Tsompani D, Galler M, Rumsby EL, Culley KL, Clark IM, Young DA. HDAC6 regulates NF-κB signalling to control chondrocyte IL-1-induced MMP and inflammatory gene expression. Sci Rep 2022; 12:6640. [PMID: 35459919 PMCID: PMC9033835 DOI: 10.1038/s41598-022-10518-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 04/06/2022] [Indexed: 11/09/2022] Open
Abstract
Elevated pro-inflammatory signalling coupled with catabolic metalloproteinase expression is a common feature of arthritis, leading to cartilage damage, deterioration of the joint architecture and the associated pain and immobility. Countering these processes, histone deacetylase inhibitors (HDACi) have been shown to suppress matrix metalloproteinase (MMP) expression, block cytokine-induced signalling and reduce the cartilage degradation in animal models of the arthritis. In order to establish which specific HDACs account for these chondro-protective effects an HDAC1-11 RNAi screen was performed. HDAC6 was required for both the interleukin (IL)-1 induction of MMP expression and pro-inflammatory interleukin expression in chondrocytes, implicating an effect on NF-κB signalling. Depletion of HDAC6 post-transcriptionally up-regulated inhibitor of κB (IκB), prevented the nuclear translocation of NF-κB subunits and down-regulated NF-κB reporter activation. The pharmacological inhibition of HDAC6 reduced MMP expression in chondrocytes and cartilage collagen release. This work highlights the important role of HDAC6 in pro-inflammatory signalling and metalloproteinase gene expression, and identifies a part for HDAC6 in the NF-κB signalling pathway. By confirming the protection of cartilage this work supports the inhibition of HDAC6 as a possible therapeutic strategy in arthritis.
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Affiliation(s)
- Matt J Barter
- Biosciences Institute, Central Parkway, Newcastle University, Newcastle upon Tyne, NE1 3BZ, UK.
| | - Andrew Butcher
- Department of Musculoskeletal and Ageing Science, Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool, UK
| | - Hui Wang
- Arthritis and Regenerative Medicine Laboratory, Aberdeen Centre for Arthritis and Musculoskeletal Health, University of Aberdeen, Aberdeen, UK
| | - Dimitra Tsompani
- GSK Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, UK
| | - Martin Galler
- Biosciences Institute, Central Parkway, Newcastle University, Newcastle upon Tyne, NE1 3BZ, UK
| | - Ellen L Rumsby
- Northern Care Alliance NHS Foundation Trust, Mayo Building, Salford Royal, Stott Lane, Salford, M6 8HD, UK
| | - Kirsty L Culley
- Anglia Innovation Partnership LLP, Centrum, Norwich Research Park, Norwich, UK
| | - Ian M Clark
- School of Biological Sciences, University of East Anglia, Norwich, UK
| | - David A Young
- Biosciences Institute, Central Parkway, Newcastle University, Newcastle upon Tyne, NE1 3BZ, UK
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7
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Wang F, Li S, Rosencrans WM, Cheng KW, Stott GM, Mroczkowski B, Chou TF. Sulforaphane is Synergistic with CB-5083 and Inhibits Colony Formation of CB-5083-Resistant HCT116 Cells. ChemMedChem 2022; 17:e202200030. [PMID: 35451199 DOI: 10.1002/cmdc.202200030] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 04/04/2022] [Indexed: 11/09/2022]
Abstract
Human p97 is a potential drug target in oncology. Mutation-driven drug resistance is an obstacle to the long-term efficacy of targeted therapy. We found that the ATPase activity for one of the CB-5083-resistant p97 mutants was reduced, which also attenuated the degradation of K48 ubiquitinated proteins in cells. To understand how p97 mutant cells with significantly reduced ATPase activity can still grow, we discovered reduced levels of CHOP and NF-κB activation in the p97 mutant cells and these cellular changes can potentially protect HCT116 cells from death due to lowered p97 activity. In addition, the NF-kB inhibitor Sulforaphane reduces proliferation of CB-5083 resistant cells and acts synergistically with CB-5083 to block proliferation of the parental HCT116 cells. The combination of Sulforaphane and CB-5083 may be a useful treatment strategy to combat CB-5083 resistance.
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Affiliation(s)
- Feng Wang
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Shan Li
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - William M Rosencrans
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Kai-Wen Cheng
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Gordon M Stott
- NExT Program Support, Applied/Developmental Research Directorate, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Barbara Mroczkowski
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, MD 20892, USA
| | - Tsui-Fen Chou
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA.,Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA 91125, USA
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8
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Ghalandary M, Li Y, Fröhlich T, Magg T, Liu Y, Rohlfs M, Hollizeck S, Conca R, Schwerd T, Uhlig HH, Bufler P, Koletzko S, Muise AM, Snapper SB, Hauck F, Klein C, Kotlarz D. Valosin-containing protein-regulated endoplasmic reticulum stress causes NOD2-dependent inflammatory responses. Sci Rep 2022; 12:3906. [PMID: 35273242 PMCID: PMC8913691 DOI: 10.1038/s41598-022-07804-1] [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: 04/05/2021] [Accepted: 02/24/2022] [Indexed: 11/24/2022] Open
Abstract
NOD2 polymorphisms may affect sensing of the bacterial muramyl dipeptide (MDP) and trigger perturbed inflammatory responses. Genetic screening of a patient with immunodeficiency and enteropathy revealed a rare homozygous missense mutation in the first CARD domain of NOD2 (ENST00000300589; c.160G > A, p.E54K). Biochemical assays confirmed impaired NOD2-dependent signaling and proinflammatory cytokine production in patient's cells and heterologous cellular models with overexpression of the NOD2 mutant. Immunoprecipitation-coupled mass spectrometry unveiled the ATPase valosin-containing protein (VCP) as novel interaction partner of wildtype NOD2, while the binding to the NOD2 variant p.E54K was abrogated. Knockdown of VCP in coloncarcinoma cells led to impaired NF-κB activity and IL8 expression upon MDP stimulation. In contrast, tunicamycin-induced ER stress resulted in increased IL8, CXCL1, and CXCL2 production in cells with knockdown of VCP, while enhanced expression of these proinflammatory molecules was abolished upon knockout of NOD2. Taken together, these data suggest that VCP-mediated inflammatory responses upon ER stress are NOD2-dependent.
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Affiliation(s)
- Maryam Ghalandary
- Dr. von Hauner Children's Hospital, Department of Pediatrics, University Hospital, Ludwig-Maximilians-Universität (LMU) Munich, 80337, Munich, Germany
| | - Yue Li
- Dr. von Hauner Children's Hospital, Department of Pediatrics, University Hospital, Ludwig-Maximilians-Universität (LMU) Munich, 80337, Munich, Germany
| | - Thomas Fröhlich
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, LMU Munich, Munich, Germany
| | - Thomas Magg
- Dr. von Hauner Children's Hospital, Department of Pediatrics, University Hospital, Ludwig-Maximilians-Universität (LMU) Munich, 80337, Munich, Germany
| | - Yanshan Liu
- Dr. von Hauner Children's Hospital, Department of Pediatrics, University Hospital, Ludwig-Maximilians-Universität (LMU) Munich, 80337, Munich, Germany
| | - Meino Rohlfs
- Dr. von Hauner Children's Hospital, Department of Pediatrics, University Hospital, Ludwig-Maximilians-Universität (LMU) Munich, 80337, Munich, Germany
| | - Sebastian Hollizeck
- Dr. von Hauner Children's Hospital, Department of Pediatrics, University Hospital, Ludwig-Maximilians-Universität (LMU) Munich, 80337, Munich, Germany
| | - Raffaele Conca
- Dr. von Hauner Children's Hospital, Department of Pediatrics, University Hospital, Ludwig-Maximilians-Universität (LMU) Munich, 80337, Munich, Germany
| | - Tobias Schwerd
- Dr. von Hauner Children's Hospital, Department of Pediatrics, University Hospital, Ludwig-Maximilians-Universität (LMU) Munich, 80337, Munich, Germany
| | - Holm H Uhlig
- Translational Gastroenterology Unit and Department of Pediatrics, and Biomedical Research Centre, University of Oxford, Oxford, UK
| | - Philip Bufler
- Dr. von Hauner Children's Hospital, Department of Pediatrics, University Hospital, Ludwig-Maximilians-Universität (LMU) Munich, 80337, Munich, Germany
- Department of Pediatric Gastroenterology, Nephrology and Metabolic Diseases, Charité Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität Zu Berlin, Berlin, Germany
| | - Sibylle Koletzko
- Dr. von Hauner Children's Hospital, Department of Pediatrics, University Hospital, Ludwig-Maximilians-Universität (LMU) Munich, 80337, Munich, Germany
- Department of Pediatrics, School of Medicine Collegium, Medicum University of Warmia and Mazury, Olsztyn, Poland
| | - Aleixo M Muise
- SickKids Inflammatory Bowel Disease Center, Research Institute, Hospital for Sick Children, Toronto, ON, M5G1X8, Canada
- Cell Biology Program, Research Institute, Hospital for Sick Children, Toronto, ON, M5G1X8, Canada
- VEO-IBD Consortium, University Hospital, LMU Munich, 80337, Munich, Germany
- Division of Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, Hospital for Sick Children, University of Toronto, Toronto, ON, M5G1X8, Canada
- Department of Biochemistry, University of Toronto, Toronto, ON, M5G1A8, Canada
| | - Scott B Snapper
- VEO-IBD Consortium, University Hospital, LMU Munich, 80337, Munich, Germany
- Division of Gastroenterology, Hepatology and Nutrition, Boston Children's Hospital, Boston, MA, 02115, USA
- Department of Medicine, Harvard Medical School, Boston, MA, 02115, USA
- Division of Gastroenterology, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Fabian Hauck
- Dr. von Hauner Children's Hospital, Department of Pediatrics, University Hospital, Ludwig-Maximilians-Universität (LMU) Munich, 80337, Munich, Germany
| | - Christoph Klein
- Dr. von Hauner Children's Hospital, Department of Pediatrics, University Hospital, Ludwig-Maximilians-Universität (LMU) Munich, 80337, Munich, Germany
- VEO-IBD Consortium, University Hospital, LMU Munich, 80337, Munich, Germany
- Gene Center, LMU Munich, Munich, Germany
- Deutsche Zentrum für Infektionsforschung (DZIF), Inhoffenstraße 7, 38124 Braunschweig, Germany
| | - Daniel Kotlarz
- Dr. von Hauner Children's Hospital, Department of Pediatrics, University Hospital, Ludwig-Maximilians-Universität (LMU) Munich, 80337, Munich, Germany.
- VEO-IBD Consortium, University Hospital, LMU Munich, 80337, Munich, Germany.
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9
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Popović KJ, Popović DJ, Miljković D, Popović JK, Lalošević D, Poša M, Čapo I. Disulfiram and metformin combination anticancer effect reversible partly by antioxidant nitroglycerin and completely by NF-κB activator mebendazole in hamster fibrosarcoma. Biomed Pharmacother 2021; 143:112168. [PMID: 34536762 DOI: 10.1016/j.biopha.2021.112168] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 09/02/2021] [Accepted: 09/03/2021] [Indexed: 12/16/2022] Open
Abstract
We investigated the anticancer effect of disulfiram and metformin combination on fibrosarcoma in hamsters. Hamsters of both sexes (~ 70 g) were randomly allocated to control and experimental groups (8 animals per group). In all 10 groups, 2 × 106 BHK-21/C13 cells in 1 ml were injected subcutaneously into the animals' backs. Peroral treatments were carried out with disulfiram 50 mg/kg daily, or with metformin 500 mg/kg daily, or with their combination. Validation and rescue grups were treated by double doses of the single therapy and by the combination with addition of rescue daily doses of ROS inhibitor nitroglycerin 25 mg/kg or NF-κB stimulator mebendazole 460 mg/kg, via a gastric probe after tumor inoculation. After 19 days all animals were sacrificed. Blood samples were collected for hematological and biochemical analyses, the tumors were excised and weighed, and their diameters and volumes were measured. The tumor samples were pathohistologically and immunohistochemically assessed (Ki-67, PCNA, CD34, CD31, COX4, Cytochrome C, GLUT1, iNOS), and the main organs were toxicologically tested. The combination of disulfiram and metformin significantly inhibited fibrosarcoma growth in hamsters without toxicity, compared to monotherapy or control. The single treatments did not show significant antisarcoma effect. Co-treatment with nitroglycerin partly rescued tumor progression, probably by ROS inhibition, while mebendazole completely blocked anticancer activity of the disulfiram and metformin combination, most likely by NF-κB stimulation. Combination of disulfiram with metformin may be used as an effective and safe candidate for novel nontoxic adjuvant and relapse prevention anticancer therapy.
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Affiliation(s)
- Kosta J Popović
- Department of Pharmacy, Faculty of Medicine, University of Novi Sad, 21000 Novi Sad, Serbia.
| | - Dušica J Popović
- Department of Histology and Embryology, Faculty of Medicine, University of Novi Sad, 21000 Novi Sad, Serbia
| | - Dejan Miljković
- Department of Histology and Embryology, Faculty of Medicine, University of Novi Sad, 21000 Novi Sad, Serbia
| | - Jovan K Popović
- Department of Pharmacology, Toxicology and Clinical Pharmacology, Faculty of Medicine, University of Novi Sad, 21000 Novi Sad, Serbia
| | - Dušan Lalošević
- Department of Histology and Embryology, Faculty of Medicine, University of Novi Sad, 21000 Novi Sad, Serbia
| | - Mihalj Poša
- Department of Pharmacy, Faculty of Medicine, University of Novi Sad, 21000 Novi Sad, Serbia
| | - Ivan Čapo
- Department of Histology and Embryology, Faculty of Medicine, University of Novi Sad, 21000 Novi Sad, Serbia
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10
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Tábuas-Pereira M, Santana I, Kun-Rodrigues C, Bras J, Guerreiro R. CYLD variants in frontotemporal dementia associated with severe memory impairment in a Portuguese cohort. Brain 2020; 143:e67. [PMID: 32666117 DOI: 10.1093/brain/awaa183] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Affiliation(s)
- Miguel Tábuas-Pereira
- Neurology Department, Centro Hospitalar e Universitário de Coimbra, Coimbra, Portugal.,Faculty of Medicine, University of Coimbra, Coimbra, Portugal
| | - Isabel Santana
- Neurology Department, Centro Hospitalar e Universitário de Coimbra, Coimbra, Portugal.,Faculty of Medicine, University of Coimbra, Coimbra, Portugal
| | - Célia Kun-Rodrigues
- Center for Neurodegenerative Science, Van Andel Research Institute, Grand Rapids, Michigan, USA
| | - Jose Bras
- Center for Neurodegenerative Science, Van Andel Research Institute, Grand Rapids, Michigan, USA.,Division of Psychiatry and Behavioral Medicine, Michigan State University College of Human Medicine, Grand Rapids, MI, USA
| | - Rita Guerreiro
- Center for Neurodegenerative Science, Van Andel Research Institute, Grand Rapids, Michigan, USA.,Division of Psychiatry and Behavioral Medicine, Michigan State University College of Human Medicine, Grand Rapids, MI, USA
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11
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Chen Y, Jin J. The application of ubiquitin ligases in the PROTAC drug design. Acta Biochim Biophys Sin (Shanghai) 2020; 52:776-790. [PMID: 32506133 DOI: 10.1093/abbs/gmaa053] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 06/25/2019] [Accepted: 06/26/2019] [Indexed: 12/13/2022] Open
Abstract
Protein ubiquitylation plays important roles in many biological activities. Protein ubiquitylation is a unique process that is mainly controlled by ubiquitin ligases. The ubiquitin-proteasome system (UPS) is the main process to degrade short-lived and unwanted proteins in eukaryotes. Many components in the UPS are attractive drug targets. Recent studies indicated that ubiquitin ligases can be employed as tools in proteolysis-targeting chimeras (PROTACs) for drug discovery. In this review article, we will discuss the recent progress of the application of ubiquitin ligases in the PROTAC drug design. We will also discuss advantages and existing problems of PROTACs. Moreover, we will propose a few principles for selecting ubiquitin ligases in PROTAC applications.
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Affiliation(s)
- Yilin Chen
- Life Science Institute, Zhejiang University, Hangzhou 310058, China
| | - Jianping Jin
- Life Science Institute, Zhejiang University, Hangzhou 310058, China
- Zhejiang Provincial Key Laboratory for Drug Evaluation and Clinical Research, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China
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12
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Ramanathan HN, Zhang S, Douam F, Mar KB, Chang J, Yang PL, Schoggins JW, Ploss A, Lindenbach BD. A Sensitive Yellow Fever Virus Entry Reporter Identifies Valosin-Containing Protein (VCP/p97) as an Essential Host Factor for Flavivirus Uncoating. mBio 2020; 11:e00467-20. [PMID: 32291299 PMCID: PMC7157815 DOI: 10.1128/mbio.00467-20] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 03/16/2020] [Indexed: 01/17/2023] Open
Abstract
While the basic mechanisms of flavivirus entry and fusion are understood, little is known about the postfusion events that precede RNA replication, such as nucleocapsid disassembly. We describe here a sensitive, conditionally replication-defective yellow fever virus (YFV) entry reporter, YFVΔSK/Nluc, to quantitively monitor the translation of incoming, virus particle-delivered genomes. We validated that YFVΔSK/Nluc gene expression can be neutralized by YFV-specific antisera and requires known flavivirus entry pathways and cellular factors, including clathrin- and dynamin-mediated endocytosis, endosomal acidification, YFV E glycoprotein-mediated fusion, and cellular LY6E and RPLP1 expression. The initial round of YFV translation was shown to require cellular ubiquitylation, consistent with recent findings that dengue virus capsid protein must be ubiquitylated in order for nucleocapsid uncoating to occur. Importantly, translation of incoming YFV genomes also required valosin-containing protein (VCP)/p97, a cellular ATPase that unfolds and extracts ubiquitylated client proteins from large complexes. RNA transfection and washout experiments showed that VCP/p97 functions at a postfusion, pretranslation step in YFV entry. Finally, VCP/p97 activity was required by other flaviviruses in mammalian cells and by YFV in mosquito cells. Together, these data support a critical role for VCP/p97 in the disassembly of incoming flavivirus nucleocapsids during a postfusion step in virus entry.IMPORTANCE Flaviviruses are an important group of RNA viruses that cause significant human disease. The mechanisms by which flavivirus nucleocapsids are disassembled during virus entry remain unclear. Here, we used a yellow fever virus entry reporter, which expresses a sensitive reporter enzyme but does not replicate, to show that nucleocapsid disassembly requires the cellular protein-disaggregating enzyme valosin-containing protein, also known as p97.
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Affiliation(s)
- Harish N Ramanathan
- Department of Microbial Pathogenesis, Yale University, New Haven, Connecticut, USA
| | - Shuo Zhang
- Department of Microbial Pathogenesis, Yale University, New Haven, Connecticut, USA
| | - Florian Douam
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA
| | - Katrina B Mar
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Jinhong Chang
- Department of Experimental Therapeutics, The Baruch S. Blumberg Institute, Doylestown, Pennsylvania, USA
| | - Priscilla L Yang
- Department of Microbiology and the Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - John W Schoggins
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Alexander Ploss
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA
| | - Brett D Lindenbach
- Department of Microbial Pathogenesis, Yale University, New Haven, Connecticut, USA
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13
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Figuerola-Conchas A, Saarbach J, Daguer JP, Cieren A, Barluenga S, Winssinger N, Gotta M. Small-Molecule Modulators of the ATPase VCP/p97 Affect Specific p97 Cellular Functions. ACS Chem Biol 2020; 15:243-253. [PMID: 31790201 DOI: 10.1021/acschembio.9b00832] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
VCP/p97 belongs to the AAA+ ATPase family and has an essential role in several cellular processes ranging from cell division to protein homeostasis. Compounds targeting p97 inhibit the main ATPase domain and cause cell death. Here, using PNA-encoded chemical libraries, we have identified two small molecules that target the regulatory domain of p97, comprising the N-terminal and the D1 ATPase domains, and do not cause cell death. One molecule, NW1028, inhibits the degradation of a p97-dependent reporter, whereas the other, NW1030, increases it. ATPase assays show that NW1028 and NW1030 do not affect the main catalytic domain of p97. Mapping of the binding site using a photoaffinity conjugate points to a cleft at the interface of the N-terminal and the D1 ATPase domains. We have therefore discovered two new compounds that bind to the regulatory domain of p97 and modulate specific p97 cellular functions. Using these compounds, we have revealed a role for p97 in the regulation of mitotic spindle orientation in HeLa cells.
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Affiliation(s)
- Ainoa Figuerola-Conchas
- Department of Cell Physiology and Metabolism, University of Geneva, 1211 Geneva 4, Switzerland
- National Centre of Competence in Research (NCCR) in Chemical Biology, University of Geneva, Geneva, Switzerland
| | - Jacques Saarbach
- Department of Cell Physiology and Metabolism, University of Geneva, 1211 Geneva 4, Switzerland
- National Centre of Competence in Research (NCCR) in Chemical Biology, University of Geneva, Geneva, Switzerland
| | - Jean-Pierre Daguer
- National Centre of Competence in Research (NCCR) in Chemical Biology, University of Geneva, Geneva, Switzerland
- Department of Organic Chemistry, University of Geneva, 1211 Geneva 4, Switzerland
| | - Adeline Cieren
- Department of Cell Physiology and Metabolism, University of Geneva, 1211 Geneva 4, Switzerland
- National Centre of Competence in Research (NCCR) in Chemical Biology, University of Geneva, Geneva, Switzerland
| | - Sofia Barluenga
- National Centre of Competence in Research (NCCR) in Chemical Biology, University of Geneva, Geneva, Switzerland
- Department of Organic Chemistry, University of Geneva, 1211 Geneva 4, Switzerland
| | - Nicolas Winssinger
- National Centre of Competence in Research (NCCR) in Chemical Biology, University of Geneva, Geneva, Switzerland
- Department of Organic Chemistry, University of Geneva, 1211 Geneva 4, Switzerland
| | - Monica Gotta
- Department of Cell Physiology and Metabolism, University of Geneva, 1211 Geneva 4, Switzerland
- National Centre of Competence in Research (NCCR) in Chemical Biology, University of Geneva, Geneva, Switzerland
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14
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Shi W, Ding R, Zhou PP, Fang Y, Wan R, Chen Y, Jin J. Coordinated Actions Between p97 and Cullin-RING Ubiquitin Ligases for Protein Degradation. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1217:61-78. [PMID: 31898222 DOI: 10.1007/978-981-15-1025-0_5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The cullin-RING ubiquitin ligases comprise the largest subfamily of ubiquitin ligases. They control ubiquitylation and degradation of a large number of protein substrates in eukaryotes. p97 is an ATPase domain-containing protein segregase. It plays essential roles in post-ubiquitylational events in the ubiquitin-proteasome pathway. Together with its cofactors, p97 collaborates with ubiquitin ligases to extract ubiquitylated substrates and deliver them to the proteasome for proteolysis. Here we review the structure, functions, and mechanisms of p97 in cellular protein degradation in coordination with its cofactors and the cullin-RING ubiquitin ligases.
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Affiliation(s)
- Wenbo Shi
- Life Science Institute, Zhejiang University, HangZhou, China
| | - Ran Ding
- Life Science Institute, Zhejiang University, HangZhou, China
| | - Pei Pei Zhou
- Life Science Institute, Zhejiang University, HangZhou, China
| | - Yuan Fang
- Life Science Institute, Zhejiang University, HangZhou, China
| | - Ruixi Wan
- Life Science Institute, Zhejiang University, HangZhou, China
| | - Yilin Chen
- Life Science Institute, Zhejiang University, HangZhou, China
| | - Jianping Jin
- Life Science Institute, Zhejiang University, HangZhou, China.
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15
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Structure of the PUB Domain from Ubiquitin Regulatory X Domain Protein 1 (UBXD1) and Its Interaction with the p97 AAA+ ATPase. Biomolecules 2019; 9:biom9120876. [PMID: 31847414 PMCID: PMC6995525 DOI: 10.3390/biom9120876] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 12/11/2019] [Accepted: 12/11/2019] [Indexed: 01/19/2023] Open
Abstract
AAA+ ATPase p97/valosin-containing protein (VCP)/Cdc48 is a key player in various cellular stress responses in which it unfolds ubiquitinated proteins to facilitate their degradation by the proteasome. P97 works in different cellular processes using alternative sets of cofactors and is implicated in multiple degenerative diseases. Ubiquitin regulatory X domain protein 1 (UBXD1) has been linked to pathogenesis and is unique amongst p97 cofactors because it interacts with both termini of p97. Its N-domain binds to the N-domain and N/D1 interface of p97 and regulates its ATPase activity. The PUB (peptide:N-glycanase and UBA or UBX-containing proteins) domain binds the p97 C-terminus, but how it controls p97 function is still unknown. Here we present the NMR structure of UBXD1-PUB together with binding studies, mutational analysis, and a model of UBXD1-PUB in complex with the p97 C-terminus. While the binding pocket is conserved among PUB domains, UBXD1-PUB features a unique loop and turn regions suggesting a role in coordinating interaction with downstream regulators and substrate processing
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16
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Feldman D, Singh A, Schmid-Burgk JL, Carlson RJ, Mezger A, Garrity AJ, Zhang F, Blainey PC. Optical Pooled Screens in Human Cells. Cell 2019; 179:787-799.e17. [PMID: 31626775 PMCID: PMC6886477 DOI: 10.1016/j.cell.2019.09.016] [Citation(s) in RCA: 139] [Impact Index Per Article: 27.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 07/08/2019] [Accepted: 09/13/2019] [Indexed: 01/06/2023]
Abstract
Genetic screens are critical for the systematic identification of genes underlying cellular phenotypes. Pooling gene perturbations greatly improves scalability but is not compatible with imaging of complex and dynamic cellular phenotypes. Here, we introduce a pooled approach for optical genetic screens in mammalian cells. We use targeted in situ sequencing to demultiplex a library of genetic perturbations following image-based phenotyping. We screened a set of 952 genes across millions of cells for involvement in nuclear factor κB (NF-κB) signaling by imaging the translocation of RelA (p65) to the nucleus. Screening at a single time point across 3 cell lines recovered 15 known pathway components, while repeating the screen with live-cell imaging revealed a role for Mediator complex subunits in regulating the duration of p65 nuclear retention. These results establish a highly multiplexed approach to image-based screens of spatially and temporally defined phenotypes with pooled libraries.
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Affiliation(s)
- David Feldman
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Physics, MIT, Cambridge, MA 02142, USA
| | - Avtar Singh
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Rebecca J Carlson
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Health Sciences and Technology, MIT, Cambridge, MA 02142, USA
| | - Anja Mezger
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
| | | | - Feng Zhang
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Biological Engineering, MIT, Cambridge, MA 02142, USA; McGovern Institute for Brain Research at MIT, Cambridge, MA 02142, USA; Department of Brain and Cognitive Science, MIT, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, MIT, Cambridge, MA 02142, USA
| | - Paul C Blainey
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Biological Engineering, MIT, Cambridge, MA 02142, USA; Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA 02142, USA.
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17
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Blythe EE, Gates SN, Deshaies RJ, Martin A. Multisystem Proteinopathy Mutations in VCP/p97 Increase NPLOC4·UFD1L Binding and Substrate Processing. Structure 2019; 27:1820-1829.e4. [PMID: 31623962 DOI: 10.1016/j.str.2019.09.011] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 08/19/2019] [Accepted: 09/20/2019] [Indexed: 11/25/2022]
Abstract
Valosin-containing protein (VCP)/p97 is an essential ATP-dependent protein unfoldase. Dominant mutations in p97 cause multisystem proteinopathy (MSP), a disease affecting the brain, muscle, and bone. Despite the identification of numerous pathways that are perturbed in MSP, the molecular-level defects of these p97 mutants are not completely understood. Here, we use biochemistry and cryoelectron microscopy to explore the effects of MSP mutations on the unfoldase activity of p97 in complex with its substrate adaptor NPLOC4⋅UFD1L (UN). We show that all seven analyzed MSP mutants unfold substrates faster. Mutant homo- and heterohexamers exhibit tighter UN binding and faster substrate processing. Our structural studies suggest that the increased UN affinity originates from a decoupling of p97's nucleotide state and the positioning of its N-terminal domains. Together, our data support a gain-of-function model for p97-UN-dependent processes in MSP and underscore the importance of N-terminal domain movements for adaptor recruitment and substrate processing by p97.
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Affiliation(s)
- Emily E Blythe
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; Department of Molecular & Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Stephanie N Gates
- Department of Molecular & Cell Biology, University of California, Berkeley, CA 94720, USA; Howard Hughes Medical Institute, University of California, Berkeley, CA 94720, USA; California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Raymond J Deshaies
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; Amgen Research, Thousand Oaks, CA 91320, USA
| | - Andreas Martin
- Department of Molecular & Cell Biology, University of California, Berkeley, CA 94720, USA; Howard Hughes Medical Institute, University of California, Berkeley, CA 94720, USA; California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA.
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18
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Ufd1 phosphorylation at serine 229 negatively regulates endoplasmic reticulum-associated degradation by inhibiting the interaction of Ufd1 with VCP. Biochem J 2019; 476:2561-2577. [PMID: 31477623 DOI: 10.1042/bcj20190254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 08/29/2019] [Accepted: 08/30/2019] [Indexed: 11/17/2022]
Abstract
Misfolded proteins in the endoplasmic reticulum (ER) are removed through multistep processes termed ER-associated degradation (ERAD). Valosin-containing protein (VCP) plays a crucial role in ERAD as the interaction of ubiquitin fusion degradation protein 1 (Ufd1) with VCP via its SHP box motif (228F-S-G-S-G-N-R-L235) is required for ERAD. However, the mechanisms by which the VCP-Ufd1 interaction is regulated are not well understood. Here, we found that the serine 229 residue located in the Ufd1 SHP box is phosphorylated in vitro and in vivo by cyclic adenosine monophosphate-dependent protein kinase A (PKA), with this process being enhanced by either forskolin (an adenylyl cyclase activator) or calyculin A (a protein phosphatase inhibitor). Moreover, a phosphomimetic mutant (S229D) of Ufd1 as well as treatment by forskolin, calyculin A, or activated PKA strongly reduced Ufd1 binding affinity for VCP. Consistent with this, the Ufd1 S229D mutant significantly inhibited ERAD leading to the accumulation of ERAD substrates such as a tyrosinase mutant (C89R) and 3-hydroxy-3-methylglutaryl coenzyme A reductase. However, a non-phosphorylatable Ufd1 mutant (S229A) retained VCP-binding ability and was less effective in blocking ERAD. Collectively, our results support that Ufd1 S229 phosphorylation status mediated by PKA serves as a key regulatory point for the VCP-Ufd1 interaction and functional ERAD.
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19
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Bright F, Werry EL, Dobson-Stone C, Piguet O, Ittner LM, Halliday GM, Hodges JR, Kiernan MC, Loy CT, Kassiou M, Kril JJ. Neuroinflammation in frontotemporal dementia. Nat Rev Neurol 2019; 15:540-555. [PMID: 31324897 DOI: 10.1038/s41582-019-0231-z] [Citation(s) in RCA: 138] [Impact Index Per Article: 27.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/14/2019] [Indexed: 12/12/2022]
Abstract
Frontotemporal dementia (FTD) refers to a group of progressive neurodegenerative disorders with different pathological signatures, genetic variability and complex disease mechanisms, for which no effective treatments exist. Despite advances in understanding the underlying pathology of FTD, sensitive and specific fluid biomarkers for this disease are lacking. As in other types of dementia, mounting evidence suggests that neuroinflammation is involved in the progression of FTD, including cortical inflammation, microglial activation, astrogliosis and differential expression of inflammation-related proteins in the periphery. Furthermore, an overlap between FTD and autoimmune disease has been identified. The most substantial evidence, however, comes from genetic studies, and several FTD-related genes are also implicated in neuroinflammation. This Review discusses specific evidence of neuroinflammatory mechanisms in FTD and describes how advances in our understanding of these mechanisms, in FTD as well as in other neurodegenerative diseases, might facilitate the development and implementation of diagnostic tools and disease-modifying treatments for FTD.
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Affiliation(s)
- Fiona Bright
- School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
| | - Eryn L Werry
- School of Chemistry, Faculty of Science, University of Sydney, Sydney, NSW, Australia
| | - Carol Dobson-Stone
- Brain and Mind Centre, University of Sydney, Sydney, NSW, Australia.,Central Clinical School, Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia.,School of Medical Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Olivier Piguet
- Brain and Mind Centre, University of Sydney, Sydney, NSW, Australia.,School of Psychology, Faculty of Science, University of Sydney, Sydney, NSW, Australia.,Centre of Excellence in Cognition and its Disorders, Australian Research Council, Sydney, NSW, Australia
| | - Lars M Ittner
- Dementia Research Centre, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW, Australia
| | - Glenda M Halliday
- Brain and Mind Centre, University of Sydney, Sydney, NSW, Australia.,Central Clinical School, Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
| | - John R Hodges
- Brain and Mind Centre, University of Sydney, Sydney, NSW, Australia.,Central Clinical School, Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia.,Centre of Excellence in Cognition and its Disorders, Australian Research Council, Sydney, NSW, Australia
| | - Matthew C Kiernan
- Brain and Mind Centre, University of Sydney, Sydney, NSW, Australia.,Central Clinical School, Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia.,Institute of Clinical Neurosciences, Royal Prince Alfred Hospital, Sydney, NSW, Australia
| | - Clement T Loy
- Sydney School of Public Health, Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
| | - Michael Kassiou
- School of Chemistry, Faculty of Science, University of Sydney, Sydney, NSW, Australia
| | - Jillian J Kril
- School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia.
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20
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Zhang X, Hu P, Ding SY, Sun T, Liu L, Han S, DeLeo AB, Sadagopan A, Guo W, Wang X. Induction of autophagy-dependent apoptosis in cancer cells through activation of ER stress: an uncovered anti-cancer mechanism by anti-alcoholism drug disulfiram. Am J Cancer Res 2019; 9:1266-1281. [PMID: 31285958 PMCID: PMC6610050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 05/25/2019] [Indexed: 06/09/2023] Open
Abstract
UNLABELLED Due to its potent anticancer activity, there is interest in repurposing of the FDA-approved anti-alcoholism drug, disulfiram (DSF). DSF forms potent complexes with copper (DSF/Cu) that induce apoptosis of many types of cancer cells. Here, we investigated the role of DSF/Cu in autophagy, a mechanism of cell death or survival, and its interplay with DSF/Cu induced apoptosis of human pancreatic and breast cancer cells. METHODS Levels of autophagy and apoptosis were assessed by Western blot, flow cytometry and immunofluorescence analysis. Cell viability was measured by MTT assays. Activation of inositol-requiring enzyme 1α (IRE1α)-mRNA X-box binding protein 1 (XBP1) pathway and spliced XBP1 (XBP1s) expression were analyzed by Western blot, Phos-tag gel assay, RT-PCR, qRT-PCR and flow cytometry. RESULTS The apoptosis induced by DSF/Cu in pancreatic and breast cancer cells is autophagy dependent. This is accomplished by activating IRE1α, the sensor of unfolded protein response (UPR) via promotion of phosphorylation of IRE1α and its downstream XBP1 splicing into active XBP1s. CONCLUSIONS DSF/Cu induces ER-stress through activation of IRE1α-XBP1 pathway which is responsible, at least in part, for induction of autophagy-dependent apoptosis of cancer cells. Insight into the ER-stress inducing ability by DSF/Cu may open a new research area for rational design of innovative therapeutic strategies for pancreatic and breast cancers.
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Affiliation(s)
- Xiao Zhang
- Division of Surgical Oncology, Department of Surgery, Massachusetts General Hospital, Harvard Medical SchoolBoston, MA, USA
- Key Laboratory of Antibody Technology, National Health Commission, Nanjing Medical UniversityNanjing, Jiangsu, China
| | - Pan Hu
- Division of Surgical Oncology, Department of Surgery, Massachusetts General Hospital, Harvard Medical SchoolBoston, MA, USA
| | - Shi-Ying Ding
- Department of Orthopaedic Surgery, Massachusetts General Hospital, Harvard Medical SchoolBoston, MA, USA
| | - Ting Sun
- Division of Surgical Oncology, Department of Surgery, Massachusetts General Hospital, Harvard Medical SchoolBoston, MA, USA
| | - Ling Liu
- Division of Surgical Oncology, Department of Surgery, Massachusetts General Hospital, Harvard Medical SchoolBoston, MA, USA
| | - Shiwei Han
- Division of Surgical Oncology, Department of Surgery, Massachusetts General Hospital, Harvard Medical SchoolBoston, MA, USA
| | - Albert B DeLeo
- Division of Surgical Oncology, Department of Surgery, Massachusetts General Hospital, Harvard Medical SchoolBoston, MA, USA
| | - Ananthan Sadagopan
- Division of Surgical Oncology, Department of Surgery, Massachusetts General Hospital, Harvard Medical SchoolBoston, MA, USA
| | - Wei Guo
- Division of Surgical Oncology, Department of Surgery, Massachusetts General Hospital, Harvard Medical SchoolBoston, MA, USA
| | - Xinhui Wang
- Division of Surgical Oncology, Department of Surgery, Massachusetts General Hospital, Harvard Medical SchoolBoston, MA, USA
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21
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Ballar Kırmızıbayrak P, Erbaykent Tepedelen B. Endoplazmik retikulum-aracılı protein yıkım yolağında görev yapan p97/VCP ve Ufd1-Npl4 adlı proteinlerin NF-κB yolağına etkisinin prostat kanser hücre hattında incelenmesi. EGE TIP DERGISI 2019. [DOI: 10.19161/etd.418150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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22
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Li H, Cui Y, Wei J, Liu C, Chen Y, Cui CP, Li L, Zhang X, Zhang L. VCP/p97 increases BMP signaling by accelerating ubiquitin ligase Smurf1 degradation. FASEB J 2018; 33:2928-2943. [PMID: 30335548 DOI: 10.1096/fj.201801173r] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The bone morphogenetic protein (BMP)-Smad signaling pathway plays a crucial role in the control of bone homeostasis by regulating osteoblast activity. It is known that the ubiquitin ligase Smad ubiquitination regulatory factor (Smurf)1 is a master negative regulator of BMP signaling, but how its stability and activity are regulated remains poorly understood. Our study showed that valosin-containing protein/p97, the mutations of which lead to rare forms of Paget's disease of bone (PDB)-like syndrome-such as inclusion body myopathy (IBM) associated with Paget's disease of bone and frontotemporal dementia (IBM-PFD)-together with its adaptor nuclear protein localization (NPL)4, specifically interact with Smurf1 and deliver the ubiquitinated Smurf1 for degradation. Depletion of either p97 or NPL4 resulted in the elevation of Smurf1 protein level and decreased BMP signaling accordingly. Mechanically, a typical proline, glutamic acid, serine, and threonine motif specifically existing in Smurf1 is necessary for its recognition and degradation by p97, and this process is dependent on p97 ATPase activity. More importantly, compared with p97 WT, PDB-associated mutation of p97 (mainly A232E) harboring the higher ATPase activity of p97 further promoted Smurf1 degradation, thus increasing BMP signaling activity. Our findings first establish a link between p97 and Smurf1, providing an in-depth understanding of how Smurf1 is regulated, as well as the mechanism of p97-related bone diseases.-Li, H., Cui, Y., Wei, J., Liu, C., Chen, Y., Cui, C.-P., Li, L., Zhang, X., Zhang, L. VCP/p97 increases BMP signaling by accelerating ubiquitin ligase Smurf1 degradation.
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Affiliation(s)
- Haiwen Li
- State Key Laboratory of Proteomics, National Center of Protein Sciences, Beijing Institute of Lifeomics, Beijing, China.,Department of Neurosciences, School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
| | - Yu Cui
- State Key Laboratory of Proteomics, National Center of Protein Sciences, Beijing Institute of Lifeomics, Beijing, China
| | - Jun Wei
- Department of General Surgery, Shanghai Fengxian Central Hospital Graduate Training Base, Fengxian Hospital, Southern Medical University, Shanghai, China
| | - Chao Liu
- State Key Laboratory of Proteomics, National Center of Protein Sciences, Beijing Institute of Lifeomics, Beijing, China
| | - Yuhan Chen
- State Key Laboratory of Proteomics, National Center of Protein Sciences, Beijing Institute of Lifeomics, Beijing, China
| | - Chun-Ping Cui
- State Key Laboratory of Proteomics, National Center of Protein Sciences, Beijing Institute of Lifeomics, Beijing, China
| | - Lei Li
- State Key Laboratory of Proteomics, National Center of Protein Sciences, Beijing Institute of Lifeomics, Beijing, China
| | - Xueli Zhang
- Department of General Surgery, Shanghai Fengxian Central Hospital Graduate Training Base, Fengxian Hospital, Southern Medical University, Shanghai, China
| | - Lingqiang Zhang
- State Key Laboratory of Proteomics, National Center of Protein Sciences, Beijing Institute of Lifeomics, Beijing, China
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23
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Parisi E, Yahya G, Flores A, Aldea M. Cdc48/p97 segregase is modulated by cyclin-dependent kinase to determine cyclin fate during G1 progression. EMBO J 2018; 37:embj.201798724. [PMID: 29950310 DOI: 10.15252/embj.201798724] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Revised: 05/14/2018] [Accepted: 06/12/2018] [Indexed: 01/26/2023] Open
Abstract
Cells sense myriad signals during G1, and a rapid response to prevent cell cycle entry is of crucial importance for proper development and adaptation. Cln3, the most upstream G1 cyclin in budding yeast, is an extremely short-lived protein subject to ubiquitination and proteasomal degradation. On the other hand, nuclear accumulation of Cln3 depends on chaperones that are also important for its degradation. However, how these processes are intertwined to control G1-cyclin fate is not well understood. Here, we show that Cln3 undergoes a challenging ubiquitination step required for both degradation and full activation. Segregase Cdc48/p97 prevents degradation of ubiquitinated Cln3, and concurrently stimulates its ER release and nuclear accumulation to trigger Start. Cdc48/p97 phosphorylation at conserved Cdk-target sites is important for recruitment of specific cofactors and, in both yeast and mammalian cells, to attain proper G1-cyclin levels and activity. Cdk-dependent modulation of Cdc48 would subjugate G1 cyclins to fast and reversible state switching, thus arresting cells promptly in G1 at developmental or environmental checkpoints, but also resuming G1 progression immediately after proliferative signals reappear.
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Affiliation(s)
- Eva Parisi
- Molecular Biology Institute of Barcelona IBMB-CSIC, Barcelona, Catalonia, Spain
| | - Galal Yahya
- Molecular Biology Institute of Barcelona IBMB-CSIC, Barcelona, Catalonia, Spain.,Department of Microbiology and Immunology, School of Pharmacy, Zagazig University, Zagazig, Egypt
| | - Alba Flores
- Molecular Biology Institute of Barcelona IBMB-CSIC, Barcelona, Catalonia, Spain
| | - Martí Aldea
- Molecular Biology Institute of Barcelona IBMB-CSIC, Barcelona, Catalonia, Spain .,Departament de Ciències Bàsiques, Universitat Internacional de Catalunya, Barcelona, Catalonia, Spain
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24
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Hülsmann J, Kravic B, Weith M, Gstaiger M, Aebersold R, Collins BC, Meyer H. AP-SWATH Reveals Direct Involvement of VCP/p97 in Integrated Stress Response Signaling Through Facilitating CReP/PPP1R15B Degradation. Mol Cell Proteomics 2018; 17:1295-1307. [PMID: 29599191 DOI: 10.1074/mcp.ra117.000471] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 03/07/2018] [Indexed: 12/27/2022] Open
Abstract
The ubiquitin-directed AAA-ATPase VCP/p97 facilitates degradation of damaged or misfolded proteins in diverse cellular stress response pathways. Resolving the complexity of its interactions with partner and substrate proteins and understanding its links to stress signaling is therefore a major challenge. Here, we used affinity-purification SWATH mass spectrometry (AP-SWATH) to identify proteins that specifically interact with the substrate-trapping mutant, p97-E578Q. AP-SWATH identified differential interactions over a large detection range from abundant p97 cofactors to pathway-specific partners and individual ligases such as RNF185 and MUL1 that were trapped in p97-E578Q complexes. In addition, we identified various substrate proteins and candidates including the PP1 regulator CReP/PPP1R15B that dephosphorylates eIF2α and thus counteracts attenuation of translation by stress-kinases. We provide evidence that p97 with its Ufd1-Npl4 adapter ensures rapid constitutive turnover and balanced levels of CReP in unperturbed cells. Moreover, we show that p97-mediated degradation, together with a reduction in CReP synthesis, is essential for timely stress-induced reduction of CReP levels and, consequently, for robust eIF2α phosphorylation to enforce the stress response. Thus, our results demonstrate that p97 not only facilitates bulk degradation of misfolded proteins upon stress, but also directly modulates the integrated stress response at the level of signaling.
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Affiliation(s)
- Julia Hülsmann
- From the ‡Molecular Biology I, Centre for Medical Biotechnology, Faculty of Biology, University of Duisburg-Essen, 45141 Essen, Germany
| | - Bojana Kravic
- From the ‡Molecular Biology I, Centre for Medical Biotechnology, Faculty of Biology, University of Duisburg-Essen, 45141 Essen, Germany
| | - Matthias Weith
- From the ‡Molecular Biology I, Centre for Medical Biotechnology, Faculty of Biology, University of Duisburg-Essen, 45141 Essen, Germany
| | - Matthias Gstaiger
- §Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Ruedi Aebersold
- §Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland.,¶Faculty of Science, University of Zurich, Zurich, Switzerland
| | - Ben C Collins
- §Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland;
| | - Hemmo Meyer
- From the ‡Molecular Biology I, Centre for Medical Biotechnology, Faculty of Biology, University of Duisburg-Essen, 45141 Essen, Germany;
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25
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Pöhler R, Krahn JH, van den Boom J, Dobrynin G, Kaschani F, Eggenweiler HM, Zenke FT, Kaiser M, Meyer H. A Non-Competitive Inhibitor of VCP/p97 and VPS4 Reveals Conserved Allosteric Circuits in Type I and II AAA ATPases. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201711429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Robert Pöhler
- Molecular Biology I, Centre for Medical Biotechnology; University of Duisburg-Essen; 45117 Essen Germany
| | - Jan H. Krahn
- Chemical Biology, Centre for Medical Biotechnology; University of Duisburg-Essen; 45117 Essen Germany
| | - Johannes van den Boom
- Molecular Biology I, Centre for Medical Biotechnology; University of Duisburg-Essen; 45117 Essen Germany
| | - Grzegorz Dobrynin
- Molecular Biology I, Centre for Medical Biotechnology; University of Duisburg-Essen; 45117 Essen Germany
| | - Farnusch Kaschani
- Chemical Biology, Centre for Medical Biotechnology; University of Duisburg-Essen; 45117 Essen Germany
| | - Hans-Michael Eggenweiler
- Medicinal Chemistry DA and Translational Innovation Platform Oncology, Global R&D, Healthcare; Merck KGaA; Frankfurter Str. 250 64293 Darmstadt Germany
| | - Frank T. Zenke
- Medicinal Chemistry DA and Translational Innovation Platform Oncology, Global R&D, Healthcare; Merck KGaA; Frankfurter Str. 250 64293 Darmstadt Germany
| | - Markus Kaiser
- Chemical Biology, Centre for Medical Biotechnology; University of Duisburg-Essen; 45117 Essen Germany
| | - Hemmo Meyer
- Molecular Biology I, Centre for Medical Biotechnology; University of Duisburg-Essen; 45117 Essen Germany
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26
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Pöhler R, Krahn JH, van den Boom J, Dobrynin G, Kaschani F, Eggenweiler HM, Zenke FT, Kaiser M, Meyer H. A Non-Competitive Inhibitor of VCP/p97 and VPS4 Reveals Conserved Allosteric Circuits in Type I and II AAA ATPases. Angew Chem Int Ed Engl 2018; 57:1576-1580. [PMID: 29271116 DOI: 10.1002/anie.201711429] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Revised: 12/15/2017] [Indexed: 01/16/2023]
Abstract
AAA ATPases have pivotal functions in diverse cellular processes essential for survival and proliferation. Revealing strategies for chemical inhibition of this class of enzymes is therefore of great interest for the development of novel chemotherapies or chemical tools. Here, we characterize the compound MSC1094308 as a reversible, allosteric inhibitor of the type II AAA ATPase human ubiquitin-directed unfoldase (VCP)/p97 and the type I AAA ATPase VPS4B. Subsequent proteomic, genetic and biochemical studies indicate that MSC1094308 binds to a previously characterized drugable hotspot of p97, thereby inhibiting the D2 ATPase activity. Our results furthermore indicate that a similar allosteric site exists in VPS4B, suggesting conserved allosteric circuits and drugable sites in both type I and II AAA ATPases. Our results may thus guide future chemical tool and drug discovery efforts for the biomedically relevant AAA ATPases.
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Affiliation(s)
- Robert Pöhler
- Molecular Biology I, Centre for Medical Biotechnology, University of Duisburg-Essen, 45117, Essen, Germany
| | - Jan H Krahn
- Chemical Biology, Centre for Medical Biotechnology, University of Duisburg-Essen, 45117, Essen, Germany
| | - Johannes van den Boom
- Molecular Biology I, Centre for Medical Biotechnology, University of Duisburg-Essen, 45117, Essen, Germany
| | - Grzegorz Dobrynin
- Molecular Biology I, Centre for Medical Biotechnology, University of Duisburg-Essen, 45117, Essen, Germany
| | - Farnusch Kaschani
- Chemical Biology, Centre for Medical Biotechnology, University of Duisburg-Essen, 45117, Essen, Germany
| | - Hans-Michael Eggenweiler
- Medicinal Chemistry DA and Translational Innovation Platform Oncology, Global R&D, Healthcare, Merck KGaA, Frankfurter Str. 250, 64293, Darmstadt, Germany
| | - Frank T Zenke
- Medicinal Chemistry DA and Translational Innovation Platform Oncology, Global R&D, Healthcare, Merck KGaA, Frankfurter Str. 250, 64293, Darmstadt, Germany
| | - Markus Kaiser
- Chemical Biology, Centre for Medical Biotechnology, University of Duisburg-Essen, 45117, Essen, Germany
| | - Hemmo Meyer
- Molecular Biology I, Centre for Medical Biotechnology, University of Duisburg-Essen, 45117, Essen, Germany
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27
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Skrott Z, Mistrik M, Andersen KK, Friis S, Majera D, Gursky J, Ozdian T, Bartkova J, Turi Z, Moudry P, Kraus M, Michalova M, Vaclavkova J, Dzubak P, Vrobel I, Pouckova P, Sedlacek J, Miklovicova A, Kutt A, Li J, Mattova J, Driessen C, Dou QP, Olsen J, Hajduch M, Cvek B, Deshaies RJ, Bartek J. Alcohol-abuse drug disulfiram targets cancer via p97 segregase adaptor NPL4. Nature 2017; 552:194-199. [PMID: 29211715 PMCID: PMC5730499 DOI: 10.1038/nature25016] [Citation(s) in RCA: 496] [Impact Index Per Article: 70.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Accepted: 11/08/2017] [Indexed: 12/21/2022]
Abstract
Cancer incidence is rising and this global challenge is further exacerbated by tumour resistance to available medicines. A promising approach to such unmet need for improved cancer treatment is drug repurposing. Here we highlight the potential for repurposing disulfiram (Antabuse), an old alcohol-aversion drug effective against diverse cancer types in preclinical studies. Our nationwide epidemiological study reveals that patients who continuously used disulfiram have a lower risk of death from cancer compared to those who stopped using the drug at their diagnosis. Moreover, we identify ditiocarb-copper complex as the metabolite of disulfiram responsible for anticancer effects, and provide methods to detect its preferential accumulation in tumours and candidate biomarkers for impact in cells and tissues. Finally, our functional and biophysical analyses reveal the long-sought molecular target of disulfiram’s tumour suppressing effects as NPL4, an adapter of p97/VCP segregase essential for protein turnover involved in multiple regulatory and stress-response cellular pathways.
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Affiliation(s)
- Zdenek Skrott
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University, Olomouc, Czech Republic
| | - Martin Mistrik
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University, Olomouc, Czech Republic
| | | | - Søren Friis
- Danish Cancer Society Research Center, DK-2100 Copenhagen, Denmark
| | - Dusana Majera
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University, Olomouc, Czech Republic
| | - Jan Gursky
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University, Olomouc, Czech Republic
| | - Tomas Ozdian
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University, Olomouc, Czech Republic
| | - Jirina Bartkova
- Danish Cancer Society Research Center, DK-2100 Copenhagen, Denmark.,Science for Life Laboratory, Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
| | - Zsofia Turi
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University, Olomouc, Czech Republic
| | - Pavel Moudry
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University, Olomouc, Czech Republic
| | - Marianne Kraus
- Kantonsspital St Gallen, Department Oncology/Hematology, St Gallen, Switzerland
| | - Martina Michalova
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University, Olomouc, Czech Republic
| | - Jana Vaclavkova
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University, Olomouc, Czech Republic
| | - Petr Dzubak
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University, Olomouc, Czech Republic
| | - Ivo Vrobel
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University, Olomouc, Czech Republic
| | - Pavla Pouckova
- Institute of Biophysics and Informatics, First Faculty of Medicine, Charles University, 120 00 Prague 2, Czech Republic
| | - Jindrich Sedlacek
- Department of Cell Biology & Genetics, Palacky University, Olomouc, Czech Republic
| | | | - Anne Kutt
- Danish Cancer Society Research Center, DK-2100 Copenhagen, Denmark
| | - Jing Li
- Division of Biology and Biological Engineering, Caltech, Pasadena, California 91125, USA
| | - Jana Mattova
- Institute of Biophysics and Informatics, First Faculty of Medicine, Charles University, 120 00 Prague 2, Czech Republic
| | - Christoph Driessen
- Kantonsspital St Gallen, Department Oncology/Hematology, St Gallen, Switzerland
| | - Q Ping Dou
- Barbara Ann Karmanos Cancer Institute and Department of Oncology, School of Medicine, Wayne State University, Detroit, Michigan, USA.,School of Basic Medical Sciences, Affiliated Tumor Hospital of Guangzhou Medical University, Guangzhou 511436, China
| | - Jørgen Olsen
- Danish Cancer Society Research Center, DK-2100 Copenhagen, Denmark
| | - Marian Hajduch
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University, Olomouc, Czech Republic
| | - Boris Cvek
- Department of Cell Biology & Genetics, Palacky University, Olomouc, Czech Republic
| | - Raymond J Deshaies
- Division of Biology and Biological Engineering, Caltech, Pasadena, California 91125, USA.,Howard Hughes Medical Institute, Caltech, Pasadena, California 91125, USA
| | - Jiri Bartek
- Danish Cancer Society Research Center, DK-2100 Copenhagen, Denmark.,Science for Life Laboratory, Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
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28
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VCP/p97-Mediated Unfolding as a Principle in Protein Homeostasis and Signaling. Mol Cell 2017; 69:182-194. [PMID: 29153394 DOI: 10.1016/j.molcel.2017.10.028] [Citation(s) in RCA: 262] [Impact Index Per Article: 37.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Revised: 10/06/2017] [Accepted: 10/20/2017] [Indexed: 01/14/2023]
Abstract
The AAA+-type ATPase p97 governs an ever-expanding number of cellular processes reaching from degradation of damaged proteins and organelles to key signaling events and chromatin regulation with thousands of client proteins. With its relevance for cellular homeostasis and genome stability, it is linked to muscular and neuronal degeneration and, conversely, constitutes an attractive anti-cancer drug target. Its molecular function is ATP-driven protein unfolding, which is directed by ubiquitin and assisted by a host of cofactor proteins. This activity underlies p97's diverse ability to pull proteins out of membranes, unfold proteins for proteasomal degradation, or segregate proteins from partners for downstream activity. Recent advances in structural analysis and biochemical reconstitution have underscored this notion, resolved detailed molecular motions within the p97 hexamer, and suggested substrate threading through the central channel of the p97 hexamer as the driving mechanism. We will discuss the mechanisms and open questions in the context of the diverse cellular activities.
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29
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Ye Y, Tang WK, Zhang T, Xia D. A Mighty "Protein Extractor" of the Cell: Structure and Function of the p97/CDC48 ATPase. Front Mol Biosci 2017; 4:39. [PMID: 28660197 PMCID: PMC5468458 DOI: 10.3389/fmolb.2017.00039] [Citation(s) in RCA: 129] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Accepted: 05/22/2017] [Indexed: 12/13/2022] Open
Abstract
p97/VCP (known as Cdc48 in S. cerevisiae or TER94 in Drosophila) is one of the most abundant cytosolic ATPases. It is highly conserved from archaebacteria to eukaryotes. In conjunction with a large number of cofactors and adaptors, it couples ATP hydrolysis to segregation of polypeptides from immobile cellular structures such as protein assemblies, membranes, ribosome, and chromatin. This often results in proteasomal degradation of extracted polypeptides. Given the diversity of p97 substrates, this "segregase" activity has profound influence on cellular physiology ranging from protein homeostasis to DNA lesion sensing, and mutations in p97 have been linked to several human diseases. Here we summarize our current understanding of the structure and function of this important cellular machinery and discuss the relevant clinical implications.
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Affiliation(s)
- Yihong Ye
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of HealthBethesda, MD, United States
| | - Wai Kwan Tang
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of HealthBethesda, MD, United States
| | - Ting Zhang
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of HealthBethesda, MD, United States
| | - Di Xia
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of HealthBethesda, MD, United States
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30
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Schimmack G, Schorpp K, Kutzner K, Gehring T, Brenke JK, Hadian K, Krappmann D. YOD1/TRAF6 association balances p62-dependent IL-1 signaling to NF-κB. eLife 2017; 6. [PMID: 28244869 PMCID: PMC5340530 DOI: 10.7554/elife.22416] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2016] [Accepted: 02/26/2017] [Indexed: 12/25/2022] Open
Abstract
The ubiquitin ligase TRAF6 is a key regulator of canonical IκB kinase (IKK)/NF-κB signaling in response to interleukin-1 (IL-1) stimulation. Here, we identified the deubiquitinating enzyme YOD1 (OTUD2) as a novel interactor of TRAF6 in human cells. YOD1 binds to the C-terminal TRAF homology domain of TRAF6 that also serves as the interaction surface for the adaptor p62/Sequestosome-1, which is required for IL-1 signaling to NF-κB. We show that YOD1 competes with p62 for TRAF6 association and abolishes the sequestration of TRAF6 to cytosolic p62 aggregates by a non-catalytic mechanism. YOD1 associates with TRAF6 in unstimulated cells but is released upon IL-1β stimulation, thereby facilitating TRAF6 auto-ubiquitination as well as NEMO/IKKγ substrate ubiquitination. Further, IL-1 triggered IKK/NF-κB signaling and induction of target genes is decreased by YOD1 overexpression and augmented after YOD1 depletion. Hence, our data define that YOD1 antagonizes TRAF6/p62-dependent IL-1 signaling to NF-κB. DOI:http://dx.doi.org/10.7554/eLife.22416.001
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Affiliation(s)
- Gisela Schimmack
- Research Unit Cellular Signal Integration, Institute of Molecular Toxicology and Pharmacology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
| | - Kenji Schorpp
- Assay Development and Screening Platform, Institute of Molecular Toxicology and Pharmacology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
| | - Kerstin Kutzner
- Research Unit Cellular Signal Integration, Institute of Molecular Toxicology and Pharmacology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
| | - Torben Gehring
- Research Unit Cellular Signal Integration, Institute of Molecular Toxicology and Pharmacology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
| | - Jara Kerstin Brenke
- Assay Development and Screening Platform, Institute of Molecular Toxicology and Pharmacology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
| | - Kamyar Hadian
- Assay Development and Screening Platform, Institute of Molecular Toxicology and Pharmacology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
| | - Daniel Krappmann
- Research Unit Cellular Signal Integration, Institute of Molecular Toxicology and Pharmacology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
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31
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A bead-based cleavage method for large-scale identification of protease substrates. Sci Rep 2016; 6:22645. [PMID: 26935269 PMCID: PMC4776233 DOI: 10.1038/srep22645] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Accepted: 02/16/2016] [Indexed: 01/25/2023] Open
Abstract
Proteolysis is a major form of post translational modification which occurs when a protease cleaves peptide bonds in a target protein to modify its activity. Tracking protease substrates is indispensable for understanding its cellular functions. However, it is difficult to directly identify protease substrates because the end products of proteolysis, the cleaved protein fragments, must be identified among the pool of cellular proteins. Here we present a bead-based cleavage approach using immobilized proteome as the screening library to identify protease substrates. This method enables efficient separation of proteolyzed proteins from background protein mixture. Using caspase-3 as the model protease, we have identified 1159 high confident substrates, among which, strikingly, 43.9% of substrates undergo degradation during apoptosis. The huge number of substrates and positive support of in vivo evidence indicate that the BBC method is a powerful tool for protease substrates identification.
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32
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Elliott PR, Komander D. Regulation of Met1-linked polyubiquitin signalling by the deubiquitinase OTULIN. FEBS J 2015; 283:39-53. [PMID: 26503766 PMCID: PMC4765238 DOI: 10.1111/febs.13547] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2015] [Revised: 08/25/2015] [Accepted: 10/02/2015] [Indexed: 12/25/2022]
Abstract
Modification of proteins with Met1‐linked ‘linear’ ubiquitin chains has emerged as a key regulatory signal to control inflammatory signalling via the master regulator, the transcription factor nuclear factor κB (NF‐κB). While the assembly machinery, the linear ubiquitin chain assembly complex (LUBAC), and receptors for this ubiquitin chain type have been known for years, it was less clear which deubiquitinating enzymes (DUBs) hydrolyse Met1 linkages specifically. In 2013, two labs reported the previously unannotated protein FAM105B/OTULIN to be this missing Met1 linkage‐specific DUB. Structural studies have revealed how OTULIN achieves its remarkable specificity, employing a mechanism of ubiquitin‐assisted catalysis in which a glutamate residue on the substrate complements the active site of the enzyme. The specificity of OTULIN enables it to regulate global levels of Met1‐linked polyubiquitin in cells. This ability led to investigations of NF‐κB activation from new angles, and also revealed involvement of Met1‐polyubiquitin in Wnt signalling. Interestingly, OTULIN directly interacts with LUBAC, and this interaction is dynamic and can be regulated by OTULIN phosphorylation. This provides a new paradigm for how individual linkage types can be regulated by dedicated enzyme complexes mediating assembly and removal. Here we review what has been learned about OTULIN's mechanism, regulation and function, discuss the open questions in the field, and discuss how DUBs regulate the NF‐κB response.
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Affiliation(s)
- Paul R Elliott
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - David Komander
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
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33
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Hao Q, Jiao S, Shi Z, Li C, Meng X, Zhang Z, Wang Y, Song X, Wang W, Zhang R, Zhao Y, Wong CCL, Zhou Z. A non-canonical role of the p97 complex in RIG-I antiviral signaling. EMBO J 2015; 34:2903-20. [PMID: 26471729 DOI: 10.15252/embj.201591888] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Accepted: 09/17/2015] [Indexed: 01/13/2023] Open
Abstract
RIG-I is a well-studied sensor of viral RNA that plays a key role in innate immunity. p97 regulates a variety of cellular events such as protein quality control, membrane reassembly, DNA repair, and the cell cycle. Here, we report a new role for p97 with Npl4-Ufd1 as its cofactor in reducing antiviral innate immune responses by facilitating proteasomal degradation of RIG-I. The p97 complex is able to directly bind both non-ubiquitinated RIG-I and the E3 ligase RNF125, promoting K48-linked ubiquitination of RIG-I at residue K181. Viral infection significantly strengthens the interaction between RIG-I and the p97 complex by a conformational change of RIG-I that exposes the CARDs and through K63-linked ubiquitination of these CARDs. Disruption of the p97 complex enhances RIG-I antiviral signaling. Consistently, administration of compounds targeting p97 ATPase activity was shown to inhibit viral replication and protect mice from vesicular stomatitis virus (VSV) infection. Overall, our study uncovered a previously unrecognized role for the p97 complex in protein ubiquitination and revealed the p97 complex as a potential drug target in antiviral therapy.
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Affiliation(s)
- Qian Hao
- National Center for Protein Science Shanghai, State Key Laboratory of Cell Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Shi Jiao
- National Center for Protein Science Shanghai, State Key Laboratory of Cell Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Zhubing Shi
- National Center for Protein Science Shanghai, State Key Laboratory of Cell Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Chuanchuan Li
- National Center for Protein Science Shanghai, State Key Laboratory of Cell Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Xia Meng
- National Center for Protein Science Shanghai, State Key Laboratory of Cell Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Zhen Zhang
- National Center for Protein Science Shanghai, State Key Laboratory of Cell Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yanyan Wang
- National Center for Protein Science Shanghai, State Key Laboratory of Cell Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Xiaomin Song
- National Center for Protein Science Shanghai, State Key Laboratory of Cell Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Wenjia Wang
- National Center for Protein Science Shanghai, State Key Laboratory of Cell Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Rongguang Zhang
- National Center for Protein Science Shanghai, State Key Laboratory of Cell Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yun Zhao
- National Center for Protein Science Shanghai, State Key Laboratory of Cell Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Catherine C L Wong
- National Center for Protein Science Shanghai, State Key Laboratory of Cell Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Zhaocai Zhou
- National Center for Protein Science Shanghai, State Key Laboratory of Cell Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China School of Life Science and Technology, ShanghaiTech University, Shanghai, China
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34
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Schweitzer K, Pralow A, Naumann M. p97/VCP promotes Cullin-RING-ubiquitin-ligase/proteasome-dependent degradation of IκBα and the preceding liberation of RelA from ubiquitinated IκBα. J Cell Mol Med 2015; 20:58-70. [PMID: 26463447 PMCID: PMC4717852 DOI: 10.1111/jcmm.12702] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2015] [Accepted: 08/25/2015] [Indexed: 12/21/2022] Open
Abstract
Cullin‐RING‐ubiquitin‐ligase (CRL)‐dependent ubiquitination of the nuclear factor kappa B (NF‐κB) inhibitor IκBα and its subsequent degradation by the proteasome usually precede NF‐κB/RelA nuclear activity. Through removal of the CRL‐activating modification of their cullin subunit with the ubiquitin (Ub)‐like modifier NEDD8, the COP9 signalosome (CSN) opposes CRL Ub‐ligase activity. While RelA phosphorylation was observed to mediate NF‐κB activation independent of Ub‐proteasome‐pathway (UPP)‐dependent turnover of IκBα in some studies, a strict requirement of the p97/VCP ATPase for both, IκBα degradation and NF‐κB activation, was reported in others. In this study, we thus aimed to reconcile the mechanism for tumour necrosis factor (TNF)‐induced NF‐κB activation. We found that inducible phosphorylation of RelA is accomplished in an IKK‐complex‐dependent manner within the NF‐κB/RelA‐IκBα‐complex contemporaneous with the phosphorylation of IκBα, and that RelA phosphorylation is not sufficient to dissociate NF‐κB/RelA from IκBα. Subsequent to CRL‐dependent IκBα ubiquitination functional p97/VCP is essentially required for efficient liberation of (phosphorylated) RelA from IκBα, preceding p97/VCP‐promoted timely and efficient degradation of IκBα as well as simultaneous NF‐κB/RelA nuclear translocation. Collectively, our data add new facets to the knowledge about maintenance of IκBα and RelA expression, likely depending on p97/VCP‐supported scheduled basal NF‐κB activity, and the mechanism of TNF‐induced NF‐κB activation.
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Affiliation(s)
- Katrin Schweitzer
- Institute of Experimental Internal Medicine, Medical Faculty, Otto von Guericke University, Magdeburg, Germany
| | - Alexander Pralow
- Institute of Experimental Internal Medicine, Medical Faculty, Otto von Guericke University, Magdeburg, Germany
| | - Michael Naumann
- Institute of Experimental Internal Medicine, Medical Faculty, Otto von Guericke University, Magdeburg, Germany
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35
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Greenblatt MB, Park KH, Oh H, Kim JM, Shin DY, Lee JM, Lee JW, Singh A, Lee KY, Hu D, Xiao C, Charles JF, Penninger JM, Lotinun S, Baron R, Ghosh S, Shim JH. CHMP5 controls bone turnover rates by dampening NF-κB activity in osteoclasts. ACTA ACUST UNITED AC 2015. [PMID: 26195726 PMCID: PMC4516796 DOI: 10.1084/jem.20150407] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
Physiological bone remodeling requires that bone formation by osteoblasts be tightly coupled to bone resorption by osteoclasts. However, relatively little is understood about how this coupling is regulated. Here, we demonstrate that modulation of NF-κB signaling in osteoclasts via a novel activity of charged multivesicular body protein 5 (CHMP5) is a key determinant of systemic rates of bone turnover. A conditional deletion of CHMP5 in osteoclasts leads to increased bone resorption by osteoclasts coupled with exuberant bone formation by osteoblasts, resembling an early onset, polyostotic form of human Paget's disease of bone (PDB). These phenotypes are reversed by haploinsufficiency for Rank, as well as by antiresorptive treatments, including alendronate, zolendronate, and OPG-Fc. Accordingly, CHMP5-deficient osteoclasts display increased RANKL-induced NF-κB activation and osteoclast differentiation. Biochemical analysis demonstrated that CHMP5 cooperates with the PDB genetic risk factor valosin-containing protein (VCP/p97) to stabilize the inhibitor of NF-κBα (IκBα), down-regulating ubiquitination of IκBα via the deubiquitinating enzyme USP15. Thus, CHMP5 tunes NF-κB signaling downstream of RANK in osteoclasts to dampen osteoclast differentiation, osteoblast coupling and bone turnover rates, and disruption of CHMP5 activity results in a PDB-like skeletal disorder.
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Affiliation(s)
- Matthew B Greenblatt
- Department of Pathology, Brigham and Women's Hospital, Boston, MA 02115 Department of Medicine and Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, NY 10065
| | - Kwang Hwan Park
- Department of Medicine and Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, NY 10065 Department of Microbiology, Brain Korea 21 PLUS Project for Medical Sciences and Department of Orthopaedic Surgery, Yonsei University College of Medicine, Seoul 120-752, Republic of Korea Department of Microbiology, Brain Korea 21 PLUS Project for Medical Sciences and Department of Orthopaedic Surgery, Yonsei University College of Medicine, Seoul 120-752, Republic of Korea
| | - Hwanhee Oh
- Department of Medicine and Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, NY 10065
| | - Jung-Min Kim
- Department of Medicine and Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, NY 10065
| | - Dong Yeon Shin
- Department of Medicine and Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, NY 10065
| | - Jae Myun Lee
- Department of Microbiology, Brain Korea 21 PLUS Project for Medical Sciences and Department of Orthopaedic Surgery, Yonsei University College of Medicine, Seoul 120-752, Republic of Korea
| | - Jin Woo Lee
- Department of Microbiology, Brain Korea 21 PLUS Project for Medical Sciences and Department of Orthopaedic Surgery, Yonsei University College of Medicine, Seoul 120-752, Republic of Korea
| | - Anju Singh
- National Center for Advancing Translational Sciences/National Institutes of Health, Rockville, MD 20850
| | - Ki-young Lee
- Department of Molecular Cell Biology and Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon 440-746, Republic of Korea
| | - Dorothy Hu
- Endocrine Unit, Massachusetts General Hospital, Boston, MA 02114
| | - Changchun Xiao
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037
| | - Julia F Charles
- Department of Medicine, Division of Rheumatology, Allergy, and Immunology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115
| | - Josef M Penninger
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, 1030 Vienna, Austria
| | - Sutada Lotinun
- Department of Oral Medicine, Infection and Immunity, Harvard School of Dental Medicine, Boston, MA 02115 Department of Physiology and STAR on Craniofacial and Skeletal Disorders, Faculty of Dentistry, Chulalongkorn University, Bangkok 10330, Thailand
| | - Roland Baron
- Department of Oral Medicine, Infection and Immunity, Harvard School of Dental Medicine, Boston, MA 02115
| | - Sankar Ghosh
- Department of Microbiology and Immunology, Columbia University, College of Physicians and Surgeons, New York, NY 10032
| | - Jae-Hyuck Shim
- Department of Medicine and Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, NY 10065
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36
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Zhang Z, Wang Y, Li C, Shi Z, Hao Q, Wang W, Song X, Zhao Y, Jiao S, Zhou Z. The Transitional Endoplasmic Reticulum ATPase p97 Regulates the Alternative Nuclear Factor NF-κB Signaling via Partial Degradation of the NF-κB Subunit p100. J Biol Chem 2015; 290:19558-68. [PMID: 26112410 DOI: 10.1074/jbc.m114.630061] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Indexed: 12/12/2022] Open
Abstract
Partial degradation of the p100 subunit to generate p52 subunit is a hallmark of the alternative NF-κB pathway, which has been implicated in cancer. Here, we uncovered a role of the p97-Npl4-Ufd1 complex in mediating p100-to-p52 processing and therefore positively regulating the alternative NF-κB pathway. We observed an elevation of p97 mRNA levels in lymphoma patients, which positively correlates with NFKB2 expression, a downstream target gene of the alternative NF-κB pathway. Moreover, NFKB2 mRNA levels were aberrantly down-regulated in patients with inclusion body myopathy associated with Paget's disease of the bone and frontotemporal dementia (IBMPFD), a disease caused by mutation of p97. Inactivation of p97 or depletion of the p97-Npl4-Ufd1 complex inhibits the processing of p100 into p52, decreasing transcription of the downstream target genes. Further analyses reveal that the p97-Npl4-Ufd1 complex interacts with F-box and WD repeats protein SCF(βTrCP) complex to regulate the partial degradation of p100, a process involving K48- and K11-linked ubiquitination. In line with this, in LPS-induced lung damage mice model, generation of p52 is significantly decreased in p97-KD mice compared with mock mice. Finally, abrogation of p97 ATPase activity by its specific inhibitor DBeQ, efficiently decreased proliferation of lymphoma cells. Collectively, our study revealed a regulatory role of the p97-Npl4-Ufd1 complex in regulating p100 partial degradation, highlighting the potential of p97 as a drug target for cancers with aberrant activation of the alternative NF-κB pathway.
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Affiliation(s)
- Zhao Zhang
- From the National Center for Protein Science Shanghai, State Key Laboratory of Cell Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yanyan Wang
- From the National Center for Protein Science Shanghai, State Key Laboratory of Cell Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Chuanchuan Li
- From the National Center for Protein Science Shanghai, State Key Laboratory of Cell Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Zhubing Shi
- From the National Center for Protein Science Shanghai, State Key Laboratory of Cell Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China, and
| | - Qian Hao
- From the National Center for Protein Science Shanghai, State Key Laboratory of Cell Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Wenjia Wang
- From the National Center for Protein Science Shanghai, State Key Laboratory of Cell Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Xiaomin Song
- From the National Center for Protein Science Shanghai, State Key Laboratory of Cell Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yun Zhao
- From the National Center for Protein Science Shanghai, State Key Laboratory of Cell Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Shi Jiao
- From the National Center for Protein Science Shanghai, State Key Laboratory of Cell Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China,
| | - Zhaocai Zhou
- From the National Center for Protein Science Shanghai, State Key Laboratory of Cell Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China, School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
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37
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Yılmaz ZB, Kofahl B, Beaudette P, Baum K, Ipenberg I, Weih F, Wolf J, Dittmar G, Scheidereit C. Quantitative dissection and modeling of the NF-κB p100-p105 module reveals interdependent precursor proteolysis. Cell Rep 2014; 9:1756-1769. [PMID: 25482563 DOI: 10.1016/j.celrep.2014.11.014] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Revised: 10/20/2014] [Accepted: 11/08/2014] [Indexed: 12/26/2022] Open
Abstract
The mechanisms that govern proteolytic maturation or complete destruction of the precursor proteins p100 and p105 are fundamental to homeostasis and activation of NF-κB; however, they remain poorly understood. Using mass-spectrometry-based quantitative analysis of noncanonical LTβR-induced signaling, we demonstrate that stimulation induces simultaneous processing of both p100 and p105. The precursors not only form hetero-oligomers but also interact with the ATPase VCP/p97, and their induced proteolysis strictly depends on the signal response domain (SRD) of p100, suggesting that the SRD-targeting proteolytic machinery acts in cis and in trans. Separation of cellular pools by isotope labeling revealed synchronous dynamics of p105 and p100 proteolysis. The generation of p50 and p52 from their precursors depends on functional VCP/p97. We have developed quantitative mathematical models that describe the dynamics of the system and predict that p100-p105 complexes are signal responsive.
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Affiliation(s)
- Zekiye Buket Yılmaz
- Signal Transduction Laboratory, Max Delbrück Center for Molecular Medicine, Robert-Rössle-Strasse 10, 13125 Berlin, Germany.
| | - Bente Kofahl
- Mathematical Modeling Group, Max Delbrück Center for Molecular Medicine, Robert-Rössle-Strasse 10, 13125 Berlin, Germany
| | - Patrick Beaudette
- Signal Transduction Laboratory, Max Delbrück Center for Molecular Medicine, Robert-Rössle-Strasse 10, 13125 Berlin, Germany; Mass Spectrometry Group, Max Delbrück Center for Molecular Medicine, Robert-Rössle-Strasse 10, 13125 Berlin, Germany
| | - Katharina Baum
- Mathematical Modeling Group, Max Delbrück Center for Molecular Medicine, Robert-Rössle-Strasse 10, 13125 Berlin, Germany
| | - Inbal Ipenberg
- Signal Transduction Laboratory, Max Delbrück Center for Molecular Medicine, Robert-Rössle-Strasse 10, 13125 Berlin, Germany
| | - Falk Weih
- Leibniz-Institute for Age Research-Fritz-Lipmann-Institute, Beutenbergstrasse 11, 07745 Jena, Germany
| | - Jana Wolf
- Mathematical Modeling Group, Max Delbrück Center for Molecular Medicine, Robert-Rössle-Strasse 10, 13125 Berlin, Germany
| | - Gunnar Dittmar
- Mass Spectrometry Group, Max Delbrück Center for Molecular Medicine, Robert-Rössle-Strasse 10, 13125 Berlin, Germany
| | - Claus Scheidereit
- Signal Transduction Laboratory, Max Delbrück Center for Molecular Medicine, Robert-Rössle-Strasse 10, 13125 Berlin, Germany.
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38
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Abstract
Genomic alterations may make cancer cells more dependent than normal cells on mechanisms of proteostasis, including protein folding and degradation. This proposition is the basis for the clinical use of proteasome inhibitors to treat multiple myeloma and mantle cell lymphoma. However, proteasome inhibitors have not proved effective in treating other cancers, and this has called into question the general applicability of this approach. Here, I consider possible explanations for this apparently limited applicability, and discuss whether inhibiting other broadly acting components of the ubiquitin-proteasome system - including ubiquitin-activating enzyme and the AAA-ATPase p97/VCP - might be more generally effective in cancer therapy.
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Affiliation(s)
- Raymond J Deshaies
- Division of Biology and Biological Engineering and Howard Hughes Medical Institute, California Institute of Technology, Pasadena 91107, CA, USA.
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39
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Meyer H, Weihl CC. The VCP/p97 system at a glance: connecting cellular function to disease pathogenesis. J Cell Sci 2014; 127:3877-83. [PMID: 25146396 DOI: 10.1242/jcs.093831] [Citation(s) in RCA: 285] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The ATPase valosin-containing protein (VCP)/p97 has emerged as a central and important element of the ubiquitin system. Together with a network of cofactors, it regulates an ever-expanding range of processes that stretch into almost every aspect of cellular physiology. Its main role in proteostasis and key functions in signaling pathways are of relevance to degenerative diseases and genomic stability. In this Cell Science at a Glance and the accompanying poster, we give a brief overview of this complex system. In addition, we discuss the pathogenic basis for VCP/p97-associated diseases and then highlight in more detail new exciting links to the translational stress response and RNA biology that further underscore the significance of the VCP/p97 system.
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Affiliation(s)
- Hemmo Meyer
- Centre for Medical Biotechnology, Faculty of Biology, University of Duisburg-Essen, 45117 Essen, Germany
| | - Conrad C Weihl
- Department of Neurology and Hope Center for Neurological Disorders, Washington University School of Medicine, St Louis, MO 63110, USA
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40
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Schaeffer V, Akutsu M, Olma MH, Gomes LC, Kawasaki M, Dikic I. Binding of OTULIN to the PUB domain of HOIP controls NF-κB signaling. Mol Cell 2014; 54:349-61. [PMID: 24726327 DOI: 10.1016/j.molcel.2014.03.016] [Citation(s) in RCA: 147] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2013] [Revised: 01/24/2014] [Accepted: 02/28/2014] [Indexed: 10/25/2022]
Abstract
Linear ubiquitin chains are implicated in the regulation of the NF-κB pathway, immunity, and inflammation. They are synthesized by the LUBAC complex containing the catalytic subunit HOIL-1-interacting protein (HOIP) and are disassembled by the linear ubiquitin-specific deubiquitinase OTULIN. Little is known about the regulation of these opposing activities. Here we demonstrate that HOIP and OTULIN interact and act as a bimolecular editing pair for linear ubiquitin signals in vivo. The HOIP PUB domain binds to the PUB interacting motif (PIM) of OTULIN and the chaperone VCP/p97. Structural studies revealed the basis of high-affinity interaction with the OTULIN PIM. The conserved Tyr56 of OTULIN makes critical contacts with the HOIP PUB domain, and its phosphorylation negatively regulates this interaction. Functionally, HOIP binding to OTULIN is required for the recruitment of OTULIN to the TNF receptor complex and to counteract HOIP-dependent activation of the NF-κB pathway.
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Affiliation(s)
- Veronique Schaeffer
- Institute of Biochemistry II, Goethe University Faculty of Medicine, 60590 Frankfurt am Main, Germany
| | - Masato Akutsu
- Institute of Biochemistry II, Goethe University Faculty of Medicine, 60590 Frankfurt am Main, Germany; Buchmann Institute for Molecular Life Sciences, Goethe University, 60438 Frankfurt am Main, Germany
| | - Michael H Olma
- Institute of Biochemistry II, Goethe University Faculty of Medicine, 60590 Frankfurt am Main, Germany
| | - Ligia C Gomes
- Buchmann Institute for Molecular Life Sciences, Goethe University, 60438 Frankfurt am Main, Germany
| | - Masato Kawasaki
- Structural Biology Research Center, Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Tsukuba, Ibaraki, 305-0801, Japan
| | - Ivan Dikic
- Institute of Biochemistry II, Goethe University Faculty of Medicine, 60590 Frankfurt am Main, Germany; Buchmann Institute for Molecular Life Sciences, Goethe University, 60438 Frankfurt am Main, Germany.
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