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Begalli F, Bennett J, Capece D, Verzella D, D'Andrea D, Tornatore L, Franzoso G. Unlocking the NF-κB Conundrum: Embracing Complexity to Achieve Specificity. Biomedicines 2017; 5:E50. [PMID: 28829404 PMCID: PMC5618308 DOI: 10.3390/biomedicines5030050] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Revised: 08/04/2017] [Accepted: 08/10/2017] [Indexed: 12/12/2022] Open
Abstract
Transcription factors of the nuclear factor κB (NF-κB) family are central coordinating regulators of the host defence responses to stress, injury and infection. Aberrant NF-κB activation also contributes to the pathogenesis of some of the most common current threats to global human health, including chronic inflammatory diseases, autoimmune disorders, diabetes, vascular diseases and the majority of cancers. Accordingly, the NF-κB pathway is widely considered an attractive therapeutic target in a broad range of malignant and non-malignant diseases. Yet, despite the aggressive efforts by the pharmaceutical industry to develop a specific NF-κB inhibitor, none has been clinically approved, due to the dose-limiting toxicities associated with the global suppression of NF-κB. In this review, we summarise the main strategies historically adopted to therapeutically target the NF-κB pathway with an emphasis on oncology, and some of the emerging strategies and newer agents being developed to pharmacologically inhibit this pathway.
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Affiliation(s)
- Federica Begalli
- Centre for Cell Signalling and Inflammation, Department of Medicine, Imperial College London, London W12 0NN, UK.
| | - Jason Bennett
- Centre for Cell Signalling and Inflammation, Department of Medicine, Imperial College London, London W12 0NN, UK.
| | - Daria Capece
- Centre for Cell Signalling and Inflammation, Department of Medicine, Imperial College London, London W12 0NN, UK.
| | - Daniela Verzella
- Centre for Cell Signalling and Inflammation, Department of Medicine, Imperial College London, London W12 0NN, UK.
| | - Daniel D'Andrea
- Centre for Cell Signalling and Inflammation, Department of Medicine, Imperial College London, London W12 0NN, UK.
| | - Laura Tornatore
- Centre for Cell Signalling and Inflammation, Department of Medicine, Imperial College London, London W12 0NN, UK.
| | - Guido Franzoso
- Centre for Cell Signalling and Inflammation, Department of Medicine, Imperial College London, London W12 0NN, UK.
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Molluscum Contagiosum Virus MC159 Abrogates cIAP1-NEMO Interactions and Inhibits NEMO Polyubiquitination. J Virol 2017; 91:JVI.00276-17. [PMID: 28515292 DOI: 10.1128/jvi.00276-17] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Accepted: 05/05/2017] [Indexed: 12/20/2022] Open
Abstract
Molluscum contagiosum virus (MCV) is a dermatotropic poxvirus that causes benign skin lesions. MCV lesions persist because of virally encoded immune evasion molecules that inhibit antiviral responses. The MCV MC159 protein suppresses NF-κB activation, a powerful antiviral response, via interactions with the NF-κB essential modulator (NEMO) subunit of the IκB kinase (IKK) complex. Binding of MC159 to NEMO does not disrupt the IKK complex, implying that MC159 prevents IKK activation via an as-yet-unidentified strategy. Here, we demonstrated that MC159 inhibited NEMO polyubiquitination, a posttranslational modification required for IKK and downstream NF-κB activation. Because MCV cannot be propagated in cell culture, MC159 was expressed independent of infection or during a surrogate vaccinia virus infection to identify how MC159 prevented polyubiquitination. Cellular inhibitor of apoptosis protein 1 (cIAP1) is a cellular E3 ligase that ubiquitinates NEMO. Mutational analyses revealed that MC159 and cIAP1 each bind to the same NEMO region, suggesting that MC159 may competitively inhibit cIAP1-NEMO interactions. Indeed, MC159 prevented cIAP1-NEMO interactions. MC159 also diminished cIAP1-mediated NEMO polyubiquitination and cIAP1-induced NF-κB activation. These data suggest that MC159 competitively binds to NEMO to prevent cIAP1-induced NEMO polyubiquitination. To our knowledge, this is the first report of a viral protein disrupting NEMO-cIAP1 interactions to strategically suppress IKK activation. All viruses must antagonize antiviral signaling events for survival. We hypothesize that MC159 inhibits NEMO polyubiquitination as a clever strategy to manipulate the host cell environment to the benefit of the virus.IMPORTANCE Molluscum contagiosum virus (MCV) is a human-specific poxvirus that causes persistent skin neoplasms. The persistence of MCV has been attributed to viral downregulation of host cell immune responses such as NF-κB activation. We show here that the MCV MC159 protein interacts with the NEMO subunit of the IKK complex to prevent NEMO interactions with the cIAP1 E3 ubiquitin ligase. This interaction correlates with a dampening of cIAP1 to polyubiquitinate NEMO and to activate NF-κB. This inhibition of cIAP1-NEMO interactions is a new viral strategy to minimize IKK activation and to control NEMO polyubiquitination. This research provides new insights into mechanisms that persistent viruses may use to cause long-term infection of host cells.
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Wu F, Zhu J, Li H, Zhu L. Structural analysis of recombinant human ubiquitin-conjugating enzyme UbcH5c. Acta Pharm Sin B 2017; 7:390-394. [PMID: 28540177 PMCID: PMC5430876 DOI: 10.1016/j.apsb.2016.12.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2016] [Revised: 12/04/2016] [Accepted: 12/19/2016] [Indexed: 11/30/2022] Open
Abstract
UbcH5c belongs to the ubiquitin-conjugating enzyme family and plays an important role in catalyzing ubiquitination during TNF-α--triggered NF-κB activation. Therefore, UbcH5c is a potent therapeutic target for the treatment of inflammatory and autoimmune diseases induced by aberrant activation of NF-κB. In this study, we established a stable expression system for recombinant UbcH5c and solved the crystal structure of UbcH5c belonging to space group P22121 with one molecule in the asymmetric unit. This study provides the basis for further study of UbcH5c including the design of UbcH5c inhibitors.
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Affiliation(s)
| | | | - Honglin Li
- Corresponding authors. Tel.: +86 21 64253379.
| | - Lili Zhu
- Corresponding authors. Tel.: +86 21 64253379.
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Markovinovic A, Cimbro R, Ljutic T, Kriz J, Rogelj B, Munitic I. Optineurin in amyotrophic lateral sclerosis: Multifunctional adaptor protein at the crossroads of different neuroprotective mechanisms. Prog Neurobiol 2017; 154:1-20. [PMID: 28456633 DOI: 10.1016/j.pneurobio.2017.04.005] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2017] [Revised: 04/09/2017] [Accepted: 04/16/2017] [Indexed: 12/12/2022]
Abstract
When optineurin mutations showed up on the amyotrophic lateral sclerosis (ALS) landscape in 2010, they differed from most other ALS-causing genes. They seemed to act by loss- rather than gain-of-function, and it was unclear how a polyubiquitin-binding adaptor protein, which was proposed to regulate a variety of cellular functions including cell signaling and vesicle trafficking, could mediate neuroprotection. This review discusses the considerable progress that has been made since then. A large number of mutations in optineurin and optineurin-interacting proteins TANK-binding kinase (TBK1) and p62/SQSTM-1 have been found in the ALS patients, suggesting a common neuroprotective pathway. Moreover, functional studies of the ALS-causing optineurin mutations and the recently established optineurin ubiquitin-binding deficient and knockout mouse models helped identify three major mechanisms likely to mediate neuroprotection: regulation of autophagy, mitigation of (chronic) inflammatory signaling, and blockade of necroptosis. These three processes crosstalk, and require multiple levels of control, many of which can be mediated by optineurin. Based on the role of optineurin in multiple processes and the unexpected finding that targeted optineurin deletion in microglia and oligodendrocytes ultimately leads to the same phenotype of axonal degeneration despite different initial defects, we propose that the failure of the weakest link in the optineurin neuroprotective network is sufficient to disturb homeostasis and set-off the domino effect that could ultimately lead to neurodegeneration.
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Affiliation(s)
- Andrea Markovinovic
- Laboratory of Molecular Immunology, Department of Biotechnology, University of Rijeka, 51000 Rijeka, Croatia
| | - Raffaello Cimbro
- Division of Rheumatology, Johns Hopkins School of Medicine, Baltimore, MD 21224, USA
| | - Tereza Ljutic
- Laboratory of Molecular Immunology, Department of Biotechnology, University of Rijeka, 51000 Rijeka, Croatia
| | - Jasna Kriz
- Department of Psychiatry and Neuroscience, Faculty of Medicine, Research Centre of the Mental Health Institute of Quebec, Laval University, Quebec, Quebec G1J 2G3, Canada
| | - Boris Rogelj
- Department of Biotechnology, Jožef Stefan Institute, Faculty of Chemistry and Chemical Technology, University of Ljubljana, Biomedical Research Institute BRIS, SI-1000 Ljubljana, Slovenia
| | - Ivana Munitic
- Laboratory of Molecular Immunology, Department of Biotechnology, University of Rijeka, 51000 Rijeka, Croatia.
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Rittinger K, Ikeda F. Linear ubiquitin chains: enzymes, mechanisms and biology. Open Biol 2017; 7:170026. [PMID: 28446710 PMCID: PMC5413910 DOI: 10.1098/rsob.170026] [Citation(s) in RCA: 79] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Accepted: 03/21/2017] [Indexed: 12/14/2022] Open
Abstract
Ubiquitination is a versatile post-translational modification that regulates a multitude of cellular processes. Its versatility is based on the ability of ubiquitin to form multiple types of polyubiquitin chains, which are recognized by specific ubiquitin receptors to induce the required cellular response. Linear ubiquitin chains are linked through Met 1 and have been established as important players of inflammatory signalling and apoptotic cell death. These chains are generated by a ubiquitin E3 ligase complex called the linear ubiquitin chain assembly complex (LUBAC) that is thus far the only E3 ligase capable of forming linear ubiquitin chains. The complex consists of three subunits, HOIP, HOIL-1L and SHARPIN, each of which have specific roles in the observed biological functions of LUBAC. Furthermore, LUBAC has been found to be associated with OTULIN and CYLD, deubiquitinases that disassemble linear chains and counterbalance the E3 ligase activity of LUBAC. Gene mutations in HOIP, HOIL-1L and OTULIN are found in human patients who suffer from autoimmune diseases, and HOIL-1L mutations are also found in myopathy patients. In this paper, we discuss the mechanisms of linear ubiquitin chain generation and disassembly by their respective enzymes and review our current understanding of their biological functions and association with human diseases.
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Affiliation(s)
- Katrin Rittinger
- Molecular Structure of Cell Signalling Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Fumiyo Ikeda
- Institute of Molecular Biotechnology (IMBA), Dr Bohr-gasse 3, 1030 Vienna, Austria
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56
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Goru SK, Kadakol A, Gaikwad AB. Hidden targets of ubiquitin proteasome system: To prevent diabetic nephropathy. Pharmacol Res 2017; 120:170-179. [PMID: 28363724 DOI: 10.1016/j.phrs.2017.03.024] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/18/2017] [Accepted: 03/21/2017] [Indexed: 12/21/2022]
Abstract
Diabetic nephropathy (DN) is the major cause of end stage renal failure. Although, several therapeutic targets have emerged to prevent the progression of DN, the number of people with DN still continues to rise worldwide, suggesting an urgent need of novel targets to prevent DN completely. Currently, the role of ubiquitin proteasome system (UPS) has been highlighted in the pathogenesis and progression of various diseases like obesity, insulin resistance, atherosclerosis, cancers, neurodegerative disorders and including secondary complications of diabetes. UPS mainly involves in protein homeostatis through ubiquitination (post translational modification) and proteasomal degradation of various proteins. Ubiquitination, not only involves in proteasomal degradation, but also directs the substrate proteins to participate in multitude of cell signalling pathways. However, very little is known about ubiquitination and UPS in the progression of DN. This review mainly focuses on UPS and its components including E2 conjugating enzymes, E3 ligases and deubiquitinases (DUBs) in the development of DN and thus may help us to find novel therapeutic targets with in UPS to prevent DN completely in future.
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Affiliation(s)
- Santosh Kumar Goru
- Laboratory of Molecular Pharmacology, Department of Pharmacy, Birla Institute of Technology and Science Pilani, Pilani Campus, Rajasthan 333031, India
| | - Almesh Kadakol
- Laboratory of Molecular Pharmacology, Department of Pharmacy, Birla Institute of Technology and Science Pilani, Pilani Campus, Rajasthan 333031, India
| | - Anil Bhanudas Gaikwad
- Laboratory of Molecular Pharmacology, Department of Pharmacy, Birla Institute of Technology and Science Pilani, Pilani Campus, Rajasthan 333031, India.
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Filipčík P, Curry JR, Mace PD. When Worlds Collide-Mechanisms at the Interface between Phosphorylation and Ubiquitination. J Mol Biol 2017; 429:1097-1113. [PMID: 28235544 DOI: 10.1016/j.jmb.2017.02.011] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Revised: 02/13/2017] [Accepted: 02/14/2017] [Indexed: 02/08/2023]
Abstract
Phosphorylation and ubiquitination are pervasive post-translational modifications that impact all processes inside eukaryotic cells. The role of each modification has been studied for decades, and functional interplay between the two has long been demonstrated and even more widely postulated. However, our understanding of the molecular features that allow phosphorylation to control protein ubiquitination and ubiquitin to control phosphorylation has only recently begun to build. Here, we review examples of regulation between ubiquitination and phosphorylation, aiming to describe mechanisms at the molecular level. In general, these examples illustrate phosphorylation as a versatile switch throughout ubiquitination pathways, and ubiquitination primarily impacting kinase signalling in a more emphatic manner through scaffolding or degradation. Examples of regulation between these two processes are likely to grow even further as advances in molecular biology, proteomics, and computation allow a system-level understanding of signalling. Many new cases could involve similar principles to those described here, but the extensive co-regulation of these two systems leaves no doubt that they still have many surprises in store.
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Affiliation(s)
- Pavel Filipčík
- Biochemistry Department, School of Biomedical Sciences, University of Otago, P.O. Box 56, 710 Cumberland Street, Dunedin 9054, New Zealand
| | - Jack R Curry
- Biochemistry Department, School of Biomedical Sciences, University of Otago, P.O. Box 56, 710 Cumberland Street, Dunedin 9054, New Zealand
| | - Peter D Mace
- Biochemistry Department, School of Biomedical Sciences, University of Otago, P.O. Box 56, 710 Cumberland Street, Dunedin 9054, New Zealand.
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58
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Investigations of human myosin VI targeting using optogenetically controlled cargo loading. Proc Natl Acad Sci U S A 2017; 114:E1607-E1616. [PMID: 28193860 DOI: 10.1073/pnas.1614716114] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Myosins play countless critical roles in the cell, each requiring it to be activated at a specific location and time. To control myosin VI with this specificity, we created an optogenetic tool for activating myosin VI by fusing the light-sensitive Avena sativa phototropin1 LOV2 domain to a peptide from Dab2 (LOVDab), a myosin VI cargo protein. Our approach harnesses the native targeting and activation mechanism of myosin VI, allowing direct inferences on myosin VI function. LOVDab robustly recruits human full-length myosin VI to various organelles in vivo and hinders peroxisome motion in a light-controllable manner. LOVDab also activates myosin VI in an in vitro gliding filament assay. Our data suggest that protein and lipid cargoes cooperate to activate myosin VI, allowing myosin VI to integrate Ca2+, lipid, and protein cargo signals in the cell to deploy in a site-specific manner.
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59
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Chen S, Yang X, Cheng W, Ma Y, Shang Y, Cao L, Chen S, Chen Y, Wang M, Guo D. Immune regulator ABIN1 suppresses HIV-1 transcription by negatively regulating the ubiquitination of Tat. Retrovirology 2017; 14:12. [PMID: 28193275 PMCID: PMC5304394 DOI: 10.1186/s12977-017-0338-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Accepted: 01/31/2017] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND A20-binding inhibitor of NF-κB activation (ABIN1), an important immune regulator, was previously shown to be involved in HIV-1 replication. However, the reported studies done with overexpressed ABIN1 provided controversial results. RESULTS Here we identified ABIN1 as a suppressor of HIV-1 transcription since transient knockdown of ABIN1 led to increased HIV-1 replication both in transformed Jurkat T cell line and in primary human CD4+ T lymphocytes. Depletion of ABIN1 specifically enhanced the HIV-1 transcription from the integrated genome during viral life cycle, but not the earlier steps such as reverse transcription or integration. Immunoprecipitation assays revealed that ABIN1 specifically inhibits the proto-oncogene HDM2 catalyzed K63-linked polyubiquitination of Tat at Lys71, which is critical for the transactivation activity of Tat. The ubiquitin chain binding activity of ABIN1 carried by UBAN domain turned out to be essential for the inhibitory role of ABIN1. The results of immunofluorescence localization experiments suggested that ABIN1 may obstruct Tat ubiquitination by redistributing some of HDM2 from the nucleus to the cytoplasm. CONCLUSIONS Our findings have revealed ABIN1 as intrinsic suppressor of HIV-1 mRNA transcription by regulating the ubiquitination of Tat.
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Affiliation(s)
- Shiyou Chen
- State Key Laboratory of Virology and Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, 430072, People's Republic of China
| | - Xiaodan Yang
- State Key Laboratory of Virology and Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, 430072, People's Republic of China
| | - Weijia Cheng
- Clinical Laboratory, General Hospital of the Yangtze River Shipping, Wuhan, 430010, People's Republic of China
| | - Yuhong Ma
- School of Basic Medical Sciences, Wuhan University, Wuhan, 430071, People's Republic of China
| | - Yafang Shang
- State Key Laboratory of Virology and Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, 430072, People's Republic of China
| | - Liu Cao
- State Key Laboratory of Virology and Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, 430072, People's Republic of China
| | - Shuliang Chen
- School of Basic Medical Sciences, Wuhan University, Wuhan, 430071, People's Republic of China
| | - Yu Chen
- State Key Laboratory of Virology and Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, 430072, People's Republic of China
| | - Min Wang
- School of Basic Medical Sciences, Wuhan University, Wuhan, 430071, People's Republic of China.
| | - Deyin Guo
- State Key Laboratory of Virology and Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, 430072, People's Republic of China. .,School of Basic Medical Sciences, Wuhan University, Wuhan, 430071, People's Republic of China. .,School of Basic Medicine (Shenzhen), Sun Yat-sen University, Guangzhou, 510080, People's Republic of China.
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60
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Montecalvo A, Watkins SC, Orange J, Kane LP. Inducible turnover of optineurin regulates T cell activation. Mol Immunol 2017; 85:9-17. [PMID: 28192730 DOI: 10.1016/j.molimm.2017.01.027] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Revised: 01/13/2017] [Accepted: 01/28/2017] [Indexed: 12/28/2022]
Abstract
Optineurin (Optn) is an adaptor protein with homology to NF-κB essential modulator (NEMO), the regulatory subunit of the IκB kinase (IKK) complex. Dysregulation of Optn has been linked to neurodegenerative, autoimmune and bone diseases. Optn shares a high degree of homology with NEMO, but is not part of the same high-molecular weight complex containing IKKα and IKKβ. Despite its homology with NEMO and the fact that it has been the subject of extensive study in several cell types, there are no published studies addressing the role of Optn during T cell activation. Here we demonstrate that ectopic expression of Optn down-regulates TCR-induced NF-κB activation and TNF-α production, in a manner dependent on ubiquitin-binding. Conversely, knock-down of Optn enhances NF-κB activation and the production of TNF-α. Consistent with a negative regulatory role for this protein, we observed transient loss of Optn after TCR stimulation in both cell lines and in primary murine T cells. The acute loss of Optn appears to be due to both protein degradation and exocytosis, the latter via activation-induced exosomes. This study therefore provides novel information regarding the role of Optn during TCR activation, suggesting the possible importance of Optn during inflammation and/or autoimmune diseases.
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Affiliation(s)
- Angela Montecalvo
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, United States
| | - Simon C Watkins
- Department of Cell Biology and Physiology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, United States
| | - Jordan Orange
- Texas Children's Hospital, Houston, TX 77030, United States
| | - Lawrence P Kane
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, United States.
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Shibata Y, Tokunaga F, Goto E, Komatsu G, Gohda J, Saeki Y, Tanaka K, Takahashi H, Sawasaki T, Inoue S, Oshiumi H, Seya T, Nakano H, Tanaka Y, Iwai K, Inoue JI. HTLV-1 Tax Induces Formation of the Active Macromolecular IKK Complex by Generating Lys63- and Met1-Linked Hybrid Polyubiquitin Chains. PLoS Pathog 2017; 13:e1006162. [PMID: 28103322 PMCID: PMC5283754 DOI: 10.1371/journal.ppat.1006162] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Revised: 01/31/2017] [Accepted: 01/01/2017] [Indexed: 11/18/2022] Open
Abstract
The Tax protein of human T-cell leukemia virus type 1 (HTLV-1) is crucial for the development of adult T-cell leukemia (ATL), a highly malignant CD4+ T cell neoplasm. Among the multiple aberrant Tax-induced effects on cellular processes, persistent activation of transcription factor NF-κB, which is activated only transiently upon physiological stimulation, is essential for leukemogenesis. We and others have shown that Tax induces activation of the IκB kinase (IKK) complex, which is a critical step in NF-κB activation, by generating Lys63-linked polyubiquitin chains. However, the molecular mechanism underlying Tax-induced IKK activation is controversial and not fully understood. Here, we demonstrate that Tax recruits linear (Met1-linked) ubiquitin chain assembly complex (LUBAC) to the IKK complex and that Tax fails to induce IKK activation in cells that lack LUBAC activity. Mass spectrometric analyses revealed that both Lys63-linked and Met1-linked polyubiquitin chains are associated with the IKK complex. Furthermore, treatment of the IKK-associated polyubiquitin chains with Met1-linked-chain-specific deubiquitinase (OTULIN) resulted in the reduction of high molecular weight polyubiquitin chains and the generation of short Lys63-linked ubiquitin chains, indicating that Tax can induce the generation of Lys63- and Met1-linked hybrid polyubiquitin chains. We also demonstrate that Tax induces formation of the active macromolecular IKK complex and that the blocking of Tax-induced polyubiquitin chain synthesis inhibited formation of the macromolecular complex. Taken together, these results lead us to propose a novel model in which the hybrid-chain-dependent oligomerization of the IKK complex triggered by Tax leads to trans-autophosphorylation-mediated IKK activation.
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Affiliation(s)
- Yuri Shibata
- Division of Cellular and Molecular Biology, Department of Cancer Biology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Fuminori Tokunaga
- Department of Pathobiochemistry, Graduate School of Medicine, Osaka City University, Osaka, Japan
| | - Eiji Goto
- Department of Pathobiochemistry, Graduate School of Medicine, Osaka City University, Osaka, Japan
| | - Ginga Komatsu
- Division of Cellular and Molecular Biology, Department of Cancer Biology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Jin Gohda
- Research Center for Asian Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Yasushi Saeki
- Laboratory of Protein Metabolism, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Keiji Tanaka
- Laboratory of Protein Metabolism, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | | | | | - Satoshi Inoue
- Department of Anti-Aging Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Hiroyuki Oshiumi
- Department of Microbiology and Immunology, Graduate School of Medicine, Hokkaido University, Sapporo, Japan
| | - Tsukasa Seya
- Department of Microbiology and Immunology, Graduate School of Medicine, Hokkaido University, Sapporo, Japan
| | - Hiroyasu Nakano
- Department of Biochemistry, Toho University School of Medicine, Tokyo, Japan
| | - Yuetsu Tanaka
- Division of Immunology, Faculty of Medicine, University of the Ryukyus, Okinawa, Japan
| | - Kazuhiro Iwai
- Department of Molecular and Cellular Physiology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Jun-ichiro Inoue
- Division of Cellular and Molecular Biology, Department of Cancer Biology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- * E-mail:
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Zheng Q, Huang T, Zhang L, Zhou Y, Luo H, Xu H, Wang X. Dysregulation of Ubiquitin-Proteasome System in Neurodegenerative Diseases. Front Aging Neurosci 2016; 8:303. [PMID: 28018215 PMCID: PMC5156861 DOI: 10.3389/fnagi.2016.00303] [Citation(s) in RCA: 186] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Accepted: 11/29/2016] [Indexed: 12/15/2022] Open
Abstract
The ubiquitin-proteasome system (UPS) is one of the major protein degradation pathways, where abnormal UPS function has been observed in cancer and neurological diseases. Many neurodegenerative diseases share a common pathological feature, namely intracellular ubiquitin-positive inclusions formed by aggregate-prone neurotoxic proteins. This suggests that dysfunction of the UPS in neurodegenerative diseases contributes to the accumulation of neurotoxic proteins and to instigate neurodegeneration. Here, we review recent findings describing various aspects of UPS dysregulation in neurodegenerative disorders such as Alzheimer’s disease, Parkinson’s disease, and Huntington’s disease.
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Affiliation(s)
- Qiuyang Zheng
- Fujian Provincial Key Laboratory of Neurodegenerative Disease and Aging Research, Institute of Neuroscience, College of Medicine, Collaborative Innovation Center for Brain Science, Xiamen University Xiamen, China
| | - Timothy Huang
- Neuroscience Initiative, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA USA
| | - Lishan Zhang
- Fujian Provincial Key Laboratory of Neurodegenerative Disease and Aging Research, Institute of Neuroscience, College of Medicine, Collaborative Innovation Center for Brain Science, Xiamen University Xiamen, China
| | - Ying Zhou
- Fujian Provincial Key Laboratory of Neurodegenerative Disease and Aging Research, Institute of Neuroscience, College of Medicine, Collaborative Innovation Center for Brain Science, Xiamen University Xiamen, China
| | - Hong Luo
- Fujian Provincial Key Laboratory of Neurodegenerative Disease and Aging Research, Institute of Neuroscience, College of Medicine, Collaborative Innovation Center for Brain Science, Xiamen University Xiamen, China
| | - Huaxi Xu
- Fujian Provincial Key Laboratory of Neurodegenerative Disease and Aging Research, Institute of Neuroscience, College of Medicine, Collaborative Innovation Center for Brain Science, Xiamen UniversityXiamen, China; Neuroscience Initiative, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CAUSA
| | - Xin Wang
- Fujian Provincial Key Laboratory of Neurodegenerative Disease and Aging Research, Institute of Neuroscience, College of Medicine, Collaborative Innovation Center for Brain Science, Xiamen University Xiamen, China
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Super-resolution microscopy reveals a preformed NEMO lattice structure that is collapsed in incontinentia pigmenti. Nat Commun 2016; 7:12629. [PMID: 27586688 PMCID: PMC5025789 DOI: 10.1038/ncomms12629] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Accepted: 07/18/2016] [Indexed: 12/26/2022] Open
Abstract
The NF-κB pathway has critical roles in cancer, immunity and inflammatory responses. Understanding the mechanism(s) by which mutations in genes involved in the pathway cause disease has provided valuable insight into its regulation, yet many aspects remain unexplained. Several lines of evidence have led to the hypothesis that the regulatory/sensor protein NEMO acts as a biological binary switch. This hypothesis depends on the formation of a higher-order structure, which has yet to be identified using traditional molecular techniques. Here we use super-resolution microscopy to reveal the existence of higher-order NEMO lattice structures dependent on the presence of polyubiquitin chains before NF-κB activation. Such structures may permit proximity-based trans-autophosphorylation, leading to cooperative activation of the signalling cascade. We further show that NF-κB activation results in modification of these structures. Finally, we demonstrate that these structures are abrogated in cells derived from incontinentia pigmenti patients. NEMO is a member of the IKK complex that binds ubiquitin, involved in NF-κB signalling and proposed to form higher order structures. Here the authors use super-resolution microscopy to detect the presence of NEMO lattices in cells, that are modified by NF-κB treatment and abrogated by mutations affecting NEMO ubiquitin binding.
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64
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Meena NP, Zhu G, Mittelstadt PR, Giardino Torchia ML, Pourcelot M, Arnoult D, Ashwell JD, Munitic I. The TBK1-binding domain of optineurin promotes type I interferon responses. FEBS Lett 2016; 590:1498-508. [PMID: 27086836 DOI: 10.1002/1873-3468.12176] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Revised: 04/05/2016] [Accepted: 04/07/2016] [Indexed: 01/24/2023]
Abstract
Pathogen-associated molecular pattern (PAMP) recognition leads to TANK-binding kinase (TBK1) polyubiquitination and activation by transautophosphorylation, resulting in IFN-β production. Here, we describe a mouse model of optineurin insufficiency (OptnΔ(157) ) in which the TBK1-interacting N-terminus of optineurin was deleted. PAMP-stimulated cells from OptnΔ(157) mice had reduced TBK1 activity, no phosphorylation of optineurin Ser(187) , and mounted low IFN-β responses. In contrast to pull-down assays where the presence of N-terminus was sufficient for TBK1 binding, both the N-terminal and the ubiquitin-binding regions of optineurin were needed for PAMP-induced binding. This report establishes optineurin as a positive regulator TBK1 via a bipartite interaction between these molecules.
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Affiliation(s)
- Netra Pal Meena
- Laboratory of Immune Cell Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Guozhi Zhu
- Laboratory of Immune Cell Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Paul R Mittelstadt
- Laboratory of Immune Cell Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | | | - Marie Pourcelot
- INSERM, UMR_S 1197, Hôpital Paul Brousse, Villejuif, France.,Université Paris-Saclay, Villejuif, France
| | - Damien Arnoult
- INSERM, UMR_S 1197, Hôpital Paul Brousse, Villejuif, France.,Université Paris-Saclay, Villejuif, France
| | - Jonathan D Ashwell
- Laboratory of Immune Cell Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Ivana Munitic
- Laboratory of Immune Cell Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.,Laboratory of Molecular Immunology, Department of Biotechnology, University of Rijeka, Croatia
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Abstract
Protein ubiquitination is a dynamic multifaceted post-translational modification involved in nearly all aspects of eukaryotic biology. Once attached to a substrate, the 76-amino acid protein ubiquitin is subjected to further modifications, creating a multitude of distinct signals with distinct cellular outcomes, referred to as the 'ubiquitin code'. Ubiquitin can be ubiquitinated on seven lysine (Lys) residues or on the N-terminus, leading to polyubiquitin chains that can encompass complex topologies. Alternatively or in addition, ubiquitin Lys residues can be modified by ubiquitin-like molecules (such as SUMO or NEDD8). Finally, ubiquitin can also be acetylated on Lys, or phosphorylated on Ser, Thr or Tyr residues, and each modification has the potential to dramatically alter the signaling outcome. While the number of distinctly modified ubiquitin species in cells is mind-boggling, much progress has been made to characterize the roles of distinct ubiquitin modifications, and many enzymes and receptors have been identified that create, recognize or remove these ubiquitin modifications. We here provide an overview of the various ubiquitin modifications present in cells, and highlight recent progress on ubiquitin chain biology. We then discuss the recent findings in the field of ubiquitin acetylation and phosphorylation, with a focus on Ser65-phosphorylation and its role in mitophagy and Parkin activation.
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Affiliation(s)
- Kirby N Swatek
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - David Komander
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
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66
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Shen WC, Li HY, Chen GC, Chern Y, Tu PH. Mutations in the ubiquitin-binding domain of OPTN/optineurin interfere with autophagy-mediated degradation of misfolded proteins by a dominant-negative mechanism. Autophagy 2016; 11:685-700. [PMID: 25484089 DOI: 10.4161/auto.36098] [Citation(s) in RCA: 118] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
OPTN (optineurin) is an autophagy receptor and mutations in the OPTN gene result in familial glaucoma (E50K) and amyotrophic lateral sclerosis (ALS) (E478G). However, the mechanisms through which mutant OPTN leads to human diseases remain to be characterized. Here, we demonstrated that OPTN colocalized with inclusion bodies (IBs) formed by mutant HTT/huntingtin protein (mHTT) in R6/2 transgenic mice and IBs formed by 81QNmHTT (nuclear form), 109QmHTT (cytoplasmic form) or the truncated form of TARDBP/TDP-43 (TARDBP(ND251)) in Neuro2A cells. This colocalization required the ubiquitin (Ub)-binding domain (UbBD, amino acids 424 to 511) of OPTN. Overexpression of wild-type (WT) OPTN decreased IBs through K63-linked polyubiquitin-mediated autophagy. E50K or 210 to 410Δ (with amino acids 210 to 410 deleted) whose mutation or deletion was outside the UbBD decreased the IBs formed by 109QmHTT or TARDBP(ND251), as was the case with WT OPTN. In contrast, UbBD mutants, including E478G, D474N, UbBDΔ, 411 to 520Δ and 210 to 520Δ, increased accumulation of IBs. UbBD mutants (E478G, UbBDΔ) retained a substantial ability to interact with WT OPTN, and were found to colocalize with polyubiquitinated IBs, which might occur indirectly through their WT partner in a WT-mutant complex. They decreased autophagic flux evidenced by alteration in LC3 level and turnover and in the number of LC3-positive puncta under stresses like starvation or formation of IBs. UbBD mutants exhibited a weakened interaction with MYO6 (myosin VI) and TOM1 (target of myb1 homolog [chicken]), important for autophagosome maturation, in cells or sorted 109QmHtt IBs. Taken together, our data indicated that UbBD mutants acted as dominant-negative traps through the formation of WT-mutant hybrid complexes to compromise the maturation of autophagosomes, which in turn interfered with OPTN-mediated autophagy and clearance of IBs.
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Key Words
- ALS, amyotrophic lateral sclerosis
- Ab, antibody
- BafA1, bafilomycin A1
- CCD, coiled-coil domain
- Ef, FRET efficiency
- FT, filter-trap assay
- HD, Huntington disease
- IBs, inclusion bodies
- IP, immunoprecipitation
- K48, lysine 48
- K63, lysine 63
- LIR, LC3-interacting region
- MYO6, myosin VI
- OPTN, optineurin
- PBS, phosphate-buffered saline
- PFA, paraformaldehyde
- TARDBP/TDP-43
- TARDBP/TDP-43, TAR DNA-binding protein
- TBK1, TANK-binding kinase 1
- TUBA, alpha tubulin
- UPS, ubiquitin-proteasome system
- Ub, ubiquitin B/C/D
- UbBD, ubiquitin-binding domain
- WB, western blot
- WT, wild type
- autophagy
- dominant-negative
- huntingtin
- mHTT, mutant huntingtin
- optineurin
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Affiliation(s)
- Wen-Chuan Shen
- a Taiwan International Graduate Program in Molecular Medicine; National Yang-Ming University and Academia Sinica ; Taipei , Taiwan
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67
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Defects in autophagy caused by glaucoma-associated mutations in optineurin. Exp Eye Res 2016; 144:54-63. [DOI: 10.1016/j.exer.2015.08.020] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Revised: 07/14/2015] [Accepted: 08/18/2015] [Indexed: 11/30/2022]
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68
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Kupka S, Reichert M, Draber P, Walczak H. Formation and removal of poly-ubiquitin chains in the regulation of tumor necrosis factor-induced gene activation and cell death. FEBS J 2016; 283:2626-39. [PMID: 26749412 DOI: 10.1111/febs.13644] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Revised: 12/21/2015] [Accepted: 01/05/2016] [Indexed: 12/17/2022]
Abstract
Tumor necrosis factor (TNF) is a potent cytokine known for its involvement in inflammation, repression of tumorigenesis and activation of immune cells. Consequently, accurate regulation of the TNF signaling pathway is crucial for preventing the potent noxious effects of TNF. These pathological conditions include chronic inflammation, septic shock, cachexia and cancer. The TNF signaling cascade utilizes a complex network of post-translational modifications to control the cellular response following its activation. Next to phosphorylation, the ubiquitination of signaling complex components is probably the most important modification. This process is mediated by a specialist class of enzymes, the ubiquitin ligases. Equally important is the class of dedicated ubiquitin-specific proteases, the deubiquitinases. Together with ubiquitin binding proteins, this ubiquitination-deubiquitination system enables the dynamics of signaling complexes. In TNF signaling, these dynamics translate into the precise regulation of the induction of gene activation or cell death. Here, we review and discuss current knowledge of TNF signaling regulation by the ubiquitin system.
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Affiliation(s)
- Sebastian Kupka
- Centre for Cell Death, Cancer, and Inflammation (CCCI), UCL Cancer Institute, University College London, London, UK
| | - Matthias Reichert
- Centre for Cell Death, Cancer, and Inflammation (CCCI), UCL Cancer Institute, University College London, London, UK
| | - Peter Draber
- Centre for Cell Death, Cancer, and Inflammation (CCCI), UCL Cancer Institute, University College London, London, UK
| | - Henning Walczak
- Centre for Cell Death, Cancer, and Inflammation (CCCI), UCL Cancer Institute, University College London, London, UK
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69
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Recruitment of A20 by the C-terminal domain of NEMO suppresses NF-κB activation and autoinflammatory disease. Proc Natl Acad Sci U S A 2016; 113:1612-7. [PMID: 26802121 DOI: 10.1073/pnas.1518163113] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Receptor-induced NF-κB activation is controlled by NEMO, the NF-κB essential modulator. Hypomorphic NEMO mutations result in X-linked ectodermal dysplasia with anhidrosis and immunodeficiency, also referred to as NEMO syndrome. Here we describe a distinct group of patients with NEMO C-terminal deletion (ΔCT-NEMO) mutations. Individuals harboring these mutations develop inflammatory skin and intestinal disease in addition to ectodermal dysplasia with anhidrosis and immunodeficiency. Both primary cells from these patients, as well as reconstituted cell lines with this deletion, exhibited increased IκB kinase (IKK) activity and production of proinflammatory cytokines. Unlike previously described loss-of-function mutations, ΔCT-NEMO mutants promoted increased NF-κB activation in response to TNF and Toll-like receptor stimulation. Investigation of the underlying mechanisms revealed impaired interactions with A20, a negative regulator of NF-κB activation, leading to prolonged accumulation of K63-ubiquitinated RIP within the TNFR1 signaling complex. Recruitment of A20 to the C-terminal domain of NEMO represents a novel mechanism limiting NF-κB activation by NEMO, and its absence results in autoinflammatory disease.
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70
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Mathis BJ, Lai Y, Qu C, Janicki JS, Cui T. CYLD-mediated signaling and diseases. Curr Drug Targets 2016; 16:284-94. [PMID: 25342597 DOI: 10.2174/1389450115666141024152421] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2014] [Revised: 09/26/2014] [Accepted: 10/03/2014] [Indexed: 02/07/2023]
Abstract
The conserved cylindromatosis (CYLD) codes for a deubiquitinating enzyme and is a crucial regulator of diverse cellular processes such as immune responses, inflammation, death, and proliferation. It directly regulates multiple key signaling cascades, such as the Nuclear Factor kappa B [NFkB] and the Mitogen-Activated Protein Kinase (MAPK) pathways, by its catalytic activity on polyubiquitinated key intermediates. Several lines of emerging evidence have linked CYLD to the pathogenesis of various maladies, including cancer, poor infection control, lung fibrosis, neural development, and now cardiovascular dysfunction. While CYLD-mediated signaling is cell type and stimuli specific, the activity of CYLD is tightly controlled by phosphorylation and other regulators such as Snail. This review explores a broad selection of current and past literature regarding CYLD's expression, function and regulation with emerging reports on its role in cardiovascular disease.
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Affiliation(s)
| | | | | | | | - Taixing Cui
- Department of Cell Biology and Anatomy, University of South Carolina School of Medicine, Columbia, SC 29209, USA.
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71
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Inhibition of Canonical NF-κB Signaling by a Small Molecule Targeting NEMO-Ubiquitin Interaction. Sci Rep 2016; 6:18934. [PMID: 26740240 PMCID: PMC4703965 DOI: 10.1038/srep18934] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Accepted: 11/30/2015] [Indexed: 12/16/2022] Open
Abstract
The IκB kinase (IKK) complex acts as the gatekeeper of canonical NF-κB signaling, thereby regulating immunity, inflammation and cancer. It consists of the catalytic subunits IKKα and IKKβ and the regulatory subunit NEMO/IKKγ. Here, we show that the ubiquitin binding domain (UBAN) in NEMO is essential for IKK/NF-κB activation in response to TNFα, but not IL-1β stimulation. By screening a natural compound library we identified an anthraquinone derivative that acts as an inhibitor of NEMO-ubiquitin binding (iNUB). Using biochemical and NMR experiments we demonstrate that iNUB binds to NEMOUBAN and competes for interaction with methionine-1-linked linear ubiquitin chains. iNUB inhibited NF-κB activation upon UBAN-dependent TNFα and TCR/CD28, but not UBAN-independent IL-1β stimulation. Moreover, iNUB was selectively killing lymphoma cells that are addicted to chronic B-cell receptor triggered IKK/NF-κB activation. Thus, iNUB disrupts the NEMO-ubiquitin protein-protein interaction interface and thereby inhibits physiological and pathological NF-κB signaling.
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72
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Heo JM, Ordureau A, Paulo JA, Rinehart J, Harper JW. The PINK1-PARKIN Mitochondrial Ubiquitylation Pathway Drives a Program of OPTN/NDP52 Recruitment and TBK1 Activation to Promote Mitophagy. Mol Cell 2015; 60:7-20. [PMID: 26365381 DOI: 10.1016/j.molcel.2015.08.016] [Citation(s) in RCA: 608] [Impact Index Per Article: 67.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Revised: 08/12/2015] [Accepted: 08/19/2015] [Indexed: 12/22/2022]
Abstract
Damaged mitochondria are detrimental to cellular homeostasis. One mechanism for removal of damaged mitochondria involves the PINK1-PARKIN pathway, which poly-ubiquitylates damaged mitochondria to promote mitophagy. We report that assembly of ubiquitin chains on mitochondria triggers autophagy adaptor recruitment concomitantly with activation of the TBK1 kinase, which physically associates with OPTN, NDP52, and SQSTM1. TBK1 activation in HeLa cells requires OPTN and NDP52 and OPTN ubiquitin chain binding. In addition to the known role of S177 phosphorylation in OPTN on ATG8 recruitment, TBK1-dependent phosphorylation on S473 and S513 promotes ubiquitin chain binding in vitro as well as TBK1 activation, OPTN mitochondrial retention, and efficient mitophagy in vivo. These data reveal a self-reinforcing positive feedback mechanism that coordinates TBK1-dependent autophagy adaptor phosphorylation with the assembly of ubiquitin chains on mitochondria to facilitate efficient mitophagy, and mechanistically links genes mutated in Parkinson's disease and amyotrophic lateral sclerosis in a common selective autophagy pathway.
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Affiliation(s)
- Jin-Mi Heo
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Alban Ordureau
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Joao A Paulo
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Jesse Rinehart
- Department of Cellular & Molecular Physiology, Systems Biology Institute, Yale University School of Medicine, New Haven, CT 06520, USA
| | - J Wade Harper
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA.
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73
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Zhao Y, Ma CA, Wu L, Iwai K, Ashwell JD, Oltz EM, Ballard DW, Jain A. CYLD and the NEMO Zinc Finger Regulate Tumor Necrosis Factor Signaling and Early Embryogenesis. J Biol Chem 2015. [PMID: 26224629 DOI: 10.1074/jbc.m115.658096] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
NF-κB essential modulator (NEMO) and cylindromatosis protein (CYLD) are intracellular proteins that regulate the NF-κB signaling pathway. Although mice with either CYLD deficiency or an alteration in the zinc finger domain of NEMO (K392R) are born healthy, we found that the combination of these two gene defects in double mutant (DM) mice is early embryonic lethal but can be rescued by the absence of TNF receptor 1 (TNFR1). Notably, NEMO was not recruited into the TNFR1 complex of DM cells, and consequently NF-κB induction by TNF was severely impaired and DM cells were sensitized to TNF-induced cell death. Interestingly, the TNF signaling defects can be fully rescued by reconstitution of DM cells with CYLD lacking ubiquitin hydrolase activity but not with CYLD mutated in TNF receptor-associated factor 2 (TRAF2) or NEMO binding sites. Therefore, our data demonstrate an unexpected non-catalytic function for CYLD as an adapter protein between TRAF2 and the NEMO zinc finger that is important for TNF-induced NF-κB signaling during embryogenesis.
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Affiliation(s)
- Yongge Zhao
- From the Laboratory of Host Defenses, NIAID, National Institutes of Health, Bethesda, Maryland 20892,
| | - Chi A Ma
- From the Laboratory of Host Defenses, NIAID, National Institutes of Health, Bethesda, Maryland 20892
| | - Liming Wu
- From the Laboratory of Host Defenses, NIAID, National Institutes of Health, Bethesda, Maryland 20892
| | - Kazuhiro Iwai
- the Department of Molecular and Cellular Physiology, Graduate School of Medicine, Kyoto University, Kyoto, 606-8501, Japan
| | - Jonathan D Ashwell
- the Laboratory of Immune Cell Biology, NCI, National Institutes of Health, Bethesda, Maryland 20892
| | - Eugene M Oltz
- the Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri 63110, and
| | - Dean W Ballard
- the Department of Pathology, Microbiology and Immunology, Vanderbilt University, Nashville, Tennessee 37232
| | - Ashish Jain
- From the Laboratory of Host Defenses, NIAID, National Institutes of Health, Bethesda, Maryland 20892,
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74
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Le Henaff C, Mansouri R, Modrowski D, Zarka M, Geoffroy V, Marty C, Tarantino N, Laplantine E, Marie PJ. Increased NF-κB Activity and Decreased Wnt/β-Catenin Signaling Mediate Reduced Osteoblast Differentiation and Function in ΔF508 Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) Mice. J Biol Chem 2015; 290:18009-18017. [PMID: 26060255 DOI: 10.1074/jbc.m115.646208] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Indexed: 01/11/2023] Open
Abstract
The prevalent human ΔF508 mutation in the cystic fibrosis transmembrane conductance regulator (CFTR) is associated with reduced bone formation and bone loss in mice. The molecular mechanisms by which the ΔF508-CFTR mutation causes alterations in bone formation are poorly known. In this study, we analyzed the osteoblast phenotype in ΔF508-CFTR mice and characterized the signaling mechanisms underlying this phenotype. Ex vivo studies showed that the ΔF508-CFTR mutation negatively impacted the differentiation of bone marrow stromal cells into osteoblasts and the activity of osteoblasts, demonstrating that the ΔF508-CFTR mutation alters both osteoblast differentiation and function. Treatment with a CFTR corrector rescued the abnormal collagen gene expression in ΔF508-CFTR osteoblasts. Mechanistic analysis revealed that NF-κB signaling and transcriptional activity were increased in mutant osteoblasts. Functional studies showed that the activation of NF-κB transcriptional activity in mutant osteoblasts resulted in increased β-catenin phosphorylation, reduced osteoblast β-catenin expression, and altered expression of Wnt/β-catenin target genes. Pharmacological inhibition of NF-κB activity or activation of canonical Wnt signaling rescued Wnt target gene expression and corrected osteoblast differentiation and function in bone marrow stromal cells and osteoblasts from ΔF508-CFTR mice. Overall, the results show that the ΔF508-CFTR mutation impairs osteoblast differentiation and function as a result of overactive NF-κB and reduced Wnt/β-catenin signaling. Moreover, the data indicate that pharmacological inhibition of NF-κB or activation of Wnt/β-catenin signaling can rescue the abnormal osteoblast differentiation and function induced by the prevalent ΔF508-CFTR mutation, suggesting novel therapeutic strategies to correct the osteoblast dysfunctions in cystic fibrosis.
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Affiliation(s)
- Carole Le Henaff
- UMR-1132 INSERM, 75475 Paris; Université Paris Diderot, Sorbonne Paris Cité, 75013 Paris
| | - Rafik Mansouri
- UMR-1132 INSERM, 75475 Paris; Université Paris Diderot, Sorbonne Paris Cité, 75013 Paris
| | - Dominique Modrowski
- UMR-1132 INSERM, 75475 Paris; Université Paris Diderot, Sorbonne Paris Cité, 75013 Paris
| | - Mylène Zarka
- UMR-1132 INSERM, 75475 Paris; Université Paris Diderot, Sorbonne Paris Cité, 75013 Paris
| | - Valérie Geoffroy
- UMR-1132 INSERM, 75475 Paris; Université Paris Diderot, Sorbonne Paris Cité, 75013 Paris
| | - Caroline Marty
- UMR-1132 INSERM, 75475 Paris; Université Paris Diderot, Sorbonne Paris Cité, 75013 Paris
| | - Nadine Tarantino
- Laboratoire de Signalisation et Pathogenèse, Institut Pasteur, 75015 Paris, France
| | - Emmanuel Laplantine
- Laboratoire de Signalisation et Pathogenèse, Institut Pasteur, 75015 Paris, France
| | - Pierre J Marie
- UMR-1132 INSERM, 75475 Paris; Université Paris Diderot, Sorbonne Paris Cité, 75013 Paris.
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75
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Bansal M, Swarup G, Balasubramanian D. Functional analysis of optineurin and some of its disease-associated mutants. IUBMB Life 2015; 67:120-8. [DOI: 10.1002/iub.1355] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Revised: 01/07/2015] [Accepted: 01/16/2015] [Indexed: 12/27/2022]
Affiliation(s)
- Megha Bansal
- Centre for Cellular and Molecular Biology; Hyderabad Telangana India
| | - Ghanshyam Swarup
- Centre for Cellular and Molecular Biology; Hyderabad Telangana India
| | - Dorairajan Balasubramanian
- Brien Holden Eye Research Centre, Hyderabad Eye Research Foundation, L.V. Prasad Eye Institute; Hyderabad Telangana India
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76
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Rare mendelian primary immunodeficiency diseases associated with impaired NF-κB signaling. Genes Immun 2015; 16:239-46. [PMID: 25764117 PMCID: PMC4457537 DOI: 10.1038/gene.2015.3] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Revised: 01/07/2015] [Accepted: 01/09/2015] [Indexed: 12/14/2022]
Abstract
Mendelian Primary Immunodeficiency Diseases (MPIDs) are rare disorders affecting distinct constituents of the innate and adaptive immune system. Although they are genetically heterogeneous a substantial group of MPIDs is due to mutations in genes affecting the NF-κB transcription pathway, essential for cell proliferation, cell survival, and involved in innate immunity and in inflammation. Many of these genes encode for crucial regulatory components of NF-κB pathway and their mutations are associated with immunological and developmental signs somehow overlapping in patients with MPIDs. At present nine different MPIDs listed in the OMIM are caused by mutations in at least nine different genes strictly involved in the NF-κB pathway that result in defects in immune responses. We will report here on the distinct function of each causative gene, on the impaired NF-κB step and more in general on the molecular mechanisms underlining the pathogenesis of the disease. Overall, the MPIDs affecting NF-κB signalosome require a careful integrated diagnosis and appropriate genetic tests to be molecularly identified. Their discovery at an ever-increasing rate will help to establish common therapeutic strategy for a subclass of immunodeficient patients.
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77
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Dubosclard V, Fontan E, Agou F. Use of fluorescence spectroscopy for quantitative investigations of ubiquitin interactions with the ubiquitin-binding domains of NEMO. Methods Mol Biol 2015; 1280:321-37. [PMID: 25736758 DOI: 10.1007/978-1-4939-2422-6_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/21/2023]
Abstract
Ubiquitin serves as a signal for a variety of cellular processes and its specific interaction with ubiquitin-binding domain (UBD) regulates key cellular events including protein degradation, cell-cycle control, DNA repair, and kinase activation. Several binding mechanisms for isolated UBDs have been reported in recent years. However, little is known about the mechanism through which proteins containing multiple-UBDs achieve specificity for a particular oligomer of polyUb. The NF-κB essential modulator (NEMO, also known IKKγ), which plays a key role in the NF-κB signaling pathway, belongs to the latter family of proteins since it contains two distal NOA (also known UBAN/CC2-LZ/NUB) and ZF UBDs, separated by an unstructured proline-rich linker of about 40 residues in length. Here, we show a new procedure for fast purification of this bipartite domain. We also describe the use of intrinsic fluorescence spectroscopy for quantitative investigations of ubiquitin interactions between two distal ubiquitin-binding domains of NEMO (NOA and ZF). This spectroscopic method has many advantages over other techniques like GST pulldown and Biacore's SPR for monitoring avid interactions between two UBDs, especially when UBDs are located at significant distance from each other within the protein.
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Affiliation(s)
- Virginie Dubosclard
- Unité de Signalisation Moléculaire et Activation Cellulaire, Département de Biologie Cellulaire et Infection, Institut Pasteur, 25 rue du Dr. Roux, 75015, Paris, France
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78
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Brubaker SW, Bonham KS, Zanoni I, Kagan JC. Innate immune pattern recognition: a cell biological perspective. Annu Rev Immunol 2015; 33:257-90. [PMID: 25581309 DOI: 10.1146/annurev-immunol-032414-112240] [Citation(s) in RCA: 988] [Impact Index Per Article: 109.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Receptors of the innate immune system detect conserved determinants of microbial and viral origin. Activation of these receptors initiates signaling events that culminate in an effective immune response. Recently, the view that innate immune signaling events rely on and operate within a complex cellular infrastructure has become an important framework for understanding the regulation of innate immunity. Compartmentalization within this infrastructure provides the cell with the ability to assign spatial information to microbial detection and regulate immune responses. Several cell biological processes play a role in the regulation of innate signaling responses; at the same time, innate signaling can engage cellular processes as a form of defense or to promote immunological memory. In this review, we highlight these aspects of cell biology in pattern-recognition receptor signaling by focusing on signals that originate from the cell surface, from endosomal compartments, and from within the cytosol.
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Affiliation(s)
- Sky W Brubaker
- Division of Gastroenterology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts 02115; , , ,
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79
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Vincendeau M, Krappmann D, Hadian K. In vitro detection of NEMO-ubiquitin binding using DELFIA and microscale thermophoresis assays. Methods Mol Biol 2015; 1280:311-20. [PMID: 25736757 DOI: 10.1007/978-1-4939-2422-6_18] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Canonical NF-κB signaling in response to various stimuli converges at the level of the IκB kinase (IKK) complex to ultimately activate NF-κB. To achieve this, the IKK complex uses one of its regulatory subunit (IKKγ/NEMO) to sense ubiquitin chains formed by upstream complexes. Various studies have shown that different Ubiquitin chains are involved in the binding of NEMO and thereby the activation of NF-κB. We have utilized two distinct biochemical methods, i.e., Dissociation-Enhanced Lanthanide Fluorescence Immunoassay (DELFIA) and Microscale Thermophoresis (MST), to detect the interaction of NEMO to linear and K63-linked Ubiquitin chains, respectively. Here, we describe the brief basis of the methods and a detailed underlying protocol.
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Affiliation(s)
- Michelle Vincendeau
- Research Unit Cellular Signal Integration, Institute of Molecular Toxicology and Pharmacology, Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
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80
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Erpapazoglou Z, Walker O, Haguenauer-Tsapis R. Versatile roles of k63-linked ubiquitin chains in trafficking. Cells 2014; 3:1027-88. [PMID: 25396681 PMCID: PMC4276913 DOI: 10.3390/cells3041027] [Citation(s) in RCA: 131] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Revised: 10/14/2014] [Accepted: 10/21/2014] [Indexed: 12/11/2022] Open
Abstract
Modification by Lys63-linked ubiquitin (UbK63) chains is the second most abundant form of ubiquitylation. In addition to their role in DNA repair or kinase activation, UbK63 chains interfere with multiple steps of intracellular trafficking. UbK63 chains decorate many plasma membrane proteins, providing a signal that is often, but not always, required for their internalization. In yeast, plants, worms and mammals, this same modification appears to be critical for efficient sorting to multivesicular bodies and subsequent lysosomal degradation. UbK63 chains are also one of the modifications involved in various forms of autophagy (mitophagy, xenophagy, or aggrephagy). Here, in the context of trafficking, we report recent structural studies investigating UbK63 chains assembly by various E2/E3 pairs, disassembly by deubiquitylases, and specifically recognition as sorting signals by receptors carrying Ub-binding domains, often acting in tandem. In addition, we address emerging and unanticipated roles of UbK63 chains in various recycling pathways that function by activating nucleators required for actin polymerization, as well as in the transient recruitment of signaling molecules at the plasma or ER membrane. In this review, we describe recent advances that converge to elucidate the mechanisms underlying the wealth of trafficking functions of UbK63 chains.
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Affiliation(s)
- Zoi Erpapazoglou
- Institut Jacques Monod-CNRS, UMR 7592, Université-Paris Diderot, Sorbonne Paris Cité, F-75205 Paris, France.
| | - Olivier Walker
- Institut des Sciences Analytiques, UMR5280, Université de Lyon/Université Lyon 1, 69100 Villeurbanne, France.
| | - Rosine Haguenauer-Tsapis
- Institut Jacques Monod-CNRS, UMR 7592, Université-Paris Diderot, Sorbonne Paris Cité, F-75205 Paris, France.
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81
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Hooper C, Jackson SS, Coughlin EE, Coon JJ, Miyamoto S. Covalent modification of the NF-κB essential modulator (NEMO) by a chemical compound can regulate its ubiquitin binding properties in vitro. J Biol Chem 2014; 289:33161-74. [PMID: 25296760 DOI: 10.1074/jbc.m114.582478] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Post-translational modification by ubiquitin plays important roles in multiple physiological and pathological processes. Ubiquitin-binding proteins play a critical role in recognizing and relaying polyubiquitin-based signaling. NEMO (NF-κB Essential Modulator) is a central player in canonical NF-κB signaling whose major function is to bind to Lys-63- and/or M1- (or linear) linked polyubiquitin chains generated in response to cell stimulation. Here we show that Withaferin A (WA), a steroidal lactone, causes a change in NEMO's interaction with specific types of polyubiquitin chains in vitro. WA induces full-length recombinant NEMO to bind to long Lys-48-linked polyubiquitin chains but not tetra-ubiquitin species. Significantly, the UBAN (ubiquitin binding in ABIN and NEMO) domain, essential for the ability of NEMO to bind M1/Lys-63-linked polyubiquitin, is dispensable for the WA-induced gain-of-function activity. Mass spectrometric analysis demonstrated that WA covalently modifies NEMO on a cysteine residue within the C-terminal zinc finger (ZF) domain. Point mutations to the ZF can reverse the WA-induced Lys-48-polyubiquitin binding phenotype. Our study demonstrates the feasibility of directly altering the ubiquitin interaction properties of an ubiquitin-binding protein by a chemical compound, thereby shedding light on a novel drug class to potentially alter polyubiquitin-based cellular processes.
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Affiliation(s)
- Christopher Hooper
- From the McArdle Laboratory for Cancer Research, Department of Oncology, Cellular and Molecular Biology Program, University of Wisconsin-Madison, Madison, Wisconsin 53705 and
| | - Shawn S Jackson
- From the McArdle Laboratory for Cancer Research, Department of Oncology, Cellular and Molecular Biology Program, University of Wisconsin-Madison, Madison, Wisconsin 53705 and Medical Scientist Training Program, and
| | - Emma E Coughlin
- Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, Wisconsin 53706
| | - Joshua J Coon
- Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, Wisconsin 53706 Department of Chemistry, Department of Biomolecular Chemistry, and
| | - Shigeki Miyamoto
- From the McArdle Laboratory for Cancer Research, Department of Oncology, Cellular and Molecular Biology Program, University of Wisconsin-Madison, Madison, Wisconsin 53705 and Medical Scientist Training Program, and
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82
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Withaferin A disrupts ubiquitin-based NEMO reorganization induced by canonical NF-κB signaling. Exp Cell Res 2014; 331:58-72. [PMID: 25304104 DOI: 10.1016/j.yexcr.2014.09.034] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Revised: 09/03/2014] [Accepted: 09/27/2014] [Indexed: 01/18/2023]
Abstract
The NF-κB family of transcription factors regulates numerous cellular processes, including cell proliferation and survival responses. The constitutive activation of NF-κB has also emerged as an important oncogenic driver in many malignancies, such as activated B-cell like diffuse large B cell lymphoma, among others. In this study, we investigated the impact and mechanisms of action of Withaferin A, a naturally produced steroidal lactone, against both signal-inducible as well as constitutive NF-κB activities. We found that Withaferin A is a robust inhibitor of canonical and constitutive NF-κB activities, leading to apoptosis of certain lymphoma lines. In the canonical pathway induced by TNF, Withaferin A did not disrupt RIP1 polyubiquitination or NEMO-IKKβ interaction and was a poor direct IKKβ inhibitor, but prevented the formation of TNF-induced NEMO foci which colocalized with TNF ligand. While GFP-NEMO efficiently formed TNF-induced foci, a GFP-NEMO(Y308S) mutant that is defective in binding to polyubiquitin chains did not form foci. Our study reveals that Withaferin A is a novel type of IKK inhibitor which acts by disrupting NEMO reorganization into ubiquitin-based signaling structures in vivo.
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83
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Liu L, Hua Y, Wang D, Shan L, Zhang Y, Zhu J, Jin H, Li H, Hu Z, Zhang W. A sesquiterpene lactone from a medicinal herb inhibits proinflammatory activity of TNF-α by inhibiting ubiquitin-conjugating enzyme UbcH5. ACTA ACUST UNITED AC 2014; 21:1341-1350. [PMID: 25200604 DOI: 10.1016/j.chembiol.2014.07.021] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Revised: 07/22/2014] [Accepted: 07/25/2014] [Indexed: 01/06/2023]
Abstract
UbcH5 is the key ubiquitin-conjugating enzyme catalyzing ubiquitination during TNF-α-triggered NF-κB activation. Here, we identified an herb-derived sesquiterpene lactone compound IJ-5 as a preferential inhibitor of UbcH5 and explored its therapeutic value in inflammatory and autoimmune disease models. IJ-5 suppresses TNF-α-induced NF-κB activation and inflammatory gene transcription by inhibiting the ubiquitination of receptor-interacting protein 1 and NF-κB essential modifier, which is essential to IκB kinase activation. Mechanistic investigations revealed that IJ-5 preferentially binds to and inactivates UbcH5 by forming a covalent adduct with its active site cysteine and thereby preventing ubiquitin conjugation to UbcH5. In preclinical models, pretreatment of IJ-5 exhibited potent anti-inflammatory activity against TNF-α- and D-galactosamine-induced hepatitis and collagen-induced arthritis. These findings highlight the potential of UbcH5 as a therapeutic target for anti-TNF-α interventions and provide an interesting lead compound for the development of new anti-inflammation agents.
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Affiliation(s)
- Li Liu
- Department of Phytochemistry, School of Pharmacy, Second Military Medical University, Shanghai 200433, China
| | - Yaping Hua
- Department of Natural Medicinal Chemistry, School of Pharmacy, Shanghai JiaoTong University, Shanghai 200240, China
| | - Dan Wang
- Department of Phytochemistry, School of Pharmacy, Second Military Medical University, Shanghai 200433, China
| | - Lei Shan
- Department of Phytochemistry, School of Pharmacy, Second Military Medical University, Shanghai 200433, China
| | - Yuan Zhang
- Shanghai Key Laboratory of New Drug Design, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Junsheng Zhu
- Shanghai Key Laboratory of New Drug Design, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Huizi Jin
- Department of Natural Medicinal Chemistry, School of Pharmacy, Shanghai JiaoTong University, Shanghai 200240, China
| | - Honglin Li
- Shanghai Key Laboratory of New Drug Design, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Zhenlin Hu
- Department of Biochemical Pharmacy, School of Pharmacy, Second Military Medical University, Shanghai 200433, China.
| | - Weidong Zhang
- Department of Phytochemistry, School of Pharmacy, Second Military Medical University, Shanghai 200433, China.
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84
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Fiil BK, Gyrd-Hansen M. Met1-linked ubiquitination in immune signalling. FEBS J 2014; 281:4337-50. [PMID: 25060092 PMCID: PMC4286102 DOI: 10.1111/febs.12944] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2014] [Revised: 07/14/2014] [Accepted: 07/22/2014] [Indexed: 12/25/2022]
Abstract
N-terminal methionine-linked ubiquitin (Met1-Ub), or linear ubiquitin, has emerged as a central post-translational modification in innate immune signalling. The molecular machinery that assembles, senses and, more recently, disassembles Met1-Ub has been identified, and technical advances have enabled the identification of physiological substrates for Met1-Ub in response to activation of innate immune receptors. These discoveries have significantly advanced our understanding of how nondegradative ubiquitin modifications control proinflammatory responses mediated by nuclear factor-κB and mitogen-activated protein kinases. In this review, we discuss the current data on Met1-Ub function and regulation, and point to some of the questions that still remain unanswered.
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Affiliation(s)
- Berthe K Fiil
- Department of Disease Biology, Novo Nordisk Foundation Centre for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
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85
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Involvement of A20 in the molecular switch that activates the non-canonical NF-кB pathway. Sci Rep 2014; 3:2568. [PMID: 24008839 PMCID: PMC3764444 DOI: 10.1038/srep02568] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2013] [Accepted: 08/19/2013] [Indexed: 12/13/2022] Open
Abstract
The non-canonical NF-κB pathway is crucial for the immune system. A critical event in activation of the non-canonical pathway is the attenuation of NF-κB-inducing kinase (NIK) degradation, which is promoted by continuous polyubiquitination of NIK catalyzed by the NIK ubiquitin-ligase complex composed of cellular inhibitor of apoptosis protein 1 and 2 (cIAP1/2), TNF receptor-associated factor 2 (TRAF2), and TRAF3. However, the molecular mechanism of stimulation-dependent NIK stabilization remains poorly understood. Here, we show that A20, a ubiquitin-editing enzyme, promotes efficient activation of the non-canonical pathway independent of its catalytic activity. A20 directly binds to cIAP1 through the seventh zinc finger of A20, resulting in dissociation of the TRAF2/TRAF3 interaction, thereby inactivating the ligase complex to stabilize NIK. Given that A20 negatively regulates the canonical pathway, A20 is likely involved in the molecular switch that promotes the transition from canonical to non-canonical activation for proper control of the immune system.
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86
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Mechanism underlying IκB kinase activation mediated by the linear ubiquitin chain assembly complex. Mol Cell Biol 2014; 34:1322-35. [PMID: 24469399 DOI: 10.1128/mcb.01538-13] [Citation(s) in RCA: 90] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The linear ubiquitin chain assembly complex (LUBAC) ligase, consisting of HOIL-1L, HOIP, and SHARPIN, specifically generates linear polyubiquitin chains. LUBAC-mediated linear polyubiquitination has been implicated in NF-κB activation. NEMO, a component of the IκB kinase (IKK) complex, is a substrate of LUBAC, but the precise molecular mechanism underlying linear chain-mediated NF-κB activation has not been fully elucidated. Here, we demonstrate that linearly polyubiquitinated NEMO activates IKK more potently than unanchored linear chains. In mutational analyses based on the crystal structure of the complex between the HOIP NZF1 and NEMO CC2-LZ domains, which are involved in the HOIP-NEMO interaction, NEMO mutations that impaired linear ubiquitin recognition activity and prevented recognition by LUBAC synergistically suppressed signal-induced NF-κB activation. HOIP NZF1 bound to NEMO and ubiquitin simultaneously, and HOIP NZF1 mutants defective in interaction with either NEMO or ubiquitin could not restore signal-induced NF-κB activation. Furthermore, linear chain-mediated activation of IKK2 involved homotypic interaction of the IKK2 kinase domain. Collectively, these results demonstrate that linear polyubiquitination of NEMO plays crucial roles in IKK activation and that this modification involves the HOIP NZF1 domain and recognition of NEMO-conjugated linear ubiquitin chains by NEMO on another IKK complex.
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87
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Tarantino N, Tinevez JY, Crowell EF, Boisson B, Henriques R, Mhlanga M, Agou F, Israël A, Laplantine E. TNF and IL-1 exhibit distinct ubiquitin requirements for inducing NEMO-IKK supramolecular structures. J Cell Biol 2014; 204:231-45. [PMID: 24446482 PMCID: PMC3897181 DOI: 10.1083/jcb.201307172] [Citation(s) in RCA: 301] [Impact Index Per Article: 30.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2013] [Accepted: 12/09/2013] [Indexed: 11/22/2022] Open
Abstract
Nuclear factor κB (NF-κB) essential modulator (NEMO), a regulatory component of the IκB kinase (IKK) complex, controls NF-κB activation through its interaction with ubiquitin chains. We show here that stimulation with interleukin-1 (IL-1) and TNF induces a rapid and transient recruitment of NEMO into punctate structures that are anchored at the cell periphery. These structures are enriched in activated IKK kinases and ubiquitinated NEMO molecules, which suggests that they serve as organizing centers for the activation of NF-κB. These NEMO-containing structures colocalize with activated TNF receptors but not with activated IL-1 receptors. We investigated the involvement of nondegradative ubiquitination in the formation of these structures, using cells deficient in K63 ubiquitin chains or linear ubiquitin chain assembly complex (LUBAC)-mediated linear ubiquitination. Our results indicate that, unlike TNF, IL-1 requires K63-linked and linear ubiquitin chains to recruit NEMO into higher-order complexes. Thus, different mechanisms are involved in the recruitment of NEMO into supramolecular complexes, which appear to be essential for NF-κB activation.
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Affiliation(s)
- Nadine Tarantino
- Unité de Signalisation Moléculaire et Activation Cellulaire and Laboratoire Trafic Membranaire et Division Cellulaire, Institut Pasteur, Centre National de la Recherche Scientifique URA 2582, Paris 75015, France
| | - Jean-Yves Tinevez
- Plateforme d’Imagerie Dynamique and Computational Imaging and Modeling Group, Institut Pasteur, Paris 75015, France
| | - Elizabeth Faris Crowell
- Unité de Signalisation Moléculaire et Activation Cellulaire and Laboratoire Trafic Membranaire et Division Cellulaire, Institut Pasteur, Centre National de la Recherche Scientifique URA 2582, Paris 75015, France
| | - Bertrand Boisson
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY 10065
| | - Ricardo Henriques
- Plateforme d’Imagerie Dynamique and Computational Imaging and Modeling Group, Institut Pasteur, Paris 75015, France
- Gene Expression and Biophysics Unit, Instituto de Medicina Molecular, Faculdade de Medicina Universidade de Lisboa, Lisboa, 1649-028 Portugal
- Medical Research Council Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, England, UK
| | - Musa Mhlanga
- Gene Expression and Biophysics Unit, Instituto de Medicina Molecular, Faculdade de Medicina Universidade de Lisboa, Lisboa, 1649-028 Portugal
- Gene Expression and Biophysics Group, Synthetic Biology Emerging Research Area, Biosciences Unit, Council for Scientific and Industrial Research, Pretoria, Gauteng 0001, South Africa
| | - Fabrice Agou
- Unité de Signalisation Moléculaire et Activation Cellulaire and Laboratoire Trafic Membranaire et Division Cellulaire, Institut Pasteur, Centre National de la Recherche Scientifique URA 2582, Paris 75015, France
| | - Alain Israël
- Unité de Signalisation Moléculaire et Activation Cellulaire and Laboratoire Trafic Membranaire et Division Cellulaire, Institut Pasteur, Centre National de la Recherche Scientifique URA 2582, Paris 75015, France
| | - Emmanuel Laplantine
- Unité de Signalisation Moléculaire et Activation Cellulaire and Laboratoire Trafic Membranaire et Division Cellulaire, Institut Pasteur, Centre National de la Recherche Scientifique URA 2582, Paris 75015, France
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88
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Abstract
The ubiquitin system plays a pivotal role in the regulation of immune responses. This system includes a large family of E3 ubiquitin ligases of over 700 proteins and about 100 deubiquitinating enzymes, with the majority of their biological functions remaining unknown. Over the last decade, through a combination of genetic, biochemical, and molecular approaches, tremendous progress has been made in our understanding of how the process of protein ubiquitination and its reversal deubiquitination controls the basic aspect of the immune system including lymphocyte development, differentiation, activation, and tolerance induction and regulates the pathophysiological abnormalities such as autoimmunity, allergy, and malignant formation. In this review, we selected some of the published literature to discuss the roles of protein-ubiquitin conjugation and deubiquitination in T-cell activation and anergy, regulatory T-cell and T-helper cell differentiation, regulation of NF-κB signaling, and hematopoiesis in both normal and dysregulated conditions. A comprehensive understanding of the relationship between the ubiquitin system and immunity will provide insight into the molecular mechanisms of immune regulation and at the same time will advance new therapeutic intervention for human immunological diseases.
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Affiliation(s)
- Yoon Park
- La Jolla Institute for Allergy and Immunology, La Jolla, California, USA
| | - Hyung-seung Jin
- La Jolla Institute for Allergy and Immunology, La Jolla, California, USA
| | - Daisuke Aki
- La Jolla Institute for Allergy and Immunology, La Jolla, California, USA
| | - Jeeho Lee
- La Jolla Institute for Allergy and Immunology, La Jolla, California, USA
| | - Yun-Cai Liu
- La Jolla Institute for Allergy and Immunology, La Jolla, California, USA.
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89
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Hinz M, Scheidereit C. The IκB kinase complex in NF-κB regulation and beyond. EMBO Rep 2013; 15:46-61. [PMID: 24375677 DOI: 10.1002/embr.201337983] [Citation(s) in RCA: 374] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The IκB kinase (IKK) complex is the signal integration hub for NF-κB activation. Composed of two serine-threonine kinases (IKKα and IKKβ) and the regulatory subunit NEMO (also known as IKKγ), the IKK complex integrates signals from all NF-κB activating stimuli to catalyze the phosphorylation of various IκB and NF-κB proteins, as well as of other substrates. Since the discovery of the IKK complex components about 15 years ago, tremendous progress has been made in the understanding of the IKK architecture and its integration into signaling networks. In addition to the control of NF-κB, IKK subunits mediate the crosstalk with other pathways, thereby extending the complexity of their biological function. This review summarizes recent advances in IKK biology and focuses on emerging aspects of IKK structure, regulation and function.
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Affiliation(s)
- Michael Hinz
- Max Delbrück Center for Molecular Medicine, Berlin, Germany
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90
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Munitic I, Torchia MLG, Meena NP, Zhu G, Li CC, Ashwell JD. Optineurin insufficiency impairs IRF3 but not NF-κB activation in immune cells. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2013; 191:6231-40. [PMID: 24244017 PMCID: PMC3886234 DOI: 10.4049/jimmunol.1301696] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Optineurin is a widely expressed polyubiquitin-binding protein that has been implicated in regulating cell signaling via its NF-κB essential modulator-homologous C-terminal ubiquitin (Ub)-binding region. Its functions are controversial, with in vitro studies finding that optineurin suppressed TNF-mediated NF-κB activation and virus-induced activation of IFN regulatory factor 3 (IRF3), whereas bone marrow-derived macrophages (BMDMs) from mice carrying an optineurin Ub-binding point mutation had normal TLR-mediated NF-κB activation and diminished IRF3 activation. We have generated a mouse model in which the entire Ub-binding C-terminal region is deleted (Optn(470T)). Akin to C-terminal optineurin mutations found in patients with certain neurodegenerative diseases, Optn(470T) was expressed at substantially lower levels than the native protein, allowing assessment not only of the lack of Ub binding, but also of protein insufficiency. Embryonic lethality with incomplete penetrance was observed for 129 × C57BL/6 Optn(470T/470T) mice, but after further backcrossing to C57BL/6, offspring viability was restored. Moreover, the mice that survived were indistinguishable from wild type littermates and had normal immune cell distributions. Activation of NF-κB in Optn(470T) BMDM and BM-derived dendritic cells with TNF or via TLR4, T cells via the TCR, and B cells with LPS or anti-CD40 was normal. In contrast, optineurin and/or its Ub-binding function was necessary for optimal TANK binding kinase 1 and IRF3 activation, and both Optn(470T) BMDMs and bone marrow-derived dendritic cells had diminished IFN-β production upon LPS stimulation. Importantly, Optn(470T) mice produced less IFN-β upon LPS challenge. Therefore, endogenous optineurin is dispensable for NF-κB activation but necessary for optimal IRF3 activation in immune cells.
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Affiliation(s)
- Ivana Munitic
- Laboratory of Immune Cell Biology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892
| | | | - Netra Pal Meena
- Laboratory of Immune Cell Biology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892
| | - Guozhi Zhu
- Laboratory of Immune Cell Biology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892
| | - Caiyi C. Li
- Laboratory of Immune Cell Biology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892
| | - Jonathan D. Ashwell
- Laboratory of Immune Cell Biology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892
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91
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Ofengeim D, Yuan J. Regulation of RIP1 kinase signalling at the crossroads of inflammation and cell death. Nat Rev Mol Cell Biol 2013; 14:727-36. [PMID: 24129419 DOI: 10.1038/nrm3683] [Citation(s) in RCA: 450] [Impact Index Per Article: 40.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Receptor-interacting protein 1 (RIP1) kinase has emerged as a key upstream regulator that controls inflammatory signalling as well as the activation of multiple cell death pathways, including apoptosis and necroptosis. The ability of RIP1 to modulate these key cellular events is tightly controlled by ubiquitylation, deubiquitylation and the interaction of RIP1 with a class of ubiquitin receptors. The modification of RIP1 may thus provide a unique 'ubiquitin code' that determines whether a cell activates nuclear factor-κB (NF-κB) to promote inflammatory signalling or induces cell death by apoptosis or necroptosis. Targeting RIP1 might be a novel therapeutic strategy for the treatment of both acute and chronic human diseases.
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Affiliation(s)
- Dimitry Ofengeim
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
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92
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Nelson DE, Randle SJ, Laman H. Beyond ubiquitination: the atypical functions of Fbxo7 and other F-box proteins. Open Biol 2013; 3:130131. [PMID: 24107298 PMCID: PMC3814724 DOI: 10.1098/rsob.130131] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
F-box proteins (FBPs) are substrate-recruiting subunits of Skp1-cullin1-FBP (SCF)-type E3 ubiquitin ligases. To date, 69 FBPs have been identified in humans, but ubiquitinated substrates have only been identified for a few, with the majority of FBPs remaining ‘orphans’. In recent years, a growing body of work has identified non-canonical, SCF-independent roles for about 12% of the human FBPs. These atypical FBPs affect processes as diverse as transcription, cell cycle regulation, mitochondrial dynamics and intracellular trafficking. Here, we provide a general review of FBPs, with a particular emphasis on these expanded functions. We review Fbxo7 as an exemplar of this special group as it has well-defined roles in both SCF and non-SCF complexes. We review its function as a cell cycle regulator, via its ability to stabilize p27 protein and Cdk6 complexes, and as a proteasome regulator, owing to its high affinity binding to PI31. We also highlight recent advances in our understanding of Fbxo7 function in Parkinson's disease, where it functions in the regulation of mitophagy with PINK1 and Parkin. We postulate that a few extraordinary FBPs act as platforms that seamlessly segue their canonical and non-canonical functions to integrate different cellular pathways and link their regulation.
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Affiliation(s)
- David E Nelson
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QP, UK
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93
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Ngadjeua F, Chiaravalli J, Traincard F, Raynal B, Fontan E, Agou F. Two-sided ubiquitin binding of NF-κB essential modulator (NEMO) zinc finger unveiled by a mutation associated with anhidrotic ectodermal dysplasia with immunodeficiency syndrome. J Biol Chem 2013; 288:33722-33737. [PMID: 24100029 DOI: 10.1074/jbc.m113.483305] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Hypomorphic mutations in the X-linked human NEMO gene result in various forms of anhidrotic ectodermal dysplasia with immunodeficiency. NEMO function is mediated by two distal ubiquitin binding domains located in the regulatory C-terminal domain of the protein: the coiled-coil 2-leucine zipper (CC2-LZ) domain and the zinc finger (ZF) domain. Here, we investigated the effect of the D406V mutation found in the NEMO ZF of an ectodermal dysplasia with immunodeficiency patients. This point mutation does not impair the folding of NEMO ZF or mono-ubiquitin binding but is sufficient to alter NEMO function, as NEMO-deficient fibroblasts and Jurkat T lymphocytes reconstituted with full-length D406V NEMO lead to partial and strong defects in NF-κB activation, respectively. To further characterize the ubiquitin binding properties of NEMO ZF, we employed di-ubiquitin (di-Ub) chains composed of several different linkages (Lys-48, Lys-63, and linear (Met-1-linked)). We showed that the pathogenic mutation preferentially impairs the interaction with Lys-63 and Met-1-linked di-Ub, which correlates with its ubiquitin binding defect in vivo. Furthermore, sedimentation velocity and gel filtration showed that NEMO ZF, like other NEMO related-ZFs, binds mono-Ub and di-Ub with distinct stoichiometries, indicating the presence of a new Ub site within the NEMO ZF. Extensive mutagenesis was then performed on NEMO ZF and characterization of mutants allowed the proposal of a structural model of NEMO ZF in interaction with a Lys-63 di-Ub chain.
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Affiliation(s)
- Flora Ngadjeua
- Institut Pasteur, Unité de Biochimie Structurale et Cellulaire, Department of Structural Biology and Chemistry, CNRS, UMR 3528, 25/28 rue du Dr. Roux 75724 Paris cedex 15, France; Université Pierre et Marie Curie, Cellule Pasteur UPMC, rue du Dr. Roux 75015 Paris, France
| | - Jeanne Chiaravalli
- Institut Pasteur, Unité de Biochimie Structurale et Cellulaire, Department of Structural Biology and Chemistry, CNRS, UMR 3528, 25/28 rue du Dr. Roux 75724 Paris cedex 15, France
| | - François Traincard
- Institut Pasteur, Unité de Biochimie Structurale et Cellulaire, Department of Structural Biology and Chemistry, CNRS, UMR 3528, 25/28 rue du Dr. Roux 75724 Paris cedex 15, France
| | - Bertrand Raynal
- Plateforme de Biophysique des Macromolécules et de leurs Interactions, Institut Pasteur, Department of Structural Biology and Chemistry, CNRS, UMR 3528, 25/28 rue du Dr. Roux 75724 Paris cedex 15, France
| | - Elisabeth Fontan
- Institut Pasteur, Unité de Biochimie Structurale et Cellulaire, Department of Structural Biology and Chemistry, CNRS, UMR 3528, 25/28 rue du Dr. Roux 75724 Paris cedex 15, France
| | - Fabrice Agou
- Institut Pasteur, Unité de Biochimie Structurale et Cellulaire, Department of Structural Biology and Chemistry, CNRS, UMR 3528, 25/28 rue du Dr. Roux 75724 Paris cedex 15, France.
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94
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Abstract
The transcription factor NF-κB is a family of proteins involved in signaling pathways essential for normal cellular functions and development. Deletion of various components of this pathway resulted with abnormal skeletal development. Research in the last decade has established that NF-κB signaling mediates RANK ligand-induced osteoclastogenesis. Consistently, it was shown that inhibition of NF-κB was an effective approach to inhibit osteoclast formation and bone resorptive activity. Identification of the molecular machinery underlying NF-κB activation permitted osteoclast-specific deletion of the major components of this pathway. As a result, it was clear that deletion of members of the proximal IKK kinase complex and the distal NF-κB subunits and downstream regulators affected skeletal development. These studies provided several targets of therapeutic intervention in osteolytic diseases. NF-κB activity has been also described as the centerpiece of inflammatory responses and is considered a potent mediator of inflammatory osteolysis. Indeed, inflammatory insults exacerbate physiologic RANKL-induced NF-κB signals leading to exaggerated responses and to inflammatory osteolysis. These superimposed NF-κB activities appear to underlie several bone pathologies. This review will describe the individual roles of NF-κB molecules in bone resorption and inflammatory osteolysis.
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Affiliation(s)
- Y Abu-Amer
- Department of Orthopedic Surgery, Department of Cell Biology & Physiology, Washington University School of Medicine, 660S. Euclid Avenue, Saint Louis, MO 63110, USA.
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95
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Caster DJ, Korte EA, Nanda SK, McLeish KR, Oliver RK, G'sell RT, Sheehan RM, Freeman DW, Coventry SC, Kelly JA, Guthridge JM, James JA, Sivils KL, Alarcon-Riquelme ME, Scofield RH, Adrianto I, Gaffney PM, Stevens AM, Freedman BI, Langefeld CD, Tsao BP, Pons-Estel BA, Jacob CO, Kamen DL, Gilkeson GS, Brown EE, Alarcon GS, Edberg JC, Kimberly RP, Martin J, Merrill JT, Harley JB, Kaufman KM, Reveille JD, Anaya JM, Criswell LA, Vila LM, Petri M, Ramsey-Goldman R, Bae SC, Boackle SA, Vyse TJ, Niewold TB, Cohen P, Powell DW. ABIN1 dysfunction as a genetic basis for lupus nephritis. J Am Soc Nephrol 2013; 24:1743-54. [PMID: 23970121 DOI: 10.1681/asn.2013020148] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The genetic factors underlying the pathogenesis of lupus nephritis associated with systemic lupus erythematosus are largely unknown, although animal studies indicate that nuclear factor (NF)-κB is involved. We reported previously that a knockin mouse expressing an inactive form of ABIN1 (ABIN1[D485N]) develops lupus-like autoimmune disease and demonstrates enhanced activation of NF-κB and mitogen-activated protein kinases in immune cells after toll-like receptor stimulation. In the current study, we show that ABIN1[D485N] mice develop progressive GN similar to class III and IV lupus nephritis in humans. To investigate the clinical relevance of ABIN1 dysfunction, we genotyped five single-nucleotide polymorphisms in the gene encoding ABIN1, TNIP1, in samples from European-American, African American, Asian, Gullah, and Hispanic participants in the Large Lupus Association Study 2. Comparing cases of systemic lupus erythematosus with nephritis and cases of systemic lupus erythematosus without nephritis revealed strong associations with lupus nephritis at rs7708392 in European Americans and rs4958881 in African Americans. Comparing cases of systemic lupus erythematosus with nephritis and healthy controls revealed a stronger association at rs7708392 in European Americans but not at rs4958881 in African Americans. Our data suggest that variants in the TNIP1 gene are associated with the risk for lupus nephritis and could be mechanistically involved in disease development via aberrant regulation of NF-κB and mitogen-activated protein kinase activity.
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96
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Liu S, Chen J, Cai X, Wu J, Chen X, Wu YT, Sun L, Chen ZJ. MAVS recruits multiple ubiquitin E3 ligases to activate antiviral signaling cascades. eLife 2013; 2:e00785. [PMID: 23951545 PMCID: PMC3743401 DOI: 10.7554/elife.00785] [Citation(s) in RCA: 272] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2013] [Accepted: 07/01/2013] [Indexed: 12/18/2022] Open
Abstract
RNA virus infections are detected by the RIG-I family of receptors, which induce type-I interferons through the mitochondrial protein MAVS. MAVS forms large prion-like polymers that activate the cytosolic kinases IKK and TBK1, which in turn activate NF-κB and IRF3, respectively, to induce interferons. Here we show that MAVS polymers recruit several TRAF proteins, including TRAF2, TRAF5, and TRAF6, through distinct TRAF-binding motifs. Mutations of these motifs that disrupted MAVS binding to TRAFs abrogated its ability to activate IRF3. IRF3 activation was also abolished in cells lacking TRAF2, 5, and 6. These TRAF proteins promoted ubiquitination reactions that recruited NEMO to the MAVS signaling complex, leading to the activation of IKK and TBK1. These results delineate the mechanism of MAVS signaling and reveal that TRAF2, 5, and 6, which are normally associated with NF-κB activation, also play a crucial role in IRF3 activation in antiviral immune responses. DOI:http://dx.doi.org/10.7554/eLife.00785.001 The innate immune system can detect and destroy viruses, bacteria and other pathogens that enter the human body. In particular, inside cells, viral RNA can bind to and activate a protein called RIG-I. This protein switches on another protein, called MAVS, which can activate other copies of itself. These MAVS molecules then aggregate together on the membrane of mitochondria and send a signal that leads to the production of small proteins, called cytokines, which stimulate an inflammatory response and ultimately neutralize the virus. Although many of the proteins that are activated by MAVS in the innate immunity signaling pathway have been identified, precisely how MAVS transmits this signal is unknown. Now, Liu et al. explore how this protein can propagate signals in the innate immune response by monitoring activation of the transcription factors IRF3 and NF-κB, which transcribe cytokine genes. Previous studies have suggested that a protein known as ubiquitin is needed to activate RIG-I, and that this protein collaborates with MAVS to signal through the innate immunity pathway. Liu et al. found that a group of proteins including TRAF2, TRAF5, TRAF6 and LUBAC relay the antiviral signal by binding to MAVS. These so-called ‘E3 ligases’ string ubiquitin together in chains called polyubiquitin, which is essential for activating signaling after, or downstream of, MAVS; however, the association of these E3 ligases with MAVS also requires that multiple copies of MAVS cluster together. MAVS, the TRAF proteins and LUBAC collectively recruit other innate immunity pathway proteins to activate IRF3 and NF-κB, and thus transcription of the genes that control the innate immunity response. Together, these results show the intricate interplay of proteins needed to eliminate viruses from the body. DOI:http://dx.doi.org/10.7554/eLife.00785.002
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Affiliation(s)
- Siqi Liu
- Department of Molecular Biology , University of Texas Southwestern Medical Center , Dallas , United States
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97
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Defective immune responses in mice lacking LUBAC-mediated linear ubiquitination in B cells. EMBO J 2013; 32:2463-76. [PMID: 23942237 DOI: 10.1038/emboj.2013.184] [Citation(s) in RCA: 90] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2013] [Accepted: 07/25/2013] [Indexed: 11/08/2022] Open
Abstract
The linear ubiquitin chain assembly complex (LUBAC) plays a crucial role in activating the canonical NF-κB pathway, which is important for B-cell development and function. Here, we describe a mouse model (B-HOIP(Δlinear)) in which the linear polyubiquitination activity of LUBAC is specifically ablated in B cells. Canonical NF-κB and ERK activation, mediated by the tumour necrosis factor (TNF) receptor superfamily receptors CD40 and TACI, was impaired in B cells from B-HOIP(Δlinear) mice due to defective activation of the IKK complex; however, B-cell receptor (BCR)-mediated activation of the NF-κB and ERK pathways was unaffected. B-HOIP(Δlinear) mice show impaired B1-cell development and defective antibody responses to thymus-dependent and thymus-independent II antigens. Taken together, these data suggest that LUBAC-mediated linear polyubiquitination is essential for B-cell development and activation, possibly via canonical NF-κB and ERK activation induced by the TNF receptor superfamily, but not by the BCR.
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98
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Liu X, Wang Q, Chen W, Wang C. Dynamic regulation of innate immunity by ubiquitin and ubiquitin-like proteins. Cytokine Growth Factor Rev 2013; 24:559-70. [PMID: 23953672 DOI: 10.1016/j.cytogfr.2013.07.002] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2013] [Revised: 07/16/2013] [Accepted: 07/18/2013] [Indexed: 12/21/2022]
Abstract
Protein post-translational modifications (PTMs) are central to the host innate immune regulations. Dynamically, PTMs fine-tune the spatial and temporary responses of immune- and non-immune-cells, in accordance with extracellular and intracellular stresses. Ubiquitin and ubiquitin-like proteins (Ubls) are emerging as the important multi-functional signals, controlling the activation, stability, affinity and location of many signaling proteins. Recent investigations, at the molecular-cellular-animal models, have shed new light on the versatility of the ubiquitin, SUMO and ISG15, for shaping the strength and duration of the innate immune responses. This review summarizes our current knowledge on the functions and regulatory mechanisms of the ubiquitin and Ubls in the innate immunity, the first line of host defense against microbial infection.
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Affiliation(s)
- Xing Liu
- State Key Laboratory of Cell Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
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99
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Innate immune-directed NF-κB signaling requires site-specific NEMO ubiquitination. Cell Rep 2013; 4:352-61. [PMID: 23871670 DOI: 10.1016/j.celrep.2013.06.036] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2013] [Revised: 06/05/2013] [Accepted: 06/25/2013] [Indexed: 11/23/2022] Open
Abstract
While the I kappa kinase (IKK) scaffolding protein NF-κB essential modulator (NEMO) binds to polyubiquitin chains to transmit inflammatory signals, NEMO itself is also ubiquitinated in response to a variety of inflammatory agonists. Although there have been hints that polyubiquitination of NEMO is essential for avoiding inflammatory disorders, the in vivo physiologic role of NEMO ubiquitination is unknown. In this work, we knock in a NEMO allele in which two major inflammatory agonist-induced ubiquitination sites cannot be ubiquitinated. We show that mice with a nonubiquitinatable NEMO allele display embryonic lethality. Heterozygous females develop inflammatory skin lesions, decreased B cell numbers, and hypercellular spleens. Embryonic lethality can be complemented by mating onto a TNFR1(-/-) background, at the cost of severe steatohepatitis and early mortality, and we also show that NEMO ubiquitination is required for optimal innate immune signaling responses. These findings suggest that NEMO ubiquitination is crucial for NF-κB activity in response to innate immune agonists.
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100
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IRF-1-binding site in the first intron mediates interferon-γ-induced optineurin promoter activation. Biochem Biophys Res Commun 2013; 437:179-84. [DOI: 10.1016/j.bbrc.2013.06.065] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2013] [Accepted: 06/18/2013] [Indexed: 12/20/2022]
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