51
|
Abstract
Ubiquitination (also known as ubiquitylation) is a post-translational modification that creates versatility in cell signalling and regulates a multitude of cellular processes. Its versatility lies in the capacity to form eight different inter-ubiquitin linkages through the seven lysine residues of ubiquitin and through its N-terminal methionine (M1). The latter, referred to as linear or M1 linkage, is created by the linear ubiquitin chain assembly complex (LUBAC), the only E3 ligase known to date that is capable of forming linear ubiquitin chains de novo Linear ubiquitin chains are crucial modulators of innate and adaptive immune responses, and act by regulating inflammatory and cell death signalling. In this Cell Science at a Glance article and the accompanying poster, we review the current knowledge on the role of LUBAC and linear ubiquitination in immune signalling and human physiology. We specifically focus on the role for LUBAC in signalling that is induced by the cytokine tumour necrosis factor (TNF) and its role in inflammation, gene activation and cell death. Furthermore, we highlight the roles of deubiquitinases (DUBs) that cleave M1 linkages and add an additional layer in the control of LUBAC-mediated immune signalling.
Collapse
Affiliation(s)
- Maureen Spit
- Centre for Cell Death, Cancer, and Inflammation (CCCI), UCL Cancer Institute, University College London, 72 Huntley Street, London WC1E 6DD, UK
| | - Eva Rieser
- Centre for Cell Death, Cancer, and Inflammation (CCCI), UCL Cancer Institute, University College London, 72 Huntley Street, London WC1E 6DD, UK
| | - Henning Walczak
- Centre for Cell Death, Cancer, and Inflammation (CCCI), UCL Cancer Institute, University College London, 72 Huntley Street, London WC1E 6DD, UK
| |
Collapse
|
52
|
Lafont E, Draber P, Rieser E, Reichert M, Kupka S, de Miguel D, Draberova H, von Mässenhausen A, Bhamra A, Henderson S, Wojdyla K, Chalk A, Surinova S, Linkermann A, Walczak H. TBK1 and IKKε prevent TNF-induced cell death by RIPK1 phosphorylation. Nat Cell Biol 2018; 20:1389-1399. [PMID: 30420664 PMCID: PMC6268100 DOI: 10.1038/s41556-018-0229-6] [Citation(s) in RCA: 182] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Accepted: 10/08/2018] [Indexed: 12/20/2022]
Abstract
The linear-ubiquitin chain assembly complex (LUBAC) modulates signalling via various immune receptors. In tumour necrosis factor (TNF) signalling, linear (also known as M1) ubiquitin enables full gene activation and prevents cell death. However, the mechanisms underlying cell death prevention remain ill-defined. Here, we show that LUBAC activity enables TBK1 and IKKε recruitment to and activation at the TNF receptor 1 signalling complex (TNFR1-SC). While exerting only limited effects on TNF-induced gene activation, TBK1 and IKKε are essential to prevent TNF-induced cell death. Mechanistically, TBK1 and IKKε phosphorylate the kinase RIPK1 in the TNFR1-SC, thereby preventing RIPK1-dependent cell death. This activity is essential in vivo, as it prevents TNF-induced lethal shock. Strikingly, NEMO (also known as IKKγ), which mostly, but not exclusively, binds the TNFR1-SC via M1 ubiquitin, mediates the recruitment of the adaptors TANK and NAP1 (also known as AZI2). TANK is constitutively associated with both TBK1 and IKKε, while NAP1 is associated with TBK1. We discovered a previously unrecognized cell death checkpoint that is mediated by TBK1 and IKKε, and uncovered an essential survival function for NEMO, whereby it enables the recruitment and activation of these non-canonical IKKs to prevent TNF-induced cell death.
Collapse
Affiliation(s)
- Elodie Lafont
- 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
- Laboratory of Adaptive Immunity, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Eva Rieser
- 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
| | - Sebastian Kupka
- Centre for Cell Death, Cancer and Inflammation (CCCI), UCL Cancer Institute, University College London, London, UK
| | - Diego de Miguel
- Centre for Cell Death, Cancer and Inflammation (CCCI), UCL Cancer Institute, University College London, London, UK
| | - Helena Draberova
- Centre for Cell Death, Cancer and Inflammation (CCCI), UCL Cancer Institute, University College London, London, UK
- Laboratory of Adaptive Immunity, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Anne von Mässenhausen
- Division of Nephrology, Department of Internal Medicine III, University Hospital Carl Gustav Carus at the Technical University Dresden, Dresden, Germany
| | - Amandeep Bhamra
- Proteomics Research Core Facility, UCL Cancer Institute, University College London, London, UK
| | - Stephen Henderson
- Bill Lyons Informatics Centre (BLIC), UCL Cancer Institute, University College London, London, UK
| | - Katarzyna Wojdyla
- Proteomics Research Core Facility, UCL Cancer Institute, University College London, London, UK
| | - Avigayil Chalk
- Laboratory of Adaptive Immunity, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Silvia Surinova
- Laboratory of Adaptive Immunity, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
- Proteomics Research Core Facility, UCL Cancer Institute, University College London, London, UK
| | - Andreas Linkermann
- Division of Nephrology, Department of Internal Medicine III, University Hospital Carl Gustav Carus at the Technical University Dresden, Dresden, Germany
| | - Henning Walczak
- Centre for Cell Death, Cancer and Inflammation (CCCI), UCL Cancer Institute, University College London, London, UK.
| |
Collapse
|
53
|
HOIL1 Is Essential for the Induction of Type I and III Interferons by MDA5 and Regulates Persistent Murine Norovirus Infection. J Virol 2018; 92:JVI.01368-18. [PMID: 30209176 DOI: 10.1128/jvi.01368-18] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 09/06/2018] [Indexed: 12/13/2022] Open
Abstract
The linear ubiquitin chain assembly complex (LUBAC), composed of heme-oxidized IRP2 ubiquitin ligase 1 (HOIL1), HOIL1-interacting protein (HOIP), and SHANK-associated RH domain-interacting protein (SHARPIN), is a crucial regulator of multiple immune signaling pathways. In humans, HOIL1 or HOIP deficiency is associated with an immune disorder involving autoinflammation, immunodeficiency, and inflammatory bowel disease (IBD)-like symptoms. During viral infection, LUBAC is reported to inhibit the induction of interferon (IFN) by the cytosolic RNA sensor retinoic acid-inducible gene I (RIG-I). Surprisingly, we found that HOIL1 is essential for the induction of both type I and type III IFNs, as well as the phosphorylation of IFN regulatory factor 3 (IRF3), during murine norovirus (MNoV) infection in cultured dendritic cells. The RIG-I-like receptor, melanoma differentiation-associated protein 5 (MDA5), is also required for IFN induction and IRF3 phosphorylation during MNoV infection. Furthermore, HOIL1 and MDA5 were required for IFN induction after Theiler's murine encephalomyelitis virus infection and poly(I·C) transfection, but not Sendai virus or vesicular stomatitis virus infection, indicating that HOIL1 and LUBAC are required selectively for MDA5 signaling. Moreover, Hoil1 - / - mice exhibited defective control of acute and persistent murine norovirus infection and defective regulation of MNoV persistence by the microbiome as also observed previously for mice deficient in interferon lambda (IFN-λ) receptor, signal transducer and activator of transcription factor 1 (STAT1), and IRF3. These data indicate that LUBAC plays a critical role in IFN induction to control RNA viruses sensed by MDA5.IMPORTANCE Human noroviruses are a leading cause of gastroenteritis throughout the world but are challenging to study in vivo and in vitro Murine norovirus (MNoV) provides a tractable genetic and small-animal model to study norovirus biology and immune responses. Interferons are critical mediators of antiviral immunity, but excessive expression can dysregulate the immune system. IFN-λ plays an important role at mucosal surfaces, including the gastrointestinal tract, and both IFN-λ and commensal enteric bacteria are important modulators of persistent MNoV infection. LUBAC, of which HOIL1 is a component, is reported to inhibit type I IFN induction after RIG-I stimulation. We show, in contrast, that HOIL1 is critical for type I and III IFN induction during infection with MNoV, a virus that preferentially activates MDA5. Moreover, HOIL1 regulates MNoV infection in vivo These data reveal distinct functions for LUBAC in these closely related signaling pathways and in modulation of IFN expression.
Collapse
|
54
|
Cyclophilin J limits inflammation through the blockage of ubiquitin chain sensing. Nat Commun 2018; 9:4381. [PMID: 30348973 PMCID: PMC6197184 DOI: 10.1038/s41467-018-06756-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 09/26/2018] [Indexed: 01/16/2023] Open
Abstract
Maintaining innate immune homeostasis is important for individual health. Npl4 zinc finger (NZF) domain-mediated ubiquitin chain sensing is reported to function in the nuclear factor-kappa B (NF-κB) signal pathway, but the regulatory mechanism remains elusive. Here we show that cyclophilin J (CYPJ), a member of the peptidylprolyl isomerase family, is induced by inflammation. CYPJ interacts with the NZF domain of transform growth factor-β activated kinase 1 binding protein 2 and 3 as well as components of the linear ubiquitin chain assembly complex to block the binding of ubiquitin-chain and negatively regulates NF-κB signaling. Mice with Cypj deficiency are susceptible to lipopolysaccharide and heat-killed Listeria monocytogenes-induced sepsis and dextran sulfate sodium-induced colitis. These findings identify CYPJ as a negative feedback regulator of the NF-κB signaling pathway, and provide insights for understanding the homeostasis of innate immunity.
Collapse
|
55
|
E3 ligase FBXW7 aggravates TMPD-induced systemic lupus erythematosus by promoting cell apoptosis. Cell Mol Immunol 2018; 15:1057-1070. [PMID: 30275535 DOI: 10.1038/s41423-018-0167-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Accepted: 08/17/2018] [Indexed: 12/11/2022] Open
Abstract
Systemic lupus erythematosus (SLE) is a systemic autoimmune disease, and the pathogenesis of SLE has not been fully elucidated. The E3 ubiquitin ligase FBXW7 has been well characterized in cancer as a tumor suppressor that can promote the ubiquitination and subsequent degradation of various oncoproteins; however, the potential role of FBXW7 in autoimmune diseases is unclear. In the present study, we identified that FBXW7 is a crucial exacerbating factor for SLE development and progression in a mouse model induced by 2, 6, 10, 14-tetramethylpentadecane (TMPD). Myeloid cell-specific FBXW7-deficient (Lysm+FBXW7f/f) C57BL/6 mice showed decreased immune complex accumulation, glomerulonephritis, glomerular mesangial cell proliferation, and base-membrane thickness in the kidney. Lysm+FBXW7f/f mice produced fewer anti-Sm/RNP and anti-ANA autoantibodies and showed a decreased MHC II expression in B cells. In Lysm+FBXW7f/f mice, we observed that cell apoptosis was reduced and that fewer CD11b+Ly6Chi inflammatory monocytes were recruited to the peritoneal cavity. Consistently, diffuse pulmonary hemorrhage (DPH) was also decreased in Lysm+FBXW7f/f mice. Mechanistically, we clarified that FBXW7 promoted TMPD-induced cell apoptosis by catalyzing MCL1 degradation through K48-linked ubiquitination. Our work revealed that FBXW7 expression in myeloid cells played a crucial role in TMPD-induced SLE progression in mice, which may provide novel ideas and theoretical support for understanding the pathogenesis of SLE.
Collapse
|
56
|
LUBAC prevents lethal dermatitis by inhibiting cell death induced by TNF, TRAIL and CD95L. Nat Commun 2018; 9:3910. [PMID: 30254289 PMCID: PMC6156229 DOI: 10.1038/s41467-018-06155-8] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Accepted: 08/17/2018] [Indexed: 12/13/2022] Open
Abstract
The linear ubiquitin chain assembly complex (LUBAC), composed of HOIP, HOIL-1 and SHARPIN, is required for optimal TNF-mediated gene activation and to prevent cell death induced by TNF. Here, we demonstrate that keratinocyte-specific deletion of HOIP or HOIL-1 (E-KO) results in severe dermatitis causing postnatal lethality. We provide genetic and pharmacological evidence that the postnatal lethal dermatitis in HoipE-KO and Hoil-1E-KO mice is caused by TNFR1-induced, caspase-8-mediated apoptosis that occurs independently of the kinase activity of RIPK1. In the absence of TNFR1, however, dermatitis develops in adulthood, triggered by RIPK1-kinase-activity-dependent apoptosis and necroptosis. Strikingly, TRAIL or CD95L can redundantly induce this disease-causing cell death, as combined loss of their respective receptors is required to prevent TNFR1-independent dermatitis. These findings may have implications for the treatment of patients with mutations that perturb linear ubiquitination and potentially also for patients with inflammation-associated disorders that are refractory to inhibition of TNF alone. TNF mediated inflammation is critical in autoimmune mediated pathology, however many patients are refractory to current anti-TNF therapeutics. Here the authors show induction of several death ligands, in addition to TNF is sufficient to cause fatal dermatitis in a LUBAC deficient murine model of disease.
Collapse
|
57
|
Juilland M, Thome M. Holding All the CARDs: How MALT1 Controls CARMA/CARD-Dependent Signaling. Front Immunol 2018; 9:1927. [PMID: 30214442 PMCID: PMC6125328 DOI: 10.3389/fimmu.2018.01927] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 08/06/2018] [Indexed: 01/20/2023] Open
Abstract
The scaffold proteins CARMA1-3 (encoded by the genes CARD11, -14 and -10) and CARD9 play major roles in signaling downstream of receptors with immunoreceptor tyrosine activation motifs (ITAMs), G-protein coupled receptors (GPCR) and receptor tyrosine kinases (RTK). These receptors trigger the formation of oligomeric CARMA/CARD-BCL10-MALT1 (CBM) complexes via kinases of the PKC family. The CBM in turn regulates gene expression by the activation of NF-κB and AP-1 transcription factors and controls transcript stability. The paracaspase MALT1 is the only CBM component having an enzymatic (proteolytic) activity and has therefore recently gained attention as a potential drug target. Here we review recent advances in the understanding of the molecular function of the protease MALT1 and summarize how MALT1 scaffold and protease function contribute to the transmission of CBM signals. Finally, we will highlight how dysregulation of MALT1 function can cause pathologies such as immunodeficiency, autoimmunity, psoriasis, and cancer.
Collapse
Affiliation(s)
- Mélanie Juilland
- Department of Biochemistry, University of Lausanne, Epalinges, Switzerland
| | - Margot Thome
- Department of Biochemistry, University of Lausanne, Epalinges, Switzerland
| |
Collapse
|
58
|
Katsuya K, Hori Y, Oikawa D, Yamamoto T, Umetani K, Urashima T, Kinoshita T, Ayukawa K, Tokunaga F, Tamaru M. High-Throughput Screening for Linear Ubiquitin Chain Assembly Complex (LUBAC) Selective Inhibitors Using Homogenous Time-Resolved Fluorescence (HTRF)-Based Assay System. SLAS DISCOVERY 2018; 23:1018-1029. [PMID: 30071751 DOI: 10.1177/2472555218793066] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The nuclear factor κB (NF-κB) pathway is critical for regulating immune and inflammatory responses, and uncontrolled NF-κB activation is closely associated with various inflammatory diseases and malignant tumors. The Met1-linked linear ubiquitin chain, which is generated by linear ubiquitin chain assembly complex (LUBAC), is important for regulating NF-κB activation. This process occurs through the linear ubiquitination of NF-κB essential modulator, a regulatory subunit of the canonical inhibitor of the NF-κB kinase complex. In this study, we have established a robust and efficient high-throughput screening (HTS) platform to explore LUBAC inhibitors, which may be used as tool compounds to elucidate the pathophysiological role of LUBAC. The HTS platform consisted of both cell-free and cell-based assays: (1) cell-free LUBAC-mediated linear ubiquitination assay using homogenous time-resolved fluorescence technology and (2) cell-based LUBAC assay using the NF-κB luciferase reporter gene assay. By using the HTS platform, we performed a high-throughput chemical library screen and identified several hit compounds with selectivity against a counterassay. Liquid chromatography-mass spectrometry analysis revealed that these compounds contain a chemically reactive lactone structure, which is transformed to give reactive α,β-unsaturated carbonyl compounds. Further investigation revealed that the reactive group of these compounds is essential for the inhibition of LUBAC activity.
Collapse
Affiliation(s)
- Ken Katsuya
- 1 Biological Research Laboratories, Central Pharmaceutical Research Institute, Japan Tobacco Inc., Takatsuki, Osaka, Japan
| | - Yuji Hori
- 1 Biological Research Laboratories, Central Pharmaceutical Research Institute, Japan Tobacco Inc., Takatsuki, Osaka, Japan
| | - Daisuke Oikawa
- 2 Department of Pathobiochemistry, Graduate School of Medicine, Osaka City University, Abeno-ku, Osaka, Japan
| | - Tomohisa Yamamoto
- 1 Biological Research Laboratories, Central Pharmaceutical Research Institute, Japan Tobacco Inc., Takatsuki, Osaka, Japan
| | - Kayo Umetani
- 1 Biological Research Laboratories, Central Pharmaceutical Research Institute, Japan Tobacco Inc., Takatsuki, Osaka, Japan
| | - Toshiki Urashima
- 1 Biological Research Laboratories, Central Pharmaceutical Research Institute, Japan Tobacco Inc., Takatsuki, Osaka, Japan
| | - Tomomi Kinoshita
- 1 Biological Research Laboratories, Central Pharmaceutical Research Institute, Japan Tobacco Inc., Takatsuki, Osaka, Japan
| | - Kumiko Ayukawa
- 1 Biological Research Laboratories, Central Pharmaceutical Research Institute, Japan Tobacco Inc., Takatsuki, Osaka, Japan
| | - Fuminori Tokunaga
- 2 Department of Pathobiochemistry, Graduate School of Medicine, Osaka City University, Abeno-ku, Osaka, Japan
| | - Masahiro Tamaru
- 1 Biological Research Laboratories, Central Pharmaceutical Research Institute, Japan Tobacco Inc., Takatsuki, Osaka, Japan
| |
Collapse
|
59
|
Magnani ND, Dada LA, Sznajder JI. Ubiquitin-proteasome signaling in lung injury. Transl Res 2018; 198:29-39. [PMID: 29752900 PMCID: PMC6986356 DOI: 10.1016/j.trsl.2018.04.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 04/15/2018] [Accepted: 04/16/2018] [Indexed: 12/21/2022]
Abstract
Cell homeostasis requires precise coordination of cellular proteins function. Ubiquitination is a post-translational modification that modulates protein half-life and function and is tightly regulated by ubiquitin E3 ligases and deubiquitinating enzymes. Lung injury can progress to acute respiratory distress syndrome that is characterized by an inflammatory response and disruption of the alveolocapillary barrier resulting in alveolar edema accumulation and hypoxemia. Ubiquitination plays an important role in the pathobiology of acute lung injury as it regulates the proteins modulating the alveolocapillary barrier and the inflammatory response. Better understanding of the signaling pathways regulated by ubiquitination may lead to novel therapeutic approaches by targeting specific elements of the ubiquitination pathways.
Collapse
Affiliation(s)
- Natalia D Magnani
- Pulmonary and Critical Care Division, Northwestern Feinberg School of Medicine, Chicago, Illinois
| | - Laura A Dada
- Pulmonary and Critical Care Division, Northwestern Feinberg School of Medicine, Chicago, Illinois
| | - Jacob I Sznajder
- Pulmonary and Critical Care Division, Northwestern Feinberg School of Medicine, Chicago, Illinois.
| |
Collapse
|
60
|
Aalto AL, Mohan AK, Schwintzer L, Kupka S, Kietz C, Walczak H, Broemer M, Meinander A. M1-linked ubiquitination by LUBEL is required for inflammatory responses to oral infection in Drosophila. Cell Death Differ 2018; 26:860-876. [PMID: 30026495 PMCID: PMC6462001 DOI: 10.1038/s41418-018-0164-x] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Revised: 06/20/2018] [Accepted: 07/02/2018] [Indexed: 01/04/2023] Open
Abstract
Post-translational modifications such as ubiquitination play a key role in regulation of inflammatory nuclear factor-κB (NF-κB) signalling. The Drosophila IκB kinase γ (IKKγ) Kenny is a central regulator of the Drosophila Imd pathway responsible for activation of the NF-κB Relish. We found the Drosophila E3 ligase and HOIL-1L interacting protein (HOIP) orthologue linear ubiquitin E3 ligase (LUBEL) to catalyse formation of M1-linked linear ubiquitin (M1-Ub) chains in flies in a signal-dependent manner upon bacterial infection. Upon activation of the Imd pathway, LUBEL modifies Kenny with M1-Ub chains. Interestingly, the LUBEL-mediated M1-Ub chains seem to be targeted both directly to Kenny and to K63-linked ubiquitin chains conjugated to Kenny by DIAP2. This suggests that DIAP2 and LUBEL work together to promote Kenny-mediated activation of Relish. We found LUBEL-mediated M1-Ub chain formation to be required for flies to survive oral infection with Gram-negative bacteria, for activation of Relish-mediated expression of antimicrobial peptide genes and for pathogen clearance during oral infection. Interestingly, LUBEL is not required for mounting an immune response against systemic infection, as Relish-mediated antimicrobial peptide genes can be expressed in the absence of LUBEL during septic injury. Finally, transgenic induction of LUBEL-mediated M1-Ub drives expression of antimicrobial peptide genes and hyperplasia in the midgut in the absence of infection. This suggests that M1-Ub chains are important for Imd signalling and immune responses in the intestinal epithelia, and that enhanced M1-Ub chain formation is able to drive chronic intestinal inflammation in flies.
Collapse
Affiliation(s)
- Anna L Aalto
- Department of Cell Biology, Faculty of Science and Engineering, BioCity, Åbo Akademi University, 20520, Turku, Finland
| | - Aravind K Mohan
- Department of Cell Biology, Faculty of Science and Engineering, BioCity, Åbo Akademi University, 20520, Turku, Finland
| | - Lukas Schwintzer
- German Center for Neurodegenerative Diseases (DZNE), 53127, Bonn, Germany
| | - Sebastian Kupka
- Centre for Cell Death, Cancer and Inflammation (CCCI), UCL Cancer Institute, London, WC1E 6BT, UK
| | - Christa Kietz
- Department of Cell Biology, Faculty of Science and Engineering, BioCity, Åbo Akademi University, 20520, Turku, Finland
| | - Henning Walczak
- Centre for Cell Death, Cancer and Inflammation (CCCI), UCL Cancer Institute, London, WC1E 6BT, UK
| | - Meike Broemer
- German Center for Neurodegenerative Diseases (DZNE), 53127, Bonn, Germany
| | - Annika Meinander
- Department of Cell Biology, Faculty of Science and Engineering, BioCity, Åbo Akademi University, 20520, Turku, Finland.
| |
Collapse
|
61
|
Liu J, Pan L. Structural bases of the assembly, recognition and disassembly of linear ubiquitin chain. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2018; 1865:1410-1422. [PMID: 29981772 DOI: 10.1016/j.bbamcr.2018.07.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Revised: 06/25/2018] [Accepted: 07/03/2018] [Indexed: 12/31/2022]
Abstract
Linear ubiquitin chain is a latest discovered type of poly-ubiquitin chain that is broadly involved in innate immune and inflammatory pathways. Dysfunctions in its assembly, recognition or disassembly are intimately related with numerous immunodeficiency or autoimmune diseases. Our understanding of the molecular mechanism for linear ubiquitin chain formation, recognition and disassembly has being significantly evolved in recent years, with particular contribution from the biochemical and structural characterizations of related proteins. Here, we focus on the relevant proteins for the synthesis, recognition and digestion of linear ubiquitin chain, and review recent findings to summarize currently known molecular mechanism from a perspective of structural biology.
Collapse
Affiliation(s)
- Jianping Liu
- State Key Laboratory of Bioorganic and Natural Products Chemistry, University of Chinese Academy of Sciences, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, People's Republic of China
| | - Lifeng Pan
- State Key Laboratory of Bioorganic and Natural Products Chemistry, University of Chinese Academy of Sciences, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, People's Republic of China; Collaborative Innovation Center of Chemistry for Life Sciences, University of Chinese Academy of Sciences, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, People's Republic of China.
| |
Collapse
|
62
|
Chen X, Zhao Q, Xie Q, Xing Y, Chen Z. MCPIP1 negatively regulate cellular antiviral innate immune responses through DUB and disruption of TRAF3-TBK1-IKKε complex. Biochem Biophys Res Commun 2018; 503:830-836. [PMID: 29920243 PMCID: PMC7092953 DOI: 10.1016/j.bbrc.2018.06.083] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Accepted: 06/16/2018] [Indexed: 01/12/2023]
Abstract
IFNβ innate immune plays an essential role in antiviral immune. Previous reports suggested that many important regulatory proteins in innate immune pathway may be modified by ubiquitin and that many de-ubiquitination (DUB) proteins may affect immunity. Monocyte chemotactic protein-inducing protein 1 (MCPIP1), one of the CCCH Zn finger-containing proteins, was reported to have DUB function, but its effect on IFNβ innate immune was not fully understood. In this study, we uncovered a novel mechanism that may explain how MCPIP1 efficiently inhibits IFNβ innate immune. It was found that MCPIP1 negatively regulates the IFNβ expression activated by RIG-I, STING, TBK1, IRF3. Furthermore, MCPIP1 inhibits the nuclear translocation of IRF3 upon stimulation with virus, which plays a key role in type I IFN expression. Additionally, MCPIP1 interacts with important modulators of IFNβ expression pathway including IPS1, TRAF3, TBK1 and IKKε. Meanwhile, the interaction between the components in TRAF3-TBK1-IKKε complex was disrupted by MCPIP1. These results collectively suggest MCPIP1 as an innate immune regulator encoded by the host and point to a new mechanism through which MCPIP1 negatively regulates IRF3 activation and type I IFNβ expression.
Collapse
Affiliation(s)
- Xiaojuan Chen
- Division of Infection and Immunity, Department of Biological Technology, Beijing Institute of Radiation Medicine, Beijing, 100850, China
| | - Qian Zhao
- Division of Infection and Immunity, Department of Biological Technology, Beijing Institute of Radiation Medicine, Beijing, 100850, China
| | - Qing Xie
- Division of Infection and Immunity, Department of Biological Technology, Beijing Institute of Radiation Medicine, Beijing, 100850, China
| | - Yaling Xing
- Division of Infection and Immunity, Department of Biological Technology, Beijing Institute of Radiation Medicine, Beijing, 100850, China.
| | - Zhongbin Chen
- Division of Infection and Immunity, Department of Biological Technology, Beijing Institute of Radiation Medicine, Beijing, 100850, China.
| |
Collapse
|
63
|
Liu J, Wang Y, Gong Y, Fu T, Hu S, Zhou Z, Pan L. Structural Insights into SHARPIN-Mediated Activation of HOIP for the Linear Ubiquitin Chain Assembly. Cell Rep 2018; 21:27-36. [PMID: 28978479 DOI: 10.1016/j.celrep.2017.09.031] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Revised: 08/15/2017] [Accepted: 09/07/2017] [Indexed: 11/25/2022] Open
Abstract
The linear ubiquitin chain assembly complex (LUBAC) is the sole identified E3 ligase complex that catalyzes the formation of linear ubiquitin chain, and it is composed of HOIP, HOIL-1L, and SHARPIN. The E3 activity of HOIP can be effectively activated by HOIL-1L or SHARPIN, deficiency of which leads to severe immune system disorders. However, the underlying mechanism governing the HOIP-SHARPIN interaction and the SHARPIN-mediated activation of HOIP remains elusive. Here, we biochemically and structurally demonstrate that the UBL domain of SHARPIN specifically binds to the UBA domain of HOIP and thereby associates with and activates HOIP. We further uncover that SHARPIN and HOIL-1L can separately or synergistically bind to distinct sites of HOIP UBA with induced allosteric effects and thereby facilitate the E2 loading of HOIP for its activation. Thus, our findings provide mechanistic insights into the assembly and activation of LUBAC.
Collapse
Affiliation(s)
- Jianping Liu
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, People's Republic of China
| | - Yingli Wang
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, People's Republic of China
| | - Yukang Gong
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, People's Republic of China
| | - Tao Fu
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, People's Republic of China
| | - Shichen Hu
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, People's Republic of China
| | - Zixuan Zhou
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, People's Republic of China
| | - Lifeng Pan
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, People's Republic of China.
| |
Collapse
|
64
|
Tang Y, Tu H, Liu G, Zheng G, Wang M, Li L, Zhao X, Lin X. RNF31 Regulates Skin Homeostasis by Protecting Epidermal Keratinocytes from Cell Death. THE JOURNAL OF IMMUNOLOGY 2018; 200:4117-4124. [DOI: 10.4049/jimmunol.1800172] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Accepted: 04/13/2018] [Indexed: 11/19/2022]
|
65
|
Fennell LM, Rahighi S, Ikeda F. Linear ubiquitin chain-binding domains. FEBS J 2018; 285:2746-2761. [PMID: 29679476 DOI: 10.1111/febs.14478] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2017] [Revised: 03/08/2018] [Accepted: 04/13/2018] [Indexed: 12/25/2022]
Abstract
Ubiquitin modification (ubiquitination) of target proteins can vary with respect to chain lengths, linkage type, and chain forms, such as homologous, mixed, and branched ubiquitin chains. Thus, ubiquitination can generate multiple unique surfaces on a target protein substrate. Ubiquitin-binding domains (UBDs) recognize ubiquitinated substrates, by specifically binding to these unique surfaces, modulate the formation of cellular signaling complexes and regulate downstream signaling cascades. Among the eight different homotypic chain types, Met1-linked (also termed linear) chains are the only chains in which linkage occurs on a non-Lys residue of ubiquitin. Linear ubiquitin chains have been implicated in immune responses, cell death and autophagy, and several UBDs - specific for linear ubiquitin chains - have been identified. In this review, we describe the main principles of ubiquitin recognition by UBDs, focusing on linear ubiquitin chains and their roles in biology.
Collapse
Affiliation(s)
- Lilian M Fennell
- Institute of Molecular Biotechnology (IMBA), Vienna Biocenter (VBC), Austria
| | - Simin Rahighi
- Chapman University School of Pharmacy (CUSP), Harry and Diane Health Science Campus, Chapman University, Irvine, CA, USA
| | - Fumiyo Ikeda
- Institute of Molecular Biotechnology (IMBA), Vienna Biocenter (VBC), Austria
| |
Collapse
|
66
|
Peltzer N, Darding M, Montinaro A, Draber P, Draberova H, Kupka S, Rieser E, Fisher A, Hutchinson C, Taraborrelli L, Hartwig T, Lafont E, Haas TL, Shimizu Y, Böiers C, Sarr A, Rickard J, Alvarez-Diaz S, Ashworth MT, Beal A, Enver T, Bertin J, Kaiser W, Strasser A, Silke J, Bouillet P, Walczak H. LUBAC is essential for embryogenesis by preventing cell death and enabling haematopoiesis. Nature 2018; 557:112-117. [PMID: 29695863 PMCID: PMC5947819 DOI: 10.1038/s41586-018-0064-8] [Citation(s) in RCA: 155] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Accepted: 03/16/2018] [Indexed: 01/17/2023]
Abstract
The Linear Ubiquitin chain Assembly Complex (LUBAC) is required for optimal gene activation and prevention of cell death upon activation of immune receptors, including TNFR11. Deficiency in the LUBAC components SHARPIN or HOIP in mice results in severe inflammation in adulthood or embryonic lethality, respectively, due to deregulation of TNFR1-mediated cell death2–8. In humans, deficiency in the third LUBAC component, HOIL-1, causes autoimmunity and inflammatory disease, similar to HOIP deficiency, whereas HOIL-1 deficiency in mice was reported to cause no overt phenotype9–11. By creating HOIL-1-deficient mice, we here show that HOIL-1 is, however, as essential for LUBAC function as HOIP, albeit for different reasons: whereas HOIP is LUBAC’s catalytically active component, HOIL-1 is required for LUBAC assembly, stability and optimal retention in the TNFR1-signalling complex (TNFR1-SC), thereby preventing aberrant cell death. Both, HOIL-1 and HOIP prevent embryonic lethality at mid-gestation by interfering with aberrant TNFR1-mediated endothelial cell death, which only partially depends on RIPK1 kinase activity. Co-deletion of Caspase-8 with RIPK3 or MLKL prevents cell death in Hoil-1-/- embryos, yet only combined loss of Caspase-8 with MLKL results in viable HOIL-1-deficient mice. Interestingly, Ripk3-/-Caspase-8-/-Hoil-1-/- embryos die at late-gestation due to haematopoietic defects that are rescued by co-deletion of RIPK1 but not MLKL. Collectively, these results demonstrate that both, HOIP and HOIL-1 are essential LUBAC components and are required for embryogenesis by preventing aberrant cell death. Furthermore, they unveil that, when LUBAC and Caspase-8 are absent, RIPK3 prevents RIPK1 from inducing embryonic lethality by causing defects in foetal haematopoiesis.
Collapse
Affiliation(s)
- Nieves Peltzer
- UCL Cancer Institute, University College London, London, UK
| | | | | | - Peter Draber
- UCL Cancer Institute, University College London, London, UK.,Laboratory of Adaptive Immunity, Institute of Molecular Genetics, Czech Academy of Sciences, Prague, Czech Republic
| | - Helena Draberova
- UCL Cancer Institute, University College London, London, UK.,Laboratory of Adaptive Immunity, Institute of Molecular Genetics, Czech Academy of Sciences, Prague, Czech Republic
| | | | - Eva Rieser
- UCL Cancer Institute, University College London, London, UK
| | - Amanda Fisher
- University of Texas Health Science Center, San Antonio, TX, USA
| | | | | | | | - Elodie Lafont
- UCL Cancer Institute, University College London, London, UK
| | - Tobias L Haas
- Institute of General Pathology, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Yutaka Shimizu
- UCL Cancer Institute, University College London, London, UK
| | | | - Aida Sarr
- UCL Cancer Institute, University College London, London, UK
| | - James Rickard
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.,Department of Medical Biology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Silvia Alvarez-Diaz
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.,Department of Medical Biology, The University of Melbourne, Melbourne, Victoria, Australia
| | | | - Allison Beal
- Pattern Recognition Receptor Discovery Performance Unit, Immuno-Inflammation Therapeutic Area, GlaxoSmithKline, Collegeville, PA, USA
| | - Tariq Enver
- UCL Cancer Institute, University College London, London, UK
| | - John Bertin
- Pattern Recognition Receptor Discovery Performance Unit, Immuno-Inflammation Therapeutic Area, GlaxoSmithKline, Collegeville, PA, USA
| | - William Kaiser
- University of Texas Health Science Center, San Antonio, TX, USA
| | - Andreas Strasser
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.,Department of Medical Biology, The University of Melbourne, Melbourne, Victoria, Australia
| | - John Silke
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.,Department of Medical Biology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Philippe Bouillet
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.,Department of Medical Biology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Henning Walczak
- UCL Cancer Institute, University College London, London, UK.
| |
Collapse
|
67
|
Tang Y, Kwon H, Neel BA, Kasher-Meron M, Pessin JB, Yamada E, Pessin JE. The fructose-2,6-bisphosphatase TIGAR suppresses NF-κB signaling by directly inhibiting the linear ubiquitin assembly complex LUBAC. J Biol Chem 2018; 293:7578-7591. [PMID: 29650758 DOI: 10.1074/jbc.ra118.002727] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Revised: 04/05/2018] [Indexed: 12/28/2022] Open
Abstract
The systems integration of whole-body metabolism and immune signaling are central homeostatic mechanisms necessary for maintenance of normal physiology, and dysregulation of these processes leads to a variety of chronic disorders. However, the intracellular mechanisms responsible for cell-autonomous cross-talk between the inflammatory signaling pathways and metabolic flux have remained enigmatic. In this study, we discovered that the fructose-2,6-bisphosphatase TIGAR (Tp53-induced glycolysis and apoptosis regulator) critically regulates NF-κB activation. We found that TIGAR potently inhibits NF-κB-dependent gene expression by suppressing the upstream activation of IKKβ phosphorylation and kinase activation. This inhibition occurred through a direct binding competition between NEMO and TIGAR for association with the linear ubiquitination assembly complex (LUBAC). This competition prevented linear ubiquitination of NEMO, which is required for activation of IKKβ and other downstream targets. Furthermore, a TIGAR phosphatase activity-deficient mutant was equally effective as WT TIGAR in inhibiting NEMO linear ubiquitination, IKKβ phosphorylation/activation, and NF-κB signaling, indicating that TIGAR's effect on NF-κB signaling is due to its interaction with LUBAC. Physiologically, TIGAR knockout mice displayed enhanced adipose tissue NF-κB signaling, whereas adipocyte-specific overexpression of TIGAR suppressed adipose tissue NF-κB signaling. Together, these results demonstrate that TIGAR has a nonenzymatic molecular function that modulates the NF-κB signaling pathway by directly inhibiting the E3 ligase activity of LUBAC.
Collapse
Affiliation(s)
- Yan Tang
- From the Department of Medicine, Albert Einstein College of Medicine, Bronx, New York 10461
| | - Hyokjoon Kwon
- the Rutgers Robert Wood Johnson School of Medicine, Rutgers University, Piscataway, New Jersey 08854
| | | | - Michal Kasher-Meron
- From the Department of Medicine, Albert Einstein College of Medicine, Bronx, New York 10461
| | - Jacob B Pessin
- From the Department of Medicine, Albert Einstein College of Medicine, Bronx, New York 10461
| | - Eijiro Yamada
- the Department of Medicine and Molecular Science, Gunma University Graduate School of Medicine, Maebashi 371-8511, Japan, and
| | - Jeffrey E Pessin
- From the Department of Medicine, Albert Einstein College of Medicine, Bronx, New York 10461, .,the Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, New York 10461
| |
Collapse
|
68
|
Klein T, Eckhard U, Dufour A, Solis N, Overall CM. Proteolytic Cleavage-Mechanisms, Function, and "Omic" Approaches for a Near-Ubiquitous Posttranslational Modification. Chem Rev 2017; 118:1137-1168. [PMID: 29265812 DOI: 10.1021/acs.chemrev.7b00120] [Citation(s) in RCA: 123] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Proteases enzymatically hydrolyze peptide bonds in substrate proteins, resulting in a widespread, irreversible posttranslational modification of the protein's structure and biological function. Often regarded as a mere degradative mechanism in destruction of proteins or turnover in maintaining physiological homeostasis, recent research in the field of degradomics has led to the recognition of two main yet unexpected concepts. First, that targeted, limited proteolytic cleavage events by a wide repertoire of proteases are pivotal regulators of most, if not all, physiological and pathological processes. Second, an unexpected in vivo abundance of stable cleaved proteins revealed pervasive, functionally relevant protein processing in normal and diseased tissue-from 40 to 70% of proteins also occur in vivo as distinct stable proteoforms with undocumented N- or C-termini, meaning these proteoforms are stable functional cleavage products, most with unknown functional implications. In this Review, we discuss the structural biology aspects and mechanisms of catalysis by different protease classes. We also provide an overview of biological pathways that utilize specific proteolytic cleavage as a precision control mechanism in protein quality control, stability, localization, and maturation, as well as proteolytic cleavage as a mediator in signaling pathways. Lastly, we provide a comprehensive overview of analytical methods and approaches to study activity and substrates of proteolytic enzymes in relevant biological models, both historical and focusing on state of the art proteomics techniques in the field of degradomics research.
Collapse
Affiliation(s)
- Theo Klein
- Life Sciences Institute, Department of Oral Biological and Medical Sciences, and ‡Department of Biochemistry and Molecular Biology, University of British Columbia , Vancouver, British Columbia V6T 1Z4, Canada
| | - Ulrich Eckhard
- Life Sciences Institute, Department of Oral Biological and Medical Sciences, and ‡Department of Biochemistry and Molecular Biology, University of British Columbia , Vancouver, British Columbia V6T 1Z4, Canada
| | - Antoine Dufour
- Life Sciences Institute, Department of Oral Biological and Medical Sciences, and ‡Department of Biochemistry and Molecular Biology, University of British Columbia , Vancouver, British Columbia V6T 1Z4, Canada
| | - Nestor Solis
- Life Sciences Institute, Department of Oral Biological and Medical Sciences, and ‡Department of Biochemistry and Molecular Biology, University of British Columbia , Vancouver, British Columbia V6T 1Z4, Canada
| | - Christopher M Overall
- Life Sciences Institute, Department of Oral Biological and Medical Sciences, and ‡Department of Biochemistry and Molecular Biology, University of British Columbia , Vancouver, British Columbia V6T 1Z4, Canada
| |
Collapse
|
69
|
Aguilar-Alonso F, Whiting AL, Kim YJ, Bernal F. Biophysical and biological evaluation of optimized stapled peptide inhibitors of the linear ubiquitin chain assembly complex (LUBAC). Bioorg Med Chem 2017; 26:1179-1188. [PMID: 29246782 DOI: 10.1016/j.bmc.2017.11.047] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Revised: 11/17/2017] [Accepted: 11/29/2017] [Indexed: 10/18/2022]
Abstract
Linear ubiquitylation, in which ubiquitin units are covalently linked through N- and C-terminal amino acids, is a unique cellular signaling mechanism. This process is controlled by a single E3 ubiquitin ligase, the linear ubiquitin chain assembly complex (LUBAC), which is composed of three proteins - HOIL-1L, HOIP and SHARPIN. LUBAC is involved in the activation of the canonical NF-κB pathway and has been linked to NF-κB dependent malignancies. In this work, we present HOIP-based stapled alpha-helical peptides designed to inhibit LUBAC through the disruption of the HOIL-1L-HOIP interaction and loss of the functional complex. We find our HOIP peptides to be active LUBAC ubiquitylation inhibitors in vitro, though through interaction with HOIP rather than HOIL. Active peptides were shown to have inhibitory effects on cell viability, reduced NF-κB activity and decreased production of NF-κB related gene products. This work further demonstrates the potential of LUBAC as a therapeutic target and of the use of stapled peptides as inhibitors of protein-protein interactions.
Collapse
Affiliation(s)
- Francisco Aguilar-Alonso
- Laboratory of Protein Dynamics and Signaling, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, United States
| | - Amanda L Whiting
- Laboratory of Protein Dynamics and Signaling, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, United States
| | - Ye Joon Kim
- Laboratory of Protein Dynamics and Signaling, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, United States
| | - Federico Bernal
- Laboratory of Protein Dynamics and Signaling, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, United States.
| |
Collapse
|
70
|
Tsuchiya Y, Osaki K, Kanamoto M, Nakao Y, Takahashi E, Higuchi T, Kamata H. Distinct B subunits of PP2A regulate the NF-κB signalling pathway through dephosphorylation of IKKβ, IκBα and RelA. FEBS Lett 2017; 591:4083-4094. [PMID: 29139553 PMCID: PMC5767752 DOI: 10.1002/1873-3468.12912] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Revised: 10/04/2017] [Accepted: 10/25/2017] [Indexed: 12/23/2022]
Abstract
PP2A is composed of a scaffolding subunit (A), a catalytic subunit (C) and a regulatory subunit (B) that is classified into four families including B, B′, B′′ and B′′′/striatin. Here, we found that a distinct PP2A complex regulates NF‐κB signalling by dephosphorylation of IKKβ, IκBα and RelA/p65. The PP2A core enzyme AC dimer and the holoenzyme AB′′′C trimer dephosphorylate IKKβ, IκBα and RelA, whereas the ABC trimer dephosphorylates IκBα but not IKKβ and RelA in cells. In contrast, AB′C and AB′′C trimers have little effect on dephosphorylation of these signalling proteins. These results suggest that different forms of PP2A regulate NF‐κB pathway signalling through multiple steps each in a different manner, thereby finely tuning NF‐κB‐ and IKKβ‐mediated cellular responses.
Collapse
Affiliation(s)
- Yoshihiro Tsuchiya
- Laboratory of Biomedical Chemistry, Department of Molecular Medical Science, Graduate School of Biomedical Science, Hiroshima University, Japan
| | - Keiko Osaki
- Laboratory of Biomedical Chemistry, Department of Molecular Medical Science, Graduate School of Biomedical Science, Hiroshima University, Japan
| | - Mayu Kanamoto
- Laboratory of Biomedical Chemistry, Department of Molecular Medical Science, Graduate School of Biomedical Science, Hiroshima University, Japan
| | - Yuki Nakao
- Laboratory of Biomedical Chemistry, Department of Molecular Medical Science, Graduate School of Biomedical Science, Hiroshima University, Japan
| | - Ena Takahashi
- Laboratory of Biomedical Chemistry, Department of Molecular Medical Science, Graduate School of Biomedical Science, Hiroshima University, Japan
| | - Toru Higuchi
- Laboratory of Biomedical Chemistry, Department of Molecular Medical Science, Graduate School of Biomedical Science, Hiroshima University, Japan
| | - Hideaki Kamata
- Laboratory of Biomedical Chemistry, Department of Molecular Medical Science, Graduate School of Biomedical Science, Hiroshima University, Japan
| |
Collapse
|
71
|
Zhou B, Zeng L. Conventional and unconventional ubiquitination in plant immunity. MOLECULAR PLANT PATHOLOGY 2017; 18:1313-1330. [PMID: 27925369 PMCID: PMC6638253 DOI: 10.1111/mpp.12521] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Revised: 11/23/2016] [Accepted: 11/27/2016] [Indexed: 05/16/2023]
Abstract
Ubiquitination is one of the most abundant types of protein post-translational modification (PTM) in plant cells. The importance of ubiquitination in the regulation of many aspects of plant immunity has been increasingly appreciated in recent years. Most of the studies linking ubiquitination to the plant immune system, however, have been focused on the E3 ubiquitin ligases and the conventional ubiquitination that leads to the degradation of the substrate proteins by the 26S proteasome. By contrast, our knowledge about the role of unconventional ubiquitination that often serves as non-degradative, regulatory signal remains a significant gap. We discuss, in this review, the recent advances in our understanding of ubiquitination in the modulation of plant immunity, with a particular focus on the E3 ubiquitin ligases. We approach the topic from a perspective of two broadly defined types of ubiquitination in an attempt to highlight the importance, yet current scarcity, in our knowledge about the regulation of plant immunity by unconventional ubiquitination.
Collapse
Affiliation(s)
- Bangjun Zhou
- Center for Plant Science Innovation and Department of Plant PathologyUniversity of NebraskaLincolnNE68583USA
| | - Lirong Zeng
- Center for Plant Science Innovation and Department of Plant PathologyUniversity of NebraskaLincolnNE68583USA
- Southern Regional Collaborative Innovation Center for Grain and Oil CropsHunan Agricultural UniversityChangsha410128China
| |
Collapse
|
72
|
Imaizumi T, Hayakari R, Watanabe S, Aizawa T, Matsumiya T, Yoshida H, Tsuruga K, Kawaguchi S, Tanaka H. Cylindromatosis (CYLD), a Deubiquitinase, Attenuates Inflammatory Signaling Pathways by Activating Toll-Like Receptor 3 in Human Mesangial Cells. Kidney Blood Press Res 2017; 42:942-950. [PMID: 29166644 DOI: 10.1159/000485084] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 07/22/2017] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND/AIMS Cylindromatosis (CYLD), a deubiquitinase, negatively regulates nuclear factor-κB in various cells. However, its potential roles in glomerular inflammation remain unclear. Because the activation of the Toll-like receptor 3 (TLR3)/type I interferon (IFN) pathways plays a pivotal role in chronic kidney diseases (CKD), we examined the role of CYLD in the TLR3 signaling in cultured human mesangial cells (MCs). METHODS We stimulated CYLD-silenced MCs with polyinosinic-polycytidylic acid (poly IC), a synthetic analogue of dsRNA, and studied representative TLR3/IFN-β pathways (i.e., TLR3/IFN-β/retinoic acid-inducible gene-I (RIG-I)/CCL5, and TLR3/IFN-β/melanoma differentiation associated gene 5 (MDA5)/CXCL10 axes) using RT-PCR, western blotting, and ELISA. We also used immunofluorescence staining and microscopy to examine mesangial CYLD expression in biopsied specimens from patients with CKD. RESULTS CYLD silencing resulted in an increase of poly IC-induced RIG-I and MDA5 protein levels and increased CCL5 and CXCL10 mRNA and protein expression, but unexpectedly decreased mRNA expressions of RIG-I and MDA5. Interestingly, CYLD silencing did not affect IFN-β or the phosphorylated STAT1 (signal transducers and activator of transcription protein 1). CYLD was highly expressed in biopsied specimens from patients with proliferative lupus nephritis (LN). CONCLUSION CYLD inhibits post-transcriptional regulation of RIG-I and MDA5 expression following TLR3 activation in MCs. CYLD may be involved in the pathogenesis of CKD, especially pathogenesis of LN.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | - Shogo Kawaguchi
- Department of Gastroenterology and Hematology, Hirosaki University Graduate School of Medicine, Hirosaki, Japan
| | - Hiroshi Tanaka
- Department of Pediatrics, Hirosaki, Japan
- Department of School Health Science, Hirosaki University Faculty of Education, Hirosaki, Japan
| |
Collapse
|
73
|
Abstract
Pathogen-associated molecular patterns (PAMPs) and damage-associated molecular patterns (DAMPs) are recognized by different cellular pathogen recognition receptors (PRRs), which are expressed on cell membrane or in the cytoplasm of cells of the innate immune system. Nucleic acids derived from pathogens or from certain cellular conditions represent a large category of PAMPs/DAMPs that trigger production of type I interferons (IFN-I) in addition to pro-inflammatory cytokines, by specifically binding to intracellular Toll-like receptors or cytosolic receptors. These cytosolic receptors, which are not related to TLRs and we call them “Toll-free” receptors, include the RNA-sensing RIG-I like receptors (RLRs), the DNA-sensing HIN200 family, and cGAS, amongst others. Viruses have evolved myriad strategies to evoke both host cellular and viral factors to evade IFN-I-mediated innate immune responses, to facilitate their infection, replication, and establishment of latency. This review outlines these “Toll-free” innate immune pathways and recent updates on their regulation, with focus on cellular and viral factors with enzyme activities.
Collapse
Affiliation(s)
- Ling Wang
- Department of Internal Medicine, Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA.,Center of Excellence for Inflammation, Infectious Diseases and Immunity, Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA
| | - Shunbin Ning
- Department of Internal Medicine, Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA.,Center of Excellence for Inflammation, Infectious Diseases and Immunity, Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA
| |
Collapse
|
74
|
Hrdinka M, Gyrd-Hansen M. The Met1-Linked Ubiquitin Machinery: Emerging Themes of (De)regulation. Mol Cell 2017; 68:265-280. [PMID: 29053955 DOI: 10.1016/j.molcel.2017.09.001] [Citation(s) in RCA: 90] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Revised: 07/21/2017] [Accepted: 08/31/2017] [Indexed: 01/24/2023]
Abstract
The linear ubiquitin chain assembly complex, LUBAC, is the only known mammalian ubiquitin ligase that makes methionine 1 (Met1)-linked polyubiquitin (also referred to as linear ubiquitin). A decade after LUBAC was discovered as a cellular activity of unknown function, there are now many lines of evidence connecting Met1-linked polyubiquitin to NF-κB signaling, cell death, inflammation, immunity, and cancer. We now know that Met1-linked polyubiquitin has potent signaling functions and that its deregulation is connected to disease. Indeed, mutations and deficiencies in several factors involved in conjugation and deconjugation of Met1-linked polyubiquitin have been implicated in immune-related disorders. Here, we discuss current knowledge and recent insights into the role and regulation of Met1-linked polyubiquitin, with an emphasis on the mechanisms controlling the function of LUBAC.
Collapse
Affiliation(s)
- Matous Hrdinka
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Old Road Campus Research Building, Oxford OX3 7DQ, UK
| | - Mads Gyrd-Hansen
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Old Road Campus Research Building, Oxford OX3 7DQ, UK.
| |
Collapse
|
75
|
Abstract
Purpose of review The CARMA1/BCL10/MALT1 (CBM) complex is a multimeric signaling complex controlling several important aspects of lymphocyte activation. Gain-of-function mutations in the genes encoding CBM proteins or their upstream regulators are associated with lymphoid malignancies, whereas loss-of-function mutations lead to immunodeficiency. This review reports on recent findings advancing our understanding of how CBM proteins contribute to malignant and nonmalignant hematological diseases in humans. Recent findings Somatic gain-of-function mutations of CARMA1 (also known as CARD11), originally described for patients with diffuse large B-cell lymphoma, have recently been identified in patients with acute T-cell leukemia/lymphoma or Sézary syndrome, and in patients with a B-cell lymphoproliferative disorder known as BENTA. Loss-of-function mutations of CARMA1 and MALT1, on the other hand, have been reported to underlie human immunodeficiency. Lately, it has become clear that CBM-dependent signaling promotes lymphomagenesis not only via NF-κB activation, but also via the AP-1 family of transcription factors. The identification of new substrates of the protease MALT1 and the characterization of mice expressing catalytically inactive MALT1 have deepened our understanding of how the CBM complex controls lymphocyte proliferation through promoting MALT1's protease activity. Summary The discovery of CARMA1 gain-of-function mutations in T-cell malignancies and BENTA patients, as well as the association of CARMA1 and MALT1 mutations with human immunodeficiency highlight the importance of CBM proteins in the regulation of lymphocyte functions, and suggest that the protease activity of MALT1 might be targeted to treat specific lymphoid malignancies.
Collapse
|
76
|
Joshi RN, Binai NA, Marabita F, Sui Z, Altman A, Heck AJR, Tegnér J, Schmidt A. Phosphoproteomics Reveals Regulatory T Cell-Mediated DEF6 Dephosphorylation That Affects Cytokine Expression in Human Conventional T Cells. Front Immunol 2017; 8:1163. [PMID: 28993769 PMCID: PMC5622166 DOI: 10.3389/fimmu.2017.01163] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Accepted: 09/01/2017] [Indexed: 12/25/2022] Open
Abstract
Regulatory T cells (Tregs) control key events of immune tolerance, primarily by suppression of effector T cells. We previously revealed that Tregs rapidly suppress T cell receptor (TCR)-induced calcium store depletion in conventional CD4+CD25− T cells (Tcons) independently of IP3 levels, consequently inhibiting NFAT signaling and effector cytokine expression. Here, we study Treg suppression mechanisms through unbiased phosphoproteomics of primary human Tcons upon TCR stimulation and Treg-mediated suppression, respectively. Tregs induced a state of overall decreased phosphorylation as opposed to TCR stimulation. We discovered novel phosphosites (T595_S597) in the DEF6 (SLAT) protein that were phosphorylated upon TCR stimulation and conversely dephosphorylated upon coculture with Tregs. Mutation of these DEF6 phosphosites abrogated interaction of DEF6 with the IP3 receptor and affected NFAT activation and cytokine transcription in primary Tcons. This novel mechanism and phosphoproteomics data resource may aid in modifying sensitivity of Tcons to Treg-mediated suppression in autoimmune disease or cancer.
Collapse
Affiliation(s)
- Rubin N Joshi
- Unit of Computational Medicine, Center for Molecular Medicine, Department of Medicine Solna, Karolinska University Hospital, Science for Life Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Nadine A Binai
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, Netherlands.,Netherlands Proteomics Centre, Utrecht, Netherlands
| | - Francesco Marabita
- Unit of Computational Medicine, Center for Molecular Medicine, Department of Medicine Solna, Karolinska University Hospital, Science for Life Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Zhenhua Sui
- Division of Cell Biology, La Jolla Institute for Allergy and Immunology, La Jolla, CA, United States
| | - Amnon Altman
- Division of Cell Biology, La Jolla Institute for Allergy and Immunology, La Jolla, CA, United States
| | - Albert J R Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, Netherlands.,Netherlands Proteomics Centre, Utrecht, Netherlands
| | - Jesper Tegnér
- Unit of Computational Medicine, Center for Molecular Medicine, Department of Medicine Solna, Karolinska University Hospital, Science for Life Laboratory, Karolinska Institutet, Stockholm, Sweden.,Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.,Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Angelika Schmidt
- Unit of Computational Medicine, Center for Molecular Medicine, Department of Medicine Solna, Karolinska University Hospital, Science for Life Laboratory, Karolinska Institutet, Stockholm, Sweden
| |
Collapse
|
77
|
Ma X, Zhao J, Yang F, Liu H, Qi W. Ubiquitin conjugating enzyme E2 L3 promoted tumor growth of NSCLC through accelerating p27kip1 ubiquitination and degradation. Oncotarget 2017; 8:84193-84203. [PMID: 29137415 PMCID: PMC5663587 DOI: 10.18632/oncotarget.20449] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Accepted: 07/26/2017] [Indexed: 02/03/2023] Open
Abstract
The molecular pathogenesis of human lung cancer has not been completely clarified. Here, we reported that UBE2L3, a member of the ubiquitin-conjugating enzymes (E2s), were overexpressed in non-small-cell lung cancer (NSCLC) tissues compared with the non-tumor tissues. High expression of UBE2L3 was correlated with advanced tumor stage and adverse outcomes. Knockdown of UBE2L3 inhibited NSCLC cell growth while ectopic expression of UBE2L3 promoted NSCLC cell growth in a cell cycle dependent manner. The results of subcutaneous tumor xenograft studies revealed that knockdown of UBE2L3 attenuated the in vivo tumor growth. Mechanistically, we observed that UBE2L3 could interact with F-box protein Skp2, a member of the SCF (Skp2) ubiquitin ligase complex, and thus promoted the ubiquitination and proteasomal degradation of p27kip1. Furthermore, NSCLC cases with high level of UBE2L3 and low level of p27kip1 had worst prognosis, suggesting that combination of UBE2L3 and p27kip1 is a more powerful prognostic marker for NSCLC patients. Taken together, the current study presented a novel marker for predicting prognosis and a potential therapeutic target for NSCLC patients.
Collapse
Affiliation(s)
- Xingjie Ma
- Department of Cardiothoracic Surgery, The First Affiliated Hospital of Jiaxing University, Jiaxing, Zhejiang, China
| | - Junjie Zhao
- Department of Cardiothoracic Surgery, The First Affiliated Hospital of Jiaxing University, Jiaxing, Zhejiang, China
| | - Fan Yang
- Department of Cardiothoracic Surgery, The First Affiliated Hospital of Jiaxing University, Jiaxing, Zhejiang, China
| | - Haitao Liu
- Department of Cardiothoracic Surgery, The First Affiliated Hospital of Jiaxing University, Jiaxing, Zhejiang, China
| | - Weibo Qi
- Department of Cardiothoracic Surgery, The First Affiliated Hospital of Jiaxing University, Jiaxing, Zhejiang, China
| |
Collapse
|
78
|
Dove KK, Klevit RE. RING-Between-RING E3 Ligases: Emerging Themes amid the Variations. J Mol Biol 2017; 429:3363-3375. [PMID: 28827147 DOI: 10.1016/j.jmb.2017.08.008] [Citation(s) in RCA: 99] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Revised: 08/09/2017] [Accepted: 08/10/2017] [Indexed: 11/30/2022]
Abstract
Covalent, reversible, post-translational modification of cellular proteins with the small modifier, ubiquitin (Ub), regulates virtually every known cellular process in eukaryotes. The process is carried out by a trio of enzymes: a Ub-activating (E1) enzyme, a Ub-conjugating (E2) enzyme, and a Ub ligase (E3) enzyme. RING-in-Between-RING (RBR) E3s constitute one of three classes of E3 ligases and are defined by a RING-HECT-hybrid mechanism that utilizes a E2-binding RING domain and a second domain (called RING2) that contains an active site Cys required for the formation of an obligatory E3~Ub intermediate. Albeit a small class, RBR E3s in humans regulate diverse cellular process. This review focuses on non-Parkin members such as HOIP/HOIL-1L (the only E3s known to generate linear Ub chains), HHARI and TRIAD1, both of which have been recently demonstrated to work together with Cullin RING E3 ligases. We provide a brief historical background and highlight, summarize, and discuss recent developments in the young field of RBR E3s. Insights reviewed here include new understandings of the RBR Ub-transfer mechanism, specifically the role of RING1 and various Ub-binding sites, brief structural comparisons among members, and different modes of auto-inhibition and activation.
Collapse
Affiliation(s)
- Katja K Dove
- Department of Biochemistry, University of Washington, Seattle, WA, United States
| | - Rachel E Klevit
- Department of Biochemistry, University of Washington, Seattle, WA, United States.
| |
Collapse
|
79
|
Immune defects caused by mutations in the ubiquitin system. J Allergy Clin Immunol 2017; 139:743-753. [PMID: 28270366 DOI: 10.1016/j.jaci.2016.11.031] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Revised: 10/19/2016] [Accepted: 11/29/2016] [Indexed: 12/18/2022]
Abstract
The importance of the ubiquitin system in health and disease has been widely recognized in recent decades, with better understanding of the various components of the system and their function. Ubiquitination, which is essential to almost all biological processes in eukaryotes, was also found to play an important role in innate and adaptive immune responses. Thus it is not surprising that mutations in genes coding for components of the ubiquitin system cause immune dysregulation. The first defect in the system was described 30 years ago and is due to mutations in the nuclear factor κB (NF-κB) essential modulator, a key regulator of the NF-κB pathway. With use of novel sequencing techniques, many additional mutations in different genes involved in ubiquitination and related to immune system function were identified. This can be clearly illustrated in mutations in the different activation pathways of NF-κB, which result in aberrations in production of various proinflammatory cytokines. The inherited diseases typically manifest with immunodeficiency, autoimmunity, or autoinflammation. In this perspective we provide a short description of the ubiquitin system, with specific emphasis given to its role in the immune system. The various immunodeficiency conditions identified thus far in association with defective ubiquitination are discussed in more detail.
Collapse
|
80
|
Affiliation(s)
- Mads Gyrd-Hansen
- Nuffield Department of Clinical Medicine, Ludwig Institute for Cancer Research, University of Oxford, Old Road Campus Research Building, Oxford OX3 7DQ, UK
| |
Collapse
|
81
|
Brazee P, Dada LA, Sznajder JI. Role of Linear Ubiquitination in Health and Disease. Am J Respir Cell Mol Biol 2017; 54:761-8. [PMID: 26848516 DOI: 10.1165/rcmb.2016-0014tr] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The covalent attachment of ubiquitin to target proteins is one of the most prevalent post-translational modifications, regulating a myriad of cellular processes including cell growth, survival, and metabolism. Recently, a novel RING E3 ligase complex was described, called linear ubiquitin assembly complex (LUBAC), which is capable of connecting ubiquitin molecules in a novel head-to-tail fashion via the N-terminal methionine residue. LUBAC is a heteromeric complex composed of heme-oxidized iron-responsive element-binding protein 2 ubiquitin ligase-1L (HOIL-1L), HOIL-1L-interacting protein, and shank-associated RH domain-interacting protein (SHARPIN). The essential role of LUBAC-generated linear chains for activation of nuclear factor-κB (NF-κB) signaling was first described in the activation of tumor necrosis factor-α receptor signaling complex. A decade of research has identified additional pathways that use LUBAC for downstream signaling, including CD40 ligand and the IL-1β receptor, as well as cytosolic pattern recognition receptors including nucleotide-binding oligomerization domain containing 2 (NOD2), retinoic acid-inducible gene 1 (RIG-1), and the NOD-like receptor family, pyrin domain containing 3 inflammasome (NLRP3). Even though the three components of the complex are required for full activation of NF-κB, the individual components of LUBAC regulate specific cell type- and stimuli-dependent effects. In humans, autosomal defects in LUBAC are associated with both autoinflammation and immunodeficiency, with additional disorders described in mice. Moreover, in the lung epithelium, HOIL-1L ubiquitinates target proteins independently of the other LUBAC components, adding another layer of complexity to the function and regulation of LUBAC. Although many advances have been made, the diverse functions of linear ubiquitin chains and the regulation of LUBAC are not yet completely understood. In this review, we discuss the various roles of linear ubiquitin chains and point to areas of study that would benefit from further investigation into LUBAC-mediated signaling pathways in lung pathophysiology.
Collapse
Affiliation(s)
- Patricia Brazee
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Northwestern University, Chicago, Illinois
| | - Laura A Dada
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Northwestern University, Chicago, Illinois
| | - Jacob I Sznajder
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Northwestern University, Chicago, Illinois
| |
Collapse
|
82
|
A Naturally Occurring Recombinant Enterovirus Expresses a Torovirus Deubiquitinase. J Virol 2017; 91:JVI.00450-17. [PMID: 28490584 DOI: 10.1128/jvi.00450-17] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Accepted: 04/26/2017] [Indexed: 11/20/2022] Open
Abstract
Enteroviruses (EVs) are implicated in a wide range of diseases in humans and animals. In this study, a novel enterovirus (enterovirus species G [EVG]) (EVG 08/NC_USA/2015) was isolated from a diagnostic sample from a neonatal pig diarrhea case and identified by using metagenomics and complete genome sequencing. The viral genome shares 75.4% nucleotide identity with a prototypic EVG strain (PEV9 UKG/410/73). Remarkably, a 582-nucleotide insertion, flanked by 3Cpro cleavage sites at the 5' and 3' ends, was found in the 2C/3A junction region of the viral genome. This insertion encodes a predicted protease with 54 to 68% amino acid identity to torovirus (ToV) papain-like protease (PLP) (ToV-PLP). Structural homology modeling predicts that this protease adopts a fold and a catalytic site characteristic of minimal PLP catalytic domains. This structure is similar to those of core catalytic domains of the foot-and-mouth disease virus leader protease and coronavirus PLPs, which act as deubiquitinating and deISGylating (interferon [IFN]-stimulated gene 15 [ISG15]-removing) enzymes on host cell substrates. Importantly, the recombinant ToV-PLP protein derived from this novel enterovirus also showed strong deubiquitination and deISGylation activities and demonstrated the ability to suppress IFN-β expression. Using reverse genetics, we generated a ToV-PLP knockout recombinant virus. Compared to the wild-type virus, the ToV-PLP knockout mutant virus showed impaired growth and induced higher expression levels of innate immune genes in infected cells. These results suggest that ToV-PLP functions as an innate immune antagonist; enterovirus G may therefore gain fitness through the acquisition of ToV-PLP from a recombination event.IMPORTANCE Enteroviruses comprise a highly diversified group of viruses. Genetic recombination has been considered a driving force for viral evolution; however, recombination between viruses from two different orders is a rare event. In this study, we identified a special case of cross-order recombination between enterovirus G (order Picornavirales) and torovirus (order Nidovirales). This naturally occurring recombination event may have broad implications for other picornaviral and/or nidoviral species. Importantly, we demonstrated that the exogenous ToV-PLP gene that was inserted into the EVG genome encodes a deubiquitinase/deISGylase and potentially suppresses host cellular innate immune responses. Our results provide insights into how a gain of function through genetic recombination, in particular cross-order recombination, may improve the ability of a virus to evade host immunity.
Collapse
|
83
|
Geoepidemiology and Immunologic Features of Autoinflammatory Diseases: a Comprehensive Review. Clin Rev Allergy Immunol 2017; 54:454-479. [DOI: 10.1007/s12016-017-8613-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
|
84
|
Shimizu Y, Peltzer N, Sevko A, Lafont E, Sarr A, Draberova H, Walczak H. The Linear ubiquitin chain assembly complex acts as a liver tumor suppressor and inhibits hepatocyte apoptosis and hepatitis. Hepatology 2017; 65:1963-1978. [PMID: 28120397 PMCID: PMC5485060 DOI: 10.1002/hep.29074] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Revised: 01/09/2017] [Accepted: 01/18/2017] [Indexed: 02/05/2023]
Abstract
Linear ubiquitination is a key posttranslational modification that regulates immune signaling and cell death pathways, notably tumor necrosis factor receptor 1 (TNFR1) signaling. The only known enzyme complex capable of forming linear ubiquitin chains under native conditions to date is the linear ubiquitin chain assembly complex, of which the catalytic core component is heme-oxidized iron regulatory protein 2 ubiquitin ligase-1-interacting protein (HOIP). To understand the underlying mechanisms of maintenance of liver homeostasis and the role of linear ubiquitination specifically in liver parenchymal cells, we investigated the physiological role of HOIP in the liver parenchyma. To do so, we created mice harboring liver parenchymal cell-specific deletion of HOIP (HoipΔhep mice) by crossing Hoip-floxed mice with albumin-Cre mice. HOIP deficiency in liver parenchymal cells triggered tumorigenesis at 18 months of age preceded by spontaneous hepatocyte apoptosis and liver inflammation within the first month of life. In line with the emergence of inflammation, HoipΔhep mice displayed enhanced liver regeneration and DNA damage. In addition, consistent with increased apoptosis, HOIP-deficient hepatocytes showed enhanced caspase activation and endogenous formation of a death-inducing signaling complex which activated caspase-8. Unexpectedly, exacerbated caspase activation and apoptosis were not dependent on TNFR1, whereas ensuing liver inflammation and tumorigenesis were promoted by TNFR1 signaling. CONCLUSION The linear ubiquitin chain assembly complex serves as a previously undescribed tumor suppressor in the liver, restraining TNFR1-independent apoptosis in hepatocytes which, in its absence, is causative of TNFR1-mediated inflammation, resulting in hepatocarcinogenesis. (Hepatology 2017;65:1963-1978).
Collapse
Affiliation(s)
- Yutaka Shimizu
- Centre for Cell Death, Cancer and Inflammation, UCL Cancer InstituteUniversity College LondonLondonUK
| | - Nieves Peltzer
- Centre for Cell Death, Cancer and Inflammation, UCL Cancer InstituteUniversity College LondonLondonUK
| | - Alexandra Sevko
- Centre for Cell Death, Cancer and Inflammation, UCL Cancer InstituteUniversity College LondonLondonUK
| | - Elodie Lafont
- Centre for Cell Death, Cancer and Inflammation, UCL Cancer InstituteUniversity College LondonLondonUK
| | - Aida Sarr
- Centre for Cell Death, Cancer and Inflammation, UCL Cancer InstituteUniversity College LondonLondonUK
| | - Helena Draberova
- Centre for Cell Death, Cancer and Inflammation, UCL Cancer InstituteUniversity College LondonLondonUK
| | - Henning Walczak
- Centre for Cell Death, Cancer and Inflammation, UCL Cancer InstituteUniversity College LondonLondonUK
| |
Collapse
|
85
|
Lafont E, Kantari-Mimoun C, Draber P, De Miguel D, Hartwig T, Reichert M, Kupka S, Shimizu Y, Taraborrelli L, Spit M, Sprick MR, Walczak H. The linear ubiquitin chain assembly complex regulates TRAIL-induced gene activation and cell death. EMBO J 2017; 36:1147-1166. [PMID: 28258062 PMCID: PMC5412822 DOI: 10.15252/embj.201695699] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Revised: 01/30/2017] [Accepted: 02/13/2017] [Indexed: 01/08/2023] Open
Abstract
The linear ubiquitin chain assembly complex (LUBAC) is the only known E3 ubiquitin ligase which catalyses the generation of linear ubiquitin linkages de novo LUBAC is a crucial component of various immune receptor signalling pathways. Here, we show that LUBAC forms part of the TRAIL-R-associated complex I as well as of the cytoplasmic TRAIL-induced complex II In both of these complexes, HOIP limits caspase-8 activity and, consequently, apoptosis whilst being itself cleaved in a caspase-8-dependent manner. Yet, by limiting the formation of a RIPK1/RIPK3/MLKL-containing complex, LUBAC also restricts TRAIL-induced necroptosis. We identify RIPK1 and caspase-8 as linearly ubiquitinated targets of LUBAC following TRAIL stimulation. Contrary to its role in preventing TRAIL-induced RIPK1-independent apoptosis, HOIP presence, but not its activity, is required for preventing necroptosis. By promoting recruitment of the IKK complex to complex I, LUBAC also promotes TRAIL-induced activation of NF-κB and, consequently, the production of cytokines, downstream of FADD, caspase-8 and cIAP1/2. Hence, LUBAC controls the TRAIL signalling outcome from complex I and II, two platforms which both trigger cell death and gene activation.
Collapse
Affiliation(s)
- Elodie Lafont
- Centre for Cell Death, Cancer and Inflammation (CCCI), UCL Cancer Institute, University College London, London, UK
| | - Chahrazade Kantari-Mimoun
- 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
| | - Diego De Miguel
- Centre for Cell Death, Cancer and Inflammation (CCCI), UCL Cancer Institute, University College London, London, UK
| | - Torsten Hartwig
- 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
| | - Sebastian Kupka
- Centre for Cell Death, Cancer and Inflammation (CCCI), UCL Cancer Institute, University College London, London, UK
| | - Yutaka Shimizu
- Centre for Cell Death, Cancer and Inflammation (CCCI), UCL Cancer Institute, University College London, London, UK
| | - Lucia Taraborrelli
- Centre for Cell Death, Cancer and Inflammation (CCCI), UCL Cancer Institute, University College London, London, UK
| | - Maureen Spit
- Centre for Cell Death, Cancer and Inflammation (CCCI), UCL Cancer Institute, University College London, London, UK
| | - Martin R Sprick
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGMBH), Heidelberg, Germany
| | - Henning Walczak
- Centre for Cell Death, Cancer and Inflammation (CCCI), UCL Cancer Institute, University College London, London, UK
| |
Collapse
|
86
|
Aksentijevich I, Zhou Q. NF-κB Pathway in Autoinflammatory Diseases: Dysregulation of Protein Modifications by Ubiquitin Defines a New Category of Autoinflammatory Diseases. Front Immunol 2017. [PMID: 28469620 DOI: 10.3389/fimmu.2017.00399)] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
Autoinflammatory diseases are caused by defects in genes that regulate the innate immunity. Recently, the scope of autoinflammation has been broadened to include diseases that result from dysregulations in protein modifications by the highly conserved ubiquitin (Ub) peptides. Thus far these diseases consist of linear ubiquitin chain assembly complex (LUBAC) and OTULIN deficiencies, and haploinsufficiency of A20. The LUBAC is critical for linear ubiquitination of key signaling molecules in immune response pathways, while deubiquitinase enzymes, OTULIN and TNFAIP3/A20, reverse the effects of ubiquitination by hydrolyzing linear (Met1) and Lys63 (K63) Ub moieties, respectively, from conjugated proteins. Consequently, OTULIN or A20-deficient cells have an excess of Met1 or K63 Ub chains on NEMO, RIPK1, and other target substrates, which lead to constitutive activation of the NF-kB pathway. Mutant cells produce elevated levels of many proinflammatory cytokines and respond to therapy with cytokine inhibitors. Patients with an impairment in LUBAC stability have compromised NF-kB responses in non-immune cells such as fibroblasts, while their monocytes are hyperresponsive to IL-1β. Discoveries of germline mutations in enzymes that regulate protein modifications by Ub define a new category of autoinflammatory diseases caused by upregulations in the NF-kB signaling. The primary aim of this review is to summarize the latest developments in our understanding of the etiology of autoinflammation.
Collapse
Affiliation(s)
- Ivona Aksentijevich
- Inflammatory Disease Section, National Human Genome Research Institute, Bethesda, MD, USA
| | - Qing Zhou
- Inflammatory Disease Section, National Human Genome Research Institute, Bethesda, MD, USA
| |
Collapse
|
87
|
Aksentijevich I, Zhou Q. NF-κB Pathway in Autoinflammatory Diseases: Dysregulation of Protein Modifications by Ubiquitin Defines a New Category of Autoinflammatory Diseases. Front Immunol 2017; 8:399. [PMID: 28469620 PMCID: PMC5395695 DOI: 10.3389/fimmu.2017.00399] [Citation(s) in RCA: 133] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Accepted: 03/21/2017] [Indexed: 11/24/2022] Open
Abstract
Autoinflammatory diseases are caused by defects in genes that regulate the innate immunity. Recently, the scope of autoinflammation has been broadened to include diseases that result from dysregulations in protein modifications by the highly conserved ubiquitin (Ub) peptides. Thus far these diseases consist of linear ubiquitin chain assembly complex (LUBAC) and OTULIN deficiencies, and haploinsufficiency of A20. The LUBAC is critical for linear ubiquitination of key signaling molecules in immune response pathways, while deubiquitinase enzymes, OTULIN and TNFAIP3/A20, reverse the effects of ubiquitination by hydrolyzing linear (Met1) and Lys63 (K63) Ub moieties, respectively, from conjugated proteins. Consequently, OTULIN or A20-deficient cells have an excess of Met1 or K63 Ub chains on NEMO, RIPK1, and other target substrates, which lead to constitutive activation of the NF-kB pathway. Mutant cells produce elevated levels of many proinflammatory cytokines and respond to therapy with cytokine inhibitors. Patients with an impairment in LUBAC stability have compromised NF-kB responses in non-immune cells such as fibroblasts, while their monocytes are hyperresponsive to IL-1β. Discoveries of germline mutations in enzymes that regulate protein modifications by Ub define a new category of autoinflammatory diseases caused by upregulations in the NF-kB signaling. The primary aim of this review is to summarize the latest developments in our understanding of the etiology of autoinflammation.
Collapse
Affiliation(s)
- Ivona Aksentijevich
- Inflammatory Disease Section, National Human Genome Research Institute, Bethesda, MD, USA
| | - Qing Zhou
- Inflammatory Disease Section, National Human Genome Research Institute, Bethesda, MD, USA
| |
Collapse
|
88
|
Hoss F, Rodriguez-Alcazar JF, Latz E. Assembly and regulation of ASC specks. Cell Mol Life Sci 2017; 74:1211-1229. [PMID: 27761594 PMCID: PMC11107573 DOI: 10.1007/s00018-016-2396-6] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Revised: 09/28/2016] [Accepted: 10/10/2016] [Indexed: 12/11/2022]
Abstract
The inflammasome adapter ASC links activated inflammasome sensors to the effector molecule pro-caspase-1. Recruitment of pro-caspase-1 to ASC promotes the autocatalytic activation of caspase-1, which leads to the release of pro-inflammatory cytokines, such as IL-1β. Upon triggering of inflammasome sensors, ASC assembles into large helical fibrils that interact with each other serving as a supramolecular signaling platform termed the ASC speck. Alternative splicing, post-translational modifications of ASC, as well as interaction with other proteins can perturb ASC function. In several inflammatory diseases, ASC specks can be found in the extracellular space and its presence correlates with poor prognosis. Here, we review the role of ASC in inflammation, and focus on the structural mechanisms that lead to ASC speck formation, the regulation of ASC function during inflammasome assembly, and the importance of ASC specks in disease.
Collapse
Affiliation(s)
- Florian Hoss
- Institute of Innate Immunity, University Hospitals, University of Bonn, Sigmund-Freud-Straße 25, 53127, Bonn, Germany
| | - Juan F Rodriguez-Alcazar
- Institute of Innate Immunity, University Hospitals, University of Bonn, Sigmund-Freud-Straße 25, 53127, Bonn, Germany
| | - Eicke Latz
- Institute of Innate Immunity, University Hospitals, University of Bonn, Sigmund-Freud-Straße 25, 53127, Bonn, Germany.
- Department of Infectious Diseases and Immunology, University of Massachusetts Medical School, Worcester, MA, USA.
- German Center for Neurodegenerative Diseases, Bonn, Germany.
- Department of Cancer Research and Molecular Medicine, Centre of Molecular Inflammation Research, Norwegian University of Science and Technology, Trondheim, Norway.
| |
Collapse
|
89
|
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.
Collapse
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
| |
Collapse
|
90
|
Internally tagged ubiquitin: a tool to identify linear polyubiquitin-modified proteins by mass spectrometry. Nat Methods 2017; 14:504-512. [DOI: 10.1038/nmeth.4228] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Accepted: 02/13/2017] [Indexed: 12/23/2022]
|
91
|
Hewings DS, Flygare JA, Bogyo M, Wertz IE. Activity-based probes for the ubiquitin conjugation-deconjugation machinery: new chemistries, new tools, and new insights. FEBS J 2017; 284:1555-1576. [PMID: 28196299 PMCID: PMC7163952 DOI: 10.1111/febs.14039] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Revised: 01/21/2017] [Accepted: 02/10/2017] [Indexed: 12/17/2022]
Abstract
The reversible post‐translational modification of proteins by ubiquitin and ubiquitin‐like proteins regulates almost all cellular processes, by affecting protein degradation, localization, and complex formation. Deubiquitinases (DUBs) are proteases that remove ubiquitin modifications or cleave ubiquitin chains. Most DUBs are cysteine proteases, which makes them well suited for study by activity‐based probes. These DUB probes report on deubiquitinase activity by reacting covalently with the active site in an enzyme‐catalyzed manner. They have proven to be important tools to study DUB selectivity and proteolytic activity in different settings, to identify novel DUBs, and to characterize deubiquitinase inhibitors. Inspired by the efficacy of activity‐based probes for DUBs, several groups have recently reported probes for the ubiquitin conjugation machinery (E1, E2, and E3 enzymes). Many of these enzymes, while not proteases, also posses active site cysteine residues and can be targeted by covalent probes. In this review, we will discuss how features of the probe (cysteine‐reactive group, recognition element, and reporter tag) affect reactivity and suitability for certain experimental applications. We will also review the diverse applications of the current probes, and discuss the need for new probe types to study emerging aspects of ubiquitin biology.
Collapse
Affiliation(s)
- David S Hewings
- Discovery Chemistry, Genentech, South San Francisco, CA, USA.,Early Discovery Biochemistry, Genentech, South San Francisco, CA, USA.,Discovery Oncology, Genentech, South San Francisco, CA, USA.,Department of Pathology, Stanford University School of Medicine, CA, USA
| | - John A Flygare
- Discovery Chemistry, Genentech, South San Francisco, CA, USA
| | - Matthew Bogyo
- Department of Pathology, Stanford University School of Medicine, CA, USA
| | - Ingrid E Wertz
- Early Discovery Biochemistry, Genentech, South San Francisco, CA, USA.,Discovery Oncology, Genentech, South San Francisco, CA, USA
| |
Collapse
|
92
|
Abstract
The ubiquitin proteasome system controls the concentrations of regulatory proteins and removes damaged and misfolded proteins from cells. Proteins are targeted to the protease at the center of this system, the proteasome, by ubiquitin tags, but ubiquitin is also used as a signal in other cellular processes. Specificity is conferred by the size and structure of the ubiquitin tags, which are recognized by receptors associated with the different cellular processes. However, the ubiquitin code remains ambiguous, and the same ubiquitin tag can target different proteins to different fates. After binding substrate protein at the ubiquitin tag, the proteasome initiates degradation at a disordered region in the substrate. The proteasome has pronounced preferences for the initiation site, and its recognition represents a second component of the degradation signal.
Collapse
Affiliation(s)
- Houqing Yu
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712;
| | - Andreas Matouschek
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712;
| |
Collapse
|
93
|
Goto E, Tokunaga F. Decreased linear ubiquitination of NEMO and FADD on apoptosis with caspase-mediated cleavage of HOIP. Biochem Biophys Res Commun 2017; 485:152-159. [PMID: 28189684 DOI: 10.1016/j.bbrc.2017.02.040] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Accepted: 02/07/2017] [Indexed: 01/30/2023]
Abstract
NF-κB is crucial to regulate immune and inflammatory responses and cell survival. LUBAC generates a linear ubiquitin chain and activates NF-κB through ubiquitin ligase (E3) activity in the HOIP subunit. Here, we show that HOIP is predominantly cleaved by caspase at Asp390 upon apoptosis, and that is subjected to proteasomal degradation. We identified that FADD, as well as NEMO, is a substrate for LUBAC. Although the C-terminal fragment of HOIP retains NF-κB activity, linear ubiquitination of NEMO and FADD decreases upon apoptosis. Moreover, the N-terminal fragment of HOIP binds with deubiquitinases, such as OTULIN and CYLD-SPATA2. These results indicate that caspase-mediated cleavage of HOIP divides critical functional regions of HOIP, and that this regulates linear (de)ubiquitination of substrates upon apoptosis.
Collapse
Affiliation(s)
- Eiji Goto
- Department of Pathobiochemistry, Graduate School of Medicine, Osaka City University, Osaka 545-8585, Japan
| | - Fuminori Tokunaga
- Department of Pathobiochemistry, Graduate School of Medicine, Osaka City University, Osaka 545-8585, Japan.
| |
Collapse
|
94
|
The Linear Ubiquitin Assembly Complex Modulates Latent Membrane Protein 1 Activation of NF-κB and Interferon Regulatory Factor 7. J Virol 2017; 91:JVI.01138-16. [PMID: 27903798 DOI: 10.1128/jvi.01138-16] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Accepted: 11/14/2016] [Indexed: 12/11/2022] Open
Abstract
Recently, linear ubiquitin assembly complex (LUBAC)-mediated linear ubiquitination has come into focus due to its emerging role in activation of NF-κB in different biological contexts. However, the role of LUBAC in LMP1 signaling leading to NF-κB and interferon regulatory factor 7 (IRF7) activation has not been investigated. We show here that RNF31, the key component of LUBAC, interacts with LMP1 and IRF7 in Epstein-Barr virus (EBV)-transformed cells and that LUBAC stimulates linear ubiquitination of NEMO and IRF7. Consequently, LUBAC is required for LMP1 signaling to full activation of NF-κB but inhibits LMP1-stimulated IRF7 transcriptional activity. The protein levels of RNF31 and LMP1 are correlated in EBV-transformed cells. Knockdown of RNF31 in EBV-transformed IB4 cells by RNA interference negatively regulates the expression of the genes downstream of LMP1 signaling and results in a decrease of cell proliferation. These lines of evidence indicate that LUBAC-mediated linear ubiquitination plays crucial roles in regulating LMP1 signaling and functions. IMPORTANCE We show here that LUBAC-mediated linear ubiquitination is required for LMP1 activation of NF-κB but inhibits LMP1-mediated IRF7 activation. Our findings provide novel mechanisms underlying EBV-mediated oncogenesis and may have a broad impact on IRF7-mediated immune responses.
Collapse
|
95
|
Regulation of Linear Ubiquitin Chain Assembly Complex by Caspase-Mediated Cleavage of RNF31. Mol Cell Biol 2016; 36:3010-3018. [PMID: 27669734 DOI: 10.1128/mcb.00474-16] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Accepted: 09/19/2016] [Indexed: 01/11/2023] Open
Abstract
Cell death and survival signaling pathways have opposed but fundamental functions for various cellular processes and maintain cell homeostasis through cross talk. Here we report a novel mechanism of interaction between these two pathways through the cleavage of RNF31 by caspases. RNF31, a component of the linear ubiquitin chain assembly complex (LUBAC), regulates cell survival by inducing linear ubiquitination of NF-κB signaling components. We found that RNF31 is cleaved under apoptosis conditions through various stimulations. The effector caspases caspase 3 and caspase 6 are responsible for this event, and aspartates 348, 387, and 390 were identified as target sites for this cleavage. Cleavage of RNF31 suppressed its ability to activate NF-κB signaling; thus, mutation of cleavage sites inhibited the induction of apoptosis by treatment with tumor necrosis factor alpha (TNF-α). Our findings elucidate a novel regulatory loop between cell death and the survival signal and may provide guidance for the development of therapeutic strategies for cancers through the sensitization of tumor cells to death-inducing drugs.
Collapse
|
96
|
Klein T, Viner RI, Overall CM. Quantitative proteomics and terminomics to elucidate the role of ubiquitination and proteolysis in adaptive immunity. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2016; 374:rsta.2015.0372. [PMID: 27644975 PMCID: PMC5031638 DOI: 10.1098/rsta.2015.0372] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Accepted: 06/27/2016] [Indexed: 06/06/2023]
Abstract
Adaptive immunity is the specialized defence mechanism in vertebrates that evolved to eliminate pathogens. Specialized lymphocytes recognize specific protein epitopes through antigen receptors to mount potent immune responses, many of which are initiated by nuclear factor-kappa B activation and gene transcription. Most, if not all, pathways in adaptive immunity are further regulated by post-translational modification (PTM) of signalling proteins, e.g. phosphorylation, citrullination, ubiquitination and proteolytic processing. The importance of PTMs is reflected by genetic or acquired defects in these pathways that lead to a dysfunctional immune response. Here we discuss the state of the art in targeted proteomics and systems biology approaches to dissect the PTM landscape specifically regarding ubiquitination and proteolysis in B- and T-cell activation. Recent advances have occurred in methods for specific enrichment and targeted quantitation. Together with improved instrument sensitivity, these advances enable the accurate analysis of often rare PTM events that are opaque to conventional proteomics approaches, now rendering in-depth analysis and pathway dissection possible. We discuss published approaches, including as a case study the profiling of the N-terminome of lymphocytes of a rare patient with a genetic defect in the paracaspase protease MALT1, a key regulator protease in antigen-driven signalling, which was manifested by elevated linear ubiquitination.This article is part of the themed issue 'Quantitative mass spectrometry'.
Collapse
Affiliation(s)
- Theo Klein
- Centre for Blood Research, University of British Columbia, Vancouver, BC Canada V6T 1Z3 Department of Oral Biological and Medical Sciences, Faculty of Dentistry, University of British Columbia, Vancouver, BC Canada V6T 1Z3 Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC Canada V6T 1Z3
| | - Rosa I Viner
- Thermo Fisher Scientific, San Jose, CA 95134, USA
| | - Christopher M Overall
- Centre for Blood Research, University of British Columbia, Vancouver, BC Canada V6T 1Z3 Department of Oral Biological and Medical Sciences, Faculty of Dentistry, University of British Columbia, Vancouver, BC Canada V6T 1Z3 Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC Canada V6T 1Z3
| |
Collapse
|
97
|
Gao S, Pan M, Zheng Y, Huang Y, Zheng Q, Sun D, Lu L, Tan X, Tan X, Lan H, Wang J, Wang T, Wang J, Liu L. Monomer/Oligomer Quasi-Racemic Protein Crystallography. J Am Chem Soc 2016; 138:14497-14502. [PMID: 27768314 DOI: 10.1021/jacs.6b09545] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Racemic or quasi-racemic crystallography recently emerges as a useful technology for solution of the crystal structures of biomacromolecules. It remains unclear to what extent the biomacromolecules of opposite handedness can differ from each other in racemic or quasi-racemic crystallography. Here we report a finding that monomeric d-ubiquitin (Ub) has propensity to cocrystallize with different dimers, trimers, and even a tetramer of l-Ub. In these cocrystals the unconnected monomeric d-Ubs can self-assemble to form pseudomirror images of different oligomers of l-Ub. This monomer/oligomer cocrystallization phenomenon expands the concept of racemic crystallography. Using the monomer/oligomer cocrystallization technology we obtained, for the first time the X-ray structures of linear M1-linked tri- and tetra-Ubs and a K11/K63-branched tri-Ub.
Collapse
Affiliation(s)
- Shuai Gao
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Department of Chemistry and ‡State Key Laboratory of Biomembrane and Membrane Biotechnology, Center for Structural Biology, School of Life Sciences, Tsinghua University , Beijing 100084, China
| | - Man Pan
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Department of Chemistry and ‡State Key Laboratory of Biomembrane and Membrane Biotechnology, Center for Structural Biology, School of Life Sciences, Tsinghua University , Beijing 100084, China
| | - Yong Zheng
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Department of Chemistry and ‡State Key Laboratory of Biomembrane and Membrane Biotechnology, Center for Structural Biology, School of Life Sciences, Tsinghua University , Beijing 100084, China
| | - Yichao Huang
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Department of Chemistry and ‡State Key Laboratory of Biomembrane and Membrane Biotechnology, Center for Structural Biology, School of Life Sciences, Tsinghua University , Beijing 100084, China
| | - Qingyun Zheng
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Department of Chemistry and ‡State Key Laboratory of Biomembrane and Membrane Biotechnology, Center for Structural Biology, School of Life Sciences, Tsinghua University , Beijing 100084, China
| | - Demeng Sun
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Department of Chemistry and ‡State Key Laboratory of Biomembrane and Membrane Biotechnology, Center for Structural Biology, School of Life Sciences, Tsinghua University , Beijing 100084, China
| | - Lining Lu
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Department of Chemistry and ‡State Key Laboratory of Biomembrane and Membrane Biotechnology, Center for Structural Biology, School of Life Sciences, Tsinghua University , Beijing 100084, China
| | - Xiaodan Tan
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Department of Chemistry and ‡State Key Laboratory of Biomembrane and Membrane Biotechnology, Center for Structural Biology, School of Life Sciences, Tsinghua University , Beijing 100084, China
| | - Xianglong Tan
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Department of Chemistry and ‡State Key Laboratory of Biomembrane and Membrane Biotechnology, Center for Structural Biology, School of Life Sciences, Tsinghua University , Beijing 100084, China
| | - Huan Lan
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Department of Chemistry and ‡State Key Laboratory of Biomembrane and Membrane Biotechnology, Center for Structural Biology, School of Life Sciences, Tsinghua University , Beijing 100084, China
| | - Jiaxing Wang
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Department of Chemistry and ‡State Key Laboratory of Biomembrane and Membrane Biotechnology, Center for Structural Biology, School of Life Sciences, Tsinghua University , Beijing 100084, China
| | - Tian Wang
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Department of Chemistry and ‡State Key Laboratory of Biomembrane and Membrane Biotechnology, Center for Structural Biology, School of Life Sciences, Tsinghua University , Beijing 100084, China
| | - Jiawei Wang
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Department of Chemistry and ‡State Key Laboratory of Biomembrane and Membrane Biotechnology, Center for Structural Biology, School of Life Sciences, Tsinghua University , Beijing 100084, China
| | - Lei Liu
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Department of Chemistry and ‡State Key Laboratory of Biomembrane and Membrane Biotechnology, Center for Structural Biology, School of Life Sciences, Tsinghua University , Beijing 100084, China
| |
Collapse
|
98
|
Asaoka T, Almagro J, Ehrhardt C, Tsai I, Schleiffer A, Deszcz L, Junttila S, Ringrose L, Mechtler K, Kavirayani A, Gyenesei A, Hofmann K, Duchek P, Rittinger K, Ikeda F. Linear ubiquitination by LUBEL has a role in Drosophila heat stress response. EMBO Rep 2016; 17:1624-1640. [PMID: 27702987 PMCID: PMC5090701 DOI: 10.15252/embr.201642378] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Accepted: 09/05/2016] [Indexed: 12/17/2022] Open
Abstract
The HOIP ubiquitin E3 ligase generates linear ubiquitin chains by forming a complex with HOIL‐1L and SHARPIN in mammals. Here, we provide the first evidence of linear ubiquitination induced by a HOIP orthologue in Drosophila. We identify Drosophila CG11321, which we named Linear Ubiquitin E3 ligase (LUBEL), and find that it catalyzes linear ubiquitination in vitro. We detect endogenous linear ubiquitin chain‐derived peptides by mass spectrometry in Drosophila Schneider 2 cells and adult flies. Furthermore, using CRISPR/Cas9 technology, we establish linear ubiquitination‐defective flies by mutating residues essential for the catalytic activity of LUBEL. Linear ubiquitination signals accumulate upon heat shock in flies. Interestingly, flies with LUBEL mutations display reduced survival and climbing defects upon heat shock, which is also observed upon specific LUBEL depletion in muscle. Thus, LUBEL is involved in the heat response by controlling linear ubiquitination in flies.
Collapse
Affiliation(s)
- Tomoko Asaoka
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna, Austria
| | - Jorge Almagro
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna, Austria
| | - Christine Ehrhardt
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna, Austria
| | - Isabella Tsai
- Molecular Structure of Cell Signalling Laboratory, The Francis Crick Institute, London, UK
| | - Alexander Schleiffer
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna, Austria.,Research Institute of Molecular Pathology (IMP), Vienna, Austria
| | - Luiza Deszcz
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna, Austria
| | - Sini Junttila
- Vienna Biocenter Core Facilities GmbH (VBCF), Vienna, Austria
| | - Leonie Ringrose
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna, Austria.,Humboldt-Universität zu Berlin IRI for the Life Sciences, Berlin, Germany
| | - Karl Mechtler
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna, Austria.,Research Institute of Molecular Pathology (IMP), Vienna, Austria
| | | | - Attila Gyenesei
- Vienna Biocenter Core Facilities GmbH (VBCF), Vienna, Austria
| | - Kay Hofmann
- Institute for Genetics, University of Cologne, Cologne, Germany
| | - Peter Duchek
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna, Austria
| | - Katrin Rittinger
- Molecular Structure of Cell Signalling Laboratory, The Francis Crick Institute, London, UK
| | - Fumiyo Ikeda
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna, Austria
| |
Collapse
|
99
|
Abstract
Ubiquitin chains assembled via the N-terminal methionine (Met1 or linear ubiquitin), conjugated by the linear ubiquitin chain assembly complex (LUBAC), participate in NF-κΒ-dependent inflammatory signaling and immune responses. A recent report in Cell finds that OTULIN, a deubiquitinase that selectively cleaves Met1-linked ubiquitin chains, is essential for restraining inflammation in vivo.
Collapse
|
100
|
Won M, Byun HS, Park KA, Hur GM. Post-translational control of NF-κB signaling by ubiquitination. Arch Pharm Res 2016; 39:1075-84. [PMID: 27287455 DOI: 10.1007/s12272-016-0772-2] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Accepted: 06/03/2016] [Indexed: 01/01/2023]
Abstract
The transcription factor nuclear factor-kappa B (NF-κB) controls a number of essential cellular functions, including the immune response, cell proliferation, and apoptosis. NF-κB signaling must be engaged temporally and spatially and well orchestrated to prevent aberrant activation because loss of normal regulation of NF-κB is a major contributor to a variety of pathological diseases, including inflammatory diseases, autoimmune diseases, and cancers. Thus, understanding the molecular mechanisms controlling NF-κB activation is an important part of treatment of these relevant diseases. Although NF-κB transcriptional activity is largely regulated by nuclear translocation, post-translational modification of NF-κB signaling components, including phosphorylation, ubiquitination, acetylation, and methylation, has emerged as an important mechanism affecting activity. Many proteins have been shown to ubiquitinate and regulate NF-κB activation at the receptor signaling complex in response to a variety of ligands, such as tumor necrosis factor, interleukin-1, and Toll-like receptor ligands. In this review, we discuss our current knowledge of ubiquitination patterns and their functional role in NF-κB regulation.
Collapse
Affiliation(s)
- Minho Won
- Research Institute for Medical Science, College of Medicine, Chungnam National University, Daejeon, 35015, Republic of Korea
| | - Hee Sun Byun
- Research Institute for Medical Science, College of Medicine, Chungnam National University, Daejeon, 35015, Republic of Korea
| | - Kyeong Ah Park
- Research Institute for Medical Science, College of Medicine, Chungnam National University, Daejeon, 35015, Republic of Korea
| | - Gang Min Hur
- Research Institute for Medical Science, College of Medicine, Chungnam National University, Daejeon, 35015, Republic of Korea. .,Department of Pharmacology, Research Institute for Medical Science, College of Medicine, Chungnam National University, Daejeon, 35015, Republic of Korea.
| |
Collapse
|