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Brazee PL, Morales-Nebreda L, Magnani ND, Garcia JG, Misharin AV, Ridge KM, Budinger GRS, Iwai K, Dada LA, Sznajder JI. Linear ubiquitin assembly complex regulates lung epithelial-driven responses during influenza infection. J Clin Invest 2020; 130:1301-1314. [PMID: 31714898 DOI: 10.1172/jci128368] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 11/06/2019] [Indexed: 12/25/2022] Open
Abstract
Influenza A virus (IAV) is among the most common causes of pneumonia-related death worldwide. Pulmonary epithelial cells are the primary target for viral infection and replication and respond by releasing inflammatory mediators that recruit immune cells to mount the host response. Severe lung injury and death during IAV infection result from an exuberant host inflammatory response. The linear ubiquitin assembly complex (LUBAC), composed of SHARPIN, HOIL-1L, and HOIP, is a critical regulator of NF-κB-dependent inflammation. Using mice with lung epithelial-specific deletions of HOIL-1L or HOIP in a model of IAV infection, we provided evidence that, while a reduction in the inflammatory response was beneficial, ablation of the LUBAC-dependent lung epithelial-driven response worsened lung injury and increased mortality. Moreover, we described a mechanism for the upregulation of HOIL-1L in infected and noninfected cells triggered by the activation of type I IFN receptor and mediated by IRF1, which was maladaptive and contributed to hyperinflammation. Thus, we propose that lung epithelial LUBAC acts as a molecular rheostat that could be selectively targeted to modulate the immune response in patients with severe IAV-induced pneumonia.
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Affiliation(s)
- Patricia L Brazee
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Luisa Morales-Nebreda
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Natalia D Magnani
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Joe Gn Garcia
- Department of Medicine, University of Arizona, Tucson, Arizona, USA
| | - Alexander V Misharin
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Karen M Ridge
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Northwestern University, Chicago, Illinois, USA
| | - G R Scott Budinger
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Kazuhiro Iwai
- Department of Molecular and Cellular Physiology, Graduate School of Medicine, Kyoto University, Yoshida-konoe-cho, Kyoto, Japan
| | - Laura A Dada
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Jacob I Sznajder
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Northwestern University, Chicago, Illinois, USA
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52
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Li L, Bai J, Fan H, Yan J, Li S, Jiang P. E2 ubiquitin-conjugating enzyme UBE2L6 promotes Senecavirus A proliferation by stabilizing the viral RNA polymerase. PLoS Pathog 2020; 16:e1008970. [PMID: 33104725 PMCID: PMC7588118 DOI: 10.1371/journal.ppat.1008970] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 09/08/2020] [Indexed: 12/29/2022] Open
Abstract
Senecavirus A (SVA), discovered in 2002, is an emerging pathogen of swine that has since been reported in numerous pork producing countries. To date, the mechanism of SVA replication remains poorly understood. In this study, utilizing iTRAQ analysis we found that UBE2L6, an E2 ubiquitin-conjugating enzyme, is up-regulated in SVA-infected BHK-21 cells, and that its overexpression promotes SVA replication. We determined that UBE2L6 interacts with, and ubiquitinates the RNA-dependent RNA polymerase of SVA, (the 3D protein) and this ubiquitination serves to inhibit the degradation of 3D. UBE2L6-mediated ubiquitination of 3D requires a cystine at residue 86 in UBE2L6, and lysines at residues 169 and 321 in 3D. Virus with mutations in 3D (rK169R and rK321R) exhibited significantly decreased replication compared to wild type SVA and the repaired viruses, rK169R(R) and rK321R(R). These data indicate that UBE2L6, the enzyme, targets the 3D polymerase, the substrate, during SVA infection to facilitate replication. Senecavirus A (SVA) is a newly emerging pathogen causing swine idiopathic vesicular disease and epidemic transient neonatal losses. Infections have been reported in many pork producing countries, yet the mechanism of SVA replication remains poorly understood. In this study, we found that UBE2L6, an E2 ubiquitin-conjugating enzyme, is up-regulated in SVA-infected BHK-21 cells. The viral RNA dependent RNA polymerase (RdRp) 3D is ubiquitinated by UBE2L6, and the lysines at residues 169 and 321 of 3D are the required ubiquitination sites. The level of replication of recombinant viruses harboring ubiquitination-deficient 3D was significantly decreased compared to parental SVA. Our data demonstrate that UBE2L6 ubiquitinates SVA 3D, thereby facilitating SVA infection. These results may make it possible to identify novel targets for disease treatment.
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Affiliation(s)
- Liang Li
- Key Laboratory of Animal Diseases Diagnostic and Immunology, Ministry of Agriculture, MOE International Joint Collaborative Research Laboratory for Animal Health & Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Juan Bai
- Key Laboratory of Animal Diseases Diagnostic and Immunology, Ministry of Agriculture, MOE International Joint Collaborative Research Laboratory for Animal Health & Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, China
- * E-mail: (JB); (PJ)
| | - Hui Fan
- Key Laboratory of Animal Diseases Diagnostic and Immunology, Ministry of Agriculture, MOE International Joint Collaborative Research Laboratory for Animal Health & Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Junfang Yan
- Key Laboratory of Animal Diseases Diagnostic and Immunology, Ministry of Agriculture, MOE International Joint Collaborative Research Laboratory for Animal Health & Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Shihai Li
- Key Laboratory of Animal Diseases Diagnostic and Immunology, Ministry of Agriculture, MOE International Joint Collaborative Research Laboratory for Animal Health & Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Ping Jiang
- Key Laboratory of Animal Diseases Diagnostic and Immunology, Ministry of Agriculture, MOE International Joint Collaborative Research Laboratory for Animal Health & Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, China
- * E-mail: (JB); (PJ)
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53
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Green JL, Wu Y, Encheva V, Lasonder E, Prommaban A, Kunzelmann S, Christodoulou E, Grainger M, Truongvan N, Bothe S, Sharma V, Song W, Pinzuti I, Uthaipibull C, Srichairatanakool S, Birault V, Langsley G, Schindelin H, Stieglitz B, Snijders AP, Holder AA. Ubiquitin activation is essential for schizont maturation in Plasmodium falciparum blood-stage development. PLoS Pathog 2020; 16:e1008640. [PMID: 32569299 PMCID: PMC7332102 DOI: 10.1371/journal.ppat.1008640] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 07/02/2020] [Accepted: 05/17/2020] [Indexed: 11/19/2022] Open
Abstract
Ubiquitylation is a common post translational modification of eukaryotic proteins and in the human malaria parasite, Plasmodium falciparum (Pf) overall ubiquitylation increases in the transition from intracellular schizont to extracellular merozoite stages in the asexual blood stage cycle. Here, we identify specific ubiquitylation sites of protein substrates in three intraerythrocytic parasite stages and extracellular merozoites; a total of 1464 sites in 546 proteins were identified (data available via ProteomeXchange with identifier PXD014998). 469 ubiquitylated proteins were identified in merozoites compared with only 160 in the preceding intracellular schizont stage, suggesting a large increase in protein ubiquitylation associated with merozoite maturation. Following merozoite invasion of erythrocytes, few ubiquitylated proteins were detected in the first intracellular ring stage but as parasites matured through trophozoite to schizont stages the apparent extent of ubiquitylation increased. We identified commonly used ubiquitylation motifs and groups of ubiquitylated proteins in specific areas of cellular function, for example merozoite pellicle proteins involved in erythrocyte invasion, exported proteins, and histones. To investigate the importance of ubiquitylation we screened ubiquitin pathway inhibitors in a parasite growth assay and identified the ubiquitin activating enzyme (UBA1 or E1) inhibitor MLN7243 (TAK-243) to be particularly effective. This small molecule was shown to be a potent inhibitor of recombinant PfUBA1, and a structural homology model of MLN7243 bound to the parasite enzyme highlights avenues for the development of P. falciparum specific inhibitors. We created a genetically modified parasite with a rapamycin-inducible functional deletion of uba1; addition of either MLN7243 or rapamycin to the recombinant parasite line resulted in the same phenotype, with parasite development blocked at the schizont stage. Nuclear division and formation of intracellular structures was interrupted. These results indicate that the intracellular target of MLN7243 is UBA1, and this activity is essential for the final differentiation of schizonts to merozoites.
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Affiliation(s)
- Judith L. Green
- Malaria Parasitology Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Yang Wu
- Malaria Parasitology Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Vesela Encheva
- Mass Spectrometry Proteomics, The Francis Crick Institute, London, United Kingdom
| | - Edwin Lasonder
- School of Biomedical Science, University of Plymouth, Plymouth, United Kingdom
| | - Adchara Prommaban
- Malaria Parasitology Laboratory, The Francis Crick Institute, London, United Kingdom
- Department of Biochemistry, Chiang Mai University, Chiang Mai, Thailand
| | - Simone Kunzelmann
- Structural Biology Science Technology Platform, The Francis Crick Institute, London, United Kingdom
| | - Evangelos Christodoulou
- Structural Biology Science Technology Platform, The Francis Crick Institute, London, United Kingdom
| | - Munira Grainger
- Malaria Parasitology Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Ngoc Truongvan
- Rudolf Virchow Center for Experimental Biomedicine, Universität Würzburg, Würzburg, Germany
| | - Sebastian Bothe
- Department of Chemistry and Pharmacy, University of Würzburg, Würzburg, Germany
| | - Vikram Sharma
- School of Biomedical Science, University of Plymouth, Plymouth, United Kingdom
| | - Wei Song
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Irene Pinzuti
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Chairat Uthaipibull
- National Center for Genetic Engineering and Biotechnology, Khlong Luang, Thailand
| | | | | | - Gordon Langsley
- Laboratoire de Biologie Cellulaire Comparative des Apicomplexes, Institut Cochin, Université Paris Descartes, Paris, France
| | - Hermann Schindelin
- Rudolf Virchow Center for Experimental Biomedicine, Universität Würzburg, Würzburg, Germany
| | - Benjamin Stieglitz
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | | | - Anthony A. Holder
- Malaria Parasitology Laboratory, The Francis Crick Institute, London, United Kingdom
- * E-mail:
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The HOIL-1L ligase modulates immune signalling and cell death via monoubiquitination of LUBAC. Nat Cell Biol 2020; 22:663-673. [PMID: 32393887 DOI: 10.1038/s41556-020-0517-9] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Accepted: 04/06/2020] [Indexed: 12/21/2022]
Abstract
The linear ubiquitin chain assembly complex (LUBAC), which consists of HOIP, SHARPIN and HOIL-1L, promotes NF-κB activation and protects against cell death by generating linear ubiquitin chains. LUBAC contains two RING-IBR-RING (RBR) ubiquitin ligases (E3), and the HOIP RBR is responsible for catalysing linear ubiquitination. We found that HOIL-1L RBR plays a crucial role in regulating LUBAC. HOIL-1L RBR conjugates monoubiquitin onto all LUBAC subunits, followed by HOIP-mediated conjugation of linear chains onto monoubiquitin, and these linear chains attenuate the functions of LUBAC. The introduction of E3-defective HOIL-1L mutants into cells augmented linear ubiquitination, which protected the cells against Salmonella infection and cured dermatitis caused by reduced LUBAC levels due to SHARPIN loss. Our results reveal a regulatory mode of E3 ligases in which the accessory E3 in LUBAC downregulates the main E3 by providing preferred substrates for autolinear ubiquitination. Thus, inhibition of HOIL-1L E3 represents a promising strategy for treating severe infections or immunodeficiency.
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55
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Oikawa D, Sato Y, Ito H, Tokunaga F. Linear Ubiquitin Code: Its Writer, Erasers, Decoders, Inhibitors, and Implications in Disorders. Int J Mol Sci 2020; 21:ijms21093381. [PMID: 32403254 PMCID: PMC7246992 DOI: 10.3390/ijms21093381] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 05/01/2020] [Accepted: 05/06/2020] [Indexed: 12/12/2022] Open
Abstract
The linear ubiquitin chain assembly complex (LUBAC) is a ubiquitin ligase composed of the Heme-oxidized IRP2 ubiquitin ligase-1L (HOIL-1L), HOIL-1L-interacting protein (HOIP), and Shank-associated RH domain interactor (SHARPIN) subunits. LUBAC specifically generates the N-terminal Met1-linked linear ubiquitin chain and regulates acquired and innate immune responses, such as the canonical nuclear factor-κB (NF-κB) and interferon antiviral pathways. Deubiquitinating enzymes, OTULIN and CYLD, physiologically bind to HOIP and control its function by hydrolyzing the linear ubiquitin chain. Moreover, proteins containing linear ubiquitin-specific binding domains, such as NF-κB-essential modulator (NEMO), optineurin, A20-binding inhibitors of NF-κB (ABINs), and A20, modulate the functions of LUBAC, and the dysregulation of the LUBAC-mediated linear ubiquitination pathway induces cancer and inflammatory, autoimmune, and neurodegenerative diseases. Therefore, inhibitors of LUBAC would be valuable to facilitate investigations of the molecular and cellular bases for LUBAC-mediated linear ubiquitination and signal transduction, and for potential therapeutic purposes. We identified and characterized α,β-unsaturated carbonyl-containing chemicals, named HOIPINs (HOIP inhibitors), as LUBAC inhibitors. We summarize recent advances in elucidations of the pathophysiological functions of LUBAC-mediated linear ubiquitination and identifications of its regulators, toward the development of LUBAC inhibitors.
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Affiliation(s)
- Daisuke Oikawa
- Department of Pathobiochemistry, Graduate School of Medicine, Osaka City University, Osaka 545-8585, Japan;
| | - Yusuke Sato
- Center for Research on Green Sustainable Chemistry, Tottori University, Tottori 680-8552, Japan;
| | - Hidefumi Ito
- Department of Neurology, Faculty of Medicine, Wakayama Medical University, Wakayama 641-8510, Japan;
| | - Fuminori Tokunaga
- Department of Pathobiochemistry, Graduate School of Medicine, Osaka City University, Osaka 545-8585, Japan;
- Correspondence: ; Tel.: +81-6-6645-3720
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56
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Molecular bases for HOIPINs-mediated inhibition of LUBAC and innate immune responses. Commun Biol 2020; 3:163. [PMID: 32246052 PMCID: PMC7125101 DOI: 10.1038/s42003-020-0882-8] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2019] [Accepted: 02/27/2020] [Indexed: 12/31/2022] Open
Abstract
The NF-κB and interferon antiviral signaling pathways play pivotal roles in inflammatory and innate immune responses. The LUBAC ubiquitin ligase complex, composed of the HOIP, HOIL-1L, and SHARPIN subunits, activates the canonical NF-κB pathway through Met1-linked linear ubiquitination. We identified small-molecule chemical inhibitors of LUBAC, HOIPIN-1 and HOIPIN-8. Here we show that HOIPINs down-regulate not only the proinflammatory cytokine-induced canonical NF-κB pathway, but also various pathogen-associated molecular pattern-induced antiviral pathways. Structural analyses indicated that HOIPINs inhibit the RING-HECT-hybrid reaction in HOIP by modifying the active Cys885, and residues in the C-terminal LDD domain, such as Arg935 and Asp936, facilitate the binding of HOIPINs to LUBAC. HOIPINs effectively induce cell death in activated B cell-like diffuse large B cell lymphoma cells, and alleviate imiquimod-induced psoriasis in model mice. These results reveal the molecular and cellular bases of LUBAC inhibition by HOIPINs, and demonstrate their potential therapeutic uses. Daisuke Oikawa et al. provide structural insights into how small-molecule inhibitors of LUBAC ubiquitin ligase, HOIPINs, bind to LUBAC. They find that HOIPINs trigger apoptosis in lymphoma cells and alleviate psoriasis in mice, suggesting the potential therapeutic utility of HOIPINs.
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57
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Regulation of the linear ubiquitination of STAT1 controls antiviral interferon signaling. Nat Commun 2020; 11:1146. [PMID: 32123171 PMCID: PMC7052135 DOI: 10.1038/s41467-020-14948-z] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 02/10/2020] [Indexed: 12/15/2022] Open
Abstract
Linear ubiquitination is a critical regulator of inflammatory signaling pathways. However, linearly ubiquitinated substrates and the biological significance of linear ubiquitination is incompletely understood. Here, we show that STAT1 has linear ubiquitination at Lys511 and Lys652 residues in intact cells, which inhibits STAT1 binding to the type-I interferon receptor IFNAR2, thereby restricting STAT1 activation and resulting in type-I interferon signaling homeostasis. Linear ubiquitination of STAT1 is removed rapidly by OTULIN upon type-I interferon stimulation, which facilitates activation of interferon-STAT1 signaling. Furthermore, viruses induce HOIP expression through the NF-κB pathway, which in turn increases linear ubiquitination of STAT1 and thereby inhibits interferon antiviral response. Consequently, HOIL-1L heterozygous mice have active STAT1 signaling and enhanced responses to type-I interferons. These findings demonstrate a linear ubiquitination-mediated switch between homeostasis and activation of type-I interferon signaling, and suggest potential strategies for clinical antiviral therapy.
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58
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Meschede J, Šadić M, Furthmann N, Miedema T, Sehr DA, Müller-Rischart AK, Bader V, Berlemann LA, Pilsl A, Schlierf A, Barkovits K, Kachholz B, Rittinger K, Ikeda F, Marcus K, Schaefer L, Tatzelt J, Winklhofer KF. The parkin-coregulated gene product PACRG promotes TNF signaling by stabilizing LUBAC. Sci Signal 2020; 13:13/617/eaav1256. [PMID: 32019898 DOI: 10.1126/scisignal.aav1256] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The Parkin-coregulated gene (PACRG), which encodes a protein of unknown function, shares a bidirectional promoter with Parkin (PRKN), which encodes an E3 ubiquitin ligase. Because PRKN is important in mitochondrial quality control and protection against stress, we tested whether PACRG also affected these pathways in various cultured human cell lines and in mouse embryonic fibroblasts. PACRG did not play a role in mitophagy but did play a role in tumor necrosis factor (TNF) signaling. Similarly to Parkin, PACRG promoted nuclear factor κB (NF-κB) activation in response to TNF. TNF-induced nuclear translocation of the NF-κB subunit p65 and NF-κB-dependent transcription were decreased in PACRG-deficient cells. Defective canonical NF-κB activation in the absence of PACRG was accompanied by a decrease in linear ubiquitylation mediated by the linear ubiquitin chain assembly complex (LUBAC), which is composed of the two E3 ubiquitin ligases HOIP and HOIL-1L and the adaptor protein SHARPIN. Upon TNF stimulation, PACRG was recruited to the activated TNF receptor complex and interacted with LUBAC components. PACRG functionally replaced SHARPIN in this context. In SHARPIN-deficient cells, PACRG prevented LUBAC destabilization, restored HOIP-dependent linear ubiquitylation, and protected cells from TNF-induced apoptosis. This function of PACRG in positively regulating TNF signaling may help to explain the association of PACRG and PRKN polymorphisms with an increased susceptibility to intracellular pathogens.
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Affiliation(s)
- Jens Meschede
- Molecular Cell Biology, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, 44801 Bochum, Germany
| | - Maria Šadić
- Neurobiochemistry, Adolf Butenandt Institute, Ludwig Maximilians University, 80336 Munich, Germany
| | - Nikolas Furthmann
- Molecular Cell Biology, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, 44801 Bochum, Germany
| | - Tim Miedema
- Molecular Cell Biology, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, 44801 Bochum, Germany
| | - Dominik A Sehr
- Molecular Cell Biology, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, 44801 Bochum, Germany
| | | | - Verian Bader
- Molecular Cell Biology, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, 44801 Bochum, Germany
| | - Lena A Berlemann
- Molecular Cell Biology, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, 44801 Bochum, Germany
| | - Anna Pilsl
- Neurobiochemistry, Adolf Butenandt Institute, Ludwig Maximilians University, 80336 Munich, Germany
| | - Anita Schlierf
- Neurobiochemistry, Adolf Butenandt Institute, Ludwig Maximilians University, 80336 Munich, Germany
| | - Katalin Barkovits
- Medizinisches Proteom-Center, Ruhr University Bochum, 44801 Bochum, Germany
| | - Barbara Kachholz
- Molecular Cell Biology, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, 44801 Bochum, Germany
| | | | - Fumiyo Ikeda
- Institute of Molecular Biotechnology (IMBA), 1030 Vienna, Austria
| | - Katrin Marcus
- Medizinisches Proteom-Center, Ruhr University Bochum, 44801 Bochum, Germany
| | - Liliana Schaefer
- Pharmacenter Frankfurt/ZAFES, Institute for General Pharmacology and Toxicology, Goethe University, 60590 Frankfurt am Main, Germany
| | - Jörg Tatzelt
- Neurobiochemistry, Adolf Butenandt Institute, Ludwig Maximilians University, 80336 Munich, Germany.,Biochemistry of Neurodegenerative Diseases, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, 44801 Bochum, Germany
| | - Konstanze F Winklhofer
- Molecular Cell Biology, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, 44801 Bochum, Germany. .,Neurobiochemistry, Adolf Butenandt Institute, Ludwig Maximilians University, 80336 Munich, Germany
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59
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Tsai YCI, Johansson H, Dixon D, Martin S, Chung CW, Clarkson J, House D, Rittinger K. Single-Domain Antibodies as Crystallization Chaperones to Enable Structure-Based Inhibitor Development for RBR E3 Ubiquitin Ligases. Cell Chem Biol 2020; 27:83-93.e9. [PMID: 31813847 PMCID: PMC6963773 DOI: 10.1016/j.chembiol.2019.11.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 10/15/2019] [Accepted: 11/14/2019] [Indexed: 01/14/2023]
Abstract
Protein ubiquitination plays a key role in the regulation of cellular processes, and misregulation of the ubiquitin system is linked to many diseases. So far, development of tool compounds that target enzymes of the ubiquitin system has been slow and only a few specific inhibitors are available. Here, we report the selection of single-domain antibodies (single-dAbs) based on a human scaffold that recognize the catalytic domain of HOIP, a subunit of the multi-component E3 LUBAC and member of the RBR family of E3 ligases. Some of these dAbs affect ligase activity and provide mechanistic insight into the ubiquitin transfer mechanism of different E2-conjugating enzymes. Furthermore, we show that the co-crystal structure of a HOIP RBR/dAb complex serves as a robust platform for soaking of ligands that target the active site cysteine of HOIP, thereby providing easy access to structure-based ligand design for this important class of E3 ligases.
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Affiliation(s)
- Yi-Chun Isabella Tsai
- Molecular Structure of Cell Signalling Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Henrik Johansson
- Molecular Structure of Cell Signalling Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; Crick-GSK Biomedical LinkLabs, GlaxoSmithKline, Gunnels Wood Road, Stevenage SG1 2NY, UK
| | - David Dixon
- R&D Medicinal Science & Technology, GlaxoSmithKline, Gunnels Wood Road, Stevenage SG1 2NY, UK
| | - Stephen Martin
- Structural Biology Science Technology Platform, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Chun-Wa Chung
- Crick-GSK Biomedical LinkLabs, GlaxoSmithKline, Gunnels Wood Road, Stevenage SG1 2NY, UK; R&D Medicinal Science & Technology, GlaxoSmithKline, Gunnels Wood Road, Stevenage SG1 2NY, UK
| | - Jane Clarkson
- R&D Medicinal Science & Technology, GlaxoSmithKline, Gunnels Wood Road, Stevenage SG1 2NY, UK
| | - David House
- Crick-GSK Biomedical LinkLabs, GlaxoSmithKline, Gunnels Wood Road, Stevenage SG1 2NY, UK
| | - Katrin Rittinger
- Molecular Structure of Cell Signalling Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK.
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60
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Dittmar G, Winklhofer KF. Linear Ubiquitin Chains: Cellular Functions and Strategies for Detection and Quantification. Front Chem 2020; 7:915. [PMID: 31998699 PMCID: PMC6966713 DOI: 10.3389/fchem.2019.00915] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 12/16/2019] [Indexed: 01/06/2023] Open
Abstract
Ubiquitination of proteins is a sophisticated post-translational modification implicated in the regulation of an ever-growing abundance of cellular processes. Recent insights into different layers of complexity have shaped the concept of the ubiquitin code. Key players in determining this code are the number of ubiquitin moieties attached to a substrate, the architecture of polyubiquitin chains, and post-translational modifications of ubiquitin itself. Ubiquitination can induce conformational changes of substrates and alter their interactive profile, resulting in the formation of signaling complexes. Here we focus on a distinct type of ubiquitination that is characterized by an inter-ubiquitin linkage through the N-terminal methionine, called M1-linked or linear ubiquitination. Formation, recognition, and disassembly of linear ubiquitin chains are highly specific processes that are implicated in immune signaling, cell death regulation and protein quality control. Consistent with their role in influencing signaling events, linear ubiquitin chains are formed in a transient and spatially regulated manner, making their detection and quantification challenging.
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Affiliation(s)
- Gunnar Dittmar
- Proteomics of Cellular Signalling, Quantitative Biology Unit, Luxembourg Institute of Health, Strassen, Luxembourg
| | - Konstanze F Winklhofer
- Department of Molecular Cell Biology, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, Bochum, Germany
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61
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Abstract
The ubiquitylation of NF-κB essential modulator (NEMO) is part of the intracellular immune signalling pathway. Monoubiquitylated NEMO is required for exploring the mechanism of NEMO linear ubiquitylation by LUBAC (linear ubiquitin chain assembly complex), but is not accessible by biological techniques. Here we perform the chemical ubiquitylation of NEMO using a ligation auxiliary, which only requires a two-step synthesis, and is easily installed onto the lysine side-chain. Chemical ligation occurs directly on the lysine ε amine and remains efficient below pH 7. We show that ubiquitylated NEMO has similar affinity to linear diubiquitin chains as unmodified NEMO. The proximal ubiquitin of chemically synthesised NEMOCoZi-Ub is accepted as a substrate for linear extension by the (RING-Between-RING) RBR domain of HOIL-1-interacting protein (HOIP) alone. Our results indicate that NEMO linear ubiquitylation consists of two-steps, an initial priming event and a separate extension step requiring different LUBAC components.
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62
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The E3 ligase HOIL-1 catalyses ester bond formation between ubiquitin and components of the Myddosome in mammalian cells. Proc Natl Acad Sci U S A 2019; 116:13293-13298. [PMID: 31209050 PMCID: PMC6613137 DOI: 10.1073/pnas.1905873116] [Citation(s) in RCA: 92] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The linear ubiquitin assembly complex (LUBAC) comprises 3 components: HOIP, HOIL-1, and Sharpin, of which HOIP and HOIL-1 are both members of the RBR subfamily of E3 ubiquitin ligases. HOIP catalyses the formation of Met1-linked ubiquitin oligomers (also called linear ubiquitin), but the function of the E3 ligase activity of HOIL-1 is unknown. Here, we report that HOIL-1 is an atypical E3 ligase that forms oxyester bonds between the C terminus of ubiquitin and serine and threonine residues in its substrates. Exploiting the sensitivity of HOIL-1-generated oxyester bonds to cleavage by hydroxylamine, and macrophages from knock-in mice expressing the E3 ligase-inactive HOIL-1[C458S] mutant, we identify IRAK1, IRAK2, and MyD88 as physiological substrates of the HOIL-1 E3 ligase during Toll-like receptor signaling. HOIL-1 is a monoubiquitylating E3 ubiquitin ligase that initiates the de novo synthesis of polyubiquitin chains that are attached to these proteins in macrophages. HOIL-1 also catalyses its own monoubiquitylation in cells and most probably the monoubiquitylation of Sharpin, in which ubiquitin is also attached by an oxyester bond. Our study establishes that oxyester-linked ubiquitylation is used as an intracellular signaling mechanism.
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van Well EM, Bader V, Patra M, Sánchez-Vicente A, Meschede J, Furthmann N, Schnack C, Blusch A, Longworth J, Petrasch-Parwez E, Mori K, Arzberger T, Trümbach D, Angersbach L, Showkat C, Sehr DA, Berlemann LA, Goldmann P, Clement AM, Behl C, Woerner AC, Saft C, Wurst W, Haass C, Ellrichmann G, Gold R, Dittmar G, Hipp MS, Hartl FU, Tatzelt J, Winklhofer KF. A protein quality control pathway regulated by linear ubiquitination. EMBO J 2019; 38:e100730. [PMID: 30886048 PMCID: PMC6484417 DOI: 10.15252/embj.2018100730] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Revised: 02/12/2019] [Accepted: 02/13/2019] [Indexed: 12/22/2022] Open
Abstract
Neurodegenerative diseases are characterized by the accumulation of misfolded proteins in the brain. Insights into protein quality control mechanisms to prevent neuronal dysfunction and cell death are crucial in developing causal therapies. Here, we report that various disease-associated protein aggregates are modified by the linear ubiquitin chain assembly complex (LUBAC). HOIP, the catalytic component of LUBAC, is recruited to misfolded Huntingtin in a p97/VCP-dependent manner, resulting in the assembly of linear polyubiquitin. As a consequence, the interactive surface of misfolded Huntingtin species is shielded from unwanted interactions, for example with the low complexity sequence domain-containing transcription factor Sp1, and proteasomal degradation of misfolded Huntingtin is facilitated. Notably, all three core LUBAC components are transcriptionally regulated by Sp1, linking defective LUBAC expression to Huntington's disease. In support of a protective activity of linear ubiquitination, silencing of OTULIN, a deubiquitinase with unique specificity for linear polyubiquitin, decreases proteotoxicity, whereas silencing of HOIP has the opposite effect. These findings identify linear ubiquitination as a protein quality control mechanism and hence a novel target for disease-modifying strategies in proteinopathies.
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Affiliation(s)
- Eva M van Well
- Department of Molecular Cell Biology, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, Bochum, Germany
| | - Verian Bader
- Department of Molecular Cell Biology, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, Bochum, Germany
| | - Maria Patra
- Neurobiochemistry, Adolf Butenandt Institute, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Ana Sánchez-Vicente
- Department of Molecular Cell Biology, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, Bochum, Germany
| | - Jens Meschede
- Department of Molecular Cell Biology, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, Bochum, Germany
| | - Nikolas Furthmann
- Department of Molecular Cell Biology, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, Bochum, Germany
| | - Cathrin Schnack
- Department of Molecular Cell Biology, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, Bochum, Germany
| | - Alina Blusch
- Department of Neurology, St Josef Hospital, Ruhr University Bochum, Bochum, Germany
| | - Joseph Longworth
- Proteome and Genome Research Unit, Department of Oncology, Luxembourg Institute of Health, Strassen, Luxembourg
| | | | - Kohji Mori
- Biomedical Center (BMC), Ludwig-Maximilians-University Munich, Munich, Germany
| | - Thomas Arzberger
- Department of Psychiatry and Psychotherapy, Ludwig-Maximilians-University Munich, Munich, Germany
- Centre for Neuropathology and Prion Research, Ludwig-Maximilians-University Munich, Munich, Germany
- German Center for Neurodegenerative Diseases (DZNE) Munich, Munich, Germany
| | - Dietrich Trümbach
- Institute of Developmental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Lena Angersbach
- Department of Molecular Cell Biology, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, Bochum, Germany
| | - Cathrin Showkat
- Department of Molecular Cell Biology, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, Bochum, Germany
| | - Dominik A Sehr
- Department of Molecular Cell Biology, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, Bochum, Germany
| | - Lena A Berlemann
- Department of Molecular Cell Biology, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, Bochum, Germany
| | - Petra Goldmann
- Department of Molecular Cell Biology, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, Bochum, Germany
| | - Albrecht M Clement
- Institute for Pathobiochemistry, University Medical Center of the Johannes Gutenberg-University, Mainz, Germany
| | - Christian Behl
- Institute for Pathobiochemistry, University Medical Center of the Johannes Gutenberg-University, Mainz, Germany
| | - Andreas C Woerner
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Carsten Saft
- Department of Neurology, St Josef Hospital, Ruhr University Bochum, Bochum, Germany
| | - Wolfgang Wurst
- German Center for Neurodegenerative Diseases (DZNE) Munich, Munich, Germany
- Institute of Developmental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Developmental Genetics, Technical University Munich, Neuherberg, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Christian Haass
- Biomedical Center (BMC), Ludwig-Maximilians-University Munich, Munich, Germany
- German Center for Neurodegenerative Diseases (DZNE) Munich, Munich, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Gisa Ellrichmann
- Department of Neurology, St Josef Hospital, Ruhr University Bochum, Bochum, Germany
| | - Ralf Gold
- Department of Neurology, St Josef Hospital, Ruhr University Bochum, Bochum, Germany
| | - Gunnar Dittmar
- Proteome and Genome Research Unit, Department of Oncology, Luxembourg Institute of Health, Strassen, Luxembourg
| | - Mark S Hipp
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Martinsried, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - F Ulrich Hartl
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Martinsried, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Jörg Tatzelt
- Neurobiochemistry, Adolf Butenandt Institute, Ludwig-Maximilians-University Munich, Munich, Germany
- Department of Biochemistry of Neurodegenerative Diseases, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, Bochum, Germany
- Cluster of Excellence RESOLV, Bochum, Germany
| | - Konstanze F Winklhofer
- Department of Molecular Cell Biology, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, Bochum, Germany
- Neurobiochemistry, Adolf Butenandt Institute, Ludwig-Maximilians-University Munich, Munich, Germany
- German Center for Neurodegenerative Diseases (DZNE) Munich, Munich, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
- Cluster of Excellence RESOLV, Bochum, Germany
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Scott DC, Schulman BA. Dual-color pulse-chase ubiquitination assays to simultaneously monitor substrate priming and extension. Methods Enzymol 2019; 618:29-48. [PMID: 30850057 DOI: 10.1016/bs.mie.2019.01.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Many fundamental discoveries in ubiquitin-proteasome research have relied on reconstitution of activities from purified or recombinantly expressed components. These include landmark discoveries of E1-E2-E3 mechanisms, in which ubiquitin (UB) is initially activated and then covalently shuttled between enzyme active sites and ultimately ligated to substrate or substrate-linked UBs during polyubiquitination. However, recent studies have unearthed enormous variations on the E1-E2-E3 theme; for example, one E3 may employ two distinct E2s, or two different E3s may act in a single assembly or in series, to prime substrates directly with UB and subsequently decorate them with myriad types of polyubiquitin chains. To dissect this complexity, it can be helpful to monitor specific UB transfer reactions in isolation, rather than the end-point products formed upon mixing all enzymes in a cascade. Pulse-chase assays enable observation of a single reaction step and also allow one to differentially label UBs carried by different enzymes within the same tube. In such assays, the "pulse" reaction generates a thioester-linked enzyme~UB intermediate, while the "chase" monitors UB transfer to downstream components over time. Here, we describe pulse-chase assays for detecting fluorescent-UB in E2~UB intermediates. These assays enable direct assessment of particular ligation reactions, alone and in combination, to explore roles of multiple enzymatic cascades in the same tube. We anticipate this technique can be adapted to many different E2s, as well as thioester-forming E3s, to dissect ubiquitination by many distinct enzyme cascades.
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Affiliation(s)
- Daniel C Scott
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, United States
| | - Brenda A Schulman
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, United States; Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany.
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Johansson H, Isabella Tsai YC, Fantom K, Chung CW, Kümper S, Martino L, Thomas DA, Eberl HC, Muelbaier M, House D, Rittinger K. Fragment-Based Covalent Ligand Screening Enables Rapid Discovery of Inhibitors for the RBR E3 Ubiquitin Ligase HOIP. J Am Chem Soc 2019; 141:2703-2712. [PMID: 30657686 PMCID: PMC6383986 DOI: 10.1021/jacs.8b13193] [Citation(s) in RCA: 82] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
![]()
Modification
of proteins with polyubiquitin chains is a key regulatory
mechanism to control cellular behavior and alterations in the ubiquitin
system are linked to many diseases. Linear (M1-linked) polyubiquitin
chains play pivotal roles in several cellular signaling pathways mediating
immune and inflammatory responses and apoptotic cell death. These
chains are formed by the linear ubiquitin chain assembly complex (LUBAC),
a multiprotein E3 ligase that consists of 3 subunits, HOIP, HOIL-1L,
and SHARPIN. Herein, we describe the discovery of inhibitors targeting
the active site cysteine of the catalytic subunit HOIP using fragment-based
covalent ligand screening. We report the synthesis of a diverse library
of electrophilic fragments and demonstrate an integrated use of protein
LC–MS, biochemical ubiquitination assays, chemical synthesis,
and protein crystallography to enable the first structure-based development
of covalent inhibitors for an RBR E3 ligase. Furthermore, using cell-based
assays and chemoproteomics, we demonstrate that these compounds effectively
penetrate mammalian cells to label and inhibit HOIP and NF-κB
activation, making them suitable hits for the development of selective
probes to study LUBAC biology. Our results illustrate the power of
fragment-based covalent ligand screening to discover lead compounds
for challenging targets, which holds promise to be a general approach
for the development of cell-permeable inhibitors of thioester-forming
E3 ubiquitin ligases.
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Affiliation(s)
- Henrik Johansson
- Crick-GSK Biomedical LinkLabs , GlaxoSmithKline , Gunnels Wood Road , Stevenage SG1 2NY , United Kingdom.,Molecular Structure of Cell Signalling Laboratory , The Francis Crick Institute , 1 Midland Road , London NW1 1AT , United Kingdom
| | - Yi-Chun Isabella Tsai
- Molecular Structure of Cell Signalling Laboratory , The Francis Crick Institute , 1 Midland Road , London NW1 1AT , United Kingdom
| | - Ken Fantom
- R&D Platform Technology & Science , GlaxoSmithKline , Gunnels Wood Road , Stevenage SG1 2NY , United Kingdom
| | - Chun-Wa Chung
- Crick-GSK Biomedical LinkLabs , GlaxoSmithKline , Gunnels Wood Road , Stevenage SG1 2NY , United Kingdom.,R&D Platform Technology & Science , GlaxoSmithKline , Gunnels Wood Road , Stevenage SG1 2NY , United Kingdom
| | - Sandra Kümper
- Crick-GSK Biomedical LinkLabs , GlaxoSmithKline , Gunnels Wood Road , Stevenage SG1 2NY , United Kingdom.,Molecular Structure of Cell Signalling Laboratory , The Francis Crick Institute , 1 Midland Road , London NW1 1AT , United Kingdom
| | - Luigi Martino
- Molecular Structure of Cell Signalling Laboratory , The Francis Crick Institute , 1 Midland Road , London NW1 1AT , United Kingdom
| | - Daniel A Thomas
- R&D Platform Technology & Science , GlaxoSmithKline , Gunnels Wood Road , Stevenage SG1 2NY , United Kingdom
| | - H Christian Eberl
- Cellzome GmbH, a GlaxoSmithKline Company , Meyerhofstraße 1 , Heidelberg 69117 , Germany
| | - Marcel Muelbaier
- Cellzome GmbH, a GlaxoSmithKline Company , Meyerhofstraße 1 , Heidelberg 69117 , Germany
| | - David House
- Crick-GSK Biomedical LinkLabs , GlaxoSmithKline , Gunnels Wood Road , Stevenage SG1 2NY , United Kingdom
| | - Katrin Rittinger
- Molecular Structure of Cell Signalling Laboratory , The Francis Crick Institute , 1 Midland Road , London NW1 1AT , United Kingdom
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66
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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.
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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
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67
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Katsuya K, Oikawa D, Iio K, Obika S, Hori Y, Urashima T, Ayukawa K, Tokunaga F. Small-molecule inhibitors of linear ubiquitin chain assembly complex (LUBAC), HOIPINs, suppress NF-κB signaling. Biochem Biophys Res Commun 2019; 509:700-706. [PMID: 30611571 DOI: 10.1016/j.bbrc.2018.12.164] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 12/26/2018] [Indexed: 11/18/2022]
Abstract
Nuclear factor-κB (NF-κB) is a crucial transcription factor family involved in the regulation of immune and inflammatory responses and cell survival. The linear ubiquitin chain assembly complex (LUBAC), composed of the HOIL-1L, HOIP, and SHARPIN subunits, specifically generates Met1-linked linear ubiquitin chains through the ubiquitin ligase activity in HOIP, and activates the NF-κB pathway. We recently identified a chemical inhibitor of LUBAC, which we named HOIPIN-1 (HOIP inhibitor-1). To improve the potency of HOIPIN-1, we synthesized 7 derivatives (HOIPIN-2∼8), and analyzed their effects on LUBAC and NF-κB activation. Among them, HOIPIN-8 suppressed the linear ubiquitination activity by recombinant LUBAC at an IC50 value of 11 nM, corresponding to a 255-fold increase over that of HOIPIN-1. Furthermore, as compared with HOIPIN-1, HOIPIN-8 showed 10-fold and 4-fold enhanced inhibitory activities on LUBAC- and TNF-α-induced NF-κB activation respectively, without cytotoxicity. These results indicated that HOIPIN-8 is a powerful tool to explore the physiological functions of LUBAC.
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Affiliation(s)
- Ken Katsuya
- Biological Research Laboratories, Central Pharmaceutical Research Institute, Japan Tobacco Inc., Osaka, 569-1125, Japan
| | - Daisuke Oikawa
- Department of Pathobiochemistry, Graduate School of Medicine, Osaka City University, Osaka, 545-8585, Japan
| | - Kiyosei Iio
- Chemical Research Laboratories, Central Pharmaceutical Research Institute, Japan Tobacco Inc., Osaka, 569-1125, Japan
| | - Shingo Obika
- Chemical Research Laboratories, Central Pharmaceutical Research Institute, Japan Tobacco Inc., Osaka, 569-1125, Japan
| | - Yuji Hori
- Biological Research Laboratories, Central Pharmaceutical Research Institute, Japan Tobacco Inc., Osaka, 569-1125, Japan
| | - Toshiki Urashima
- Biological Research Laboratories, Central Pharmaceutical Research Institute, Japan Tobacco Inc., Osaka, 569-1125, Japan
| | - Kumiko Ayukawa
- Biological Research Laboratories, Central Pharmaceutical Research Institute, Japan Tobacco Inc., Osaka, 569-1125, Japan
| | - Fuminori Tokunaga
- Department of Pathobiochemistry, Graduate School of Medicine, Osaka City University, Osaka, 545-8585, Japan.
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68
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Poush JA, Blouin NA, Di Bona KR, Lažetić V, Fay DS. Regulation of germ cell development by ARI1 family ubiquitin ligases in C. elegans. Sci Rep 2018; 8:17737. [PMID: 30531803 PMCID: PMC6288150 DOI: 10.1038/s41598-018-35691-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 11/09/2018] [Indexed: 11/25/2022] Open
Abstract
RING-between-RING (RBR) E3 ubiquitin ligases are implicated in various developmental processes, and mutations in genes encoding RBR proteins HHARI/ARIH1 and Parkin are associated with human diseases. Here we show by phylogenetic analysis that the ARI1 family has undergone a dramatic expansion within the Caenorhabditis clade in recent history, a characteristic shared by some genes involved in germline development. We then examined the effects of deleting all ARI1 family members in the nematode Caenorhabditis elegans, which to our knowledge represents the first complete knockout of ARI1 function in a metazoan. Hermaphrodites that lacked or had strongly reduced ARI1 activity had low fecundity and were partially defective in initiation of oocyte differentiation. We provide evidence that the C. elegans ARI1s likely function downstream or in parallel to FBF-1 and FBF-2, two closely related RNA-binding proteins that are required for the switch from spermatogenesis to oogenesis during late larval development. Previous studies have shown that the E2 enzymes UBC-18/UBCH7 and UBC-3/CDC34 can functionally collaborate with ARI1 family members. Our data indicated that UBC-18, but not UBC-3, specifically cooperates with the ARI1s in germline development. These findings provide new insights into the functions of RING-between-RING proteins and Ariadne E3s during development.
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Affiliation(s)
- Julian A Poush
- Department of Molecular Biology, College of Agriculture and Natural Resources, University of Wyoming, Laramie, WY, 82071, USA
| | - Nicolas A Blouin
- Department of Molecular Biology, College of Agriculture and Natural Resources, University of Wyoming, Laramie, WY, 82071, USA
- Wyoming INBRE Bioinformatics Core, Laramie, USA
| | - Kristin R Di Bona
- Department of Molecular Biology, College of Agriculture and Natural Resources, University of Wyoming, Laramie, WY, 82071, USA
| | - Vladimir Lažetić
- Department of Molecular Biology, College of Agriculture and Natural Resources, University of Wyoming, Laramie, WY, 82071, USA
| | - David S Fay
- Department of Molecular Biology, College of Agriculture and Natural Resources, University of Wyoming, Laramie, WY, 82071, USA.
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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.
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70
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Zhu F, Yi G, Liu X, Zhu F, Zhao A, Wang A, Zhu R, Chen Z, Zhao B, Fang S, Yu X, Lin R, Liang R, Li D, Zhao W, Zhang Z, Guo W, Zhang S, Ge S, Fan X, Zhao G, Li B. Ring finger protein 31-mediated atypical ubiquitination stabilizes forkhead box P3 and thereby stimulates regulatory T-cell function. J Biol Chem 2018; 293:20099-20111. [PMID: 30389786 DOI: 10.1074/jbc.ra118.005802] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Revised: 10/21/2018] [Indexed: 01/05/2023] Open
Abstract
The CD4+CD25+FOXP3+ regulatory T (Treg) cells are critical for maintaining immune tolerance in healthy individuals and are reported to restrict anti-inflammatory responses and thereby promote tumor progression, suggesting them as a target in the development of antitumor immunotherapy. Forkhead box P3 (FOXP3) is a key transcription factor governing Treg lineage differentiation and their immune-suppressive function. Here, using Treg cells, as well as HEK-293T and Jurkat T cells, we report that the stability of FOXP3 is directly and positively regulated by the E3 ubiquitin ligase ring finger protein 31 (RNF31), which catalyzes the conjugation of atypical ubiquitin chains to the FOXP3 protein. We observed that shRNA-mediated RNF31 knockdown in human Treg cells decreases FOXP3 protein levels and increases levels of interferon-γ, resulting in a Th1 helper cell-like phenotype. Human Treg cells that ectopically expressed RNF31 displayed stronger immune-suppressive capacity, suggesting that RNF31 positively regulates both FOXP3 stability and Treg cell function. Moreover, we found that RNF31 is up-regulated in Treg cells that infiltrate human gastric tumor tissues compared with their counterparts residing in peripheral and normal tissue. We also found that elevated RNF31 expression in intratumoral Treg cells is associated with poor survival of gastric cancer patients, suggesting that RNF31 supports the immune-suppressive functions of Treg cells. Our results suggest that RNF31 could be a potential therapeutic target in immunity-based interventions against human gastric cancer.
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Affiliation(s)
- Fuxiang Zhu
- From the Shanghai Institute of Immunology and Department of Immunology and Microbiology, Shanghai JiaoTong University School of Medicine, Shanghai 200025,; the Unit of Molecular Immunology, Institut Pasteur of Shanghai, University of Chinese Academy of Sciences, Shanghai 200025
| | - Gang Yi
- From the Shanghai Institute of Immunology and Department of Immunology and Microbiology, Shanghai JiaoTong University School of Medicine, Shanghai 200025,; the Shanghai Key laboratory of Bio-energy Crops, School of Life Science, Shanghai University, Shanghai 200025
| | - Xu Liu
- the Department of Gastrointestinal Surgery, RenJi Hospital, School of Medicine, Shanghai Jiao Tong University, 160 Pujian Rd., Shanghai 200025
| | - Fangming Zhu
- the Shanghai Key laboratory of Bio-energy Crops, School of Life Science, Shanghai University, Shanghai 200025
| | - Anna Zhao
- From the Shanghai Institute of Immunology and Department of Immunology and Microbiology, Shanghai JiaoTong University School of Medicine, Shanghai 200025
| | - Aiting Wang
- From the Shanghai Institute of Immunology and Department of Immunology and Microbiology, Shanghai JiaoTong University School of Medicine, Shanghai 200025,; the Unit of Molecular Immunology, Institut Pasteur of Shanghai, University of Chinese Academy of Sciences, Shanghai 200025
| | - Ruihong Zhu
- the Unit of Molecular Immunology, Institut Pasteur of Shanghai, University of Chinese Academy of Sciences, Shanghai 200025
| | - Zuojia Chen
- the Unit of Molecular Immunology, Institut Pasteur of Shanghai, University of Chinese Academy of Sciences, Shanghai 200025
| | - Binbin Zhao
- From the Shanghai Institute of Immunology and Department of Immunology and Microbiology, Shanghai JiaoTong University School of Medicine, Shanghai 200025,; the Unit of Molecular Immunology, Institut Pasteur of Shanghai, University of Chinese Academy of Sciences, Shanghai 200025
| | - Sijie Fang
- the Department of Ophthalmology, Shanghai Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai 200025
| | - Xiao Yu
- the Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Henan Key Laboratory of Digestive Organ Transplantation, Henan 450052, and
| | - Ruirong Lin
- the Department of Biliary-Pancreatic Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200025, China
| | - Rui Liang
- From the Shanghai Institute of Immunology and Department of Immunology and Microbiology, Shanghai JiaoTong University School of Medicine, Shanghai 200025
| | - Dan Li
- From the Shanghai Institute of Immunology and Department of Immunology and Microbiology, Shanghai JiaoTong University School of Medicine, Shanghai 200025
| | - Wenyi Zhao
- the Department of Gastrointestinal Surgery, RenJi Hospital, School of Medicine, Shanghai Jiao Tong University, 160 Pujian Rd., Shanghai 200025
| | - Zizhen Zhang
- the Department of Gastrointestinal Surgery, RenJi Hospital, School of Medicine, Shanghai Jiao Tong University, 160 Pujian Rd., Shanghai 200025
| | - Wenzhi Guo
- the Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Henan Key Laboratory of Digestive Organ Transplantation, Henan 450052, and
| | - Shuijun Zhang
- the Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Henan Key Laboratory of Digestive Organ Transplantation, Henan 450052, and
| | - Shengfang Ge
- the Department of Ophthalmology, Shanghai Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai 200025
| | - Xianqun Fan
- the Department of Ophthalmology, Shanghai Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai 200025
| | - Gang Zhao
- the Department of Gastrointestinal Surgery, RenJi Hospital, School of Medicine, Shanghai Jiao Tong University, 160 Pujian Rd., Shanghai 200025,.
| | - Bin Li
- From the Shanghai Institute of Immunology and Department of Immunology and Microbiology, Shanghai JiaoTong University School of Medicine, Shanghai 200025,.
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71
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Whitcomb EA, Tsai YC, Basappa J, Liu K, Le Feuvre AK, Weissman AM, Taylor A. Stabilization of p27 Kip1/CDKN1B by UBCH7/UBE2L3 catalyzed ubiquitinylation: a new paradigm in cell-cycle control. FASEB J 2018; 33:1235-1247. [PMID: 30113882 DOI: 10.1096/fj.201800960r] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Ubiquitinylation drives many cellular processes by targeting proteins for proteasomal degradation. Ubiquitin conjugation enzymes promote ubiquitinylation and, thus, degradation of protein substrates. Ubiquitinylation is a well-known posttranslational modification controlling cell-cycle transitions and levels or/and activation levels of ubiquitin-conjugating enzymes change during development and cell cycle. Progression through the cell cycle is tightly controlled by CDK inhibitors such as p27Kip1. Here we show that, in contrast to promoting its degradation, the ubiquitin-conjugating enzyme UBCH7/UBE2L3 specifically protects p27Kip1 from degradation. Overexpression of UBCH7/UBE2L3 stabilizes p27Kip1 and delays the G1-to-S transition, while depletion of UBCH7/UBE2L3 increases turnover of p27Kip1. Levels of p21Cip1/Waf1, p57Kip2, cyclin A and cyclin E, all of which are also involved in regulating the G1/S transition are not affected by UBCH7/UBE2L3 depletion. The effect of UBCH7/UBE2L3 on p27Kip1 is not due to alteration of the levels of any of the ubiquitin ligases known to ubiquitinylate p27Kip1. Rather, UBCH7/UBE2L3 catalyzes the conjugation of heterotypic ubiquitin chains on p27Kip1 that are proteolytically incompetent. These data reveal new controls and concepts about the ubiquitin proteasome system in which a ubiquitin-conjugating enzyme selectively inhibits and may even protect, rather than promote degradation of a crucial cell-cycle regulatory molecule.-Whitcomb, E. A., Tsai, Y. C., Basappa, J., Liu, K., Le Feuvre, A. K., Weissman, A. M., Taylor, A. Stabilization of p27Kip1/CDKN1B by UBCH7/UBE2L3 catalyzed ubiquitinylation: a new paradigm in cell-cycle control.
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Affiliation(s)
- Elizabeth A Whitcomb
- Laboratory for Nutrition and Vision Research Jean Mayer-U.S. Department of Agriculture (JM-USDA) Human Nutrition Research Center on Aging, Tufts University, Boston, Massachusetts, USA
| | - Yien Che Tsai
- Laboratory of Protein Dynamics and Signaling, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, USA
| | - Johnvesly Basappa
- Laboratory for Nutrition and Vision Research Jean Mayer-U.S. Department of Agriculture (JM-USDA) Human Nutrition Research Center on Aging, Tufts University, Boston, Massachusetts, USA
| | - Ke Liu
- Laboratory for Nutrition and Vision Research Jean Mayer-U.S. Department of Agriculture (JM-USDA) Human Nutrition Research Center on Aging, Tufts University, Boston, Massachusetts, USA
| | - Aurélie K Le Feuvre
- Laboratory for Nutrition and Vision Research Jean Mayer-U.S. Department of Agriculture (JM-USDA) Human Nutrition Research Center on Aging, Tufts University, Boston, Massachusetts, USA
| | - Allan M Weissman
- Laboratory of Protein Dynamics and Signaling, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, USA
| | - Allen Taylor
- Laboratory for Nutrition and Vision Research Jean Mayer-U.S. Department of Agriculture (JM-USDA) Human Nutrition Research Center on Aging, Tufts University, Boston, Massachusetts, USA
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72
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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.
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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.
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73
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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.
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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.
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74
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Mechanism of parkin activation by phosphorylation. Nat Struct Mol Biol 2018; 25:623-630. [PMID: 29967542 DOI: 10.1038/s41594-018-0088-7] [Citation(s) in RCA: 107] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Accepted: 06/12/2018] [Indexed: 12/25/2022]
Abstract
Mutations in the ubiquitin ligase parkin are responsible for a familial form of Parkinson's disease. Parkin and the PINK1 kinase regulate a quality-control system for mitochondria. PINK1 phosphorylates ubiquitin on the outer membrane of damaged mitochondria, thus leading to recruitment and activation of parkin via phosphorylation of its ubiquitin-like (Ubl) domain. Here, we describe the mechanism of parkin activation by phosphorylation. The crystal structure of phosphorylated Bactrocera dorsalis (oriental fruit fly) parkin in complex with phosphorylated ubiquitin and an E2 ubiquitin-conjugating enzyme reveals that the key activating step is movement of the Ubl domain and release of the catalytic RING2 domain. Hydrogen/deuterium exchange and NMR experiments with the various intermediates in the activation pathway confirm and extend the interpretation of the crystal structure to mammalian parkin. Our results rationalize previously unexplained Parkinson's disease mutations and the presence of internal linkers that allow large domain movements in parkin.
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75
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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.
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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.
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76
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Koliopoulos MG, Lethier M, van der Veen AG, Haubrich K, Hennig J, Kowalinski E, Stevens RV, Martin SR, Reis e Sousa C, Cusack S, Rittinger K. Molecular mechanism of influenza A NS1-mediated TRIM25 recognition and inhibition. Nat Commun 2018; 9:1820. [PMID: 29739942 PMCID: PMC5940772 DOI: 10.1038/s41467-018-04214-8] [Citation(s) in RCA: 115] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Accepted: 04/13/2018] [Indexed: 02/04/2023] Open
Abstract
RIG-I is a viral RNA sensor that induces the production of type I interferon (IFN) in response to infection with a variety of viruses. Modification of RIG-I with K63-linked poly-ubiquitin chains, synthesised by TRIM25, is crucial for activation of the RIG-I/MAVS signalling pathway. TRIM25 activity is targeted by influenza A virus non-structural protein 1 (NS1) to suppress IFN production and prevent an efficient host immune response. Here we present structures of the human TRIM25 coiled-coil-PRYSPRY module and of complexes between the TRIM25 coiled-coil domain and NS1. These structures show that binding of NS1 interferes with the correct positioning of the PRYSPRY domain of TRIM25 required for substrate ubiquitination and provide a mechanistic explanation for how NS1 suppresses RIG-I ubiquitination and hence downstream signalling. In contrast, the formation of unanchored K63-linked poly-ubiquitin chains is unchanged by NS1 binding, indicating that RING dimerisation of TRIM25 is not affected by NS1.
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Affiliation(s)
- Marios G Koliopoulos
- Molecular Structure of Cell Signalling Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Mathilde Lethier
- European Molecular Biology Laboratory, 71 Avenue des Martyrs, 38042, Grenoble, Cedex 9, France
| | | | - Kevin Haubrich
- Structural and Computational Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117, Heidelberg, Germany
| | - Janosch Hennig
- Structural and Computational Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117, Heidelberg, Germany
| | - Eva Kowalinski
- European Molecular Biology Laboratory, 71 Avenue des Martyrs, 38042, Grenoble, Cedex 9, France
| | - Rebecca V Stevens
- Molecular Structure of Cell Signalling Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Stephen R Martin
- Structural Biology Science Technology Platform, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Caetano Reis e Sousa
- Immunobiology Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Stephen Cusack
- European Molecular Biology Laboratory, 71 Avenue des Martyrs, 38042, Grenoble, Cedex 9, France
| | - Katrin Rittinger
- Molecular Structure of Cell Signalling Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.
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77
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Walden H, Rittinger K. RBR ligase-mediated ubiquitin transfer: a tale with many twists and turns. Nat Struct Mol Biol 2018; 25:440-445. [PMID: 29735995 DOI: 10.1038/s41594-018-0063-3] [Citation(s) in RCA: 87] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Accepted: 03/29/2018] [Indexed: 12/28/2022]
Abstract
RBR ligases are an enigmatic class of E3 ubiquitin ligases that combine properties of RING and HECT-type E3s and undergo multilevel regulation through autoinhibition, post-translational modifications, multimerization and interaction with binding partners. Here, we summarize recent progress in RBR structures and function, which has uncovered commonalities in the mechanisms by which different family members transfer ubiquitin through a multistep process. However, these studies have also highlighted clear differences in the activity of different family members, suggesting that each RBR ligase has evolved specific properties to fit the biological process it regulates.
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Affiliation(s)
- Helen Walden
- Institute of Molecular Cell and Systems Biology, University of Glasgow, Glasgow, Scotland, UK.
| | - Katrin Rittinger
- Molecular Structure of Cell Signalling Laboratory, The Francis Crick Institute, London, UK.
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78
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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: 27] [Impact Index Per Article: 4.5] [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.
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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
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79
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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: 157] [Impact Index Per Article: 26.2] [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.
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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.
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80
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Pao KC, Wood NT, Knebel A, Rafie K, Stanley M, Mabbitt PD, Sundaramoorthy R, Hofmann K, van Aalten DMF, Virdee S. Activity-based E3 ligase profiling uncovers an E3 ligase with esterification activity. Nature 2018; 556:381-385. [PMID: 29643511 DOI: 10.1038/s41586-018-0026-1] [Citation(s) in RCA: 172] [Impact Index Per Article: 28.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2017] [Accepted: 03/07/2018] [Indexed: 12/21/2022]
Abstract
Ubiquitination is initiated by transfer of ubiquitin (Ub) from a ubiquitin-activating enzyme (E1) to a ubiquitin-conjugating enzyme (E2), producing a covalently linked intermediate (E2-Ub) 1 . Ubiquitin ligases (E3s) of the 'really interesting new gene' (RING) class recruit E2-Ub via their RING domain and then mediate direct transfer of ubiquitin to substrates 2 . By contrast, 'homologous to E6-AP carboxy terminus' (HECT) E3 ligases undergo a catalytic cysteine-dependent transthiolation reaction with E2-Ub, forming a covalent E3-Ub intermediate3,4. Additionally, RING-between-RING (RBR) E3 ligases have a canonical RING domain that is linked to an ancillary domain. This ancillary domain contains a catalytic cysteine that enables a hybrid RING-HECT mechanism 5 . Ubiquitination is typically considered a post-translational modification of lysine residues, as there are no known human E3 ligases with non-lysine activity. Here we perform activity-based protein profiling of HECT or RBR-like E3 ligases and identify the neuron-associated E3 ligase MYCBP2 (also known as PHR1) as the apparent single member of a class of RING-linked E3 ligase with esterification activity and intrinsic selectivity for threonine over serine. MYCBP2 contains two essential catalytic cysteine residues that relay ubiquitin to its substrate via thioester intermediates. Crystallographic characterization of this class of E3 ligase, which we designate RING-Cys-relay (RCR), provides insights into its mechanism and threonine selectivity. These findings implicate non-lysine ubiquitination in cellular regulation of higher eukaryotes and suggest that E3 enzymes have an unappreciated mechanistic diversity.
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Affiliation(s)
- Kuan-Chuan Pao
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
| | - Nicola T Wood
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
| | - Axel Knebel
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
| | - Karim Rafie
- Division of Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, UK
| | - Mathew Stanley
- Division of Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, UK
| | - Peter D Mabbitt
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
| | | | - Kay Hofmann
- Institute for Genetics, University of Cologne, Cologne, Germany
| | - Daan M F van Aalten
- Division of Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, UK
| | - Satpal Virdee
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK.
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81
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Determinants of E2-ubiquitin conjugate recognition by RBR E3 ligases. Sci Rep 2018; 8:68. [PMID: 29311602 PMCID: PMC5758712 DOI: 10.1038/s41598-017-18513-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 12/13/2017] [Indexed: 12/25/2022] Open
Abstract
RING-between-RING (RBR) ubiquitin ligases work with multiple E2 enzymes and function through an E3-ubiquitin thioester intermediate. The RBR module comprises three domains, RING1, IBR and RING2 that collaborate to transfer ubiquitin from the E2~Ub conjugate, recognised by RING1, onto a catalytic cysteine in RING2 and finally onto the substrate in a multi-step reaction. Recent studies have shown that RING1 domains bind E2~Ub conjugates in an open conformation to supress ubiquitin transfer onto lysine residues and promote formation of the E3 thioester intermediate. However, how the nature of the E2 influences the ubiquitin transfer process is currently unclear. We report here a detailed characterization of the RBR/E2-conjugate recognition step that indicates that this mechanism depends on the nature of the E2 enzyme and differs between UbcH5 and UbcH7. In the case of UbcH5~Ub an interaction with ubiquitin is necessary to stabilize the transfer complex while recognition of UbcH7~Ub is driven primarily by E2-RING1 contacts. Furthermore our analysis suggests that RBRs, in isolation and in complex with ubiquitin-loaded E2s, are dynamic species and that their intrinsic flexibility might be a key aspect of their catalytic mechanism.
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82
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Abstract
The availability of different polyubiquitin chains of specific linkage types has changed the appreciation of the specificity in the ubiquitin (Ub) system. Numerous E2 Ub-conjugating enzymes and E3 Ub ligases, Ub-binding domains (UBDs), and deubiquitinases (DUBs) are now known to assemble, bind, or hydrolyze individual linkage types, respectively. Biochemical and structural studies of these processes require milligram quantities of pure polyUb. Here we describe protocols that allow the enzymatic synthesis and purification of six of the eight homotypic polyUb chains through the use of chain-specific Ub ligases and DUBs.
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Affiliation(s)
- Martin A Michel
- Division of Protein and Nucleic Acid Chemistry, MRC Laboratory of Molecular Biology, Cambridge, UK
| | - David Komander
- Division of Protein and Nucleic Acid Chemistry, MRC Laboratory of Molecular Biology, Cambridge, UK.
| | - Paul R Elliott
- Division of Protein and Nucleic Acid Chemistry, MRC Laboratory of Molecular Biology, Cambridge, UK.
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83
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Reiter KH, Klevit RE. Characterization of RING-Between-RING E3 Ubiquitin Transfer Mechanisms. Methods Mol Biol 2018; 1844:3-17. [PMID: 30242699 DOI: 10.1007/978-1-4939-8706-1_1] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Protein ubiquitination is an essential posttranslational modification that regulates nearly all cellular processes. E3 ligases catalyze the final transfer of ubiquitin (Ub) onto substrates and thus are important temporal regulators of ubiquitin modifications in the cell. E3s are classified by their distinct transfer mechanisms. RING E3s act as scaffolds to facilitate the transfer of Ub from E2-conjugating enzymes directly onto substrates, while HECT E3s form an E3~Ub thioester intermediate prior to Ub transfer. A third class, RING-Between-RING (RBR) E3s, are classified as RING/HECT hybrids based on their ability to engage the E2~Ub conjugate via a RING1 domain while subsequently forming an obligate E3~Ub intermediate prior to substrate modification. RBRs comprise the smallest class of E3s, consisting of only 14 family members in humans, yet their dysfunction has been associated with neurodegenerative diseases, susceptibility to infection, inflammation, and cancer. Additionally, their activity is suppressed by auto-inhibitory domains that block their catalytic activity, suggesting their regulation has important cellular consequences. Here, we identify technical hurdles faced in studying RBR E3s and provide protocols and guidelines to overcome these challenges.
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Affiliation(s)
| | - Rachel E Klevit
- Department of Biochemistry, University of Washington, Seattle, WA, USA.
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84
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Kobayashi F, Nishiuchi T, Takaki K, Konno H. Ubiquitin chain specificities of E6AP E3 ligase and its HECT domain. Biochem Biophys Res Commun 2017; 496:686-692. [PMID: 29288669 DOI: 10.1016/j.bbrc.2017.12.076] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Accepted: 12/14/2017] [Indexed: 01/11/2023]
Abstract
Ubiquitination of target proteins is accomplished by isopeptide bond formation between the carboxy group of the C-terminal glycine (Gly) residue of ubiquitin (Ub) and the ɛ-amino group of lysine (Lys) on the target proteins. The formation of an isopeptide bond between Ubs that gives rise to a poly-Ub chain on the target proteins and the types of poly-Ub chains formed depend on which of the seven Lys residues or N-terminal methionine (Met) residue on Ub is used for chain elongation. To understand the linkage specificity mechanism of Ub chains on E3, the previous study established an assay to monitor the formation of a free diubiquitin chain (Ub2 chain synthesis assay) by HECT type E3 ligase. In this study, we investigated Ub2 chain specificity using E6AP HECT domain. We here demonstrate the importance of the N-terminal domain of full length E6AP for Ub2 chain specificity.
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Affiliation(s)
- Fuminori Kobayashi
- Graduate School of Natural Science & Technology, Kanazawa University, Kanazawa 920-1192, Japan
| | - Takumi Nishiuchi
- Institute for Gene Research Center, Bio-AFM Frontier Research Center, Kanazawa University, Kanazawa 920-1192, Japan
| | - Kento Takaki
- Graduate School of Natural Science & Technology, Kanazawa University, Kanazawa 920-1192, Japan
| | - Hiroki Konno
- Institute for Gene Research Center, Bio-AFM Frontier Research Center, Kanazawa University, Kanazawa 920-1192, Japan.
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85
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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: 98] [Impact Index Per Article: 14.0] [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.
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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.
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86
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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: 103] [Impact Index Per Article: 14.7] [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.
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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.
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87
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Structural insights into the mechanism and E2 specificity of the RBR E3 ubiquitin ligase HHARI. Nat Commun 2017; 8:211. [PMID: 28790309 PMCID: PMC5548887 DOI: 10.1038/s41467-017-00272-6] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Accepted: 06/15/2017] [Indexed: 12/19/2022] Open
Abstract
RING-in-between-RING (RBR) ubiquitin (Ub) E3 ligases function with Ub E2s through a RING/HECT hybrid mechanism to conjugate Ub to target proteins. Here, we report the crystal structure of the RBR E3, HHARI, in complex with a UbcH7 ~ Ub thioester mimetic which reveals the molecular basis for the specificity of this cognate E2/RBR E3 pair. The structure also reveals mechanistically important conformational changes in the RING1 and UBA-like domains of HHARI that accompany UbcH7 ~ Ub binding and provides a molecular basis by which HHARI recruits E2 ~ Ub in an ‘open’ conformation. In addition to optimally functioning with an E2 that solely performs transthiolation, our data suggests that HHARI prevents spurious discharge of Ub from E2 to lysine residues by: (1) harboring structural elements that block E2 ~ Ub from adopting a ‘closed’ conformation and (2) participating in contacts to ubiquitin that promote an open E2 ~ Ub conformation. HHARI is a RING-in-between-RING (RBR) ubiquitin (Ub) E3 ligase. Here the authors present the crystal structure of HHARI with the UbcH7 ~ Ub thioester intermediate mimetic, which reveals that HHARI binds this E2 ~ Ub in an open conformation and explains the specificity of this cognate RBR E3/E2 pair.
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88
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Chen H, Wu G, Gao S, Guo R, Zhao Z, Yuan H, Liu S, Wu J, Lu X, Yuan X, Yu Z, Zu X, Xie N, Yang N, Hu Z, Sun Q, Zhang W. Discovery of Potent Small-Molecule Inhibitors of Ubiquitin-Conjugating Enzyme UbcH5c from α-Santonin Derivatives. J Med Chem 2017; 60:6828-6852. [PMID: 28696694 DOI: 10.1021/acs.jmedchem.6b01829] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
As a therapeutic target for antitumor necrosis factor (TNF)-α interventions, UbcH5c is one of the key ubiquitin-conjugating enzymes catalyzing ubiquitination during TNF-α-triggered nuclear factor kappa B (NF-κB) activation. In the present study, three series of analogues were designed and synthesized from α-santonin, and their UbcH5c inhibitory activities were screened by Western blotting and NF-κB luciferase assay. Further BIAcore, in-gel fluorescence imaging, and immunoprecipitation assays demonstrated that compound 6d exhibited robust and specific inhibition of UbcH5c, exceeding that of the positive compound 1 (IJ-5). Mechanistic investigations revealed that compound 6d preferentially bound to and inactivated UbcH5c by forming a covalent adduct with its active site Cys85. Furthermore, compound 6d exhibited potent anti-inflammatory activity against complete Freund's adjuvant-induced adjuvant arthritis in vivo. These findings suggest that the novel α-santonin-derived UbcH5c inhibitor 6d is a promising lead compound for the development of new antirheumatoid arthritis (RA) agent.
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Affiliation(s)
- Hao Chen
- School of Pharmacy, Second Military Medical University , Shanghai 200433, China
| | - Guozhen Wu
- School of Pharmacy, Second Military Medical University , Shanghai 200433, China
| | - Shuang Gao
- School of Pharmacy, Second Military Medical University , Shanghai 200433, China
| | - Ruihua Guo
- School of Pharmacy, Second Military Medical University , Shanghai 200433, China
| | - Zeng Zhao
- School of Pharmacy, Second Military Medical University , Shanghai 200433, China
| | - Hu Yuan
- Shanghai Institute of Pharmaceutical Industry , Shanghai 200040, China
| | - Shanxiang Liu
- School of Pharmacy, Second Military Medical University , Shanghai 200433, China
| | - Jian Wu
- Progenra, Inc. , 277 Great Valley Parkway, Malvern, Pennsylvania 19355, United States
| | - Xiaolong Lu
- Lifesensors, Inc. , 271 Great Valley Parkway, Malvern, Pennsylvania 19355, United States
| | - Xing Yuan
- School of Pharmacy, Second Military Medical University , Shanghai 200433, China
| | - Zongmin Yu
- School of Pharmacy, Second Military Medical University , Shanghai 200433, China
| | - Xianpeng Zu
- School of Pharmacy, Second Military Medical University , Shanghai 200433, China
| | - Ning Xie
- State Key Laboratory of Innovative Natural Medicine and TCM Injections, Jiangxi Qingfeng Pharmaceutical Co., Ltd. , Ganzhou 341000, Jiangxi, China
| | - Niao Yang
- School of Pharmacy, Second Military Medical University , Shanghai 200433, China
| | - Zhenlin Hu
- School of Pharmacy, Second Military Medical University , Shanghai 200433, China
| | - Qingyan Sun
- Shanghai Institute of Pharmaceutical Industry , Shanghai 200040, China
| | - Weidong Zhang
- School of Pharmacy, Second Military Medical University , Shanghai 200433, China.,Shanghai Institute of Pharmaceutical Industry , Shanghai 200040, China.,Institute of Interdisciplinary Research Complex, Shanghai University of Traditional Chinese Medicine , Shanghai 201210, China
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89
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Molecular basis for specificity of the Met1-linked polyubiquitin signal. Biochem Soc Trans 2017; 44:1581-1602. [PMID: 27913667 PMCID: PMC5135002 DOI: 10.1042/bst20160227] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Revised: 10/03/2016] [Accepted: 10/07/2016] [Indexed: 12/27/2022]
Abstract
The post-translational modification of proteins provides a rapid and versatile system for regulating all signalling pathways. Protein ubiquitination is one such type of post-translational modification involved in controlling numerous cellular processes. The unique ability of ubiquitin to form polyubiquitin chains creates a highly complex code responsible for different subsequent signalling outcomes. Specialised enzymes ('writers') generate the ubiquitin code, whereas other enzymes ('erasers') disassemble it. Importantly, the ubiquitin code is deciphered by different ubiquitin-binding proteins ('readers') functioning to elicit particular cellular responses. Ten years ago, the methionine1 (Met1)-linked (linear) polyubiquitin code was first identified and the intervening years have witnessed a seismic shift in our understanding of Met1-linked polyubiquitin in cellular processes, particularly inflammatory signalling. This review will discuss the molecular mechanisms of specificity determination within Met1-linked polyubiquitin signalling.
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90
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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.
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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
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91
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Abstract
Ubiquitin E3 ligases control every aspect of eukaryotic biology by promoting protein ubiquitination and degradation. At the end of a three-enzyme cascade, ubiquitin ligases mediate the transfer of ubiquitin from an E2 ubiquitin-conjugating enzyme to specific substrate proteins. Early investigations of E3s of the RING (really interesting new gene) and HECT (homologous to the E6AP carboxyl terminus) types shed light on their enzymatic activities, general architectures, and substrate degron-binding modes. Recent studies have provided deeper mechanistic insights into their catalysis, activation, and regulation. In this review, we summarize the current progress in structure-function studies of ubiquitin ligases as well as exciting new discoveries of novel classes of E3s and diverse substrate recognition mechanisms. Our increased understanding of ubiquitin ligase function and regulation has provided the rationale for developing E3-targeting therapeutics for the treatment of human diseases.
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Affiliation(s)
- Ning Zheng
- Howard Hughes Medical Institute and Department of Pharmacology, University of Washington, Seattle, Washington 98195; ,
| | - Nitzan Shabek
- Howard Hughes Medical Institute and Department of Pharmacology, University of Washington, Seattle, Washington 98195; ,
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92
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Mechanism and disease association of E2-conjugating enzymes: lessons from UBE2T and UBE2L3. Biochem J 2017; 473:3401-3419. [PMID: 27729585 PMCID: PMC5095918 DOI: 10.1042/bcj20160028] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Accepted: 08/09/2016] [Indexed: 02/07/2023]
Abstract
Ubiquitin signalling is a fundamental eukaryotic regulatory system, controlling diverse cellular functions. A cascade of E1, E2, and E3 enzymes is required for assembly of distinct signals, whereas an array of deubiquitinases and ubiquitin-binding modules edit, remove, and translate the signals. In the centre of this cascade sits the E2-conjugating enzyme, relaying activated ubiquitin from the E1 activating enzyme to the substrate, usually via an E3 ubiquitin ligase. Many disease states are associated with dysfunction of ubiquitin signalling, with the E3s being a particular focus. However, recent evidence demonstrates that mutations or impairment of the E2s can lead to severe disease states, including chromosome instability syndromes, cancer predisposition, and immunological disorders. Given their relevance to diseases, E2s may represent an important class of therapeutic targets. In the present study, we review the current understanding of the mechanism of this important family of enzymes, and the role of selected E2s in disease.
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93
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Dove KK, Olszewski JL, Martino L, Duda DM, Wu XS, Miller DJ, Reiter KH, Rittinger K, Schulman BA, Klevit RE. Structural Studies of HHARI/UbcH7∼Ub Reveal Unique E2∼Ub Conformational Restriction by RBR RING1. Structure 2017; 25:890-900.e5. [PMID: 28552575 PMCID: PMC5462532 DOI: 10.1016/j.str.2017.04.013] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Revised: 03/07/2017] [Accepted: 04/28/2017] [Indexed: 12/02/2022]
Abstract
RING-between-RING (RBR) E3s contain RING1 domains that are structurally similar yet mechanistically distinct from canonical RING domains. Both types of E3 bind E2∼ubiquitin (E2∼Ub) via their RINGs but canonical RING E3s promote closed E2∼Ub conformations required for direct Ub transfer from the E2 to substrate, while RBR RING1s promote open E2∼Ub to favor Ub transfer to the E3 active site. This different RING/E2∼Ub conformation determines its direct target, which for canonical RING E3s is typically a substrate or substrate-linked Ub, but is the E3 active-site cysteine in the case of RBR-type E3s. Here we show that a short extension of HHARI RING1, namely Zn2+-loop II, not present in any RING E3s, acts as a steric wedge to disrupt closed E2∼Ub, providing a structural explanation for the distinctive RING1-dependent conformational restriction mechanism utilized by RBR E3s.
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Affiliation(s)
- Katja K Dove
- Department of Biochemistry, University of Washington, 1705 Northeast Pacific Street, Seattle, WA 98195, USA
| | - Jennifer L Olszewski
- Department of Structural Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Luigi Martino
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - David M Duda
- Department of Structural Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA; Howard Hughes Medical Institute, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Xiaoli S Wu
- Department of Biochemistry, University of Washington, 1705 Northeast Pacific Street, Seattle, WA 98195, USA
| | - Darcie J Miller
- Department of Structural Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Katherine H Reiter
- Department of Biochemistry, University of Washington, 1705 Northeast Pacific Street, Seattle, WA 98195, USA
| | | | - Brenda A Schulman
- Department of Structural Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA; Howard Hughes Medical Institute, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA.
| | - Rachel E Klevit
- Department of Biochemistry, University of Washington, 1705 Northeast Pacific Street, Seattle, WA 98195, USA.
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94
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Chemical ubiquitination for decrypting a cellular code. Biochem J 2017; 473:1297-314. [PMID: 27208213 PMCID: PMC5298413 DOI: 10.1042/bj20151195] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Accepted: 02/15/2016] [Indexed: 02/06/2023]
Abstract
The modification of proteins with ubiquitin (Ub) is an important regulator of eukaryotic biology and deleterious perturbation of this process is widely linked to the onset of various diseases. The regulatory capacity of the Ub signal is high and, in part, arises from the capability of Ub to be enzymatically polymerised to form polyubiquitin (polyUb) chains of eight different linkage types. These distinct polyUb topologies can then be site-specifically conjugated to substrate proteins to elicit a number of cellular outcomes. Therefore, to further elucidate the biological significance of substrate ubiquitination, methodologies that allow the production of defined polyUb species, and substrate proteins that are site-specifically modified with them, are essential to progress our understanding. Many chemically inspired methods have recently emerged which fulfil many of the criteria necessary for achieving deeper insight into Ub biology. With a view to providing immediate impact in traditional biology research labs, the aim of this review is to provide an overview of the techniques that are available for preparing Ub conjugates and polyUb chains with focus on approaches that use recombinant protein building blocks. These approaches either produce a native isopeptide, or analogue thereof, that can be hydrolysable or non-hydrolysable by deubiquitinases. The most significant biological insights that have already been garnered using such approaches will also be summarized.
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95
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Kumar A, Chaugule VK, Condos TEC, Barber KR, Johnson C, Toth R, Sundaramoorthy R, Knebel A, Shaw GS, Walden H. Parkin-phosphoubiquitin complex reveals cryptic ubiquitin-binding site required for RBR ligase activity. Nat Struct Mol Biol 2017; 24:475-483. [PMID: 28414322 PMCID: PMC5420311 DOI: 10.1038/nsmb.3400] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Accepted: 03/16/2017] [Indexed: 12/20/2022]
Abstract
RING-between-RING (RBR) E3 ligases are a class of ubiquitin ligases distinct from RING or HECT E3 ligases. An important RBR ligase is Parkin, mutations in which lead to early-onset hereditary Parkinsonism. Parkin and other RBR ligases share a catalytic RBR module but are usually autoinhibited and activated via distinct mechanisms. Recent insights into Parkin regulation predict large, unknown conformational changes during Parkin activation. However, current data on active RBR ligases reflect the absence of regulatory domains. Therefore, it remains unclear how individual RBR ligases are activated, and whether they share a common mechanism. We now report the crystal structure of a human Parkin-phosphoubiquitin complex, which shows that phosphoubiquitin binding induces movement in the 'in-between RING' (IBR) domain to reveal a cryptic ubiquitin-binding site. Mutation of this site negatively affects Parkin's activity. Furthermore, ubiquitin binding promotes cooperation between Parkin molecules, which suggests a role for interdomain association in the RBR ligase mechanism.
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Affiliation(s)
- Atul Kumar
- MRC Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences University of Dundee, Dundee, UK
| | - Viduth K Chaugule
- MRC Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences University of Dundee, Dundee, UK
| | - Tara E C Condos
- Department of Biochemistry, Schulich School of Medicine and
Dentistry, University of Western Ontario, London, ON, Canada
| | - Kathryn R Barber
- Department of Biochemistry, Schulich School of Medicine and
Dentistry, University of Western Ontario, London, ON, Canada
| | - Clare Johnson
- MRC Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences University of Dundee, Dundee, UK
| | - Rachel Toth
- MRC Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences University of Dundee, Dundee, UK
| | | | - Axel Knebel
- MRC Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences University of Dundee, Dundee, UK
| | - Gary S Shaw
- Department of Biochemistry, Schulich School of Medicine and
Dentistry, University of Western Ontario, London, ON, Canada
| | - Helen Walden
- MRC Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences University of Dundee, Dundee, UK
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96
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Ubiquitin and Parkinson's disease through the looking glass of genetics. Biochem J 2017; 474:1439-1451. [PMID: 28408429 PMCID: PMC5390927 DOI: 10.1042/bcj20160498] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2016] [Revised: 02/20/2017] [Accepted: 02/20/2017] [Indexed: 12/12/2022]
Abstract
Biochemical alterations found in the brains of Parkinson's disease (PD) patients indicate that cellular stress is a major driver of dopaminergic neuronal loss. Oxidative stress, mitochondrial dysfunction, and ER stress lead to impairment of the homeostatic regulation of protein quality control pathways with a consequent increase in protein misfolding and aggregation and failure of the protein degradation machinery. Ubiquitin signalling plays a central role in protein quality control; however, prior to genetic advances, the detailed mechanisms of how impairment in the ubiquitin system was linked to PD remained mysterious. The discovery of mutations in the α-synuclein gene, which encodes the main protein misfolded in PD aggregates, together with mutations in genes encoding ubiquitin regulatory molecules, including PTEN-induced kinase 1 (PINK1), Parkin, and FBX07, has provided an opportunity to dissect out the molecular basis of ubiquitin signalling disruption in PD, and this knowledge will be critical for developing novel therapeutic strategies in PD that target the ubiquitin system.
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97
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Rittinger K, Ikeda F. Linear ubiquitin chains: enzymes, mechanisms and biology. Open Biol 2017; 7:170026. [PMID: 28446710 PMCID: PMC5413910 DOI: 10.1098/rsob.170026] [Citation(s) in RCA: 79] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Accepted: 03/21/2017] [Indexed: 12/14/2022] Open
Abstract
Ubiquitination is a versatile post-translational modification that regulates a multitude of cellular processes. Its versatility is based on the ability of ubiquitin to form multiple types of polyubiquitin chains, which are recognized by specific ubiquitin receptors to induce the required cellular response. Linear ubiquitin chains are linked through Met 1 and have been established as important players of inflammatory signalling and apoptotic cell death. These chains are generated by a ubiquitin E3 ligase complex called the linear ubiquitin chain assembly complex (LUBAC) that is thus far the only E3 ligase capable of forming linear ubiquitin chains. The complex consists of three subunits, HOIP, HOIL-1L and SHARPIN, each of which have specific roles in the observed biological functions of LUBAC. Furthermore, LUBAC has been found to be associated with OTULIN and CYLD, deubiquitinases that disassemble linear chains and counterbalance the E3 ligase activity of LUBAC. Gene mutations in HOIP, HOIL-1L and OTULIN are found in human patients who suffer from autoimmune diseases, and HOIL-1L mutations are also found in myopathy patients. In this paper, we discuss the mechanisms of linear ubiquitin chain generation and disassembly by their respective enzymes and review our current understanding of their biological functions and association with human diseases.
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Affiliation(s)
- Katrin Rittinger
- Molecular Structure of Cell Signalling Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Fumiyo Ikeda
- Institute of Molecular Biotechnology (IMBA), Dr Bohr-gasse 3, 1030 Vienna, Austria
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98
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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]
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99
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Determination of the pK a of the N-terminal amino group of ubiquitin by NMR. Sci Rep 2017; 7:43748. [PMID: 28252051 PMCID: PMC5333110 DOI: 10.1038/srep43748] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Accepted: 01/26/2017] [Indexed: 12/26/2022] Open
Abstract
Ubiquitination regulates nearly every aspect of cellular life. It is catalysed by a cascade of three enzymes and results in the attachment of the C-terminal carboxylate of ubiquitin to a lysine side chain in the protein substrate. Chain extension occurs via addition of subsequent ubiquitin molecules to either one of the seven lysine residues of ubiquitin, or via its N-terminal α-amino group to build linear ubiquitin chains. The pKa of lysine side chains is around 10.5 and hence E3 ligases require a mechanism to deprotonate the amino group at physiological pH to produce an effective nucleophile. In contrast, the pKa of N-terminal α-amino groups of proteins can vary significantly, with reported values between 6.8 and 9.1, raising the possibility that linear chain synthesis may not require a general base. In this study we use NMR spectroscopy to determine the pKa for the N-terminal α-amino group of methionine1 of ubiquitin for the first time. We show that it is 9.14, one of the highest pKa values ever reported for this amino group, providing a rational for the observed need for a general base in the E3 ligase HOIP, which synthesizes linear ubiquitin chains.
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100
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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.
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