1
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Davidson S, Shibata Y, Collard S, Zheng H, Kong K, Sun JM, Laohamonthonkul P, Cerra A, Kratina T, Li MW, Russell C, van Beek A, Kirk EP, Walsh R, Alqanatish J, Almojali A, Alsuwairi W, Alrasheed A, Lalaoui N, Gray PE, Komander D, Masters SL. Dominant negative OTULIN-related autoinflammatory syndrome. J Exp Med 2024; 221:e20222171. [PMID: 38630025 PMCID: PMC11022884 DOI: 10.1084/jem.20222171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 11/19/2023] [Accepted: 02/21/2024] [Indexed: 04/19/2024] Open
Abstract
OTU deubiquitinase with linear linkage specificity (OTULIN) regulates inflammation and cell death by deubiquitinating linear ubiquitin chains generated by the linear ubiquitin chain assembly complex (LUBAC). Biallelic loss-of-function mutations causes OTULIN-related autoinflammatory syndrome (ORAS), while OTULIN haploinsuffiency has not been associated with spontaneous inflammation. However, herein, we identify two patients with the heterozygous mutation p.Cys129Ser in OTULIN. Consistent with ORAS, we observed accumulation of linear ubiquitin chains, increased sensitivity to TNF-induced death, and dysregulation of inflammatory signaling in patient cells. While the C129S mutation did not affect OTULIN protein stability or binding capacity to LUBAC and linear ubiquitin chains, it did ablate OTULIN deubiquitinase activity. Loss of activity facilitated the accumulation of autoubiquitin chains on LUBAC. Altered ubiquitination of LUBAC inhibits its recruitment to the TNF receptor signaling complex, promoting TNF-induced cell death and disease pathology. By reporting the first dominant negative mutation driving ORAS, this study expands our clinical understanding of OTULIN-associated pathology.
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Affiliation(s)
- Sophia Davidson
- Inflammation Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, Australia
| | - Yuri Shibata
- Department of Medical Biology, The University of Melbourne, Parkville, Australia
- Ubiquitin Signalling Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
| | - Sophie Collard
- Inflammation Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, Australia
| | - Hongyu Zheng
- Inflammation Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, Australia
| | - Klara Kong
- Inflammation Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, Australia
| | - June M. Sun
- Inflammation Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, Australia
| | - Pawat Laohamonthonkul
- Inflammation Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, Australia
| | - Anthony Cerra
- Department of Medical Biology, The University of Melbourne, Parkville, Australia
- Ubiquitin Signalling Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
| | - Tobias Kratina
- Peter MacCallum Cancer Centre, Melbourne, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Australia
| | | | | | - Margaret W.Y. Li
- School of Clinical Medicine, University of New South Wales, Randwick, Australia
- Department of Immunology and Infectious Diseases, Sydney Children’s Hospital, Randwick, Australia
| | - Carolyn Russell
- Department of Paediatric Surgery, Sydney Children’s Hospital, Randwick, Australia
| | - Anna van Beek
- Department of General Paediatrics, Sydney Children’s Hospital, Randwick, Australia
| | - Edwin P. Kirk
- School of Clinical Medicine, University of New South Wales, Randwick, Australia
- Centre for Clinical Genetics, Sydney Children’s Hospital, Randwick, Australia
- New South Wales Health Pathology Randwick Genomics Laboratory, Randwick, Australia
| | - Rebecca Walsh
- New South Wales Health Pathology Randwick Genomics Laboratory, Randwick, Australia
| | - Jubran Alqanatish
- Pediatric Rheumatology, King Abdullah Specialist Children’s Hospital, National Guard Health Affairs, Riyadh, Saudi Arabia
- King Abdullah International Medical Research Center, Riyadh, Saudi Arabia
- College of Medicine, King Saud Bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | - Abdullah Almojali
- Pediatric Rheumatology, King Abdullah Specialist Children’s Hospital, National Guard Health Affairs, Riyadh, Saudi Arabia
- King Abdullah International Medical Research Center, Riyadh, Saudi Arabia
- College of Medicine, King Saud Bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | - Wafaa Alsuwairi
- Pediatric Rheumatology, King Abdullah Specialist Children’s Hospital, National Guard Health Affairs, Riyadh, Saudi Arabia
- King Abdullah International Medical Research Center, Riyadh, Saudi Arabia
- College of Medicine, King Saud Bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | - Abdulrahman Alrasheed
- Pediatric Rheumatology, King Abdullah Specialist Children’s Hospital, National Guard Health Affairs, Riyadh, Saudi Arabia
- King Abdullah International Medical Research Center, Riyadh, Saudi Arabia
- College of Medicine, King Saud Bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | - Najoua Lalaoui
- Inflammation Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
- Peter MacCallum Cancer Centre, Melbourne, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Australia
| | - Paul E. Gray
- Department of Immunology and Infectious Diseases, Sydney Children’s Hospital, Randwick, Australia
- University of Western Sydney, Sydney, Australia
| | - David Komander
- Department of Medical Biology, The University of Melbourne, Parkville, Australia
- Ubiquitin Signalling Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
| | - Seth L. Masters
- Inflammation Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, Australia
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Australia
- Department of Molecular and Translational Science, Monash University, Clayton, Australia
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2
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Dou B, Jiang G, Peng W, Liu C. OTULIN deficiency: focus on innate immune system impairment. Front Immunol 2024; 15:1371564. [PMID: 38774872 PMCID: PMC11106414 DOI: 10.3389/fimmu.2024.1371564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 04/04/2024] [Indexed: 05/24/2024] Open
Abstract
OTULIN deficiency is a complex disease characterized by a wide range of clinical manifestations, including skin rash, joint welling, lipodystrophy to pulmonary abscess, and sepsis shock. This disease is mechanistically linked to mutations in the OTULIN gene, resulting in an immune disorder that compromises the body's ability to effectively combat pathogens and foreign stimuli. The OTULIN gene is responsible for encoding a deubiquitinating enzyme crucial for hydrolyzing Met1-poly Ub chains, and its dysfunction leads to dysregulated immune responses. Patients with OTULIN deficiency often exhibit an increase in monocytes, including neutrophils and macrophages, along with inflammatory clinical features. The onset of symptoms typically occurs at an early age. However, individuals with OTULIN haploinsufficiency are particularly susceptible to life-threatening staphylococcal infections. Currently, the most effective treatment for patients with OTULIN biallelic mutations involves the use of TNF-blocking agents, which target the dysregulated immune response. In conclusion, OTULIN deficiency presents a complex clinical picture with diverse manifestations, attributed to mutations in the OTULIN gene. Understanding the underlying mechanisms is crucial for developing targeted therapeutic interventions to address this challenging condition. Further research into the pathophysiology of OTULIN deficiency is essential for improving clinical management and outcomes for affected individuals.
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Affiliation(s)
- Bo Dou
- Central South University, Xiangya Hospital, Pediatric Department, Changsha, Hunan, China
| | - Gang Jiang
- Hunan Normal University, Hunan Provincial People's Hospital, Department of Respiratory Medicine, Changsha, Hunan, China
| | - Wang Peng
- Central South University, Xiangya Hospital, Pediatric Department, Changsha, Hunan, China
| | - Chentao Liu
- Central South University, Xiangya Hospital, Pediatric Department, Changsha, Hunan, China
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3
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Asanomi Y, Kimura T, Shimoda N, Shigemizu D, Niida S, Ozaki K. CRISPR/Cas9-mediated knock-in cells of the late-onset Alzheimer's disease-risk variant, SHARPIN G186R, reveal reduced NF-κB pathway and accelerated Aβ secretion. J Hum Genet 2024; 69:171-176. [PMID: 38351238 PMCID: PMC11043039 DOI: 10.1038/s10038-024-01224-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 12/27/2023] [Accepted: 01/25/2024] [Indexed: 04/26/2024]
Affiliation(s)
- Yuya Asanomi
- Medical Genome Center, Research Institute, National Center for Geriatrics and Gerontology, Obu, Aichi, Japan
| | - Tetsuaki Kimura
- Medical Genome Center, Research Institute, National Center for Geriatrics and Gerontology, Obu, Aichi, Japan
| | - Nobuyoshi Shimoda
- Medical Genome Center, Research Institute, National Center for Geriatrics and Gerontology, Obu, Aichi, Japan
| | - Daichi Shigemizu
- Medical Genome Center, Research Institute, National Center for Geriatrics and Gerontology, Obu, Aichi, Japan
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Shumpei Niida
- Center for Core Facility Administration, Research Institute, National Center for Geriatrics and Gerontology, Obu, Aichi, Japan
| | - Kouichi Ozaki
- Medical Genome Center, Research Institute, National Center for Geriatrics and Gerontology, Obu, Aichi, Japan.
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.
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4
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Din MAU, Lin Y, Wang N, Wang B, Mao F. Ferroptosis and the ubiquitin-proteasome system: exploring treatment targets in cancer. Front Pharmacol 2024; 15:1383203. [PMID: 38666028 PMCID: PMC11043542 DOI: 10.3389/fphar.2024.1383203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Accepted: 04/02/2024] [Indexed: 04/28/2024] Open
Abstract
Ferroptosis is an emerging mode of programmed cell death fueled by iron buildup and lipid peroxidation. Recent evidence points to the function of ferroptosis in the aetiology and development of cancer and other disorders. Consequently, harnessing iron death for disease treatment has diverted the interest of the researchers in the field of basic and clinical research. The ubiquitin-proteasome system (UPS) represents a primary protein degradation pathway in eukaryotes. It involves labelling proteins to be degraded by ubiquitin (Ub), followed by recognition and degradation by the proteasome. Dysfunction of the UPS can contribute to diverse pathological processes, emphasizing the importance of maintaining organismal homeostasis. The regulation of protein stability is a critical component of the intricate molecular mechanism underlying iron death. Moreover, the intricate involvement of the UPS in regulating iron death-related molecules and signaling pathways, providing valuable insights for targeted treatment strategies. Besides, it highlights the potential of ferroptosis as a promising target for cancer therapy, emphasizing the combination between ferroptosis and the UPS. The molecular mechanisms underlying ferroptosis, including key regulators such as glutathione peroxidase 4 (GPX4), cysteine/glutamate transporter (system XC-), and iron metabolism, are thoroughly examined, alongside the role of the UPS in modulating the abundance and activity of crucial proteins for ferroptotic cell death, such as GPX4, and nuclear factor erythroid 2-related factor 2 (NRF2). As a pivotal regulatory system for macromolecular homeostasis, the UPS substantially impacts ferroptosis by directly or indirectly modulating iron death-related molecules or associated signaling pathways. This review explores the involvement of the UPS in regulating iron death-related molecules and signaling pathways, providing valuable insights for the targeted treatment of diseases associated with ferroptosis.
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Affiliation(s)
- Muhammad Azhar Ud Din
- Key Laboratory of Medical Science and Laboratory Medicine of Jiangsu Province, School of Medicine Jiangsu University, Zhenjiang, Jiangsu, China
- Department of Laboratory Medicine, Lianyungang Clinical College, Jiangsu University, Lianyungang, Jiangsu, China
| | - Yan Lin
- The People’s Hospital of Danyang, Affiliated Danyang Hospital of Nantong University, Zhenjiang, Jiangsu, China
| | - Naijian Wang
- Key Laboratory of Medical Science and Laboratory Medicine of Jiangsu Province, School of Medicine Jiangsu University, Zhenjiang, Jiangsu, China
| | - Bo Wang
- Key Laboratory of Medical Science and Laboratory Medicine of Jiangsu Province, School of Medicine Jiangsu University, Zhenjiang, Jiangsu, China
| | - Fei Mao
- Key Laboratory of Medical Science and Laboratory Medicine of Jiangsu Province, School of Medicine Jiangsu University, Zhenjiang, Jiangsu, China
- Department of Laboratory Medicine, Lianyungang Clinical College, Jiangsu University, Lianyungang, Jiangsu, China
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5
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Fu Y, Li L, Zhang X, Deng Z, Wu Y, Chen W, Liu Y, He S, Wang J, Xie Y, Tu Z, Lyu Y, Wei Y, Wang S, Cui CP, Liu CH, Zhang L. Systematic HOIP interactome profiling reveals critical roles of linear ubiquitination in tissue homeostasis. Nat Commun 2024; 15:2974. [PMID: 38582895 PMCID: PMC10998861 DOI: 10.1038/s41467-024-47289-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 03/27/2024] [Indexed: 04/08/2024] Open
Abstract
Linear ubiquitination catalyzed by HOIL-1-interacting protein (HOIP), the key component of the linear ubiquitination assembly complex, plays fundamental roles in tissue homeostasis by executing domain-specific regulatory functions. However, a proteome-wide analysis of the domain-specific interactome of HOIP across tissues is lacking. Here, we present a comprehensive mass spectrometry-based interactome profiling of four HOIP domains in nine mouse tissues. The interaction dataset provides a high-quality HOIP interactome resource with an average of approximately 90 interactors for each bait per tissue. HOIP tissue interactome presents a systematic understanding of linear ubiquitination functions in each tissue and also shows associations of tissue functions to genetic diseases. HOIP domain interactome characterizes a set of previously undefined linear ubiquitinated substrates and elucidates the cross-talk among HOIP domains in physiological and pathological processes. Moreover, we show that linear ubiquitination of Integrin-linked protein kinase (ILK) decreases focal adhesion formation and promotes the detachment of Shigella flexneri-infected cells. Meanwhile, Hoip deficiency decreases the linear ubiquitination of Smad ubiquitination regulatory factor 1 (SMURF1) and enhances its E3 activity, finally causing a reduced bone mass phenotype in mice. Overall, our work expands the knowledge of HOIP-interacting proteins and provides a platform for further discovery of linear ubiquitination functions in tissue homeostasis.
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Affiliation(s)
- Yesheng Fu
- State Key Laboratory of Medical Proteomics, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 100850, China
| | - Lei Li
- State Key Laboratory of Medical Proteomics, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 100850, China
| | - Xin Zhang
- State Key Laboratory of Medical Proteomics, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 100850, China
| | - Zhikang Deng
- State Key Laboratory of Medical Proteomics, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 100850, China
| | - Ying Wu
- State Key Laboratory of Medical Proteomics, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 100850, China
| | - Wenzhe Chen
- State Key Laboratory of Medical Proteomics, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 100850, China
| | - Yuchen Liu
- State Key Laboratory of Medical Proteomics, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 100850, China
| | - Shan He
- State Key Laboratory of Medical Proteomics, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 100850, China
| | - Jian Wang
- State Key Laboratory of Medical Proteomics, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 100850, China
| | - Yuping Xie
- State Key Laboratory of Medical Proteomics, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 100850, China
| | - Zhiwei Tu
- State Key Laboratory of Medical Proteomics, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 100850, China
| | - Yadi Lyu
- State Key Laboratory of Medical Proteomics, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 100850, China
| | - Yange Wei
- State Key Laboratory of Medical Proteomics, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 100850, China
| | - Shujie Wang
- State Key Laboratory of Medical Proteomics, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 100850, China
| | - Chun-Ping Cui
- State Key Laboratory of Medical Proteomics, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 100850, China
| | - Cui Hua Liu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, 101408, China.
| | - Lingqiang Zhang
- State Key Laboratory of Medical Proteomics, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 100850, China.
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6
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Furthmann N, Bader V, Angersbach L, Blusch A, Goel S, Sánchez-Vicente A, Krause LJ, Chaban SA, Grover P, Trinkaus VA, van Well EM, Jaugstetter M, Tschulik K, Damgaard RB, Saft C, Ellrichmann G, Gold R, Koch A, Englert B, Westenberger A, Klein C, Jungbluth L, Sachse C, Behrends C, Glatzel M, Hartl FU, Nakamura K, Christine CW, Huang EJ, Tatzelt J, Winklhofer KF. NEMO reshapes the α-Synuclein aggregate interface and acts as an autophagy adapter by co-condensation with p62. Nat Commun 2023; 14:8368. [PMID: 38114471 PMCID: PMC10730909 DOI: 10.1038/s41467-023-44033-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 11/28/2023] [Indexed: 12/21/2023] Open
Abstract
NEMO is a ubiquitin-binding protein which regulates canonical NF-κB pathway activation in innate immune signaling, cell death regulation and host-pathogen interactions. Here we identify an NF-κB-independent function of NEMO in proteostasis regulation by promoting autophagosomal clearance of protein aggregates. NEMO-deficient cells accumulate misfolded proteins upon proteotoxic stress and are vulnerable to proteostasis challenges. Moreover, a patient with a mutation in the NEMO-encoding IKBKG gene resulting in defective binding of NEMO to linear ubiquitin chains, developed a widespread mixed brain proteinopathy, including α-synuclein, tau and TDP-43 pathology. NEMO amplifies linear ubiquitylation at α-synuclein aggregates and promotes the local concentration of p62 into foci. In vitro, NEMO lowers the threshold concentrations required for ubiquitin-dependent phase transition of p62. In summary, NEMO reshapes the aggregate surface for efficient autophagosomal clearance by providing a mobile phase at the aggregate interphase favoring co-condensation with p62.
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Affiliation(s)
- Nikolas Furthmann
- Department Molecular Cell Biology, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, 44801, Bochum, Germany
| | - Verian Bader
- Department Molecular Cell Biology, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, 44801, Bochum, Germany
- Department Biochemistry of Neurodegenerative Diseases, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, 44801, Bochum, Germany
| | - Lena Angersbach
- Department Molecular Cell Biology, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, 44801, Bochum, Germany
| | - Alina Blusch
- Department of Neurology, St Josef Hospital, Ruhr University Bochum, 44791, Bochum, Germany
| | - Simran Goel
- Department Molecular Cell Biology, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, 44801, Bochum, Germany
| | - Ana Sánchez-Vicente
- Department Molecular Cell Biology, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, 44801, Bochum, Germany
| | - Laura J Krause
- Department Molecular Cell Biology, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, 44801, Bochum, Germany
- Cluster of Excellence RESOLV, 44801, Bochum, Germany
| | - Sarah A Chaban
- Department Molecular Cell Biology, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, 44801, Bochum, Germany
| | - Prerna Grover
- Department Biochemistry of Neurodegenerative Diseases, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, 44801, Bochum, Germany
| | - Victoria A Trinkaus
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, 82152, Martinsried, Germany
| | - Eva M van Well
- Department Molecular Cell Biology, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, 44801, Bochum, Germany
| | - Maximilian Jaugstetter
- Analytical Chemistry II, Faculty of Chemistry and Biochemistry, Ruhr University Bochum, 44801, Bochum, Germany
| | - Kristina Tschulik
- Cluster of Excellence RESOLV, 44801, Bochum, Germany
- Analytical Chemistry II, Faculty of Chemistry and Biochemistry, Ruhr University Bochum, 44801, Bochum, Germany
| | - Rune Busk Damgaard
- Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800, Kongens Lyngby, Denmark
| | - Carsten Saft
- Department of Neurology, St Josef Hospital, Ruhr University Bochum, 44791, Bochum, Germany
| | - Gisa Ellrichmann
- Department of Neurology, St Josef Hospital, Ruhr University Bochum, 44791, Bochum, Germany
- Department of Neurology, Klinikum Dortmund, University Witten/Herdecke, 44135, Dortmund, Germany
| | - Ralf Gold
- Department of Neurology, St Josef Hospital, Ruhr University Bochum, 44791, Bochum, Germany
| | - Arend Koch
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Neuropathology, Charitéplatz 1, 10117, Berlin, Germany
| | - Benjamin Englert
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Neuropathology, Charitéplatz 1, 10117, Berlin, Germany
- Center for Neuropathology and Prion Research, Ludwig-Maximilians University, 81377, Munich, Germany
| | - Ana Westenberger
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany
| | - Christine Klein
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany
| | - Lisa Jungbluth
- Ernst-Ruska Centre for Microscopy and Spectroscopy with Electrons (ER-C-3/Structural Biology), Forschungszentrum Jülich, Jülich, Germany
- Institute for Biological Information Processing (IBI-6/Cellular Structural Biology), Forschungszentrum Jülich, Jülich, Germany
| | - Carsten Sachse
- Ernst-Ruska Centre for Microscopy and Spectroscopy with Electrons (ER-C-3/Structural Biology), Forschungszentrum Jülich, Jülich, Germany
- Institute for Biological Information Processing (IBI-6/Cellular Structural Biology), Forschungszentrum Jülich, Jülich, Germany
- Department of Biology, Heinrich Heine University, Düsseldorf, Germany
| | - Christian Behrends
- Munich Cluster for Systems Neurology, Faculty of Medicine, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Markus Glatzel
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20251, Hamburg, Germany
| | - F Ulrich Hartl
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, 82152, Martinsried, Germany
- Munich Cluster for Systems Neurology (SyNergy), 81377, Munich, Germany
| | - Ken Nakamura
- Gladstone Institute of Neurological Disease, Gladstone Institutes, San Francisco, CA, USA
- Department of Neurology, University of California, San Francisco, CA, USA
| | - Chadwick W Christine
- Department of Neurology, University of California, San Francisco, CA, USA
- Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA
| | - Eric J Huang
- Department of Neurology, University of California, San Francisco, CA, USA
- Department of Pathology, University of California, San Francisco, CA, USA
| | - Jörg Tatzelt
- Department Biochemistry of Neurodegenerative Diseases, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, 44801, Bochum, Germany
- Cluster of Excellence RESOLV, 44801, Bochum, Germany
| | - Konstanze F Winklhofer
- Department Molecular Cell Biology, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, 44801, Bochum, Germany.
- Cluster of Excellence RESOLV, 44801, Bochum, Germany.
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7
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Hu S, Wang L. The potential role of ubiquitination and deubiquitination in melanogenesis. Exp Dermatol 2023; 32:2062-2071. [PMID: 37846904 DOI: 10.1111/exd.14953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 08/31/2023] [Accepted: 10/03/2023] [Indexed: 10/18/2023]
Abstract
Melanogenesis is a critical biochemical process in which melanocytes produce melanin, a crucial element involved in the formation of coat colour in mammals. According to several earlier studies, melanocytes' post-translational modifications of proteins primarily control melanogenesis. Among the many post-translational changes that can affect melanin production, ubiquitination and deubiquitination can keep melanin production going by changing how proteins that are related to melanin are broken down or kept stable. Ubiquitination and deubiquitination maintain ubiquitin homeostasis, which is a highly dynamic process in balance under the action of E3 ubiquitin ligase and deubiquitinating enzymes. However, the regulatory mechanisms underlying ubiquitination and deubiquitination in melanogenesis are yet to be thoroughly investigated. As a result, there has been a growing focus on exploring the potential correlation between melanogenesis, ubiquitination and deubiquitination. This study discusses the mechanisms of ubiquitination and deubiquitination in the context of melanogenesis, a crucial process for enhancing mammalian coat coloration and addressing pigment-related diseases.
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Affiliation(s)
- Shuaishuai Hu
- College of Life Science, Luoyang Normal University, Luoyang, China
| | - Lu Wang
- College of Life Science, Luoyang Normal University, Luoyang, China
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8
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Wehrmann M, Vilchez D. The emerging role and therapeutic implications of bacterial and parasitic deubiquitinating enzymes. Front Immunol 2023; 14:1303072. [PMID: 38077335 PMCID: PMC10703165 DOI: 10.3389/fimmu.2023.1303072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 11/03/2023] [Indexed: 12/18/2023] Open
Abstract
Deubiquitinating enzymes (DUBs) are emerging as key factors for the infection of human cells by pathogens such as bacteria and parasites. In this review, we discuss the most recent studies on the role of deubiquitinase activity in exploiting and manipulating ubiquitin (Ub)-dependent host processes during infection. The studies discussed here highlight the importance of DUB host-pathogen research and underscore the therapeutic potential of inhibiting pathogen-specific DUB activity to prevent infectious diseases.
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Affiliation(s)
- Markus Wehrmann
- Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
- Institute for Integrated Stress Response Signaling, Faculty of Medicine, University Hospital Cologne, Cologne, Germany
| | - David Vilchez
- Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
- Institute for Integrated Stress Response Signaling, Faculty of Medicine, University Hospital Cologne, Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
- Institute for Genetics, University of Cologne, Cologne, Germany
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9
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De Meyer F, Afonina IS. Novel role for linear ubiquitination in regulating NFAT1 stability. FEBS J 2023; 290:4196-4199. [PMID: 36974504 DOI: 10.1111/febs.16776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Accepted: 03/14/2023] [Indexed: 03/29/2023]
Abstract
Linear ubiquitination is an important post-translational modification regulating the activation of numerous proinflammatory signalling mediators. Deregulated linear ubiquitination has been implicated in the pathogenesis of several inflammatory and autoimmune diseases. In this issue, Miao et al. have identified a novel role for linear ubiquitination in the stabilisation of the NFAT1 transcription factor, leading to enhanced NFAT1-mediated gene expression, which might have functional implications in patients with Kawasaki disease.
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Affiliation(s)
- Femke De Meyer
- Unit of Molecular Signal Transduction in Inflammation, VIB-UGent Center for Inflammation Research, Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Belgium
| | - Inna S Afonina
- Unit of Molecular Signal Transduction in Inflammation, VIB-UGent Center for Inflammation Research, Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Belgium
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10
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Kuang X, Zhang Z, Li D, Bao W, Pan J, Zhou P, Chen H, Gao Z, Xie X, Yang C, Zhu G, Zhou Z, Tang R, Feng Z, Zhou L, Feng X, Wang L, Yang J, Jiang L. Peptidase inhibitor (PI16) impairs bladder cancer metastasis by inhibiting NF-κB activation via disrupting multiple-site ubiquitination of NEMO. Cell Mol Biol Lett 2023; 28:62. [PMID: 37525118 PMCID: PMC10388466 DOI: 10.1186/s11658-023-00465-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Accepted: 06/14/2023] [Indexed: 08/02/2023] Open
Abstract
BACKGROUND Bladder cancer (BLCA) is a malignancy that frequently metastasizes and leads to poor patient prognosis. It is essential to understand the molecular mechanisms underlying the progression and metastasis of BLCA and identify potential biomarkers. METHODS The expression of peptidase inhibitor 16 (PI16) was analysed using quantitative PCR, immunoblotting and immunohistochemistry assays. The functional roles of PI16 were evaluated using wound healing, transwell, and human umbilical vein endothelial cell tube formation assays, as well as in vivo tumour models. The effects of PI16 on nuclear factor κB (NF-κB) signalling activation were examined using luciferase reporter gene systems, immunoblotting and immunofluorescence assays. Co-immunoprecipitation was used to investigate the interaction of PI16 with annexin-A1 (ANXA1) and NEMO. RESULTS PI16 expression was downregulated in bladder cancer tissues, and lower PI16 levels correlated with disease progression and poor survival in patients with BLCA. Overexpressing PI16 inhibited BLCA cell growth, motility, invasion and angiogenesis in vitro and in vivo, while silencing PI16 had the opposite effects. Mechanistically, PI16 inhibited the activation of the NF-κB pathway by interacting with ANXA1, which inhibited K63 and M1 ubiquitination of NEMO. CONCLUSIONS These results indicate that PI16 functions as a tumour suppressor in BLCA by inhibiting tumour growth and metastasis. Additionally, PI16 may serve as a potential biomarker for metastatic BLCA.
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Affiliation(s)
- Xiangqin Kuang
- Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou, 510095, China
- Guangzhou Municipal and Guangdong Provincial Key Laboratory of Protein Modification and Degradation, School of Basic Medical Science, Guangzhou Medical University, Guangzhou, 511436, China
- Department of Medical Imaging, Health Science Center, Hubei Minzu University, Enshi, 445000, China
| | - Zhuojun Zhang
- Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou, 510095, China
- Guangzhou Municipal and Guangdong Provincial Key Laboratory of Protein Modification and Degradation, School of Basic Medical Science, Guangzhou Medical University, Guangzhou, 511436, China
| | - Difeng Li
- Guangzhou Municipal and Guangdong Provincial Key Laboratory of Protein Modification and Degradation, School of Basic Medical Science, Guangzhou Medical University, Guangzhou, 511436, China
- Department of Pathology, School of Medicine, Women's Hospital, Zhejiang University, 310006, Hangzhou, China
| | - Wenhao Bao
- Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou, 510095, China
- Guangzhou Municipal and Guangdong Provincial Key Laboratory of Protein Modification and Degradation, School of Basic Medical Science, Guangzhou Medical University, Guangzhou, 511436, China
| | - Jinyuan Pan
- Department of Oncology, Huanggang Central Hospital of Yangtze University, Huanggang, 438000, China
| | - Ping Zhou
- Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou, 510095, China
- Guangzhou Municipal and Guangdong Provincial Key Laboratory of Protein Modification and Degradation, School of Basic Medical Science, Guangzhou Medical University, Guangzhou, 511436, China
| | - Han Chen
- Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou, 510095, China
- Guangzhou Municipal and Guangdong Provincial Key Laboratory of Protein Modification and Degradation, School of Basic Medical Science, Guangzhou Medical University, Guangzhou, 511436, China
| | - Zhiqing Gao
- Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou, 510095, China
- Guangzhou Municipal and Guangdong Provincial Key Laboratory of Protein Modification and Degradation, School of Basic Medical Science, Guangzhou Medical University, Guangzhou, 511436, China
| | - Xiaoyi Xie
- Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou, 510095, China
- Guangzhou Municipal and Guangdong Provincial Key Laboratory of Protein Modification and Degradation, School of Basic Medical Science, Guangzhou Medical University, Guangzhou, 511436, China
| | - Chunxiao Yang
- Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou, 510095, China
- Guangzhou Municipal and Guangdong Provincial Key Laboratory of Protein Modification and Degradation, School of Basic Medical Science, Guangzhou Medical University, Guangzhou, 511436, China
| | - Ge Zhu
- Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou, 510095, China
- Guangzhou Municipal and Guangdong Provincial Key Laboratory of Protein Modification and Degradation, School of Basic Medical Science, Guangzhou Medical University, Guangzhou, 511436, China
| | - Zhongqiu Zhou
- Meishan Women and Children's Hospital, Alliance Hospital of West China Second University Hospital, Sichuan University, Meishan, 620000, China
| | - Ruiming Tang
- The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People's Hospital, Guangzhou, 511518, China
| | - Zhengfu Feng
- The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People's Hospital, Guangzhou, 511518, China
| | - Lihuan Zhou
- The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People's Hospital, Guangzhou, 511518, China
| | - Xiaoli Feng
- The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People's Hospital, Guangzhou, 511518, China
| | - Lan Wang
- Department of Pathogen Biology and Immunology, School of Basic Courses, Guangdong Pharmaceutical University, Guangzhou, 510006, China
| | - Jianan Yang
- Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou, 510095, China.
- Department of Urologic Oncosurgery, Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou, 510095, China.
| | - Lili Jiang
- Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou, 510095, China.
- Guangzhou Municipal and Guangdong Provincial Key Laboratory of Protein Modification and Degradation, School of Basic Medical Science, Guangzhou Medical University, Guangzhou, 511436, China.
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11
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Carman LE, Samulevich ML, Aneskievich BJ. Repressive Control of Keratinocyte Cytoplasmic Inflammatory Signaling. Int J Mol Sci 2023; 24:11943. [PMID: 37569318 PMCID: PMC10419196 DOI: 10.3390/ijms241511943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 07/17/2023] [Accepted: 07/20/2023] [Indexed: 08/13/2023] Open
Abstract
The overactivity of keratinocyte cytoplasmic signaling contributes to several cutaneous inflammatory and immune pathologies. An important emerging complement to proteins responsible for this overactivity is signal repression brought about by several proteins and protein complexes with the native role of limiting inflammation. The signaling repression by these proteins distinguishes them from transmembrane receptors, kinases, and inflammasomes, which drive inflammation. For these proteins, defects or deficiencies, whether naturally arising or in experimentally engineered skin inflammation models, have clearly linked them to maintaining keratinocytes in a non-activated state or returning cells to a post-inflamed state after a signaling event. Thus, together, these proteins help to resolve acute inflammatory responses or limit the development of chronic cutaneous inflammatory disease. We present here an integrated set of demonstrated or potentially inflammation-repressive proteins or protein complexes (linear ubiquitin chain assembly complex [LUBAC], cylindromatosis lysine 63 deubiquitinase [CYLD], tumor necrosis factor alpha-induced protein 3-interacting protein 1 [TNIP1], A20, and OTULIN) for a comprehensive view of cytoplasmic signaling highlighting protein players repressing inflammation as the needed counterpoints to signal activators and amplifiers. Ebb and flow of players on both sides of this inflammation equation would be of physiological advantage to allow acute response to damage or pathogens and yet guard against chronic inflammatory disease. Further investigation of the players responsible for repressing cytoplasmic signaling would be foundational to developing new chemical-entity pharmacologics to stabilize or enhance their function when clinical intervention is needed to restore balance.
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Affiliation(s)
- Liam E. Carman
- Graduate Program in Pharmacology & Toxicology, University of Connecticut, Storrs, CT 06269-3092, USA; (L.E.C.); (M.L.S.)
| | - Michael L. Samulevich
- Graduate Program in Pharmacology & Toxicology, University of Connecticut, Storrs, CT 06269-3092, USA; (L.E.C.); (M.L.S.)
| | - Brian J. Aneskievich
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, CT 06269-3092, USA
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12
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Goel S, Oliva R, Jeganathan S, Bader V, Krause LJ, Kriegler S, Stender ID, Christine CW, Nakamura K, Hoffmann JE, Winter R, Tatzelt J, Winklhofer KF. Linear ubiquitination induces NEMO phase separation to activate NF-κB signaling. Life Sci Alliance 2023; 6:e202201607. [PMID: 36720498 PMCID: PMC9889916 DOI: 10.26508/lsa.202201607] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 01/09/2023] [Accepted: 01/09/2023] [Indexed: 02/02/2023] Open
Abstract
The NF-κB essential modulator NEMO is the core regulatory component of the inhibitor of κB kinase complex, which is a critical checkpoint in canonical NF-κB signaling downstream of innate and adaptive immune receptors. In response to various stimuli, such as TNF or IL-1β, NEMO binds to linear or M1-linked ubiquitin chains generated by LUBAC, promoting its oligomerization and subsequent activation of the associated kinases. Here we show that M1-ubiquitin chains induce phase separation of NEMO and the formation of NEMO assemblies in cells after exposure to IL-1β. Phase separation is promoted by both binding of NEMO to linear ubiquitin chains and covalent linkage of M1-ubiquitin to NEMO and is essential but not sufficient for its phase separation. Supporting the functional relevance of NEMO phase separation in signaling, a pathogenic NEMO mutant, which is impaired in both binding and linkage to linear ubiquitin chains, does not undergo phase separation and is defective in mediating IL-1β-induced NF-κB activation.
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Affiliation(s)
- Simran Goel
- Department Molecular Cell Biology, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, Bochum, Germany
| | - Rosario Oliva
- Physical Chemistry I-Biophysical Chemistry, Department of Chemistry and Chemical Biology, TU Dortmund University, Dortmund, Germany
- Department of Chemical Sciences, University of Naples Federico II, Naples, Italy
| | - Sadasivam Jeganathan
- Department Molecular Cell Biology, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, Bochum, Germany
| | - Verian Bader
- Department Molecular Cell Biology, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, Bochum, Germany
- Department Biochemistry of Neurodegenerative Diseases, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, Bochum, Germany
| | - Laura J Krause
- Department Molecular Cell Biology, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, Bochum, Germany
- RESOLV Cluster of Excellence, Ruhr University Bochum, Bochum, Germany
| | - Simon Kriegler
- Physical Chemistry I-Biophysical Chemistry, Department of Chemistry and Chemical Biology, TU Dortmund University, Dortmund, Germany
| | - Isabelle D Stender
- Protein Chemistry Facility, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | | | - Ken Nakamura
- Department of Neurology, UCSF, San Francisco, CA, USA
- Gladstone Institute of Neurological Disease, Gladstone Institutes, San Francisco, CA, USA
| | - Jan-Erik Hoffmann
- Protein Chemistry Facility, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Roland Winter
- Physical Chemistry I-Biophysical Chemistry, Department of Chemistry and Chemical Biology, TU Dortmund University, Dortmund, Germany
- RESOLV Cluster of Excellence, Ruhr University Bochum, Bochum, Germany
| | - Jörg Tatzelt
- RESOLV Cluster of Excellence, Ruhr University Bochum, Bochum, Germany
- Department Biochemistry of Neurodegenerative Diseases, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, Bochum, Germany
| | - Konstanze F Winklhofer
- Department Molecular Cell Biology, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, Bochum, Germany
- RESOLV Cluster of Excellence, Ruhr University Bochum, Bochum, Germany
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13
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Wu Z, Berlemann LA, Bader V, Sehr DA, Dawin E, Covallero A, Meschede J, Angersbach L, Showkat C, Michaelis JB, Münch C, Rieger B, Namgaladze D, Herrera MG, Fiesel FC, Springer W, Mendes M, Stepien J, Barkovits K, Marcus K, Sickmann A, Dittmar G, Busch KB, Riedel D, Brini M, Tatzelt J, Cali T, Winklhofer KF. LUBAC assembles a ubiquitin signaling platform at mitochondria for signal amplification and transport of NF-κB to the nucleus. EMBO J 2022; 41:e112006. [PMID: 36398858 PMCID: PMC9753471 DOI: 10.15252/embj.2022112006] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 10/20/2022] [Accepted: 10/25/2022] [Indexed: 11/19/2022] Open
Abstract
Mitochondria are increasingly recognized as cellular hubs to orchestrate signaling pathways that regulate metabolism, redox homeostasis, and cell fate decisions. Recent research revealed a role of mitochondria also in innate immune signaling; however, the mechanisms of how mitochondria affect signal transduction are poorly understood. Here, we show that the NF-κB pathway activated by TNF employs mitochondria as a platform for signal amplification and shuttling of activated NF-κB to the nucleus. TNF treatment induces the recruitment of HOIP, the catalytic component of the linear ubiquitin chain assembly complex (LUBAC), and its substrate NEMO to the outer mitochondrial membrane, where M1- and K63-linked ubiquitin chains are generated. NF-κB is locally activated and transported to the nucleus by mitochondria, leading to an increase in mitochondria-nucleus contact sites in a HOIP-dependent manner. Notably, TNF-induced stabilization of the mitochondrial kinase PINK1 furthermore contributes to signal amplification by antagonizing the M1-ubiquitin-specific deubiquitinase OTULIN. Overall, our study reveals a role for mitochondria in amplifying TNF-mediated NF-κB activation, both serving as a signaling platform, as well as a transport mode for activated NF-κB to the nuclear.
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Affiliation(s)
- Zhixiao Wu
- Department Molecular Cell Biology, Institute of Biochemistry and PathobiochemistryRuhr University BochumBochumGermany
| | - Lena A Berlemann
- Department Molecular Cell Biology, Institute of Biochemistry and PathobiochemistryRuhr University BochumBochumGermany
| | - Verian Bader
- Department Molecular Cell Biology, Institute of Biochemistry and PathobiochemistryRuhr University BochumBochumGermany
- Department Biochemistry of Neurodegenerative Diseases, Institute of Biochemistry and PathobiochemistryRuhr University BochumBochumGermany
| | - Dominik A Sehr
- Department Molecular Cell Biology, Institute of Biochemistry and PathobiochemistryRuhr University BochumBochumGermany
| | - Eva Dawin
- Department Molecular Cell Biology, Institute of Biochemistry and PathobiochemistryRuhr University BochumBochumGermany
- Leibniz‐Institut für Analytische Wissenschaften—ISAS—e.VDortmundGermany
| | | | - Jens Meschede
- Department Molecular Cell Biology, Institute of Biochemistry and PathobiochemistryRuhr University BochumBochumGermany
| | - Lena Angersbach
- Department Molecular Cell Biology, Institute of Biochemistry and PathobiochemistryRuhr University BochumBochumGermany
| | - Cathrin Showkat
- Department Molecular Cell Biology, Institute of Biochemistry and PathobiochemistryRuhr University BochumBochumGermany
| | - Jonas B Michaelis
- Faculty of Medicine, Institute of Biochemistry IIGoethe University FrankfurtFrankfurt am MainGermany
| | - Christian Münch
- Faculty of Medicine, Institute of Biochemistry IIGoethe University FrankfurtFrankfurt am MainGermany
| | - Bettina Rieger
- Institute for Integrative Cell Biology and Physiology, Faculty of BiologyUniversity of MünsterMünsterGermany
| | - Dmitry Namgaladze
- Institute of Biochemistry I, Faculty of MedicineGoethe‐University FrankfurtFrankfurtGermany
| | - Maria Georgina Herrera
- Department Molecular Cell Biology, Institute of Biochemistry and PathobiochemistryRuhr University BochumBochumGermany
| | - Fabienne C Fiesel
- Department of NeuroscienceMayo ClinicJacksonvilleFLUSA
- Neuroscience PhD ProgramMayo Clinic Graduate School of Biomedical SciencesJacksonvilleFLUSA
| | - Wolfdieter Springer
- Department of NeuroscienceMayo ClinicJacksonvilleFLUSA
- Neuroscience PhD ProgramMayo Clinic Graduate School of Biomedical SciencesJacksonvilleFLUSA
| | - Marta Mendes
- Proteomics of Cellular Signaling, Department of Infection and ImmunityLuxembourg Institute of HealthStrassenLuxembourg
| | - Jennifer Stepien
- Medizinisches Proteom‐CenterRuhr‐Universität BochumBochumGermany
- Medical Proteome Analysis, Center for Protein Diagnostics (PRODI)Ruhr‐University BochumBochumGermany
| | - Katalin Barkovits
- Medizinisches Proteom‐CenterRuhr‐Universität BochumBochumGermany
- Medical Proteome Analysis, Center for Protein Diagnostics (PRODI)Ruhr‐University BochumBochumGermany
| | - Katrin Marcus
- Medizinisches Proteom‐CenterRuhr‐Universität BochumBochumGermany
- Medical Proteome Analysis, Center for Protein Diagnostics (PRODI)Ruhr‐University BochumBochumGermany
| | - Albert Sickmann
- Leibniz‐Institut für Analytische Wissenschaften—ISAS—e.VDortmundGermany
| | - Gunnar Dittmar
- Proteomics of Cellular Signaling, Department of Infection and ImmunityLuxembourg Institute of HealthStrassenLuxembourg
- Department of Life Sciences and MedicineUniversity of LuxembourgBelvauxLuxembourg
| | - Karin B Busch
- Institute for Integrative Cell Biology and Physiology, Faculty of BiologyUniversity of MünsterMünsterGermany
| | - Dietmar Riedel
- Laboratory for Electron MicroscopyMax Planck Institute for Multidisciplinary SciencesGöttingenGermany
| | - Marisa Brini
- Department of BiologyUniversity of PaduaPaduaItaly
- Centro Studi per la Neurodegenerazione (CESNE)University of PadovaPaduaItaly
| | - Jörg Tatzelt
- Department Biochemistry of Neurodegenerative Diseases, Institute of Biochemistry and PathobiochemistryRuhr University BochumBochumGermany
- RESOLV Cluster of ExcellenceRuhr University BochumBochumGermany
| | - Tito Cali
- Department of Biomedical SciencesUniversity of PaduaPaduaItaly
- Centro Studi per la Neurodegenerazione (CESNE)University of PadovaPaduaItaly
- Padua Neuroscience Center (PNC)University of PaduaPaduaItaly
| | - Konstanze F Winklhofer
- Department Molecular Cell Biology, Institute of Biochemistry and PathobiochemistryRuhr University BochumBochumGermany
- RESOLV Cluster of ExcellenceRuhr University BochumBochumGermany
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14
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Martín-Rufo R, de la Vega-Barranco G, Lecona E. Ubiquitin and SUMO as timers during DNA replication. Semin Cell Dev Biol 2022; 132:62-73. [PMID: 35210137 DOI: 10.1016/j.semcdb.2022.02.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 02/12/2022] [Accepted: 02/14/2022] [Indexed: 12/14/2022]
Abstract
Every time a cell copies its DNA the genetic material is exposed to the acquisition of mutations and genomic alterations that corrupt the information passed on to daughter cells. A tight temporal regulation of DNA replication is necessary to ensure the full copy of the DNA while preventing the appearance of genomic instability. Protein modification by ubiquitin and SUMO constitutes a very complex and versatile system that allows the coordinated control of protein stability, activity and interactome. In chromatin, their action is complemented by the AAA+ ATPase VCP/p97 that recognizes and removes ubiquitylated and SUMOylated factors from specific cellular compartments. The concerted action of the ubiquitin/SUMO system and VCP/p97 determines every step of DNA replication enforcing the ordered activation/inactivation, loading/unloading and stabilization/destabilization of replication factors. Here we analyze the mechanisms used by ubiquitin/SUMO and VCP/p97 to establish molecular timers throughout DNA replication and their relevance in maintaining genome stability. We propose that these PTMs are the main molecular watch of DNA replication from origin recognition to replisome disassembly.
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Affiliation(s)
- Rodrigo Martín-Rufo
- Chromatin, Cancer and the Ubiquitin System lab, Centre for Molecular Biology Severo Ochoa (CBMSO, CSIC-UAM), Department of Genome Dynamics and Function, Madrid 28049, Spain
| | - Guillermo de la Vega-Barranco
- Chromatin, Cancer and the Ubiquitin System lab, Centre for Molecular Biology Severo Ochoa (CBMSO, CSIC-UAM), Department of Genome Dynamics and Function, Madrid 28049, Spain
| | - Emilio Lecona
- Chromatin, Cancer and the Ubiquitin System lab, Centre for Molecular Biology Severo Ochoa (CBMSO, CSIC-UAM), Department of Genome Dynamics and Function, Madrid 28049, Spain.
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15
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Chen Y, Liu Y, Jiang K, Wen Z, Cao X, Wu S. Linear ubiquitination of LKB1 activates AMPK pathway to inhibit NLRP3 inflammasome response and reduce chondrocyte pyroptosis in osteoarthritis. J Orthop Translat 2022; 39:1-11. [PMID: 36514784 PMCID: PMC9719095 DOI: 10.1016/j.jot.2022.11.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 10/11/2022] [Accepted: 11/07/2022] [Indexed: 12/03/2022] Open
Abstract
Background Osteoarthritis (OA) is the most common chronic disease. It is characterized by high levels of clinical heterogeneity and low inflammation. Therefore, elucidation of the mechanisms that regulate gene expression is critical for developing effective OA therapies. This study aimed to explore the role of LKB1/AMPK in the progression of OA. Methods Anterior cruciate ligament transection (ACLT) was performed on Sprague Dawley (SD) rats right knee to construct OA model, followed by AICAR [AMP-activated protein kinase (AMPK) activator] treatment. The level changes [AMPK, IL-10, IL-13, IL-1β, TNF-α, IL-6, ASC, Caspase-1, Ki67, and hibit Nod-like receptor protein 3 (NLRP3)] and the degree of tissue injury were assessed by western blot, Immunohistochemical (IHC), Enzyme-linked immunosorbent assay (ELISA), Hematoxylin-eosin staining (HE), Immunofluorescence (IF), Terminal deoxynucleotidyl transferase dUTP nick-end labeling (TUNEL) assay, and Safranin O and Fast Green staining (S-O). Human chondrocytes were induced by LPS to construct a cellular inflammatory model, and then transfected with oe-AMPK or oe-HOIL-1-interacting protein (HOIP). Cell viability/apoptotic and intracellular content of AMPK, HOIP, IL-1β, IL-10, IL-13, TNF-α, IL-6, ASC, NLRP3 and Caspase-1 were measured by western blot, ELISA, CCK-8, IF, flow cytometry and TUNEL assays. Results After AICAR treatment with OA rats, the expression of p-AMPK, IL-10, IL-13, Ki67 and Bcl-2 increased, the level of NLRP3 inflammasome, TNF-α, IL-6, Bax and Caspase-3 levels were decreased, and tissue damage and apoptosis were significantly alleviated. After transfected with oe-LKB1, chondrocyte activity and LKB1 linear ubiquitination were enhanced, and the level of HOIP, p-AMPK, IL-10 and IL-13 were increased. In contrast, NLRP3 inflammasome (ASC, NLRP3, Caspase-1, IL-1β, and cleaved Caspase-1), TNF-α, and IL-6 levels decreased, apoptosis rate and TUNEL positive rate were attenuated. Conclusion LKB1/AMPK pathway significantly ameliorated NLRP3 inflammasome response and chondrocyte injury. Activation of AMPK pathway by linear ubiquitination of LKB1 may be a potential target for OA treatment. The translational potential of this article This study highlights the importance of the LKB1/AMPK pathway in NLRP3 inflammatory body response and chondrocyte injury. Activation of LKB1 by modulating linear ubiquitination may be a potential target for OA treatment.
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Affiliation(s)
- Yang Chen
- Department of Orthopedics, Third Xiangya Hospital of Central South University, Changsha, 410013, China,Department of Orthopedics, Haikou People's Hospital/Haikou Affiliated Hospital of Central South University, Xiangya School of Medicine, Hai Kou, 570100, China
| | - Yiheng Liu
- Department of Orthopedics, Haikou People's Hospital/Haikou Affiliated Hospital of Central South University, Xiangya School of Medicine, Hai Kou, 570100, China
| | - Kai Jiang
- Department of Orthopedics, Second Xiangya Hospital of Central South University, Changsha, 410011, China
| | - Zi Wen
- Department of Orthopedics, Third Xiangya Hospital of Central South University, Changsha, 410013, China
| | - Xu Cao
- Department of Orthopedics, Third Xiangya Hospital of Central South University, Changsha, 410013, China,Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, 310022, China,Corresponding author. Department of Orthopedics, Third Xiangya Hospital of Central South University, Changsha, 410013, China.
| | - Song Wu
- Department of Orthopedics, Third Xiangya Hospital of Central South University, Changsha, 410013, China,Corresponding author.
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16
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Kelsall IR. Non-lysine ubiquitylation: Doing things differently. Front Mol Biosci 2022; 9:1008175. [PMID: 36200073 PMCID: PMC9527308 DOI: 10.3389/fmolb.2022.1008175] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Accepted: 09/01/2022] [Indexed: 11/23/2022] Open
Abstract
The post-translational modification of proteins with ubiquitin plays a central role in nearly all aspects of eukaryotic biology. Historically, studies have focused on the conjugation of ubiquitin to lysine residues in substrates, but it is now clear that ubiquitylation can also occur on cysteine, serine, and threonine residues, as well as on the N-terminal amino group of proteins. Paradigm-shifting reports of non-proteinaceous substrates have further extended the reach of ubiquitylation beyond the proteome to include intracellular lipids and sugars. Additionally, results from bacteria have revealed novel ways to ubiquitylate (and deubiquitylate) substrates without the need for any of the enzymatic components of the canonical ubiquitylation cascade. Focusing mainly upon recent findings, this review aims to outline the current understanding of non-lysine ubiquitylation and speculate upon the molecular mechanisms and physiological importance of this non-canonical modification.
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17
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Chen Z, Song M, Wang T, Gao J, Lin F, Dai H, Zhang C. Role of circRNA in E3 Modification under Human Disease. Biomolecules 2022; 12:biom12091320. [PMID: 36139159 PMCID: PMC9496110 DOI: 10.3390/biom12091320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 09/12/2022] [Accepted: 09/13/2022] [Indexed: 11/16/2022] Open
Abstract
Circular RNA (circRNA) is often regarded as a special kind of non-coding RNA, involved in the regulation mechanism of various diseases, such as tumors, neurological diseases, and inflammation. In a broad spectrum of biological processes, the modification of the 76-amino acid ubiquitin protein generates a large number of signals with different cellular results. Each modification may change the result of signal transduction and participate in the occurrence and development of diseases. Studies have found that circRNA-mediated ubiquitination plays an important role in a variety of diseases. This review first introduces the characteristics of circRNA and ubiquitination and summarizes the mechanism of circRNA in the regulation of ubiquitination in various diseases. It is hoped that the emergence of circRNA-mediated ubiquitination can broaden the diagnosis and prognosis of the disease.
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Affiliation(s)
- Zishuo Chen
- Guangdong Provincial Key Laboratory of Single Cell Technology and Application, Southern Medical University, Guangzhou 510515, China
| | - Minkai Song
- Division of Orthopaedic Surgery, Department of Orthopaedics, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Ting Wang
- Guangdong Provincial Key Laboratory of Single Cell Technology and Application, Southern Medical University, Guangzhou 510515, China
| | - Jiawen Gao
- Division of Spinal Surgery, Department of Orthopaedics, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Fei Lin
- Guangdong Provincial Key Laboratory of Single Cell Technology and Application, Southern Medical University, Guangzhou 510515, China
| | - Hui Dai
- Hospital Office, Ganzhou People’s Hospital, Ganzhou 341000, China
- Hospital Office, Ganzhou Hospital-Nanfang Hospital, Southern Medical University, Ganzhou 341000, China
- Correspondence: (H.D.); (C.Z.)
| | - Chao Zhang
- Guangdong Provincial Key Laboratory of Single Cell Technology and Application, Southern Medical University, Guangzhou 510515, China
- Hospital Office, Ganzhou Hospital-Nanfang Hospital, Southern Medical University, Ganzhou 341000, China
- Correspondence: (H.D.); (C.Z.)
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18
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Aalto A, Martínez‐Chacón G, Kietz C, Tsyganova N, Kreutzer J, Kallio P, Broemer M, Meinander A. M1-linked ubiquitination facilitates NF-κB activation and survival during sterile inflammation. FEBS J 2022; 289:5180-5197. [PMID: 35263507 PMCID: PMC9543601 DOI: 10.1111/febs.16425] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 12/17/2021] [Accepted: 03/07/2022] [Indexed: 01/03/2023]
Abstract
Methionine 1 (M1)-linked ubiquitination plays a key role in the regulation of inflammatory nuclear factor-κB (NF-κB) signalling and is important for clearance of pathogen infection in Drosophila melanogaster. M1-linked ubiquitin (M1-Ub) chains are assembled by the linear ubiquitin E3 ligase (LUBEL) in flies. Here, we have studied the role of LUBEL in sterile inflammation induced by different types of cellular stresses. We have found that the LUBEL catalyses formation of M1-Ub chains in response to hypoxic, oxidative and mechanical stress conditions. LUBEL is shown to be important for flies to survive low oxygen conditions and paraquat-induced oxidative stress. This protective action seems to be driven by stress-induced activation of the NF-κB transcription factor Relish via the immune deficiency (Imd) pathway. In addition to LUBEL, the intracellular mediators of Relish activation, including the transforming growth factor activating kinase 1 (Tak1), Drosophila inhibitor of apoptosis (IAP) Diap2, the IκB kinase γ (IKKγ) Kenny and the initiator caspase Death-related ced-3/Nedd2-like protein (Dredd), but not the membrane receptor peptidoglycan recognition protein (PGRP)-LC, are shown to be required for sterile inflammatory response and survival. Finally, we showed that the stress-induced upregulation of M1-Ub chains in response to hypoxia, oxidative and mechanical stress is also induced in mammalian cells and protects from stress-induced cell death. Taken together, our results suggest that M1-Ub chains are important for NF-κB signalling in inflammation induced by stress conditions often observed in chronic inflammatory diseases and cancer.
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Affiliation(s)
- Anna Aalto
- Faculty of Science and Engineering, Cell BiologyÅbo Akademi University, BioCityTurkuFinland
| | | | - Christa Kietz
- Faculty of Science and Engineering, Cell BiologyÅbo Akademi University, BioCityTurkuFinland
| | - Nadezhda Tsyganova
- Faculty of Science and Engineering, Cell BiologyÅbo Akademi University, BioCityTurkuFinland
| | - Joose Kreutzer
- Faculty of Medicine and Health TechnologyBioMediTechTampere UniversityFinland
| | - Pasi Kallio
- Faculty of Medicine and Health TechnologyBioMediTechTampere UniversityFinland
| | - Meike Broemer
- German Center for Neurodegenerative Diseases (DZNE)BonnGermany
| | - Annika Meinander
- Faculty of Science and Engineering, Cell BiologyÅbo Akademi University, BioCityTurkuFinland
- InFLAMES Research Flagship CenterÅbo Akademi UniversityTurkuFinland
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19
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Zheng Q, Su Z, Yu Y, Liu L. Recent progress in dissecting ubiquitin signals with chemical biology tools. Curr Opin Chem Biol 2022; 70:102187. [PMID: 35961065 DOI: 10.1016/j.cbpa.2022.102187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 06/15/2022] [Accepted: 06/30/2022] [Indexed: 11/28/2022]
Abstract
Protein ubiquitination regulates almost all eukaryotic cellular processes, and is of very high complexity due to the diversity of ubiquitin (Ub) modifications including mono-, multiply mono-, homotypic poly-, and even heterotypic poly-ubiquitination. To accurately elucidate the role of each specific Ub signal in different cells with spatiotemporal resolutions, a variety of chemical biology tools have been developed. In this review, we summarize some recently developed chemical biology tools for ubiquitination studies and their applications in molecular and cellular biology.
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Affiliation(s)
- Qingyun Zheng
- School of Medicine, Shanghai Engineering Research Center of Organ Repair, Shanghai University, Shanghai 200444, China; Tsinghua-Peking Center for Life Sciences, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (MOE), Department of Chemistry, Tsinghua University, Beijing, 100084, China
| | - Zhen Su
- School of Medicine, Shanghai Engineering Research Center of Organ Repair, Shanghai University, Shanghai 200444, China
| | - Yuanyuan Yu
- School of Medicine, Shanghai Engineering Research Center of Organ Repair, Shanghai University, Shanghai 200444, China.
| | - Lei Liu
- Tsinghua-Peking Center for Life Sciences, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (MOE), Department of Chemistry, Tsinghua University, Beijing, 100084, China.
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20
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Abstract
Yuri Shibata and David Komander discuss the composition, regulation and functions of the linear ubiquitin chain assembly complex (LUBAC).
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Affiliation(s)
- Yuri Shibata
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia, and Department of Medical Biology, University of Melbourne, Melbourne, VIC 3000, Australia.
| | - David Komander
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia, and Department of Medical Biology, University of Melbourne, Melbourne, VIC 3000, Australia.
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21
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Zhang X, Meng T, Cui S, Liu D, Pang Q, Wang P. Roles of ubiquitination in the crosstalk between tumors and the tumor microenvironment (Review). Int J Oncol 2022; 61:84. [PMID: 35616129 PMCID: PMC9170352 DOI: 10.3892/ijo.2022.5374] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 04/27/2022] [Indexed: 11/06/2022] Open
Abstract
The interaction between a tumor and the tumor microenvironment (TME) plays a key role in tumorigenesis and tumor progression. Ubiquitination, a crucial post-translational modification for regulating protein degradation and turnover, plays a role in regulating the crosstalk between a tumor and the TME. Thus, identifying the roles of ubiquitination in the process may assist researchers to investigate the mechanisms underlying tumorigenesis and tumor progression. In the present review article, new insights into the substrates for ubiquitination that are involved in the regulation of hypoxic environments, angiogenesis, chronic inflammation-mediated tumor formation, and the function of cancer-associated fibroblasts and infiltrating immune cells (tumor-associated macrophages, T-cells, myeloid-derived suppressor cells, dendritic cells, and natural killer cells) are summarized. In addition, the potential targets of the ubiquitination proteasome system within the TME for cancer therapy and their therapeutic effects are reviewed and discussed.
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Affiliation(s)
- Xiuzhen Zhang
- Anti‑aging and Regenerative Medicine Research Institution, School of Life Sciences and Medicine, Shandong University of Technology, Zibo, Shandong 255000, P.R. China
| | - Tong Meng
- Tongji University Cancer Center, Shanghai Tenth People's Hospital of Tongji University, School of Medicine, Tongji University, Shanghai 200092, P.R. China
| | - Shuaishuai Cui
- School of Life Sciences and Medicine, Shandong University of Technology, Zibo, Shandong 255000, P.R. China
| | - Dongwu Liu
- Anti‑aging and Regenerative Medicine Research Institution, School of Life Sciences and Medicine, Shandong University of Technology, Zibo, Shandong 255000, P.R. China
| | - Qiuxiang Pang
- Anti‑aging and Regenerative Medicine Research Institution, School of Life Sciences and Medicine, Shandong University of Technology, Zibo, Shandong 255000, P.R. China
| | - Ping Wang
- Tongji University Cancer Center, Shanghai Tenth People's Hospital of Tongji University, School of Medicine, Tongji University, Shanghai 200092, P.R. China
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22
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Beck DB, Werner A, Kastner DL, Aksentijevich I. Disorders of ubiquitylation: unchained inflammation. Nat Rev Rheumatol 2022; 18:435-447. [PMID: 35523963 PMCID: PMC9075716 DOI: 10.1038/s41584-022-00778-4] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/31/2022] [Indexed: 12/31/2022]
Abstract
Ubiquitylation is an essential post-translational modification that regulates intracellular signalling networks by triggering proteasomal substrate degradation, changing the activity of substrates or mediating changes in proteins that interact with substrates. Hundreds of enzymes participate in reversible ubiquitylation of proteins, some acting globally and others targeting specific proteins. Ubiquitylation is essential for innate immune responses, as it facilitates rapid regulation of inflammatory pathways, thereby ensuring sufficient but not excessive responses. A growing number of inborn errors of immunity are attributed to dysregulated ubiquitylation. These genetic disorders exhibit broad clinical manifestations, ranging from susceptibility to infection to autoinflammatory and/or autoimmune features, lymphoproliferation and propensity to malignancy. Many autoinflammatory disorders result from disruption of components of the ubiquitylation machinery and lead to overactivation of innate immune cells. An understanding of the disorders of ubiquitylation in autoinflammatory diseases could enable the development of novel management strategies.
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Affiliation(s)
- David B Beck
- Inflammatory Disease Section, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.,Center for Human Genetics and Genomics, New York University, New York, NY, USA.,Division of Rheumatology, Department of Medicine, New York University, New York, NY, USA
| | - Achim Werner
- Stem Cell Biochemistry Unit, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD, USA
| | - Daniel L Kastner
- Inflammatory Disease Section, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Ivona Aksentijevich
- Inflammatory Disease Section, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.
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23
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Screening of OTULIN gene mutation with targeted next generation sequencing in Turkish populations and in silico analysis of these mutations. Mol Biol Rep 2022; 49:4643-4652. [PMID: 35294702 DOI: 10.1007/s11033-022-07312-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 03/01/2022] [Indexed: 10/18/2022]
Abstract
BACKGROUND OTULIN-related autoinflammatory syndrome (ORAS) is an autosomal recessive disease characterized by systemic inflammation, recurrent fever. Due to limited knowledge about the OTULIN DNA variants that cause ORAS, the diagnosis and treatment of this disease is difficult. In this study, we aim to identify OTULIN DNA variants responsible for the genetic pathology of ORAS and observe the effects of these variants on the OTULIN protein structure and the function with different bioinformatics approaches. METHODS The present study included 3230 individuals with the suspicion of an autoinflammatory disease who were referred to Ege University Children's Hospital Molecular Medicine Laboratory. OTULIN variants were detected using a panel consisting of 37 different autoinflammatory diseases (AID) genes via targeted Next-Generation Sequencing. RESULTS As a result of the study, DNA variants associated with various AID were detected in 65% of the individuals to whom the panel was applied. Among these variants, only three different OTULIN variants (p.Val82Ile, p.Gln115His and p.Leu131_Arg132insLeuCysThrGlu) were detected. The pathogenic effects of the variants detected in the OTULIN gene were determined by using Polyphen2 as "Probably Pathogenic" for the p.Val82Ile and "benign" for the p.Gln115His. At the same time, the effects of these variants on the structure and function of the OTULIN protein were investigated by in silico approaches. Both variants reduce protein stability and binding affinity. CONCLUSION The results of the current study suggest that the evaluation of OTULIN variants with in silico approaches will contribute to the development of personalized treatments by diagnosing the disease specific to the variant.
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24
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Zinngrebe J, Moepps B, Monecke T, Gierschik P, Schlichtig F, Barth TFE, Strauß G, Boldrin E, Posovszky C, Schulz A, Beringer O, Rieser E, Jacobsen E, Lorenz MR, Schwarz K, Pannicke U, Walczak H, Niessing D, Schuetz C, Fischer‐Posovszky P, Debatin K. Compound heterozygous variants in OTULIN are associated with fulminant atypical late-onset ORAS. EMBO Mol Med 2022; 14:e14901. [PMID: 35170849 PMCID: PMC8899767 DOI: 10.15252/emmm.202114901] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 01/21/2022] [Accepted: 01/24/2022] [Indexed: 01/11/2023] Open
Abstract
Autoinflammatory diseases are a heterogenous group of disorders defined by fever and systemic inflammation suggesting involvement of genes regulating innate immune responses. Patients with homozygous loss-of-function variants in the OTU-deubiquitinase OTULIN suffer from neonatal-onset OTULIN-related autoinflammatory syndrome (ORAS) characterized by fever, panniculitis, diarrhea, and arthritis. Here, we describe an atypical form of ORAS with distinct clinical manifestation of the disease caused by two new compound heterozygous variants (c.258G>A (p.M86I)/c.500G>C (p.W167S)) in the OTULIN gene in a 7-year-old affected by a life-threatening autoinflammatory episode with sterile abscess formation. On the molecular level, we find binding of OTULIN to linear ubiquitin to be compromised by both variants; however, protein stability and catalytic activity is most affected by OTULIN variant p.W167S. These molecular changes together lead to increased levels of linear ubiquitin linkages in patient-derived cells triggering the disease. Our data indicate that the spectrum of ORAS patients is more diverse than previously thought and, thus, supposedly asymptomatic individuals might also be affected. Based on our results, we propose to subdivide the ORAS into classical and atypical entities.
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Affiliation(s)
- Julia Zinngrebe
- Department of Pediatrics and Adolescent MedicineUlm University Medical CenterUlmGermany
| | - Barbara Moepps
- Institute of Pharmacology and ToxicologyUlm UniversityUlmGermany
| | - Thomas Monecke
- Institute of Pharmaceutical BiotechnologyUlm UniversityUlmGermany
| | - Peter Gierschik
- Institute of Pharmacology and ToxicologyUlm UniversityUlmGermany
| | - Ferdinand Schlichtig
- Department of Pediatrics and Adolescent MedicineUlm University Medical CenterUlmGermany
| | | | - Gudrun Strauß
- Department of Pediatrics and Adolescent MedicineUlm University Medical CenterUlmGermany
| | - Elena Boldrin
- Department of Pediatrics and Adolescent MedicineUlm University Medical CenterUlmGermany
| | - Carsten Posovszky
- Department of Pediatrics and Adolescent MedicineUlm University Medical CenterUlmGermany
| | - Ansgar Schulz
- Department of Pediatrics and Adolescent MedicineUlm University Medical CenterUlmGermany
| | - Ortraud Beringer
- Department of Pediatrics and Adolescent MedicineUlm University Medical CenterUlmGermany
| | - Eva Rieser
- Institute of Biochemistry I & CECAD Research CenterUniversity of CologneCologneGermany
| | - Eva‐Maria Jacobsen
- Department of Pediatrics and Adolescent MedicineUlm University Medical CenterUlmGermany
| | | | - Klaus Schwarz
- Institute for Transfusion MedicineUlm UniversityUlmGermany
- Institute for Clinical Transfusion Medicine and Immunogenetics UlmGerman Red Cross Blood Service Baden‐Wuerttemberg – HessenUlmGermany
| | | | - Henning Walczak
- Institute of Biochemistry I & CECAD Research CenterUniversity of CologneCologneGermany
- UCL Cancer InstituteLondonUK
| | - Dierk Niessing
- Institute of Pharmaceutical BiotechnologyUlm UniversityUlmGermany
| | | | | | - Klaus‐Michael Debatin
- Department of Pediatrics and Adolescent MedicineUlm University Medical CenterUlmGermany
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25
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Schulze-Niemand E, Naumann M, Stein M. Substrate-assisted activation and selectivity of the bacterial RavD effector deubiquitinylase. Proteins 2021; 90:947-958. [PMID: 34825414 DOI: 10.1002/prot.26286] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 11/02/2021] [Accepted: 11/22/2021] [Indexed: 11/12/2022]
Abstract
Deubiquitinylases (DUBs) catalyze the peptide bond cleavage of specific ubiquitin linkages at distinct protein substrates. Pathogens from viruses and bacteria independently developed effector proteins with DUB activity to mimic host DUB functions and circumvent immune responses. The effector protein RavD from Legionella pneumophila cleaves linear ubiquitin chains with an exclusive methionine-1 selectivity. It thus performs as a functional analogue of the human DUB OTULIN, which achieves its selectivity only via a specialized proximal ubiquitin S1' binding site as well as a substrate-assisted activation of the catalytic triad. An analysis of the crystal structures of bacterial RavD in its free and di-ubiquitin-bound forms, in order to rationalize the structural basis for its selectivity and activation mechanism, is not fully conclusive. As these ambiguities might arise from the introduced double mutation of the di-ubiquitin substrate in the RavD-di-ubiquitin complex crystal structure, biomolecular modeling, and molecular dynamics sampling (1-2 μs for each system of RavD and OTULIN) were employed to reconstitute the physiological RavD-di-ubiquitin complex. The simulations show that the distal S1 ubiquitin binding sites of RavD and OTULIN are similar in terms of interface area, composition, and ubiquitin binding affinity. The proximal S1' site of RavD, in contrast, is significantly smaller and ubiquitin binding is weaker and more flexible than in OTULIN. Upon substrate access, the residues of the catalytic triad of RavD show a reduction of flexibility and a conformational transition toward a catalytically active state. Thus, the enzymatic activation of RavD is presumably also substrate-assisted and a clear rationale for the common M1-substrate selectivity.
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Affiliation(s)
- Eric Schulze-Niemand
- Institute for Experimental Internal Medicine, Medical Faculty, Otto-von-Guericke University, Magdeburg, Germany.,Molecular Simulations and Design Group, Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
| | - Michael Naumann
- Institute for Experimental Internal Medicine, Medical Faculty, Otto-von-Guericke University, Magdeburg, Germany
| | - Matthias Stein
- Molecular Simulations and Design Group, Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
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26
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Delvecchio VS, Fierro C, Giovannini S, Melino G, Bernassola F. Emerging roles of the HECT-type E3 ubiquitin ligases in hematological malignancies. Discov Oncol 2021; 12:39. [PMID: 35201500 PMCID: PMC8777521 DOI: 10.1007/s12672-021-00435-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 09/13/2021] [Indexed: 02/07/2023] Open
Abstract
Ubiquitination-mediated proteolysis or regulation of proteins, ultimately executed by E3 ubiquitin ligases, control a wide array of cellular processes, including transcription, cell cycle, autophagy and apoptotic cell death. HECT-type E3 ubiquitin ligases can be distinguished from other subfamilies of E3 ubiquitin ligases because they have a C-terminal HECT domain that directly catalyzes the covalent attachment of ubiquitin to their substrate proteins. Deregulation of HECT-type E3-mediated ubiquitination plays a prominent role in cancer development and chemoresistance. Several members of this subfamily are indeed frequently deregulated in human cancers as a result of genetic mutations and altered expression or activity. HECT-type E3s contribute to tumorigenesis by regulating the ubiquitination rate of substrates that function as either tumour suppressors or oncogenes. While the pathological roles of the HECT family members in solid tumors are quite well established, their contribution to the pathogenesis of hematological malignancies has only recently emerged. This review aims to provide a comprehensive overview of the involvement of the HECT-type E3s in leukemogenesis.
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Affiliation(s)
- Vincenza Simona Delvecchio
- Department of Experimental Medicine, TOR, University of Rome “Tor Vergata”, Via Montpellier 1, 00133 Rome, Italy
| | - Claudia Fierro
- Department of Experimental Medicine, TOR, University of Rome “Tor Vergata”, Via Montpellier 1, 00133 Rome, Italy
| | - Sara Giovannini
- Department of Experimental Medicine, TOR, University of Rome “Tor Vergata”, Via Montpellier 1, 00133 Rome, Italy
| | - Gerry Melino
- Department of Experimental Medicine, TOR, University of Rome “Tor Vergata”, Via Montpellier 1, 00133 Rome, Italy
| | - Francesca Bernassola
- Department of Experimental Medicine, TOR, University of Rome “Tor Vergata”, Via Montpellier 1, 00133 Rome, Italy
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27
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Shibata Y, Komander D. Linear ubiquitin chains break blood vessel branches. Cell Res 2021; 31:1045-1046. [PMID: 34429523 PMCID: PMC8486837 DOI: 10.1038/s41422-021-00553-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Affiliation(s)
- Yuri Shibata
- grid.1042.7Ubiquitin Signalling Division, Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, 3052 Melbourne Australia
| | - David Komander
- grid.1042.7Ubiquitin Signalling Division, Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, 3052 Melbourne Australia
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28
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Pruneda JN, Damgaard RB. Ester-linked ubiquitination by HOIL-1 controls immune signalling by shaping the linear ubiquitin landscape. FEBS J 2021; 288:5903-5908. [PMID: 34322999 DOI: 10.1111/febs.16118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 07/08/2021] [Indexed: 11/29/2022]
Abstract
Ester-linked ubiquitination of serine or threonine residues - or even lipids - has emerged as a new regulatory earmark in cell signalling. Petrova et al. (2021) now reveal that ubiquitin esterification by the atypical ubiquitin ligase HOIL-1, a component of the LUBAC complex, is critical for proper formation of linear ubiquitin chains and control of immune signalling in T cells and macrophages. Surprisingly, ester-linked ubiquitination can either promote or inhibit linear ubiquitin conjugation and cytokine production depending on the receptor and immune cell engaged. Comment on: https://doi.org/10.1111/febs.15896.
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Affiliation(s)
- Jonathan N Pruneda
- Department of Molecular Microbiology & Immunology, Oregon Health & Science University, Portland, OR, USA
| | - Rune Busk Damgaard
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
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29
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Siraj A, Lim DY, Tayara H, Chong KT. UbiComb: A Hybrid Deep Learning Model for Predicting Plant-Specific Protein Ubiquitylation Sites. Genes (Basel) 2021; 12:genes12050717. [PMID: 34064731 PMCID: PMC8151217 DOI: 10.3390/genes12050717] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 05/06/2021] [Accepted: 05/07/2021] [Indexed: 12/11/2022] Open
Abstract
Protein ubiquitylation is an essential post-translational modification process that performs a critical role in a wide range of biological functions, even a degenerative role in certain diseases, and is consequently used as a promising target for the treatment of various diseases. Owing to the significant role of protein ubiquitylation, these sites can be identified by enzymatic approaches, mass spectrometry analysis, and combinations of multidimensional liquid chromatography and tandem mass spectrometry. However, these large-scale experimental screening techniques are time consuming, expensive, and laborious. To overcome the drawbacks of experimental methods, machine learning and deep learning-based predictors were considered for prediction in a timely and cost-effective manner. In the literature, several computational predictors have been published across species; however, predictors are species-specific because of the unclear patterns in different species. In this study, we proposed a novel approach for predicting plant ubiquitylation sites using a hybrid deep learning model by utilizing convolutional neural network and long short-term memory. The proposed method uses the actual protein sequence and physicochemical properties as inputs to the model and provides more robust predictions. The proposed predictor achieved the best result with accuracy values of 80% and 81% and F-scores of 79% and 82% on the 10-fold cross-validation and an independent dataset, respectively. Moreover, we also compared the testing of the independent dataset with popular ubiquitylation predictors; the results demonstrate that our model significantly outperforms the other methods in prediction classification results.
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Affiliation(s)
- Arslan Siraj
- Department of Electronics and Information Engineering, Jeonbuk National University, Jeonju 54896, Korea; (A.S.); (D.Y.L.)
| | - Dae Yeong Lim
- Department of Electronics and Information Engineering, Jeonbuk National University, Jeonju 54896, Korea; (A.S.); (D.Y.L.)
| | - Hilal Tayara
- School of International Engineering and Science, Jeonbuk National University, Jeonju 54896, Korea
- Correspondence: (H.T.); (K.T.C.)
| | - Kil To Chong
- Department of Electronics and Information Engineering, Jeonbuk National University, Jeonju 54896, Korea; (A.S.); (D.Y.L.)
- Advanced Electronics and Information Research Center, Jeonbuk National University, Jeonju 54896, Korea
- Correspondence: (H.T.); (K.T.C.)
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30
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Damgaard RB. The ubiquitin system: from cell signalling to disease biology and new therapeutic opportunities. Cell Death Differ 2021; 28:423-426. [PMID: 33446876 PMCID: PMC7862391 DOI: 10.1038/s41418-020-00703-w] [Citation(s) in RCA: 78] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 11/27/2020] [Indexed: 12/17/2022] Open
Affiliation(s)
- Rune Busk Damgaard
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, 2800, Kgs. Lyngby, Denmark.
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