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Sun Q, Sui Y, Li S, Zhou R, Fu Z, Luo J, Zhao W. RNF8-mediated multi-ubiquitination of MCM7: Linking disassembly of the CMG helicase with DNA damage response in human cells. Life Sci 2024; 353:122912. [PMID: 39004272 DOI: 10.1016/j.lfs.2024.122912] [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: 04/13/2024] [Revised: 06/26/2024] [Accepted: 07/10/2024] [Indexed: 07/16/2024]
Abstract
DNA damage causes genomic instability. To maintain genome integrity, cells have evolved DNA damage response, which is involved in replication fork disassembly and DNA replication termination. However, the mechanism underlying the regulation of replication fork disassembly and its connection with DNA damage repair remain elusive. The CMG-MCM7 subunit ubiquitination functions on the eukaryotic replication fork disassembly at replication termination. Until now, only ubiquitin ligases CUL2LRR1 have been reported catalyzing MCM7 ubiquitination in human cells. This study discovered that in human cells, the ubiquitin ligase RNF8 catalyzes K63-linked multi-ubiquitination of MCM7 at K145 both in vivo and in vitro. The multi-ubiquitination of MCM7 is dynamically regulated during the cell cycle, primarily presenting on chromatin during the late S phase. Additionally, MCM7 polyubiquitylation is promoted by RNF168 and BRCA1 during DNA replication termination. Upon DNA damage, the RNF8-mediated polyubiquitination of MCM7 decreased significantly during the late S phase. This study highlights the novel role of RNF8-catalyzed polyubiquitination of MCM7 in the regulation of replication fork disassembly in human cells and linking it to DNA damage response.
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Affiliation(s)
- Qianqian Sun
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing 10005, China
| | - Yaqi Sui
- School of Life Sciences, Chongqing University; Chongqing 401331, China
| | - Shirui Li
- School of Life Sciences, Chongqing University; Chongqing 401331, China
| | - Rui Zhou
- School of Life Sciences, Chongqing University; Chongqing 401331, China
| | - Zhisong Fu
- School of Life Sciences, Chongqing University; Chongqing 401331, China
| | - Jing Luo
- School of Life Sciences, Chongqing University; Chongqing 401331, China
| | - Wenhui Zhao
- School of Life Sciences, Chongqing University; Chongqing 401331, China.
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2
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Ming T, Liu H, Yuan M, Tian J, Fang Q, Liu Y, Kong Q, Wang Q, Song X, Xia Z, Wu X. The deubiquitinase OTUD1 deubiquitinates TIPE2 and plays a protective role in sepsis-induced lung injury by targeting TAK1-mediated MAPK and NF-κB signaling. Biochem Pharmacol 2024; 227:116418. [PMID: 38996928 DOI: 10.1016/j.bcp.2024.116418] [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: 04/16/2024] [Revised: 06/05/2024] [Accepted: 07/09/2024] [Indexed: 07/14/2024]
Abstract
Ovarian tumor domain-containing protease 1 (OTUD1) is a critical negative regulator that promotes innate immune homeostasis and is extensively involved in the pathogenesis of sepsis. In this study, we performed a powerful integration of multiomics analysis and an experimental mechanistic investigation to elucidate the immunoregulatory role of OTUD1 in sepsis at the clinical, animal and cellular levels. Our study revealed the upregulation of OTUD1 expression and the related distinctive alterations observed via multiomics profiling in clinical and experimental sepsis. Importantly, in vivo and in vitro, OTUD1 was shown to negatively regulate inflammatory responses and play a protective role in sepsis-induced pathological lung injury by mechanistically inhibiting the activation of the transforming growth factor-beta-activated kinase 1 (TAK1)-mediated mitogen-activated protein kinase (MAPK) and nuclear factor kappa-B (NF-κB) signaling pathways in the present study. Subsequently, we probed the molecular mechanisms underlying OTUD1's regulation of NF-κB and MAPK pathways by pinpointing the target proteins that OTUD1 can deubiquitinate. Drawing upon prior research conducted in our laboratory, it has been demonstrated that tumor necrosis factor-α-induced protein 8-like 2 (TIPE2) performs a protective function in septic lung injury and septic encephalopathy by suppressing the NF-κB and MAPK pathways. Hence, we hypothesized that TIPE2 might be a target protein of OTUD1. Additional experiments, including Co-IP, immunofluorescence co-localization, and Western blotting, revealed that OTUD1 indeed has the ability to deubiquitinate TIPE2. In summary, OTUD1 holds potential as an immunoregulatory and inflammatory checkpoint agent, and could serve as a promising therapeutic target for sepsis-induced lung injury.
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Affiliation(s)
- Tingqian Ming
- Department of Anesthesiology, Renmin Hospital of Wuhan University, Wuhan, Hubei 430060, PR China
| | - Huifan Liu
- Department of Anesthesiology and Critical Care Medicine, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, 430071, PR China
| | - Min Yuan
- Department of Anesthesiology, Renmin Hospital of Wuhan University, Wuhan, Hubei 430060, PR China
| | - Jingyuan Tian
- Department of Anesthesiology, Renmin Hospital of Wuhan University, Wuhan, Hubei 430060, PR China
| | - Qing Fang
- Department of Anesthesiology and Critical Care Medicine, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, 430071, PR China
| | - Yuping Liu
- Department of Anesthesiology and Critical Care Medicine, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, 430071, PR China
| | - Qian Kong
- Department of Anesthesiology, Renmin Hospital of Wuhan University, Wuhan, Hubei 430060, PR China
| | - Qian Wang
- Department of Anesthesiology, Renmin Hospital of Wuhan University, Wuhan, Hubei 430060, PR China
| | - Xuemin Song
- Department of Anesthesiology and Critical Care Medicine, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, 430071, PR China
| | - Zhongyuan Xia
- Department of Anesthesiology, Renmin Hospital of Wuhan University, Wuhan, Hubei 430060, PR China.
| | - Xiaojing Wu
- Department of Anesthesiology, Renmin Hospital of Wuhan University, Wuhan, Hubei 430060, PR China.
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3
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Li Z, Gilbert C, Peng H, Pollet N. Discovery of numerous novel Helitron-like elements in eukaryote genomes using HELIANO. Nucleic Acids Res 2024:gkae679. [PMID: 39119924 DOI: 10.1093/nar/gkae679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2024] [Revised: 07/19/2024] [Accepted: 07/25/2024] [Indexed: 08/10/2024] Open
Abstract
Helitron-like elements (HLEs) are widespread eukaryotic DNA transposons employing a rolling-circle transposition mechanism. Despite their prevalence in fungi, animals, and plant genomes, identifying Helitrons remains a formidable challenge. We introduce HELIANO, a software for annotating and classifying autonomous and non-autonomous HLE sequences from whole genomes. HELIANO overcomes several limitations of existing tools in speed and accuracy, demonstrated through benchmarking and its application to the complex genomes of frogs (Xenopus tropicalis and Xenopus laevis) and rice (Oryza sativa), where it uncovered numerous previously unidentified HLEs. In an extensive analysis of 404 eukaryote genomes, we found HLEs widely distributed across phyla, with exceptions in specific taxa. HELIANO's application led to the discovery of numerous new HLEs in land plants and identified 20 protein domains captured by certain autonomous HLE families. A comprehensive phylogenetic analysis further classified HLEs into two primary clades, HLE1 and HLE2, and revealed nine subgroups, some of which are enriched within specific taxa. The future use of HELIANO promises to improve the global analysis of HLEs across genomes, significantly advancing our understanding of this fascinating transposon superfamily.
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Affiliation(s)
- Zhen Li
- Université Paris-Saclay, CNRS, IRD, UMR Évolution, Génomes, Comportement et Écologie, 91198 Gif-sur-Yvette, France
| | - Clément Gilbert
- Université Paris-Saclay, CNRS, IRD, UMR Évolution, Génomes, Comportement et Écologie, 91198 Gif-sur-Yvette, France
| | - Haoran Peng
- Crop Genome Dynamics Group, Agroscope, 1260 Nyon, Switzerland
| | - Nicolas Pollet
- Université Paris-Saclay, CNRS, IRD, UMR Évolution, Génomes, Comportement et Écologie, 91198 Gif-sur-Yvette, France
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4
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Li Z, Tian Y, Zong H, Wang X, Li D, Keranmu A, Xin S, Ye B, Bai R, Chen W, Yang G, Ye L, Wang S. Deubiquitinating enzyme OTUD4 stabilizes RBM47 to induce ATF3 transcription: a novel mechanism underlying the restrained malignant properties of ccRCC cells. Apoptosis 2024; 29:1051-1069. [PMID: 38553613 DOI: 10.1007/s10495-024-01953-6] [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] [Accepted: 03/03/2024] [Indexed: 07/23/2024]
Abstract
Dysregulation of deubiquitination contributes to various diseases, including cancer, and aberrant expression of deubiquitinating enzymes is involved in carcinoma progression. As a member of the ovarian tumor (OTU) deubiquitinases, OTUD4 is considered a tumor suppressor in many kinds of malignancies. The biological characteristics and mechanisms of OTUD4 in clear cell renal cell carcinoma (ccRCC) remain unclear. The downregulation of OTUD4 in ccRCC was confirmed based on the TCGA database and a validation cohort of 30-paired ccRCC and para-carcinoma samples. Moreover, OTUD4 expression was detected by immunohistochemistry in 50 cases of ccRCC tissues, and patients with lower levels of OTUD4 showed larger tumor size (p = 0.015). TCGA data revealed that patients with high expression of OTUD4 had a longer overall survival rate. In vitro and in vivo studies revealed that downregulation of OTUD4 was essential for tumor cell growth and metastasis in ccRCC, and OTUD4 overexpression inhibited these malignant phenotypes. We further found that OTUD4 sensitized ccRCC cells to Erastin-induced ferroptosis, and ferrostain-1 inhibited OTUD4-induced ferroptotic cell death. Mechanistic studies indicated that OTUD4 functioned as an anti-proliferative and anti-metastasic factor through the regulation of RNA-binding protein 47 (RBM47)-mediated activating transcription factor 3 (ATF3). OTUD4 directly interacted with RBM47 and promoted its stability via deubiquitination events. RBM47 was critical in ccRCC progression by regulating ATF3 mRNA stability, thereby promoting ATF3-mediated ferroptosis. RBM47 interference abolished the suppressive role of OTUD4 overexpression in ccRCC. Our findings provide mechanistic insight into OTUD4 of ccRCC progression and indicate a novel critical pathway OTUD4/RBM47/ATF3 may serve as a potential therapeutic pathway for ccRCC.
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Affiliation(s)
- Ziyao Li
- Department of Urology, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
- School of Electrical Engineering of Zhengzhou University, Zhengzhou, China
- Center for Frontier Medical Engineering of Chiba University, Chiba, Japan
| | - Ye Tian
- Department of Urology, Guizhou Provincial People's Hospital, Guiyang, China
| | - Huafeng Zong
- Department of Pathology, Dalian Friendship Hospital, Dalian, China
| | - Xuelei Wang
- Department of Urology, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Dongyang Li
- Department of Urology, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Adili Keranmu
- Department of Urology, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Shiyong Xin
- Department of Urology, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Bowen Ye
- Department of Urology, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Rong Bai
- Department of Pharmacy, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Weihua Chen
- Department of Urology, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Guosheng Yang
- Department of Urology, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Lin Ye
- Department of Urology, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China.
| | - Siyan Wang
- Health Management Center, Huizhou Third People's Hospital, Guangzhou Medical University, Huizhou, China.
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5
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Pruneda JN, Nguyen JV, Nagai H, Kubori T. Bacterial usurpation of the OTU deubiquitinase fold. FEBS J 2024; 291:3303-3316. [PMID: 36636866 PMCID: PMC10338644 DOI: 10.1111/febs.16725] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 12/10/2022] [Accepted: 01/10/2023] [Indexed: 01/14/2023]
Abstract
The extensive cellular signalling events controlled by posttranslational ubiquitination are tightly regulated through the action of specialized proteases termed deubiquitinases. Among them, the OTU family of deubiquitinases can play very specialized roles in the regulation of discrete subtypes of ubiquitin signals that control specific cellular functions. To exert control over host cellular functions, some pathogenic bacteria have usurped the OTU deubiquitinase fold as a secreted virulence factor that interferes with ubiquitination inside infected cells. Herein, we provide a review of the function of bacterial OTU deubiquitinases during infection, the structural basis for their deubiquitinase activities and the bioinformatic approaches leading to their identification. Understanding bacterial OTU deubiquitinases holds the potential for discoveries not only in bacterial pathogenesis but in eukaryotic biology as well.
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Affiliation(s)
- Jonathan N. Pruneda
- Department of Molecular Microbiology & Immunology, Oregon Health & Science University, Portland, OR 97239, USA
| | - Justine V. Nguyen
- Department of Molecular Microbiology & Immunology, Oregon Health & Science University, Portland, OR 97239, USA
| | - Hiroki Nagai
- Department of Microbiology, Graduate School of Medicine, Gifu University, Gifu, Gifu 501-1194, Japan
- Center for One Medicine Innovative Translational Research, Gifu University Institute for Advanced Study, Gifu, Gifu 501-1194, Japan
| | - Tomoko Kubori
- Department of Microbiology, Graduate School of Medicine, Gifu University, Gifu, Gifu 501-1194, Japan
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6
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McDade E, Liu H, Bui Q, Hassenstab J, Gordon B, Benzinger T, Shen Y, Timsina J, Wang L, Sung YJ, Karch C, Renton A, Daniels A, Morris J, Xiong C, Ibanez L, Perrin R, Llibre-Guerra JJ, Day G, Supnet-Bell C, Xu X, Berman S, Chhatwal J, Ikeuchi T, Kasuga K, Niimi Y, Huey E, Schofield P, Brooks W, Ryan N, Jucker M, Laske C, Levin J, Vöglein J, Roh JH, Lopera F, Bateman R, Cruchaga C. Ubiquitin-Proteasome System in the Different Stages of Dominantly Inherited Alzheimer's Disease. RESEARCH SQUARE 2024:rs.3.rs-4202125. [PMID: 39108475 PMCID: PMC11302696 DOI: 10.21203/rs.3.rs-4202125/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 08/23/2024]
Abstract
This study explored the role of the ubiquitin-proteasome system (UPS) in dominantly inherited Alzheimer's disease (DIAD) by examining changes in cerebrospinal fluid (CSF) levels of UPS proteins along with disease progression, AD imaging biomarkers (PiB PET, tau PET), neurodegeneration imaging measures (MRI, FDG PET), and Clinical Dementia Rating® (CDR®). Using the SOMAscan assay, we detected subtle increases in specific ubiquitin enzymes associated with proteostasis in mutation carriers (MCs) up to two decades before the estimated symptom onset. This was followed by more pronounced elevations of UPS-activating enzymes, including E2 and E3 proteins, and ubiquitin-related modifiers. Our findings also demonstrated consistent correlations between UPS proteins and CSF biomarkers such as Aβ42/40 ratio, total tau, various phosphorylated tau species to total tau ratios (ptau181/T181, ptauT205/T205, ptauS202/S202, ptauT217/T217), and MTBR-tau243, alongside Neurofilament light chain (NfL) and the CDR®. Notably, a positive association was observed with imaging markers (PiB PET, tau PET) and a negative correlation with markers of neurodegeneration (FDG PET, MRI), highlighting a significant link between UPS dysregulation and neurodegenerative processes. The correlations suggest that the increase in multiple UPS proteins with rising tau levels and tau-tangle associated markers, indicating a potential role for the UPS in relation to misfolded tau/neurofibrillary tangles (NFTs) and symptom onset. These findings indicate that elevated CSF UPS proteins in DIAD MCs could serve as early indicators of disease progression and suggest a link between UPS dysregulation and amyloid plaque, tau tangles formation, implicating the UPS as a potential therapeutic target in AD pathogenesis.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Alan Renton
- Nash Family Department of Neuroscience and Ronald Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA: Departments of Neurology and Genetics and Ge
| | | | | | | | | | | | | | | | | | | | | | - Jasmeer Chhatwal
- Massachusetts General Hospital, Brigham and Women's Hospital, Harvard Medical School
| | | | - Kensaku Kasuga
- Department of Molecular Genetics, Brain Research Institute, Niigata University
| | | | | | | | | | | | | | | | | | | | | | | | - Randall Bateman
- Department of Neurology, Washington University School of Medicine
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7
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Rossio V, Paulo JA, Liu X, Gygi SP, King RW. Specificity profiling of deubiquitylases against endogenously generated ubiquitin-protein conjugates. Cell Chem Biol 2024; 31:1349-1362.e5. [PMID: 38810651 PMCID: PMC11260241 DOI: 10.1016/j.chembiol.2024.05.001] [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: 02/05/2024] [Revised: 03/15/2024] [Accepted: 05/01/2024] [Indexed: 05/31/2024]
Abstract
Deubiquitylating enzymes (DUBs) remove ubiquitin from proteins thereby regulating their stability or activity. Our understanding of DUB-substrate specificity is limited because DUBs are typically not compared to each other against many physiological substrates. By broadly inhibiting DUBs in Xenopus egg extract, we generated hundreds of ubiquitylated proteins and compared the ability of 30 DUBs to deubiquitylate them using quantitative proteomics. We identified five high-impact DUBs (USP7, USP9X, USP36, USP15, and USP24) that each reduced ubiquitylation of over 10% of the isolated proteins. Candidate substrates of high-impact DUBs showed substantial overlap and were enriched for disordered regions, suggesting this feature may promote substrate recognition. Other DUBs showed lower impact and non-overlapping specificity, targeting distinct non-disordered proteins including complexes such as the ribosome or the proteasome. Altogether our study identifies candidate DUB substrates and defines patterns of functional redundancy and specificity, revealing substrate characteristics that may influence DUB-substrate recognition.
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Affiliation(s)
- Valentina Rossio
- Department of Cell Biology, Blavatnik Institute at Harvard Medical School, Boston, MA 02115, USA
| | - Joao A Paulo
- Department of Cell Biology, Blavatnik Institute at Harvard Medical School, Boston, MA 02115, USA
| | - Xinyue Liu
- Department of Cell Biology, Blavatnik Institute at Harvard Medical School, Boston, MA 02115, USA
| | - Steven P Gygi
- Department of Cell Biology, Blavatnik Institute at Harvard Medical School, Boston, MA 02115, USA
| | - Randall W King
- Department of Cell Biology, Blavatnik Institute at Harvard Medical School, Boston, MA 02115, USA.
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8
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Lange SM, McFarland MR, Lamoliatte F, Carroll T, Krshnan L, Pérez-Ràfols A, Kwasna D, Shen L, Wallace I, Cole I, Armstrong LA, Knebel A, Johnson C, De Cesare V, Kulathu Y. VCP/p97-associated proteins are binders and debranching enzymes of K48-K63-branched ubiquitin chains. Nat Struct Mol Biol 2024:10.1038/s41594-024-01354-y. [PMID: 38977901 DOI: 10.1038/s41594-024-01354-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 06/13/2024] [Indexed: 07/10/2024]
Abstract
Branched ubiquitin (Ub) chains constitute a sizable fraction of Ub polymers in human cells. Despite their abundance, our understanding of branched Ub function in cell signaling has been stunted by the absence of accessible methods and tools. Here we identify cellular branched-chain-specific binding proteins and devise approaches to probe K48-K63-branched Ub function. We establish a method to monitor cleavage of linkages within complex Ub chains and unveil ATXN3 and MINDY as debranching enzymes. We engineer a K48-K63 branch-specific nanobody and reveal the molecular basis of its specificity in crystal structures of nanobody-branched Ub chain complexes. Using this nanobody, we detect increased K48-K63-Ub branching following valosin-containing protein (VCP)/p97 inhibition and after DNA damage. Together with our discovery that multiple VCP/p97-associated proteins bind to or debranch K48-K63-linked Ub, these results suggest a function for K48-K63-branched chains in VCP/p97-related processes.
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Affiliation(s)
- Sven M Lange
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK.
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA.
| | - Matthew R McFarland
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
| | - Frederic Lamoliatte
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
| | - Thomas Carroll
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
| | - Logesvaran Krshnan
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
| | - Anna Pérez-Ràfols
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
| | - Dominika Kwasna
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
- Malopolska Centre of Biotechnology (MCB), Jagiellonian University, Krakow, Poland
| | - Linnan Shen
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
| | - Iona Wallace
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
| | - Isobel Cole
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
| | - Lee A Armstrong
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
| | - Axel Knebel
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
| | - Clare Johnson
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
| | - Virginia De Cesare
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
| | - Yogesh Kulathu
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK.
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9
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Gangaram B, Lee V, Slavotinek A. Biallelic OTUD6B variants associated with a Kabuki syndrome-like disorder in three siblings: A clinical report and literature review. Am J Med Genet A 2024; 194:e63567. [PMID: 38389298 DOI: 10.1002/ajmg.a.63567] [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: 09/11/2023] [Revised: 01/19/2024] [Accepted: 02/01/2024] [Indexed: 02/24/2024]
Abstract
Biallelic variants in the OTUD6B gene have been reported in the literature in association with an intellectual developmental disorder featuring dysmorphic facies, seizures, and distal limb abnormalities. Physical differences described for affected individuals suggest that the disorder may be clinically recognizable, but previous publications have reported an initial clinical suspicion for Kabuki syndrome (KS) in some affected individuals. Here, we report on three siblings with biallelic variants in OTUD6B co-segregating with neurodevelopmental delay, shared physical differences, and other clinical findings similar to those of previously reported individuals. However, clinical manifestations such as long palpebral fissures, prominent and cupped ears, developmental delay, growth deficiency, persistent fetal fingertip pads, vertebral anomaly, and seizures in the proband were initially suggestive of KS. In addition, previously unreported clinical manifestations such as delayed eruption of primary dentition, soft doughy skin with reduced sweating, and mirror movements present in our patients suggest an expansion of the phenotype, and we perform a literature review to update on current information related to OTUD6B and human gene-disease association.
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Affiliation(s)
- Balram Gangaram
- Division of Medical Genetics, Department of Pediatrics, University of California, San Francisco, California, USA
| | - Virgina Lee
- Division of Child Neurology, University of California, San Francisco, California, USA
| | - Anne Slavotinek
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
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10
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Owashi Y, Arai H, Adachi-Hagimori T, Kageyama D. Rickettsia induces strong cytoplasmic incompatibility in a predatory insect. Proc Biol Sci 2024; 291:20240680. [PMID: 39079670 PMCID: PMC11288687 DOI: 10.1098/rspb.2024.0680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Accepted: 05/21/2024] [Indexed: 08/03/2024] Open
Abstract
Rickettsia, a group of intracellular bacteria found in eukaryotes, exhibits diverse lifestyles, with some acting as vertebrate pathogens transmitted by arthropod vectors and others serving as maternally transmitted arthropod endosymbionts, some of which manipulate host reproduction for their own benefit. Two phenotypes, namely male-killing and parthenogenesis induction are known as Rickettsia-induced host reproductive manipulations, but it remains unknown whether Rickettsia can induce other types of host manipulation. In this study, we discovered that Rickettsia induced strong cytoplasmic incompatibility (CI), in which uninfected females produce no offspring when mated with infected males, in the predatory insect Nesidiocoris tenuis (Hemiptera: Miridae). Molecular phylogenetic analysis revealed that the Rickettsia strain was related to Rickettsia bellii, a common insect endosymbiont. Notably, this strain carried plasmid-encoded homologues of the CI-inducing factors (namely cifA-like and cifB-like genes), typically found in Wolbachia, which are well-known CI-inducing endosymbionts. Protein domain prediction revealed that the cifB-like gene encodes PD-(D/E)XK nuclease and deubiquitinase domains, which are responsible for Wolbachia-induced CI, as well as ovarian tumour-like (OTU-like) cysteine protease and ankyrin repeat domains. These findings suggest that Rickettsia and Wolbachia endosymbionts share underlying mechanisms of CI and that CI-inducing ability was acquired by microbes through horizontal plasmid transfer.
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Affiliation(s)
- Yuta Owashi
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), 1-2 Owashi, Tsukuba, Ibaraki 305-0851, Japan
| | - Hiroshi Arai
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), 1-2 Owashi, Tsukuba, Ibaraki 305-0851, Japan
| | - Tetsuya Adachi-Hagimori
- Laboratory of Applied Entomology, University of Miyazaki, 1-1 Gakuenkibanadai-Nishi, Miyazaki 889-2192, Japan
| | - Daisuke Kageyama
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), 1-2 Owashi, Tsukuba, Ibaraki 305-0851, Japan
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11
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Bejan DS, Lacoursiere RE, Pruneda JN, Cohen MS. Discovery of ester-linked ubiquitylation of PARP10 mono-ADP-ribosylation in cells: a dual post-translational modification on Glu/Asp side chains. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.27.600929. [PMID: 38979324 PMCID: PMC11230417 DOI: 10.1101/2024.06.27.600929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
The prevailing view on post-translational modifications (PTMs) is that amino acid side chains in proteins are modified with a single PTM at any given time. However, a growing body of work has demonstrated crosstalk between different PTMs, some occurring on the same residue. Such interplay is seen with ADP-ribosylation and ubiquitylation, where specialized E3 ligases ubiquitylate targets for proteasomal degradation in an ADP-ribosylation-dependent manner. More recently, the DELTEX family of E3 ligases was reported to catalyze ubiquitylation of the 3'- hydroxy group of the adenine-proximal ribose of free NAD + and ADP-ribose in vitro , generating a non-canonical ubiquitin ester-linked species. In this report, we show, for the first time, that this dual PTM occurs in cells on mono-ADP-ribosylated (MARylated) PARP10 on Glu/Asp sites to form a MAR ubiquitin ester (MARUbe). We term this process m ono- A DP-ribosyl ub iquit ylation or MARUbylation. Using chemical and enzymatic treatments, including a newly characterized bacterial deubiquitinase with esterase-specific activity, we discovered that PARP10 MARUbylation is extended with K11-linked polyubiquitin chains. Finally, mechanistic studies using proteasomal and ubiquitin-activating enzyme inhibitors demonstrated that PARP10 MARUbylation leads to its proteasomal degradation, providing a functional role for this new PTM in regulating protein turnover.
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Yang M, Wei Y, He X, Xia C. The deubiquitinating protein OTUD6B promotes lung adenocarcinoma progression by stabilizing RIPK1. Biol Direct 2024; 19:46. [PMID: 38880876 PMCID: PMC11181667 DOI: 10.1186/s13062-024-00489-8] [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: 04/19/2024] [Accepted: 06/12/2024] [Indexed: 06/18/2024] Open
Abstract
BACKGROUND There is growing evidence indicating that deubiquitinating enzymes may contribute to tumor progression and can serve as promising therapeutic targets. METHODS The overexpression of deubiquitinase OTUD6B in lung adenocarcinoma (LUAD) and its adjacent tissues was analyzed by immunohistochemistry and TCGA/GO database. Survival analysis further supported OTUD6B as a potential target for LUAD treatment. We assessed the effect of OTUD6B on LUAD cell growth using cell viability assays and conducted TUNEL staining, migration, and invasion experiments to investigate the impact of OTUD6B on the apoptosis and metastasis of LUAD cells. Additionally, we established a transplanted tumor model in nude mice to validate our findings in vivo. Finally, using IP mass spectrometry and co-IP experiments, we screened and confirmed the influence of RIPK1 as a substrate of OTUD6B in LUAD. RESULTS OTUD6B is highly overexpressed in human LUAD and predicts poor prognosis in LUAD patients. OTUD6B knockdown inhibited the proliferation of LUAD cells and enhanced apoptosis and inhibited metastasis in LUAD cells suppressed. A549 xenografts revealed that OTUD6B deletion can slow down tumour growth. Additionally, OTUD6B can bind to RIPK1, reduce its ubiquitination level and increase its protein stability. CONCLUSIONS Our results suggest that OTUD6B is a promising clinical target for LUAD treatment and that targeting OTUD6B may constitute an effective anti-LUAD strategy.
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Affiliation(s)
- Miaomiao Yang
- Department of Nephrology, Henan Provincial Key Laboratory of Kidney Disease and Immunology, Henan Provincial Clinical Research Center for Kidney Disease, Henan Provincial People's Hospital and People's Hospital of Zhengzhou University, 7 Weiwu Road, Zhengzhou, 450053, Henan, China.
| | - Yujie Wei
- National Engineering Laboratory for Internet Medical Systems and Applications, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, No. 1 Jianshe Road, Erqi District, Zhengzhou, 450052, Henan, China
| | - Xin He
- Department of Clinical Laboratory, The Fifth Affiliated Hospital of Zhengzhou University, No.3 Kangfuqian Street, Erqi District, Zhengzhou, China
| | - Changwei Xia
- Heart Center of Henan Provincial People's Hospital, Central China Fuwai Hospital of Zhengzhou University, Fuwai Central China Cardiovascular Hospital and Central China Branch of National Center Fuwai Cardiovascular Diseases, Zhengzhou, China.
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13
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Liu Y, Tang B, Wang H, Lu M. Otud6b induces pulmonary arterial hypertension by mediating the Calpain-1/HIF-1α signaling pathway. Cell Mol Life Sci 2024; 81:258. [PMID: 38878112 PMCID: PMC11335297 DOI: 10.1007/s00018-024-05291-3] [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: 01/18/2024] [Revised: 05/20/2024] [Accepted: 05/24/2024] [Indexed: 06/29/2024]
Abstract
Pulmonary hypertension (PAH) is a cardiopulmonary disease in which pulmonary artery pressure continues to rise, leading to right heart failure and death. Otud6b is a member of the ubiquitin family and is involved in cell proliferation, apoptosis and inflammation. The aim of this study was to understand the role and mechanism of Otud6b in PAH. C57BL/6 and Calpain-1 knockout (KO) mice were exposed to a PAH model induced by 10% oxygen. Human pulmonary artery endothelial cells (HPACEs) and human pulmonary artery smooth muscle cells (HPASMCs) were exposed to 3% oxygen to establish an in vitro model. Proteomics was used to determine the role of Otud6b and its relationship to Calpain-1/HIF-1α signaling. The increased expression of Otud6b is associated with the progression of PAH. ROtud6b activates Otud6b, induces HIF-1α activation, increases the production of ET-1 and VEGF, and further aggravates endothelial injury. Reducing Otud6b expression by tracheal infusion of siOtud6b has the opposite effect, improving hemodynamic and cardiac response to PAH, reducing the release of Calpain-1 and HIF-1α, and eliminating the pro-inflammatory and apoptotic effects of Otud6b. At the same time, we also found that blocking Calpain-1 reduced the effect of Otud6b on HIF-1α, and inhibiting HIF-1α reduced the expression of Calpain-1 and Otud6b. Our study shows that increased Otud6b expression during hypoxia promotes the development of PAH models through a positive feedback loop between HIF-1α and Calpain-1. Therefore, we use Otud6b as a biomarker of PAH severity, and regulating Otud6b expression may be an effective target for the treatment of PAH.
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MESH Headings
- Animals
- Humans
- Male
- Mice
- Calpain/metabolism
- Calpain/genetics
- Disease Models, Animal
- Endopeptidases/metabolism
- Endopeptidases/genetics
- Endothelial Cells/metabolism
- Hypertension, Pulmonary/metabolism
- Hypertension, Pulmonary/pathology
- Hypertension, Pulmonary/genetics
- Hypoxia-Inducible Factor 1, alpha Subunit/metabolism
- Hypoxia-Inducible Factor 1, alpha Subunit/genetics
- Mice, Inbred C57BL
- Mice, Knockout
- Myocytes, Smooth Muscle/metabolism
- Myocytes, Smooth Muscle/pathology
- Pulmonary Arterial Hypertension/metabolism
- Pulmonary Arterial Hypertension/pathology
- Pulmonary Arterial Hypertension/genetics
- Pulmonary Artery/metabolism
- Pulmonary Artery/pathology
- Signal Transduction
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Affiliation(s)
- Yu Liu
- Key Laboratory of Cardiovascular and Cerebrovascular Drug Research of Liaoning Province, Jinzhou Medical University, Jinzhou, China
- School of Pharmacy, Harbin Medical University, Harbin, China
| | - Bailin Tang
- Key Laboratory of Cardiovascular and Cerebrovascular Drug Research of Liaoning Province, Jinzhou Medical University, Jinzhou, China
- Tongji Medical College of Basic Sciences, Huazhong University of Science and Technology, Wuhan, China
| | - Hongxin Wang
- Key Laboratory of Cardiovascular and Cerebrovascular Drug Research of Liaoning Province, Jinzhou Medical University, Jinzhou, China
| | - Meili Lu
- Key Laboratory of Cardiovascular and Cerebrovascular Drug Research of Liaoning Province, Jinzhou Medical University, Jinzhou, China.
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14
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Xu F, Chen H, Zhou C, Zang T, Wang R, Shen S, Li C, Yu Y, Pei Z, Shen L, Qian J, Ge J. Targeting deubiquitinase OTUB1 protects vascular smooth muscle cells in atherosclerosis by modulating PDGFRβ. Front Med 2024; 18:465-483. [PMID: 38644399 DOI: 10.1007/s11684-024-1056-8] [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: 07/20/2023] [Accepted: 12/04/2023] [Indexed: 04/23/2024]
Abstract
Atherosclerosis is a chronic artery disease that causes various types of cardiovascular dysfunction. Vascular smooth muscle cells (VSMCs), the main components of atherosclerotic plaque, switch from contractile to synthetic phenotypes during atherogenesis. Ubiquitylation is crucial in regulating VSMC phenotypes in atherosclerosis, and it can be reversely regulated by deubiquitinases. However, the specific effects of deubiquitinases on atherosclerosis have not been thoroughly elucidated. In this study, RNAi screening in human aortic smooth muscle cells was performed to explore the effects of OTU family deubiquitinases, which revealed that silencing OTUB1 inhibited PDGF-BB-stimulated VSMC phenotype switch. Further in vivo studies using Apoe-/- mice revealed that knockdown of OTUB1 in VSMCs alleviated atherosclerosis plaque burden in the advanced stage and led to a stable plaque phenotype. Moreover, VSMC proliferation and migration upon PDGF-BB stimulation could be inhibited by silencing OTUB1 in vitro. Unbiased RNA-sequencing data indicated that knocking down OTUB1 influenced VSMC differentiation, adhesion, and proliferation. Mass spectrometry of ubiquitinated protein confirmed that proteins related to cell growth and migration were differentially ubiquitylated. Mechanistically, we found that OTUB1 recognized the K707 residue ubiquitylation of PDGFRβ with its catalytic triad, thereby reducing the K48-linked ubiquitylation of PDGFRβ. Inhibiting OTUB1 in VSMCs could promote PDGFRβ degradation via the ubiquitin-proteasome pathway, so it was beneficial in preventing VSMCs' phenotype switch. These findings revealed that knocking down OTUB1 ameliorated VSMCs' phenotype switch and atherosclerosis progression, indicating that OTUB1 could be a valuable translational therapeutic target in the future.
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Affiliation(s)
- Fei Xu
- Department of Cardiology and Laboratory of Heart Valve Disease, West China Hospital, Sichuan University, Chengdu, 610041, China
- Department of Cardiology, Zhongshan Hospital, Fudan University, Research Unit of Cardiovascular Techniques and Devices, Chinese Academy of Medical Sciences, Shanghai, 200032, China
- Shanghai Institute of Cardiovascular Diseases, Shanghai, 200032, China
- National Clinical Research Center for Interventional Medicine & Shanghai Clinical Research Center for Interventional Medicine (19MC1910300), Shanghai, 200032, China
| | - Han Chen
- Department of Cardiology, Zhongshan Hospital, Fudan University, Research Unit of Cardiovascular Techniques and Devices, Chinese Academy of Medical Sciences, Shanghai, 200032, China
- Shanghai Institute of Cardiovascular Diseases, Shanghai, 200032, China
- National Clinical Research Center for Interventional Medicine & Shanghai Clinical Research Center for Interventional Medicine (19MC1910300), Shanghai, 200032, China
| | - Changyi Zhou
- Department of Cardiology, Zhongshan Hospital, Fudan University, Research Unit of Cardiovascular Techniques and Devices, Chinese Academy of Medical Sciences, Shanghai, 200032, China
- Shanghai Institute of Cardiovascular Diseases, Shanghai, 200032, China
- National Clinical Research Center for Interventional Medicine & Shanghai Clinical Research Center for Interventional Medicine (19MC1910300), Shanghai, 200032, China
| | - Tongtong Zang
- Department of Cardiology, Zhongshan Hospital, Fudan University, Research Unit of Cardiovascular Techniques and Devices, Chinese Academy of Medical Sciences, Shanghai, 200032, China
- Shanghai Institute of Cardiovascular Diseases, Shanghai, 200032, China
- National Clinical Research Center for Interventional Medicine & Shanghai Clinical Research Center for Interventional Medicine (19MC1910300), Shanghai, 200032, China
| | - Rui Wang
- Department of Cardiology, Zhongshan Hospital, Fudan University, Research Unit of Cardiovascular Techniques and Devices, Chinese Academy of Medical Sciences, Shanghai, 200032, China
- Shanghai Institute of Cardiovascular Diseases, Shanghai, 200032, China
- National Clinical Research Center for Interventional Medicine & Shanghai Clinical Research Center for Interventional Medicine (19MC1910300), Shanghai, 200032, China
| | - Shutong Shen
- Department of Cardiology, Zhongshan Hospital, Fudan University, Research Unit of Cardiovascular Techniques and Devices, Chinese Academy of Medical Sciences, Shanghai, 200032, China
- Shanghai Institute of Cardiovascular Diseases, Shanghai, 200032, China
- National Clinical Research Center for Interventional Medicine & Shanghai Clinical Research Center for Interventional Medicine (19MC1910300), Shanghai, 200032, China
| | - Chaofu Li
- Department of Cardiology, Zhongshan Hospital, Fudan University, Research Unit of Cardiovascular Techniques and Devices, Chinese Academy of Medical Sciences, Shanghai, 200032, China
- Shanghai Institute of Cardiovascular Diseases, Shanghai, 200032, China
- National Clinical Research Center for Interventional Medicine & Shanghai Clinical Research Center for Interventional Medicine (19MC1910300), Shanghai, 200032, China
| | - Yue Yu
- Department of Cardiology, Zhongshan Hospital, Fudan University, Research Unit of Cardiovascular Techniques and Devices, Chinese Academy of Medical Sciences, Shanghai, 200032, China
- Shanghai Institute of Cardiovascular Diseases, Shanghai, 200032, China
- National Clinical Research Center for Interventional Medicine & Shanghai Clinical Research Center for Interventional Medicine (19MC1910300), Shanghai, 200032, China
| | - Zhiqiang Pei
- Department of Cardiology, Zhongshan Hospital, Fudan University, Research Unit of Cardiovascular Techniques and Devices, Chinese Academy of Medical Sciences, Shanghai, 200032, China
- Shanghai Institute of Cardiovascular Diseases, Shanghai, 200032, China
- National Clinical Research Center for Interventional Medicine & Shanghai Clinical Research Center for Interventional Medicine (19MC1910300), Shanghai, 200032, China
| | - Li Shen
- Department of Cardiology, Zhongshan Hospital, Fudan University, Research Unit of Cardiovascular Techniques and Devices, Chinese Academy of Medical Sciences, Shanghai, 200032, China.
- Shanghai Institute of Cardiovascular Diseases, Shanghai, 200032, China.
- National Clinical Research Center for Interventional Medicine & Shanghai Clinical Research Center for Interventional Medicine (19MC1910300), Shanghai, 200032, China.
| | - Juying Qian
- Department of Cardiology, Zhongshan Hospital, Fudan University, Research Unit of Cardiovascular Techniques and Devices, Chinese Academy of Medical Sciences, Shanghai, 200032, China.
- Shanghai Institute of Cardiovascular Diseases, Shanghai, 200032, China.
- National Clinical Research Center for Interventional Medicine & Shanghai Clinical Research Center for Interventional Medicine (19MC1910300), Shanghai, 200032, China.
| | - Junbo Ge
- Department of Cardiology, Zhongshan Hospital, Fudan University, Research Unit of Cardiovascular Techniques and Devices, Chinese Academy of Medical Sciences, Shanghai, 200032, China.
- Shanghai Institute of Cardiovascular Diseases, Shanghai, 200032, China.
- National Clinical Research Center for Interventional Medicine & Shanghai Clinical Research Center for Interventional Medicine (19MC1910300), Shanghai, 200032, China.
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15
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Liu Y, Yuan J, Zhang Y, Qin F, Bai X, Sun W, Chen T, Liu F, Zheng Y, Qi X, Zhao W, Liu B, Gao C. OTUD5 promotes the inflammatory immune response by enhancing MyD88 oligomerization and Myddosome formation. Cell Death Differ 2024; 31:753-767. [PMID: 38605168 PMCID: PMC11164869 DOI: 10.1038/s41418-024-01293-7] [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: 12/24/2023] [Revised: 03/23/2024] [Accepted: 04/02/2024] [Indexed: 04/13/2024] Open
Abstract
Myddosome is an oligomeric complex required for the transmission of inflammatory signals from TLR/IL1Rs and consists of MyD88 and IRAK family kinases. However, the molecular basis for the self-assemble of Myddosome proteins and regulation of intracellular signaling remains poorly understood. Here, we identify OTUD5 acts as an essential regulator for MyD88 oligomerization and Myddosome formation. OTUD5 directly interacts with MyD88 and cleaves its K11-linked polyubiquitin chains at Lys95, Lys231 and Lys250. This polyubiquitin cleavage enhances MyD88 oligomerization after LPS stimulation, which subsequently promotes the recruitment of downstream IRAK4 and IRAK2 to form Myddosome and the activation of NF-κB and MAPK signaling and production of inflammatory cytokines. Consistently, Otud5-deficient mice are less susceptible to LPS- and CLP-induced sepsis. Taken together, our findings reveal a positive regulatory role of OTUD5 in MyD88 oligomerization and Myddosome formation, which provides new sights into the treatment of inflammatory diseases.
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Affiliation(s)
- Yaxing Liu
- Key Laboratory of Infection and Immunity of Shandong Province & Key Laboratory for Experimental Teratology of Ministry of Education, Shandong University, Jinan, Shandong, 250012, P.R. China
- Department of Immunology, School of Basic Medical Sciences, Shandong University, Jinan, Shandong, 250012, P.R. China
| | - Jiahua Yuan
- Key Laboratory of Infection and Immunity of Shandong Province & Key Laboratory for Experimental Teratology of Ministry of Education, Shandong University, Jinan, Shandong, 250012, P.R. China
- Department of Immunology, School of Basic Medical Sciences, Shandong University, Jinan, Shandong, 250012, P.R. China
| | - Yuling Zhang
- Key Laboratory of Infection and Immunity of Shandong Province & Key Laboratory for Experimental Teratology of Ministry of Education, Shandong University, Jinan, Shandong, 250012, P.R. China
- Department of Immunology, School of Basic Medical Sciences, Shandong University, Jinan, Shandong, 250012, P.R. China
| | - Fei Qin
- Key Laboratory of Infection and Immunity of Shandong Province & Key Laboratory for Experimental Teratology of Ministry of Education, Shandong University, Jinan, Shandong, 250012, P.R. China
- Department of Immunology, School of Basic Medical Sciences, Shandong University, Jinan, Shandong, 250012, P.R. China
| | - Xuemei Bai
- Key Laboratory of Infection and Immunity of Shandong Province & Key Laboratory for Experimental Teratology of Ministry of Education, Shandong University, Jinan, Shandong, 250012, P.R. China
- Department of Immunology, School of Basic Medical Sciences, Shandong University, Jinan, Shandong, 250012, P.R. China
| | - Wanwei Sun
- Key Laboratory of Infection and Immunity of Shandong Province & Key Laboratory for Experimental Teratology of Ministry of Education, Shandong University, Jinan, Shandong, 250012, P.R. China
- Department of Immunology, School of Basic Medical Sciences, Shandong University, Jinan, Shandong, 250012, P.R. China
| | - Tian Chen
- Key Laboratory of Infection and Immunity of Shandong Province & Key Laboratory for Experimental Teratology of Ministry of Education, Shandong University, Jinan, Shandong, 250012, P.R. China
- Department of Pathogenic Biology, School of Basic Medical Sciences, Shandong University, Jinan, Shandong, 250012, P. R. China
| | - Feng Liu
- Key Laboratory of Infection and Immunity of Shandong Province & Key Laboratory for Experimental Teratology of Ministry of Education, Shandong University, Jinan, Shandong, 250012, P.R. China
- Department of Immunology, School of Basic Medical Sciences, Shandong University, Jinan, Shandong, 250012, P.R. China
| | - Yi Zheng
- Key Laboratory of Infection and Immunity of Shandong Province & Key Laboratory for Experimental Teratology of Ministry of Education, Shandong University, Jinan, Shandong, 250012, P.R. China
- Department of Immunology, School of Basic Medical Sciences, Shandong University, Jinan, Shandong, 250012, P.R. China
| | - Xiaopeng Qi
- Advanced Medical Research Institute, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, P. R. China
| | - Wei Zhao
- Key Laboratory of Infection and Immunity of Shandong Province & Key Laboratory for Experimental Teratology of Ministry of Education, Shandong University, Jinan, Shandong, 250012, P.R. China
- Department of Pathogenic Biology, School of Basic Medical Sciences, Shandong University, Jinan, Shandong, 250012, P. R. China
| | - Bingyu Liu
- Key Laboratory of Infection and Immunity of Shandong Province & Key Laboratory for Experimental Teratology of Ministry of Education, Shandong University, Jinan, Shandong, 250012, P.R. China.
- Department of Immunology, School of Basic Medical Sciences, Shandong University, Jinan, Shandong, 250012, P.R. China.
| | - Chengjiang Gao
- Key Laboratory of Infection and Immunity of Shandong Province & Key Laboratory for Experimental Teratology of Ministry of Education, Shandong University, Jinan, Shandong, 250012, P.R. China.
- Department of Immunology, School of Basic Medical Sciences, Shandong University, Jinan, Shandong, 250012, P.R. China.
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16
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Majumder S, Srivastava M, Alam P, Saha S, Kumari R, Chand AK, Asthana S, Sen S, Maiti TK. Hotspot site microenvironment in the deubiquitinase OTUB1 drives its stability and aggregation. J Biol Chem 2024; 300:107315. [PMID: 38663827 PMCID: PMC11154711 DOI: 10.1016/j.jbc.2024.107315] [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: 01/27/2024] [Revised: 03/30/2024] [Accepted: 04/15/2024] [Indexed: 05/30/2024] Open
Abstract
Lewy bodies (LB) are aberrant protein accumulations observed in the brain cells of individuals affected by Parkinson's disease (PD). A comprehensive analysis of LB proteome identified over a hundred proteins, many co-enriched with α-synuclein, a major constituent of LB. Within this context, OTUB1, a deubiquitinase detected in LB, exhibits amyloidogenic properties, yet the mechanisms underlying its aggregation remain elusive. In this study, we identify two critical sites in OTUB1-namely, positions 133 and 173-that significantly impact its amyloid aggregation. Substituting alanine at position 133 and lysine at position 173 enhances both thermodynamic and kinetic stability, effectively preventing amyloid aggregation. Remarkably, lysine at position 173 demonstrates the highest stability without compromising enzymatic activity. The increased stability and inhibition of amyloid aggregation are attributed mainly to the changes in the specific microenvironment at the hotspot. In our exploration of the in-vivo co-occurrence of α-synuclein and OTUB1 in LB, we observed a synergistic modulation of each other's aggregation. Collectively, our study unveils the molecular determinants influencing OTUB1 aggregation, shedding light on the role of specific residues in modulating aggregation kinetics and structural transition. These findings contribute valuable insights into the complex interplay of amino acid properties and protein aggregation, with potential implications for understanding broader aspects of protein folding and aggregation phenomena.
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Affiliation(s)
- Sushanta Majumder
- Functional Proteomics Laboratory, Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad, India
| | - Mitul Srivastava
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, India
| | - Parvez Alam
- Spectroscopy Laboratory, School of Physical Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Sandhini Saha
- Functional Proteomics Laboratory, Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad, India
| | - Raniki Kumari
- Functional Proteomics Laboratory, Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad, India
| | - Ajay Kumar Chand
- Spectroscopy Laboratory, School of Physical Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Shailendra Asthana
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, India
| | - Sobhan Sen
- Spectroscopy Laboratory, School of Physical Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Tushar Kanti Maiti
- Functional Proteomics Laboratory, Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad, India.
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Ma K, Xian W, Liu H, Shu R, Ge J, Luo ZQ, Liu X, Qiu J. Bacterial ubiquitin ligases hijack the host deubiquitinase OTUB1 to inhibit MTORC1 signaling and promote autophagy. Autophagy 2024:1-16. [PMID: 38818749 DOI: 10.1080/15548627.2024.2353492] [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: 09/05/2023] [Accepted: 05/05/2024] [Indexed: 06/01/2024] Open
Abstract
Many bacterial pathogens have evolved effective strategies to interfere with the ubiquitination network to evade clearance by the innate immune system. Here, we report that OTUB1, one of the most abundant deubiquitinases (DUBs) in mammalian cells, is subjected to both canonical and noncanonical ubiquitination during Legionella pneumophila infection. The effectors SidC and SdcA catalyze OTUB1 ubiquitination at multiple lysine residues, resulting in its association with a Legionella-containing vacuole. Lysine ubiquitination by SidC and SdcA promotes interactions between OTUB1 and DEPTOR, an inhibitor of the MTORC1 pathway, thus suppressing MTORC1 signaling. The inhibition of MTORC1 leads to suppression of host protein synthesis and promotion of host macroautophagy/autophagy during L. pneumophila infection. In addition, members of the SidE family effectors (SidEs) induce phosphoribosyl (PR)-linked ubiquitination of OTUB1 at Ser16 and Ser18 and block its DUB activity. The levels of the lysine and serine ubiquitination of OTUB1 are further regulated by effectors that function to antagonize the activities of SidC, SdcA and SidEs, including Lem27, DupA, DupB, SidJ and SdjA. Our study reveals an effectors-mediated complicated mechanism in regulating the activity of a host DUB.Abbreviations: BafA1: bafilomycin A1; BMDMs: bone marrow-derived macrophages; DUB: deubiquitinase; Dot/Icm: defective for organelle trafficking/intracellular multiplication; DEPTOR: DEP domain containing MTOR interacting protein; GAPDH: glyceraldehyde-3-phosphate dehydrogenase; L. pneumophila: Legionella pneumophila; LCV: Legionella-containing vacuole; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; MOI: multiplicity of infection; MTORC1: mechanistic target of rapamycin kinase complex 1; OTUB1: OTU deubiquitinase, ubiquitin aldehyde binding 1; PR-Ub: phosphoribosyl (PR)-linked ubiquitin; PTM: posttranslational modification; SDS-PAGE: sodium dodecyl sulfate-polyacrylamide gel electrophoresis; SidEs: SidE family effectors; Ub: ubiquitin.
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Affiliation(s)
- Kelong Ma
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, College of Veterinary Medicine, Jilin University, Center for Pathogen Biology and Infectious Diseases, The First Hospital of Jilin University, Changchun, China
| | - Wei Xian
- Department of Microbiology and Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Hongtao Liu
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, College of Veterinary Medicine, Jilin University, Center for Pathogen Biology and Infectious Diseases, The First Hospital of Jilin University, Changchun, China
| | - Rundong Shu
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, College of Veterinary Medicine, Jilin University, Center for Pathogen Biology and Infectious Diseases, The First Hospital of Jilin University, Changchun, China
| | - Jinli Ge
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, College of Veterinary Medicine, Jilin University, Center for Pathogen Biology and Infectious Diseases, The First Hospital of Jilin University, Changchun, China
| | - Zhao-Qing Luo
- Purdue Institute for Inflammation, Immunology and Infectious Disease and Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Xiaoyun Liu
- Department of Microbiology and Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
- NHC Key Laboratory of Medical Immunology, Peking University, Beijing, China
| | - Jiazhang Qiu
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, College of Veterinary Medicine, Jilin University, Center for Pathogen Biology and Infectious Diseases, The First Hospital of Jilin University, Changchun, China
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18
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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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19
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Kim HJ, Choi Y, Lee Y, Hwangbo M, Kim J. OTUD6A orchestrates complex modulation of TEAD4-mediated transcriptional programs. FEBS Lett 2024; 598:1045-1060. [PMID: 38594215 DOI: 10.1002/1873-3468.14861] [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: 01/04/2024] [Revised: 02/28/2024] [Accepted: 03/02/2024] [Indexed: 04/11/2024]
Abstract
TEAD transcription factors play a central role in the Hippo signaling pathway. In this study, we focused on transcriptional enhancer factor TEF-3 (TEAD4), exploring its regulation by the deubiquitinase OTU domain-containing protein 6A (OTUD6A). We identified OTUD6A as a TEAD4-interacting deubiquitinase, positively influencing TEAD-driven transcription without altering TEAD4 stability. Structural analyses revealed specific interaction domains: the N-terminal domain of OTUD6A and the YAP-binding domain of TEAD4. Functional assays demonstrated the positive impact of OTUD6A on the transcription of YAP-TEAD target genes. Despite no impact on TEAD4 nuclear localization, OTUD6A selectively modulated nuclear interactions, enhancing YAP-TEAD4 complex formation while suppressing VGLL4 (transcription cofactor vestigial-like protein 4)-TEAD4 interaction. Critically, OTUD6A facilitated YAP-TEAD4 complex binding to target gene promoters. Our study unveils the regulatory landscape of OTUD6A on TEAD4, providing insights into diseases regulated by YAP-TEAD complexes.
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Affiliation(s)
- Hyo Jin Kim
- Department of Life Sciences, Sogang University, Seoul, Korea
| | - Yunsik Choi
- Department of Life Sciences, Sogang University, Seoul, Korea
| | - Yuri Lee
- Department of Life Sciences, Sogang University, Seoul, Korea
| | - Mi Hwangbo
- Department of Life Sciences, Sogang University, Seoul, Korea
| | - Jongchan Kim
- Department of Life Sciences, Sogang University, Seoul, Korea
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20
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Chen Y, Xue H, Jin J. Applications of protein ubiquitylation and deubiquitylation in drug discovery. J Biol Chem 2024; 300:107264. [PMID: 38582446 PMCID: PMC11087986 DOI: 10.1016/j.jbc.2024.107264] [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: 07/09/2023] [Revised: 03/29/2024] [Accepted: 04/01/2024] [Indexed: 04/08/2024] Open
Abstract
The ubiquitin (Ub)-proteasome system (UPS) is the major machinery mediating specific protein turnover in eukaryotic cells. By ubiquitylating unwanted, damaged, or harmful proteins and driving their degradation, UPS is involved in many important cellular processes. Several new UPS-based technologies, including molecular glue degraders and PROTACs (proteolysis-targeting chimeras) to promote protein degradation, and DUBTACs (deubiquitinase-targeting chimeras) to increase protein stability, have been developed. By specifically inducing the interactions between different Ub ligases and targeted proteins that are not otherwise related, molecular glue degraders and PROTACs degrade targeted proteins via the UPS; in contrast, by inducing the proximity of targeted proteins to deubiquitinases, DUBTACs are created to clear degradable poly-Ub chains to stabilize targeted proteins. In this review, we summarize the recent research progress in molecular glue degraders, PROTACs, and DUBTACs and their applications. We discuss immunomodulatory drugs, sulfonamides, cyclin-dependent kinase-targeting molecular glue degraders, and new development of PROTACs. We also introduce the principle of DUBTAC and its applications. Finally, we propose a few future directions of these three technologies related to targeted protein homeostasis.
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Affiliation(s)
- Yilin Chen
- Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Haoan Xue
- Life Sciences Institute, Zhejiang University, Hangzhou, China; Center for Life Sciences, Shaoxing Institute, Zhejiang University, Shaoxing, China
| | - Jianping Jin
- Life Sciences Institute, Zhejiang University, Hangzhou, China; Center for Life Sciences, Shaoxing Institute, Zhejiang University, Shaoxing, China; Cancer Center, Zhejiang University, Hangzhou, China.
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21
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Kong L, Jin X. Dysregulation of deubiquitination in breast cancer. Gene 2024; 902:148175. [PMID: 38242375 DOI: 10.1016/j.gene.2024.148175] [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: 10/25/2023] [Revised: 12/04/2023] [Accepted: 01/16/2024] [Indexed: 01/21/2024]
Abstract
Breast cancer (BC) is a highly frequent malignant tumor that poses a serious threat to women's health and has different molecular subtypes, histological subtypes, and biological features, which act by activating oncogenic factors and suppressing cancer inhibitors. The ubiquitin-proteasome system (UPS) is the main process contributing to protein degradation, and deubiquitinases (DUBs) are reverse enzymes that counteract this process. There is growing evidence that dysregulation of DUBs is involved in the occurrence of BC. Herein, we review recent research findings in BC-associated DUBs, describe their nature, classification, and functions, and discuss the potential mechanisms of DUB-related dysregulation in BC. Furthermore, we present the successful treatment of malignant cancer with DUB inhibitors, as well as analyzing the status of targeting aberrant DUBs in BC.
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Affiliation(s)
- Lili Kong
- Department of Biochemistry and Molecular Biology, Zhejiang Key Laboratory of Pathophysiology, Health Science Center, Ningbo 315211, Zhejiang, China
| | - Xiaofeng Jin
- Department of Biochemistry and Molecular Biology, Zhejiang Key Laboratory of Pathophysiology, Health Science Center, Ningbo 315211, Zhejiang, China.
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22
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Song X, Xia B, Gao X, Liu X, Lv H, Wang S, Xiao Q, Luo H. Related cellular signaling and consequent pathophysiological outcomes of ubiquitin specific protease 24. Life Sci 2024; 342:122512. [PMID: 38395384 DOI: 10.1016/j.lfs.2024.122512] [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: 11/25/2023] [Revised: 02/17/2024] [Accepted: 02/18/2024] [Indexed: 02/25/2024]
Abstract
Ubiquitin-specific protease 24 (USP24) is an essential member of the deubiquitinating protease family found in eukaryotes. It engages in interactions with multiple proteins, including p53, MCL-1, E2F4, and FTH1, among others. Through these interactions, USP24 plays a critical role in regulating vital cellular processes such as cell cycle control, DNA damage response, cellular iron autophagy, and apoptosis. Increased levels of USP24 have been observed in various cancer types, including bladder cancer, lung cancer, myeloma, hepatocellular carcinoma, and gastric cancer. However, in certain tumors like kidney cancer, USP24 is significantly downregulated, and the specific mechanism behind this remains unclear. Currently, there are no officially approved USP24 inhibitors available for clinical use. Some existing inhibitors targeting USP24 have shown promising effects in treating malignancies; however, their precise mode of action and information regarding binding sites are not well understood. Moreover, further optimization is required to enhance the selectivity and efficacy of these inhibitors. This review aims to provide a comprehensive overview of recent advancements in understanding the cellular functions of USP24, its association with various diseases, and the development of small-molecule inhibitors that target this protein. In conclusion, USP24 represents a promising therapeutic target for various diseases, and ongoing research will contribute to validating its role and facilitating the development of effective treatments.
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Affiliation(s)
- Xiaoyang Song
- School of Basic Medical Sciences, Shandong Second Medical University, Weifang 261053, China
| | - Boyu Xia
- School of Basic Medical Sciences, Shandong Second Medical University, Weifang 261053, China
| | - Xinrong Gao
- School of Basic Medical Sciences, Shandong Second Medical University, Weifang 261053, China
| | - Xinying Liu
- School of Basic Medical Sciences, Shandong Second Medical University, Weifang 261053, China
| | - Hongyuan Lv
- School of Basic Medical Sciences, Shandong Second Medical University, Weifang 261053, China
| | - Shiwei Wang
- School of Basic Medical Sciences, Shandong Second Medical University, Weifang 261053, China
| | - Qinpei Xiao
- School of Basic Medical Sciences, Shandong Second Medical University, Weifang 261053, China
| | - Hao Luo
- School of Basic Medical Sciences, Shandong Second Medical University, Weifang 261053, China.
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23
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Cai H, Wu X, Mao J, Tong Z, Yan D, Weng Y, Zheng Q. Sequential release of interacting proteins and Ub-modifying enzymes by disulfide heterotypic ubiquitin reagents. Bioorg Chem 2024; 145:107186. [PMID: 38387394 DOI: 10.1016/j.bioorg.2024.107186] [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: 09/30/2023] [Revised: 01/31/2024] [Accepted: 02/06/2024] [Indexed: 02/24/2024]
Abstract
Heterotypic ubiquitin (Ub) chains have emerged as fundamental components in a wide range of cellular processes. The integrative identification of Ub-interacting proteins (readers) and Ub-modifying enzymes (writers and erasers) that selectively recognize and regulate heterotypic ubiquitination may provide crucial insights into these processes. In this study, we employed the bifunctional molecule-assisted (CAET) strategy to develop a type of disulfide bond-activated heterotypic Ub reagents, which allowed to enrich heterotypic Ub-interacting proteins and modifying enzymes simultaneously. The sequential release of readers which are non-covalently bound and writers or erasers which are covalently conjugated by using urea and reductant, respectively, combined with label-free quantitative (LFQ) MS indicated that these heterotypic Ub reagents would facilitate future investigations into functional roles played by heterotypic Ub chains.
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Affiliation(s)
- Hongyi Cai
- Institute of Translational Medicine, National Center for Translational Medicine (Shanghai), Shanghai Jiao Tong University, Shanghai 200240, China; Tsinghua-Peking Joint Center for Life Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Xiangwei Wu
- Tsinghua-Peking Joint Center for Life Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Junxiong Mao
- Institute of Translational Medicine, National Center for Translational Medicine (Shanghai), Shanghai Jiao Tong University, Shanghai 200240, China; Tsinghua-Peking Joint Center for Life Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Zebin Tong
- Institute of Translational Medicine, National Center for Translational Medicine (Shanghai), Shanghai Jiao Tong University, Shanghai 200240, China
| | - Dingfei Yan
- MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, 100084 Beijing, China
| | - Yicheng Weng
- Institute of Translational Medicine, National Center for Translational Medicine (Shanghai), Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Qingyun Zheng
- Institute of Translational Medicine, National Center for Translational Medicine (Shanghai), Shanghai Jiao Tong University, Shanghai 200240, China.
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24
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Ci M, Zhao G, Li C, Liu R, Hu X, Pan J, Shen Y, Zhang G, Li Y, Zhang L, Liang P, Cui H. OTUD4 promotes the progression of glioblastoma by deubiquitinating CDK1 and activating MAPK signaling pathway. Cell Death Dis 2024; 15:179. [PMID: 38429268 PMCID: PMC10907623 DOI: 10.1038/s41419-024-06569-x] [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: 07/15/2023] [Revised: 02/15/2024] [Accepted: 02/21/2024] [Indexed: 03/03/2024]
Abstract
Glioblastoma, IDH-Wild type (GBM, CNS WHO Grade 4) is a highly heterogeneous and aggressive primary malignant brain tumor with high morbidity, high mortality, and poor patient prognosis. The global burden of GBM is increasing notably due to limited treatment options, drug delivery problems, and the lack of characteristic molecular targets. OTU deubiquitinase 4 (OTUD4) is a potential predictive factor for several cancers such as breast cancer, liver cancer, and lung cancer. However, its function in GBM remains unknown. In this study, we found that high expression of OTUD4 is positively associated with poor prognosis in GBM patients. Moreover, we provided in vitro and in vivo evidence that OTUD4 promotes the proliferation and invasion of GBM cells. Mechanism studies showed that, on the one hand, OTUD4 directly interacts with cyclin-dependent kinase 1 (CDK1) and stabilizes CDK1 by removing its K11, K29, and K33-linked polyubiquitination. On the other hand, OTUD4 binds to fibroblast growth factor receptor 1 (FGFR1) and reduces FGFR1's K6 and K27-linked polyubiquitination, thereby indirectly stabilizing CDK1, ultimately influencing the activation of the downstream MAPK signaling pathway. Collectively, our results revealed that OTUD4 promotes GBM progression via OTUD4-CDK1-MAPK axis, and may be a prospective therapeutic target for GBM treatment.
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Affiliation(s)
- Mingxin Ci
- State Key Laboratory of Resource Insects, Medical Research Institute, Southwest University, Chongqing, 400715, China
- Jinfeng Laboratory, Chongqing, 401329, China
| | - Gaichao Zhao
- State Key Laboratory of Resource Insects, Medical Research Institute, Southwest University, Chongqing, 400715, China
- Jinfeng Laboratory, Chongqing, 401329, China
| | - Chongyang Li
- State Key Laboratory of Resource Insects, Medical Research Institute, Southwest University, Chongqing, 400715, China
- Jinfeng Laboratory, Chongqing, 401329, China
| | - Ruochen Liu
- State Key Laboratory of Resource Insects, Medical Research Institute, Southwest University, Chongqing, 400715, China
- Jinfeng Laboratory, Chongqing, 401329, China
| | - Xiaosong Hu
- State Key Laboratory of Resource Insects, Medical Research Institute, Southwest University, Chongqing, 400715, China
- Jinfeng Laboratory, Chongqing, 401329, China
| | - Jun Pan
- State Key Laboratory of Resource Insects, Medical Research Institute, Southwest University, Chongqing, 400715, China
- Jinfeng Laboratory, Chongqing, 401329, China
| | - Yang Shen
- State Key Laboratory of Resource Insects, Medical Research Institute, Southwest University, Chongqing, 400715, China
- Jinfeng Laboratory, Chongqing, 401329, China
| | - Guanghui Zhang
- State Key Laboratory of Resource Insects, Medical Research Institute, Southwest University, Chongqing, 400715, China
- Jinfeng Laboratory, Chongqing, 401329, China
| | - Yongsen Li
- State Key Laboratory of Resource Insects, Medical Research Institute, Southwest University, Chongqing, 400715, China
- Jinfeng Laboratory, Chongqing, 401329, China
| | - Li Zhang
- Department of Radiology and Nuclear Medicine, The First Hospital of HeBei Medical University, Hebei, 050000, China.
| | - Ping Liang
- Department of Neurosurgery, Children's Hospital of Chongqing Medical University, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing, 400014, China.
| | - Hongjuan Cui
- State Key Laboratory of Resource Insects, Medical Research Institute, Southwest University, Chongqing, 400715, China.
- Jinfeng Laboratory, Chongqing, 401329, China.
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25
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Wang Q, Liang S, Qian J, Xu J, Zheng Q, Wang M, Guo X, Min J, Wu G, Zhuang Z, Luo W, Liang G. OTUD1 promotes isoprenaline- and myocardial infarction-induced heart failure by targeting PDE5A in cardiomyocytes. Biochim Biophys Acta Mol Basis Dis 2024; 1870:167018. [PMID: 38185350 DOI: 10.1016/j.bbadis.2024.167018] [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: 09/02/2023] [Revised: 12/29/2023] [Accepted: 01/01/2024] [Indexed: 01/09/2024]
Abstract
Heart failure represents a major cause of death worldwide. Recent research has emphasized the potential role of protein ubiquitination/deubiquitination protein modification in cardiac pathology. Here, we investigate the role of the ovarian tumor deubiquitinase 1 (OTUD1) in isoprenaline (ISO)- and myocardial infarction (MI)-induced heart failure and its molecular mechanism. OTUD1 protein levels were raised markedly in murine cardiomyocytes after MI and ISO treatment. OTUD1 deficiency attenuated myocardial hypertrophy and cardiac dysfunction induced by ISO infusion or MI operation. In vitro, OTUD1 knockdown in neonatal rat ventricular myocytes (NRVMs) attenuated ISO-induced injuries, while OTUD1 overexpression aggravated the pathological changes. Mechanistically, LC-MS/MS and Co-IP studies showed that OTUD1 bound directly to the GAF1 and PDEase domains of PDE5A. OTUD1 was found to reverse K48 ubiquitin chain in PDE5A through cysteine at position 320 of OTUD1, preventing its proteasomal degradation. PDE5A could inactivates the cGMP-PKG-SERCA2a signaling axis which dysregulate the calcium handling in cardiomyocytes, and leading to the cardiomyocyte injuries. In conclusion, OTUD1 promotes heart failure by deubiquitinating and stabilizing PDE5A in cardiomyocytes. These findings have identified PDE5A as a new target of OTUD1 and emphasize the potential of OTUD1 as a target for treating heart failure.
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Affiliation(s)
- Qinyan Wang
- The Affiliated Cangnan Hospital and Chemical Biology Research Center, Wenzhou Medical University, Wenzhou 325000, Zhejiang, China; Department of Cardiology and Medical Research Center, The First Affiliated Hospital, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Shiqi Liang
- The Affiliated Cangnan Hospital and Chemical Biology Research Center, Wenzhou Medical University, Wenzhou 325000, Zhejiang, China; Department of Cardiology and Medical Research Center, The First Affiliated Hospital, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Jinfu Qian
- Department of Cardiology and Medical Research Center, The First Affiliated Hospital, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Jiachen Xu
- Department of Cardiology and Medical Research Center, The First Affiliated Hospital, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Qingsong Zheng
- The Affiliated Cangnan Hospital and Chemical Biology Research Center, Wenzhou Medical University, Wenzhou 325000, Zhejiang, China
| | - Mengyang Wang
- Department of Pharmacology, College of Pharmacy, Beihua University, Jilin, Jilin 132013, China
| | - Xiaochen Guo
- The Affiliated Cangnan Hospital and Chemical Biology Research Center, Wenzhou Medical University, Wenzhou 325000, Zhejiang, China
| | - Julian Min
- The Affiliated Cangnan Hospital and Chemical Biology Research Center, Wenzhou Medical University, Wenzhou 325000, Zhejiang, China
| | - Gaojun Wu
- Department of Cardiology and Medical Research Center, The First Affiliated Hospital, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Zaishou Zhuang
- The Affiliated Cangnan Hospital and Chemical Biology Research Center, Wenzhou Medical University, Wenzhou 325000, Zhejiang, China
| | - Wu Luo
- The Affiliated Cangnan Hospital and Chemical Biology Research Center, Wenzhou Medical University, Wenzhou 325000, Zhejiang, China; Department of Cardiology and Medical Research Center, The First Affiliated Hospital, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China.
| | - Guang Liang
- The Affiliated Cangnan Hospital and Chemical Biology Research Center, Wenzhou Medical University, Wenzhou 325000, Zhejiang, China; Department of Cardiology and Medical Research Center, The First Affiliated Hospital, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China; School of Pharmaceutical Sciences, Hangzhou Medical College, Hangzhou, Zhejiang 311399, China.
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26
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Zheng LL, Wang LT, Pang YW, Sun LP, Shi L. Recent advances in the development of deubiquitinases inhibitors as antitumor agents. Eur J Med Chem 2024; 266:116161. [PMID: 38262120 DOI: 10.1016/j.ejmech.2024.116161] [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: 11/01/2023] [Revised: 01/12/2024] [Accepted: 01/16/2024] [Indexed: 01/25/2024]
Abstract
Ubiquitination is a type of post-translational modification that covalently links ubiquitin to a target protein, which plays a critical role in modulating protein activity, stability, and localization. In contrast, this process is reversed by deubiquitinases (DUBs), which remove ubiquitin from ubiquitinated substrates. Dysregulation of DUBs is associated with several human diseases, such as cancer, inflammation, neurodegenerative disorders, and autoimmune diseases. Thus, DUBs have become promising targets for drug development. Although the physiological and pathological effects of DUBs are increasingly well understood, the clinical drug discovery of selective DUB inhibitors has been challenging. Herein, we summarize the structures and functions of main classes of DUBs and discuss the recent progress in developing selective small-molecule DUB inhibitors as antitumor agents.
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Affiliation(s)
- Li-Li Zheng
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 211198, China
| | - Li-Ting Wang
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 211198, China
| | - Ye-Wei Pang
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 211198, China
| | - Li-Ping Sun
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 211198, China.
| | - Lei Shi
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 211198, China.
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27
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Xia J, Yang Y, Chen X, Song K, Ma G, Yang Y, Yao C, Du A. An apicoplast-localized deubiquitinase contributes to the cell growth and apicoplast homeostasis of Toxoplasma gondii. Vet Res 2024; 55:10. [PMID: 38233899 PMCID: PMC10795397 DOI: 10.1186/s13567-023-01261-y] [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: 09/02/2023] [Accepted: 11/17/2023] [Indexed: 01/19/2024] Open
Abstract
Toxoplasma gondii is among the most important parasites worldwide. The apicoplast is a unique organelle shared by all Apicomplexan protozoa. Increasing lines of evidence suggest that the apicoplast possesses its own ubiquitination system. Deubiquitination is a crucial step executed by deubiquitinase (DUB) during protein ubiquitination. While multiple components of ubiquitination have been identified in T. gondii, the deubiquitinases involved remain unknown. The aim of the current study was to delineate the localization of TgOTU7 and elucidate its functions. TgOTU7 was specifically localized at the apicoplast, and its expression was largely regulated during the cell cycle. Additionally, TgOTU7 efficiently breaks down ubiquitin chains, exhibits linkage-nonspecific deubiquitinating activity and is critical for the lytic cycle and apicoplast biogenesis, similar to the transcription of the apicoplast genome and the nuclear genes encoding apicoplast-targeted proteins. Taken together, the results indicate that the newly described deubiquitinase TgOTU7 specifically localizes to the apicoplast and affects the cell growth and apicoplast homeostasis of T. gondii.
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Affiliation(s)
- Jie Xia
- Institute of Preventive Veterinary Medicine and Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, China
| | - Yimin Yang
- Institute of Preventive Veterinary Medicine and Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, China
| | - Xueqiu Chen
- Institute of Preventive Veterinary Medicine and Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, China
| | - Kaiyue Song
- Institute of Preventive Veterinary Medicine and Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, China
| | - Guangxu Ma
- Institute of Preventive Veterinary Medicine and Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, China
| | - Yi Yang
- Institute of Preventive Veterinary Medicine and Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, China
| | - Chaoqun Yao
- Department of Biomedical Sciences and One Health Center for Zoonoses and Tropical Veterinary Medicine, Ross University School of Veterinary Medicine, P.O. Box 334, Basseterre, Saint Kitts and Nevis.
| | - Aifang Du
- Institute of Preventive Veterinary Medicine and Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, China.
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28
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Wu M, Sun L, Song T. OTUB1-mediated inhibition of ubiquitination: a growing list of effectors, multiplex mechanisms, and versatile functions. Front Mol Biosci 2024; 10:1261273. [PMID: 38264570 PMCID: PMC10803509 DOI: 10.3389/fmolb.2023.1261273] [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: 07/19/2023] [Accepted: 12/19/2023] [Indexed: 01/25/2024] Open
Abstract
Protein ubiquitination plays a pivotal role in protein homeostasis. Ubiquitination may regulate the stability, activity, protein-protein interaction, and localization of a protein. Ubiquitination is subject to regulation by two groups of counteracting enzymes, the E3 ubiquitin ligases and deubiquitinases. Consistently, deubiquitinases are involved in essentially all biological processes. OTUB1, an OTU-family deubiquitinase, is a critical regulator of development, cancer, DNA damage response, and immune response. OTUB1 antagonizes the ubiquitination of a wide-spectrum of proteins through at least two different mechanisms. Besides direct deubiquitination, OTUB1 can also inhibit ubiquitination by non-canonically blocking ubiquitin transfer from certain ubiquitin-conjugases (E2). In this review, we start with a general background of protein ubiquitination and deubiquitination. Next, we introduce the basic characteristics of OTUB1 and then elaborate on the updated biological functions of OTUB1. Afterwards, we discuss potential mechanisms underlying the versatility and specificity of OTUB1 functions. In the end, we discuss the perspective that OTUB1 can be a potential therapeutic target for cancer.
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Affiliation(s)
- Miaomiao Wu
- Deparment of Obstetrics and Gynecology, Shuyang Hospital of Traditional Chinese Medicine, Suqian, China
| | - Lidong Sun
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- Cell Architecture Research Institute, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Tanjing Song
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- Cell Architecture Research Institute, Huazhong University of Science and Technology, Wuhan, Hubei, China
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Ren W, Xu Z, Chang Y, Ju F, Wu H, Liang Z, Zhao M, Wang N, Lin Y, Xu C, Chen S, Rao Y, Lin C, Yang J, Liu P, Zhang J, Huang C, Xia N. Pharmaceutical targeting of OTUB2 sensitizes tumors to cytotoxic T cells via degradation of PD-L1. Nat Commun 2024; 15:9. [PMID: 38167274 PMCID: PMC10761827 DOI: 10.1038/s41467-023-44466-7] [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: 01/25/2023] [Accepted: 12/14/2023] [Indexed: 01/05/2024] Open
Abstract
PD-1 is a co-inhibitory receptor expressed by CD8+ T cells which limits their cytotoxicity. PD-L1 expression on cancer cells contributes to immune evasion by cancers, thus, understanding the mechanisms that regulate PD-L1 protein levels in cancers is important. Here we identify tumor-cell-expressed otubain-2 (OTUB2) as a negative regulator of antitumor immunity, acting through the PD-1/PD-L1 axis in various human cancers. Mechanistically, OTUB2 directly interacts with PD-L1 to disrupt the ubiquitination and degradation of PD-L1 in the endoplasmic reticulum. Genetic deletion of OTUB2 markedly decreases the expression of PD-L1 proteins on the tumor cell surface, resulting in increased tumor cell sensitivity to CD8+ T-cell-mediated cytotoxicity. To underscore relevance in human patients, we observe a significant correlation between OTUB2 expression and PD-L1 abundance in human non-small cell lung cancer. An inhibitor of OTUB2, interfering with its deubiquitinase activity without disrupting the OTUB2-PD-L1 interaction, successfully reduces PD-L1 expression in tumor cells and suppressed tumor growth. Together, these results reveal the roles of OTUB2 in PD-L1 regulation and tumor evasion and lays down the proof of principle for OTUB2 targeting as therapeutic strategy for cancer treatment.
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Affiliation(s)
- Wenfeng Ren
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, Department of Laboratory Medicine, School of Public Health, Xiamen University, Xiamen, Fujian, 361102, China
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen, Fujian, 361102, China
| | - Zilong Xu
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, Department of Laboratory Medicine, School of Public Health, Xiamen University, Xiamen, Fujian, 361102, China
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen, Fujian, 361102, China
| | - Yating Chang
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, Department of Laboratory Medicine, School of Public Health, Xiamen University, Xiamen, Fujian, 361102, China
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen, Fujian, 361102, China
- School of Life Sciences, Xiamen University, Xiamen, Fujian, 361102, China
| | - Fei Ju
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, Department of Laboratory Medicine, School of Public Health, Xiamen University, Xiamen, Fujian, 361102, China
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen, Fujian, 361102, China
| | - Hongning Wu
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, Department of Laboratory Medicine, School of Public Health, Xiamen University, Xiamen, Fujian, 361102, China
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen, Fujian, 361102, China
- School of Life Sciences, Xiamen University, Xiamen, Fujian, 361102, China
| | - Zhiqi Liang
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, Department of Laboratory Medicine, School of Public Health, Xiamen University, Xiamen, Fujian, 361102, China
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen, Fujian, 361102, China
- School of Life Sciences, Xiamen University, Xiamen, Fujian, 361102, China
| | - Min Zhao
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, Department of Laboratory Medicine, School of Public Health, Xiamen University, Xiamen, Fujian, 361102, China
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen, Fujian, 361102, China
| | - Naizhen Wang
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, Department of Laboratory Medicine, School of Public Health, Xiamen University, Xiamen, Fujian, 361102, China
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen, Fujian, 361102, China
| | - Yanhua Lin
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, Department of Laboratory Medicine, School of Public Health, Xiamen University, Xiamen, Fujian, 361102, China
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen, Fujian, 361102, China
| | - Chenhang Xu
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, Department of Laboratory Medicine, School of Public Health, Xiamen University, Xiamen, Fujian, 361102, China
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen, Fujian, 361102, China
- School of Life Sciences, Xiamen University, Xiamen, Fujian, 361102, China
| | - Shengming Chen
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, Department of Laboratory Medicine, School of Public Health, Xiamen University, Xiamen, Fujian, 361102, China
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen, Fujian, 361102, China
| | - Yipeng Rao
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, Department of Laboratory Medicine, School of Public Health, Xiamen University, Xiamen, Fujian, 361102, China
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen, Fujian, 361102, China
| | - Chaolong Lin
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, Department of Laboratory Medicine, School of Public Health, Xiamen University, Xiamen, Fujian, 361102, China
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen, Fujian, 361102, China
| | - Jianxin Yang
- Department of Hepatobiliary & Pancreatic Surgery, The National Key Clinical Specialty, Zhongshan Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, Fujian, 361004, China
- Fujian Provincial Key Laboratory and Chronic Liver Disease and Hepatocellular Carcinoma, Xiamen, Fujian, 361004, China
| | - Pingguo Liu
- Department of Hepatobiliary & Pancreatic Surgery, The National Key Clinical Specialty, Zhongshan Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, Fujian, 361004, China.
- Fujian Provincial Key Laboratory and Chronic Liver Disease and Hepatocellular Carcinoma, Xiamen, Fujian, 361004, China.
| | - Jun Zhang
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, Department of Laboratory Medicine, School of Public Health, Xiamen University, Xiamen, Fujian, 361102, China.
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen, Fujian, 361102, China.
| | - Chenghao Huang
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, Department of Laboratory Medicine, School of Public Health, Xiamen University, Xiamen, Fujian, 361102, China.
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen, Fujian, 361102, China.
| | - Ningshao Xia
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, Department of Laboratory Medicine, School of Public Health, Xiamen University, Xiamen, Fujian, 361102, China.
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen, Fujian, 361102, China.
- School of Life Sciences, Xiamen University, Xiamen, Fujian, 361102, China.
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Tey PY, Dufner A, Knobeloch KP, Pruneda JN, Clague MJ, Urbé S. Rapid turnover of CTLA4 is associated with a complex architecture of reversible ubiquitylation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.31.573735. [PMID: 38260548 PMCID: PMC10802369 DOI: 10.1101/2023.12.31.573735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
The immune checkpoint regulator CTLA4 is an unusually short-lived membrane protein. Here we show that its lysosomal degradation is dependent on ubiquitylation at Lysine residues 203 and 213. Inhibition of the v-ATPase partially restores CTLA4 levels following cycloheximide treatment, but also reveals a fraction that is secreted in exosomes. The endosomal deubiquitylase, USP8, interacts with CTLA4 and its loss enhances CTLA4 ubiquitylation in cancer cells, mouse CD4+ T cells and in cancer cell-derived exosomes. Depletion of the USP8 adapter protein, HD-PTP, but not ESCRT-0 recapitulates this cellular phenotype, but shows distinct properties vis-à-vis exosome incorporation. Re-expression of wild-type USP8, but neither a catalytically inactive, nor a localization-compromised ΔMIT domain mutant can rescue delayed degradation of CTLA4, or counteract its accumulation in clustered endosomes. UbiCRest analysis of CTLA4-associated ubiquitin chain linkages identifies a complex mixture of conventional Lys63- and more unusual Lys27- and Lys29-linked polyubiquitin chains that may underly the rapidity of protein turnover.
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Affiliation(s)
- Pei Yee Tey
- Biochemistry, Cell and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Crown St., Liverpool, L69 3BX, UK
| | - Almut Dufner
- Institute of Neuropathology, Medical Faculty, University of Freiburg, 79106 Freiburg, Germany; Signalling Research Centres BIOSS and CIBSS, University of Freiburg, 79104 Freiburg, Germany
| | - Klaus-Peter Knobeloch
- Institute of Neuropathology, Medical Faculty, University of Freiburg, 79106 Freiburg, Germany; Signalling Research Centres BIOSS and CIBSS, University of Freiburg, 79104 Freiburg, Germany
| | - Jonathan N. Pruneda
- Department of Molecular Microbiology & Immunology, Oregon Health & Science University, Portland, OR 97239, USA
| | - Michael J. Clague
- Biochemistry, Cell and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Crown St., Liverpool, L69 3BX, UK
| | - Sylvie Urbé
- Biochemistry, Cell and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Crown St., Liverpool, L69 3BX, UK
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Tian W, Li H, Li Y, Guo J, Wang H, Yang B, Li P, Cui X, Liu L. A novel missense variant in OTUD5 causes X-linked multiple congenital anomalies-neurodevelopmental syndrome. Mol Genet Genomic Med 2024; 12:e2325. [PMID: 38037881 PMCID: PMC10767676 DOI: 10.1002/mgg3.2325] [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: 07/13/2023] [Revised: 10/13/2023] [Accepted: 11/10/2023] [Indexed: 12/02/2023] Open
Abstract
BACKGROUND The OTUD5 gene encodes a deubiquitinating enzyme (DUB) of the OTU family. Variants of OTUD5 are associated with X-linked multiple congenital anomalies-neurodevelopmental syndrome (MCAND). The case described in this study expands the clinical and molecular spectrum of OTUD5. METHODS Trio-based clinical exome sequencing (trio-CES) was performed on a Chinese boy with a clinical phenotype and both of his parents. Sanger sequencing was employed for validation of the variant detected. RESULTS The patient presented with characteristic facial features, intellectual disability, motor/language/cognitive, and global developmental delays, limb contractures, and kidney abnormalities, and trio-CES identified a de novo missense variant, c.1305T>A, of the OTUD5 gene. DISCUSSION We describe OTUD5 gene variation in the Chinese population, with the first report of this variant. Additionally, we provide a comprehensive summary of all published cases of MCAND to date, in order to elucidate the primary clinical features of the syndrome and the variability in phenotype severity. This case expands the genetic and clinical phenotypic spectrum of OTUD5-associated MCAND.
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Affiliation(s)
- Weifang Tian
- Prenatal Diagnosis Center, The Third Affiliated Hospital of Zhengzhou University, Maternal and Child Health Hospital of Henan ProvinceZhengzhouChina
| | - Haiyu Li
- Prenatal Diagnosis Center, The Third Affiliated Hospital of Zhengzhou University, Maternal and Child Health Hospital of Henan ProvinceZhengzhouChina
| | - Ying Li
- Prenatal Diagnosis Center, The Third Affiliated Hospital of Zhengzhou University, Maternal and Child Health Hospital of Henan ProvinceZhengzhouChina
| | - Jing Guo
- Prenatal Diagnosis Center, The Third Affiliated Hospital of Zhengzhou University, Maternal and Child Health Hospital of Henan ProvinceZhengzhouChina
| | - Handuo Wang
- Prenatal Diagnosis Center, The Third Affiliated Hospital of Zhengzhou University, Maternal and Child Health Hospital of Henan ProvinceZhengzhouChina
| | - Bo Yang
- Prenatal Diagnosis Center, The Third Affiliated Hospital of Zhengzhou University, Maternal and Child Health Hospital of Henan ProvinceZhengzhouChina
| | - Pengyun Li
- Prenatal Diagnosis Center, The Third Affiliated Hospital of Zhengzhou University, Maternal and Child Health Hospital of Henan ProvinceZhengzhouChina
| | - Xueyin Cui
- Prenatal Diagnosis Center, The Third Affiliated Hospital of Zhengzhou University, Maternal and Child Health Hospital of Henan ProvinceZhengzhouChina
| | - Ling Liu
- Prenatal Diagnosis Center, The Third Affiliated Hospital of Zhengzhou University, Maternal and Child Health Hospital of Henan ProvinceZhengzhouChina
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Rossio V, Paulo JA, Liu X, Gygi SP, King RW. Substrate identification and specificity profiling of deubiquitylases against endogenously-generated ubiquitin-protein conjugates. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.20.572581. [PMID: 38187689 PMCID: PMC10769257 DOI: 10.1101/2023.12.20.572581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Deubiquitylating enzymes (DUBs) remove ubiquitin from proteins thereby regulating their stability or activity. Our understanding of DUB-substrate specificity is limited because DUBs are typically not compared to each other against many physiological substrates. By broadly inhibiting DUBs in Xenopus egg extract, we generated hundreds of ubiquitylated proteins and compared the ability of 30 DUBs to deubiquitylate them using quantitative proteomics. We identified five high impact DUBs (USP7, USP9X, USP36, USP15 and USP24) that each reduced ubiquitylation of over ten percent of the isolated proteins. Candidate substrates of high impact DUBs showed substantial overlap and were enriched for disordered regions, suggesting this feature may promote substrate recognition. Other DUBs showed lower impact and non-overlapping specificity, targeting distinct non-disordered proteins including complexes such as the ribosome or the proteasome. Altogether our study identifies candidate DUB substrates and defines patterns of functional redundancy and specificity, revealing substrate characteristics that may influence DUB-substrate recognition.
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Du B, Zhang J, Kong L, Shi H, Zhang D, Wang X, Yang C, Li P, Yao R, Liang C, Wu L, Huang Z. Ovarian Tumor Domain-Containing 7B Attenuates Pathological Cardiac Hypertrophy by Inhibiting Ubiquitination and Degradation of Krüppel-Like Factor 4. J Am Heart Assoc 2023; 12:e029745. [PMID: 38084712 PMCID: PMC10863784 DOI: 10.1161/jaha.123.029745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 08/15/2023] [Indexed: 12/20/2023]
Abstract
BACKGROUND Cardiac hypertrophy (CH) is a well-established risk factor for many cardiovascular diseases and a primary cause of mortality and morbidity among older adults. Currently, no pharmacological interventions have been specifically tailored to treat CH. OTUD7B (ovarian tumor domain-containing 7B) is a member of the ovarian tumor-related protease (OTU) family that regulates many important cell signaling pathways. However, the role of OTUD7B in the development of CH is unclear. Therefore, we investigated the role of OTUD7B in CH. METHODS AND RESULTS OTUD7B knockout mice were used to assay the role of OTUD7B in CH after transverse aortic coarctation surgery. We further assayed the specific functions of OTUD7B in isolated neonatal rat cardiomyocytes. We found that OTUD7B expression decreased in hypertrophic mice hearts and phenylephrine-stimulated neonatal rat cardiomyocytes. Furthermore, OTUD7B deficiency exacerbated transverse aortic coarctation surgery-induced myocardial hypertrophy, abnormal cardiac function, and fibrosis. In cardiac myocytes, OTUD7B knockdown promoted phenylephrine stimulation-induced myocardial hypertrophy, whereas OTUD7B overexpression had the opposite effect. An immunoprecipitation-mass spectrometry analysis showed that OTUD7B directly binds to KLF4 (Krüppel-like factor 4). Additional molecular experiments showed that OTUD7B impedes KLF4 degradation by inhibiting lysine residue at 48 site-linked ubiquitination and suppressing myocardial hypertrophy by activating the serine/threonine kinase pathway. CONCLUSIONS These results demonstrate that the OTUD7B-KLF4 axis is a novel molecular target for CH treatment.
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Affiliation(s)
- Bin‐Bin Du
- Cardiovascular Hospital, The First Affiliated Hospital of Zhengzhou University, Zhengzhou UniversityZhengzhouChina
| | - Jie‐Lei Zhang
- Department of EndocrinologyThe First Affiliated Hospital of Zhengzhou University, Zhengzhou UniversityZhengzhouChina
| | - Ling‐Yao Kong
- Cardiovascular Hospital, The First Affiliated Hospital of Zhengzhou University, Zhengzhou UniversityZhengzhouChina
| | - Hui‐Ting Shi
- Cardiovascular Hospital, The First Affiliated Hospital of Zhengzhou University, Zhengzhou UniversityZhengzhouChina
| | - Dian‐Hong Zhang
- Cardiovascular Hospital, The First Affiliated Hospital of Zhengzhou University, Zhengzhou UniversityZhengzhouChina
| | - Xing Wang
- Cardiovascular Hospital, The First Affiliated Hospital of Zhengzhou University, Zhengzhou UniversityZhengzhouChina
| | - Chun‐Lei Yang
- Cardiovascular Hospital, The First Affiliated Hospital of Zhengzhou University, Zhengzhou UniversityZhengzhouChina
| | - Peng‐Cheng Li
- Cardiovascular Hospital, The First Affiliated Hospital of Zhengzhou University, Zhengzhou UniversityZhengzhouChina
| | - Rui Yao
- Cardiovascular Hospital, The First Affiliated Hospital of Zhengzhou University, Zhengzhou UniversityZhengzhouChina
| | - Cui Liang
- Cardiovascular Hospital, The First Affiliated Hospital of Zhengzhou University, Zhengzhou UniversityZhengzhouChina
| | - Lei‐Ming Wu
- Cardiovascular Hospital, The First Affiliated Hospital of Zhengzhou University, Zhengzhou UniversityZhengzhouChina
| | - Zhen Huang
- Cardiovascular Hospital, The First Affiliated Hospital of Zhengzhou University, Zhengzhou UniversityZhengzhouChina
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Abstract
Ubiquitination is an essential regulator of most, if not all, signalling pathways, and defects in cellular signalling are central to cancer initiation, progression and, eventually, metastasis. The attachment of ubiquitin signals by E3 ubiquitin ligases is directly opposed by the action of approximately 100 deubiquitinating enzymes (DUBs) in humans. Together, DUBs and E3 ligases coordinate ubiquitin signalling by providing selectivity for different substrates and/or ubiquitin signals. The balance between ubiquitination and deubiquitination is exquisitely controlled to ensure properly coordinated proteostasis and response to cellular stimuli and stressors. Not surprisingly, then, DUBs have been associated with all hallmarks of cancer. These relationships are often complex and multifaceted, highlighted by the implication of multiple DUBs in certain hallmarks and by the impact of individual DUBs on multiple cancer-associated pathways, sometimes with contrasting cancer-promoting and cancer-inhibiting activities, depending on context and tumour type. Although it is still understudied, the ever-growing knowledge of DUB function in cancer physiology will eventually identify DUBs that warrant specific inhibition or activation, both of which are now feasible. An integrated appreciation of the physiological consequences of DUB modulation in relevant cancer models will eventually lead to the identification of patient populations that will most likely benefit from DUB-targeted therapies.
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Affiliation(s)
- Grant Dewson
- Ubiquitin Signalling Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia.
- Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia.
| | - Pieter J A Eichhorn
- Curtin Medical School, Curtin University, Perth, Western Australia, Australia.
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.
| | - David Komander
- Ubiquitin Signalling Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia.
- Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia.
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Ren J, Yu P, Liu S, Li R, Niu X, Chen Y, Zhang Z, Zhou F, Zhang L. Deubiquitylating Enzymes in Cancer and Immunity. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2303807. [PMID: 37888853 PMCID: PMC10754134 DOI: 10.1002/advs.202303807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Revised: 08/30/2023] [Indexed: 10/28/2023]
Abstract
Deubiquitylating enzymes (DUBs) maintain relative homeostasis of the cellular ubiquitome by removing the post-translational modification ubiquitin moiety from substrates. Numerous DUBs have been demonstrated specificity for cleaving a certain type of ubiquitin linkage or positions within ubiquitin chains. Moreover, several DUBs perform functions through specific protein-protein interactions in a catalytically independent manner, which further expands the versatility and complexity of DUBs' functions. Dysregulation of DUBs disrupts the dynamic equilibrium of ubiquitome and causes various diseases, especially cancer and immune disorders. This review summarizes the Janus-faced roles of DUBs in cancer including proteasomal degradation, DNA repair, apoptosis, and tumor metastasis, as well as in immunity involving innate immune receptor signaling and inflammatory and autoimmune disorders. The prospects and challenges for the clinical development of DUB inhibitors are further discussed. The review provides a comprehensive understanding of the multi-faced roles of DUBs in cancer and immunity.
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Affiliation(s)
- Jiang Ren
- The Eighth Affiliated HospitalSun Yat‐sen UniversityShenzhen518033P. R. China
| | - Peng Yu
- Zhongshan Institute for Drug DiscoveryShanghai Institute of Materia MedicaChinese Academy of SciencesZhongshanGuangdongP. R. China
| | - Sijia Liu
- International Biomed‐X Research CenterSecond Affiliated Hospital of Zhejiang University School of MedicineZhejiang UniversityHangzhouP. R. China
- Key Laboratory of Precision Diagnosis and Treatment for Hepatobiliary and Pancreatic Tumor of Zhejiang ProvinceHangzhou310058China
| | - Ran Li
- The Eighth Affiliated HospitalSun Yat‐sen UniversityShenzhen518033P. R. China
| | - Xin Niu
- MOE Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling NetworkLife Sciences InstituteZhejiang UniversityHangzhou310058P. R. China
| | - Yan Chen
- The Eighth Affiliated HospitalSun Yat‐sen UniversityShenzhen518033P. R. China
| | - Zhenyu Zhang
- Department of NeurosurgeryThe First Affiliated Hospital of Zhengzhou UniversityZhengzhouHenan450003P. R. China
| | - Fangfang Zhou
- Institutes of Biology and Medical ScienceSoochow UniversitySuzhou215123P. R. China
| | - Long Zhang
- The Eighth Affiliated HospitalSun Yat‐sen UniversityShenzhen518033P. R. China
- International Biomed‐X Research CenterSecond Affiliated Hospital of Zhejiang University School of MedicineZhejiang UniversityHangzhouP. R. China
- MOE Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling NetworkLife Sciences InstituteZhejiang UniversityHangzhou310058P. R. China
- Cancer CenterZhejiang UniversityHangzhouZhejiang310058P. R. China
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Shestoperova EI, Strieter ER. Uncovering DUB Selectivity through an Ion Mobility-Based Assessment of Ubiquitin Chain Isomers. Anal Chem 2023; 95:17416-17423. [PMID: 37962301 PMCID: PMC11103383 DOI: 10.1021/acs.analchem.3c04622] [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] [Indexed: 11/15/2023]
Abstract
Ubiquitination is a reversible post-translational modification that maintains cellular homeostasis and regulates protein turnover. Deubiquitinases (DUBs) are a large family of proteases that catalyze the removal of ubiquitin (Ub) along with the dismantling and editing of Ub chains. Assessing the activity and selectivity of DUBs is critical for defining physiological functions. Despite numerous methods for evaluating DUB activity, none are capable of assessing activity and selectivity in the context of multicomponent mixtures of native unlabeled Ub conjugates. Here, we report an ion mobility (IM)-based approach for measuring DUB selectivity in the context of unlabeled mixtures of Ub chains. We show that IM-mass spectrometry (IM-MS) can be used to assess the selectivity of DUBs in a time-dependent manner. Moreover, using the branched Ub chain selective DUB UCH37/UCHL5 along with a mixture of Ub trimers, a strong preference for branched Ub trimers bearing K6 and K48 linkages is revealed. Our results demonstrate that IM-MS is a powerful method for evaluating DUB selectivity under conditions more physiologically relevant than single-component mixtures.
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Affiliation(s)
- Elizaveta I Shestoperova
- Department of Chemistry, University of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
| | - Eric R Strieter
- Department of Chemistry, University of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
- Molecular & Cellular Biology Graduate Program, University of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
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Yang Y, Mei L, Chen J, Chen X, Wang Z, Liu L, Yang A. Legionella pneumophila-mediated host posttranslational modifications. J Mol Cell Biol 2023; 15:mjad032. [PMID: 37156500 PMCID: PMC10720952 DOI: 10.1093/jmcb/mjad032] [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: 09/16/2022] [Revised: 01/17/2023] [Accepted: 05/06/2023] [Indexed: 05/10/2023] Open
Abstract
Legionella pneumophila is a Gram-negative bacterium ubiquitously present in freshwater environments and causes a serious type of pneumonia called Legionnaires' disease. During infections, L. pneumophila releases over 300 effector proteins into host cells through an Icm/Dot type IV secretion system to manipulate the host defense system for survival within the host. Notably, certain effector proteins mediate posttranslational modifications (PTMs), serving as useful approaches exploited by L. pneumophila to modify host proteins. Some effectors catalyze the addition of host protein PTMs, while others mediate the removal of PTMs from host proteins. In this review, we summarize L. pneumophila effector-mediated PTMs of host proteins, including phosphorylation, ubiquitination, glycosylation, AMPylation, phosphocholination, methylation, and ADP-ribosylation, as well as dephosphorylation, deubiquitination, deAMPylation, deADP-ribosylation, dephosphocholination, and delipidation. We describe their molecular mechanisms and biological functions in the regulation of bacterial growth and Legionella-containing vacuole biosynthesis and in the disruption of host immune and defense machinery.
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Affiliation(s)
- Yi Yang
- School of Life Sciences, Chongqing University, Chongqing 401331, China
| | - Ligang Mei
- School of Life Sciences, Chongqing University, Chongqing 401331, China
| | - Jing Chen
- School of Life Sciences, Chongqing University, Chongqing 401331, China
| | - Xiaorong Chen
- School of Life Sciences, Chongqing University, Chongqing 401331, China
| | - Zhuolin Wang
- School of Life Sciences, Chongqing University, Chongqing 401331, China
| | - Lu Liu
- School of Life Sciences, Chongqing University, Chongqing 401331, China
| | - Aimin Yang
- School of Life Sciences, Chongqing University, Chongqing 401331, China
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Zheng S, Li Y, Song X, Wu M, Yu L, Huang G, Liu T, Zhang L, Shang M, Zhu Q, Gao C, Chen L, Liu H. OTUD1 ameliorates cerebral ischemic injury through inhibiting inflammation by disrupting K63-linked deubiquitination of RIP2. J Neuroinflammation 2023; 20:281. [PMID: 38012669 PMCID: PMC10680203 DOI: 10.1186/s12974-023-02968-7] [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: 06/19/2023] [Accepted: 11/22/2023] [Indexed: 11/29/2023] Open
Abstract
BACKGROUND Inflammatory response triggered by innate immunity plays a pivotal element in the progress of ischemic stroke. Receptor-interacting kinase 2 (RIP2) is implicated in maintaining immunity homeostasis and regulating inflammatory response. However, the underlying mechanism of RIP2 in ischemic stroke is still not well understood. Hence, the study investigated the role and the ubiquitination regulatory mechanism of RIP2 in ischemic stroke. METHODS Focal cerebral ischemia was introduced by middle cerebral artery occlusion (MCAO) in wild-type (WT) and OTUD1-deficient (OTUD1-/-) mice, oxygen glucose deprivation and reoxygenation (OGD/R) models in BV2 cells and primary cultured astrocytes were performed for monitoring of experimental stroke. GSK2983559 (GSK559), a RIP2 inhibitor was intraventricularly administered 30 min before MCAO. Mice brain tissues were collected for TTC staining and histopathology. Protein expression of RIP2, OTUD1, p-NF-κB-p65 and IκBα was determined by western blot. Localization of RIP2 and OTUD1 was examined by immunofluorescence. The change of IL-1β, IL-6 and TNF-α was detected by ELISA assay and quantitative real-time polymerase chain reaction. Immunoprecipitation and confocal microscopy were used to study the interaction of RIP2 and OTUD1. The activity of NF-κB was examined by dual-luciferase assay. RESULTS Our results showed upregulated protein levels of RIP2 and OTUD1 in microglia and astrocytes in mice subjected to focal cerebral ischemia. Inhibition of RIP2 by GSK559 ameliorated the cerebral ischemic outcome by repressing the NF-κB activity and the inflammatory response. Mechanistically, OTUD1 interacted with RIP2 and sequentially removed the K63-linked polyubiquitin chains of RIP2, thereby inhibiting NF-κB activation. Furthermore, OTUD1 deficiency exacerbated cerebral ischemic injury in response to inflammation induced by RIP2 ubiquitination. CONCLUSIONS These findings suggested that RIP2 mediated cerebral ischemic lesion via stimulating inflammatory response, and OTUD1 ameliorated brain injury after ischemia through inhibiting RIP2-induced NF-κB activation by specifically cleaving K63-linked ubiquitination of RIP2.
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Affiliation(s)
- Shengnan Zheng
- Department of Pharmacology, School of Basic Medical Sciences, Shandong University, Jinan, Shandong, 250012, People's Republic of China
| | - Yiquan Li
- Department of Pharmacology, School of Basic Medical Sciences, Shandong University, Jinan, Shandong, 250012, People's Republic of China
| | - Xiaomeng Song
- Department of Pharmacology, School of Basic Medical Sciences, Shandong University, Jinan, Shandong, 250012, People's Republic of China
| | - Mengting Wu
- Department of Pharmacology, School of Basic Medical Sciences, Shandong University, Jinan, Shandong, 250012, People's Republic of China
| | - Lu Yu
- Department of Pharmacology, School of Basic Medical Sciences, Shandong University, Jinan, Shandong, 250012, People's Republic of China
| | - Gan Huang
- Department of Pharmacology, School of Basic Medical Sciences, Shandong University, Jinan, Shandong, 250012, People's Republic of China
| | - Tengfei Liu
- Department of Pharmacology, School of Basic Medical Sciences, Shandong University, Jinan, Shandong, 250012, People's Republic of China
| | - Lei Zhang
- Key Laboratory of Infection and Immunity of Shandong Province & Department of Immunology, School of Basic Medical Sciences, Shandong University, Jinan, Shandong, 250012, People's Republic of China
| | - Mingmei Shang
- Rheumatology Unit, Department of Medicine, Solna, Karolinska Institute, Karolinska University Hospital, Stockholm, Sweden
| | - Qingfen Zhu
- Shandong Institute for Food and Drug Control, Jinan, Shandong, 250012, People's Republic of China
| | - Chengjiang Gao
- Key Laboratory of Infection and Immunity of Shandong Province & Department of Immunology, School of Basic Medical Sciences, Shandong University, Jinan, Shandong, 250012, People's Republic of China
| | - Lin Chen
- Department of Pharmacology, School of Basic Medical Sciences, Shandong University, Jinan, Shandong, 250012, People's Republic of China.
| | - Huiqing Liu
- Department of Pharmacology, School of Basic Medical Sciences, Shandong University, Jinan, Shandong, 250012, People's Republic of China.
- Department of Rehabilitation Medicine, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, People's Republic of China.
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Boll V, Hermanns T, Uthoff M, Erven I, Hörner EM, Kozjak-Pavlovic V, Baumann U, Hofmann K. Functional and structural diversity in deubiquitinases of the Chlamydia-like bacterium Simkania negevensis. Nat Commun 2023; 14:7335. [PMID: 37957213 PMCID: PMC10643670 DOI: 10.1038/s41467-023-43144-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 11/01/2023] [Indexed: 11/15/2023] Open
Abstract
Besides the regulation of many cellular pathways, ubiquitination is important for defense against invading pathogens. Some intracellular bacteria have evolved deubiquitinase (DUB) effector proteins, which interfere with the host ubiquitin system and help the pathogen to evade xenophagy and lysosomal degradation. Most intracellular bacteria encode one or two DUBs, which are often linkage-promiscuous or preferentially cleave K63-linked chains attached to bacteria or bacteria-containing vacuoles. By contrast, the respiratory pathogen Legionella pneumophila possesses a much larger number of DUB effectors, including a K6-specific enzyme belonging to the OTU family and an M1-specific DUB uniquely found in this bacterium. Here, we report that the opportunistic pathogen Simkania negevensis, which is unrelated to Legionella but has a similar lifestyle, encodes a similarly large number of DUBs, including M1- and K6-specific enzymes. Simkania DUBs are highly diverse and include DUB classes never before seen in bacteria. Interestingly, the M1- and K6-specific DUBs of Legionella and Simkania are unrelated, suggesting that their acquisition occurred independently. We characterize the DUB activity of eight Simkania-encoded enzymes belonging to five different DUB classes. We also provide a structural basis for the M1-specificity of a Simkania DUB, which most likely evolved from a eukaryotic otubain-like precursor.
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Affiliation(s)
- Vanessa Boll
- Institute for Genetics, University of Cologne, Cologne, Germany
| | - Thomas Hermanns
- Institute for Genetics, University of Cologne, Cologne, Germany
| | - Matthias Uthoff
- Institute of Biochemistry, University of Cologne, Cologne, Germany
- Bayer AG, Research & Development, Pharmaceuticals, Biologics Research, Wuppertal, Germany
| | - Ilka Erven
- Institute for Genetics, University of Cologne, Cologne, Germany
| | - Eva-Maria Hörner
- Chair of Microbiology, Biocenter, Julius Maximilian University, Würzburg, Würzburg, Germany
| | - Vera Kozjak-Pavlovic
- Chair of Microbiology, Biocenter, Julius Maximilian University, Würzburg, Würzburg, Germany
| | - Ulrich Baumann
- Institute of Biochemistry, University of Cologne, Cologne, Germany
| | - Kay Hofmann
- Institute for Genetics, University of Cologne, Cologne, Germany.
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40
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Shestoperova EI, Strieter ER. Uncovering DUB Selectivity Through Ion-Mobility-Based Assessment of Ubiquitin Chain Isomers. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.11.561976. [PMID: 37873305 PMCID: PMC10592704 DOI: 10.1101/2023.10.11.561976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Ubiquitination is a reversible posttranslational modification that maintains cellular homeostasis and regulates protein turnover. Deubiquitinases (DUBs) are a large family of proteases that catalyze the removal of ubiquitin (Ub) along with the dismantling and editing of Ub chains. Assessing the activity and selectivity of DUBs is critical for defining physiological function. Despite numerous methods for evaluating DUB activity, none are capable of assessing activity and selectivity in the context of multicomponent mixtures of native, unlabeled ubiquitin conjugates. Here we report on an ion mobility (IM)-based approach for measuring DUB selectivity in the context of unlabeled mixtures of Ub chains. We show that IM-MS can be used to assess the selectivity of DUBs in a time-dependent manner. Moreover, using the branched Ub chain selective DUB UCH37/UCHL5 along with a mixture of Ub trimers, a strong preference for branched Ub trimers bearing K6 and K48 linkages is revealed. Our results demonstrate that IM coupled with mass spectrometry (IM-MS) is a powerful method for evaluating DUB selectivity under conditions more physiologically relevant than single component mixtures.
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41
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Park Y, Dodantenna N, Kim Y, Kim T, Lee H, Yoo Y, Heo J, Lee J, Kwon M, Kang HC, Lee J, Cho H. MARCH5-dependent NLRP3 ubiquitination is required for mitochondrial NLRP3-NEK7 complex formation and NLRP3 inflammasome activation. EMBO J 2023; 42:e113481. [PMID: 37575012 PMCID: PMC10548170 DOI: 10.15252/embj.2023113481] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 07/20/2023] [Accepted: 07/23/2023] [Indexed: 08/15/2023] Open
Abstract
The NLRP3 inflammasome plays a key role in responding to pathogens, and endogenous damage and mitochondria are intensively involved in inflammasome activation. The NLRP3 inflammasome forms multiprotein complexes and its sequential assembly is important for its activation. Here, we show that NLRP3 is ubiquitinated by the mitochondria-associated E3 ligase, MARCH5. Myeloid cell-specific March5 conditional knockout (March5 cKO) mice failed to secrete IL-1β and IL-18 and exhibited an attenuated mortality rate upon LPS or Pseudomonas aeruginosa challenge. Macrophages derived from March5 cKO mice also did not produce IL-1β and IL-18 after microbial infection. Mechanistically, MARCH5 interacts with the NACHT domain of NLRP3 and promotes K27-linked polyubiquitination on K324 and K430 residues of NLRP3. Ubiquitination-defective NLRP3 mutants on K324 and K430 residues are not able to bind to NEK7, nor form NLRP3 oligomers leading to abortive ASC speck formation and diminished IL-1β production. Thus, MARCH5-dependent NLRP3 ubiquitination on the mitochondria is required for NLRP3-NEK7 complex formation and NLRP3 oligomerization. We propose that the E3 ligase MARCH5 is a regulator of NLRP3 inflammasome activation on the mitochondria.
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Affiliation(s)
- Yeon‐Ji Park
- Department of BiochemistryAjou University School of MedicineSuwonKorea
- Department of Biological SciencesGraduate School of Ajou UniversitySuwonKorea
| | | | - Yonghyeon Kim
- Department of BiochemistryAjou University School of MedicineSuwonKorea
- Department of Biological SciencesGraduate School of Ajou UniversitySuwonKorea
| | - Tae‐Hwan Kim
- College of Veterinary MedicineChungnam National UniversityDaejeonKorea
| | - Ho‐Soo Lee
- Department of BiochemistryAjou University School of MedicineSuwonKorea
| | - Young‐Suk Yoo
- Department of BiochemistryAjou University School of MedicineSuwonKorea
| | - June Heo
- Department of BiochemistryAjou University School of MedicineSuwonKorea
- Department of Biological SciencesGraduate School of Ajou UniversitySuwonKorea
| | - Jae‐Ho Lee
- Department of BiochemistryAjou University School of MedicineSuwonKorea
| | - Myung‐Hee Kwon
- Department of MicrobiologyAjou University School of MedicineSuwonKorea
| | - Ho Chul Kang
- Department of PhysiologyAjou University School of MedicineSuwonKorea
| | - Jong‐Soo Lee
- College of Veterinary MedicineChungnam National UniversityDaejeonKorea
| | - Hyeseong Cho
- Department of BiochemistryAjou University School of MedicineSuwonKorea
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42
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Song J, Zhang Y, Bai Y, Sun X, Lu Y, Guo Y, He Y, Gao M, Chi X, Heng BC, Zhang X, Li W, Xu M, Wei Y, You F, Zhang X, Lu D, Deng X. The Deubiquitinase OTUD1 Suppresses Secretory Neutrophil Polarization And Ameliorates Immunopathology of Periodontitis. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2303207. [PMID: 37639212 PMCID: PMC10602526 DOI: 10.1002/advs.202303207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 07/12/2023] [Indexed: 08/29/2023]
Abstract
Tissue-infiltrating neutrophils (TINs) secrete various signaling molecules to establish paracrine communication within the inflammatory milieu. It is imperative to identify molecular mediators that control this secretory phenotype of TINs. The present study uncovers a secretory neutrophil subset that exhibits increased pro-inflammatory cytokine production and enhanced migratory capacity which is highly related with periodontal pathogenesis. Further analysis identifies the OTU domain-containing protein 1 (OTUD1) plays a regulatory role in this secretory neutrophil polarization. In human and mouse periodontitis, the waning of inflammation is correlated with OTUD1 upregulation, whereas severe periodontitis is induced when neutrophil-intrinsic OTUD1 is depleted. Mechanistically, OTUD1 interacts with SEC23B, a component of the coat protein II complex (COPII). By removing the K63-linked polyubiquitin chains on SEC23B Lysine 81, the deubiquitinase OTUD1 negatively regulates the COPII secretory machinery and limits protein ER-to-Golgi trafficking, thus restricting the surface expression of integrin-regulated proteins, CD9 and CD47. Accordingly, blockade of protein transport by Brefeldin A (BFA) curbs recruitment of Otud1-deficient TINs and attenuates inflammation-induced alveolar bone destruction. The results thus identify OTUD1 signaling as a negative feedback loop that limits the polarization of neutrophils with secretory phenotype and highlight the potential application of BFA in the treatment of periodontal inflammation.
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Affiliation(s)
- Jia Song
- Department of Geriatric DentistryPeking University School and Hospital of StomatologyBeijing100081P. R. China
- Department of Dental Materials & Dental Medical Devices Testing CenterPeking University School and Hospital of StomatologyBeijing100081P. R. China
- National Center for Stomatology National Clinical Research Center for Oral DiseasesNational Engineering Research Center of Oral Biomaterials and Digital Medical Devices NMPAKey Laboratory for Dental Materials Beijing Laboratory of Biomedical Materials & Beijing Key Laboratory of Digital StomatologyPeking University School and Hospital of StomatologyBeijing100081P. R. China
| | - Yuning Zhang
- Department of OrthodonticsPeking University School and Hospital of StomatologyBeijing100081P. R. China
| | - Yunyang Bai
- Department of Geriatric DentistryPeking University School and Hospital of StomatologyBeijing100081P. R. China
- National Center for Stomatology National Clinical Research Center for Oral DiseasesNational Engineering Research Center of Oral Biomaterials and Digital Medical Devices NMPAKey Laboratory for Dental Materials Beijing Laboratory of Biomedical Materials & Beijing Key Laboratory of Digital StomatologyPeking University School and Hospital of StomatologyBeijing100081P. R. China
| | - Xiaowen Sun
- Department of Dental Materials & Dental Medical Devices Testing CenterPeking University School and Hospital of StomatologyBeijing100081P. R. China
| | - Yanhui Lu
- Department of Dental Materials & Dental Medical Devices Testing CenterPeking University School and Hospital of StomatologyBeijing100081P. R. China
| | - Yusi Guo
- Department of Geriatric DentistryPeking University School and Hospital of StomatologyBeijing100081P. R. China
- National Center for Stomatology National Clinical Research Center for Oral DiseasesNational Engineering Research Center of Oral Biomaterials and Digital Medical Devices NMPAKey Laboratory for Dental Materials Beijing Laboratory of Biomedical Materials & Beijing Key Laboratory of Digital StomatologyPeking University School and Hospital of StomatologyBeijing100081P. R. China
| | - Ying He
- Department of Geriatric DentistryPeking University School and Hospital of StomatologyBeijing100081P. R. China
- National Center for Stomatology National Clinical Research Center for Oral DiseasesNational Engineering Research Center of Oral Biomaterials and Digital Medical Devices NMPAKey Laboratory for Dental Materials Beijing Laboratory of Biomedical Materials & Beijing Key Laboratory of Digital StomatologyPeking University School and Hospital of StomatologyBeijing100081P. R. China
| | - Min Gao
- Department of Geriatric DentistryPeking University School and Hospital of StomatologyBeijing100081P. R. China
- National Center for Stomatology National Clinical Research Center for Oral DiseasesNational Engineering Research Center of Oral Biomaterials and Digital Medical Devices NMPAKey Laboratory for Dental Materials Beijing Laboratory of Biomedical Materials & Beijing Key Laboratory of Digital StomatologyPeking University School and Hospital of StomatologyBeijing100081P. R. China
| | - Xiaopei Chi
- Department of Geriatric DentistryPeking University School and Hospital of StomatologyBeijing100081P. R. China
- National Center for Stomatology National Clinical Research Center for Oral DiseasesNational Engineering Research Center of Oral Biomaterials and Digital Medical Devices NMPAKey Laboratory for Dental Materials Beijing Laboratory of Biomedical Materials & Beijing Key Laboratory of Digital StomatologyPeking University School and Hospital of StomatologyBeijing100081P. R. China
| | - Boon Chin Heng
- National Center for Stomatology National Clinical Research Center for Oral DiseasesNational Engineering Research Center of Oral Biomaterials and Digital Medical Devices NMPAKey Laboratory for Dental Materials Beijing Laboratory of Biomedical Materials & Beijing Key Laboratory of Digital StomatologyPeking University School and Hospital of StomatologyBeijing100081P. R. China
- Central LaboratoryPeking University School and Hospital of StomatologyBeijing100081P. R. China
| | - Xin Zhang
- Institute of Systems BiomedicineSchool of Basic Medical SciencesNHC Key Laboratory of Medical ImmunologyBeijing Key Laboratory of Tumor Systems BiologyPeking University Health Science CenterBeijing100191P. R. China
| | - Wenjing Li
- Department of Geriatric DentistryPeking University School and Hospital of StomatologyBeijing100081P. R. China
- National Center for Stomatology National Clinical Research Center for Oral DiseasesNational Engineering Research Center of Oral Biomaterials and Digital Medical Devices NMPAKey Laboratory for Dental Materials Beijing Laboratory of Biomedical Materials & Beijing Key Laboratory of Digital StomatologyPeking University School and Hospital of StomatologyBeijing100081P. R. China
| | - Mingming Xu
- Department of Geriatric DentistryPeking University School and Hospital of StomatologyBeijing100081P. R. China
- National Center for Stomatology National Clinical Research Center for Oral DiseasesNational Engineering Research Center of Oral Biomaterials and Digital Medical Devices NMPAKey Laboratory for Dental Materials Beijing Laboratory of Biomedical Materials & Beijing Key Laboratory of Digital StomatologyPeking University School and Hospital of StomatologyBeijing100081P. R. China
| | - Yan Wei
- Department of Geriatric DentistryPeking University School and Hospital of StomatologyBeijing100081P. R. China
- National Center for Stomatology National Clinical Research Center for Oral DiseasesNational Engineering Research Center of Oral Biomaterials and Digital Medical Devices NMPAKey Laboratory for Dental Materials Beijing Laboratory of Biomedical Materials & Beijing Key Laboratory of Digital StomatologyPeking University School and Hospital of StomatologyBeijing100081P. R. China
| | - Fuping You
- Institute of Systems BiomedicineSchool of Basic Medical SciencesNHC Key Laboratory of Medical ImmunologyBeijing Key Laboratory of Tumor Systems BiologyPeking University Health Science CenterBeijing100191P. R. China
| | - Xuehui Zhang
- Department of Dental Materials & Dental Medical Devices Testing CenterPeking University School and Hospital of StomatologyBeijing100081P. R. China
- National Center for Stomatology National Clinical Research Center for Oral DiseasesNational Engineering Research Center of Oral Biomaterials and Digital Medical Devices NMPAKey Laboratory for Dental Materials Beijing Laboratory of Biomedical Materials & Beijing Key Laboratory of Digital StomatologyPeking University School and Hospital of StomatologyBeijing100081P. R. China
- Peking University‐Yunnan Baiyao International Medical Research CenterBeijing100191P. R. China
| | - Dan Lu
- Institute of Systems BiomedicineSchool of Basic Medical SciencesNHC Key Laboratory of Medical ImmunologyBeijing Key Laboratory of Tumor Systems BiologyPeking University Health Science CenterBeijing100191P. R. China
| | - Xuliang Deng
- Department of Geriatric DentistryPeking University School and Hospital of StomatologyBeijing100081P. R. China
- National Center for Stomatology National Clinical Research Center for Oral DiseasesNational Engineering Research Center of Oral Biomaterials and Digital Medical Devices NMPAKey Laboratory for Dental Materials Beijing Laboratory of Biomedical Materials & Beijing Key Laboratory of Digital StomatologyPeking University School and Hospital of StomatologyBeijing100081P. R. China
- Peking University‐Yunnan Baiyao International Medical Research CenterBeijing100191P. R. China
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Xu Q, He L, Zhang S, Di X, Jiang H. Deubiquitinase OTUD3: a double-edged sword in immunity and disease. Front Cell Dev Biol 2023; 11:1237530. [PMID: 37829187 PMCID: PMC10566363 DOI: 10.3389/fcell.2023.1237530] [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: 06/09/2023] [Accepted: 08/28/2023] [Indexed: 10/14/2023] Open
Abstract
Deubiquitination is an important form of post-translational modification that regulates protein homeostasis. Ovarian tumor domain-containing proteins (OTUDs) subfamily member OTUD3 was identified as a deubiquitinating enzyme involved in the regulation of various physiological processes such as immunity and inflammation. Disturbances in these physiological processes trigger diseases in humans and animals, such as cancer, neurodegenerative diseases, diabetes, mastitis, etc. OTUD3 is aberrantly expressed in tumors and is a double-edged sword, exerting tumor-promoting or anti-tumor effects in different types of tumors affecting cancer cell proliferation, metastasis, and metabolism. OTUD3 is regulated at the transcriptional level by a number of MicroRNAs, such as miR-520h, miR-32, and miR101-3p. In addition, OTUD3 is regulated by a number of post-translational modifications, such as acetylation and ubiquitination. Therefore, understanding the regulatory mechanisms of OTUD3 expression can help provide insight into its function in human immunity and disease, offering the possibility of its use as a therapeutic target to diagnose or treat disease.
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Affiliation(s)
- Qiao Xu
- Department of Cell Biology, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Lan He
- School of Biomedical Science, Hunan University, Changsha, Hunan, China
| | - Shubing Zhang
- Department of Cell Biology, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Xiaotang Di
- Department of Cell Biology, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Hao Jiang
- Department of Biomedical Informatics, School of Life Sciences, Central South University, Changsha, Hunan, China
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44
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Shi X, Wu W, Feng Z, Fan P, Shi R, Zhang X. MARCH7-mediated ubiquitination decreases the solubility of ATG14 to inhibit autophagy. Cell Rep 2023; 42:113045. [PMID: 37632749 DOI: 10.1016/j.celrep.2023.113045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 07/07/2023] [Accepted: 08/11/2023] [Indexed: 08/28/2023] Open
Abstract
Autophagy is a fundamental biological process critical to all eukaryotic cellular life. Although autophagy has been increasingly studied, how its process is precisely coordinated remains an open question. ATG14 (ATG14L/Barkor) is known to play a crucial role in both autophagosome formation and autophagosome-lysosome fusion. However, how ATG14 is regulated, especially at the post-translation level, is still not clear. Here, we report that MARCH7 (membrane-associated ring-CH-type finger 7), an E3 ubiquitin ligase, inhibits autophagy by ubiquitinating ATG14. MARCH7 significantly promotes K6-, K11-, and K63-linked mixed polyubiquitination on ATG14, triggering the aggregation of ATG14 and reducing its solubility in cells. Functionally, we find that MARCH7 depletion decreases the number of aggresome-like induced structures (ALISs). Mechanistically, we show that ubiquitinated ATG14 has fewer interactions with STX17, leading to the inhibition of autophagy flux. Collectively, our study reveals a mechanism in regulating autophagy and suggests a potential strategy for the treatment of autophagy-related diseases.
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Affiliation(s)
- Xue Shi
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Center for Cell Lineage and Development, GIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research Centre, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, Guangdong 510530, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wenfeng Wu
- Key Laboratory of Biological Targeting Diagnosis, Therapy and Rehabilitation of Guangdong Higher Education Institutes, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou 510530, China
| | - Zhenhuan Feng
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Center for Cell Lineage and Development, GIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research Centre, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, Guangdong 510530, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Peiyang Fan
- SanQuan College, Xinxiang Medical University, Xinxiang, Henan 453003, China
| | - Ruona Shi
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Center for Cell Lineage and Development, GIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research Centre, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, Guangdong 510530, China
| | - Xiaofei Zhang
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Center for Cell Lineage and Development, GIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research Centre, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, Guangdong 510530, China; University of Chinese Academy of Sciences, Beijing 100049, China; Key Laboratory of Biological Targeting Diagnosis, Therapy and Rehabilitation of Guangdong Higher Education Institutes, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou 510530, China.
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45
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Roberts CG, Franklin TG, Pruneda JN. Ubiquitin-targeted bacterial effectors: rule breakers of the ubiquitin system. EMBO J 2023; 42:e114318. [PMID: 37555693 PMCID: PMC10505922 DOI: 10.15252/embj.2023114318] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 07/10/2023] [Accepted: 07/18/2023] [Indexed: 08/10/2023] Open
Abstract
Regulation through post-translational ubiquitin signaling underlies a large portion of eukaryotic biology. This has not gone unnoticed by invading pathogens, many of which have evolved mechanisms to manipulate or subvert the host ubiquitin system. Bacteria are particularly adept at this and rely heavily upon ubiquitin-targeted virulence factors for invasion and replication. Despite lacking a conventional ubiquitin system of their own, many bacterial ubiquitin regulators loosely follow the structural and mechanistic rules established by eukaryotic ubiquitin machinery. Others completely break these rules and have evolved novel structural folds, exhibit distinct mechanisms of regulation, or catalyze foreign ubiquitin modifications. Studying these interactions can not only reveal important aspects of bacterial pathogenesis but also shed light on unexplored areas of ubiquitin signaling and regulation. In this review, we discuss the methods by which bacteria manipulate host ubiquitin and highlight aspects that follow or break the rules of ubiquitination.
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Affiliation(s)
- Cameron G Roberts
- Department of Molecular Microbiology & ImmunologyOregon Health & Science UniversityPortlandORUSA
| | - Tyler G Franklin
- Department of Molecular Microbiology & ImmunologyOregon Health & Science UniversityPortlandORUSA
| | - Jonathan N Pruneda
- Department of Molecular Microbiology & ImmunologyOregon Health & Science UniversityPortlandORUSA
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46
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Gan J, de Vries J, Akkermans JJLL, Mohammed Y, Tjokrodirijo RTN, de Ru AH, Kim RQ, Vargas DA, Pol V, Fasan R, van Veelen PA, Neefjes J, van Dam H, Ovaa H, Sapmaz A, Geurink PP. Cellular Validation of a Chemically Improved Inhibitor Identifies Monoubiquitination on OTUB2. ACS Chem Biol 2023; 18:2003-2013. [PMID: 37642399 PMCID: PMC10510154 DOI: 10.1021/acschembio.3c00227] [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: 04/19/2023] [Accepted: 08/11/2023] [Indexed: 08/31/2023]
Abstract
Ubiquitin thioesterase OTUB2, a cysteine protease from the ovarian tumor (OTU) deubiquitinase superfamily, is often overexpressed during tumor progression and metastasis. Development of OTUB2 inhibitors is therefore believed to be therapeutically important, yet potent and selective small-molecule inhibitors targeting OTUB2 are scarce. Here, we describe the development of an improved OTUB2 inhibitor, LN5P45, comprising a chloroacethydrazide moiety that covalently reacts to the active-site cysteine residue. LN5P45 shows outstanding target engagement and proteome-wide selectivity in living cells. Importantly, LN5P45 as well as other OTUB2 inhibitors strongly induce monoubiquitination of OTUB2 on lysine 31. We present a route to future OTUB2-related therapeutics and have shown that the OTUB2 inhibitor developed in this study can help to uncover new aspects of the related biology and open new questions regarding the understanding of OTUB2 regulation at the post-translational modification level.
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Affiliation(s)
- Jin Gan
- Department
of Cell and Chemical Biology, Division of Chemical Biology and Drug
Discovery, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, The Netherlands
| | - Jelle de Vries
- Department
of Cell and Chemical Biology, Division of Chemical Biology and Drug
Discovery, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, The Netherlands
| | - Jimmy J. L. L. Akkermans
- Department
of Cell and Chemical Biology and Oncode Institute, Leiden University Medical Center LUMC, Einthovenweg 20, 2333 ZC Leiden, The Netherlands
| | - Yassene Mohammed
- Center
for Proteomics and Metabolomics, Leiden
University Medical Center, Albinusdreef 2, 2333 ZC Leiden, The Netherlands
| | - Rayman T. N. Tjokrodirijo
- Center
for Proteomics and Metabolomics, Leiden
University Medical Center, Albinusdreef 2, 2333 ZC Leiden, The Netherlands
| | - Arnoud H. de Ru
- Center
for Proteomics and Metabolomics, Leiden
University Medical Center, Albinusdreef 2, 2333 ZC Leiden, The Netherlands
| | - Robbert Q. Kim
- Department
of Cell and Chemical Biology, Division of Chemical Biology and Drug
Discovery, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, The Netherlands
| | - David A. Vargas
- Department
of Chemistry, University of Rochester, Hutchison Hall, 120 Trustee Rd, Rochester, New York 14627, United States
| | - Vito Pol
- Department
of Cell and Chemical Biology, Division of Chemical Biology and Drug
Discovery, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, The Netherlands
| | - Rudi Fasan
- Department
of Chemistry, University of Rochester, Hutchison Hall, 120 Trustee Rd, Rochester, New York 14627, United States
| | - Peter A. van Veelen
- Center
for Proteomics and Metabolomics, Leiden
University Medical Center, Albinusdreef 2, 2333 ZC Leiden, The Netherlands
| | - Jacques Neefjes
- Department
of Cell and Chemical Biology and Oncode Institute, Leiden University Medical Center LUMC, Einthovenweg 20, 2333 ZC Leiden, The Netherlands
| | - Hans van Dam
- Department
of Cell and Chemical Biology, Division of Chemical Biology and Drug
Discovery, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, The Netherlands
| | - Huib Ovaa
- Department
of Cell and Chemical Biology, Division of Chemical Biology and Drug
Discovery, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, The Netherlands
| | - Aysegul Sapmaz
- Department
of Cell and Chemical Biology, Division of Chemical Biology and Drug
Discovery, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, The Netherlands
| | - Paul P. Geurink
- Department
of Cell and Chemical Biology, Division of Chemical Biology and Drug
Discovery, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, The Netherlands
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47
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Liu Q, Mallette E, Zheng H, Zhang W. Development of an OTUD1 ubiquitin variant inhibitor. Biochem J 2023; 480:1317-1330. [PMID: 37589489 DOI: 10.1042/bcj20230119] [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: 04/11/2023] [Revised: 08/15/2023] [Accepted: 08/17/2023] [Indexed: 08/18/2023]
Abstract
OTUD1 (Ovarian tumor domain-containing deubiquitinase 1) is a member of the OTU domain-containing deubiquitinase family of enzymes involved in immunoregulation and tumorigenesis pathways. OTUD1 consists of three distinct regions: an unstructured N-terminal region, an OTU-fold catalytic domain, and a ubiquitin-interacting motif (UIM) containing region. Enhanced enzymatic activity and a strong preference for K63-linked substrates are imparted by the UIM containing region. We used phage display with a ubiquitin variant (UbV) library to identify binders for OTUD1 lacking the unstructured N-terminal region (OTUD1OTU + UIM) in an attempt to identify inhibitors bridging the catalytic domain and the UIM containing region. Two UbVs were identified (UbVOD.1 and UbVOD.2) with high affinity and specificity for OTUD1. Of the UbVs identified, UbVOD.1 inhibited OTUD1 activity towards mono-Ub and K63-linked di-Ub substrates in vitro with single-digit nanomolar IC50 and potently inhibited deubiquitinase activity with poly-Ub chains of other linkages. In vivo expression of UbVOD.1 alone was unstable, however as a di-UbV, global deubiquitination and deubiquitinase activity with the OTUD1 substrate RIPK1 were inhibited. Herein we describe the development of molecular tools for exploring the activity of OTUD1 in a cellular context, towards protein-based therapeutics.
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Affiliation(s)
- Qi Liu
- Department of Molecular and Cellular Biology, College of Biological Science, University of Guelph, Guelph N1G 2W1, Canada
| | - Evan Mallette
- Department of Molecular and Cellular Biology, College of Biological Science, University of Guelph, Guelph N1G 2W1, Canada
| | - Hui Zheng
- International Institute of Infection and Immunity, Institutes of Biology and Medical Sciences, Jiangsu Key Laboratory of Infection and Immunity, Soochow University, Suzhou, Jiangsu 215123, China
| | - Wei Zhang
- Department of Molecular and Cellular Biology, College of Biological Science, University of Guelph, Guelph N1G 2W1, Canada
- CIFAR Azrieli Global Scholars Program, Canadian Institute for Advanced Research, Toronto, ON M5G 1M1, Canada
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48
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Li Z, Li G, Li Y, Luo Y, Jiang Y, Zhang Z, Zhou Z, Liu S, Wu C, You F. Deubiquitinase OTUD6A Regulates Innate Immune Response via Targeting UBC13. Viruses 2023; 15:1761. [PMID: 37632103 PMCID: PMC10458163 DOI: 10.3390/v15081761] [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: 06/19/2023] [Revised: 07/28/2023] [Accepted: 07/31/2023] [Indexed: 08/27/2023] Open
Abstract
OTUD6A is a deubiquitinase that plays crucial roles in various human diseases. However, the precise regulatory mechanism of OTUD6A remains unclear. In this study, we found that OTUD6A significantly inhibited the production of type I interferon. Consistently, peritoneal macrophages and bone marrow-derived macrophages from Otud6a-/- mice produced more type I interferon after virus infection compared to cells from WT mice. Otud6a-/-- mice also exhibited increased resistance to lethal HSV-1 and VSV infections, as well as LPS attacks due to decreased inflammatory responses. Mechanistically, mass spectrometry results revealed that UBC13 was an OTUD6A-interacting protein, and the interaction was significantly enhanced after HSV-1 stimulation. Taken together, our findings suggest that OTUD6A plays a crucial role in the innate immune response and may serve as a potential therapeutic target for infectious disease.
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Affiliation(s)
- Zhiwei Li
- College of Life Sciences, Hebei University, Baoding 071002, China; (Z.L.); (Y.J.); (Z.Z.); (Z.Z.)
| | - Guanwen Li
- College of Life Sciences, South China Agricultural University, Guangzhou 510642, China;
| | - Yunfei Li
- Department of Systems Biomedicine, Institute of Systems Biomedicine, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China; (Y.L.); (Y.L.)
| | - Yujie Luo
- Department of Systems Biomedicine, Institute of Systems Biomedicine, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China; (Y.L.); (Y.L.)
| | - Yuhan Jiang
- College of Life Sciences, Hebei University, Baoding 071002, China; (Z.L.); (Y.J.); (Z.Z.); (Z.Z.)
| | - Ziyu Zhang
- College of Life Sciences, Hebei University, Baoding 071002, China; (Z.L.); (Y.J.); (Z.Z.); (Z.Z.)
| | - Ziyi Zhou
- College of Life Sciences, Hebei University, Baoding 071002, China; (Z.L.); (Y.J.); (Z.Z.); (Z.Z.)
| | - Shengde Liu
- Department of Gastrointestinal Oncology, Key Laboratory of Carcinogenesis and Translational Research, Peking University Cancer Hospital and Institute, Beijing 100142, China
| | - Chen Wu
- College of Life Sciences, Hebei University, Baoding 071002, China; (Z.L.); (Y.J.); (Z.Z.); (Z.Z.)
| | - Fuping You
- Department of Systems Biomedicine, Institute of Systems Biomedicine, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China; (Y.L.); (Y.L.)
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49
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Pei HZ, Peng Z, Zhuang X, Wang X, Lu B, Guo Y, Zhao Y, Zhang D, Xiao Y, Gao T, Yu L, He C, Wu S, Baek SH, Zhao ZJ, Xu X, Chen Y. miR-221/222 induce instability of p53 By downregulating deubiquitinase YOD1 in acute myeloid leukemia. Cell Death Discov 2023; 9:249. [PMID: 37454155 DOI: 10.1038/s41420-023-01537-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 06/20/2023] [Accepted: 06/28/2023] [Indexed: 07/18/2023] Open
Abstract
Acute myeloid leukemia (AML) is a hematological malignancy characterized by the impaired differentiation and uncontrolled proliferation of myeloid blasts. Tumor suppressor p53 is often downregulated in AML cells via ubiquitination-mediated degradation. While the role of E3 ligase MDM2 in p53 ubiquitination is well-accepted, little is known about the involvement of deubiquitinases (DUBs). Herein, we found that the expression of YOD1, among several DUBs, is substantially reduced in blood cells from AML patients. We identified that YOD1 deubiqutinated and stabilized p53 through interaction via N-terminus of p53 and OTU domain of YOD1. In addition, expression levels of YOD1 were suppressed by elevated miR-221/222 in AML cells through binding to the 3' untranslated region of YOD1, as verified by reporter gene assays. Treatment of cells with miR-221/222 mimics and inhibitors yielded the expected effects on YOD1 expressions, in agreement with the negative correlation observed between the expression levels of miR-221/222 and YOD1 in AML cells. Finally, overexpression of YOD1 stabilized p53, upregulated pro-apoptotic p53 downstream genes, and increased the sensitivity of AML cells to FLT3 inhibitors remarkably. Collectively, our study identified a pathway connecting miR-221/222, YOD1, and p53 in AML. Targeting miR-221/222 and stimulating YOD1 activity may improve the therapeutic effects of FLT3 inhibitors in patients with AML.
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Affiliation(s)
- Han Zhong Pei
- Department of Hematology, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, 518107, Guangdong, China
| | - Zhiyong Peng
- Nanfang-Chunfu Children's Institute of Hematology, Taixin Hospital, Dongguan, Guangdong, China
| | - Xiaomei Zhuang
- Department of Hematology, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, 518107, Guangdong, China
| | - Xiaobo Wang
- Department of Hematology, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, 518107, Guangdong, China
| | - Bo Lu
- Department of Hematology, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, 518107, Guangdong, China
| | - Yao Guo
- Department of Hematology, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, 518107, Guangdong, China
| | - Yuming Zhao
- Department of Hematology, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, 518107, Guangdong, China
| | - Dengyang Zhang
- Department of Hematology, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, 518107, Guangdong, China
| | - Yunjun Xiao
- Department of Hematology, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, 518107, Guangdong, China
| | - Tianshun Gao
- Department of Hematology, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, 518107, Guangdong, China
| | - Liuting Yu
- Department of Hematology, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, 518107, Guangdong, China
| | - Chunxiao He
- Department of Hematology, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, 518107, Guangdong, China
| | - Shunjie Wu
- Department of Hematology, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, 518107, Guangdong, China
| | - Suk-Hwan Baek
- Department of Biochemistry & Molecular Biology, College of Medicine, Yeungnam University, 170 Hyeonchung-ro, Nam-gu, Daegu, 42415, South Korea.
| | - Zhizhuang Joe Zhao
- Department of Pathology, University of Oklahoma Health Sciences Center, 940 Stanton L. Young Blvd., BMSB 451, Oklahoma City, OK, 73104, USA.
| | - Xiaojun Xu
- Department of Hematology, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, 518107, Guangdong, China.
| | - Yun Chen
- Department of Hematology, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, 518107, Guangdong, China.
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50
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Kang S, Kim G, Choi M, Jeong M, van der Heden van Noort GJ, Roh SH, Shin D. Structural insights into ubiquitin chain cleavage by Legionella ovarian tumor deubiquitinases. Life Sci Alliance 2023; 6:e202201876. [PMID: 37100438 PMCID: PMC10133868 DOI: 10.26508/lsa.202201876] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 04/17/2023] [Accepted: 04/17/2023] [Indexed: 04/28/2023] Open
Abstract
Although ubiquitin is found only in eukaryotes, several pathogenic bacteria and viruses possess proteins that hinder the host ubiquitin system. Legionella, a gram-negative intracellular bacterium, possesses an ovarian tumor (OTU) family of deubiquitinases (Lot DUBs). Herein, we describe the molecular characteristics of Lot DUBs. We elucidated the structure of the LotA OTU1 domain and revealed that entire Lot DUBs possess a characteristic extended helical lobe that is not found in other OTU-DUBs. The structural topology of an extended helical lobe is the same throughout the Lot family, and it provides an S1' ubiquitin-binding site. Moreover, the catalytic triads of Lot DUBs resemble those of the A20-type OTU-DUBs. Furthermore, we revealed a unique mechanism by which LotA OTU domains cooperate together to distinguish the length of the chain and preferentially cleave longer K48-linked polyubiquitin chains. The LotA OTU1 domain itself cleaves K6-linked ubiquitin chains, whereas it is also essential for assisting the cleavage of longer K48-linked polyubiquitin chains by the OTU2 domain. Thus, this study provides novel insights into the structure and mechanism of action of Lot DUBs.
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Affiliation(s)
- Sangwoo Kang
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul, Republic of Korea
| | - Gyuhee Kim
- School of Biological Science, Institute of Molecular Biology and Genetics, Seoul National University, Seoul, Republic of Korea
| | - Minhyeong Choi
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul, Republic of Korea
| | - Minwoo Jeong
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul, Republic of Korea
| | | | - Soung-Hun Roh
- School of Biological Science, Institute of Molecular Biology and Genetics, Seoul National University, Seoul, Republic of Korea
| | - Donghyuk Shin
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul, Republic of Korea
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