1
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Liu D, Cao J, Ding X, Xu W, Yao X, Dai M, Tai Q, Shi M, Fei K, Xu Y, Su B. Disulfiram/copper complex improves the effectiveness of the WEE1 inhibitor Adavosertib in p53 deficient non-small cell lung cancer via ferroptosis. Biochim Biophys Acta Mol Basis Dis 2024; 1870:167455. [PMID: 39111630 DOI: 10.1016/j.bbadis.2024.167455] [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: 01/03/2024] [Revised: 07/25/2024] [Accepted: 08/02/2024] [Indexed: 08/19/2024]
Abstract
Cancer cells lacking functional p53 exhibit poor prognosis, necessitating effective treatment strategies. Inhibiting WEE1, the G2/M cell cycle checkpoint gatekeeper, represents a promising approach for treating p53-deficient NSCLC. Here, we investigate the connection between p53 and WEE1, as well as explore a synergistic therapeutic approach for managing p53-deficient NSCLC. Our study reveals that p53 deficiency upregulates both protein levels and kinase activity of WEE1 by inhibiting its SUMOylation process, thereby enhancing the susceptibility of p53-deficient NSCLC to WEE1 inhibitors. Furthermore, we demonstrate that the WEE1 inhibitor Adavosertib induces intracellular lipid peroxidation, specifically in p53-deficient NSCLC cells, suggesting potential synergy with pro-oxidant reagents. Repurposing Disulfiram (DSF), an alcoholism medication used in combination with copper (Cu), exhibits pro-oxidant properties against NSCLC. The levels of WEE1 protein in p53-deficient NSCLC cells treated with DSF-Cu exhibit a time-dependent increase. Subsequent evaluation of the combination therapy involving Adavosertib and DSF-Cu reveals reduced cell viability along with smaller tumor volumes and lighter tumor weights observed in both p53-deficient cells and xenograft models while correlating with solute carrier family 7-member 11 (SLC7A11)/glutathione-regulated ferroptosis pathway activation. In conclusion, our findings elucidate the molecular interplay between p53 and WEE1 and unveil a novel synergistic therapeutic strategy for treating p53-deficient NSCLC.
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Affiliation(s)
- Di Liu
- Department of Radiation Oncology, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, PR China
| | - Jingxue Cao
- Department of Radiology, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, PR China
| | - Xi Ding
- Department of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, PR China
| | - Wen Xu
- Central Laboratory, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, PR China
| | - Xiaojuan Yao
- Central Laboratory, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, PR China
| | - Mengyuan Dai
- Central Laboratory, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, PR China
| | - Qidong Tai
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, PR China
| | - Minxing Shi
- Central Laboratory, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, PR China
| | - Ke Fei
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, PR China
| | - Yaping Xu
- Department of Radiation Oncology, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, PR China.
| | - Bo Su
- Central Laboratory, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, PR China.
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2
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Zhao S, Li Z, Zhang Q, Zhang Y, Zhang J, Fan G, Cao X, Jiu Y. Discovery of Trametinib as an orchestrator for cytoskeletal vimentin remodeling. J Mol Cell Biol 2024; 16:mjae009. [PMID: 38429984 PMCID: PMC11393047 DOI: 10.1093/jmcb/mjae009] [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: 08/28/2023] [Revised: 12/07/2023] [Accepted: 02/29/2024] [Indexed: 03/03/2024] Open
Abstract
The dynamic remodeling of the cytoskeletal network of vimentin intermediate filaments supports various cellular functions, including cell morphology, elasticity, migration, organelle localization, and resistance against mechanical or pathological stress. Currently available chemicals targeting vimentin predominantly induce network reorganization and shrinkage around the nucleus. Effective tools for long-term manipulation of vimentin network dispersion in living cells are still lacking, limiting in-depth studies on vimentin function and potential therapeutic applications. Here, we verified that a commercially available small molecule, trametinib, is capable of inducing spatial spreading of the cellular vimentin network without affecting its transcriptional or Translational regulation. Further evidence confirmed its low cytotoxicity and similar effects on different cell types. Importantly, Trametinib has no impact on the other two cytoskeletal systems, actin filaments and the microtubule network. Moreover, Trametinib regulates vimentin network dispersion rapidly and efficiently, with effects persisting for up to 48 h after drug withdrawal. We also ruled out the possibility that Trametinib directly affects the phosphorylation level of vimentin. In summary, we identified an unprecedented regulator Trametinib, which is capable of spreading the vimentin network toward the cell periphery, and thus complemented the existing repertoire of vimentin remodeling drugs in the field of cytoskeletal research.
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Affiliation(s)
- Shuangshuang Zhao
- Unit of Cell Biology and Imaging Study of Pathogen Host Interaction, The Center for Microbes, Development and Health, Key Laboratory of Molecular Virology and Immunology, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai 200031, China
| | - Zhifang Li
- Guangzhou National Laboratory, Guangzhou 510005, China
| | - Qian Zhang
- Unit of Cell Biology and Imaging Study of Pathogen Host Interaction, The Center for Microbes, Development and Health, Key Laboratory of Molecular Virology and Immunology, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yue Zhang
- Unit of Cell Biology and Imaging Study of Pathogen Host Interaction, The Center for Microbes, Development and Health, Key Laboratory of Molecular Virology and Immunology, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai 200031, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiali Zhang
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Gaofeng Fan
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Xiaobao Cao
- Guangzhou National Laboratory, Guangzhou 510005, China
| | - Yaming Jiu
- Unit of Cell Biology and Imaging Study of Pathogen Host Interaction, The Center for Microbes, Development and Health, Key Laboratory of Molecular Virology and Immunology, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai 200031, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
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3
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Gou Y, Liu D, Chen M, Wei Y, Huang X, Han C, Feng Z, Zhang C, Lu T, Peng D, Xue Y. GPS-SUMO 2.0: an updated online service for the prediction of SUMOylation sites and SUMO-interacting motifs. Nucleic Acids Res 2024; 52:W238-W247. [PMID: 38709873 PMCID: PMC11223847 DOI: 10.1093/nar/gkae346] [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: 01/31/2024] [Revised: 04/08/2024] [Accepted: 04/18/2024] [Indexed: 05/08/2024] Open
Abstract
Small ubiquitin-like modifiers (SUMOs) are tiny but important protein regulators involved in orchestrating a broad spectrum of biological processes, either by covalently modifying protein substrates or by noncovalently interacting with other proteins. Here, we report an updated server, GPS-SUMO 2.0, for the prediction of SUMOylation sites and SUMO-interacting motifs (SIMs). For predictor training, we adopted three machine learning algorithms, penalized logistic regression (PLR), a deep neural network (DNN), and a transformer, and used 52 404 nonredundant SUMOylation sites in 8262 proteins and 163 SIMs in 102 proteins. To further increase the accuracy of predicting SUMOylation sites, a pretraining model was first constructed using 145 545 protein lysine modification sites, followed by transfer learning to fine-tune the model. GPS-SUMO 2.0 exhibited greater accuracy in predicting SUMOylation sites than did other existing tools. For users, one or multiple protein sequences or identifiers can be input, and the prediction results are shown in a tabular list. In addition to the basic statistics, we integrated knowledge from 35 public resources to annotate SUMOylation sites or SIMs. The GPS-SUMO 2.0 server is freely available at https://sumo.biocuckoo.cn/. We believe that GPS-SUMO 2.0 can serve as a useful tool for further analysis of SUMOylation and SUMO interactions.
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Affiliation(s)
- Yujie Gou
- Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan430074, China
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan430074, China
| | - Dan Liu
- Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan430074, China
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan430074, China
| | - Miaomiao Chen
- Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan430074, China
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan430074, China
| | - Yuxiang Wei
- Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan430074, China
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan430074, China
| | - Xinhe Huang
- Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan430074, China
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan430074, China
| | - Cheng Han
- Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan430074, China
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan430074, China
| | - Zihao Feng
- Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan430074, China
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan430074, China
| | - Chi Zhang
- Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan430074, China
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan430074, China
| | - Teng Lu
- Computer Network Information Center, Chinese Academy of Sciences, Beijing100190, China
| | - Di Peng
- Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan430074, China
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan430074, China
| | - Yu Xue
- Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan430074, China
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan430074, China
- Nanjing University Institute of Artificial Intelligence Biomedicine, Nanjing210031, China
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4
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Connors CQ, Mauro MS, Wiles JT, Countryman AD, Martin SL, Lacroix B, Shirasu-Hiza M, Dumont J, Kasza KE, Davies TR, Canman JC. Germ fate determinants protect germ precursor cell division by reducing septin and anillin levels at the cell division plane. Mol Biol Cell 2024; 35:ar94. [PMID: 38696255 PMCID: PMC11244169 DOI: 10.1091/mbc.e24-02-0096-t] [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: 03/08/2024] [Revised: 04/22/2024] [Accepted: 04/26/2024] [Indexed: 05/04/2024] Open
Abstract
Animal cell cytokinesis, or the physical division of one cell into two, is thought to be driven by constriction of an actomyosin contractile ring at the division plane. The mechanisms underlying cell type-specific differences in cytokinesis remain unknown. Germ cells are totipotent cells that pass genetic information to the next generation. Previously, using formincyk-1(ts) mutant Caenorhabditis elegans 4-cell embryos, we found that the P2 germ precursor cell is protected from cytokinesis failure and can divide with greatly reduced F-actin levels at the cell division plane. Here, we identified two canonical germ fate determinants required for P2-specific cytokinetic protection: PIE-1 and POS-1. Neither has been implicated previously in cytokinesis. These germ fate determinants protect P2 cytokinesis by reducing the accumulation of septinUNC-59 and anillinANI-1 at the division plane, which here act as negative regulators of cytokinesis. These findings may provide insight into the regulation of cytokinesis in other cell types, especially in stem cells with high potency.
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Affiliation(s)
- Caroline Q. Connors
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY 10032
| | - Michael S. Mauro
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY 10032
| | - J. Tristian Wiles
- Department of Biological Sciences, Columbia University, New York, NY 10027
| | | | - Sophia L. Martin
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY 10032
| | - Benjamin Lacroix
- Université Paris Cité, CNRS, Institut Jacques Monod, F-75013 Paris, France
- Université de Montpellier, CNRS, Centre de Recherche en Biologie Cellulaire de Montpellier, UMR 5237 Montpellier, France
| | - Mimi Shirasu-Hiza
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032
| | - Julien Dumont
- Université Paris Cité, CNRS, Institut Jacques Monod, F-75013 Paris, France
| | - Karen E. Kasza
- Department of Mechanical Engineering, Columbia University, New York, NY 10027
| | - Timothy R. Davies
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY 10032
- Department of Biosciences, Durham University, Durham DH1 3LE, UK
| | - Julie C. Canman
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY 10032
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5
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Hao B, Chen K, Zhai L, Liu M, Liu B, Tan M. Substrate and Functional Diversity of Protein Lysine Post-translational Modifications. GENOMICS, PROTEOMICS & BIOINFORMATICS 2024; 22:qzae019. [PMID: 38862432 DOI: 10.1093/gpbjnl/qzae019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/01/2023] [Revised: 11/11/2023] [Accepted: 01/08/2024] [Indexed: 06/13/2024]
Abstract
Lysine post-translational modifications (PTMs) are widespread and versatile protein PTMs that are involved in diverse biological processes by regulating the fundamental functions of histone and non-histone proteins. Dysregulation of lysine PTMs is implicated in many diseases, and targeting lysine PTM regulatory factors, including writers, erasers, and readers, has become an effective strategy for disease therapy. The continuing development of mass spectrometry (MS) technologies coupled with antibody-based affinity enrichment technologies greatly promotes the discovery and decoding of PTMs. The global characterization of lysine PTMs is crucial for deciphering the regulatory networks, molecular functions, and mechanisms of action of lysine PTMs. In this review, we focus on lysine PTMs, and provide a summary of the regulatory enzymes of diverse lysine PTMs and the proteomics advances in lysine PTMs by MS technologies. We also discuss the types and biological functions of lysine PTM crosstalks on histone and non-histone proteins and current druggable targets of lysine PTM regulatory factors for disease therapy.
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Affiliation(s)
- Bingbing Hao
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Tianjian Laboratory of Advanced Biomedical Sciences, Institute of Advanced Biomedical Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Kaifeng Chen
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Linhui Zhai
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan 528400, China
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing 210023, China
| | - Muyin Liu
- Department of Cardiology, Shanghai Institute of Cardiovascular Diseases, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Bin Liu
- Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, College of Pharmacy, Jiangsu Ocean University, Lianyungang 222005, China
| | - Minjia Tan
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan 528400, China
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6
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Zhu G, Tong N, Zhu Y, Wang L, Wang Q. The crosstalk between SUMOylation and immune system in host-pathogen interactions. Crit Rev Microbiol 2024:1-23. [PMID: 38619159 DOI: 10.1080/1040841x.2024.2339259] [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: 10/31/2023] [Accepted: 04/01/2024] [Indexed: 04/16/2024]
Abstract
Pathogens can not only cause infectious diseases, immune system diseases, and chronic diseases, but also serve as potential triggers or initiators for certain tumors. They directly or indirectly damage human health and are one of the leading causes of global deaths. Small ubiquitin-like modifier (SUMO) modification, a type of protein post-translational modification (PTM) that occurs when SUMO groups bond covalently to particular lysine residues on substrate proteins, plays a crucial role in both innate and adaptive immunologic responses, as well as pathogen-host immune system crosstalk. SUMOylation participates in the host's defense against pathogens by regulating immune responses, while numerically vast and taxonomically diverse pathogens have evolved to exploit the cellular SUMO modification system to break through innate defenses. Here, we describe the characteristics and multiple functions of SUMOylation as a pivotal PTM mechanism, the tactics employed by various pathogens to counteract the immune system through targeting host SUMOylation, and the character of the SUMOylation system in the fight between pathogens and the host immune system. We have also included a summary of the potential anti-pathogen SUMO enzyme inhibitors. This review serves as a reference for basic research and clinical practice in the diagnosis, prognosis, and treatment of pathogenic microorganism-caused disorders.
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Affiliation(s)
- Gangli Zhu
- Guangdong Province Solid Waste Recycling and Heavy Metal Pollution Control Engineering Technology Research Center, Guangdong Polytechnic of Environment Protection Engineering, Foshan, Guangdong, China
| | - Ni Tong
- Department of Molecular Biology, State Administration of Traditional Chinese Medicine of the People's Republic of China, School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, Guangdong, China
- Shenzhen Traditional Chinese Medicine Hospital, Shenzhen, Guangdong, China
| | - Yipeng Zhu
- Guagnzhou NO.6 Middle school, Guangzhou, Guangdong, China
| | - Lize Wang
- General Department, Institute of Software Chinese Academy of Sciences, Beijing, China
| | - Qirui Wang
- Department of Molecular Biology, State Administration of Traditional Chinese Medicine of the People's Republic of China, School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, Guangdong, China
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7
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Fan SH, Li N, Huang KF, Chang YT, Wu CC, Chen SL. MyoD Over-Expression Rescues GST-bFGF Repressed Myogenesis. Int J Mol Sci 2024; 25:4308. [PMID: 38673893 PMCID: PMC11050597 DOI: 10.3390/ijms25084308] [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: 03/11/2024] [Revised: 04/10/2024] [Accepted: 04/11/2024] [Indexed: 04/28/2024] Open
Abstract
During embryogenesis, basic fibroblast growth factor (bFGF) is released from neural tube and myotome to promote myogenic fate in the somite, and is routinely used for the culture of adult skeletal muscle (SKM) stem cells (MuSC, called satellite cells). However, the mechanism employed by bFGF to promote SKM lineage and MuSC proliferation has not been analyzed in detail. Furthermore, the question of if the post-translational modification (PTM) of bFGF is important to its stemness-promoting effect has not been answered. In this study, GST-bFGF was expressed and purified from E.coli, which lacks the PTM system in eukaryotes. We found that both GST-bFGF and commercially available bFGF activated the Akt-Erk pathway and had strong cell proliferation effect on C2C12 myoblasts and MuSC. GST-bFGF reversibly compromised the myogenesis of C2C12 myoblasts and MuSC, and it increased the expression of Myf5, Pax3/7, and Cyclin D1 but strongly repressed that of MyoD, suggesting the maintenance of myogenic stemness amid repressed MyoD expression. The proliferation effect of GST-bFGF was conserved in C2C12 over-expressed with MyoD (C2C12-tTA-MyoD), implying its independence of the down-regulation of MyoD. In addition, the repressive effect of GST-bFGF on myogenic differentiation was almost totally rescued by the over-expression of MyoD. Together, these evidences suggest that (1) GST-bFGF and bFGF have similar effects on myogenic cell proliferation and differentiation, and (2) GST-bFGF can promote MuSC stemness and proliferation by differentially regulating MRFs and Pax3/7, (3) MyoD repression by GST-bFGF is reversible and independent of the proliferation effect, and (4) GST-bFGF can be a good substitute for bFGF in sustaining MuSC stemness and proliferation.
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Affiliation(s)
| | | | | | | | | | - Shen-Liang Chen
- Department of Life Sciences, National Central University, Jhongli 32001, Taiwan; (S.-H.F.); (N.L.); (K.-F.H.); (Y.-T.C.); (C.-C.W.)
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8
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Park SLL, Ramírez-Jarquín UN, Shahani N, Rivera O, Sharma M, Joshi PS, Hansalia A, Dagar S, McManus FP, Thibault P, Subramaniam S. SUMO modifies GβL and mediates mTOR signaling. J Biol Chem 2024; 300:105778. [PMID: 38395307 PMCID: PMC10982569 DOI: 10.1016/j.jbc.2024.105778] [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: 09/08/2023] [Revised: 01/25/2024] [Accepted: 02/09/2024] [Indexed: 02/25/2024] Open
Abstract
The mechanistic target of rapamycin (mTOR) signaling is influenced by multiple regulatory proteins and post-translational modifications; however, underlying mechanisms remain unclear. Here, we report a novel role of small ubiquitin-like modifier (SUMO) in mTOR complex assembly and activity. By investigating the SUMOylation status of core mTOR components, we observed that the regulatory subunit, GβL (G protein β-subunit-like protein, also known as mLST8), is modified by SUMO1, 2, and 3 isoforms. Using mutagenesis and mass spectrometry, we identified that GβL is SUMOylated at lysine sites K86, K215, K245, K261, and K305. We found that SUMO depletion reduces mTOR-Raptor (regulatory protein associated with mTOR) and mTOR-Rictor (rapamycin-insensitive companion of mTOR) complex formation and diminishes nutrient-induced mTOR signaling. Reconstitution with WT GβL but not SUMOylation-defective KR mutant GβL promotes mTOR signaling in GβL-depleted cells. Taken together, we report for the very first time that SUMO modifies GβL, influences the assembly of mTOR protein complexes, and regulates mTOR activity.
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Affiliation(s)
| | | | - Neelam Shahani
- Department of Neuroscience, The Wertheim UF Scripps Institute, Jupiter, Florida, USA
| | - Oscar Rivera
- Department of Neuroscience, The Wertheim UF Scripps Institute, Jupiter, Florida, USA
| | - Manish Sharma
- Department of Neuroscience, The Wertheim UF Scripps Institute, Jupiter, Florida, USA
| | | | - Aayushi Hansalia
- Department of Neuroscience, The Wertheim UF Scripps Institute, Jupiter, Florida, USA
| | - Sunayana Dagar
- Department of Neuroscience, The Wertheim UF Scripps Institute, Jupiter, Florida, USA
| | - Francis P McManus
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Quebec, Canada
| | - Pierre Thibault
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Quebec, Canada; Department of Chemistry, Université de Montréal, Montréal, Quebec, Canada
| | - Srinivasa Subramaniam
- Department of Neuroscience, The Wertheim UF Scripps Institute, Jupiter, Florida, USA; The Skaggs Graduate School of Chemical and Biological Sciences, The Scripps Research Institute, La Jolla, California, USA; Norman Fixel Institute for Neurological Diseases, Gainesville, Florida, USA.
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9
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Kumar J, Uppulapu SK, Kumari S, Sharma K, Paradee W, Yadav RP, Kumar V, Kumar S. P66Shc Mediates SUMO2-induced Endothelial Dysfunction. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.24.577109. [PMID: 38328241 PMCID: PMC10849724 DOI: 10.1101/2024.01.24.577109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Sumoylation is a post-translational modification that can regulate different physiological functions. Increased sumoylation, specifically conjugation of SUMO2/3 (small ubiquitin like modifier 2/3), is detrimental to vascular health. However, the molecular mechanism mediating this effect is poorly understood. Here, we demonstrate that SUMO2 modifies p66Shc, which impairs endothelial function. Using multiple approaches, we show that p66Shc is a direct target of SUMO2. Mass spectrometry identified that SUMO2 modified lysine-81 in the unique collagen homology-2 domain of p66Shc. SUMO2ylation of p66Shc increased phosphorylation at serine-36, causing it to translocate to the mitochondria. Notably, sumoylation-deficient p66Shc (p66ShcK81R) was resistant to SUMO2-induced p66ShcS36 phosphorylation and mitochondrial translocation. Ingenuity pathway analysis showed that majority of effects of p66Shc SUMO2ylation were mediated via p66ShcK81. Finally, p66ShcK81R knockin mice were resistant to SUMO2-induced endothelial dysfunction. Collectively, our work uncovers a posttranslational modification of redox protein p66Shc and identifies SUMO2-p66Shc signaling as a regulator of vascular endothelial function.
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10
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Chen Y, Liu K, Zhang G, Cheng J, Tu J. Monoclonal antibody-based systematic identification of SUMO1-modification sites reveals TFII-I SUMOylation is involved in tumor growth. J Cell Physiol 2024; 239:e31080. [PMID: 37450667 DOI: 10.1002/jcp.31080] [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: 04/29/2023] [Revised: 06/23/2023] [Accepted: 06/30/2023] [Indexed: 07/18/2023]
Abstract
SUMOylation plays an essential role in diverse physiological and pathological processes. Identification of wild-type SUMO1-modification sites by mass spectrometry is still challenging. In this study, we produced a monoclonal SUMO1C-K antibody recognizing SUMOylated peptides and proposed an efficient streamline for identification of SUMOylation sites. We identified 471 SUMOylation sites in 325 proteins from five raw data. These identified sites exhibit a high positive rate when evaluated by mutation-verified SUMOylation sites. We identified many SUMOylated proteins involved in mitochondrial metabolism and non-membrane-bounded organelles formation. We proposed a SUMOylation motif, ΨKXD/EP, where proline is required for efficient SUMOylation. We further revealed SUMOylation of TFII-I was stimulated by growth signals and was required for nucleus-localization of p-ERK1/2. Mutation of SUMOylation sites of TFII-I suppressed tumor cell growth in vitro and in vivo. Taken together, we provided a strategy for personalized identification of wild-type SUMO1-modification sites and revealed the physiological significance of TFII-I SUMOylation in this study.
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Affiliation(s)
- Yalan Chen
- Department of Biochemistry and Molecular Cell Biology, Shanghai Key Laboratory for Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Kexin Liu
- Department of Biochemistry and Molecular Cell Biology, Shanghai Key Laboratory for Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Geqiang Zhang
- Department of Biochemistry and Molecular Cell Biology, Shanghai Key Laboratory for Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jinke Cheng
- Department of Biochemistry and Molecular Cell Biology, Shanghai Key Laboratory for Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jun Tu
- Department of Biochemistry and Molecular Cell Biology, Shanghai Key Laboratory for Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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11
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Hammami NEH, Mérindol N, Plourde MB, Maisonnet T, Lebel S, Berthoux L. SUMO-3 promotes the ubiquitin-dependent turnover of TRIM55. Biochem Cell Biol 2024; 102:73-84. [PMID: 37703582 DOI: 10.1139/bcb-2023-0153] [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] [Indexed: 09/15/2023] Open
Abstract
Human muscle-specific RING fingers (MURFs) are members of the tripartite motif (TRIM) family of proteins characterized by their C-terminal subgroup one signature domain. MURFs play a role in sarcomere formation and microtubule dynamics. It was previously established that some TRIMs undergo post-translational modification by small ubiquitin-like modifier (SUMO). In this study, we explored the putative SUMOylation of MURF proteins as well as their interactions with SUMO. MURF proteins (TRIM54, TRIM55, and TRIM63) were not found to be SUMOylated. However, TRIM55 turnover by proteasomal and lysosomal degradation was higher upon overexpression of SUMO-3 but not of SUMO-1. Furthermore, it is predicted that TRIM55 contains two potential SUMO-interacting motifs (SIMs). We found that SIM1- and SIM2-mutated TRIM55 were more stable than the wild-type (WT) protein partly due to decreased degradation. Consistently, SIM-mutated TRIM55 was less polyubiquitinated than the WT protein, despite similar monoubiquitination levels. Using IF microscopy, we observed that SIM motifs influenced TRIM55 subcellular localization. In conclusion, our results suggest that SUMO-3 or SUMO-3-modified proteins modulate the localization, stability, and RING ubiquitin ligase activity of TRIM55.
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Affiliation(s)
- Nour-El-Houda Hammami
- Department of medical biology, Université du Québec à Trois-Rivières, Trois-Rivières, QC, Canada
| | - Natacha Mérindol
- Department of medical biology, Université du Québec à Trois-Rivières, Trois-Rivières, QC, Canada
| | - Mélodie B Plourde
- Department of medical biology, Université du Québec à Trois-Rivières, Trois-Rivières, QC, Canada
| | - Tara Maisonnet
- Department of medical biology, Université du Québec à Trois-Rivières, Trois-Rivières, QC, Canada
| | - Sophie Lebel
- Department of medical biology, Université du Québec à Trois-Rivières, Trois-Rivières, QC, Canada
| | - Lionel Berthoux
- Department of medical biology, Université du Québec à Trois-Rivières, Trois-Rivières, QC, Canada
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12
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Filippopoulou C, Thomé CC, Perdikari S, Ntini E, Simos G, Bohnsack KE, Chachami G. Hypoxia-driven deSUMOylation of EXOSC10 promotes adaptive changes in the transcriptome profile. Cell Mol Life Sci 2024; 81:58. [PMID: 38279024 PMCID: PMC10817850 DOI: 10.1007/s00018-023-05035-9] [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: 07/10/2023] [Revised: 10/12/2023] [Accepted: 11/06/2023] [Indexed: 01/28/2024]
Abstract
Reduced oxygen availability (hypoxia) triggers adaptive cellular responses via hypoxia-inducible factor (HIF)-dependent transcriptional activation. Adaptation to hypoxia also involves transcription-independent processes like post-translational modifications; however, these mechanisms are poorly characterized. Investigating the involvement of protein SUMOylation in response to hypoxia, we discovered that hypoxia strongly decreases the SUMOylation of Exosome subunit 10 (EXOSC10), the catalytic subunit of the RNA exosome, in an HIF-independent manner. EXOSC10 is a multifunctional exoribonuclease enriched in the nucleolus that mediates the processing and degradation of various RNA species. We demonstrate that the ubiquitin-specific protease 36 (USP36) SUMOylates EXOSC10 and we reveal SUMO1/sentrin-specific peptidase 3 (SENP3) as the enzyme-mediating deSUMOylation of EXOSC10. Under hypoxia, EXOSC10 dissociates from USP36 and translocates from the nucleolus to the nucleoplasm concomitant with its deSUMOylation. Loss of EXOSC10 SUMOylation does not detectably affect rRNA maturation but affects the mRNA transcriptome by modulating the expression levels of hypoxia-related genes. Our data suggest that dynamic modulation of EXOSC10 SUMOylation and localization under hypoxia regulates the RNA degradation machinery to facilitate cellular adaptation to low oxygen conditions.
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Affiliation(s)
- Chrysa Filippopoulou
- Laboratory of Biochemistry, Faculty of Medicine, University of Thessaly, Biopolis, 41500, Larissa, Greece
| | - Chairini C Thomé
- Department of Molecular Biology, University Medical Center Göttingen, 37073, Göttingen, Germany
| | - Sofia Perdikari
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas (FORTH), 70013, Heraklion, Greece
| | - Evgenia Ntini
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas (FORTH), 70013, Heraklion, Greece
| | - George Simos
- Laboratory of Biochemistry, Faculty of Medicine, University of Thessaly, Biopolis, 41500, Larissa, Greece
- Gerald Bronfman Department of Oncology, Faculty of Medicine, McGill University, Montreal, Canada
| | - Katherine E Bohnsack
- Department of Molecular Biology, University Medical Center Göttingen, 37073, Göttingen, Germany
| | - Georgia Chachami
- Laboratory of Biochemistry, Faculty of Medicine, University of Thessaly, Biopolis, 41500, Larissa, Greece.
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13
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Fernandez A, Corvalan K, Santis O, Mendez-Ruette M, Caviedes A, Pizarro M, Gomez MT, Batiz LF, Landgraf P, Kahne T, Rojas-Fernandez A, Wyneken U. Sumoylation in astrocytes induces changes in the proteome of the derived small extracellular vesicles which change protein synthesis and dendrite morphology in target neurons. Brain Res 2024; 1823:148679. [PMID: 37972846 DOI: 10.1016/j.brainres.2023.148679] [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: 08/25/2023] [Revised: 11/01/2023] [Accepted: 11/13/2023] [Indexed: 11/19/2023]
Abstract
Emerging evidence highlights the relevance of the protein post-translational modification by SUMO (Small Ubiquitin-like Modifier) in the central nervous system for modulating cognition and plasticity in health and disease. In these processes, astrocyte-to-neuron crosstalk mediated by extracellular vesicles (EVs) plays a yet poorly understood role. Small EVs (sEVs), including microvesicles and exosomes, contain a molecular cargo of lipids, proteins, and nucleic acids that define their biological effect on target cells. Here, we investigated whether SUMOylation globally impacts the sEV protein cargo. For this, sEVs were isolated from primary cultures of astrocytes by ultracentrifugation or using a commercial sEV isolation kit. SUMO levels were regulated: 1) via plasmids that over-express SUMO, or 2) via experimental conditions that increase SUMOylation, i.e., by using the stress hormone corticosterone, or 3) via the SUMOylation inhibitor 2-D08 (2',3',4'-trihydroxy-flavone, 2-(2,3,4-Trihydroxyphenyl)-4H-1-Benzopyran-4-one). Corticosterone and 2-D08 had opposing effects on the number of sEVs and on their protein cargo. Proteomic analysis showed that increased SUMOylation in corticosterone-treated or plasmid-transfected astrocytes increased the presence of proteins related to cell division, transcription, and protein translation in the derived sEVs. When sEVs derived from corticosterone-treated astrocytes were transferred to neurons to assess their impact on protein synthesis using the fluorescence non-canonical amino acid tagging assay (FUNCAT), we detected an increase in protein synthesis, while sEVs from 2-D08-treated astrocytes had no effect. Our results show that SUMO conjugation plays an important role in the modulation of the proteome of astrocyte-derived sEVs with a potential functional impact on neurons.
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Affiliation(s)
- Anllely Fernandez
- Centro de Investigación e Innovación Biomédica (CIIB), Facultad de Medicina, Universidad de los Andes, Santiago 7620001, Chile
| | - Katherine Corvalan
- Centro de Investigación e Innovación Biomédica (CIIB), Facultad de Medicina, Universidad de los Andes, Santiago 7620001, Chile
| | - Octavia Santis
- Centro de Investigación e Innovación Biomédica (CIIB), Facultad de Medicina, Universidad de los Andes, Santiago 7620001, Chile
| | - Maxs Mendez-Ruette
- Centro de Investigación e Innovación Biomédica (CIIB), Facultad de Medicina, Universidad de los Andes, Santiago 7620001, Chile
| | - Ariel Caviedes
- Centro de Investigación e Innovación Biomédica (CIIB), Facultad de Medicina, Universidad de los Andes, Santiago 7620001, Chile
| | - Matias Pizarro
- Centro de Investigación e Innovación Biomédica (CIIB), Facultad de Medicina, Universidad de los Andes, Santiago 7620001, Chile
| | - Maria-Teresa Gomez
- Centro de Investigación e Innovación Biomédica (CIIB), Facultad de Medicina, Universidad de los Andes, Santiago 7620001, Chile
| | - Luis Federico Batiz
- Centro de Investigación e Innovación Biomédica (CIIB), Facultad de Medicina, Universidad de los Andes, Santiago 7620001, Chile
| | - Peter Landgraf
- Institute for Pharmacology and Toxicology, Medical Faculty, Otto-von-Guericke University, Germany, 39120 Magdeburg, Germany
| | - Thilo Kahne
- Institute of Experimental Internal Medicine, Medical Faculty, Otto-von-Guericke University, 39120 Magdeburg, Germany
| | - Alejandro Rojas-Fernandez
- Instituto de Medicina & Centro Interdisciplinario de Estudios del Sistema Nervioso (CISNe), Universidad Austral de Chile, Valdivia 5110566, Chile
| | - Ursula Wyneken
- Centro de Investigación e Innovación Biomédica (CIIB), Facultad de Medicina, Universidad de los Andes, Santiago 7620001, Chile; IMPACT, Center of Interventional Medicine for Precision and Advanced Cellular Therapy, Santiago 7620001, Chile.
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14
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Ren J, Wang S, Zong Z, Pan T, Liu S, Mao W, Huang H, Yan X, Yang B, He X, Zhou F, Zhang L. TRIM28-mediated nucleocapsid protein SUMOylation enhances SARS-CoV-2 virulence. Nat Commun 2024; 15:244. [PMID: 38172120 PMCID: PMC10764958 DOI: 10.1038/s41467-023-44502-6] [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: 06/15/2023] [Accepted: 12/15/2023] [Indexed: 01/05/2024] Open
Abstract
Viruses, as opportunistic intracellular parasites, hijack the cellular machinery of host cells to support their survival and propagation. Numerous viral proteins are subjected to host-mediated post-translational modifications. Here, we demonstrate that the SARS-CoV-2 nucleocapsid protein (SARS2-NP) is SUMOylated on the lysine 65 residue, which efficiently mediates SARS2-NP's ability in homo-oligomerization, RNA association, liquid-liquid phase separation (LLPS). Thereby the innate antiviral immune response is suppressed robustly. These roles can be achieved through intermolecular association between SUMO conjugation and a newly identified SUMO-interacting motif in SARS2-NP. Importantly, the widespread SARS2-NP R203K mutation gains a novel site of SUMOylation which further increases SARS2-NP's LLPS and immunosuppression. Notably, the SUMO E3 ligase TRIM28 is responsible for catalyzing SARS2-NP SUMOylation. An interfering peptide targeting the TRIM28 and SARS2-NP interaction was screened out to block SARS2-NP SUMOylation and LLPS, and consequently inhibit SARS-CoV-2 replication and rescue innate antiviral immunity. Collectively, these data support SARS2-NP SUMOylation is critical for SARS-CoV-2 virulence, and therefore provide a strategy to antagonize SARS-CoV-2.
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Affiliation(s)
- Jiang Ren
- The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen, 518033, China
| | - Shuai Wang
- Institutes of Biology and Medical Sciences, Soochow University, Suzhou, 215123, China
| | - Zhi Zong
- MOE Key Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou, 310058, China
| | - Ting Pan
- Shenzhen Key Laboratory of Systems Medicine for Inflammatory Diseases, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Shenzhen, 518107, China
| | - Sijia Liu
- International Biomed-X Research Center, Second Affiliated Hospital of Zhejiang University, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Wei Mao
- Zhejiang Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Huizhe Huang
- Faculty of Basic Medical Sciences, Chongqing Medical University, Chongqing, 400016, China
| | - Xiaohua Yan
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Nanchang University, Nanchang, 330031, China
| | - Bing Yang
- MOE Key Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou, 310058, China
- Department of Pharmaceutical Chemistry and the Cardiovascular Research Institute, University of California, San Francisco, CA, 94158, USA
| | - Xin He
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China.
| | - Fangfang Zhou
- Institutes of Biology and Medical Sciences, Soochow University, Suzhou, 215123, China.
| | - Long Zhang
- The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen, 518033, China.
- MOE Key Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou, 310058, China.
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15
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Dong D, Du Y, Fei X, Yang H, Li X, Yang X, Ma J, Huang S, Ma Z, Zheng J, Chan DW, Shi L, Li Y, Irving AT, Yuan X, Liu X, Ni P, Hu Y, Meng G, Peng Y, Sadler A, Xu D. Inflammasome activity is controlled by ZBTB16-dependent SUMOylation of ASC. Nat Commun 2023; 14:8465. [PMID: 38123560 PMCID: PMC10733316 DOI: 10.1038/s41467-023-43945-1] [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: 07/29/2022] [Accepted: 11/24/2023] [Indexed: 12/23/2023] Open
Abstract
Inflammasome activity is important for the immune response and is instrumental in numerous clinical conditions. Here we identify a mechanism that modulates the central Caspase-1 and NLR (Nod-like receptor) adaptor protein ASC (apoptosis-associated speck-like protein containing a CARD). We show that the function of ASC in assembling the inflammasome is controlled by its modification with SUMO (small ubiquitin-like modifier) and identify that the nuclear ZBTB16 (zinc-finger and BTB domain-containing protein 16) promotes this SUMOylation. The physiological significance of this activity is demonstrated through the reduction of acute inflammatory pathogenesis caused by a constitutive hyperactive inflammasome by ablating ZBTB16 in a mouse model of Muckle-Wells syndrome. Together our findings identify an further mechanism by which ZBTB16-dependent control of ASC SUMOylation assembles the inflammasome to promote this pro-inflammatory response.
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Affiliation(s)
- Danfeng Dong
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- College of Health Sciences and Technology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yuzhang Du
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- College of Health Sciences and Technology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xuefeng Fei
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- College of Health Sciences and Technology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Hao Yang
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- College of Health Sciences and Technology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiaofang Li
- Assisted Reproduction Center, Northwest Women's and Children's Hospital, Xi'an, Shaanxi Province, 710003, China
| | - Xiaobao Yang
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- College of Health Sciences and Technology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Junrui Ma
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- College of Health Sciences and Technology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Shu Huang
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- College of Health Sciences and Technology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhihui Ma
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- College of Health Sciences and Technology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Juanjuan Zheng
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- College of Health Sciences and Technology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - David W Chan
- School of Medicine, The Chinese University of Hong Kong-Shenzhen, Shenzhen, China
| | - Liyun Shi
- Department of Microbiology and Immunology, Nanjing University of Chinese Medicine, Nanjing, China
| | - Yunqi Li
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Aaron T Irving
- Department of Clinical Laboratory Studies, Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Centre for Infection, Immunity &Cancer, Zhejiang University-University of Edinburgh Institute, Zhejiang University School of Medicine, Zhejiang University, Haining, China
| | - Xiangliang Yuan
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- College of Health Sciences and Technology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiangfan Liu
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- College of Health Sciences and Technology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Peihua Ni
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- College of Health Sciences and Technology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yiqun Hu
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- College of Health Sciences and Technology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Guangxun Meng
- The Center for Microbes, Development and Health, CAS Key Laboratory of Molecular Virology & Immunology, Shanghai Institute of Immunity and Infection, University of Chinese Academy of Sciences, Shanghai, 200031, China
| | - Yibing Peng
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
- College of Health Sciences and Technology, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Anthony Sadler
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, 27-31 Wright Street, Clayton, VIC, 3168, Australia.
- Department of Molecular and Translational Science, Monash University, Clayton, VIC, Australia.
| | - Dakang Xu
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
- College of Health Sciences and Technology, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
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16
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Connors CQ, Mauro MS, Tristian Wiles J, Countryman AD, Martin SL, Lacroix B, Shirasu-Hiza M, Dumont J, Kasza KE, Davies TR, Canman JC. Germ fate determinants protect germ precursor cell division by restricting septin and anillin levels at the division plane. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.17.566773. [PMID: 38014027 PMCID: PMC10680835 DOI: 10.1101/2023.11.17.566773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Animal cell cytokinesis, or the physical division of one cell into two, is thought to be driven by constriction of an actomyosin contractile ring at the division plane. The mechanisms underlying cell type-specific differences in cytokinesis remain unknown. Germ cells are totipotent cells that pass genetic information to the next generation. Previously, using formin cyk-1 (ts) mutant C. elegans embryos, we found that the P2 germ precursor cell is protected from cytokinesis failure and can divide without detectable F-actin at the division plane. Here, we identified two canonical germ fate determinants required for P2-specific cytokinetic protection: PIE-1 and POS-1. Neither has been implicated previously in cytokinesis. These germ fate determinants protect P2 cytokinesis by reducing the accumulation of septin UNC-59 and anillin ANI-1 at the division plane, which here act as negative regulators of cytokinesis. These findings may provide insight into cytokinetic regulation in other cell types, especially in stem cells with high potency.
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17
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Zhang Y, Ji P, Zhang M, Tran NT, Li S. Large-scale lysine crotonylation analysis reveals the role of TRAF6-Ecsit complex in endoplasmic reticulum stress in mud crab (Scylla paramamosain). DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2023; 148:104898. [PMID: 37531975 DOI: 10.1016/j.dci.2023.104898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 07/26/2023] [Accepted: 07/30/2023] [Indexed: 08/04/2023]
Abstract
Lysine crotonylation (Kcr) is a newly discovered type of post-translational modification. Although Kcr has been reported in several species, its role in crustaceans remains largely unknown. In this study, Kcr in hemocytes of mud crab (Scylla paramamosain) was characterized using pan anti-crotonyllysine antibody enrichment and high-resolution liquid chromatogram-mass spectrometry analysis after SpTRAF6 or SpEcsit silencing. Altogether, 1,800 Kcr sites with six conserved motifs were identified from 512 proteins. Subcellular localization analysis showed that the identified Kcr proteins were mainly localized to the cytoplasm, nucleus, and mitochondria. The cellular components analysis showed that the 'chromosomal region' was enriched in the hemocytes of SpTRAF6-or SpEcsit-silenced mud crabs. The KEGG and PPI analyses showed that the identified Kcr proteins in the hemocytes SpTRAF6-or SpEcsit-silenced mud crabs were related to the 'protein processing in endoplasmic reticulum'; of which the marker of endoplasmic reticulum stress (Bip) was identified to be crotonylated. These datasets present the first comprehensive analysis of the crotonylome in mud crab hemocytes, providing invaluable insights into the regulatory functions of SpTRAF6 and SpEcsit in Kcr. Additionally, our findings shed light on the potential role of these proteins in activating marker proteins during endoplasmic reticulum stress in invertebrates.
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Affiliation(s)
- Yongsheng Zhang
- Guangdong Provincial Key Laboratory of Marine Biology, Shantou University, Shantou, 515063, China; Marine Biology Institute, Shantou University, Shantou, 515063, China; STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou, 515063, China
| | - Peina Ji
- Guangdong Provincial Key Laboratory of Marine Biology, Shantou University, Shantou, 515063, China; Marine Biology Institute, Shantou University, Shantou, 515063, China; STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou, 515063, China
| | - Ming Zhang
- Guangdong Provincial Key Laboratory of Marine Biology, Shantou University, Shantou, 515063, China; Marine Biology Institute, Shantou University, Shantou, 515063, China; STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou, 515063, China
| | - Ngoc Tuan Tran
- Guangdong Provincial Key Laboratory of Marine Biology, Shantou University, Shantou, 515063, China; Marine Biology Institute, Shantou University, Shantou, 515063, China; STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou, 515063, China
| | - Shengkang Li
- Guangdong Provincial Key Laboratory of Marine Biology, Shantou University, Shantou, 515063, China; Marine Biology Institute, Shantou University, Shantou, 515063, China; STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou, 515063, China.
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18
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Li J, Krause GJ, Gui Q, Kaushik S, Rona G, Zhang Q, Liang FX, Dhabaria A, Anerillas C, Martindale JL, Vasilyev N, Askenazi M, Ueberheide B, Nudler E, Gorospe M, Cuervo AM, Pagano M. A noncanonical function of SKP1 regulates the switch between autophagy and unconventional secretion. SCIENCE ADVANCES 2023; 9:eadh1134. [PMID: 37831778 PMCID: PMC10575587 DOI: 10.1126/sciadv.adh1134] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 09/13/2023] [Indexed: 10/15/2023]
Abstract
Intracellular degradation of proteins and organelles by the autophagy-lysosome system is essential for cellular quality control and energy homeostasis. Besides degradation, endolysosomal organelles can fuse with the plasma membrane and contribute to unconventional secretion. Here, we identify a function for mammalian SKP1 in endolysosomes that is independent of its established role as an essential component of the family of SCF/CRL1 ubiquitin ligases. We found that, under nutrient-poor conditions, SKP1 is phosphorylated on Thr131, allowing its interaction with V1 subunits of the vacuolar ATPase (V-ATPase). This event, in turn, promotes V-ATPase assembly to acidify late endosomes and enhance endolysosomal degradation. Under nutrient-rich conditions, SUMOylation of phosphorylated SKP1 allows its binding to and dephosphorylation by the PPM1B phosphatase. Dephosphorylated SKP1 interacts with SEC22B to promote unconventional secretion of the content of less acidified hybrid endosomal/autophagic compartments. Collectively, our study implicates SKP1 phosphorylation as a switch between autophagy and unconventional secretion in a manner dependent on cellular nutrient status.
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Affiliation(s)
- Jie Li
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA
- Laura and Isaac Perlmutter NYU Cancer Center, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Gregory J. Krause
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Institute for Aging Research, Department of Medicine, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Qi Gui
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA
- Laura and Isaac Perlmutter NYU Cancer Center, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Susmita Kaushik
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Institute for Aging Research, Department of Medicine, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Gergely Rona
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA
- Laura and Isaac Perlmutter NYU Cancer Center, New York University Grossman School of Medicine, New York, NY 10016, USA
- Howard Hughes Medical Institute, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Qingyue Zhang
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA
- Laura and Isaac Perlmutter NYU Cancer Center, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Feng-Xia Liang
- Microscopy Laboratory, Division of Advanced Research Technologies, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Avantika Dhabaria
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA
- Laura and Isaac Perlmutter NYU Cancer Center, New York University Grossman School of Medicine, New York, NY 10016, USA
- Proteomics Laboratory, Division of Advanced Research Technologies, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Carlos Anerillas
- Laboratory of Genetics and Genomics, National Institute on Aging Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Jennifer L. Martindale
- Laboratory of Genetics and Genomics, National Institute on Aging Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Nikita Vasilyev
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA
- Laura and Isaac Perlmutter NYU Cancer Center, New York University Grossman School of Medicine, New York, NY 10016, USA
- Howard Hughes Medical Institute, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Manor Askenazi
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA
- Biomedical Hosting LLC, 33 Lewis Avenue, Arlington, MA 02474, USA
| | - Beatrix Ueberheide
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA
- Laura and Isaac Perlmutter NYU Cancer Center, New York University Grossman School of Medicine, New York, NY 10016, USA
- Proteomics Laboratory, Division of Advanced Research Technologies, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Evgeny Nudler
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA
- Laura and Isaac Perlmutter NYU Cancer Center, New York University Grossman School of Medicine, New York, NY 10016, USA
- Howard Hughes Medical Institute, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Myriam Gorospe
- Laboratory of Genetics and Genomics, National Institute on Aging Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Ana Maria Cuervo
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Institute for Aging Research, Department of Medicine, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Michele Pagano
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA
- Laura and Isaac Perlmutter NYU Cancer Center, New York University Grossman School of Medicine, New York, NY 10016, USA
- Howard Hughes Medical Institute, New York University Grossman School of Medicine, New York, NY 10016, USA
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19
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Cossart P. Raising a Bacterium to the Rank of a Model System: The Listeria Paradigm. Annu Rev Microbiol 2023; 77:1-22. [PMID: 37713460 DOI: 10.1146/annurev-micro-110422-112841] [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] [Indexed: 09/17/2023]
Abstract
My scientific career has resulted from key decisions and reorientations, sometimes taken rapidly but not always, guided by discussions or collaborations with amazing individuals from whom I learnt a lot scientifically and humanly. I had never anticipated that I would accomplish so much in what appeared as terra incognita when I started to interrogate the mechanisms underlying the virulence of the bacterium Listeria monocytogenes. All this has been possible thanks to a number of talented team members who ultimately became friends.
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Affiliation(s)
- Pascale Cossart
- Department of Cell Biology and Infection, Institut Pasteur, Paris, France;
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20
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Salas-Lloret D, Jansen NS, Nagamalleswari E, van der Meulen C, Gracheva E, de Ru AH, Otte HAM, van Veelen PA, Pichler A, Goedhart J, Vertegaal AC, González-Prieto R. SUMO-activated target traps (SATTs) enable the identification of a comprehensive E3-specific SUMO proteome. SCIENCE ADVANCES 2023; 9:eadh2073. [PMID: 37531430 PMCID: PMC10396300 DOI: 10.1126/sciadv.adh2073] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 06/28/2023] [Indexed: 08/04/2023]
Abstract
Ubiquitin and ubiquitin-like conjugation cascades consist of dedicated E1, E2, and E3 enzymes with E3s providing substrate specificity. Mass spectrometry-based approaches have enabled the identification of more than 6500 SUMO2/3 target proteins. The limited number of SUMO E3s provides the unique opportunity to systematically study E3 substrate wiring. We developed SUMO-activated target traps (SATTs) and systematically identified substrates for eight different SUMO E3s, PIAS1, PIAS2, PIAS3, PIAS4, NSMCE2, ZNF451, LAZSUL (ZNF451-3), and ZMIZ2. SATTs enabled us to identify 427 SUMO1 and 961 SUMO2/3 targets in an E3-specific manner. We found pronounced E3 substrate preference. Quantitative proteomics enabled us to measure substrate specificity of E3s, quantified using the SATT index. Furthermore, we developed the Polar SATTs web-based tool to browse the dataset in an interactive manner. Overall, we uncover E3-to-target wiring of 1388 SUMO substrates, highlighting unique and overlapping sets of substrates for eight different SUMO E3 ligases.
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Affiliation(s)
- Daniel Salas-Lloret
- Cell and Chemical Biology, Leiden University Medical Center, Leiden, Netherlands
| | - Nicolette S. Jansen
- Cell and Chemical Biology, Leiden University Medical Center, Leiden, Netherlands
| | | | - Coen van der Meulen
- Cell and Chemical Biology, Leiden University Medical Center, Leiden, Netherlands
| | - Ekaterina Gracheva
- Cell and Chemical Biology, Leiden University Medical Center, Leiden, Netherlands
| | - Arnoud H. de Ru
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, Netherlands
| | - H. Anne Marie Otte
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, Netherlands
| | - Peter A. van Veelen
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, Netherlands
| | - Andrea Pichler
- Max Plank Institute for Immunobiology and Epigenetics, Freiburg, Germany
- Institute of Biochemistry, ETH Zürich, Zürich, Switzerland
| | | | | | - Román González-Prieto
- Cell and Chemical Biology, Leiden University Medical Center, Leiden, Netherlands
- Andalusian Center for Molecular Biology and Regenerative Medicine (CABIMER), Universidad de Sevilla-CSIC-Universidad-Pablo de Olavide, Sevilla, Spain
- Departamento de Biología Celular, Facultad de Biología, Universidad de Sevilla, Sevilla, Spain
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21
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Ninova M, Holmes H, Lomenick B, Fejes Tóth K, Aravin AA. Pervasive SUMOylation of heterochromatin and piRNA pathway proteins. CELL GENOMICS 2023; 3:100329. [PMID: 37492097 PMCID: PMC10363806 DOI: 10.1016/j.xgen.2023.100329] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 03/24/2023] [Accepted: 04/26/2023] [Indexed: 07/27/2023]
Abstract
Genome regulation involves complex protein interactions that are often mediated through post-translational modifications (PTMs). SUMOylation-modification by the small ubiquitin-like modifier (SUMO)-has been implicated in numerous essential processes in eukaryotes. In Drosophila, SUMO is required for viability and fertility, with its depletion from ovaries leading to heterochromatin loss and ectopic transposon and gene activation. Here, we developed a proteomics-based strategy to uncover the Drosophila ovarian "SUMOylome," which revealed that SUMOylation is widespread among proteins involved in heterochromatin regulation and different aspects of the Piwi-interacting small RNA (piRNA) pathway that represses transposons. Furthermore, we show that SUMOylation of several piRNA pathway proteins occurs in a Piwi-dependent manner. Together, these data highlight broad implications of protein SUMOylation in epigenetic regulation and indicate novel roles of this modification in the cellular defense against genomic parasites. Finally, this work provides a resource for the study of SUMOylation in other biological contexts in the Drosophila model.
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Affiliation(s)
- Maria Ninova
- Department of Biochemistry, University of California Riverside, 3401 Watkins Drive, Boyce Hall, Riverside, CA 92521, USA
| | - Hannah Holmes
- Department of Biochemistry, University of California Riverside, 3401 Watkins Drive, Boyce Hall, Riverside, CA 92521, USA
| | - Brett Lomenick
- Proteome Exploration Laboratory of the Beckman Institute, California Institute of Technology, 1200 E. California Boulevard, Pasadena, CA 91125, USA
| | - Katalin Fejes Tóth
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 E. California Boulevard, Pasadena, CA 91125, USA
| | - Alexei A. Aravin
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 E. California Boulevard, Pasadena, CA 91125, USA
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22
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Choi WH, Yun Y, Byun I, Kim S, Lee S, Sim J, Levi S, Park SH, Jun J, Kleifeld O, Kim KP, Han D, Chiba T, Seok C, Kwon YT, Glickman MH, Lee MJ. ECPAS/Ecm29-mediated 26S proteasome disassembly is an adaptive response to glucose starvation. Cell Rep 2023; 42:112701. [PMID: 37384533 DOI: 10.1016/j.celrep.2023.112701] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 05/07/2023] [Accepted: 06/09/2023] [Indexed: 07/01/2023] Open
Abstract
The 26S proteasome comprises 20S catalytic and 19S regulatory complexes. Approximately half of the proteasomes in cells exist as free 20S complexes; however, our mechanistic understanding of what determines the ratio of 26S to 20S species remains incomplete. Here, we show that glucose starvation uncouples 26S holoenzymes into 20S and 19S subcomplexes. Subcomplex affinity purification and quantitative mass spectrometry reveal that Ecm29 proteasome adaptor and scaffold (ECPAS) mediates this structural remodeling. The loss of ECPAS abrogates 26S dissociation, reducing degradation of 20S proteasome substrates, including puromycylated polypeptides. In silico modeling suggests that ECPAS conformational changes commence the disassembly process. ECPAS is also essential for endoplasmic reticulum stress response and cell survival during glucose starvation. In vivo xenograft model analysis reveals elevated 20S proteasome levels in glucose-deprived tumors. Our results demonstrate that the 20S-19S disassembly is a mechanism adapting global proteolysis to physiological needs and countering proteotoxic stress.
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Affiliation(s)
- Won Hoon Choi
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul 03080, Korea
| | - Yejin Yun
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul 03080, Korea; Department of Biomedical Sciences, Seoul National University Graduate School, Seoul 03080, Korea
| | - Insuk Byun
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul 03080, Korea; Department of Biomedical Sciences, Seoul National University Graduate School, Seoul 03080, Korea
| | - Sumin Kim
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul 03080, Korea; Department of Biomedical Sciences, Seoul National University Graduate School, Seoul 03080, Korea
| | - Seho Lee
- Department of Chemistry, Seoul National University, Seoul 08826, Korea
| | - Jiho Sim
- Department of Chemistry, Seoul National University, Seoul 08826, Korea
| | - Shahar Levi
- Department of Biology, Technion-Israel Institute of Technology, Haifa 32000, Israel
| | - Seo Hyeong Park
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul 03080, Korea; Department of Biomedical Sciences, Seoul National University Graduate School, Seoul 03080, Korea
| | - Jeongmoo Jun
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul 03080, Korea
| | - Oded Kleifeld
- Department of Biology, Technion-Israel Institute of Technology, Haifa 32000, Israel
| | - Kwang Pyo Kim
- Department of Applied Chemistry, Institute of Natural Science, Global Center for Pharmaceutical Ingredient Materials, Kyung Hee University, Yongin 17104, Korea
| | - Dohyun Han
- Proteomics Core Facility, Biomedical Research Institute, Seoul National University Hospital, Seoul 03080, Korea
| | - Tomoki Chiba
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Ibaraki 305-8577, Japan
| | - Chaok Seok
- Department of Chemistry, Seoul National University, Seoul 08826, Korea
| | - Yong Tae Kwon
- Department of Biomedical Sciences, Seoul National University Graduate School, Seoul 03080, Korea; Ischemic/Hypoxic Disease Institute, Convergence Research Center for Dementia, Seoul National University College of Medicine, Seoul 03080, Korea
| | - Michael H Glickman
- Department of Biology, Technion-Israel Institute of Technology, Haifa 32000, Israel.
| | - Min Jae Lee
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul 03080, Korea; Department of Biomedical Sciences, Seoul National University Graduate School, Seoul 03080, Korea; Ischemic/Hypoxic Disease Institute, Convergence Research Center for Dementia, Seoul National University College of Medicine, Seoul 03080, Korea.
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23
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Hofmann S, Plank V, Groitl P, Skvorc N, Hofmann K, Luther J, Ko C, Zimmerman P, Bruss V, Stadler D, Carpentier A, Rezk S, Nassal M, Protzer U, Schreiner S. SUMO Modification of Hepatitis B Virus Core Mediates Nuclear Entry, Promyelocytic Leukemia Nuclear Body Association, and Efficient Formation of Covalently Closed Circular DNA. Microbiol Spectr 2023; 11:e0044623. [PMID: 37199632 PMCID: PMC10269885 DOI: 10.1128/spectrum.00446-23] [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: 02/05/2023] [Accepted: 04/24/2023] [Indexed: 05/19/2023] Open
Abstract
Persistence of hepatitis B virus (HBV) infection is due to a nuclear covalently closed circular DNA (cccDNA), generated from the virion-borne relaxed circular DNA (rcDNA) genome in a process likely involving numerous cell factors from the host DNA damage response (DDR). The HBV core protein mediates rcDNA transport to the nucleus and likely affects stability and transcriptional activity of cccDNA. Our study aimed at investigating the role of HBV core protein and its posttranslational modification (PTM) with SUMO (small ubiquitin-like modifiers) during the establishment of cccDNA. HBV core protein SUMO PTM was analyzed in His-SUMO-overexpressing cell lines. The impact of HBV core SUMOylation on association with cellular interaction partners and on the HBV life cycle was determined using SUMOylation-deficient mutants of the HBV core protein. Here, we show that the HBV core protein is posttranslationally modified by the addition of SUMO and that this modification impacts nuclear import of rcDNA. By using SUMOylation-deficient HBV core mutants, we show that SUMO modification is a prerequisite for the association with specific promyelocytic leukemia nuclear bodies (PML-NBs) and regulates the conversion of rcDNA to cccDNA. By in vitro SUMOylation of HBV core, we obtained evidence that SUMOylation triggers nucleocapsid disassembly, providing novel insights into the nuclear import process of rcDNA. HBV core protein SUMOylation and subsequent association with PML bodies in the nucleus constitute a key step in the conversion of HBV rcDNA to cccDNA and therefore a promising target for inhibiting formation of the HBV persistence reservoir. IMPORTANCE HBV cccDNA is formed from the incomplete rcDNA involving several host DDR proteins. The exact process and the site of cccDNA formation are poorly understood. Here, we show that HBV core protein SUMO modification is a novel PTM regulating the function of HBV core. A minor specific fraction of the HBV core protein resides with PML-NBs in the nuclear matrix. SUMO modification of HBV core protein mediates its recruitment to specific PML-NBs within the host cell. Within HBV nucleocapsids, SUMOylation of HBV core induces HBV capsid disassembly and is a prerequisite for nuclear entry of HBV core. SUMO HBV core protein association with PML-NBs is crucial for efficient conversion of rcDNA to cccDNA and for the establishment of the viral persistence reservoir. HBV core protein SUMO modification and the subsequent association with PML-NBs might constitute a potential novel target in the development of drugs targeting the cccDNA.
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Affiliation(s)
- Samuel Hofmann
- Institute of Virology, School of Medicine, Technical University of Munich, Germany
- Institute of Virology, Hannover Medical School, Hannover, Germany
| | - Verena Plank
- Institute of Virology, School of Medicine, Technical University of Munich, Germany
| | - Peter Groitl
- Institute of Virology, School of Medicine, Technical University of Munich, Germany
| | - Nathalie Skvorc
- Institute of Virology, School of Medicine, Technical University of Munich, Germany
| | - Katharina Hofmann
- Institute of Virology, School of Medicine, Technical University of Munich, Germany
- Institute of Virology, Hannover Medical School, Hannover, Germany
| | - Julius Luther
- Institute of Virology, Hannover Medical School, Hannover, Germany
| | - Chunkyu Ko
- Institute of Virology, School of Medicine, Technical University of Munich, Germany
- Institute of Virology, Helmholtz Zentrum München, Munich, Germany
| | - Peter Zimmerman
- Department of Internal Medicine II/Molecular Biology, University Hospital Freiburg, Freiburg, Germany
| | - Volker Bruss
- Institute of Virology, Helmholtz Zentrum München, Munich, Germany
| | - Daniela Stadler
- Institute of Virology, School of Medicine, Technical University of Munich, Germany
- Institute of Virology, Helmholtz Zentrum München, Munich, Germany
| | | | - Shahinda Rezk
- Institute of Virology, School of Medicine, Technical University of Munich, Germany
- Medical Research Institute, Department of Molecular and Diagnostic Microbiology, Alexandria University, Alexandria, Egypt
| | - Michael Nassal
- Department of Internal Medicine II/Molecular Biology, University Hospital Freiburg, Freiburg, Germany
| | - Ulrike Protzer
- Institute of Virology, School of Medicine, Technical University of Munich, Germany
- Institute of Virology, Helmholtz Zentrum München, Munich, Germany
- German Center for Infection Research, Munich, Germany
| | - Sabrina Schreiner
- Institute of Virology, School of Medicine, Technical University of Munich, Germany
- Institute of Virology, Hannover Medical School, Hannover, Germany
- Institute of Virology, Helmholtz Zentrum München, Munich, Germany
- German Center for Infection Research, Munich, Germany
- Cluster of Excellence RESIST (Resolving Infection Susceptibility; EXC 2155), Hannover Medical School, Hannover, Germany
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24
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Chen S, Fu X, Wang R, Li M, Yan X, Yue Z, Chen SW, Dong M, Xu A, Huang S. SUMO and PIAS repress NF-κB activation in a basal chordate. FISH & SHELLFISH IMMUNOLOGY 2023; 137:108754. [PMID: 37088348 DOI: 10.1016/j.fsi.2023.108754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 03/09/2023] [Accepted: 04/18/2023] [Indexed: 05/03/2023]
Abstract
Small ubiquitin-like modifier (SUMO) regulates various biological processes, including the MyD88/TICAMs-IRAKs-TRAF6-NF-κB pathway, one of the core immune pathways. However, its functions are inconsistent between invertebrates and vertebrates and have rarely been investigated in lower chordates, including amphioxus and fishes. Here, we investigated the SUMOylation gene system in the amphioxus, a living basal chordate. We found that amphioxus has a SUMOylation system that has a complete set of genes and preserves several ancestral traits. We proceeded to study their molecular functions using the mammal cell lines. Both amphioxus SUMO1 and SUMO2 were shown to be able to attach to NF-κB Rel and to inhibit NF-κB activation by 50-75% in a dose-dependent fashion. The inhibition by SUMO2 could be further enhanced by the addition of the SUMO E2 ligase UBC9. In comparison, while human SUMO2 inhibited RelA, human SUMO1 slightly activated RelA. We also showed that, similar to human PIAS1-4, amphioxus PIAS could serve as a SUMO E3 ligase and promote its self-SUMOylation. This suggests that amphioxus PIAS is functionally compatible in human cells. Moreover, we showed that amphioxus PIAS is not only able to inhibit NF-κB activation induced by MyD88, TICAM-like, TRAF6 and IRAK4 but also able to suppress NF-κB Rel completely in the presence of SUMO1/2 in a dose-insensitive manner. This suggests that PIAS could effectively block Rel by promoting Rel SUMOylation. In comparison, in humans, only PIAS3, but not PIAS1/2/4, has been reported to promote NF-κB SUMOylation. Taken together, the findings from amphioxus, together with those from mammals and other species, not only offer insights into the functional volatility of the animal SUMO system, but also shed light on its evolutionary transitions from amphioxus to fish, and ultimately to humans.
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Affiliation(s)
- Shenghui Chen
- Guangdong Key Laboratory of Pharmaceutical Functional Genes, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangdong, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Xianan Fu
- Guangdong Key Laboratory of Pharmaceutical Functional Genes, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangdong, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China; Center for Evolution and Conservation Biology, Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Ruihua Wang
- Guangdong Key Laboratory of Pharmaceutical Functional Genes, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangdong, China; Center for Regenerative and Translational Medicine, Guangdong Provincial Academy of Chinese Medical Sciences, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, 510632, China
| | - Mingshi Li
- Guangdong Key Laboratory of Pharmaceutical Functional Genes, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangdong, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Xinyu Yan
- Guangdong Key Laboratory of Pharmaceutical Functional Genes, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangdong, China
| | - Zirui Yue
- Guangdong Key Laboratory of Pharmaceutical Functional Genes, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangdong, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Shang-Wu Chen
- Guangdong Key Laboratory of Pharmaceutical Functional Genes, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangdong, China
| | - Meiling Dong
- Guangdong Key Laboratory of Pharmaceutical Functional Genes, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangdong, China
| | - Anlong Xu
- Guangdong Key Laboratory of Pharmaceutical Functional Genes, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangdong, China; Beijing University of Chinese Medicine, Dong San Huang Road, Chao-yang District, Beijing, 100029, China
| | - Shengfeng Huang
- Guangdong Key Laboratory of Pharmaceutical Functional Genes, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangdong, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.
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25
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Liang T, Li G, Lu Y, Hu M, Ma X. The Involvement of Ubiquitination and SUMOylation in Retroviruses Infection and Latency. Viruses 2023; 15:v15040985. [PMID: 37112965 PMCID: PMC10144533 DOI: 10.3390/v15040985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 04/15/2023] [Accepted: 04/16/2023] [Indexed: 04/29/2023] Open
Abstract
Retroviruses, especially the pathogenic human immunodeficiency virus type 1 (HIV-1), have severely threatened human health for decades. Retroviruses can form stable latent reservoirs via retroviral DNA integration into the host genome, and then be temporarily transcriptional silencing in infected cells, which makes retroviral infection incurable. Although many cellular restriction factors interfere with various steps of the life cycle of retroviruses and the formation of viral latency, viruses can utilize viral proteins or hijack cellular factors to evade intracellular immunity. Many post-translational modifications play key roles in the cross-talking between the cellular and viral proteins, which has greatly determined the fate of retroviral infection. Here, we reviewed recent advances in the regulation of ubiquitination and SUMOylation in the infection and latency of retroviruses, focusing on both host defense- and virus counterattack-related ubiquitination and SUMOylation system. We also summarized the development of ubiquitination- and SUMOylation-targeted anti-retroviral drugs and discussed their therapeutic potential. Manipulating ubiquitination or SUMOylation pathways by targeted drugs could be a promising strategy to achieve a "sterilizing cure" or "functional cure" of retroviral infection.
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Affiliation(s)
- Taizhen Liang
- State Key Laboratory of Respiratory Disease, Guangzhou Medical University, Guangzhou 511400, China
- Guangzhou Laboratory, Guangzhou International Bio-Island, Guangzhou 510005, China
| | - Guojie Li
- State Key Laboratory of Respiratory Disease, Guangzhou Medical University, Guangzhou 511400, China
- Guangzhou Laboratory, Guangzhou International Bio-Island, Guangzhou 510005, China
| | - Yunfei Lu
- Guangzhou Laboratory, Guangzhou International Bio-Island, Guangzhou 510005, China
| | - Meilin Hu
- State Key Laboratory of Respiratory Disease, Guangzhou Medical University, Guangzhou 511400, China
- Guangzhou Laboratory, Guangzhou International Bio-Island, Guangzhou 510005, China
| | - Xiancai Ma
- State Key Laboratory of Respiratory Disease, Guangzhou Medical University, Guangzhou 511400, China
- Guangzhou Laboratory, Guangzhou International Bio-Island, Guangzhou 510005, China
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
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26
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Shepelev N, Dontsova O, Rubtsova M. Post-Transcriptional and Post-Translational Modifications in Telomerase Biogenesis and Recruitment to Telomeres. Int J Mol Sci 2023; 24:5027. [PMID: 36902458 PMCID: PMC10003056 DOI: 10.3390/ijms24055027] [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: 02/02/2023] [Revised: 03/02/2023] [Accepted: 03/03/2023] [Indexed: 03/08/2023] Open
Abstract
Telomere length is associated with the proliferative potential of cells. Telomerase is an enzyme that elongates telomeres throughout the entire lifespan of an organism in stem cells, germ cells, and cells of constantly renewed tissues. It is activated during cellular division, including regeneration and immune responses. The biogenesis of telomerase components and their assembly and functional localization to the telomere is a complex system regulated at multiple levels, where each step must be tuned to the cellular requirements. Any defect in the function or localization of the components of the telomerase biogenesis and functional system will affect the maintenance of telomere length, which is critical to the processes of regeneration, immune response, embryonic development, and cancer progression. An understanding of the regulatory mechanisms of telomerase biogenesis and activity is necessary for the development of approaches toward manipulating telomerase to influence these processes. The present review focuses on the molecular mechanisms involved in the major steps of telomerase regulation and the role of post-transcriptional and post-translational modifications in telomerase biogenesis and function in yeast and vertebrates.
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Affiliation(s)
- Nikita Shepelev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117437, Russia
- Chemistry Department and Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119234, Russia
- Skolkovo Institute of Science and Technology, Moscow 121205, Russia
| | - Olga Dontsova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117437, Russia
- Chemistry Department and Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119234, Russia
- Skolkovo Institute of Science and Technology, Moscow 121205, Russia
| | - Maria Rubtsova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117437, Russia
- Chemistry Department and Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119234, Russia
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27
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Du L, Liu W, Rosen ST, Chen Y. Mechanism of SUMOylation-Mediated Regulation of Type I IFN Expression. J Mol Biol 2023; 435:167968. [PMID: 36681180 DOI: 10.1016/j.jmb.2023.167968] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Revised: 01/07/2023] [Accepted: 01/11/2023] [Indexed: 01/20/2023]
Abstract
Type I interferons (IFN) are cytokines that bridge the innate and adaptive immune response, and thus play central roles in human health, including vaccine efficacy, immune response to cancer and pathogen infection, and autoimmune disorders. Post-translational protein modifications by the small ubiquitin-like modifiers (SUMO) have recently emerged as an important regulator of type I IFN expression as shown by studies using murine and cellular models and recent human clinical trials. However, the mechanism regarding how SUMOylation regulates type I IFN expression remains poorly understood. In this study, we show that SUMOylation inhibition does not activate IFNB1 gene promoter that is regulated by known canonical pathways including cytosolic DNA. Instead, we identified a binding site for the chromatin modification enzyme, the SET Domain Bifurcated Histone Lysine Methyltransferase 1 (SETDB1), located between the IFNB1 promoter and a previously identified enhancer. We found that SETDB1 regulates IFNB1 expression and SUMOylation of SETDB1 is required for its binding and enhancing the H3K9me3 heterochromatin signal in this region. Heterochromatin, a tightly packed form of DNA, has been documented to suppress gene expression through suppressing enhancer function. Taken together, our study identified a novel mechanism of regulation of type I IFN expression, at least in part, through SUMOylation of a chromatin modification enzyme.
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Affiliation(s)
- Li Du
- Toni Stephenson Lymphoma Center, Beckman Research Institute of City of Hope, Duarte, CA, USA; Judy and Bernard Briskin Center for Multiple Myeloma Research, Beckman Research Institute of City of Hope, Duarte, CA, USA; Department of Hematology and Hematopoietic Cell Transplantation, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Wei Liu
- Toni Stephenson Lymphoma Center, Beckman Research Institute of City of Hope, Duarte, CA, USA; Department of Hematology, Xiangya Hospital, Central South University, Changsha, China
| | - Steven T Rosen
- Toni Stephenson Lymphoma Center, Beckman Research Institute of City of Hope, Duarte, CA, USA; Judy and Bernard Briskin Center for Multiple Myeloma Research, Beckman Research Institute of City of Hope, Duarte, CA, USA; Department of Hematology and Hematopoietic Cell Transplantation, Beckman Research Institute of City of Hope, Duarte, CA, USA; City of Hope Comprehensive Cancer Center, City of Hope National Medical Center, Duarte, CA, USA.
| | - Yuan Chen
- Division of Surgical Sciences, Department of Surgery and Moores Cancer Center, UC San Diego Health, San Diego, CA, USA.
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28
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Bragado L, Magalnik M, Mammi P, Romero A, Gaioli N, Pozzi B, Srebrow A. SUMO conjugation regulates the activity of the Integrator complex. Nucleic Acids Res 2022; 50:12444-12461. [PMID: 36454007 PMCID: PMC9757034 DOI: 10.1093/nar/gkac1055] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 10/13/2022] [Accepted: 11/29/2022] [Indexed: 12/03/2022] Open
Abstract
RNA polymerase II (RNAPII) transcribes small nuclear RNA (snRNA) genes in close proximity to Cajal bodies, subnuclear compartments that depend on the SUMO isopeptidase USPL1 for their assembly. We show here that overexpression of USPL1 as well as of another nuclear SUMO isopeptidase, SENP6, alters snRNA 3'-end cleavage, a process carried out by the Integrator complex. Beyond its role in snRNA biogenesis, this complex is responsible for regulating the expression of different RNAPII transcripts. While several subunits of the complex are SUMO conjugation substrates, we found that the SUMOylation of the INTS11 subunit is regulated by USPL1 and SENP6. We defined Lys381, Lys462 and Lys475 as bona fide SUMO attachment sites on INTS11 and observed that SUMOylation of this protein modulates its subcellular localization and is required for Integrator activity. Moreover, while an INTS11 SUMOylation-deficient mutant is still capable of interacting with INTS4 and INTS9, its interaction with other subunits of the complex is affected. These findings point to a regulatory role for SUMO conjugation on Integrator activity and suggest the involvement of INTS11 SUMOylation in the assembly of the complex. Furthermore, this work adds Integrator-dependent RNA processing to the growing list of cellular processes regulated by SUMO conjugation.
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Affiliation(s)
- Laureano Bragado
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Fisiología, Biología Molecular y Celular, Buenos Aires, Argentina,CONICET-Universidad de Buenos Aires, Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), Buenos Aires, Argentina
| | - Melina Magalnik
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Fisiología, Biología Molecular y Celular, Buenos Aires, Argentina,CONICET-Universidad de Buenos Aires, Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), Buenos Aires, Argentina
| | - Pablo Mammi
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Fisiología, Biología Molecular y Celular, Buenos Aires, Argentina,CONICET-Universidad de Buenos Aires, Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), Buenos Aires, Argentina
| | - Agustín Romero
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Fisiología, Biología Molecular y Celular, Buenos Aires, Argentina,CONICET-Universidad de Buenos Aires, Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), Buenos Aires, Argentina
| | - Nicolás Gaioli
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Fisiología, Biología Molecular y Celular, Buenos Aires, Argentina,CONICET-Universidad de Buenos Aires, Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), Buenos Aires, Argentina
| | - Berta Pozzi
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Fisiología, Biología Molecular y Celular, Buenos Aires, Argentina,CONICET-Universidad de Buenos Aires, Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), Buenos Aires, Argentina
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29
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Ryu HY. SUMO pathway is required for ribosome biogenesis. BMB Rep 2022; 55:535-540. [PMID: 36195568 PMCID: PMC9712707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Indexed: 12/14/2022] Open
Abstract
Ribosomes, acting as the cellular factories for protein production, are essential for all living organisms. Ribosomes are composed of both proteins and RNAs and are established through the coordination of several steps, including transcription, maturation of ribosomal RNA (rRNA), and assembly of ribosomal proteins. In particular, diverse factors required for ribosome biogenesis, such as transcription factors, small nucleolar RNA (snoRNA)-associated proteins, and assembly factors, are tightly regulated by various post-translational modifications. Among these modifications, small ubiquitin-related modifier (SUMO) targets lots of proteins required for gene expression of ribosomal proteins, rRNA, and snoRNAs, rRNA processing, and ribosome assembly. The tight control of SUMOylation affects functions and locations of substrates. This review summarizes current studies and recent progress of SUMOylation-mediated regulation of ribosome biogenesis. [BMB Reports 2022; 55(11): 535-540].
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Affiliation(s)
- Hong-Yeoul Ryu
- BK21 FOUR KNU Creative BioResearch Group, School of Life Sciences, College of National Sciences, Kyungpook National University, Daegu 41566, Korea,Brain Science and Engineering Institute, Kyungpook National University, Daegu 41566, Korea,Corresponding author. Tel: +82-53-950-6352; Fax: +82-53-955-5522; E-mail:
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30
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Ryu HY. SUMO pathway is required for ribosome biogenesis. BMB Rep 2022; 55:535-540. [PMID: 36195568 PMCID: PMC9712707 DOI: 10.5483/bmbrep.2022.55.11.130] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 09/15/2022] [Accepted: 09/26/2022] [Indexed: 12/24/2023] Open
Abstract
Ribosomes, acting as the cellular factories for protein production, are essential for all living organisms. Ribosomes are composed of both proteins and RNAs and are established through the coordination of several steps, including transcription, maturation of ribosomal RNA (rRNA), and assembly of ribosomal proteins. In particular, diverse factors required for ribosome biogenesis, such as transcription factors, small nucleolar RNA (snoRNA)-associated proteins, and assembly factors, are tightly regulated by various post-translational modifications. Among these modifications, small ubiquitin-related modifier (SUMO) targets lots of proteins required for gene expression of ribosomal proteins, rRNA, and snoRNAs, rRNA processing, and ribosome assembly. The tight control of SUMOylation affects functions and locations of substrates. This review summarizes current studies and recent progress of SUMOylation-mediated regulation of ribosome biogenesis. [BMB Reports 2022; 55(11): 535-540].
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Affiliation(s)
- Hong-Yeoul Ryu
- BK21 FOUR KNU Creative BioResearch Group, School of Life Sciences, College of National Sciences, Kyungpook National University, Daegu 41566, Korea
- Brain Science and Engineering Institute, Kyungpook National University, Daegu 41566, Korea
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31
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Ezzine C, Loison L, Montbrion N, Bôle-Feysot C, Déchelotte P, Coëffier M, Ribet D. Fatty acids produced by the gut microbiota dampen host inflammatory responses by modulating intestinal SUMOylation. Gut Microbes 2022; 14:2108280. [PMID: 35978476 PMCID: PMC9466625 DOI: 10.1080/19490976.2022.2108280] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
The gut microbiota produces a wide variety of metabolites, which interact with intestinal cells and contribute to host physiology. The effect of gut commensal bacteria on host protein SUMOylation, an essential ubiquitin-like modification involved in various intestinal functions, remains, however, unknown. Here, we show that short chain fatty acids (SCFAs) and branched chain fatty acids (BCFAs) produced by the gut microbiota increase protein SUMOylation in intestinal cells in a pH-dependent manner. We demonstrate that these metabolites inactivate intestinal deSUMOylases and promote the hyperSUMOylation of nuclear matrix-associated proteins. We further show that BCFAs inhibit the NF-κB pathway, decrease pro-inflammatory cytokine expression, and promote intestinal epithelial integrity. Together, our results reveal that fatty acids produced by gut commensal bacteria regulate intestinal physiology by modulating SUMOylation and illustrate a new mechanism of dampening of host inflammatory responses triggered by the gut microbiota.
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Affiliation(s)
- Chaima Ezzine
- Université de Rouen Normandie, INSERM UMR 1073, Nutrition, Inflammation et axe Microbiote-Intestin-Cerveau, Rouen, France,Université de Rouen Normandie, Institute for Research and Innovation in Biomedicine (IRIB), Rouen, France
| | - Léa Loison
- Université de Rouen Normandie, INSERM UMR 1073, Nutrition, Inflammation et axe Microbiote-Intestin-Cerveau, Rouen, France,Université de Rouen Normandie, Institute for Research and Innovation in Biomedicine (IRIB), Rouen, France
| | - Nadine Montbrion
- Université de Rouen Normandie, INSERM UMR 1073, Nutrition, Inflammation et axe Microbiote-Intestin-Cerveau, Rouen, France,Université de Rouen Normandie, Institute for Research and Innovation in Biomedicine (IRIB), Rouen, France
| | - Christine Bôle-Feysot
- Université de Rouen Normandie, INSERM UMR 1073, Nutrition, Inflammation et axe Microbiote-Intestin-Cerveau, Rouen, France,Université de Rouen Normandie, Institute for Research and Innovation in Biomedicine (IRIB), Rouen, France
| | - Pierre Déchelotte
- Université de Rouen Normandie, INSERM UMR 1073, Nutrition, Inflammation et axe Microbiote-Intestin-Cerveau, Rouen, France,Université de Rouen Normandie, Institute for Research and Innovation in Biomedicine (IRIB), Rouen, France,Department of Nutrition, Rouen University Hospital, CHU Rouen, Rouen, France
| | - Moïse Coëffier
- Université de Rouen Normandie, INSERM UMR 1073, Nutrition, Inflammation et axe Microbiote-Intestin-Cerveau, Rouen, France,Université de Rouen Normandie, Institute for Research and Innovation in Biomedicine (IRIB), Rouen, France,Department of Nutrition, Rouen University Hospital, CHU Rouen, Rouen, France
| | - David Ribet
- Université de Rouen Normandie, INSERM UMR 1073, Nutrition, Inflammation et axe Microbiote-Intestin-Cerveau, Rouen, France,Université de Rouen Normandie, Institute for Research and Innovation in Biomedicine (IRIB), Rouen, France,CONTACT David Ribet Université de Rouen Normandie, INSERM UMR 1073, Nutrition, Inflammation et axe Microbiote-Intestin-Cerveau, UFR Santé - 22 Boulevard Gambetta, 76000Rouen, France; Université de Rouen Normandie, Institute for Research and Innovation in Biomedicine (IRIB), Rouen, France
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32
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The Next Frontier: Translational Development of Ubiquitination, SUMOylation, and NEDDylation in Cancer. Int J Mol Sci 2022; 23:ijms23073480. [PMID: 35408841 PMCID: PMC8999128 DOI: 10.3390/ijms23073480] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 03/17/2022] [Accepted: 03/21/2022] [Indexed: 01/01/2023] Open
Abstract
Post-translational modifications of proteins ensure optimized cellular processes, including proteostasis, regulated signaling, cell survival, and stress adaptation to maintain a balanced homeostatic state. Abnormal post-translational modifications are associated with cellular dysfunction and the occurrence of life-threatening diseases, such as cancer and neurodegenerative diseases. Therefore, some of the frequently seen protein modifications have been used as disease markers, while others are targeted for developing specific therapies. The ubiquitin and ubiquitin-like post-translational modifiers, namely, small ubiquitin-like modifier (SUMO) and neuronal precursor cell-expressed developmentally down-regulated protein 8 (NEDD8), share several features, such as protein structures, enzymatic cascades mediating the conjugation process, and targeted amino acid residues. Alterations in the regulatory mechanisms lead to aberrations in biological processes during tumorigenesis, including the regulation of tumor metabolism, immunological modulation of the tumor microenvironment, and cancer stem cell stemness, besides many more. Novel insights into ubiquitin and ubiquitin-like pathways involved in cancer biology reveal a potential interplay between ubiquitination, SUMOylation, and NEDDylation. This review outlines the current understandings of the regulatory mechanisms and assay capabilities of ubiquitination, SUMOylation, and NEDDylation. It will further highlight the role of ubiquitination, SUMOylation, and NEDDylation in tumorigenesis.
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33
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Patra U, Müller S. A Tale of Usurpation and Subversion: SUMO-Dependent Integrity of Promyelocytic Leukemia Nuclear Bodies at the Crossroad of Infection and Immunity. Front Cell Dev Biol 2021; 9:696234. [PMID: 34513832 PMCID: PMC8430037 DOI: 10.3389/fcell.2021.696234] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 07/30/2021] [Indexed: 12/13/2022] Open
Abstract
Promyelocytic leukemia nuclear bodies (PML NBs) are multi-protein assemblies representing distinct sub-nuclear structures. As phase-separated molecular condensates, PML NBs exhibit liquid droplet-like consistency. A key organizer of the assembly and dynamics of PML NBs is the ubiquitin-like SUMO modification system. SUMO is covalently attached to PML and other core components of PML NBs thereby exhibiting a glue-like function by providing multivalent interactions with proteins containing SUMO interacting motifs (SIMs). PML NBs serve as the catalytic center for nuclear SUMOylation and SUMO-SIM interactions are essential for protein assembly within these structures. Importantly, however, formation of SUMO chains on PML and other PML NB-associated proteins triggers ubiquitylation and proteasomal degradation which coincide with disruption of these nuclear condensates. To date, a plethora of nuclear activities such as transcriptional and post-transcriptional regulation of gene expression, apoptosis, senescence, cell cycle control, DNA damage response, and DNA replication have been associated with PML NBs. Not surprisingly, therefore, SUMO-dependent PML NB integrity has been implicated in regulating many physiological processes including tumor suppression, metabolism, drug-resistance, development, cellular stemness, and anti-pathogen immune response. The interplay between PML NBs and viral infection is multifaceted. As a part of the cellular antiviral defense strategy, PML NB components are crucial restriction factors for many viruses and a mutual positive correlation has been found to exist between PML NBs and the interferon response. Viruses, in turn, have developed counterstrategies for disarming PML NB associated immune defense measures. On the other end of the spectrum, certain viruses are known to usurp specific PML NB components for successful replication and disruption of these sub-nuclear foci has recently been linked to the stimulation rather than curtailment of antiviral gene repertoire. Importantly, the ability of invading virions to manipulate the host SUMO modification machinery is essential for this interplay between PML NB integrity and viruses. Moreover, compelling evidence is emerging in favor of bacterial pathogens to negotiate with the SUMO system thereby modulating PML NB-directed intrinsic and innate immunity. In the current context, we will present an updated account of the dynamic intricacies between cellular PML NBs as the nuclear SUMO modification hotspots and immune regulatory mechanisms in response to viral and bacterial pathogens.
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Affiliation(s)
- Upayan Patra
- Institute of Biochemistry II, Faculty of Medicine, Goethe University, Frankfurt, Germany
| | - Stefan Müller
- Institute of Biochemistry II, Faculty of Medicine, Goethe University, Frankfurt, Germany
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34
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Thery F, Eggermont D, Impens F. Proteomics Mapping of the ISGylation Landscape in Innate Immunity. Front Immunol 2021; 12:720765. [PMID: 34447387 PMCID: PMC8383068 DOI: 10.3389/fimmu.2021.720765] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 07/16/2021] [Indexed: 01/12/2023] Open
Abstract
During infection, pathogen sensing and cytokine signaling by the host induce expression of antimicrobial proteins and specialized post-translational modifications. One such protein is ISG15, a ubiquitin-like protein (UBL) conserved among vertebrates. Similar to ubiquitin, ISG15 covalently conjugates to lysine residues in substrate proteins in a process called ISGylation. Mice deficient for ISGylation or lacking ISG15 are strongly susceptible to many viral pathogens and several intracellular bacterial pathogens. Although ISG15 was the first UBL discovered after ubiquitin, the mechanisms behind its protective activity are poorly understood. Largely, this stems from a lack of knowledge on the ISG15 substrate repertoire. To unravel the antiviral activity of ISG15, early studies used mass spectrometry-based proteomics in combination with ISG15 pulldown. Despite reporting hundreds of ISG15 substrates, these studies were unable to identify the exact sites of modification, impeding a clear understanding of the molecular consequences of protein ISGylation. More recently, a peptide-based enrichment approach revolutionized the study of ubiquitin allowing untargeted discovery of ubiquitin substrates, including knowledge of their exact modification sites. Shared molecular determinants between ISG15 and ubiquitin allowed to take advantage of this technology for proteome-wide mapping of ISG15 substrates and modification sites. In this review, we provide a comprehensive overview of mass spectrometry-based proteomics studies on protein ISGylation. We critically discuss the relevant literature, compare reported substrates and sites and make suggestions for future research.
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Affiliation(s)
- Fabien Thery
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium.,Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Denzel Eggermont
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium.,Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Francis Impens
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium.,Department of Biomolecular Medicine, Ghent University, Ghent, Belgium.,VIB Proteomics Core, VIB, Ghent, Belgium
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35
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López-Berges MS, Scheven MT, Hortschansky P, Misslinger M, Baldin C, Gsaller F, Werner ER, Krüger T, Kniemeyer O, Weber J, Brakhage AA, Haas H. The bZIP Transcription Factor HapX Is Post-Translationally Regulated to Control Iron Homeostasis in Aspergillus fumigatus. Int J Mol Sci 2021; 22:ijms22147739. [PMID: 34299357 PMCID: PMC8307855 DOI: 10.3390/ijms22147739] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 07/15/2021] [Indexed: 11/21/2022] Open
Abstract
The airborne fungus Aspergillus fumigatus causes opportunistic infections in humans with high mortality rates in immunocompromised patients. Previous work established that the bZIP transcription factor HapX is essential for virulence via adaptation to iron limitation by repressing iron-consuming pathways and activating iron acquisition mechanisms. Moreover, HapX was shown to be essential for transcriptional activation of vacuolar iron storage and iron-dependent pathways in response to iron availability. Here, we demonstrate that HapX has a very short half-life during iron starvation, which is further decreased in response to iron, while siderophore biosynthetic enzymes are very stable. We identified Fbx22 and SumO as HapX interactors and, in agreement, HapX post-translational modifications including ubiquitination of lysine161, sumoylation of lysine242 and phosphorylation of threonine319. All three modifications were enriched in the immediate adaptation from iron-limiting to iron-replete conditions. Interfering with these post-translational modifications, either by point mutations or by inactivation, of Fbx22 or SumO, altered HapX degradation, heme biosynthesis and iron resistance to different extents. Consistent with the need to precisely regulate HapX protein levels, overexpression of hapX caused significant growth defects under iron sufficiency. Taken together, our results indicate that post-translational regulation of HapX is important to control iron homeostasis in A. fumigatus.
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Affiliation(s)
- Manuel Sánchez López-Berges
- Institute of Molecular Biology, Biocenter, Medical University of Innsbruck, 6020 Innsbruck, Austria; (M.M.); (C.B.); (F.G.)
- Correspondence: (M.S.L.-B.); (A.A.B.); (H.H.)
| | - Mareike Thea Scheven
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology (Leibniz-HKI), 07745 Jena, Germany; (M.T.S.); (P.H.); (T.K.); (O.K.); (J.W.)
- Institute of Microbiology, Friedrich Schiller University Jena, 07743 Jena, Germany
| | - Peter Hortschansky
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology (Leibniz-HKI), 07745 Jena, Germany; (M.T.S.); (P.H.); (T.K.); (O.K.); (J.W.)
| | - Matthias Misslinger
- Institute of Molecular Biology, Biocenter, Medical University of Innsbruck, 6020 Innsbruck, Austria; (M.M.); (C.B.); (F.G.)
| | - Clara Baldin
- Institute of Molecular Biology, Biocenter, Medical University of Innsbruck, 6020 Innsbruck, Austria; (M.M.); (C.B.); (F.G.)
| | - Fabio Gsaller
- Institute of Molecular Biology, Biocenter, Medical University of Innsbruck, 6020 Innsbruck, Austria; (M.M.); (C.B.); (F.G.)
| | - Ernst R. Werner
- Division of Biological Chemistry, Biocenter, Innsbruck Medical University, 6020 Innsbruck, Austria;
| | - Thomas Krüger
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology (Leibniz-HKI), 07745 Jena, Germany; (M.T.S.); (P.H.); (T.K.); (O.K.); (J.W.)
| | - Olaf Kniemeyer
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology (Leibniz-HKI), 07745 Jena, Germany; (M.T.S.); (P.H.); (T.K.); (O.K.); (J.W.)
| | - Jakob Weber
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology (Leibniz-HKI), 07745 Jena, Germany; (M.T.S.); (P.H.); (T.K.); (O.K.); (J.W.)
| | - Axel A. Brakhage
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology (Leibniz-HKI), 07745 Jena, Germany; (M.T.S.); (P.H.); (T.K.); (O.K.); (J.W.)
- Institute of Microbiology, Friedrich Schiller University Jena, 07743 Jena, Germany
- Correspondence: (M.S.L.-B.); (A.A.B.); (H.H.)
| | - Hubertus Haas
- Institute of Molecular Biology, Biocenter, Medical University of Innsbruck, 6020 Innsbruck, Austria; (M.M.); (C.B.); (F.G.)
- Correspondence: (M.S.L.-B.); (A.A.B.); (H.H.)
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36
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Wrestling and Wrapping: A Perspective on SUMO Proteins in Schwann Cells. Biomolecules 2021; 11:biom11071055. [PMID: 34356679 PMCID: PMC8301837 DOI: 10.3390/biom11071055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 07/12/2021] [Accepted: 07/13/2021] [Indexed: 11/20/2022] Open
Abstract
Schwann cell development and peripheral nerve myelination are finely orchestrated multistep processes; some of the underlying mechanisms are well described and others remain unknown. Many posttranslational modifications (PTMs) like phosphorylation and ubiquitination have been reported to play a role during the normal development of the peripheral nervous system (PNS) and in demyelinating neuropathies. However, a relatively novel PTM, SUMOylation, has not been studied in these contexts. SUMOylation involves the covalent attachment of one or more small ubiquitin-like modifier (SUMO) proteins to a substrate, which affects the function, cellular localization, and further PTMs of the conjugated protein. SUMOylation also regulates other proteins indirectly by facilitating non-covalent protein–protein interaction via SUMO interaction motifs (SIM). This pathway has important consequences on diverse cellular processes, and dysregulation of this pathway has been reported in several diseases including neurological and degenerative conditions. In this article, we revise the scarce literature on SUMOylation in Schwann cells and the PNS, we propose putative substrate proteins, and we speculate on potential mechanisms underlying the possible involvement of this PTM in peripheral myelination and neuropathies.
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37
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Chen LC, Hsieh YL, Tan GYT, Kuo TY, Chou YC, Hsu PH, Hwang-Verslues WW. Differential effects of SUMO1 and SUMO2 on circadian protein PER2 stability and function. Sci Rep 2021; 11:14431. [PMID: 34257372 PMCID: PMC8277905 DOI: 10.1038/s41598-021-93933-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 07/05/2021] [Indexed: 11/09/2022] Open
Abstract
Posttranslational modification (PTM) of core circadian clock proteins, including Period2 (PER2), is required for proper circadian regulation. PER2 function is regulated by casein kinase 1 (CK1)-mediated phosphorylation and ubiquitination but little is known about other PER2 PTMs or their interaction with PER2 phosphorylation. We found that PER2 can be SUMOylated by both SUMO1 and SUMO2; however, SUMO1 versus SUMO2 conjugation had different effects on PER2 turnover and transcriptional suppressor function. SUMO2 conjugation facilitated PER2 interaction with β-TrCP leading to PER2 proteasomal degradation. In contrast, SUMO1 conjugation, mediated by E3 SUMO-protein ligase RanBP2, enhanced CK1-mediated PER2S662 phosphorylation, inhibited PER2 degradation and increased PER2 transcriptional suppressor function. PER2 K736 was critical for both SUMO1- and SUMO2-conjugation. A PER2K736R mutation was sufficient to alter PER2 protein oscillation and reduce PER2-mediated transcriptional suppression. Together, our data revealed that SUMO1 versus SUMO2 conjugation acts as a determinant of PER2 stability and function and thereby affects the circadian regulatory system and the expression of clock-controlled genes.
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Affiliation(s)
- Ling-Chih Chen
- Genomics Research Center, Academia Sinica, No. 128, Sec. 2, Academia Road, Taipei, 115, Taiwan, ROC
| | - Yung-Lin Hsieh
- Genomics Research Center, Academia Sinica, No. 128, Sec. 2, Academia Road, Taipei, 115, Taiwan, ROC
| | - Grace Y T Tan
- Genomics Research Center, Academia Sinica, No. 128, Sec. 2, Academia Road, Taipei, 115, Taiwan, ROC
| | - Tai-Yun Kuo
- Genomics Research Center, Academia Sinica, No. 128, Sec. 2, Academia Road, Taipei, 115, Taiwan, ROC
| | - Yu-Chi Chou
- Biomedical Translation Research Center (BioTReC), Academia Sinica, Taipei, 115, Taiwan, ROC
| | - Pang-Hung Hsu
- Department of Bioscience and Biotechnology, National Taiwan Ocean University, Keelung City, 202, Taiwan, ROC
| | - Wendy W Hwang-Verslues
- Genomics Research Center, Academia Sinica, No. 128, Sec. 2, Academia Road, Taipei, 115, Taiwan, ROC.
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38
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MacTaggart B, Kashina A. Posttranslational modifications of the cytoskeleton. Cytoskeleton (Hoboken) 2021; 78:142-173. [PMID: 34152688 DOI: 10.1002/cm.21679] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Revised: 06/13/2021] [Accepted: 06/16/2021] [Indexed: 12/12/2022]
Abstract
The cytoskeleton plays important roles in many essential processes at the cellular and organismal levels, including cell migration and motility, cell division, and the establishment and maintenance of cell and tissue architecture. In order to facilitate these varied functions, the main cytoskeletal components-microtubules, actin filaments, and intermediate filaments-must form highly diverse intracellular arrays in different subcellular areas and cell types. The question of how this diversity is conferred has been the focus of research for decades. One key mechanism is the addition of posttranslational modifications (PTMs) to the major cytoskeletal proteins. This posttranslational addition of various chemical groups dramatically increases the complexity of the cytoskeletal proteome and helps facilitate major global and local cytoskeletal functions. Cytoskeletal proteins undergo many PTMs, most of which are not well understood. Recent technological advances in proteomics and cell biology have allowed for the in-depth study of individual PTMs and their functions in the cytoskeleton. Here, we provide an overview of the major PTMs that occur on the main structural components of the three cytoskeletal systems-tubulin, actin, and intermediate filament proteins-and highlight the cellular function of these modifications.
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Affiliation(s)
- Brittany MacTaggart
- School of Veterinary Medicine, Department of Biomedical Sciences, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Anna Kashina
- School of Veterinary Medicine, Department of Biomedical Sciences, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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Dong J, Li Y, Zheng F, Chen W, Huang S, Zhou X, Wang K, Cai W, Liu H, Yin L, Li Q, Tang D, Dai Y. Co-occurrence of Protein Crotonylation and 2-Hydroxyisobutyrylation in the Proteome of End-Stage Renal Disease. ACS OMEGA 2021; 6:15782-15793. [PMID: 34179622 PMCID: PMC8223210 DOI: 10.1021/acsomega.1c01161] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 05/25/2021] [Indexed: 05/16/2023]
Abstract
End-stage renal disease (ESRD) is gradually becoming a major public healthcare burden worldwide. Post-translational modifications carrying epigenetic information play a crucial role in the pathogenesis of many chronic diseases. We performed lysine crotonylation (KCr) and lysine 2-hydroxyisobutyrylation (Khib) analyses with liquid chromatography-tandem mass spectrometry to obtain a comprehensive profile and reveal the specific pathogenesis of peripheral blood mononuclear cells in ESRD patients. 218 overlap proteins among differentially modified proteins (DMPs) of both 2-hydroxyisobutyrylation and crotonylation were identified. KEGG analysis enriched pathways of protein processing in endoplasmic reticulum (ER) and glycolysis/gluconeogenesis which is closely related with cell apoptosis. In Bip, a master regulator in the ER, eight sites were identified as having both KCr and Khib modifications. Five differentially KCr modification sites and three differentially Khib-modified sites were detected between ESRD patients and normal controls. Besides Bip, other proteins (GRP94, CNX, CRT, PDIs, GlcII, ERP57, Bap31, Hsp70, and Hsp90) happened both KCr and Khib modifications. Nine DMPs having both KCr and Khib modifications were related to the glycolysis/gluconeogenesis pathway containing two key regulatory enzymes of hexokinase-1 and pyruvate kinase. The two most abundant dual modification proteins were ENO1 and PGK1 with 15 sites and 8 sites, respectively. Lysine residue K228 with both KCr and Khib modifications in ENO1 was on its surface and made it accessible for p300 mediating dynamic modifications. Overall, we hypothesize that KCr and Khib comodifications may influence the number of immunocytes and further induce immune senescence in ESRD patients through the glycolysis/gluconeogenesis pathway and protein processing in the ER process, which may be a potential therapeutic direction in the future.
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Affiliation(s)
- Jingjing Dong
- Institute
of Nephrology and Blood Purification, The First Affiliated Hospital
of Jinan University, Jinan University, Guangzhou 510632, China
- Clinical
Medical Research Center, Guangdong Provincial Engineering Research
Center of Autoimmune Disease Precision Medicine, Shenzhen Engineering
Research Center of Autoimmune Disease, The Second Clinical Medical
College of Jinan University, The First Affiliated Hospital of Southern
University of Science and Technology, Shenzhen
People’s Hospital, Shenzhen, Guangdong 518020, China
| | - Yixi Li
- Institute
of Nephrology and Blood Purification, The First Affiliated Hospital
of Jinan University, Jinan University, Guangzhou 510632, China
- Clinical
Medical Research Center, Guangdong Provincial Engineering Research
Center of Autoimmune Disease Precision Medicine, Shenzhen Engineering
Research Center of Autoimmune Disease, The Second Clinical Medical
College of Jinan University, The First Affiliated Hospital of Southern
University of Science and Technology, Shenzhen
People’s Hospital, Shenzhen, Guangdong 518020, China
| | - Fengping Zheng
- Clinical
Medical Research Center, Guangdong Provincial Engineering Research
Center of Autoimmune Disease Precision Medicine, Shenzhen Engineering
Research Center of Autoimmune Disease, The Second Clinical Medical
College of Jinan University, The First Affiliated Hospital of Southern
University of Science and Technology, Shenzhen
People’s Hospital, Shenzhen, Guangdong 518020, China
| | - Wenbiao Chen
- Clinical
Medical Research Center, Guangdong Provincial Engineering Research
Center of Autoimmune Disease Precision Medicine, Shenzhen Engineering
Research Center of Autoimmune Disease, The Second Clinical Medical
College of Jinan University, The First Affiliated Hospital of Southern
University of Science and Technology, Shenzhen
People’s Hospital, Shenzhen, Guangdong 518020, China
| | - Shaoying Huang
- Clinical
Medical Research Center, Guangdong Provincial Engineering Research
Center of Autoimmune Disease Precision Medicine, Shenzhen Engineering
Research Center of Autoimmune Disease, The Second Clinical Medical
College of Jinan University, The First Affiliated Hospital of Southern
University of Science and Technology, Shenzhen
People’s Hospital, Shenzhen, Guangdong 518020, China
| | - Xianqing Zhou
- Guangxi
Key Laboratory of Metabolic Diseases Research, Affiliated No. 924
Hospital, Southern Medical University, Guilin 541002, China
| | - Kang Wang
- Clinical
Medical Research Center, Guangdong Provincial Engineering Research
Center of Autoimmune Disease Precision Medicine, Shenzhen Engineering
Research Center of Autoimmune Disease, The Second Clinical Medical
College of Jinan University, The First Affiliated Hospital of Southern
University of Science and Technology, Shenzhen
People’s Hospital, Shenzhen, Guangdong 518020, China
| | - Wanxia Cai
- Clinical
Medical Research Center, Guangdong Provincial Engineering Research
Center of Autoimmune Disease Precision Medicine, Shenzhen Engineering
Research Center of Autoimmune Disease, The Second Clinical Medical
College of Jinan University, The First Affiliated Hospital of Southern
University of Science and Technology, Shenzhen
People’s Hospital, Shenzhen, Guangdong 518020, China
| | - HaiPing Liu
- The
Second People’s Hospital of Lianping County, Heyuan517139, Guangdong , China
| | - Lianghong Yin
- Institute
of Nephrology and Blood Purification, The First Affiliated Hospital
of Jinan University, Jinan University, Guangzhou 510632, China
| | - Qiang Li
- Dongguan
Hospital of Guangzhou University of Traditional Chinese Medicine, Dongguan 523000, Guangdong, China
- . Phone: +86 0769 26385192
| | - Donge Tang
- Clinical
Medical Research Center, Guangdong Provincial Engineering Research
Center of Autoimmune Disease Precision Medicine, Shenzhen Engineering
Research Center of Autoimmune Disease, The Second Clinical Medical
College of Jinan University, The First Affiliated Hospital of Southern
University of Science and Technology, Shenzhen
People’s Hospital, Shenzhen, Guangdong 518020, China
- . Phone: +86 0755 22942106
| | - Yong Dai
- Clinical
Medical Research Center, Guangdong Provincial Engineering Research
Center of Autoimmune Disease Precision Medicine, Shenzhen Engineering
Research Center of Autoimmune Disease, The Second Clinical Medical
College of Jinan University, The First Affiliated Hospital of Southern
University of Science and Technology, Shenzhen
People’s Hospital, Shenzhen, Guangdong 518020, China
- Guangxi
Key Laboratory of Metabolic Diseases Research, Affiliated No. 924
Hospital, Southern Medical University, Guilin 541002, China
- . Phone: +86 0755 22942780
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Kim H, Ding YH, Lu S, Zuo MQ, Tan W, Conte D, Dong MQ, Mello CC. PIE-1 SUMOylation promotes germline fates and piRNA-dependent silencing in C. elegans. eLife 2021; 10:e63300. [PMID: 34003111 PMCID: PMC8131105 DOI: 10.7554/elife.63300] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 04/23/2021] [Indexed: 02/06/2023] Open
Abstract
Germlines shape and balance heredity, integrating and regulating information from both parental and foreign sources. Insights into how germlines handle information have come from the study of factors that specify or maintain the germline fate. In early Caenorhabditis elegans embryos, the CCCH zinc finger protein PIE-1 localizes to the germline where it prevents somatic differentiation programs. Here, we show that PIE-1 also functions in the meiotic ovary where it becomes SUMOylated and engages the small ubiquitin-like modifier (SUMO)-conjugating machinery. Using whole-SUMO-proteome mass spectrometry, we identify HDAC SUMOylation as a target of PIE-1. Our analyses of genetic interactions between pie-1 and SUMO pathway mutants suggest that PIE-1 engages the SUMO machinery both to preserve the germline fate in the embryo and to promote Argonaute-mediated surveillance in the adult germline.
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Affiliation(s)
- Heesun Kim
- RNA Therapeutics Institute, University of Massachusetts Medical SchoolWorcesterUnited States
| | - Yue-He Ding
- RNA Therapeutics Institute, University of Massachusetts Medical SchoolWorcesterUnited States
| | - Shan Lu
- National Institute of Biological SciencesBeijingChina
| | - Mei-Qing Zuo
- National Institute of Biological SciencesBeijingChina
| | - Wendy Tan
- RNA Therapeutics Institute, University of Massachusetts Medical SchoolWorcesterUnited States
| | - Darryl Conte
- RNA Therapeutics Institute, University of Massachusetts Medical SchoolWorcesterUnited States
| | - Meng-Qiu Dong
- National Institute of Biological SciencesBeijingChina
| | - Craig C Mello
- RNA Therapeutics Institute, University of Massachusetts Medical SchoolWorcesterUnited States
- Howard Hughes Medical InstituteChevy ChaseUnited States
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41
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Chelbi-Alix MK, Thibault P. Crosstalk Between SUMO and Ubiquitin-Like Proteins: Implication for Antiviral Defense. Front Cell Dev Biol 2021; 9:671067. [PMID: 33968942 PMCID: PMC8097047 DOI: 10.3389/fcell.2021.671067] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 03/29/2021] [Indexed: 12/19/2022] Open
Abstract
Interferon (IFN) is a crucial first line of defense against viral infection. This cytokine induces the expression of several IFN-Stimulated Genes (ISGs), some of which act as restriction factors. Upon IFN stimulation, cells also express ISG15 and SUMO, two key ubiquitin-like (Ubl) modifiers that play important roles in the antiviral response. IFN itself increases the global cellular SUMOylation in a PML-dependent manner. Mass spectrometry-based proteomics enables the large-scale identification of Ubl protein conjugates to determine the sites of modification and the quantitative changes in protein abundance. Importantly, a key difference amongst SUMO paralogs is the ability of SUMO2/3 to form poly-SUMO chains that recruit SUMO ubiquitin ligases such RING finger protein RNF4 and RNF111, thus resulting in the proteasomal degradation of conjugated substrates. Crosstalk between poly-SUMOylation and ISG15 has been reported recently, where increased poly-SUMOylation in response to IFN enhances IFN-induced ISGylation, stabilizes several ISG products in a TRIM25-dependent fashion, and results in enhanced IFN-induced antiviral activities. This contribution will highlight the relevance of the global SUMO proteome and the crosstalk between SUMO, ubiquitin and ISG15 in controlling both the stability and function of specific restriction factors that mediate IFN antiviral defense.
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Affiliation(s)
| | - Pierre Thibault
- Institute for Research in Immunology and Cancer, Montréal, QC, Canada
- Department of Chemistry, University of Montreal, Montréal, QC, Canada
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Song B, Liu D, Greco TM, Cristea IM. Post-translational modification control of viral DNA sensors and innate immune signaling. Adv Virus Res 2021; 109:163-199. [PMID: 33934827 PMCID: PMC8489191 DOI: 10.1016/bs.aivir.2021.03.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The vertebrate innate immune system confers host cells with mechanisms to protect against both evolutionarily ancient pathogens and newly emerging pathogenic strains. Innate immunity relies on the host cell's ability to distinguish between self and pathogen-derived molecules. To achieve this, the innate immune system uses germline encoded receptors called pattern recognition receptors (PRRs), which recognize various molecular signatures, including nucleic acids, proteins, lipids, glycans and glycolipids. Among these molecules, the recognition of pathogenic, mislocalized, or damaged DNA by cellular protein receptors, commonly called DNA sensors, represents a major surveillance pathway for initiating immune signaling. The ability of cells to temporally regulate DNA sensor activation and subsequent signal termination is critical for effective immune signaling. These same mechanisms are also co-opted by pathogens to promote their replication. Therefore, there is significant interest in understanding DNA sensor regulatory networks during microbial infections and autoimmune disease. One emerging aspect of DNA sensor regulation is through post-translational modifications (PTMs), including phosphorylation, acetylation, ubiquitination, ADP-ribosylation, SUMOylation, methylation, deamidation, glutamylation. In this chapter, we discuss how PTMs have been shown to positively or negatively impact DNA sensor functions via diverse mechanisms, including direct regulation of enzymatic activity, protein-protein and protein-DNA interactions, protein translocations and protein turnover. In addition, we highlight the ability of virus-induced PTMs to promote immune evasion. We also discuss the recent evidence linking PTMs on DNA sensors with human diseases and more broadly, highlight promising directions for future research on PTM-mediated regulation of DNA sensor-dependent immune signaling.
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Affiliation(s)
- Bokai Song
- Department of Molecular Biology, Princeton University, Princeton, NJ, United States
| | - Dawei Liu
- Department of Molecular Biology, Princeton University, Princeton, NJ, United States
| | - Todd M Greco
- Department of Molecular Biology, Princeton University, Princeton, NJ, United States
| | - Ileana M Cristea
- Department of Molecular Biology, Princeton University, Princeton, NJ, United States.
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43
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Impens F, Dussurget O. Three decades of listeriology through the prism of technological advances. Cell Microbiol 2021; 22:e13183. [PMID: 32185895 DOI: 10.1111/cmi.13183] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 01/28/2020] [Accepted: 01/29/2020] [Indexed: 12/15/2022]
Abstract
Decades of breakthroughs resulting from cross feeding of microbiological research and technological innovation have promoted Listeria monocytogenes to the rank of model microorganism to study host-pathogen interactions. The extraordinary capacity of this bacterium to interfere with a vast array of host cellular processes uncovered new concepts in microbiology, cell biology and infection biology. Here, we review technological advances that revealed how bacteria and host interact in space and time at the molecular, cellular, tissue and whole body scales, ultimately revolutionising our understanding of Listeria pathogenesis. With the current bloom of multidisciplinary integrative approaches, Listeria entered a new microbiology era.
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Affiliation(s)
- Francis Impens
- Center for Medical Biotechnology, VIB, Ghent, Belgium.,Department for Biomedical Medicine, Ghent University, Ghent, Belgium.,VIB Proteomics Core, VIB, Ghent, Belgium
| | - Olivier Dussurget
- Institut Pasteur, Unité de Recherche Yersinia, Paris, France.,Université de Paris, Sorbonne Paris Cité, Paris, France
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Dunphy K, Dowling P, Bazou D, O’Gorman P. Current Methods of Post-Translational Modification Analysis and Their Applications in Blood Cancers. Cancers (Basel) 2021; 13:1930. [PMID: 33923680 PMCID: PMC8072572 DOI: 10.3390/cancers13081930] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 04/04/2021] [Accepted: 04/14/2021] [Indexed: 12/12/2022] Open
Abstract
Post-translational modifications (PTMs) add a layer of complexity to the proteome through the addition of biochemical moieties to specific residues of proteins, altering their structure, function and/or localization. Mass spectrometry (MS)-based techniques are at the forefront of PTM analysis due to their ability to detect large numbers of modified proteins with a high level of sensitivity and specificity. The low stoichiometry of modified peptides means fractionation and enrichment techniques are often performed prior to MS to improve detection yields. Immuno-based techniques remain popular, with improvements in the quality of commercially available modification-specific antibodies facilitating the detection of modified proteins with high affinity. PTM-focused studies on blood cancers have provided information on altered cellular processes, including cell signaling, apoptosis and transcriptional regulation, that contribute to the malignant phenotype. Furthermore, the mechanism of action of many blood cancer therapies, such as kinase inhibitors, involves inhibiting or modulating protein modifications. Continued optimization of protocols and techniques for PTM analysis in blood cancer will undoubtedly lead to novel insights into mechanisms of malignant transformation, proliferation, and survival, in addition to the identification of novel biomarkers and therapeutic targets. This review discusses techniques used for PTM analysis and their applications in blood cancer research.
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Affiliation(s)
- Katie Dunphy
- Department of Biology, National University of Ireland, W23 F2K8 Maynooth, Ireland; (K.D.); (P.D.)
| | - Paul Dowling
- Department of Biology, National University of Ireland, W23 F2K8 Maynooth, Ireland; (K.D.); (P.D.)
| | - Despina Bazou
- Department of Haematology, Mater Misericordiae University Hospital, D07 WKW8 Dublin, Ireland;
| | - Peter O’Gorman
- Department of Haematology, Mater Misericordiae University Hospital, D07 WKW8 Dublin, Ireland;
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Walters TS, McIntosh DJ, Ingram SM, Tillery L, Motley ED, Arinze IJ, Misra S. SUMO-Modification of Human Nrf2 at K 110 and K 533 Regulates Its Nucleocytoplasmic Localization, Stability and Transcriptional Activity. Cell Physiol Biochem 2021; 55:141-159. [PMID: 33770425 PMCID: PMC8279473 DOI: 10.33594/000000351] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/15/2021] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND/AIMS Nuclear factor erythroid 2-related factor 2 (Nrf2) is a transcription factor that binds to the antioxidant response element(s) (ARE) in target gene promoters, enabling oxidatively stressed cells to respond in order to restore redox homeostasis. Post-translational modifications (PTMs) that mediate activation of Nrf2, in the cytosol and its release from Keap1, have been extensively studied but PTMs that impact its biology after activation are beginning to emerge. In this regard, PTMs like acetylation, phosphorylation, ubiquitination and sumoylation contribute towards the Nrf2 subcellular localization, and its transactivation function. We previously demonstrated that Nrf2 traffics to the promyelocytic leukemia-nuclear bodies (PML-NB), where it is a target for modification by small ubiquitin-like modifier (SUMO) proteins (sumoylation), but the site(s) for SUMO conjugation have not been determined. In this study, we aim to identify SUMO-2 conjugation site(s) and explore the impact, sumoylation of the site(s) have on Nrf2 stability, nuclear localization and transcriptional activation of its target gene expression upon oxidative stress. METHODS The putative SUMO-binding sites in Nrf2 for human isoform1 (NP_006155.2) and mouse homolog (NP_035032.1) were identified using a computer-based SUMO-predictive software (SUMOplot™). Site-directed mutagenesis, immunoblot analysis, and ARE-mediated reporter gene assays were used to assess the impact of sumoylation on these site(s) in vitro. Effect of mutation of these sumoylation sites of Nrf2 on expression of Heme Oxygenase1 (HO-1) was determined in HEK293T cell. RESULTS
Eight putative sumoylation sites were identified by SUMOplot™ analysis. Out of the eight predicted sites only one 532LKDE535 of human (h) and its homologous 524LKDE527 of mouse (m) Nrf2, exactly matches the SUMO-binding consensus motif. The other high probability SUMO-acceptor site identified was residue K110, in the motifs 109PKSD112 and 109PKQD112 of human and mouse Nrf2, respectively. Mutational analysis of putative sumoylation sites (human (h)/mouse (m)
K110, hK533 and mK525) showed that these residues are needed for SUMO-2 conjugation, nuclear localization and ARE driven transcription of reporter genes and the endogenous HO-1 expression by Nrf2. These residues also stabilized Nrf2, as evident from shorter half-lives of the mutant protein compared to wild-type Nrf2. CONCLUSION Our findings indicate that SUMO-2
mediated sumoylation of K110 and K533 in human Nrf2 regulates in part its transcriptional activity by enhancing its stabilization and nuclear localization.
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Affiliation(s)
- Treniqka S Walters
- Department of Biochemistry, Cancer Biology, Neuroscience and Pharmacology, School of Medicine, Meharry Medical College, Nashville, TN, USA
| | - Deneshia J McIntosh
- Department of Biochemistry, Cancer Biology, Neuroscience and Pharmacology, School of Medicine, Meharry Medical College, Nashville, TN, USA
| | - Shalonda M Ingram
- Department of Microbiology, Immunology and Physiology, School of Medicine, Meharry Medical College, Nashville, TN, USA
| | - Lakeisha Tillery
- Department of Microbiology, Immunology and Physiology, School of Medicine, Meharry Medical College, Nashville, TN, USA
| | - Evangeline D Motley
- Department of Microbiology, Immunology and Physiology, School of Medicine, Meharry Medical College, Nashville, TN, USA
| | - Ifeanyi J Arinze
- Department of Biochemistry, Cancer Biology, Neuroscience and Pharmacology, School of Medicine, Meharry Medical College, Nashville, TN, USA
| | - Smita Misra
- Department of Microbiology, Immunology and Physiology, School of Medicine, Meharry Medical College, Nashville, TN, USA,
- School of Graduate Studies and Research, Meharry Medical College, Nashville TN, USA
- Center for Women's Health, Meharry Medical College, Nashville TN, USA
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SUMOylation- and GAR1-Dependent Regulation of Dyskerin Nuclear and Subnuclear Localization. Mol Cell Biol 2021; 41:MCB.00464-20. [PMID: 33526451 DOI: 10.1128/mcb.00464-20] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 01/20/2021] [Indexed: 12/29/2022] Open
Abstract
The nuclear and subnuclear compartmentalization of the telomerase-associated protein and H/ACA ribonucleoprotein component dyskerin is an important although incompletely understood aspect of H/ACA ribonucleoprotein function. Four SUMOylation sites were previously identified in the C-terminal nuclear/nucleolar localization signal (N/NoLS) of dyskerin. We found that a cytoplasmic localized C-terminal truncation variant of dyskerin lacking most of the C-terminal N/NoLS represents an under-SUMOylated variant of dyskerin compared to wild-type dyskerin. We demonstrate that mimicking constitutive SUMOylation of dyskerin using a SUMO3 fusion construct can drive nuclear accumulation of this variant and that the SUMO site K467 in this N/NoLS is particularly important for the subnuclear localization of dyskerin to the nucleolus in a mature H/ACA complex assembly- and SUMO-dependent manner. We also characterize a novel SUMO-interacting motif in the mature H/ACA complex component GAR1 that mediates the interaction between dyskerin and GAR1. Mislocalization of dyskerin, either in the cytoplasm or excluded from the nucleolus, disrupts dyskerin function and leads to reduced interaction of dyskerin with the telomerase RNA. These data indicate a role for dyskerin C-terminal N/NoLS SUMOylation in regulating the nuclear and subnuclear localization of dyskerin, which is essential for dyskerin function as both a telomerase-associated protein and as an H/ACA ribonucleoprotein.
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47
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Lork M, Lieber G, Hale BG. Proteomic Approaches to Dissect Host SUMOylation during Innate Antiviral Immune Responses. Viruses 2021; 13:528. [PMID: 33806893 PMCID: PMC8004987 DOI: 10.3390/v13030528] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 03/20/2021] [Accepted: 03/22/2021] [Indexed: 12/21/2022] Open
Abstract
SUMOylation is a highly dynamic ubiquitin-like post-translational modification that is essential for cells to respond to and resolve various genotoxic and proteotoxic stresses. Virus infections also constitute a considerable stress scenario for cells, and recent research has started to uncover the diverse roles of SUMOylation in regulating virus replication, not least by impacting antiviral defenses. Here, we review some of the key findings of this virus-host interplay, and discuss the increasingly important contribution that large-scale, unbiased, proteomic methodologies are making to discoveries in this field. We highlight the latest proteomic technologies that have been specifically developed to understand SUMOylation dynamics in response to cellular stresses, and comment on how these techniques might be best applied to dissect the biology of SUMOylation during innate immunity. Furthermore, we showcase a selection of studies that have already used SUMO proteomics to reveal novel aspects of host innate defense against viruses, such as functional cross-talk between SUMO proteins and other ubiquitin-like modifiers, viral antagonism of SUMO-modified antiviral restriction factors, and an infection-triggered SUMO-switch that releases endogenous retroelement RNAs to stimulate antiviral interferon responses. Future research in this area has the potential to provide new and diverse mechanistic insights into host immune defenses.
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Affiliation(s)
| | | | - Benjamin G. Hale
- Institute of Medical Virology, University of Zürich, 8057 Zürich, Switzerland; (M.L.); (G.L.)
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48
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Stabell M, Sæther T, Røhr ÅK, Gabrielsen OS, Myklebost O. Methylation-dependent SUMOylation of the architectural transcription factor HMGA2. Biochem Biophys Res Commun 2021; 552:91-97. [PMID: 33744765 DOI: 10.1016/j.bbrc.2021.02.099] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 02/19/2021] [Indexed: 11/26/2022]
Abstract
High mobility group A2 (HMGA2) is a chromatin-associated protein involved in the regulation of stem cell function, embryogenesis and cancer development. Although the protein does not contain a consensus SUMOylation site, it is shown to be SUMOylated. In this study, we demonstrate that the first lysine residue in the reported K66KAE SUMOylation motif in HMGA2 can be methylated in vitro and in vivo by the Set7/9 methyltransferase. By editing the lysine, the increased hydrophobicity of the resulting 6-N-methyl-lysine transforms the sequence into a consensus SUMO motif. This post-translational editing dramatically increases the subsequent SUMOylation of this site. Furthermore, similar putative methylation-dependent SUMO motifs are found in a number of other chromatin factors, and we confirm methylation-dependent SUMOylation of a site in one such protein, the Polyhomeotic complex 1 homolog (PHC1). Together, these results suggest that crosstalk between methylation and SUMOylation is a general mode for regulation of chromatin function.
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Affiliation(s)
- Marianne Stabell
- Department of Tumor Biology, Institute for Cancer Research, Radiumhospitalet, Oslo University Hospital, PO Box 4953 Nydalen, N-0424, Oslo, Norway; Department of Molecular Biosciences, University of Oslo, PO Box 1066 Blindern, N-0316, Oslo, Norway
| | - Thomas Sæther
- Department of Molecular Biosciences, University of Oslo, PO Box 1066 Blindern, N-0316, Oslo, Norway
| | - Åsmund K Røhr
- Department of Molecular Biosciences, University of Oslo, PO Box 1066 Blindern, N-0316, Oslo, Norway
| | - Odd S Gabrielsen
- Department of Molecular Biosciences, University of Oslo, PO Box 1066 Blindern, N-0316, Oslo, Norway
| | - Ola Myklebost
- Department of Tumor Biology, Institute for Cancer Research, Radiumhospitalet, Oslo University Hospital, PO Box 4953 Nydalen, N-0424, Oslo, Norway; Department of Molecular Biosciences, University of Oslo, PO Box 1066 Blindern, N-0316, Oslo, Norway.
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Fairweather SJ, Shah N, Brӧer S. Heteromeric Solute Carriers: Function, Structure, Pathology and Pharmacology. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 21:13-127. [PMID: 33052588 DOI: 10.1007/5584_2020_584] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Solute carriers form one of three major superfamilies of membrane transporters in humans, and include uniporters, exchangers and symporters. Following several decades of molecular characterisation, multiple solute carriers that form obligatory heteromers with unrelated subunits are emerging as a distinctive principle of membrane transporter assembly. Here we comprehensively review experimentally established heteromeric solute carriers: SLC3-SLC7 amino acid exchangers, SLC16 monocarboxylate/H+ symporters and basigin/embigin, SLC4A1 (AE1) and glycophorin A exchanger, SLC51 heteromer Ost α-Ost β uniporter, and SLC6 heteromeric symporters. The review covers the history of the heteromer discovery, transporter physiology, structure, disease associations and pharmacology - all with a focus on the heteromeric assembly. The cellular locations, requirements for complex formation, and the functional role of dimerization are extensively detailed, including analysis of the first complete heteromer structures, the SLC7-SLC3 family transporters LAT1-4F2hc, b0,+AT-rBAT and the SLC6 family heteromer B0AT1-ACE2. We present a systematic analysis of the structural and functional aspects of heteromeric solute carriers and conclude with common principles of their functional roles and structural architecture.
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Affiliation(s)
- Stephen J Fairweather
- Research School of Biology, Australian National University, Canberra, ACT, Australia. .,Resarch School of Chemistry, Australian National University, Canberra, ACT, Australia.
| | - Nishank Shah
- Research School of Biology, Australian National University, Canberra, ACT, Australia
| | - Stefan Brӧer
- Research School of Biology, Australian National University, Canberra, ACT, Australia.
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Paakinaho V, Lempiäinen JK, Sigismondo G, Niskanen EA, Malinen M, Jääskeläinen T, Varjosalo M, Krijgsveld J, Palvimo J. SUMOylation regulates the protein network and chromatin accessibility at glucocorticoid receptor-binding sites. Nucleic Acids Res 2021; 49:1951-1971. [PMID: 33524141 PMCID: PMC7913686 DOI: 10.1093/nar/gkab032] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Revised: 01/07/2021] [Accepted: 01/12/2021] [Indexed: 12/13/2022] Open
Abstract
Glucocorticoid receptor (GR) is an essential transcription factor (TF), controlling metabolism, development and immune responses. SUMOylation regulates chromatin occupancy and target gene expression of GR in a locus-selective manner, but the mechanism of regulation has remained elusive. Here, we identify the protein network around chromatin-bound GR by using selective isolation of chromatin-associated proteins and show that the network is affected by receptor SUMOylation, with several nuclear receptor coregulators and chromatin modifiers preferring interaction with SUMOylation-deficient GR and proteins implicated in transcriptional repression preferring interaction with SUMOylation-competent GR. This difference is reflected in our chromatin binding, chromatin accessibility and gene expression data, showing that the SUMOylation-deficient GR is more potent in binding and opening chromatin at glucocorticoid-regulated enhancers and inducing expression of target loci. Blockage of SUMOylation by a SUMO-activating enzyme inhibitor (ML-792) phenocopied to a large extent the consequences of GR SUMOylation deficiency on chromatin binding and target gene expression. Our results thus show that SUMOylation modulates the specificity of GR by regulating its chromatin protein network and accessibility at GR-bound enhancers. We speculate that many other SUMOylated TFs utilize a similar regulatory mechanism.
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Affiliation(s)
- Ville Paakinaho
- Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
| | | | | | - Einari A Niskanen
- Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
| | - Marjo Malinen
- Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
- Department of Environmental and Biological Sciences, University of Eastern Finland, Joensuu, Finland
| | - Tiina Jääskeläinen
- Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
| | - Markku Varjosalo
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Jeroen Krijgsveld
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- Heidelberg University, Medical Faculty, Heidelberg, Germany
| | - Jorma J Palvimo
- Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
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