1
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Parashar S, Kaushik A, Ambasta RK, Kumar P. E2 conjugating enzymes: A silent but crucial player in ubiquitin biology. Ageing Res Rev 2025; 108:102740. [PMID: 40194666 DOI: 10.1016/j.arr.2025.102740] [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: 02/01/2025] [Revised: 03/14/2025] [Accepted: 03/19/2025] [Indexed: 04/09/2025]
Abstract
E2 conjugating enzymes serve as the linchpin of the Ubiquitin-Proteasome System (UPS), facilitating ubiquitin (Ub) transfer to substrate proteins and regulating diverse processes critical to cellular homeostasis. The interaction of E2s with E1 activating enzymes and E3 ligases singularly positions them as middlemen of the ubiquitin machinery that guides protein turnover. Structural determinants of E2 enzymes play a pivotal role in these interactions, enabling precise ubiquitin transfer and substrate specificity. Regulation of E2 enzymes is tightly controlled through mechanisms such as post-translational modifications (PTMs), allosteric control, and gene expression modulation. Specific residues that undergo PTMs highlight their impact on E2 function and their role in ubiquitin dynamics. E2 enzymes also cooperate with deubiquitinases (DUBs) to maintain proteostasis. Design of small molecule inhibitors to modulate E2 activity is emerging as promising avenue to restrict ubiquitination as a potential therapeutic intervention. Additionally, E2 enzymes have been implicated in the pathogenesis and progression of neurodegenerative disorders (NDDs), where their dysfunction contributes to disease mechanisms. In summary, examining E2 enzymes from structural and functional perspectives offers potential to advance our understanding of cellular processes and assist in discovery of new therapeutic targets.
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Affiliation(s)
- Somya Parashar
- Molecular Neuroscience and Functional Genomics Laboratory, Department of Biotechnology, Delhi Technological University (Formerly Delhi College of Engineering), Shahbad Daulatpur, Bawana Road, Delhi 110042, India
| | - Aastha Kaushik
- Molecular Neuroscience and Functional Genomics Laboratory, Department of Biotechnology, Delhi Technological University (Formerly Delhi College of Engineering), Shahbad Daulatpur, Bawana Road, Delhi 110042, India
| | - Rashmi K Ambasta
- Department of Medicine, Vanderbilt University Medical Center (VUMC), Nashville, TN, USA
| | - Pravir Kumar
- Molecular Neuroscience and Functional Genomics Laboratory, Department of Biotechnology, Delhi Technological University (Formerly Delhi College of Engineering), Shahbad Daulatpur, Bawana Road, Delhi 110042, India.
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2
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Claessens LA, Verlaan–de Vries M, Broekman N, Luijsterburg MS, Vertegaal ACO. Interaction networks of SIM-binding groove mutants reveal alternate modes of SUMO binding and profound impact on SUMO conjugation. SCIENCE ADVANCES 2025; 11:eadp2643. [PMID: 40367183 PMCID: PMC12077520 DOI: 10.1126/sciadv.adp2643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Accepted: 04/09/2025] [Indexed: 05/16/2025]
Abstract
The best-characterized mode of noncovalent SUMO interaction involves binding of a SUMO-interaction motif (SIM) to a conserved binding groove in SUMO. Our knowledge on other types of SUMO interactions is still limited. Using SIM-binding groove SUMO2/3 mutants and mass spectrometry, we identified proteins that bind to SUMO in an alternate manner. Domain-enrichment analysis characterized a group of WD40 repeat domain-containing proteins as SIM-independent SUMO interactors, and we validated direct binding of SEC13 and SEH1L to SUMO in vitro. Using AlphaFold-3 modeling and in vitro mutational analysis, we identified residues in the WD40 domain of SEC13 and SUMO2/3's C terminus involved in the interaction. Furthermore, SIM-binding groove mutants failed to interact with SUMO E3 ligases belonging to the PIAS family, RANBP2, ZNF451, and TOPORS, leading to loss of covalent conjugation to most of SUMO target proteins. Together, our dataset serves as a unique resource and offers valuable insights on the intricacies of the SUMO interactome and SUMO targets.
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Affiliation(s)
- Laura A. Claessens
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, Netherlands
| | - Matty Verlaan–de Vries
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, Netherlands
| | - Nienke Broekman
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, Netherlands
| | | | - Alfred C. O. Vertegaal
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, Netherlands
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3
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Tröster V, Wong RP, Börgel A, Cakilkaya B, Renz C, Möckel MM, Eifler-Olivi K, Marinho J, Reinberg T, Furler S, Schaefer JV, Plückthun A, Wolf E, Ulrich HD. Custom affinity probes reveal DNA-damage-induced, ssDNA-independent chromatin SUMOylation in budding yeast. Cell Rep 2025; 44:115353. [PMID: 40019834 DOI: 10.1016/j.celrep.2025.115353] [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: 08/01/2024] [Revised: 12/17/2024] [Accepted: 02/05/2025] [Indexed: 03/29/2025] Open
Abstract
The small ubiquitin-related modifier SUMO regulates cellular processes in eukaryotes either by modulating individual protein-protein interactions or with relaxed substrate selectivity by group modification. Here, we report the isolation and characterization of designed ankyrin repeat protein (DARPin)-based affinity probes directed against budding yeast SUMO (Smt3). We validate selected DARPins as compartment-specific inhibitors or neutral detection agents. Structural characterization reveals a recognition mode distinct from that of natural SUMO interactors. In vivo application pinpoints Smt3's essential function to the nucleus and demonstrates DARPin-mediated sensitization toward various stress conditions. A subset of selected clones is validated as SUMOylation reporters in cells. In this manner, we identify a DNA-damage-induced nuclear SUMOylation response that-in contrast to previously reported chromatin group SUMOylation-is independent of single-stranded DNA and the SUMO-E3 Siz2 but depends on Mms21 and likely reflects late intermediates of homologous recombination. Thus, Smt3-specific DARPins can provide insight into the dynamics of SUMOylation in defined subcellular structures.
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Affiliation(s)
- Vera Tröster
- Institute of Molecular Biology (IMB) gGmbH, 55128 Mainz, Germany
| | - Ronald P Wong
- Institute of Molecular Biology (IMB) gGmbH, 55128 Mainz, Germany
| | - Arne Börgel
- Institute of Molecular Physiology, Johannes Gutenberg University, 55128 Mainz, Germany
| | - Baris Cakilkaya
- Institute of Molecular Physiology, Johannes Gutenberg University, 55128 Mainz, Germany
| | - Christian Renz
- Institute of Molecular Biology (IMB) gGmbH, 55128 Mainz, Germany
| | - Martin M Möckel
- Institute of Molecular Biology (IMB) gGmbH, 55128 Mainz, Germany
| | | | - Joana Marinho
- Department of Biochemistry, University of Zurich, 8057 Zurich, Switzerland
| | - Thomas Reinberg
- Department of Biochemistry, University of Zurich, 8057 Zurich, Switzerland
| | - Sven Furler
- Department of Biochemistry, University of Zurich, 8057 Zurich, Switzerland
| | - Jonas V Schaefer
- Department of Biochemistry, University of Zurich, 8057 Zurich, Switzerland
| | - Andreas Plückthun
- Department of Biochemistry, University of Zurich, 8057 Zurich, Switzerland
| | - Eva Wolf
- Institute of Molecular Physiology, Johannes Gutenberg University, 55128 Mainz, Germany
| | - Helle D Ulrich
- Institute of Molecular Biology (IMB) gGmbH, 55128 Mainz, Germany.
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4
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Du L, Chen J, Du C, Chen J, Wang Z, Bao B, Zhonglin LV, Xing C, Liang M, Wang L, Xie S, Li Y, Wang Z, Li G, Zhang J, Han G. Tim-3 promotes viral infection by suppressing the USP25-TRAF3-IRF7 signaling pathway. Cell Immunol 2025; 409-410:104930. [PMID: 39946759 DOI: 10.1016/j.cellimm.2025.104930] [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: 12/06/2024] [Revised: 01/26/2025] [Accepted: 02/05/2025] [Indexed: 03/15/2025]
Abstract
Tim-3, an immune checkpoint inhibitor, plays key roles in maintaining immune homeostasis and is involved in viral evasion. However, the precise role of Tim-3 in viral infection remains to be determined. USP25 is a deubiquitinating enzyme that initiates antiviral immunity by deubiquitinating TRAF3 and triggering the antiviral signaling pathway. Here we found that Tim-3-specific knockout in myeloid cells leads to enhanced antiviral immunity in mice with vesicular stomatitis virus (VSV) encephalitis by increasing the type I interferon response. Mechanistically, Tim-3 inhibits the expression of USP25 via STAT1 and interacts with USP25 but does not regulate its posttranslational modification; as a result, Tim-3 inhibits USP25-mediated deubiquitination of TRAF3, promotes K48-linked ubiquitination and degradation of TRAF3, inhibits the phosphorylation of IRF7, and ultimately downregulates the interferon response. These findings provide new insights into the function of Tim-3 in antiviral immunity and its related clinical significance.
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Affiliation(s)
- Lin Du
- Beijing Institute of Basic Medical Sciences, Beijing, China; Joint National Laboratory for Antibody Drug Engineering, Key Laboratory of Cell and Molecular Immunology, School of Medical Sciences, Henan University, Kaifeng, China
| | - Jinjie Chen
- Beijing Institute of Basic Medical Sciences, Beijing, China; Joint National Laboratory for Antibody Drug Engineering, Key Laboratory of Cell and Molecular Immunology, School of Medical Sciences, Henan University, Kaifeng, China
| | - Chunxiao Du
- Beijing Institute of Basic Medical Sciences, Beijing, China
| | - Junrui Chen
- Beijing Institute of Basic Medical Sciences, Beijing, China
| | - Zhaoxiang Wang
- The Second Medical Center & National Clinical Research Center for Geriatric Diseases, Chinese PLA General Hospital, Beijing, China
| | - Bing Bao
- Department of Medical Information Data Service, The General Hospital of Western Theater Command, Chengdu, China
| | - L V Zhonglin
- The Second Medical Center & National Clinical Research Center for Geriatric Diseases, Chinese PLA General Hospital, Beijing, China
| | - Chen Xing
- Beijing Institute of Basic Medical Sciences, Beijing, China
| | - Meng Liang
- Beijing Institute of Basic Medical Sciences, Beijing, China
| | - Lanying Wang
- Beijing Institute of Basic Medical Sciences, Beijing, China; Joint National Laboratory for Antibody Drug Engineering, Key Laboratory of Cell and Molecular Immunology, School of Medical Sciences, Henan University, Kaifeng, China
| | - Shun Xie
- Beijing Institute of Basic Medical Sciences, Beijing, China
| | - Yuxiang Li
- Beijing Institute of Basic Medical Sciences, Beijing, China
| | - Zhiding Wang
- Beijing Institute of Basic Medical Sciences, Beijing, China
| | - Ge Li
- Beijing Institute of Basic Medical Sciences, Beijing, China.
| | - Jun Zhang
- Beijing Institute of Basic Medical Sciences, Beijing, China.
| | - Gencheng Han
- Beijing Institute of Basic Medical Sciences, Beijing, China.
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5
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Chatzikalil E, Arvanitakis K, Filippatos F, Diamantopoulos PT, Koufakis T, Solomou EE. Diagnostic and Therapeutic Implications of the SUMOylation Pathway in Acute Myeloid Leukemia. Cancers (Basel) 2025; 17:631. [PMID: 40002226 PMCID: PMC11853134 DOI: 10.3390/cancers17040631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2024] [Revised: 02/09/2025] [Accepted: 02/10/2025] [Indexed: 02/27/2025] Open
Abstract
Epigenetics encompasses heritable and stable changes in gene expression caused by external chromosomal modifications, without altering the underlying DNA sequence. Epigenetic modifications, established during early development and maintained through successive cell divisions, play a critical role in regulating gene expression. Post-translational modifications (PTMs) are a key aspect of epigenetics and are essential for modulating protein functionality, as well as regulatory cellular processes, including proliferation, differentiation, metabolic pathways, and tumorigenic events. Among these, the small ubiquitin-related modifier (SUMOylation) system is a reversible PTM mechanism that alters target protein interaction surfaces through covalent binding to lysine residues, thereby influencing protein structure and function. Acute myeloid leukemia (AML) is a highly aggressive malignancy characterized by the clonal expansion of primitive hematopoietic stem cells of the myeloid lineage in the bone marrow. Despite recent advancements in therapeutic strategies and an improved understanding of leukemogenic pathways, patient outcomes remain poor, particularly in elderly populations. Consequently, efforts have focused on developing novel agents, including co-targeting specific mutations or integrating targeted therapies into combinatorial chemotherapeutic regimens. Emerging evidence suggests that SUMOylation plays a significant role in AML pathogenesis and treatment response, representing a promising therapeutic target for advanced disease cases. This review provides a brief analysis of the functional role of the SUMOylation system in AML and highlights its potential as a therapeutic target. We also discuss current knowledge gaps and propose directions for future research to advance precision medicine approaches for AML treatment.
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Affiliation(s)
- Elena Chatzikalil
- First Department of Pediatrics, National and Kapodistrian University of Athens Medical School, 11527 Athens, Greece;
- “Aghia Sofia” Children’s Hospital ERN-PeadCan Center, 11527 Athens, Greece
| | - Konstantinos Arvanitakis
- Division of Gastroenterology and Hepatology, First Department of Internal Medicine, AHEPA University Hospital, Aristotle University of Thessaloniki, St. Kiriakidi 1, 54636 Thessaloniki, Greece;
- Basic and Translational Research Unit, Special Unit for Biomedical Research and Education, School of Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, 54636 Thessaloniki, Greece
| | - Filippos Filippatos
- First Department of Pediatrics, National and Kapodistrian University of Athens Medical School, 11527 Athens, Greece;
- “Aghia Sofia” Children’s Hospital ERN-PeadCan Center, 11527 Athens, Greece
| | - Panagiotis T. Diamantopoulos
- First Department of Internal Medicine, National and Kapodistrian University of Athens Medical School, 11527 Athens, Greece;
| | - Theocharis Koufakis
- Second Propaedeutic Department of Internal Medicine, Hippokration General Hospital, Aristotle University of Thessaloniki, 54642 Thessaloniki, Greece;
| | - Elena E. Solomou
- Department of Internal Medicine, University of Patras Medical School, 26500 Rion, Greece;
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6
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Vogel K, Isono E. Erasing marks: Functions of plant deubiquitylating enzymes in modulating the ubiquitin code. THE PLANT CELL 2024; 36:3057-3073. [PMID: 38656977 PMCID: PMC11371157 DOI: 10.1093/plcell/koae129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 03/18/2024] [Accepted: 03/25/2024] [Indexed: 04/26/2024]
Abstract
Plant cells need to respond to environmental stimuli and developmental signals accurately and promptly. Ubiquitylation is a reversible posttranslational modification that enables the adaptation of cellular proteostasis to internal or external factors. The different topologies of ubiquitin linkages serve as the structural basis for the ubiquitin code, which can be interpreted by ubiquitin-binding proteins or readers in specific processes. The ubiquitylation status of target proteins is regulated by ubiquitylating enzymes or writers, as well as deubiquitylating enzymes (DUBs) or erasers. DUBs can remove ubiquitin molecules from target proteins. Arabidopsis (A. thaliana) DUBs belong to 7 protein families and exhibit a wide range of functions and play an important role in regulating selective protein degradation processes, including proteasomal, endocytic, and autophagic protein degradation. DUBs also shape the epigenetic landscape and modulate DNA damage repair processes. In this review, we summarize the current knowledge on DUBs in plants, their cellular functions, and the molecular mechanisms involved in the regulation of plant DUBs.
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Affiliation(s)
- Karin Vogel
- Department of Biology, University of Konstanz, Konstanz 78464, Germany
| | - Erika Isono
- Department of Biology, University of Konstanz, Konstanz 78464, Germany
- Division of Molecular Cell Biology, National Institute for Basic Biology, Okazaki 444-8585 Aichi, Japan
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7
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Yang W, Mei FC, Lin W, White MA, Li L, Li Y, Pan S, Cheng X. Protein SUMOylation promotes cAMP-independent EPAC1 activation. Cell Mol Life Sci 2024; 81:283. [PMID: 38963422 PMCID: PMC11335207 DOI: 10.1007/s00018-024-05315-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Revised: 05/20/2024] [Accepted: 06/12/2024] [Indexed: 07/05/2024]
Abstract
Protein SUMOylation is a prevalent stress-response posttranslational modification crucial for maintaining cellular homeostasis. Herein, we report that protein SUMOylation modulates cellular signaling mediated by cAMP, an ancient and universal stress-response second messenger. We identify K561 as a primary SUMOylation site in exchange protein directly activated by cAMP (EPAC1) via site-specific mapping of SUMOylation using mass spectrometry. Sequence and site-directed mutagenesis analyses reveal that a functional SUMO-interacting motif in EPAC1 is required for the binding of SUMO-conjugating enzyme UBC9, formation of EPAC1 nuclear condensate, and EPAC1 cellular SUMOylation. Heat shock-induced SUMO modification of EPAC1 promotes Rap1/2 activation in a cAMP-independent manner. Structural modeling and molecular dynamics simulation studies demonstrate that SUMO substituent on K561 of EPAC1 promotes Rap1 interaction by increasing the buried surface area between the SUMOylated receptor and its effector. Our studies identify a functional SUMOylation site in EPAC1 and unveil a novel mechanism in which SUMOylation of EPAC1 leads to its autonomous activation. The findings of SUMOylation-mediated activation of EPAC1 not only provide new insights into our understanding of cellular regulation of EPAC1 but also will open up a new field of experimentation concerning the cross-talk between cAMP/EPAC1 signaling and protein SUMOylation, two major cellular stress response pathways, during cellular homeostasis.
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Affiliation(s)
- Wenli Yang
- Department of Integrative Biology and Pharmacology, The University of Texas Health Science Center, Houston, TX, USA
- Texas Therapeutics Institute, The University of Texas Health Science Center, Houston, TX, USA
- Brown Foundation Institute of Molecular Medicine, The University of Texas Health Science Center, Houston, TX, USA
| | - Fang C Mei
- Department of Integrative Biology and Pharmacology, The University of Texas Health Science Center, Houston, TX, USA
- Texas Therapeutics Institute, The University of Texas Health Science Center, Houston, TX, USA
- Brown Foundation Institute of Molecular Medicine, The University of Texas Health Science Center, Houston, TX, USA
| | - Wei Lin
- Department of Integrative Biology and Pharmacology, The University of Texas Health Science Center, Houston, TX, USA
- Texas Therapeutics Institute, The University of Texas Health Science Center, Houston, TX, USA
- Brown Foundation Institute of Molecular Medicine, The University of Texas Health Science Center, Houston, TX, USA
| | - Mark A White
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, The University of Texas Medical Branch at Galveston, Galveston, TX, USA
| | - Li Li
- Brown Foundation Institute of Molecular Medicine, The University of Texas Health Science Center, Houston, TX, USA
| | - Yue Li
- Department of Integrative Biology and Pharmacology, The University of Texas Health Science Center, Houston, TX, USA
- Cell Therapy Manufacturing Center, 2130 W Holcombe Blvd, Houston, TX, 77030, USA
| | - Sheng Pan
- Department of Integrative Biology and Pharmacology, The University of Texas Health Science Center, Houston, TX, USA
- Brown Foundation Institute of Molecular Medicine, The University of Texas Health Science Center, Houston, TX, USA
| | - Xiaodong Cheng
- Department of Integrative Biology and Pharmacology, The University of Texas Health Science Center, Houston, TX, USA.
- Texas Therapeutics Institute, The University of Texas Health Science Center, Houston, TX, USA.
- Brown Foundation Institute of Molecular Medicine, The University of Texas Health Science Center, Houston, TX, USA.
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8
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Cheng C, Yao H, Li H, Liu J, Liu Z, Wu Y, Zhu L, Hu H, Fang Z, Wu L. Blockade of the deubiquitinating enzyme USP48 degrades oncogenic HMGA2 and inhibits colorectal cancer invasion and metastasis. Acta Pharm Sin B 2024; 14:1624-1643. [PMID: 38572092 PMCID: PMC10985028 DOI: 10.1016/j.apsb.2024.01.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 12/14/2023] [Accepted: 01/08/2024] [Indexed: 04/05/2024] Open
Abstract
HMGA2, a pivotal transcription factor, functions as a versatile regulator implicated in the progression of diverse aggressive malignancies. In this study, mass spectrometry was employed to identify ubiquitin-specific proteases that potentially interact with HMGA2, and USP48 was identified as a deubiquitinating enzyme of HMGA2. The enforced expression of USP48 significantly increased HMGA2 protein levels by inhibiting its degradation, while the deprivation of USP48 promoted HMGA2 degradation, thereby suppressing tumor invasion and metastasis. We discovered that USP48 undergoes SUMOylation at lysine 258, which enhances its binding affinity to HMGA2. Through subsequent phenotypic screening of small molecules, we identified DUB-IN-2 as a remarkably potent pharmacological inhibitor of USP48. Interestingly, the small-molecule inhibitor targeting USP48 induces destabilization of HMGA2. Clinically, upregulation of USP48 or HMGA2 in cancerous tissues is indicative of poor prognosis for patients with colorectal cancer (CRC). Collectively, our study not only elucidates the regulatory mechanism of DUBs involved in HMGA2 stability and validates USP48 as a potential therapeutic target for CRC, but also identifies DUB-IN-2 as a potent inhibitor of USP48 and a promising candidate for CRC treatment.
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Affiliation(s)
- Can Cheng
- Department of General Surgery, the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230001, China
- Anhui Province Key Laboratory of Hepatopancreatobiliary Surgery, the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230001, China
| | - Hanhui Yao
- Department of General Surgery, the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230001, China
- Anhui Province Key Laboratory of Hepatopancreatobiliary Surgery, the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230001, China
| | - Heng Li
- Anhui Province Key Laboratory of Hepatopancreatobiliary Surgery, the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230001, China
- Department of Comprehensive Surgery, Anhui Provincial Cancer Hospital, West District of the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230001, China
| | - Jingwen Liu
- Anhui Provincial Hospital Health Management Center, the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230001, China
| | - Zhengyi Liu
- Department of Breast Surgery, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, People's Hospital of Henan University, Zhengzhou 450003, China
| | - Yang Wu
- Department of General Surgery, the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230001, China
- Anhui Province Key Laboratory of Hepatopancreatobiliary Surgery, the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230001, China
| | - Liang Zhu
- Department of General Surgery, the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230001, China
| | - Hejie Hu
- Department of General Surgery, the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230001, China
| | - Zhengdong Fang
- Department of General Surgery, the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230001, China
| | - Liang Wu
- Department of General Surgery, the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230001, China
- Anhui Province Key Laboratory of Hepatopancreatobiliary Surgery, the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230001, China
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9
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Yang W, Mei FC, Lin W, White MA, Li L, Li Y, Pan S, Cheng X. Protein SUMOylation promotes cAMP-independent EPAC1 activation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.08.574738. [PMID: 38260470 PMCID: PMC10802480 DOI: 10.1101/2024.01.08.574738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Exchange protein directly activated by cAMP (EPAC1) mediates the intracellular functions of a critical stress-response second messenger, cAMP. Herein, we report that EPAC1 is a cellular substrate of protein SUMOylation, a prevalent stress-response posttranslational modification. Site-specific mapping of SUMOylation by mass spectrometer leads to identifying K561 as a primary SUMOylation site in EPAC1. Sequence and site-directed mutagenesis analyses reveal a functional SUMO-interacting motif required for cellular SUMOylation of EPAC1. SUMO modification of EPAC1 mediates its heat shock-induced Rap1/2 activation in a cAMP-independent manner. Structural modeling and molecular dynamics simulation studies demonstrate that SUMO substituent on K561 of EPAC1 promotes Rap1 interaction by increasing the buried surface area between the SUMOylated receptor and its effector. Our studies identify a functional SUMOylation site in EPAC1 and unveil a novel mechanism in which SUMOylation of EPAC1 leads to its autonomous activation. The findings of SUMOylation-mediated activation of EPAC1 not only provide new insights into our understanding of cellular regulation of EPAC1 but also will open up a new field of experimentation concerning the cross-talk between cAMP/EPAC1 signaling and protein SUMOylation, two major cellular stress response pathways, during cellular homeostasis.
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10
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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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11
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Wang W, Matunis MJ. Paralogue-Specific Roles of SUMO1 and SUMO2/3 in Protein Quality Control and Associated Diseases. Cells 2023; 13:8. [PMID: 38201212 PMCID: PMC10778024 DOI: 10.3390/cells13010008] [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: 11/16/2023] [Revised: 12/13/2023] [Accepted: 12/15/2023] [Indexed: 01/12/2024] Open
Abstract
Small ubiquitin-related modifiers (SUMOs) function as post-translational protein modifications and regulate nearly every aspect of cellular function. While a single ubiquitin protein is expressed across eukaryotic organisms, multiple SUMO paralogues with distinct biomolecular properties have been identified in plants and vertebrates. Five SUMO paralogues have been characterized in humans, with SUMO1, SUMO2 and SUMO3 being the best studied. SUMO2 and SUMO3 share 97% protein sequence homology (and are thus referred to as SUMO2/3) but only 47% homology with SUMO1. To date, thousands of putative sumoylation substrates have been identified thanks to advanced proteomic techniques, but the identification of SUMO1- and SUMO2/3-specific modifications and their unique functions in physiology and pathology are not well understood. The SUMO2/3 paralogues play an important role in proteostasis, converging with ubiquitylation to mediate protein degradation. This function is achieved primarily through SUMO-targeted ubiquitin ligases (STUbLs), which preferentially bind and ubiquitylate poly-SUMO2/3 modified proteins. Effects of the SUMO1 paralogue on protein solubility and aggregation independent of STUbLs and proteasomal degradation have also been reported. Consistent with these functions, sumoylation is implicated in multiple human diseases associated with disturbed proteostasis, and a broad range of pathogenic proteins have been identified as SUMO1 and SUMO2/3 substrates. A better understanding of paralogue-specific functions of SUMO1 and SUMO2/3 in cellular protein quality control may therefore provide novel insights into disease pathogenesis and therapeutic innovation. This review summarizes current understandings of the roles of sumoylation in protein quality control and associated diseases, with a focus on the specific effects of SUMO1 and SUMO2/3 paralogues.
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Affiliation(s)
| | - Michael J. Matunis
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA;
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12
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Teo QW, Wong HH, Heunis T, Stancheva V, Hachim A, Lv H, Siu L, Ho J, Lan Y, Mok CKP, Ulferts R, Sanyal S. Usp25-Erlin1/2 activity limits cholesterol flux to restrict virus infection. Dev Cell 2023; 58:2495-2509.e6. [PMID: 37683630 PMCID: PMC10914638 DOI: 10.1016/j.devcel.2023.08.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 05/20/2023] [Accepted: 08/09/2023] [Indexed: 09/10/2023]
Abstract
Reprogramming lipid metabolic pathways is a critical feature of activating immune responses to infection. However, how these reconfigurations occur is poorly understood. Our previous screen to identify cellular deubiquitylases (DUBs) activated during influenza virus infection revealed Usp25 as a prominent hit. Here, we show that Usp25-deleted human lung epithelial A549 cells display a >10-fold increase in pathogenic influenza virus production, which was rescued upon reconstitution with the wild type but not the catalytically deficient (C178S) variant. Proteomic analysis of Usp25 interactors revealed a strong association with Erlin1/2, which we confirmed as its substrate. Newly synthesized Erlin1/2 were degraded in Usp25-/- or Usp25C178S cells, activating Srebp2, with increased cholesterol flux and attenuated TLR3-dependent responses. Our study therefore defines the function of a deubiquitylase that serves to restrict a range of viruses by reprogramming lipid biosynthetic flux to install appropriate inflammatory responses.
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Affiliation(s)
- Qi Wen Teo
- HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China; Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Ho Him Wong
- HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Tiaan Heunis
- Sir William Dunn School of Pathology, South Parks Road, University of Oxford, Oxford OX1 3RE, UK
| | - Viktoriya Stancheva
- Sir William Dunn School of Pathology, South Parks Road, University of Oxford, Oxford OX1 3RE, UK
| | - Asmaa Hachim
- Sir William Dunn School of Pathology, South Parks Road, University of Oxford, Oxford OX1 3RE, UK
| | - Huibin Lv
- HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Lewis Siu
- HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Julian Ho
- HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Yun Lan
- HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Chris Ka Pun Mok
- HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | | | - Sumana Sanyal
- Sir William Dunn School of Pathology, South Parks Road, University of Oxford, Oxford OX1 3RE, UK; HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China.
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13
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Alfaro AJ, Dittner C, Becker J, Loft A, Mhamane A, Maida A, Georgiadi A, Tsokanos F, Klepac K, Molocea C, El‐Merahbi R, Motzler K, Geppert J, Karikari RA, Szendrödi J, Feuchtinger A, Hofmann S, Karaca S, Urlaub H, Berriel Diaz M, Melchior F, Herzig S. Fasting-sensitive SUMO-switch on Prox1 controls hepatic cholesterol metabolism. EMBO Rep 2023; 24:e55981. [PMID: 37560809 PMCID: PMC10561358 DOI: 10.15252/embr.202255981] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 07/12/2023] [Accepted: 07/27/2023] [Indexed: 08/11/2023] Open
Abstract
Accumulation of excess nutrients hampers proper liver function and is linked to nonalcoholic fatty liver disease (NAFLD) in obesity. However, the signals responsible for an impaired adaptation of hepatocytes to obesogenic dietary cues remain still largely unknown. Post-translational modification by the small ubiquitin-like modifier (SUMO) allows for a dynamic regulation of numerous processes including transcriptional reprogramming. We demonstrate that specific SUMOylation of transcription factor Prox1 represents a nutrient-sensitive determinant of hepatic fasting metabolism. Prox1 is highly SUMOylated on lysine 556 in the liver of ad libitum and refed mice, while this modification is abolished upon fasting. In the context of diet-induced obesity, Prox1 SUMOylation becomes less sensitive to fasting cues. The hepatocyte-selective knock-in of a SUMOylation-deficient Prox1 mutant into mice fed a high-fat/high-fructose diet leads to a reduction of systemic cholesterol levels, associated with the induction of liver bile acid detoxifying pathways during fasting. The generation of tools to maintain the nutrient-sensitive SUMO-switch on Prox1 may thus contribute to the development of "fasting-based" approaches for the preservation of metabolic health.
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Affiliation(s)
- Ana Jimena Alfaro
- Institute for Diabetes and CancerHelmholtz MunichNeuherbergGermany
- Joint Heidelberg‐IDC Translational Diabetes Program, Inner Medicine 1Heidelberg University HospitalHeidelbergGermany
- German Center for Diabetes Research (DZD), and German Center for Cardiovascular Disease (DZHK)NeuherbergGermany
| | - Claudia Dittner
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH)Heidelberg University, DKFZ‐ZMBH AllianceHeidelbergGermany
| | - Janina Becker
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH)Heidelberg University, DKFZ‐ZMBH AllianceHeidelbergGermany
| | - Anne Loft
- Institute for Diabetes and CancerHelmholtz MunichNeuherbergGermany
- Joint Heidelberg‐IDC Translational Diabetes Program, Inner Medicine 1Heidelberg University HospitalHeidelbergGermany
- German Center for Diabetes Research (DZD), and German Center for Cardiovascular Disease (DZHK)NeuherbergGermany
- Center for Functional Genomics and Tissue Plasticity (ATLAS), SDUOdenseDenmark
| | - Amit Mhamane
- Institute for Diabetes and CancerHelmholtz MunichNeuherbergGermany
- Joint Heidelberg‐IDC Translational Diabetes Program, Inner Medicine 1Heidelberg University HospitalHeidelbergGermany
- German Center for Diabetes Research (DZD), and German Center for Cardiovascular Disease (DZHK)NeuherbergGermany
| | - Adriano Maida
- Institute for Diabetes and CancerHelmholtz MunichNeuherbergGermany
- Joint Heidelberg‐IDC Translational Diabetes Program, Inner Medicine 1Heidelberg University HospitalHeidelbergGermany
- German Center for Diabetes Research (DZD), and German Center for Cardiovascular Disease (DZHK)NeuherbergGermany
| | - Anastasia Georgiadi
- Institute for Diabetes and CancerHelmholtz MunichNeuherbergGermany
- Joint Heidelberg‐IDC Translational Diabetes Program, Inner Medicine 1Heidelberg University HospitalHeidelbergGermany
- German Center for Diabetes Research (DZD), and German Center for Cardiovascular Disease (DZHK)NeuherbergGermany
| | - Foivos‐Filippos Tsokanos
- Institute for Diabetes and CancerHelmholtz MunichNeuherbergGermany
- Joint Heidelberg‐IDC Translational Diabetes Program, Inner Medicine 1Heidelberg University HospitalHeidelbergGermany
- German Center for Diabetes Research (DZD), and German Center for Cardiovascular Disease (DZHK)NeuherbergGermany
| | - Katarina Klepac
- Institute for Diabetes and CancerHelmholtz MunichNeuherbergGermany
- Joint Heidelberg‐IDC Translational Diabetes Program, Inner Medicine 1Heidelberg University HospitalHeidelbergGermany
- German Center for Diabetes Research (DZD), and German Center for Cardiovascular Disease (DZHK)NeuherbergGermany
| | - Claudia‐Eveline Molocea
- Institute for Diabetes and CancerHelmholtz MunichNeuherbergGermany
- Joint Heidelberg‐IDC Translational Diabetes Program, Inner Medicine 1Heidelberg University HospitalHeidelbergGermany
- German Center for Diabetes Research (DZD), and German Center for Cardiovascular Disease (DZHK)NeuherbergGermany
| | - Rabih El‐Merahbi
- Institute for Diabetes and CancerHelmholtz MunichNeuherbergGermany
- Joint Heidelberg‐IDC Translational Diabetes Program, Inner Medicine 1Heidelberg University HospitalHeidelbergGermany
- German Center for Diabetes Research (DZD), and German Center for Cardiovascular Disease (DZHK)NeuherbergGermany
| | - Karsten Motzler
- Institute for Diabetes and CancerHelmholtz MunichNeuherbergGermany
- Joint Heidelberg‐IDC Translational Diabetes Program, Inner Medicine 1Heidelberg University HospitalHeidelbergGermany
- German Center for Diabetes Research (DZD), and German Center for Cardiovascular Disease (DZHK)NeuherbergGermany
| | - Julia Geppert
- Institute for Diabetes and CancerHelmholtz MunichNeuherbergGermany
- Joint Heidelberg‐IDC Translational Diabetes Program, Inner Medicine 1Heidelberg University HospitalHeidelbergGermany
- German Center for Diabetes Research (DZD), and German Center for Cardiovascular Disease (DZHK)NeuherbergGermany
| | - Rhoda Anane Karikari
- Institute for Diabetes and CancerHelmholtz MunichNeuherbergGermany
- Joint Heidelberg‐IDC Translational Diabetes Program, Inner Medicine 1Heidelberg University HospitalHeidelbergGermany
- German Center for Diabetes Research (DZD), and German Center for Cardiovascular Disease (DZHK)NeuherbergGermany
| | - Julia Szendrödi
- Joint Heidelberg‐IDC Translational Diabetes Program, Inner Medicine 1Heidelberg University HospitalHeidelbergGermany
- German Center for Diabetes Research (DZD), and German Center for Cardiovascular Disease (DZHK)NeuherbergGermany
| | | | - Susanna Hofmann
- Institute of Diabetes and Regeneration ResearchHelmholtz MunichNeuherbergGermany
| | - Samir Karaca
- Bioanalytical Mass Spectrometry GroupMax Planck Institute for Multidisciplinary SciencesGöttingenGermany
| | - Henning Urlaub
- Bioanalytical Mass Spectrometry GroupMax Planck Institute for Multidisciplinary SciencesGöttingenGermany
- Bioanalytics, Institute of Clinical ChemistryUniversity Medical Center GöttingenGöttingenGermany
| | - Mauricio Berriel Diaz
- Institute for Diabetes and CancerHelmholtz MunichNeuherbergGermany
- Joint Heidelberg‐IDC Translational Diabetes Program, Inner Medicine 1Heidelberg University HospitalHeidelbergGermany
- German Center for Diabetes Research (DZD), and German Center for Cardiovascular Disease (DZHK)NeuherbergGermany
| | - Frauke Melchior
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH)Heidelberg University, DKFZ‐ZMBH AllianceHeidelbergGermany
| | - Stephan Herzig
- Institute for Diabetes and CancerHelmholtz MunichNeuherbergGermany
- Joint Heidelberg‐IDC Translational Diabetes Program, Inner Medicine 1Heidelberg University HospitalHeidelbergGermany
- German Center for Diabetes Research (DZD), and German Center for Cardiovascular Disease (DZHK)NeuherbergGermany
- Chair Molecular Metabolic ControlTechnical University MunichMunichGermany
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14
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Zhao Z, O’Dea R, Wendrich K, Kazi N, Gersch M. Native Semisynthesis of Isopeptide-Linked Substrates for Specificity Analysis of Deubiquitinases and Ubl Proteases. J Am Chem Soc 2023; 145:20801-20812. [PMID: 37712884 PMCID: PMC10540217 DOI: 10.1021/jacs.3c04062] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Indexed: 09/16/2023]
Abstract
Post-translational modifications with ubiquitin (Ub) and ubiquitin-like proteins (Ubls) are regulated by isopeptidases termed deubiquitinases (DUBs) and Ubl proteases. Here, we describe a mild chemical method for the preparation of fluorescence polarization substrates for these enzymes that is based on the activation of C-terminal Ub/Ubl hydrazides to acyl azides and their subsequent functionalization to isopeptides. The procedure is complemented by native purification routes and thus circumvents the previous need for desulfurization and refolding. Its broad applicability was demonstrated by the generation of fully cleavable substrates for Ub, SUMO1, SUMO2, NEDD8, ISG15, and Fubi. We employed these reagents for the investigation of substrate specificities of human UCHL3, USPL1, USP2, USP7, USP16, USP18, and USP36. Pronounced selectivity of USPL1 for SUMO2/3 over SUMO1 was observed, which we rationalize with crystal structures and biochemical assays, revealing a SUMO paralogue specificity mechanism distinct from SENP family deSUMOylases. Moreover, we investigated the recently identified Fubi proteases USP16 and USP36 and found both to act as bona fide deFubiylases, harboring catalytic activity against isopeptide-linked Fubi. Surprisingly, we also noticed the activity of both enzymes toward ISG15, previously not identified in chemoproteomics, which makes USP16 and USP36 the first human DUBs with specific isopeptidase activity toward three distinct modifiers. The methods described here for the preparation of isopeptide-linked, fully folded substrates will aid in the characterization of further DUBs/Ubl proteases. More broadly, our findings highlight possible limitations associated with fluorogenic substrates and Ubl activity-based probes and stress the importance of isopeptide-containing reagents for validating isopeptidase activities and quantifying substrate specificities.
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Affiliation(s)
- Zhou Zhao
- Chemical
Genomics Centre, Max Planck Institute of
Molecular Physiology, Otto-Hahn-Str. 15, 44227 Dortmund, Germany
- Department
of Chemistry and Chemical Biology, TU Dortmund
University, Otto-Hahn-Str.
15, 44227 Dortmund, Germany
| | - Rachel O’Dea
- Chemical
Genomics Centre, Max Planck Institute of
Molecular Physiology, Otto-Hahn-Str. 15, 44227 Dortmund, Germany
- Department
of Chemistry and Chemical Biology, TU Dortmund
University, Otto-Hahn-Str.
15, 44227 Dortmund, Germany
| | - Kim Wendrich
- Chemical
Genomics Centre, Max Planck Institute of
Molecular Physiology, Otto-Hahn-Str. 15, 44227 Dortmund, Germany
- Department
of Chemistry and Chemical Biology, TU Dortmund
University, Otto-Hahn-Str.
15, 44227 Dortmund, Germany
| | - Nafizul Kazi
- Chemical
Genomics Centre, Max Planck Institute of
Molecular Physiology, Otto-Hahn-Str. 15, 44227 Dortmund, Germany
- Department
of Chemistry and Chemical Biology, TU Dortmund
University, Otto-Hahn-Str.
15, 44227 Dortmund, Germany
| | - Malte Gersch
- Chemical
Genomics Centre, Max Planck Institute of
Molecular Physiology, Otto-Hahn-Str. 15, 44227 Dortmund, Germany
- Department
of Chemistry and Chemical Biology, TU Dortmund
University, Otto-Hahn-Str.
15, 44227 Dortmund, Germany
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15
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Cheng X, Yang W, Lin W, Mei F. Paradoxes of Cellular SUMOylation Regulation: A Role of Biomolecular Condensates? Pharmacol Rev 2023; 75:979-1006. [PMID: 37137717 PMCID: PMC10441629 DOI: 10.1124/pharmrev.122.000784] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 04/20/2023] [Accepted: 04/27/2023] [Indexed: 05/05/2023] Open
Abstract
Protein SUMOylation is a major post-translational modification essential for maintaining cellular homeostasis. SUMOylation has long been associated with stress responses as a diverse array of cellular stress signals are known to trigger rapid alternations in global protein SUMOylation. In addition, while there are large families of ubiquitination enzymes, all small ubiquitin-like modifiers (SUMOs) are conjugated by a set of enzymatic machinery comprising one heterodimeric SUMO-activating enzyme, a single SUMO-conjugating enzyme, and a small number of SUMO protein ligases and SUMO-specific proteases. How a few SUMOylation enzymes specifically modify thousands of functional targets in response to diverse cellular stresses remains an enigma. Here we review recent progress toward understanding the mechanisms of SUMO regulation, particularly the potential roles of liquid-liquid phase separation/biomolecular condensates in regulating cellular SUMOylation during cellular stresses. In addition, we discuss the role of protein SUMOylation in pathogenesis and the development of novel therapeutics targeting SUMOylation. SIGNIFICANCE STATEMENT: Protein SUMOylation is one of the most prevalent post-translational modifications and plays a vital role in maintaining cellular homeostasis in response to stresses. Protein SUMOylation has been implicated in human pathogenesis, such as cancer, cardiovascular diseases, neurodegeneration, and infection. After more than a quarter century of extensive research, intriguing enigmas remain regarding the mechanism of cellular SUMOylation regulation and the therapeutic potential of targeting SUMOylation.
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Affiliation(s)
- Xiaodong Cheng
- Department of Integrative Biology & Pharmacology and Texas Therapeutics Institute, Institute of Molecular Medicine, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, Texas
| | - Wenli Yang
- Department of Integrative Biology & Pharmacology and Texas Therapeutics Institute, Institute of Molecular Medicine, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, Texas
| | - Wei Lin
- Department of Integrative Biology & Pharmacology and Texas Therapeutics Institute, Institute of Molecular Medicine, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, Texas
| | - Fang Mei
- Department of Integrative Biology & Pharmacology and Texas Therapeutics Institute, Institute of Molecular Medicine, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, Texas
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16
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Zhou L, Qin B, Yassine DM, Luo M, Liu X, Wang F, Wang Y. Structure and function of the highly homologous deubiquitinases ubiquitin specific peptidase 25 and 28: Insights into their pathophysiological and therapeutic roles. Biochem Pharmacol 2023; 213:115624. [PMID: 37245535 DOI: 10.1016/j.bcp.2023.115624] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 05/19/2023] [Accepted: 05/22/2023] [Indexed: 05/30/2023]
Abstract
Deubiquitination is the reverse process of ubiquitination, an important protein post-translational modification. Deubiquitination is assisted by deubiquitinating enzymes (DUBs), which catalyze the hydrolysis and removal of ubiquitin chains from targeted proteins and play an important role in regulating protein stability, cell signaling transduction, and programmed cell death. Ubiquitin-specific peptidases 25 and 28 (USP25 and USP28), important members of the USP subfamily of DUBs, are highly homologous, strictly regulated, and closely associated with various diseases, such as cancer and neurodegenerative diseases. Recently, the development of inhibitors targeting USP25 and USP28 for disease treatment has garnered extreme attention. Several non-selective and selective inhibitors have shown potential inhibitory effects. However, the specificity, potency, and action mechanism of these inhibitors remain to be further improved and clarified. Herein, we summarize the structure, regulation, emerging physiological roles, and target inhibition of USP25 and USP28 to provide a basis for the development of highly potent and specific inhibitors for the treatment of diseases, such as colorectal cancer, breast cancer and so on.
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Affiliation(s)
- Lihui Zhou
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, Beijing 100081, China
| | - Biying Qin
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, Beijing 100081, China
| | - Demna Mohamed Yassine
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, Beijing 100081, China
| | - Maoguo Luo
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, Beijing 100081, China
| | - Xiaoling Liu
- School of Life Sciences, Beijing University of Chinese Medicine, Beijing, China
| | - Feng Wang
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, Beijing 100081, China
| | - Yanfeng Wang
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, Beijing 100081, China.
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17
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Shao W, Sun K, Ma T, Jiang H, Hahn M, Ma Z, Jiao C, Yin Y. SUMOylation regulates low-temperature survival and oxidative DNA damage tolerance in Botrytis cinerea. THE NEW PHYTOLOGIST 2023; 238:817-834. [PMID: 36651012 DOI: 10.1111/nph.18748] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 01/13/2023] [Indexed: 06/17/2023]
Abstract
SUMOylation as one of the protein post-translational modifications plays crucial roles in multiple biological processes of eukaryotic organisms. Botrytis cinerea is a devastating fungal pathogen and capable of infecting plant hosts at low temperature. However, the molecular mechanisms of low-temperature adaptation are largely unknown in fungi. Combining with biochemical methods and biological analyses, we report that SUMOylation regulates pathogen survival at low temperature and oxidative DNA damage response during infection in B. cinerea. The heat shock protein (Hsp70) BcSsb and E3 ubiquitin ligase BcRad18 were identified as substrates of SUMOylation; moreover, their SUMOylation both requires a single unique SUMO-interacting motif (SIM). SUMOylated BcSsb regulates β-tubulin accumulation, thereby affecting the stability of microtubules and consequently mycelial growth at low temperature. On the contrary, SUMOylated BcRad18 modulates mono-ubiquitination of the sliding clamp protein proliferating cell nuclear antigen (PCNA), which is involved in response to oxidative DNA damage during infection. Our study uncovers the molecular mechanisms of SUMOylation-mediated low-temperature survival and oxidative DNA damage tolerance during infection in a devastating fungal pathogen, which provides novel insights into low-temperature adaptation and pathogenesis for postharvest pathogens as well as new targets for inhibitor invention in disease control.
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Affiliation(s)
- Wenyong Shao
- State Key Laboratory of Rice Biology, Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China
| | - Kewei Sun
- State Key Laboratory of Rice Biology, Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China
| | - Tianling Ma
- State Key Laboratory of Rice Biology, Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China
| | - Huixian Jiang
- State Key Laboratory of Rice Biology, Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China
| | - Matthias Hahn
- Department of Biology, University of Kaiserslautern, PO Box 3049, 67653, Kaiserslautern, Germany
| | - Zhonghua Ma
- State Key Laboratory of Rice Biology, Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China
| | - Chen Jiao
- State Key Laboratory of Rice Biology, Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China
| | - Yanni Yin
- State Key Laboratory of Rice Biology, Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China
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18
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Abstract
Our understanding of the ubiquitin code has greatly evolved from conventional E1, E2 and E3 enzymes that modify Lys residues on specific substrates with a single type of ubiquitin chain to more complex processes that regulate and mediate ubiquitylation. In this Review, we discuss recently discovered endogenous mechanisms and unprecedented pathways by which pathogens rewrite the ubiquitin code to promote infection. These processes include unconventional ubiquitin modifications involving ester linkages with proteins, lipids and sugars, or ubiquitylation through a phosphoribosyl bridge involving Arg42 of ubiquitin. We also introduce the enzymatic pathways that write and reverse these modifications, such as the papain-like proteases of severe acute respiratory syndrome coronavirus (SARS-CoV) and SARS-CoV-2. Furthermore, structural studies have revealed that the ultimate functions of ubiquitin are mediated not simply by straightforward recognition by ubiquitin-binding domains. Instead, elaborate multivalent interactions between ubiquitylated targets or ubiquitin chains and their readers (for example, the proteasome, the MLL1 complex or DOT1L) can elicit conformational changes that regulate protein degradation or transcription. The newly discovered mechanisms provide opportunities for innovative therapeutic interventions for diseases such as cancer and infectious diseases.
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Affiliation(s)
- Ivan Dikic
- Institute of Biochemistry II, Faculty of Medicine, Goethe University, Frankfurt, Germany.
- Buchmann Institute for Molecular Life Sciences, Goethe University, Frankfurt, Germany.
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19
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Yang Y, Zhan X, Zhang C, Shi J, Wu J, Deng X, Hong Y, Li Q, Ge S, Xu G, He F. USP25-PKM2-glycolysis axis contributes to ischemia reperfusion-induced acute kidney injury by promoting M1-like macrophage polarization and proinflammatory response. Clin Immunol 2023; 251:109279. [PMID: 36894047 DOI: 10.1016/j.clim.2023.109279] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 03/01/2023] [Accepted: 03/03/2023] [Indexed: 03/09/2023]
Abstract
M1-like macrophages have been reported to play critical roles in acute kidney injury (AKI). Here, we elucidated the role of ubiquitin-specific protease 25 (USP25) in M1-like macrophages polarization and AKI. High USP25 expression was correlated with a decline in renal function in patients with acute kidney tubular injury and in mice with AKI. In contrast, USP25 knockout reduced M1-like macrophage infiltration, suppressed M1-like polarization, and improved AKI in mice, indicating that USP25 was necessary for M1-like polarization and proinflammatory response. Immunoprecipitation assay and liquid chromatography-tandem mass spectrometry showed that the M2 isoform of pyruvate kinase, muscle (PKM2) was a target substrate of USP25. Kyoto Encyclopedia of Genes and Genomes pathway analysis indicated the USP25 regulated aerobic glycolysis and lactate production during M1-like polarization via PKM2. Further analysis showed that the USP25-PKM2-aerobic glycolysis axis positively regulated M1-like polarization and exacerbated AKI in mice, providing potential therapeutic targets for AKI treatment.
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Affiliation(s)
- Yi Yang
- Department of Nephrology, Tongji Hospital Affiliated to Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Xiaona Zhan
- Department of Nephrology, Tongji Hospital Affiliated to Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Cailin Zhang
- Department of Nephrology, Tongji Hospital Affiliated to Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Jia Shi
- Department of Nephrology, Tongji Hospital Affiliated to Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Jianliang Wu
- Department of Nephrology, The First Affiliated Hospital of Nanchang University, Nanchang 330008, China
| | - Xuan Deng
- Department of Nephrology, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
| | - Yu Hong
- Department of Nephrology, Tongji Hospital Affiliated to Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Qing Li
- Department of Nephrology, Tongji Hospital Affiliated to Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Shuwang Ge
- Department of Nephrology, Tongji Hospital Affiliated to Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Gang Xu
- Department of Nephrology, Tongji Hospital Affiliated to Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.
| | - Fan He
- Department of Nephrology, Tongji Hospital Affiliated to Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.
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20
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Feitosa WB, Morris PL. Post-ovulatory aging is associated with altered patterns for small ubiquitin-like modifier (SUMO) proteins and SUMO-specific proteases. FASEB J 2023; 37:e22816. [PMID: 36826436 DOI: 10.1096/fj.202200622r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 01/27/2023] [Accepted: 01/30/2023] [Indexed: 02/25/2023]
Abstract
Mammalian oocytes are ovulated arrested at metaphase of the second meiotic division. If they are not fertilized within a short period, the oocyte undergoes several progressive morphological, structural, and molecular changes during a process called oocyte aging. Herein, we focused on those functional events associated with proper cytoskeleton organization and those that correlate with spindle displacement and chromosome misalignment or scatter. Post-translational modifications by Small Ubiquitin-like Modifier (SUMO) proteins are involved in spindle organization and here we demonstrate that the SUMO pathway is involved in spindle morphology changes and chromosome movements during oocyte aging. SUMO-2/3 as well as the SUMO-specific proteases SENP-2 localization are affected by postovulatory aging in vitro. Consistent with these findings, UBC9 decreases during oocyte aging while differential ubiquitination patterns also correlate with in vitro oocyte aging. These results are consistent with postovulatory aging-related alterations in the posttranslational modifications of the spindle apparatus by SUMO and its SENP proteases. These findings are suggestive that such age-related changes in SUMOylation and the deSUMOylation of key target proteins in the spindle apparatus and kinetochore may be involved with spindle and chromosome alignment defects during mammalian oocyte postovulatory aging. Such findings may have implications for ART-related human oocyte aging in vitro regarding the activities of the SUMO pathway and fertilization success.
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Affiliation(s)
| | - Patricia L Morris
- Center for Biomedical Research, Population Council, New York, New York, USA.,The Rockefeller University, New York, New York, USA
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21
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Karlowitz R, van Wijk SJL. Surviving death: emerging concepts of RIPK3 and MLKL ubiquitination in the regulation of necroptosis. FEBS J 2023; 290:37-54. [PMID: 34710282 DOI: 10.1111/febs.16255] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 10/14/2021] [Accepted: 10/27/2021] [Indexed: 01/14/2023]
Abstract
Lytic forms of programmed cell death, like necroptosis, are characterised by cell rupture and the release of cellular contents, often provoking inflammatory responses. In the recent years, necroptosis has been shown to play important roles in human diseases like cancer, infections and ischaemia/reperfusion injury. Coordinated interactions between RIPK1, RIPK3 and MLKL lead to the formation of a dedicated death complex called the necrosome that triggers MLKL-mediated membrane rupture and necroptotic cell death. Necroptotic cell death is tightly controlled by post-translational modifications, among which especially phosphorylation has been characterised in great detail. Although selective ubiquitination is relatively well-explored in the early initiation stages of necroptosis, the mechanisms and functional consequences of RIPK3 and MLKL ubiquitination for necrosome function and necroptosis are only starting to emerge. This review provides an overview on how site-specific ubiquitination of RIPK3 and MLKL regulates, fine-tunes and reverses the execution of necroptotic cell death.
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Affiliation(s)
- Rebekka Karlowitz
- Institute for Experimental Cancer Research in Pediatrics, Goethe-University Frankfurt, Germany
| | - Sjoerd J L van Wijk
- Institute for Experimental Cancer Research in Pediatrics, Goethe-University Frankfurt, Germany
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22
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Lascorz J, Codina-Fabra J, Reverter D, Torres-Rosell J. SUMO-SIM interactions: From structure to biological functions. Semin Cell Dev Biol 2022; 132:193-202. [PMID: 34840078 DOI: 10.1016/j.semcdb.2021.11.007] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 11/08/2021] [Accepted: 11/08/2021] [Indexed: 12/15/2022]
Abstract
Post-translational modification by Small Ubiquitin-like Modifier (SUMO) proteins regulates numerous cellular processes. This modification involves the covalent and reversible attachment of SUMO to target proteins through an isopeptide bond, using a cascade of E1, E2 and E3 SUMOylation enzymes. Most functions of SUMO depend on the establishment of non-covalent protein-protein interactions between SUMOylated substrates and their binding partners. The vast majority of these interactions involve a conserved surface in the SUMO protein and a SUMO interacting motif (SIM), a short stretch of hydrophobic amino acids and an acidic region, in the interactor protein. Despite single SUMO-SIM interactions are relatively weak, they can have a huge impact at different levels, altering the activity, localization and stability of proteins, triggering the formation of macromolecular assemblies or inducing phase separation. Moreover, SUMO-SIM interactions are ubiquitous in most enzymes of the SUMO pathway, and play essential roles in SUMO conjugation and deconjugation. Here, we analyze the role of SUMO-SIM contacts in SUMO enzymes and targets and discuss how this humble interaction participates in SUMOylation reactions and mediates the outcome of this essential post-translational modification.
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Affiliation(s)
- Jara Lascorz
- Institut de Biotecnologia i de Biomedicina (IBB) and Dept. de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Joan Codina-Fabra
- Departament de Ciencies Mediques Basiques, Institut de Recerca Biomedica de Lleida, Universitat de Lleida, 25198 Lleida, Spain
| | - David Reverter
- Institut de Biotecnologia i de Biomedicina (IBB) and Dept. de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain.
| | - Jordi Torres-Rosell
- Departament de Ciencies Mediques Basiques, Institut de Recerca Biomedica de Lleida, Universitat de Lleida, 25198 Lleida, Spain.
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23
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Sumoylation in Physiology, Pathology and Therapy. Cells 2022; 11:cells11050814. [PMID: 35269436 PMCID: PMC8909597 DOI: 10.3390/cells11050814] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 02/22/2022] [Accepted: 02/23/2022] [Indexed: 02/04/2023] Open
Abstract
Sumoylation is an essential post-translational modification that has evolved to regulate intricate networks within emerging complexities of eukaryotic cells. Thousands of target substrates are modified by SUMO peptides, leading to changes in protein function, stability or localization, often by modulating interactions. At the cellular level, sumoylation functions as a key regulator of transcription, nuclear integrity, proliferation, senescence, lineage commitment and stemness. A growing number of prokaryotic and viral proteins are also emerging as prime sumoylation targets, highlighting the role of this modification during infection and in immune processes. Sumoylation also oversees epigenetic processes. Accordingly, at the physiological level, it acts as a crucial regulator of development. Yet, perhaps the most prominent function of sumoylation, from mammals to plants, is its role in orchestrating organismal responses to environmental stresses ranging from hypoxia to nutrient stress. Consequently, a growing list of pathological conditions, including cancer and neurodegeneration, have now been unambiguously associated with either aberrant sumoylation of specific proteins and/or dysregulated global cellular sumoylation. Therapeutic enforcement of sumoylation can also accomplish remarkable clinical responses in various diseases, notably acute promyelocytic leukemia (APL). In this review, we will discuss how this modification is emerging as a novel drug target, highlighting from the perspective of translational medicine, its potential and limitations.
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24
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Andreev VI, Yu C, Wang J, Schnabl J, Tirian L, Gehre M, Handler D, Duchek P, Novatchkova M, Baumgartner L, Meixner K, Sienski G, Patel DJ, Brennecke J. Panoramix SUMOylation on chromatin connects the piRNA pathway to the cellular heterochromatin machinery. Nat Struct Mol Biol 2022; 29:130-142. [PMID: 35173350 PMCID: PMC11749891 DOI: 10.1038/s41594-022-00721-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 12/30/2021] [Indexed: 11/09/2022]
Abstract
Nuclear Argonaute proteins, guided by small RNAs, mediate sequence-specific heterochromatin formation. The molecular principles that link Argonaute-small RNA complexes to cellular heterochromatin effectors on binding to nascent target RNAs are poorly understood. Here, we explain the mechanism by which the PIWI-interacting RNA (piRNA) pathway connects to the heterochromatin machinery in Drosophila. We find that Panoramix, a corepressor required for piRNA-guided heterochromatin formation, is SUMOylated on chromatin in a Piwi-dependent manner. SUMOylation, together with an amphipathic LxxLL motif in Panoramix's intrinsically disordered repressor domain, are necessary and sufficient to recruit Small ovary (Sov), a multi-zinc-finger protein essential for general heterochromatin formation and viability. Structure-guided mutations that eliminate the Panoramix-Sov interaction or that prevent SUMOylation of Panoramix uncouple Sov from the piRNA pathway, resulting in viable but sterile flies in which Piwi-targeted transposons are derepressed. Thus, Piwi engages the heterochromatin machinery specifically at transposon loci by coupling recruitment of a corepressor to nascent transcripts with its SUMOylation.
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Affiliation(s)
- Veselin I Andreev
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna, Austria
| | - Changwei Yu
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria
| | - Juncheng Wang
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jakob Schnabl
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna, Austria
| | - Laszlo Tirian
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria
| | - Maja Gehre
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria
| | - Dominik Handler
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria
| | - Peter Duchek
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria
| | - Maria Novatchkova
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria
| | - Lisa Baumgartner
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna, Austria
| | - Katharina Meixner
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria
| | - Grzegorz Sienski
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna, Austria
| | - Dinshaw J Patel
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Julius Brennecke
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria.
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25
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Kasera M, Ingole KD, Rampuria S, Walia Y, Gassmann W, Bhattacharjee S. Global SUMOylome Adjustments in Basal Defenses of Arabidopsis thaliana Involve Complex Interplay Between SMALL-UBIQUITIN LIKE MODIFIERs and the Negative Immune Regulator SUPPRESSOR OF rps4-RLD1. Front Cell Dev Biol 2021; 9:680760. [PMID: 34660568 PMCID: PMC8514785 DOI: 10.3389/fcell.2021.680760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 09/03/2021] [Indexed: 11/26/2022] Open
Abstract
Steady-state SUMOylome of a plant is adjusted locally during developmental transitions and more globally during stress exposures. We recently reported that basal immunity in Arabidopsis thaliana against Pseudomonas syringae pv tomato strain DC3000 (PstDC3000) is associated with strong enhancements in the net SUMOylome. Transcriptional upregulations of SUMO conjugases, suppression of protease, and increased SUMO translations accounted for this enhanced SUMOylation. Antagonistic roles of SUMO1/2 and SUMO3 isoforms further fine-tuned the SUMOylome adjustments, thus impacting defense amplitudes and immune outcomes. Loss of function of SUPPRESSOR OF rps4-RLD1 (SRFR1), a previously reported negative regulator of basal defenses, also caused constitutive increments in global SUMO-conjugates through similar modes. These suggest that SRFR1 plays a pivotal role in maintenance of SUMOylation homeostasis and its dynamic changes during immune elicitations. Here, we demonstrate that SRFR1 degradation kinetically precedes and likely provides the salicylic acid (SA) elevations necessary for the SUMOylome increments in basal defenses. We show that SRFR1 not only is a SUMOylation substrate but also interacts in planta with both SUMO1 and SUMO3. In sum1 or sum3 mutants, SRFR1 stabilities are reduced albeit by different modes. Whereas a srfr1 sum1 combination is lethal, the srfr1 sum3 plants retain developmental defects and enhanced immunity of the srfr1 parent. Together with increasing evidence of SUMOs self-regulating biochemical efficiencies of SUMOylation-machinery, we present their impositions on SRFR1 expression that in turn counter-modulates the SUMOylome. Overall, our investigations reveal multifaceted dynamics of regulated SUMOylome changes via SRFR1 in defense-developmental balance.
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Affiliation(s)
- Mritunjay Kasera
- Laboratory of Signal Transduction and Plant Resistance, UNESCO-Regional Centre for Biotechnology (RCB), NCR Biotech Science Cluster, Faridabad, India
| | - Kishor D Ingole
- Laboratory of Signal Transduction and Plant Resistance, UNESCO-Regional Centre for Biotechnology (RCB), NCR Biotech Science Cluster, Faridabad, India.,Kalinga Institute of Industrial Technology (KIIT) University, Bhubaneswar, India
| | - Sakshi Rampuria
- Laboratory of Signal Transduction and Plant Resistance, UNESCO-Regional Centre for Biotechnology (RCB), NCR Biotech Science Cluster, Faridabad, India.,Division of Plant Sciences, C. S. Bond Life Sciences Center and Interdisciplinary Plant Group, University of Missouri, Columbia, MO, United States
| | - Yashika Walia
- Laboratory of Signal Transduction and Plant Resistance, UNESCO-Regional Centre for Biotechnology (RCB), NCR Biotech Science Cluster, Faridabad, India
| | - Walter Gassmann
- Division of Plant Sciences, C. S. Bond Life Sciences Center and Interdisciplinary Plant Group, University of Missouri, Columbia, MO, United States
| | - Saikat Bhattacharjee
- Laboratory of Signal Transduction and Plant Resistance, UNESCO-Regional Centre for Biotechnology (RCB), NCR Biotech Science Cluster, Faridabad, India
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26
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Bouchard D, Wang W, Yang WC, He S, Garcia A, Matunis MJ. SUMO paralogue-specific functions revealed through systematic analysis of human knockout cell lines and gene expression data. Mol Biol Cell 2021; 32:1849-1866. [PMID: 34232706 PMCID: PMC8684707 DOI: 10.1091/mbc.e21-01-0031] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
The small ubiquitin-related modifiers (SUMOs) regulate nearly every aspect of cellular function, from gene expression in the nucleus to ion transport at the plasma membrane. In humans, the SUMO pathway has five SUMO paralogues with sequence homologies that range from 45% to 97%. SUMO1 and SUMO2 are the most distantly related paralogues and also the best studied. To what extent SUMO1, SUMO2, and the other paralogues impart unique and nonredundant effects on cellular functions, however, has not been systematically examined and is therefore not fully understood. For instance, knockout studies in mice have revealed conflicting requirements for the paralogues during development and studies in cell culture have relied largely on transient paralogue overexpression or knockdown. To address the existing gap in understanding, we first analyzed SUMO paralogue gene expression levels in normal human tissues and found unique patterns of SUMO1–3 expression across 30 tissue types, suggesting paralogue-specific functions in adult human tissues. To systematically identify and characterize unique and nonredundant functions of the SUMO paralogues in human cells, we next used CRISPR-Cas9 to knock out SUMO1 and SUMO2 expression in osteosarcoma (U2OS) cells. Analysis of these knockout cell lines revealed essential functions for SUMO1 and SUMO2 in regulating cellular morphology, promyelocytic leukemia (PML) nuclear body structure, responses to proteotoxic and genotoxic stress, and control of gene expression. Collectively, our findings reveal nonredundant regulatory roles for SUMO1 and SUMO2 in controlling essential cellular processes and provide a basis for more precise SUMO-targeting therapies.
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Affiliation(s)
- Danielle Bouchard
- Department of Biochemistry and Molecular Biology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD 21205
| | - Wei Wang
- Department of Biochemistry and Molecular Biology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD 21205
| | - Wei-Chih Yang
- Department of Biochemistry and Molecular Biology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD 21205
| | - Shuying He
- Department of Biochemistry and Molecular Biology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD 21205
| | - Anthony Garcia
- Department of Biochemistry and Molecular Biology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD 21205
| | - Michael J Matunis
- Department of Biochemistry and Molecular Biology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD 21205
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27
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Zhu W, Zheng D, Wang D, Yang L, Zhao C, Huang X. Emerging Roles of Ubiquitin-Specific Protease 25 in Diseases. Front Cell Dev Biol 2021; 9:698751. [PMID: 34249948 PMCID: PMC8262611 DOI: 10.3389/fcell.2021.698751] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 06/01/2021] [Indexed: 12/20/2022] Open
Abstract
The balance of ubiquitination and deubiquitination plays diverse roles in regulating protein stability and cellular homeostasis. Deubiquitinating enzymes catalyze the hydrolysis and removal of ubiquitin chains from target proteins and play critical roles in various disease processes, including cancer, immune responses to viral infections and neurodegeneration. This article aims to summarize roles of the deubiquitinating enzyme ubiquitin-specific protease 25 (USP25) in disease onset and progression. Previous studies have focused on the role of USP25 in antiviral immunity and neurodegenerative diseases. Recently, however, as the structural similarities and differences between USP25 and its homolog USP28 have become clear, mechanisms of action of USP25 in cancer and other diseases have been gradually revealed.
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Affiliation(s)
- Wenjing Zhu
- Division of Pulmonary Medicine, The First Affiliated Hospital, Wenzhou Medical University, Wenzhou, China
| | - Dandan Zheng
- Division of Pulmonary Medicine, The First Affiliated Hospital, Wenzhou Medical University, Wenzhou, China
| | - Dandan Wang
- Division of Pulmonary Medicine, The First Affiliated Hospital, Wenzhou Medical University, Wenzhou, China
| | - Lehe Yang
- Division of Pulmonary Medicine, The First Affiliated Hospital, Wenzhou Medical University, Wenzhou, China
| | - Chengguang Zhao
- Division of Pulmonary Medicine, The First Affiliated Hospital, Wenzhou Medical University, Wenzhou, China
- School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, China
| | - Xiaoying Huang
- Division of Pulmonary Medicine, The First Affiliated Hospital, Wenzhou Medical University, Wenzhou, China
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28
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Wang Y, Wang F. Post-Translational Modifications of Deubiquitinating Enzymes: Expanding the Ubiquitin Code. Front Pharmacol 2021; 12:685011. [PMID: 34177595 PMCID: PMC8224227 DOI: 10.3389/fphar.2021.685011] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 05/25/2021] [Indexed: 12/14/2022] Open
Abstract
Post-translational modifications such as ubiquitination play important regulatory roles in several biological processes in eukaryotes. This process could be reversed by deubiquitinating enzymes (DUBs), which remove conjugated ubiquitin molecules from target substrates. Owing to their role as essential enzymes in regulating all ubiquitin-related processes, the abundance, localization, and catalytic activity of DUBs are tightly regulated. Dysregulation of DUBs can cause dramatic physiological consequences and a variety of disorders such as cancer, and neurodegenerative and inflammatory diseases. Multiple factors, such as transcription and translation of associated genes, and the presence of accessory domains, binding proteins, and inhibitors have been implicated in several aspects of DUB regulation. Beyond this level of regulation, emerging studies show that the function of DUBs can be regulated by a variety of post-translational modifications, which significantly affect the abundance, localization, and catalytic activity of DUBs. The most extensively studied post-translational modification of DUBs is phosphorylation. Besides phosphorylation, ubiquitination, SUMOylation, acetylation, oxidation, and hydroxylation are also reported in DUBs. In this review, we summarize the current knowledge on the regulatory effects of post-translational modifications of DUBs.
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Affiliation(s)
- Yanfeng Wang
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, Beijing, China
| | - Feng Wang
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, Beijing, China
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29
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Díaz-Hernández M, Javier-Reyna R, Sotto-Ortega I, García-Rivera G, Montaño S, Betanzos A, Zanatta D, Orozco E. Protein Sumoylation Is Crucial for Phagocytosis in Entamoeba histolytica Trophozoites. Int J Mol Sci 2021; 22:ijms22115709. [PMID: 34071922 PMCID: PMC8198320 DOI: 10.3390/ijms22115709] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 05/01/2021] [Accepted: 05/06/2021] [Indexed: 01/12/2023] Open
Abstract
Posttranslational modifications provide Entamoeba histolytica proteins the timing and signaling to intervene during different processes, such as phagocytosis. However, SUMOylation has not been studied in E. histolytica yet. Here, we characterized the E. histolytica SUMO gene, its product (EhSUMO), and the relevance of SUMOylation in phagocytosis. Our results indicated that EhSUMO has an extended N-terminus that differentiates SUMO from ubiquitin. It also presents the GG residues at the C-terminus and the ΨKXE/D binding motif, both involved in target protein contact. Additionally, the E. histolytica genome possesses the enzymes belonging to the SUMOylation-deSUMOylation machinery. Confocal microscopy assays disclosed a remarkable EhSUMO membrane activity with convoluted and changing structures in trophozoites during erythrophagocytosis. SUMOylated proteins appeared in pseudopodia, phagocytic channels, and around the adhered and ingested erythrocytes. Docking analysis predicted interaction of EhSUMO with EhADH (an ALIX family protein), and immunoprecipitation and immunofluorescence assays revealed that the association increased during phagocytosis; whereas the EhVps32 (a protein of the ESCRT-III complex)-EhSUMO interaction appeared stronger since basal conditions. In EhSUMO knocked-down trophozoites, the bizarre membranous structures disappeared, and EhSUMO interaction with EhADH and EhVps32 diminished. Our results evidenced the presence of a SUMO gene in E. histolytica and the SUMOylation relevance during phagocytosis. This is supported by bioinformatics screening of many other proteins of E. histolytica involved in phagocytosis, which present putative SUMOylation sites and the ΨKXE/D binding motif.
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Affiliation(s)
- Mitzi Díaz-Hernández
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del IPN, Mexico City 07360, Mexico; (M.D.-H.); (R.J.-R.); (G.G.-R.); (A.B.); (D.Z.)
| | - Rosario Javier-Reyna
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del IPN, Mexico City 07360, Mexico; (M.D.-H.); (R.J.-R.); (G.G.-R.); (A.B.); (D.Z.)
| | - Izaid Sotto-Ortega
- Bacteriología y Laboratorio Clínico, Universidad de Santander, 200004 Valledupar, Colombia;
| | - Guillermina García-Rivera
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del IPN, Mexico City 07360, Mexico; (M.D.-H.); (R.J.-R.); (G.G.-R.); (A.B.); (D.Z.)
| | - Sarita Montaño
- Laboratorio de Bioinformática y Simulación Molecular, Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Sinaloa, Sinaloa 80030, Mexico;
| | - Abigail Betanzos
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del IPN, Mexico City 07360, Mexico; (M.D.-H.); (R.J.-R.); (G.G.-R.); (A.B.); (D.Z.)
- Consejo Nacional de Ciencia y Tecnología (Conacyt), Mexico City 03940, Mexico
| | - Dxinegueela Zanatta
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del IPN, Mexico City 07360, Mexico; (M.D.-H.); (R.J.-R.); (G.G.-R.); (A.B.); (D.Z.)
| | - Esther Orozco
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del IPN, Mexico City 07360, Mexico; (M.D.-H.); (R.J.-R.); (G.G.-R.); (A.B.); (D.Z.)
- Correspondence: ; Tel.: +52-55-5747-5642
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30
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Teramura H, Yamada K, Ito K, Kasahara K, Kikuchi T, Kioka N, Fukuda M, Kusano H, Tanaka K, Shimada H. Characterization of novel SUMO family genes in the rice genome. Genes Genet Syst 2021; 96:25-32. [PMID: 33731501 DOI: 10.1266/ggs.20-00034] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Small ubiquitin-related modifier (SUMO) is a post-translational modification factor composed of about 100 amino acid residues. Most plant species express a family of SUMO isoforms. We found three novel homologs of rice (Oryza sativa L.) SUMO genes, OsSUMO4, OsSUMO5 and OsSUMO6, in addition to the known SUMO genes OsSUMO1-OsSUMO3. Phylogenetic tree analysis revealed that rice SUMO genes have diverged considerably during their evolution. All six of these SUMO genes complemented the phenotype of the SUMO-deficient pmt3Δ mutant of fission yeast. Among the amino acid sequences of rice SUMO proteins, consensus motifs (ΨKXE/D) of the SUMO acceptor site were found in OsSUMO3, OsSUMO4, OsSUMO5 and OsSUMO6. The heat shock protein HSF7 is known to be SUMOylated in Arabidopsis thaliana. SUMOylation using a bacterial expression system revealed that the rice HSF7 homolog was modified by the six rice SUMOs, and further suggested that OsSUMO1, OsSUMO3, OsSUMO4 and OsSUMO6 are involved in its multiple SUMOylation.
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Affiliation(s)
- Hiroshi Teramura
- Department of Biological Science and Technology, Tokyo University of Science
| | - Kazuma Yamada
- Department of Biological Science and Technology, Tokyo University of Science
| | - Kahori Ito
- Department of Biological Science and Technology, Tokyo University of Science
| | - Keisuke Kasahara
- Department of Biological Science and Technology, Tokyo University of Science
| | - Tsubasa Kikuchi
- Department of Biological Science and Technology, Tokyo University of Science
| | - Naoya Kioka
- Department of Biological Science and Technology, Tokyo University of Science
| | - Masato Fukuda
- Department of Biological Science and Technology, Tokyo University of Science
| | - Hiroaki Kusano
- Department of Biological Science and Technology, Tokyo University of Science
| | - Katsunori Tanaka
- Department of Bioscience, School of Science and Technology, Kwansei Gakuin University
| | - Hiroaki Shimada
- Department of Biological Science and Technology, Tokyo University of Science
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31
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Hou Z, Shi W, Feng J, Wang W, Zheng E, Lin H, Yu C, Li L. Self-stabilizing regulation of deubiquitinating enzymes in an enzymatic activity-dependent manner. Int J Biol Macromol 2021; 181:1081-1091. [PMID: 33864866 DOI: 10.1016/j.ijbiomac.2021.04.073] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 03/30/2021] [Accepted: 04/12/2021] [Indexed: 11/18/2022]
Abstract
Deubiquitinating enzymes (DUBs) play important roles in many physiological and pathological processes by modulating the ubiquitination of their substrates. DUBs undergo post-translational modifications including ubiquitination. However, whether DUBs can reverse their own ubiquitination and regulate their own protein stability requires further investigation. To answer this question, we screened an expression library of DUBs and their enzymatic activity mutants and found that some DUBs regulated their own protein stability in an enzymatic activity- and homomeric interaction-dependent manner. Taking Ubiquitin-specific-processing protease 29 (USP29) as an example, we found that USP29 deubiquitinates itself and protects itself from proteasomal degradation. We also revealed that the N-terminal region of USP29 is critical for its protein stability. Taken together, our work demonstrates that at least some DUBs regulate their own ubiquitination and protein stability. Our findings provide novel molecular insight into the diverse regulation of DUBs.
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Affiliation(s)
- Zhenzhu Hou
- The School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Wanyan Shi
- The School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Jinan Feng
- The School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Wei Wang
- The School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Enrun Zheng
- The School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Hanbin Lin
- The School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Cheng Yu
- The School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Lisheng Li
- The School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China; Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Fujian Medical University, 1 Xueyuan Road, Minhou, Fuzhou, China.
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32
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Xia L, Jiang Y, Zhang XH, Wang XR, Wei R, Qin K, Lu Y. SUMOylation disassembles the tetrameric pyruvate kinase M2 to block myeloid differentiation of leukemia cells. Cell Death Dis 2021; 12:101. [PMID: 33473116 PMCID: PMC7817830 DOI: 10.1038/s41419-021-03400-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Leukemia arises from blockage of the differentiation/maturation of hematopoietic progenitor cells at different stages with uncontrolled proliferation of leukemic cells. However, the signal pathways that block cell differentiation remain unclear. Herein we found that SUMOylation of the M2 isoform of pyruvate kinase (PKM2), a rate-limiting glycolytic enzyme catalyzing the dephosphorylation of phosphoenolpyruvate to pyruvate, is prevalent in a variety of leukemic cell lines as well as primary samples from patients with leukemia through multiple-reaction monitoring based targeted mass spectrometry analysis. SUMOylation of PKM2 lysine 270 (K270) triggered conformation change from tetrameric to dimeric of PKM2, reduced PK activity, and led to nuclear translocation of PKM2. SUMO1 modification of PKM2 recruits and promotes degradation of RUNX1 via a SUMO-interacting motif, resulting in blockage of myeloid differentiation of NB4 and U937 leukemia cells. Replacement of wild type PKM2 with a SUMOylation-deficient mutant (K270R) abrogated the interaction with RUNX1, and the blockage of myeloid differentiation in vitro and in xenograft model. Our results establish PKM2 as an essential modulator of leukemia cell differentiation and a potential therapeutic target, which may offer synergistic effect with differentiation therapy in the treatment of leukemia.
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Affiliation(s)
- Li Xia
- Institute of Dermatology, Xinhua Hospital, Key Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of Education and Department of Core Facility of Basic Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Yue Jiang
- Department of Hematology, Dalian Key Laboratory of Hematology, Liaoning Medical Center for Hematopoietic Stem Cell Transplantation, The Second Hospital of Dalian Medical University, Dalian, China
| | - Xue-Hong Zhang
- Department of Hematology, Dalian Key Laboratory of Hematology, Liaoning Medical Center for Hematopoietic Stem Cell Transplantation, The Second Hospital of Dalian Medical University, Dalian, China
| | - Xin-Ran Wang
- Institute of Dermatology, Xinhua Hospital, Key Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of Education and Department of Core Facility of Basic Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ran Wei
- Institute of Dermatology, Xinhua Hospital, Key Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of Education and Department of Core Facility of Basic Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Kang Qin
- Institute of Dermatology, Xinhua Hospital, Key Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of Education and Department of Core Facility of Basic Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ying Lu
- Institute of Dermatology, Xinhua Hospital, Key Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of Education and Department of Core Facility of Basic Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai, China. .,Department of Hematology, Dalian Key Laboratory of Hematology, Liaoning Medical Center for Hematopoietic Stem Cell Transplantation, The Second Hospital of Dalian Medical University, Dalian, China.
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33
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González-Prieto R, Eifler-Olivi K, Claessens LA, Willemstein E, Xiao Z, Talavera Ormeno CMP, Ovaa H, Ulrich HD, Vertegaal ACO. Global non-covalent SUMO interaction networks reveal SUMO-dependent stabilization of the non-homologous end joining complex. Cell Rep 2021; 34:108691. [PMID: 33503430 DOI: 10.1016/j.celrep.2021.108691] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 12/11/2020] [Accepted: 01/05/2021] [Indexed: 12/17/2022] Open
Abstract
In contrast to our extensive knowledge on covalent small ubiquitin-like modifier (SUMO) target proteins, we are limited in our understanding of non-covalent SUMO-binding proteins. We identify interactors of different SUMO isoforms-monomeric SUMO1, monomeric SUMO2, or linear trimeric SUMO2 chains-using a mass spectrometry-based proteomics approach. We identify 379 proteins that bind to different SUMO isoforms, mainly in a preferential manner. Interestingly, XRCC4 is the only DNA repair protein in our screen with a preference for SUMO2 trimers over mono-SUMO2, as well as the only protein in our screen that belongs to the non-homologous end joining (NHEJ) DNA double-strand break repair pathway. A SUMO interaction motif (SIM) in XRCC4 regulates its recruitment to sites of DNA damage and phosphorylation of S320 by DNA-PKcs. Our data highlight the importance of non-covalent and covalent sumoylation for DNA double-strand break repair via the NHEJ pathway and provide a resource of SUMO isoform interactors.
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Affiliation(s)
- Román González-Prieto
- Department of Cell and Chemical Biology, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, the Netherlands.
| | - Karolin Eifler-Olivi
- Department of Cell and Chemical Biology, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, the Netherlands; Institute of Molecular Biology (IMB), Ackermannweg 4, 55128 Mainz, Germany
| | - Laura A Claessens
- Department of Cell and Chemical Biology, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, the Netherlands
| | - Edwin Willemstein
- Department of Cell and Chemical Biology, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, the Netherlands
| | - Zhenyu Xiao
- Department of Cell and Chemical Biology, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, the Netherlands
| | - Cami M P Talavera Ormeno
- Department of Cell and Chemical Biology, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, the Netherlands; Oncode Institute, Einthovenweg 20, 2333 ZC Leiden, the Netherlands
| | - Huib Ovaa
- Department of Cell and Chemical Biology, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, the Netherlands; Oncode Institute, Einthovenweg 20, 2333 ZC Leiden, the Netherlands
| | - Helle D Ulrich
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128 Mainz, Germany
| | - Alfred C O Vertegaal
- Department of Cell and Chemical Biology, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, the Netherlands.
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34
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Lips C, Ritterhoff T, Weber A, Janowska MK, Mustroph M, Sommer T, Klevit RE. Who with whom: functional coordination of E2 enzymes by RING E3 ligases during poly-ubiquitylation. EMBO J 2020; 39:e104863. [PMID: 33015833 PMCID: PMC7667886 DOI: 10.15252/embj.2020104863] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Revised: 08/31/2020] [Accepted: 09/10/2020] [Indexed: 11/09/2022] Open
Abstract
Protein modification with poly-ubiquitin chains is a crucial process involved in a myriad of cellular pathways. Chain synthesis requires two steps: substrate modification with ubiquitin (priming) followed by repetitive ubiquitin-to-ubiquitin attachment (elongation). RING-type E3 ligases catalyze both reactions in collaboration with specific priming and elongating E2 enzymes. We provide kinetic insight into poly-ubiquitylation during protein quality control by showing that priming is the rate-determining step in protein degradation as directed by the yeast ERAD RING E3 ligases, Hrd1 and Doa10. Doa10 cooperates with the dedicated priming E2, Ubc6, while both E3s use Ubc7 for elongation. Here, we provide direct evidence that Hrd1 uses Ubc7 also for priming. We found that Ubc6 has an unusually high basal activity that does not require strong stimulation from an E3. Doa10 exploits this property to pair with Ubc6 over Ubc7 during priming. Our work not only illuminates the mechanisms of specific E2/E3 interplay in ERAD, but also offers a basis to understand how RING E3s may have properties that are tailored to pair with their preferred E2s.
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Affiliation(s)
- Christian Lips
- Max Delbrück‐Center for Molecular Medicine in the Helmholtz AssociationBerlin‐BuchGermany
| | - Tobias Ritterhoff
- Department of BiochemistrySchool of MedicineUniversity of WashingtonSeattleWAUSA
| | - Annika Weber
- Max Delbrück‐Center for Molecular Medicine in the Helmholtz AssociationBerlin‐BuchGermany
- Present address:
MRC Laboratory of Molecular BiologyCambridgeUK
| | - Maria K Janowska
- Department of BiochemistrySchool of MedicineUniversity of WashingtonSeattleWAUSA
| | - Mandy Mustroph
- Max Delbrück‐Center for Molecular Medicine in the Helmholtz AssociationBerlin‐BuchGermany
| | - Thomas Sommer
- Max Delbrück‐Center for Molecular Medicine in the Helmholtz AssociationBerlin‐BuchGermany
- Lady Davies Guest ProfessorTechnion‐Israel Institute of TechnologyHaifaIsrael
| | - Rachel E Klevit
- Department of BiochemistrySchool of MedicineUniversity of WashingtonSeattleWAUSA
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35
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The Role of Sumoylation in the Response to Hypoxia: An Overview. Cells 2020; 9:cells9112359. [PMID: 33114748 PMCID: PMC7693722 DOI: 10.3390/cells9112359] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 10/21/2020] [Accepted: 10/22/2020] [Indexed: 02/07/2023] Open
Abstract
Sumoylation is the covalent attachment of the small ubiquitin-related modifier (SUMO) to a vast variety of proteins in order to modulate their function. Sumoylation has emerged as an important modification with a regulatory role in the cellular response to different types of stress including osmotic, hypoxic and oxidative stress. Hypoxia can occur under physiological or pathological conditions, such as ischemia and cancer, as a result of an oxygen imbalance caused by low supply and/or increased consumption. The hypoxia inducible factors (HIFs), and the proteins that regulate their fate, are critical molecular mediators of the response to hypoxia and modulate procedures such as glucose and lipid metabolism, angiogenesis, erythropoiesis and, in the case of cancer, tumor progression and metastasis. Here, we provide an overview of the sumoylation-dependent mechanisms that are activated under hypoxia and the way they influence key players of the hypoxic response pathway. As hypoxia is a hallmark of many diseases, understanding the interrelated connections between the SUMO and the hypoxic signaling pathways can open the way for future molecular therapeutic interventions.
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36
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Heras G, Namuduri AV, Traini L, Shevchenko G, Falk A, Bergström Lind S, Jia M, Tian G, Gastaldello S. Muscle RING-finger protein-1 (MuRF1) functions and cellular localization are regulated by SUMO1 post-translational modification. J Mol Cell Biol 2020; 11:356-370. [PMID: 29868881 PMCID: PMC7727263 DOI: 10.1093/jmcb/mjy036] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Revised: 05/25/2018] [Accepted: 06/01/2018] [Indexed: 01/02/2023] Open
Abstract
The muscle RING-finger protein-1 (MuRF1) is an E3 ubiquitin ligase expressed in skeletal and cardiac muscle tissues and it plays important roles in muscle remodeling. Upregulation of MuRF1 gene transcription participates in skeletal muscle atrophy, on contrary downregulation of protein expression leads to cardiac hypertrophy. MuRF1 gene point mutations have been found to generate protein aggregate myopathies defined as muscle disorder characterized by protein accumulation in muscle fibers. We have discovered that MuRF1 turned out to be also a target for a new post-translational modification arbitrated by conjugation of SUMO1 and it is mediated by the SUMO ligases E2 UBC9 and the E3 PIASγ/4. SUMOylation takes place at lysine 238 localized at the second coiled-coil protein domain that is required for efficient substrate interaction for polyubiquitination. We provided evidence that SUMOylation is essential for MuRF1 nuclear translocation and its mitochondria accumulation is enhanced in hyperglycemic conditions delivering a stabilization of the overall SUMOylated proteins in cultured myocytes. Thus, our findings add this SUMO1 post-translational modification as a new concept to understand muscle disorders related to the defect in MuRF1 activity.
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Affiliation(s)
- Gabriel Heras
- Department of Physiology and Pharmacology, Karolinska Institutet, Solnavägen 9, Quarter B5, Stockholm, Sweden
| | - Arvind Venkat Namuduri
- Department of Physiology and Pharmacology, Karolinska Institutet, Solnavägen 9, Quarter B5, Stockholm, Sweden
| | - Leonardo Traini
- Department of Physiology and Pharmacology, Karolinska Institutet, Solnavägen 9, Quarter B5, Stockholm, Sweden
| | - Ganna Shevchenko
- Department of Chemistry-BMC, Analytical Chemistry, Uppsala University, Uppsala, Sweden
| | - Alexander Falk
- Department of Chemistry-BMC, Analytical Chemistry, Uppsala University, Uppsala, Sweden
| | - Sara Bergström Lind
- Department of Chemistry-BMC, Analytical Chemistry, Uppsala University, Uppsala, Sweden
| | - Mi Jia
- Precision Medicine and Pharmacy Research Center, Binzhou Medical University, Yantai, China
| | - Geng Tian
- Precision Medicine and Pharmacy Research Center, Binzhou Medical University, Yantai, China
| | - Stefano Gastaldello
- Department of Physiology and Pharmacology, Karolinska Institutet, Solnavägen 9, Quarter B5, Stockholm, Sweden.,Precision Medicine and Pharmacy Research Center, Binzhou Medical University, Yantai, China
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37
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Hou PP, Luo LJ, Chen HZ, Chen QT, Bian XL, Wu SF, Zhou JX, Zhao WX, Liu JM, Wang XM, Zhang ZY, Yao LM, Chen Q, Zhou D, Wu Q. Ectosomal PKM2 Promotes HCC by Inducing Macrophage Differentiation and Remodeling the Tumor Microenvironment. Mol Cell 2020; 78:1192-1206.e10. [PMID: 32470318 DOI: 10.1016/j.molcel.2020.05.004] [Citation(s) in RCA: 147] [Impact Index Per Article: 29.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 03/11/2020] [Accepted: 05/01/2020] [Indexed: 12/12/2022]
Abstract
Tumor-derived extracellular vesicles are important mediators of cell-to-cell communication during tumorigenesis. Here, we demonstrated that hepatocellular carcinoma (HCC)-derived ectosomes remodel the tumor microenvironment to facilitate HCC progression in an ectosomal PKM2-dependent manner. HCC-derived ectosomal PKM2 induced not only metabolic reprogramming in monocytes but also STAT3 phosphorylation in the nucleus to upregulate differentiation-associated transcription factors, leading to monocyte-to-macrophage differentiation and tumor microenvironment remodeling. In HCC cells, sumoylation of PKM2 induced its plasma membrane targeting and subsequent ectosomal excretion via interactions with ARRDC1. The PKM2-ARRDC1 association in HCC was reinforced by macrophage-secreted cytokines/chemokines in a CCL1-CCR8 axis-dependent manner, further facilitating PKM2 excretion from HCC cells to form a feedforward regulatory loop for tumorigenesis. In the clinic, ectosomal PKM2 was clearly detected in the plasma of HCC patients. This study highlights a mechanism by which ectosomal PKM2 remodels the tumor microenvironment and reveals ectosomal PKM2 as a potential diagnostic marker for HCC.
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Affiliation(s)
- Pei-Pei Hou
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Biology, School of Life Sciences, Xiamen University, Xiamen 361102, Fujian Province, PR China
| | - Li-Juan Luo
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Biology, School of Life Sciences, Xiamen University, Xiamen 361102, Fujian Province, PR China
| | - Hang-Zi Chen
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Biology, School of Life Sciences, Xiamen University, Xiamen 361102, Fujian Province, PR China
| | - Qi-Tao Chen
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Biology, School of Life Sciences, Xiamen University, Xiamen 361102, Fujian Province, PR China
| | - Xue-Li Bian
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Biology, School of Life Sciences, Xiamen University, Xiamen 361102, Fujian Province, PR China
| | - Sheng-Fu Wu
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Biology, School of Life Sciences, Xiamen University, Xiamen 361102, Fujian Province, PR China
| | - Jia-Xin Zhou
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Biology, School of Life Sciences, Xiamen University, Xiamen 361102, Fujian Province, PR China
| | - Wen-Xiu Zhao
- Fujian Provincial Key Laboratory of Chronic Liver Disease and Hepatocellular Carcinoma, Zhong Shan Hospital, Xiamen University, Xiamen 361005, Fujian Province, PR China
| | - Jian-Ming Liu
- Fujian Provincial Key Laboratory of Chronic Liver Disease and Hepatocellular Carcinoma, Zhong Shan Hospital, Xiamen University, Xiamen 361005, Fujian Province, PR China
| | - Xiao-Min Wang
- Fujian Provincial Key Laboratory of Chronic Liver Disease and Hepatocellular Carcinoma, Zhong Shan Hospital, Xiamen University, Xiamen 361005, Fujian Province, PR China
| | - Zhi-Yuan Zhang
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Biology, School of Life Sciences, Xiamen University, Xiamen 361102, Fujian Province, PR China
| | - Lu-Ming Yao
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Biology, School of Life Sciences, Xiamen University, Xiamen 361102, Fujian Province, PR China
| | - Qinghua Chen
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Biology, School of Life Sciences, Xiamen University, Xiamen 361102, Fujian Province, PR China
| | - Dawang Zhou
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Biology, School of Life Sciences, Xiamen University, Xiamen 361102, Fujian Province, PR China
| | - Qiao Wu
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Biology, School of Life Sciences, Xiamen University, Xiamen 361102, Fujian Province, PR China.
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38
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Regulation of Deubiquitinating Enzymes by Post-Translational Modifications. Int J Mol Sci 2020; 21:ijms21114028. [PMID: 32512887 PMCID: PMC7312083 DOI: 10.3390/ijms21114028] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 06/01/2020] [Accepted: 06/01/2020] [Indexed: 01/04/2023] Open
Abstract
Ubiquitination and deubiquitination play a critical role in all aspects of cellular processes, and the enzymes involved are tightly regulated by multiple factors including posttranslational modifications like most other proteins. Dysfunction or misregulation of these enzymes could have dramatic physiological consequences, sometimes leading to diseases. Therefore, it is important to have a clear understanding of these regulatory processes. Here, we have reviewed the posttranslational modifications of deubiquitinating enzymes and their consequences on the catalytic activity, stability, abundance, localization, and interaction with the partner proteins.
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39
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Celen AB, Sahin U. Sumoylation on its 25th anniversary: mechanisms, pathology, and emerging concepts. FEBS J 2020; 287:3110-3140. [DOI: 10.1111/febs.15319] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 03/04/2020] [Accepted: 03/30/2020] [Indexed: 12/26/2022]
Affiliation(s)
- Arda B. Celen
- Department of Molecular Biology and Genetics Center for Life Sciences and Technologies Bogazici University Istanbul Turkey
| | - Umut Sahin
- Department of Molecular Biology and Genetics Center for Life Sciences and Technologies Bogazici University Istanbul Turkey
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40
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Molecular mechanisms in SUMO conjugation. Biochem Soc Trans 2020; 48:123-135. [PMID: 31872228 DOI: 10.1042/bst20190357] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 11/28/2019] [Accepted: 12/04/2019] [Indexed: 01/25/2023]
Abstract
The small ubiquitin-like modifier (SUMO) is a post-translational modifier that can regulate the function of hundreds of proteins inside the cell. SUMO belongs to the ubiquitin-like family of proteins that can be attached to target proteins by a dedicated enzymatic cascade pathway formed by E1, E2 and E3 enzymes. SUMOylation is involved in many cellular pathways, having in most instances essential roles for their correct function. In this review, we want to highlight the latest research on the molecular mechanisms that lead to the formation of the isopeptidic bond between the lysine substrate and the C-terminus of SUMO. In particular, we will focus on the recent discoveries on the catalytic function of the SUMO E3 ligases revealed by structural and biochemical approaches. Also, we will discuss important questions regarding specificity in SUMO conjugation, which it still remains as a major issue due to the small number of SUMO E3 ligases discovered so far, in contrast with the large number of SUMO conjugated proteins in the cell.
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41
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Küçükali CI, Salman B, Yüceer H, Ulusoy C, Abacı N, Ekmekci SS, Tüzün E, Bilgiç B, Hanağası HA. Small ubiquitin-related modifier (SUMO) 3 and SUMO4 gene polymorphisms in Parkinson’s disease. Neurol Res 2020; 42:451-457. [DOI: 10.1080/01616412.2020.1724464] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Cem Ismail Küçükali
- Department of Neuroscience, Istanbul University, Aziz Sancar Institute of Experimental Medicine, Istanbul, Türkiye
| | - Burcu Salman
- Department of Genetics, Istanbul University, Aziz Sancar Institute of Experimental Medicine, Istanbul, Türkiye
| | - Hande Yüceer
- Department of Neuroscience, Istanbul University, Aziz Sancar Institute of Experimental Medicine, Istanbul, Türkiye
| | - Canan Ulusoy
- Department of Neuroscience, Istanbul University, Aziz Sancar Institute of Experimental Medicine, Istanbul, Türkiye
| | - Neslihan Abacı
- Department of Genetics, Istanbul University, Aziz Sancar Institute of Experimental Medicine, Istanbul, Türkiye
| | - Sema Sırma Ekmekci
- Department of Genetics, Istanbul University, Aziz Sancar Institute of Experimental Medicine, Istanbul, Türkiye
| | - Erdem Tüzün
- Department of Neuroscience, Istanbul University, Aziz Sancar Institute of Experimental Medicine, Istanbul, Türkiye
| | - Başar Bilgiç
- Istanbul Faculty of Medicine, Department of Neurology, Istanbul University, Istanbul, Turkey
| | - Haşmet Ayhan Hanağası
- Istanbul Faculty of Medicine, Department of Neurology, Istanbul University, Istanbul, Turkey
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42
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Gusev EY, Zotova NV. Cellular Stress and General Pathological Processes. Curr Pharm Des 2020; 25:251-297. [PMID: 31198111 DOI: 10.2174/1381612825666190319114641] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 03/13/2019] [Indexed: 02/06/2023]
Abstract
From the viewpoint of the general pathology, most of the human diseases are associated with a limited number of pathogenic processes such as inflammation, tumor growth, thrombosis, necrosis, fibrosis, atrophy, pathological hypertrophy, dysplasia and metaplasia. The phenomenon of chronic low-grade inflammation could be attributed to non-classical forms of inflammation, which include many neurodegenerative processes, pathological variants of insulin resistance, atherosclerosis, and other manifestations of the endothelial dysfunction. Individual and universal manifestations of cellular stress could be considered as a basic element of all these pathologies, which has both physiological and pathophysiological significance. The review examines the causes, main phenomena, developmental directions and outcomes of cellular stress using a phylogenetically conservative set of genes and their activation pathways, as well as tissue stress and its role in inflammatory and para-inflammatory processes. The main ways towards the realization of cellular stress and its functional blocks were outlined. The main stages of tissue stress and the classification of its typical manifestations, as well as its participation in the development of the classical and non-classical variants of the inflammatory process, were also described. The mechanisms of cellular and tissue stress are structured into the complex systems, which include networks that enable the exchange of information with multidirectional signaling pathways which together make these systems internally contradictory, and the result of their effects is often unpredictable. However, the possible solutions require new theoretical and methodological approaches, one of which includes the transition to integral criteria, which plausibly reflect the holistic image of these processes.
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Affiliation(s)
- Eugeny Yu Gusev
- Laboratory of the Immunology of Inflammation, Institute of Immunology and Physiology, Yekaterinburg, Russian Federation
| | - Natalia V Zotova
- Laboratory of the Immunology of Inflammation, Institute of Immunology and Physiology, Yekaterinburg, Russian Federation.,Department of Medical Biochemistry and Biophysics, Ural Federal University named after B.N.Yeltsin, Yekaterinburg, Russian Federation
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43
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Functional analysis of deubiquitylating enzymes in tumorigenesis and development. Biochim Biophys Acta Rev Cancer 2019; 1872:188312. [DOI: 10.1016/j.bbcan.2019.188312] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 08/16/2019] [Accepted: 08/16/2019] [Indexed: 02/06/2023]
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The role of DUBs in the post-translational control of cell migration. Essays Biochem 2019; 63:579-594. [DOI: 10.1042/ebc20190022] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 09/30/2019] [Accepted: 10/01/2019] [Indexed: 12/26/2022]
Abstract
AbstractCell migration is a multifactorial/multistep process that requires the concerted action of growth and transcriptional factors, motor proteins, extracellular matrix remodeling and proteases. In this review, we focus on the role of transcription factors modulating Epithelial-to-Mesenchymal Transition (EMT-TFs), a fundamental process supporting both physiological and pathological cell migration. These EMT-TFs (Snail1/2, Twist1/2 and Zeb1/2) are labile proteins which should be stabilized to initiate EMT and provide full migratory and invasive properties. We present here a family of enzymes, the deubiquitinases (DUBs) which have a crucial role in counteracting polyubiquitination and proteasomal degradation of EMT-TFs after their induction by TGFβ, inflammatory cytokines and hypoxia. We also describe the DUBs promoting the stabilization of Smads, TGFβ receptors and other key proteins involved in transduction pathways controlling EMT.
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Abrieu A, Liakopoulos D. How Does SUMO Participate in Spindle Organization? Cells 2019; 8:E801. [PMID: 31370271 PMCID: PMC6721559 DOI: 10.3390/cells8080801] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 07/24/2019] [Accepted: 07/30/2019] [Indexed: 02/07/2023] Open
Abstract
The ubiquitin-like protein SUMO is a regulator involved in most cellular mechanisms. Recent studies have discovered new modes of function for this protein. Of particular interest is the ability of SUMO to organize proteins in larger assemblies, as well as the role of SUMO-dependent ubiquitylation in their disassembly. These mechanisms have been largely described in the context of DNA repair, transcriptional regulation, or signaling, while much less is known on how SUMO facilitates organization of microtubule-dependent processes during mitosis. Remarkably however, SUMO has been known for a long time to modify kinetochore proteins, while more recently, extensive proteomic screens have identified a large number of microtubule- and spindle-associated proteins that are SUMOylated. The aim of this review is to focus on the possible role of SUMOylation in organization of the spindle and kinetochore complexes. We summarize mitotic and microtubule/spindle-associated proteins that have been identified as SUMO conjugates and present examples regarding their regulation by SUMO. Moreover, we discuss the possible contribution of SUMOylation in organization of larger protein assemblies on the spindle, as well as the role of SUMO-targeted ubiquitylation in control of kinetochore assembly and function. Finally, we propose future directions regarding the study of SUMOylation in regulation of spindle organization and examine the potential of SUMO and SUMO-mediated degradation as target for antimitotic-based therapies.
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Affiliation(s)
- Ariane Abrieu
- CRBM, CNRS UMR5237, Université de Montpellier, 1919 route de Mende, 34090 Montpellier, France.
| | - Dimitris Liakopoulos
- CRBM, CNRS UMR5237, Université de Montpellier, 1919 route de Mende, 34090 Montpellier, France.
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Gersch M, Wagstaff JL, Toms AV, Graves B, Freund SMV, Komander D. Distinct USP25 and USP28 Oligomerization States Regulate Deubiquitinating Activity. Mol Cell 2019; 74:436-451.e7. [PMID: 30926242 PMCID: PMC6509359 DOI: 10.1016/j.molcel.2019.02.030] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Revised: 12/20/2018] [Accepted: 02/20/2019] [Indexed: 12/13/2022]
Abstract
The evolutionarily related deubiquitinating enzymes (DUBs) USP25 and USP28 comprise an identical overall domain architecture but are functionally non-redundant: USP28 stabilizes c-MYC and other nuclear proteins, and USP25 regulates inflammatory TRAF signaling. We here compare molecular features of USP25 and USP28. Active enzymes form distinctively shaped dimers, with a dimerizing insertion spatially separating independently active catalytic domains. In USP25, but not USP28, two dimers can form an autoinhibited tetramer, where a USP25-specific, conserved insertion sequence blocks ubiquitin binding. In full-length enzymes, a C-terminal domain with a previously unknown fold has no impact on oligomerization, but N-terminal regions affect the dimer-tetramer equilibrium in vitro. We confirm oligomeric states of USP25 and USP28 in cells and show that modulating oligomerization affects substrate stabilization in accordance with in vitro activity data. Our work highlights how regions outside of the catalytic domain enable a conceptually intriguing interplay of DUB oligomerization and activity.
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Affiliation(s)
- Malte Gersch
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK; Chemical Genomics Centre, Max-Planck-Institute of Molecular Physiology, Otto-Hahn-Str. 11, 44227 Dortmund, Germany; Department of Chemistry and Chemical Biology, Technical University Dortmund, Otto-Hahn-Str. 4a, 44227 Dortmund, Germany
| | - Jane L Wagstaff
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Angela V Toms
- FORMA Therapeutics, Arsenal Street, Watertown, MA 02472, USA
| | - Bradford Graves
- FORMA Therapeutics, Arsenal Street, Watertown, MA 02472, USA
| | - Stefan M V Freund
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - David Komander
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK; Ubiquitin Signalling Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia; Department of Medical Biology, The University of Melbourne, Melbourne, VIC 3010, Australia.
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Differential Oligomerization of the Deubiquitinases USP25 and USP28 Regulates Their Activities. Mol Cell 2019; 74:421-435.e10. [PMID: 30926243 DOI: 10.1016/j.molcel.2019.02.029] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 12/13/2018] [Accepted: 02/20/2019] [Indexed: 12/12/2022]
Abstract
Deubiquitinases have emerged as promising drug targets for cancer therapy. The two DUBs USP25 and USP28 share high similarity but vary in their cellular functions. USP28 is known for its tumor-promoting role, whereas USP25 is a regulator of the innate immune system and, recently, a role in tumorigenesis was proposed. We solved the structures of the catalytic domains of both proteins and established substantial differences in their activities. While USP28 is a constitutively active dimer, USP25 presents an auto-inhibited tetramer. Our data indicate that the activation of USP25 is not achieved through substrate or ubiquitin binding. USP25 cancer-associated mutations lead to activation in vitro and in vivo, thereby providing a functional link between auto-inhibition and the cancer-promoting role of the enzyme. Our work led to the identification of significant differences between USP25 and USP28 and provided the molecular basis for the development of new and highly specific anti-cancer drugs.
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48
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Sadler JBA, Lamb CA, Welburn CR, Adamson IS, Kioumourtzoglou D, Chi NW, Gould GW, Bryant NJ. The deubiquitinating enzyme USP25 binds tankyrase and regulates trafficking of the facilitative glucose transporter GLUT4 in adipocytes. Sci Rep 2019; 9:4710. [PMID: 30886164 PMCID: PMC6423145 DOI: 10.1038/s41598-019-40596-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 02/15/2019] [Indexed: 12/11/2022] Open
Abstract
Key to whole body glucose homeostasis is the ability of fat and muscle cells to sequester the facilitative glucose transporter GLUT4 in an intracellular compartment from where it can be mobilized in response to insulin. We have previously demonstrated that this process requires ubiquitination of GLUT4 while numerous other studies have identified several molecules that are also required, including the insulin-responsive aminopeptidase IRAP and its binding partner, the scaffolding protein tankyrase. In addition to binding IRAP, Tankyrase has also been shown to bind the deubiquinating enzyme USP25. Here we demonstrate that USP25 and Tankyrase interact, and colocalise with GLUT4 in insulin-sensitive cells. Furthermore depletion of USP25 from adipocytes reduces cellular levels of GLUT4 and concomitantly blunts the ability of insulin to stimulate glucose transport. Collectively, these data support our model that sorting of GLUT4 into its insulin-sensitive store involves a cycle of ubiquitination and subsequent deubiquitination.
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Affiliation(s)
- Jessica B A Sadler
- Henry Wellcome Laboratory of Cell Biology, Institute of Molecular Cell and Systems Biology, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Christopher A Lamb
- Henry Wellcome Laboratory of Cell Biology, Institute of Molecular Cell and Systems Biology, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Cassie R Welburn
- Henry Wellcome Laboratory of Cell Biology, Institute of Molecular Cell and Systems Biology, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Iain S Adamson
- Henry Wellcome Laboratory of Cell Biology, Institute of Molecular Cell and Systems Biology, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8QQ, UK
| | | | - Nai-Wen Chi
- Department of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Gwyn W Gould
- Henry Wellcome Laboratory of Cell Biology, Institute of Molecular Cell and Systems Biology, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8QQ, UK.
| | - Nia J Bryant
- Department of Biology, University of York, York, YO10 4HJ, UK.
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Eisenhardt N, Ilic D, Nagamalleswari E, Pichler A. Biochemical characterization of SUMO-conjugating enzymes by in vitro sumoylation assays. Methods Enzymol 2019; 618:167-185. [PMID: 30850051 DOI: 10.1016/bs.mie.2018.12.025] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The small ubiquitin-related modifier (SUMO) is a protein of ~10kDa that is covalently conjugated to its substrate proteins in an enzymatic process called sumoylation. This posttranslational modification is an essential regulatory mechanism that plays crucial roles in many cellular pathways. It allows rapid adaptation to environmental changes by switching protein functions due to alternate complex assemblies, changes in intracellular localization, enzymatic activity, or stability. SUMO conjugation is executed by the hierarchical action of E1, E2, and E3 enzymes. Both E2 and E3 enzymes contribute to substrate specificity but with E3 ligases being the more important for this. E1 and E2 activities are essential for all sumoylation reactions but usually-with a few exceptions-modify substrates only inefficiently. Hence, most substrates require the additional action of an E3 ligase or a cofactor. Here, we describe methods to distinguish a bona fide E3 ligase from a cofactor activity by using in vitro sumoylation assays.
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Affiliation(s)
- Nathalie Eisenhardt
- Department of Epigenetics, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Dragana Ilic
- Department of Epigenetics, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Easa Nagamalleswari
- Department of Epigenetics, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Andrea Pichler
- Department of Epigenetics, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany.
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Mms21: A Putative SUMO E3 Ligase in Candida albicans That Negatively Regulates Invasiveness and Filamentation, and Is Required for the Genotoxic and Cellular Stress Response. Genetics 2018; 211:579-595. [PMID: 30530734 DOI: 10.1534/genetics.118.301769] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Accepted: 11/28/2018] [Indexed: 12/28/2022] Open
Abstract
In the life cycle of the fungal pathogen Candida albicans, the formation of filamentous cells is a differentiation process that is critically involved in host tissue invasion, and in adaptation to host cell and environmental stresses. Here, we have used the Gene Replacement And Conditional Expression library to identify genes controlling invasiveness and filamentation; conditional repression of the library revealed 69 mutants that triggered these processes. Intriguingly, the genes encoding the small ubiquitin-like modifier (SUMO) E3 ligase Mms21, and all other tested members of the sumoylation pathway, were both nonessential and capable of triggering filamentation upon repression, suggesting an important role for sumoylation in controlling filamentation in C. albicans We have investigated Mms21 in detail. Both Mms21 nulls (mms21Δ/Δ) and SP [Siz/Pias (protein inhibitor of activated signal transducer and activator of transcription)] domain (SUMO E3 ligase domain)-deleted mutants displayed invasiveness, filamentation, and abnormal nuclear segregation; filament formation occurred even in the absence of the hyphal transcription factor Efg1. Transcriptional analysis of mms21Δ/Δ showed an increase in expression from two- to eightfold above that of the wild-type for hyphal-specific genes, including ECE1, PGA13, PGA26, HWP1, ALS1, ALS3, SOD4, SOD5, UME6, and HGC1 The Mms21-deleted mutants were unable to recover from DNA-damaging agents like methyl methane sulfonate, hydroxyurea, hydrogen peroxide, and UV radiation, suggesting that the protein is important for genotoxic stress responses. In addition, the mms21Δ/Δ mutant displayed sensitivity to cell wall and thermal stresses, and to different antifungal drugs. All these findings suggest that Mms21 plays important roles in cellular differentiation, DNA damage and cellular stress responses, and in response to antifungal drugs.
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