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Gou Y, Liu D, Chen M, Wei Y, Huang X, Han C, Feng Z, Zhang C, Lu T, Peng D, Xue Y. GPS-SUMO 2.0: an updated online service for the prediction of SUMOylation sites and SUMO-interacting motifs. Nucleic Acids Res 2024; 52:W238-W247. [PMID: 38709873 PMCID: PMC11223847 DOI: 10.1093/nar/gkae346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 04/08/2024] [Accepted: 04/18/2024] [Indexed: 05/08/2024] Open
Abstract
Small ubiquitin-like modifiers (SUMOs) are tiny but important protein regulators involved in orchestrating a broad spectrum of biological processes, either by covalently modifying protein substrates or by noncovalently interacting with other proteins. Here, we report an updated server, GPS-SUMO 2.0, for the prediction of SUMOylation sites and SUMO-interacting motifs (SIMs). For predictor training, we adopted three machine learning algorithms, penalized logistic regression (PLR), a deep neural network (DNN), and a transformer, and used 52 404 nonredundant SUMOylation sites in 8262 proteins and 163 SIMs in 102 proteins. To further increase the accuracy of predicting SUMOylation sites, a pretraining model was first constructed using 145 545 protein lysine modification sites, followed by transfer learning to fine-tune the model. GPS-SUMO 2.0 exhibited greater accuracy in predicting SUMOylation sites than did other existing tools. For users, one or multiple protein sequences or identifiers can be input, and the prediction results are shown in a tabular list. In addition to the basic statistics, we integrated knowledge from 35 public resources to annotate SUMOylation sites or SIMs. The GPS-SUMO 2.0 server is freely available at https://sumo.biocuckoo.cn/. We believe that GPS-SUMO 2.0 can serve as a useful tool for further analysis of SUMOylation and SUMO interactions.
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Affiliation(s)
- Yujie Gou
- Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan430074, China
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan430074, China
| | - Dan Liu
- Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan430074, China
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan430074, China
| | - Miaomiao Chen
- Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan430074, China
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan430074, China
| | - Yuxiang Wei
- Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan430074, China
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan430074, China
| | - Xinhe Huang
- Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan430074, China
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan430074, China
| | - Cheng Han
- Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan430074, China
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan430074, China
| | - Zihao Feng
- Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan430074, China
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan430074, China
| | - Chi Zhang
- Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan430074, China
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan430074, China
| | - Teng Lu
- Computer Network Information Center, Chinese Academy of Sciences, Beijing100190, China
| | - Di Peng
- Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan430074, China
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan430074, China
| | - Yu Xue
- Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan430074, China
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan430074, China
- Nanjing University Institute of Artificial Intelligence Biomedicine, Nanjing210031, China
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2
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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 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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3
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Vu DD, Bonucci A, Brenière M, Cisneros-Aguirre M, Pelupessy P, Wang Z, Carlier L, Bouvignies G, Cortes P, Aggarwal AK, Blackledge M, Gueroui Z, Belle V, Stark JM, Modesti M, Ferrage F. Multivalent interactions of the disordered regions of XLF and XRCC4 foster robust cellular NHEJ and drive the formation of ligation-boosting condensates in vitro. Nat Struct Mol Biol 2024:10.1038/s41594-024-01339-x. [PMID: 38898102 DOI: 10.1038/s41594-024-01339-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 05/28/2024] [Indexed: 06/21/2024]
Abstract
In mammalian cells, DNA double-strand breaks are predominantly repaired by non-homologous end joining (NHEJ). During repair, the Ku70-Ku80 heterodimer (Ku), X-ray repair cross complementing 4 (XRCC4) in complex with DNA ligase 4 (X4L4) and XRCC4-like factor (XLF) form a flexible scaffold that holds the broken DNA ends together. Insights into the architectural organization of the NHEJ scaffold and its regulation by the DNA-dependent protein kinase catalytic subunit (DNA-PKcs) were recently obtained by single-particle cryo-electron microscopy analysis. However, several regions, especially the C-terminal regions (CTRs) of the XRCC4 and XLF scaffolding proteins, have largely remained unresolved in experimental structures, which hampers the understanding of their functions. Here we used magnetic resonance techniques and biochemical assays to comprehensively characterize the interactions and dynamics of the XRCC4 and XLF CTRs at residue resolution. We show that the CTRs of XRCC4 and XLF are intrinsically disordered and form a network of multivalent heterotypic and homotypic interactions that promotes robust cellular NHEJ activity. Importantly, we demonstrate that the multivalent interactions of these CTRs lead to the formation of XLF and X4L4 condensates in vitro, which can recruit relevant effectors and critically stimulate DNA end ligation. Our work highlights the role of disordered regions in the mechanism and dynamics of NHEJ and lays the groundwork for the investigation of NHEJ protein disorder and its associated condensates inside cells with implications in cancer biology, immunology and the development of genome-editing strategies.
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Affiliation(s)
- Duc-Duy Vu
- Département de Chimie, LBM, CNRS UMR 7203, École Normale Supérieure, PSL University, Sorbonne University, Paris, France
| | - Alessio Bonucci
- Aix Marseille Univ, CNRS UMR 7281, BIP Bioénergétique et Ingénierie des Protéines, IMM, Marseille, France
| | - Manon Brenière
- Cancer Research Center of Marseille, Department of Genome Integrity, CNRS UMR7258, Inserm U1068, Institut Paoli-Calmettes, Aix-Marseille University, Marseille, France
| | - Metztli Cisneros-Aguirre
- Department of Cancer Genetics and Epigenetics, Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of the City of Hope, Duarte, CA, USA
| | - Philippe Pelupessy
- Département de Chimie, LBM, CNRS UMR 7203, École Normale Supérieure, PSL University, Sorbonne University, Paris, France
| | - Ziqing Wang
- Département de Chimie, LBM, CNRS UMR 7203, École Normale Supérieure, PSL University, Sorbonne University, Paris, France
| | - Ludovic Carlier
- Département de Chimie, LBM, CNRS UMR 7203, École Normale Supérieure, PSL University, Sorbonne University, Paris, France
| | - Guillaume Bouvignies
- Département de Chimie, LBM, CNRS UMR 7203, École Normale Supérieure, PSL University, Sorbonne University, Paris, France
| | - Patricia Cortes
- Department of Molecular, Cellular and Biomedical Sciences, CUNY School of Medicine at City College of New York, New York, NY, USA
| | - Aneel K Aggarwal
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Martin Blackledge
- Institut de Biologie Structurale (IBS), Grenoble Alpes University, CNRS, CEA, Grenoble, France
| | - Zoher Gueroui
- PASTEUR, Département de Chimie, École Normale Supérieure, PSL University, Sorbonne University, CNRS, Paris, France
| | - Valérie Belle
- Aix Marseille Univ, CNRS UMR 7281, BIP Bioénergétique et Ingénierie des Protéines, IMM, Marseille, France
| | - Jeremy M Stark
- Department of Cancer Genetics and Epigenetics, Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of the City of Hope, Duarte, CA, USA
| | - Mauro Modesti
- Cancer Research Center of Marseille, Department of Genome Integrity, CNRS UMR7258, Inserm U1068, Institut Paoli-Calmettes, Aix-Marseille University, Marseille, France.
| | - Fabien Ferrage
- Département de Chimie, LBM, CNRS UMR 7203, École Normale Supérieure, PSL University, Sorbonne University, Paris, France.
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4
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Carnie CJ, Götz MJ, Palma-Chaundler CS, Weickert P, Wanders A, Serrano-Benitez A, Li HY, Gupta V, Awwad SW, Blum CJ, Sczaniecka-Clift M, Cordes J, Zagnoli-Vieira G, D'Alessandro G, Richards SL, Gueorguieva N, Lam S, Beli P, Stingele J, Jackson SP. Decitabine cytotoxicity is promoted by dCMP deaminase DCTD and mitigated by SUMO-dependent E3 ligase TOPORS. EMBO J 2024; 43:2397-2423. [PMID: 38760575 PMCID: PMC11183266 DOI: 10.1038/s44318-024-00108-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 03/15/2024] [Accepted: 04/16/2024] [Indexed: 05/19/2024] Open
Abstract
The nucleoside analogue decitabine (or 5-aza-dC) is used to treat several haematological cancers. Upon its triphosphorylation and incorporation into DNA, 5-aza-dC induces covalent DNA methyltransferase 1 DNA-protein crosslinks (DNMT1-DPCs), leading to DNA hypomethylation. However, 5-aza-dC's clinical outcomes vary, and relapse is common. Using genome-scale CRISPR/Cas9 screens, we map factors determining 5-aza-dC sensitivity. Unexpectedly, we find that loss of the dCMP deaminase DCTD causes 5-aza-dC resistance, suggesting that 5-aza-dUMP generation is cytotoxic. Combining results from a subsequent genetic screen in DCTD-deficient cells with the identification of the DNMT1-DPC-proximal proteome, we uncover the ubiquitin and SUMO1 E3 ligase, TOPORS, as a new DPC repair factor. TOPORS is recruited to SUMOylated DNMT1-DPCs and promotes their degradation. Our study suggests that 5-aza-dC-induced DPCs cause cytotoxicity when DPC repair is compromised, while cytotoxicity in wild-type cells arises from perturbed nucleotide metabolism, potentially laying the foundations for future identification of predictive biomarkers for decitabine treatment.
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Affiliation(s)
- Christopher J Carnie
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK.
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK.
| | - Maximilian J Götz
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | | | - Pedro Weickert
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Amy Wanders
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Almudena Serrano-Benitez
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Hao-Yi Li
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Vipul Gupta
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Samah W Awwad
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | | | | | - Jacqueline Cordes
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Guido Zagnoli-Vieira
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Giuseppina D'Alessandro
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Sean L Richards
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Nadia Gueorguieva
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Simon Lam
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Petra Beli
- Institute of Molecular Biology (IMB), Mainz, Germany
- Institute of Developmental Biology and Neurobiology (IDN), Johannes Gutenberg-Universität, Mainz, Germany
| | - Julian Stingele
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany.
| | - Stephen P Jackson
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK.
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK.
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5
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Salas-Lloret D, García-Rodríguez N, Soto-Hidalgo E, González-Vinceiro L, Espejo-Serrano C, Giebel L, Mateos-Martín ML, de Ru AH, van Veelen PA, Huertas P, Vertegaal ACO, González-Prieto R. BRCA1/BARD1 ubiquitinates PCNA in unperturbed conditions to promote continuous DNA synthesis. Nat Commun 2024; 15:4292. [PMID: 38769345 PMCID: PMC11106271 DOI: 10.1038/s41467-024-48427-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 04/30/2024] [Indexed: 05/22/2024] Open
Abstract
Deficiencies in the BRCA1 tumor suppressor gene are the main cause of hereditary breast and ovarian cancer. BRCA1 is involved in the Homologous Recombination DNA repair pathway and, together with BARD1, forms a heterodimer with ubiquitin E3 activity. The relevance of the BRCA1/BARD1 ubiquitin E3 activity for tumor suppression and DNA repair remains controversial. Here, we observe that the BRCA1/BARD1 ubiquitin E3 activity is not required for Homologous Recombination or resistance to Olaparib. Using TULIP2 methodology, which enables the direct identification of E3-specific ubiquitination substrates, we identify substrates for BRCA1/BARD1. We find that PCNA is ubiquitinated by BRCA1/BARD1 in unperturbed conditions independently of RAD18. PCNA ubiquitination by BRCA1/BARD1 avoids the formation of ssDNA gaps during DNA replication and promotes continuous DNA synthesis. These results provide additional insight about the importance of BRCA1/BARD1 E3 activity in Homologous Recombination.
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Grants
- KWF-KIG 11367/2017-2 KWF Kankerbestrijding (Dutch Cancer Society)
- EMERGIA20_00276 Consejería de Economía, Innovación, Ciencia y Empleo, Junta de Andalucía (Ministry of Economy, Innovation, Science and Employment, Government of Andalucia)
- EMERGIA21_00057 Consejería de Economía, Innovación, Ciencia y Empleo, Junta de Andalucía (Ministry of Economy, Innovation, Science and Employment, Government of Andalucia)
- 310913 EC | EC Seventh Framework Programm | FP7 Ideas: European Research Council (FP7-IDEAS-ERC - Specific Programme: "Ideas" Implementing the Seventh Framework Programme of the European Community for Research, Technological Development and Demonstration Activities (2007 to 2013))
- MICIU/AEI/10.13039/501100011033 and by European Union NextGenerationEU/PRTR - Grants: CNS2022-135216 ; MICIU/AEI/10.13039/501100011033 and by European Union : PID2021-122361NA-I00
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Affiliation(s)
- Daniel Salas-Lloret
- Department of Cell and Chemical Biology, Leiden University Medical Centre, Leiden, The Netherlands
| | - Néstor García-Rodríguez
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Sevilla, Spain
- Andalusian Centre for Regenerative Medicine and Molecular Biology (CABIMER), Universidad de Sevilla-CSIC-Universidad Pablo de Olavide-Junta de Andalucía, Sevilla, Spain
| | - Emily Soto-Hidalgo
- Andalusian Centre for Regenerative Medicine and Molecular Biology (CABIMER), Universidad de Sevilla-CSIC-Universidad Pablo de Olavide-Junta de Andalucía, Sevilla, Spain
| | - Lourdes González-Vinceiro
- Andalusian Centre for Regenerative Medicine and Molecular Biology (CABIMER), Universidad de Sevilla-CSIC-Universidad Pablo de Olavide-Junta de Andalucía, Sevilla, Spain
| | - Carmen Espejo-Serrano
- Andalusian Centre for Regenerative Medicine and Molecular Biology (CABIMER), Universidad de Sevilla-CSIC-Universidad Pablo de Olavide-Junta de Andalucía, Sevilla, Spain
| | - Lisanne Giebel
- Department of Cell and Chemical Biology, Leiden University Medical Centre, Leiden, The Netherlands
| | - María Luisa Mateos-Martín
- Institute of Biomedicine of Seville, IBiS/Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, Proteomics Facility, Sevilla, Spain
| | - Arnoud H de Ru
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - Peter A van Veelen
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - Pablo Huertas
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Sevilla, Spain
- Andalusian Centre for Regenerative Medicine and Molecular Biology (CABIMER), Universidad de Sevilla-CSIC-Universidad Pablo de Olavide-Junta de Andalucía, Sevilla, Spain
| | - Alfred C O Vertegaal
- Department of Cell and Chemical Biology, Leiden University Medical Centre, Leiden, The Netherlands
| | - Román González-Prieto
- Department of Cell and Chemical Biology, Leiden University Medical Centre, Leiden, The Netherlands.
- Andalusian Centre for Regenerative Medicine and Molecular Biology (CABIMER), Universidad de Sevilla-CSIC-Universidad Pablo de Olavide-Junta de Andalucía, Sevilla, Spain.
- Departamento de Biología Celular, Facultad de Biología, Universidad de Sevilla, Sevilla, Spain.
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6
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Bhachoo JS, Garvin AJ. SUMO and the DNA damage response. Biochem Soc Trans 2024; 52:773-792. [PMID: 38629643 PMCID: PMC11088926 DOI: 10.1042/bst20230862] [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: 12/08/2023] [Revised: 03/20/2024] [Accepted: 03/25/2024] [Indexed: 04/25/2024]
Abstract
The preservation of genome integrity requires specialised DNA damage repair (DDR) signalling pathways to respond to each type of DNA damage. A key feature of DDR is the integration of numerous post-translational modification signals with DNA repair factors. These modifications influence DDR factor recruitment to damaged DNA, activity, protein-protein interactions, and ultimately eviction to enable access for subsequent repair factors or termination of DDR signalling. SUMO1-3 (small ubiquitin-like modifier 1-3) conjugation has gained much recent attention. The SUMO-modified proteome is enriched with DNA repair factors. Here we provide a snapshot of our current understanding of how SUMO signalling impacts the major DNA repair pathways in mammalian cells. We highlight repeating themes of SUMO signalling used throughout DNA repair pathways including the assembly of protein complexes, competition with ubiquitin to promote DDR factor stability and ubiquitin-dependent degradation or extraction of SUMOylated DDR factors. As SUMO 'addiction' in cancer cells is protective to genomic integrity, targeting components of the SUMO machinery to potentiate DNA damaging therapy or exacerbate existing DNA repair defects is a promising area of study.
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Affiliation(s)
- Jai S. Bhachoo
- SUMO Biology Lab, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, West Yorkshire LS2 9JT, U.K
| | - Alexander J. Garvin
- SUMO Biology Lab, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, West Yorkshire LS2 9JT, U.K
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7
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Liu JCY, Ackermann L, Hoffmann S, Gál Z, Hendriks IA, Jain C, Morlot L, Tatham MH, McLelland GL, Hay RT, Nielsen ML, Brummelkamp T, Haahr P, Mailand N. Concerted SUMO-targeted ubiquitin ligase activities of TOPORS and RNF4 are essential for stress management and cell proliferation. Nat Struct Mol Biol 2024:10.1038/s41594-024-01294-7. [PMID: 38649616 DOI: 10.1038/s41594-024-01294-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 03/26/2024] [Indexed: 04/25/2024]
Abstract
Protein SUMOylation provides a principal driving force for cellular stress responses, including DNA-protein crosslink (DPC) repair and arsenic-induced PML body degradation. In this study, using genome-scale screens, we identified the human E3 ligase TOPORS as a key effector of SUMO-dependent DPC resolution. We demonstrate that TOPORS promotes DPC repair by functioning as a SUMO-targeted ubiquitin ligase (STUbL), combining ubiquitin ligase activity through its RING domain with poly-SUMO binding via SUMO-interacting motifs, analogous to the STUbL RNF4. Mechanistically, TOPORS is a SUMO1-selective STUbL that complements RNF4 in generating complex ubiquitin landscapes on SUMOylated targets, including DPCs and PML, stimulating efficient p97/VCP unfoldase recruitment and proteasomal degradation. Combined loss of TOPORS and RNF4 is synthetic lethal even in unstressed cells, involving defective clearance of SUMOylated proteins from chromatin accompanied by cell cycle arrest and apoptosis. Our findings establish TOPORS as a STUbL whose parallel action with RNF4 defines a general mechanistic principle in crucial cellular processes governed by direct SUMO-ubiquitin crosstalk.
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Affiliation(s)
- Julio C Y Liu
- Protein Signaling Program, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Leena Ackermann
- Protein Signaling Program, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Saskia Hoffmann
- Protein Signaling Program, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Zita Gál
- Protein Signaling Program, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Ivo A Hendriks
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Charu Jain
- Protein Signaling Program, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Louise Morlot
- Protein Signaling Program, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Michael H Tatham
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, UK
| | - Gian-Luca McLelland
- Division of Biochemistry, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Ronald T Hay
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, UK
| | - Michael Lund Nielsen
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Thijn Brummelkamp
- Division of Biochemistry, The Netherlands Cancer Institute, Amsterdam, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
| | - Peter Haahr
- Division of Biochemistry, The Netherlands Cancer Institute, Amsterdam, The Netherlands.
- Department of Cellular and Molecular Medicine, Center for Gene Expression, University of Copenhagen, Copenhagen, Denmark.
| | - Niels Mailand
- Protein Signaling Program, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark.
- Department of Cellular and Molecular Medicine, Center for Chromosome Stability, University of Copenhagen, Copenhagen, Denmark.
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8
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Lachiondo-Ortega S, Rejano-Gordillo CM, Simon J, Lopitz-Otsoa F, C Delgado T, Mazan-Mamczarz K, Goikoetxea-Usandizaga N, Zapata-Pavas LE, García-Del Río A, Guerra P, Peña-Sanfélix P, Hermán-Sánchez N, Al-Abdulla R, Fernandez-Rodríguez C, Azkargorta M, Velázquez-Cruz A, Guyon J, Martín C, Zalamea JD, Egia-Mendikute L, Sanz-Parra A, Serrano-Maciá M, González-Recio I, Gonzalez-Lopez M, Martínez-Cruz LA, Pontisso P, Aransay AM, Barrio R, Sutherland JD, Abrescia NGA, Elortza F, Lujambio A, Banales JM, Luque RM, Gahete MD, Palazón A, Avila MA, G Marin JJ, De S, Daubon T, Díaz-Quintana A, Díaz-Moreno I, Gorospe M, Rodríguez MS, Martínez-Chantar ML. SUMOylation controls Hu antigen R posttranscriptional activity in liver cancer. Cell Rep 2024; 43:113924. [PMID: 38507413 PMCID: PMC11025316 DOI: 10.1016/j.celrep.2024.113924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 08/08/2023] [Accepted: 02/21/2024] [Indexed: 03/22/2024] Open
Abstract
The posttranslational modification of proteins critically influences many biological processes and is a key mechanism that regulates the function of the RNA-binding protein Hu antigen R (HuR), a hub in liver cancer. Here, we show that HuR is SUMOylated in the tumor sections of patients with hepatocellular carcinoma in contrast to the surrounding tissue, as well as in human cell line and mouse models of the disease. SUMOylation of HuR promotes major cancer hallmarks, namely proliferation and invasion, whereas the absence of HuR SUMOylation results in a senescent phenotype with dysfunctional mitochondria and endoplasmic reticulum. Mechanistically, SUMOylation induces a structural rearrangement of the RNA recognition motifs that modulates HuR binding affinity to its target RNAs, further modifying the transcriptomic profile toward hepatic tumor progression. Overall, SUMOylation constitutes a mechanism of HuR regulation that could be potentially exploited as a therapeutic strategy for liver cancer.
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Affiliation(s)
- Sofia Lachiondo-Ortega
- Liver Disease Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), 48160 Derio, Bizkaia, Spain
| | - Claudia M Rejano-Gordillo
- Liver Disease Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), 48160 Derio, Bizkaia, Spain; Department of Biochemistry and Molecular Biology, Faculty of Sciences, University of Extremadura, University Institute of Biosanitary Research of Extremadura (INUBE), 06071 Badajoz, Spain; Biofisika Institute, Consejo Superior de Investigaciones Científicas (CSIC), Departamento Bioquímica y Biología Molecular, Facultad de Ciencia y Tecnología, Universidad del País Vasco (UPV/EHU), Leioa, Spain
| | - Jorge Simon
- Liver Disease Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), 48160 Derio, Bizkaia, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Carlos III National Health Institute, Madrid, Spain
| | - Fernando Lopitz-Otsoa
- Liver Disease Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), 48160 Derio, Bizkaia, Spain
| | - Teresa C Delgado
- Liver Disease Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), 48160 Derio, Bizkaia, Spain
| | - Krystyna Mazan-Mamczarz
- Laboratory of Genetics and Genomics, National Institute on Aging (NIA), Intramural Research Program (IRP), National Institutes of Health (NIH), Baltimore, MD, USA
| | - Naroa Goikoetxea-Usandizaga
- Liver Disease Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), 48160 Derio, Bizkaia, Spain
| | - L Estefanía Zapata-Pavas
- Liver Disease Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), 48160 Derio, Bizkaia, Spain
| | - Ana García-Del Río
- Cancer Immunology and Immunotherapy Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), 48160 Derio, Bizkaia, Spain
| | - Pietro Guerra
- Unit of Internal Medicine and Hepatology (UIMH), Department of Medicine (DIMED), University of Padova, 35128 Padua, Italy
| | - Patricia Peña-Sanfélix
- Liver Disease Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), 48160 Derio, Bizkaia, Spain
| | - Natalia Hermán-Sánchez
- Maimónides Institute of Biomedical Research of Córdoba (IMIBIC), Department of Cell Biology, Physiology and Immunology of University of Córdoba, Reina Sofia University Hospital, CIBER Pathophysiology of Obesity and Nutrition (CIBERobn), 14004 Córdoba, Spain
| | - Ruba Al-Abdulla
- Instituto de Investigación, Desarrollo e Innovación en Biotecnología Sanitaria de Elche (IDiBE), Universidad Miguel Hernández, Elche, Spain; Institute of Medical Biochemistry and Molecular Biology, University Medicine of Greifswald, 17475 Greifswald, Germany
| | - Carmen Fernandez-Rodríguez
- Liver Disease Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), 48160 Derio, Bizkaia, Spain
| | - Mikel Azkargorta
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Carlos III National Health Institute, Madrid, Spain; Proteomics Platform, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Carlos III Networked Proteomics Platform (ProteoRed-ISCIII), 48160 Derio, Bizkaia, Spain
| | - Alejandro Velázquez-Cruz
- Instituto de Investigaciones Químicas (IIQ), Centro de Investigaciones Científicas Isla de la Cartuja (cicCartuja), Universidad de Sevilla, Consejo Superior de Investigaciones Científicas (CSIC), Sevilla, Spain
| | - Joris Guyon
- University of Bordeaux, INSERM, BPH, U1219, 33000 Bordeaux, France; CHU de Bordeaux, Service de Pharmacologie Médicale, 33000 Bordeaux, France
| | - César Martín
- Biofisika Institute, Consejo Superior de Investigaciones Científicas (CSIC), Departamento Bioquímica y Biología Molecular, Facultad de Ciencia y Tecnología, Universidad del País Vasco (UPV/EHU), Leioa, Spain
| | - Juan Diego Zalamea
- Structure and Cell Biology of Viruses Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), 48160 Derio, Bizkaia, Spain
| | - Leire Egia-Mendikute
- Cancer Immunology and Immunotherapy Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), 48160 Derio, Bizkaia, Spain
| | - Arantza Sanz-Parra
- Liver Disease Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), 48160 Derio, Bizkaia, Spain
| | - Marina Serrano-Maciá
- Liver Disease Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), 48160 Derio, Bizkaia, Spain
| | - Irene González-Recio
- Liver Disease Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), 48160 Derio, Bizkaia, Spain
| | - Monika Gonzalez-Lopez
- Genome Analysis Platform, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), 48160 Derio, Bizkaia, Spain
| | - Luis Alfonso Martínez-Cruz
- Liver Disease Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), 48160 Derio, Bizkaia, Spain
| | - Patrizia Pontisso
- Unit of Internal Medicine and Hepatology (UIMH), Department of Medicine (DIMED), University of Padova, 35128 Padua, Italy
| | - Ana M Aransay
- Genome Analysis Platform, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), 48160 Derio, Bizkaia, Spain
| | - Rosa Barrio
- Ubiquitin-likes and Development Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), 48160 Derio, Bizkaia, Spain
| | - James D Sutherland
- Ubiquitin-likes and Development Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), 48160 Derio, Bizkaia, Spain
| | - Nicola G A Abrescia
- Structure and Cell Biology of Viruses Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), 48160 Derio, Bizkaia, Spain; Ikerbasque, Basque Foundation for Science, Bilbao, Spain
| | - Félix Elortza
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Carlos III National Health Institute, Madrid, Spain; Proteomics Platform, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Carlos III Networked Proteomics Platform (ProteoRed-ISCIII), 48160 Derio, Bizkaia, Spain
| | - Amaia Lujambio
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Liver Cancer Program, Division of Liver Diseases, Department of Medicine, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Graduate School of Biomedical Sciences at Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jesus M Banales
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Carlos III National Health Institute, Madrid, Spain; Ikerbasque, Basque Foundation for Science, Bilbao, Spain; Department of Liver and Gastrointestinal Diseases, Biodonostia Health Research Institute, Donostia University Hospital, San Sebastian, Spain; Department of Biochemistry and Genetics, School of Sciences, University of Navarra, Pamplona, Spain
| | - Raúl M Luque
- Maimónides Institute of Biomedical Research of Córdoba (IMIBIC), Department of Cell Biology, Physiology and Immunology of University of Córdoba, Reina Sofia University Hospital, CIBER Pathophysiology of Obesity and Nutrition (CIBERobn), 14004 Córdoba, Spain
| | - Manuel D Gahete
- Maimónides Institute of Biomedical Research of Córdoba (IMIBIC), Department of Cell Biology, Physiology and Immunology of University of Córdoba, Reina Sofia University Hospital, CIBER Pathophysiology of Obesity and Nutrition (CIBERobn), 14004 Córdoba, Spain
| | - Asís Palazón
- Cancer Immunology and Immunotherapy Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), 48160 Derio, Bizkaia, Spain; Ikerbasque, Basque Foundation for Science, Bilbao, Spain
| | - Matias A Avila
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Carlos III National Health Institute, Madrid, Spain; Hepatology Program, Centro de Investigación Médica Aplicada (CIMA), University of Navarra, Pamplona, Spain; Instituto de Investigaciones Sanitarias de Navarra (IdiSNA), Pamplona, Spain
| | - Jose J G Marin
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Carlos III National Health Institute, Madrid, Spain; Experimental Hepatology and Drug Targeting (HEVEPHARM), Instituto de Investigación Biomédica de Salamanca (IBSAL), University of Salamanca, Salamanca, Spain
| | - Supriyo De
- Laboratory of Genetics and Genomics, National Institute on Aging (NIA), Intramural Research Program (IRP), National Institutes of Health (NIH), Baltimore, MD, USA
| | - Thomas Daubon
- University of Bordeaux, CNRS, IBGC, UMR 5095, Bordeaux, France
| | - Antonio Díaz-Quintana
- Instituto de Investigaciones Químicas (IIQ), Centro de Investigaciones Científicas Isla de la Cartuja (cicCartuja), Universidad de Sevilla, Consejo Superior de Investigaciones Científicas (CSIC), Sevilla, Spain
| | - Irene Díaz-Moreno
- Instituto de Investigaciones Químicas (IIQ), Centro de Investigaciones Científicas Isla de la Cartuja (cicCartuja), Universidad de Sevilla, Consejo Superior de Investigaciones Científicas (CSIC), Sevilla, Spain
| | - Myriam Gorospe
- Laboratory of Genetics and Genomics, National Institute on Aging (NIA), Intramural Research Program (IRP), National Institutes of Health (NIH), Baltimore, MD, USA
| | - Manuel S Rodríguez
- Laboratoire de Chimie de Coordination (LCC), UPR 8241, CNRS; IPBS-University of Toulouse III-Paul Sabatier, Toulouse, France
| | - María Luz Martínez-Chantar
- Liver Disease Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), 48160 Derio, Bizkaia, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Carlos III National Health Institute, Madrid, Spain.
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9
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Campos Alonso M, Knobeloch KP. In the moonlight: non-catalytic functions of ubiquitin and ubiquitin-like proteases. Front Mol Biosci 2024; 11:1349509. [PMID: 38455765 PMCID: PMC10919355 DOI: 10.3389/fmolb.2024.1349509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 02/05/2024] [Indexed: 03/09/2024] Open
Abstract
Proteases that cleave ubiquitin or ubiquitin-like proteins (UBLs) are critical players in maintaining the homeostasis of the organism. Concordantly, their dysregulation has been directly linked to various diseases, including cancer, neurodegeneration, developmental aberrations, cardiac disorders and inflammation. Given their potential as novel therapeutic targets, it is essential to fully understand their mechanisms of action. Traditionally, observed effects resulting from deficiencies in deubiquitinases (DUBs) and UBL proteases have often been attributed to the misregulation of substrate modification by ubiquitin or UBLs. Therefore, much research has focused on understanding the catalytic activities of these proteins. However, this view has overlooked the possibility that DUBs and UBL proteases might also have significant non-catalytic functions, which are more prevalent than previously believed and urgently require further investigation. Moreover, multiple examples have shown that either selective loss of only the protease activity or complete absence of these proteins can have different functional and physiological consequences. Furthermore, DUBs and UBL proteases have been shown to often contain domains or binding motifs that not only modulate their catalytic activity but can also mediate entirely different functions. This review aims to shed light on the non-catalytic, moonlighting functions of DUBs and UBL proteases, which extend beyond the hydrolysis of ubiquitin and UBL chains and are just beginning to emerge.
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Affiliation(s)
- Marta Campos Alonso
- Institute of Neuropathology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Klaus-Peter Knobeloch
- Institute of Neuropathology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- CIBSS—Centre for Integrative Biological Signalling Studies, University of Freiburg, Freiburg, Germany
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10
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Hammami NEH, Mérindol N, Plourde MB, Maisonnet T, Lebel S, Berthoux L. SUMO-3 promotes the ubiquitin-dependent turnover of TRIM55. Biochem Cell Biol 2024; 102:73-84. [PMID: 37703582 DOI: 10.1139/bcb-2023-0153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/15/2023] Open
Abstract
Human muscle-specific RING fingers (MURFs) are members of the tripartite motif (TRIM) family of proteins characterized by their C-terminal subgroup one signature domain. MURFs play a role in sarcomere formation and microtubule dynamics. It was previously established that some TRIMs undergo post-translational modification by small ubiquitin-like modifier (SUMO). In this study, we explored the putative SUMOylation of MURF proteins as well as their interactions with SUMO. MURF proteins (TRIM54, TRIM55, and TRIM63) were not found to be SUMOylated. However, TRIM55 turnover by proteasomal and lysosomal degradation was higher upon overexpression of SUMO-3 but not of SUMO-1. Furthermore, it is predicted that TRIM55 contains two potential SUMO-interacting motifs (SIMs). We found that SIM1- and SIM2-mutated TRIM55 were more stable than the wild-type (WT) protein partly due to decreased degradation. Consistently, SIM-mutated TRIM55 was less polyubiquitinated than the WT protein, despite similar monoubiquitination levels. Using IF microscopy, we observed that SIM motifs influenced TRIM55 subcellular localization. In conclusion, our results suggest that SUMO-3 or SUMO-3-modified proteins modulate the localization, stability, and RING ubiquitin ligase activity of TRIM55.
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Affiliation(s)
- Nour-El-Houda Hammami
- Department of medical biology, Université du Québec à Trois-Rivières, Trois-Rivières, QC, Canada
| | - Natacha Mérindol
- Department of medical biology, Université du Québec à Trois-Rivières, Trois-Rivières, QC, Canada
| | - Mélodie B Plourde
- Department of medical biology, Université du Québec à Trois-Rivières, Trois-Rivières, QC, Canada
| | - Tara Maisonnet
- Department of medical biology, Université du Québec à Trois-Rivières, Trois-Rivières, QC, Canada
| | - Sophie Lebel
- Department of medical biology, Université du Québec à Trois-Rivières, Trois-Rivières, QC, Canada
| | - Lionel Berthoux
- Department of medical biology, Université du Québec à Trois-Rivières, Trois-Rivières, QC, Canada
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11
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Fernandez A, Corvalan K, Santis O, Mendez-Ruette M, Caviedes A, Pizarro M, Gomez MT, Batiz LF, Landgraf P, Kahne T, Rojas-Fernandez A, Wyneken U. Sumoylation in astrocytes induces changes in the proteome of the derived small extracellular vesicles which change protein synthesis and dendrite morphology in target neurons. Brain Res 2024; 1823:148679. [PMID: 37972846 DOI: 10.1016/j.brainres.2023.148679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 11/01/2023] [Accepted: 11/13/2023] [Indexed: 11/19/2023]
Abstract
Emerging evidence highlights the relevance of the protein post-translational modification by SUMO (Small Ubiquitin-like Modifier) in the central nervous system for modulating cognition and plasticity in health and disease. In these processes, astrocyte-to-neuron crosstalk mediated by extracellular vesicles (EVs) plays a yet poorly understood role. Small EVs (sEVs), including microvesicles and exosomes, contain a molecular cargo of lipids, proteins, and nucleic acids that define their biological effect on target cells. Here, we investigated whether SUMOylation globally impacts the sEV protein cargo. For this, sEVs were isolated from primary cultures of astrocytes by ultracentrifugation or using a commercial sEV isolation kit. SUMO levels were regulated: 1) via plasmids that over-express SUMO, or 2) via experimental conditions that increase SUMOylation, i.e., by using the stress hormone corticosterone, or 3) via the SUMOylation inhibitor 2-D08 (2',3',4'-trihydroxy-flavone, 2-(2,3,4-Trihydroxyphenyl)-4H-1-Benzopyran-4-one). Corticosterone and 2-D08 had opposing effects on the number of sEVs and on their protein cargo. Proteomic analysis showed that increased SUMOylation in corticosterone-treated or plasmid-transfected astrocytes increased the presence of proteins related to cell division, transcription, and protein translation in the derived sEVs. When sEVs derived from corticosterone-treated astrocytes were transferred to neurons to assess their impact on protein synthesis using the fluorescence non-canonical amino acid tagging assay (FUNCAT), we detected an increase in protein synthesis, while sEVs from 2-D08-treated astrocytes had no effect. Our results show that SUMO conjugation plays an important role in the modulation of the proteome of astrocyte-derived sEVs with a potential functional impact on neurons.
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Affiliation(s)
- Anllely Fernandez
- Centro de Investigación e Innovación Biomédica (CIIB), Facultad de Medicina, Universidad de los Andes, Santiago 7620001, Chile
| | - Katherine Corvalan
- Centro de Investigación e Innovación Biomédica (CIIB), Facultad de Medicina, Universidad de los Andes, Santiago 7620001, Chile
| | - Octavia Santis
- Centro de Investigación e Innovación Biomédica (CIIB), Facultad de Medicina, Universidad de los Andes, Santiago 7620001, Chile
| | - Maxs Mendez-Ruette
- Centro de Investigación e Innovación Biomédica (CIIB), Facultad de Medicina, Universidad de los Andes, Santiago 7620001, Chile
| | - Ariel Caviedes
- Centro de Investigación e Innovación Biomédica (CIIB), Facultad de Medicina, Universidad de los Andes, Santiago 7620001, Chile
| | - Matias Pizarro
- Centro de Investigación e Innovación Biomédica (CIIB), Facultad de Medicina, Universidad de los Andes, Santiago 7620001, Chile
| | - Maria-Teresa Gomez
- Centro de Investigación e Innovación Biomédica (CIIB), Facultad de Medicina, Universidad de los Andes, Santiago 7620001, Chile
| | - Luis Federico Batiz
- Centro de Investigación e Innovación Biomédica (CIIB), Facultad de Medicina, Universidad de los Andes, Santiago 7620001, Chile
| | - Peter Landgraf
- Institute for Pharmacology and Toxicology, Medical Faculty, Otto-von-Guericke University, Germany, 39120 Magdeburg, Germany
| | - Thilo Kahne
- Institute of Experimental Internal Medicine, Medical Faculty, Otto-von-Guericke University, 39120 Magdeburg, Germany
| | - Alejandro Rojas-Fernandez
- Instituto de Medicina & Centro Interdisciplinario de Estudios del Sistema Nervioso (CISNe), Universidad Austral de Chile, Valdivia 5110566, Chile
| | - Ursula Wyneken
- Centro de Investigación e Innovación Biomédica (CIIB), Facultad de Medicina, Universidad de los Andes, Santiago 7620001, Chile; IMPACT, Center of Interventional Medicine for Precision and Advanced Cellular Therapy, Santiago 7620001, Chile.
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12
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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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13
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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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14
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D’Alessandro G, Morales-Juarez DA, Richards SL, Nitiss KC, Serrano-Benitez A, Wang J, Thomas JC, Gupta V, Voigt A, Belotserkovskaya R, Goh CG, Bowden AR, Galanty Y, Beli P, Nitiss JL, Zagnoli-Vieira G, Jackson SP. RAD54L2 counters TOP2-DNA adducts to promote genome stability. SCIENCE ADVANCES 2023; 9:eadl2108. [PMID: 38055822 PMCID: PMC10699776 DOI: 10.1126/sciadv.adl2108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 11/07/2023] [Indexed: 12/08/2023]
Abstract
The catalytic cycle of topoisomerase 2 (TOP2) enzymes proceeds via a transient DNA double-strand break (DSB) intermediate termed the TOP2 cleavage complex (TOP2cc), in which the TOP2 protein is covalently bound to DNA. Anticancer agents such as etoposide operate by stabilizing TOP2ccs, ultimately generating genotoxic TOP2-DNA protein cross-links that require processing and repair. Here, we identify RAD54 like 2 (RAD54L2) as a factor promoting TOP2cc resolution. We demonstrate that RAD54L2 acts through a novel mechanism together with zinc finger protein associated with tyrosyl-DNA phosphodiesterase 2 (TDP2) and TOP2 (ZATT/ZNF451) and independent of TDP2. Our work suggests a model wherein RAD54L2 recognizes sumoylated TOP2 and, using its ATPase activity, promotes TOP2cc resolution and prevents DSB exposure. These findings suggest RAD54L2-mediated TOP2cc resolution as a potential mechanism for cancer therapy resistance and highlight RAD54L2 as an attractive candidate for drug discovery.
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Affiliation(s)
- Giuseppina D’Alessandro
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | | | - Sean L. Richards
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | | | - Almudena Serrano-Benitez
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Juanjuan Wang
- Institute of Molecular Biology (IMB), Chromatin Biology & Proteomics, Mainz, Germany
| | - John C. Thomas
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Vipul Gupta
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Andrea Voigt
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Rimma Belotserkovskaya
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Chen Gang Goh
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Anne Ramsay Bowden
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Yaron Galanty
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Petra Beli
- Institute of Molecular Biology (IMB), Chromatin Biology & Proteomics, Mainz, Germany
- Institute of Developmental Biology and Neurobiology (IDN), Johannes Gutenberg-Universität, Mainz, Germany
| | | | - Guido Zagnoli-Vieira
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Stephen P. Jackson
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
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15
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Zhang H, Xiong Y, Sun Y, Park JM, Su D, Feng X, Keast S, Tang M, Huang M, Wang C, Srivastava M, Yang C, Zhu D, Chen Z, Li S, Yin L, Pommier Y, Chen J. RAD54L2-mediated DNA damage avoidance pathway specifically preserves genome integrity in response to topoisomerase 2 poisons. SCIENCE ADVANCES 2023; 9:eadi6681. [PMID: 38055811 PMCID: PMC10699775 DOI: 10.1126/sciadv.adi6681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 11/07/2023] [Indexed: 12/08/2023]
Abstract
Type II topoisomerases (TOP2) form transient TOP2 cleavage complexes (TOP2ccs) during their catalytic cycle to relieve topological stress. TOP2ccs are covalently linked TOP2-DNA intermediates that are reversible but can be trapped by TOP2 poisons. Trapped TOP2ccs block transactions on DNA and generate genotoxic stress, which are the mechanisms of action of TOP2 poisons. How cells avoid TOP2cc accumulation remains largely unknown. In this study, we uncovered RAD54 like 2 (RAD54L2) as a key factor that mediates a TOP2-specific DNA damage avoidance pathway. RAD54L2 deficiency conferred unique sensitivity to treatment with TOP2 poisons. RAD54L2 interacted with TOP2A/TOP2B and ZATT/ZNF451 and promoted the turnover of TOP2 from DNA with or without TOP2 poisons. Additionally, inhibition of proteasome activity enhanced the chromatin binding of RAD54L2, which in turn led to the removal of TOP2 from chromatin. In conclusion, we propose that RAD54L2-mediated TOP2 turnover is critically important for the avoidance of potential TOP2-linked DNA damage under physiological conditions and in response to TOP2 poisons.
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Affiliation(s)
- Huimin Zhang
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Yun Xiong
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Yilun Sun
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, NCI, NIH, Bethesda, MD 20892, USA
| | - Jeong-Min Park
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Dan Su
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Xu Feng
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Sarah Keast
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Mengfan Tang
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Min Huang
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Chao Wang
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Mrinal Srivastava
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Chang Yang
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Dandan Zhu
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Zhen Chen
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Siting Li
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Ling Yin
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Yves Pommier
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, NCI, NIH, Bethesda, MD 20892, USA
| | - Junjie Chen
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
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16
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Claessens LA, Verlaan-de Vries M, de Graaf IJ, Vertegaal ACO. SENP6 regulates localization and nuclear condensation of DNA damage response proteins by group deSUMOylation. Nat Commun 2023; 14:5893. [PMID: 37735495 PMCID: PMC10514054 DOI: 10.1038/s41467-023-41623-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 09/12/2023] [Indexed: 09/23/2023] Open
Abstract
The SUMO protease SENP6 maintains genomic stability, but mechanistic understanding of this process remains limited. We find that SENP6 deconjugates SUMO2/3 polymers on a group of DNA damage response proteins, including BRCA1-BARD1, 53BP1, BLM and ERCC1-XPF. SENP6 maintains these proteins in a hypo-SUMOylated state under unstressed conditions and counteracts their polySUMOylation after hydroxyurea-induced stress. Co-depletion of RNF4 leads to a further increase in SUMOylation of BRCA1, BARD1 and BLM, suggesting that SENP6 antagonizes targeting of these proteins by RNF4. Functionally, depletion of SENP6 results in uncoordinated recruitment and persistence of SUMO2/3 at UVA laser and ionizing radiation induced DNA damage sites. Additionally, SUMO2/3 and DNA damage response proteins accumulate in nuclear bodies, in a PML-independent manner driven by multivalent SUMO-SIM interactions. These data illustrate coordinated regulation of SUMOylated DNA damage response proteins by SENP6, governing their timely localization at DNA damage sites and nuclear condensation state.
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Affiliation(s)
- Laura A Claessens
- Cell and Chemical Biology, Leiden University Medical Centre, Leiden, The Netherlands
| | | | - Ilona J de Graaf
- Cell and Chemical Biology, Leiden University Medical Centre, Leiden, The Netherlands
| | - Alfred C O Vertegaal
- Cell and Chemical Biology, Leiden University Medical Centre, Leiden, The Netherlands.
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17
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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: 2] [Impact Index Per Article: 2.0] [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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18
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Salas-Lloret D, Jansen NS, Nagamalleswari E, van der Meulen C, Gracheva E, de Ru AH, Otte HAM, van Veelen PA, Pichler A, Goedhart J, Vertegaal AC, González-Prieto R. SUMO-activated target traps (SATTs) enable the identification of a comprehensive E3-specific SUMO proteome. SCIENCE ADVANCES 2023; 9:eadh2073. [PMID: 37531430 PMCID: PMC10396300 DOI: 10.1126/sciadv.adh2073] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 06/28/2023] [Indexed: 08/04/2023]
Abstract
Ubiquitin and ubiquitin-like conjugation cascades consist of dedicated E1, E2, and E3 enzymes with E3s providing substrate specificity. Mass spectrometry-based approaches have enabled the identification of more than 6500 SUMO2/3 target proteins. The limited number of SUMO E3s provides the unique opportunity to systematically study E3 substrate wiring. We developed SUMO-activated target traps (SATTs) and systematically identified substrates for eight different SUMO E3s, PIAS1, PIAS2, PIAS3, PIAS4, NSMCE2, ZNF451, LAZSUL (ZNF451-3), and ZMIZ2. SATTs enabled us to identify 427 SUMO1 and 961 SUMO2/3 targets in an E3-specific manner. We found pronounced E3 substrate preference. Quantitative proteomics enabled us to measure substrate specificity of E3s, quantified using the SATT index. Furthermore, we developed the Polar SATTs web-based tool to browse the dataset in an interactive manner. Overall, we uncover E3-to-target wiring of 1388 SUMO substrates, highlighting unique and overlapping sets of substrates for eight different SUMO E3 ligases.
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Affiliation(s)
- Daniel Salas-Lloret
- Cell and Chemical Biology, Leiden University Medical Center, Leiden, Netherlands
| | - Nicolette S. Jansen
- Cell and Chemical Biology, Leiden University Medical Center, Leiden, Netherlands
| | | | - Coen van der Meulen
- Cell and Chemical Biology, Leiden University Medical Center, Leiden, Netherlands
| | - Ekaterina Gracheva
- Cell and Chemical Biology, Leiden University Medical Center, Leiden, Netherlands
| | - Arnoud H. de Ru
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, Netherlands
| | - H. Anne Marie Otte
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, Netherlands
| | - Peter A. van Veelen
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, Netherlands
| | - Andrea Pichler
- Max Plank Institute for Immunobiology and Epigenetics, Freiburg, Germany
- Institute of Biochemistry, ETH Zürich, Zürich, Switzerland
| | | | | | - Román González-Prieto
- Cell and Chemical Biology, Leiden University Medical Center, Leiden, Netherlands
- Andalusian Center for Molecular Biology and Regenerative Medicine (CABIMER), Universidad de Sevilla-CSIC-Universidad-Pablo de Olavide, Sevilla, Spain
- Departamento de Biología Celular, Facultad de Biología, Universidad de Sevilla, Sevilla, Spain
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19
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Vu DD, Bonucci A, Brenière M, Cisneros-Aguirre M, Pelupessy P, Wang Z, Carlier L, Bouvignies G, Cortes P, Aggarwal AK, Blackledge M, Gueroui Z, Belle V, Stark JM, Modesti M, Ferrage F. Multivalent interactions of the disordered regions of XLF and XRCC4 foster robust cellular NHEJ and drive the formation of ligation-boosting condensates in vitro. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.12.548668. [PMID: 37503201 PMCID: PMC10369993 DOI: 10.1101/2023.07.12.548668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
In mammalian cells, DNA double-strand breaks are predominantly repaired by non-homologous end joining (NHEJ). During repair, the Ku70/80 heterodimer (Ku), XRCC4 in complex with DNA Ligase 4 (X4L4), and XLF form a flexible scaffold that holds the broken DNA ends together. Insights into the architectural organization of the NHEJ scaffold and its regulation by the DNA-dependent protein kinase catalytic subunit (DNA-PKcs) have recently been obtained by single-particle cryo-electron microscopy analysis. However, several regions, especially the C-terminal regions (CTRs) of the XRCC4 and XLF scaffolding proteins, have largely remained unresolved in experimental structures, which hampers the understanding of their functions. Here, we used magnetic resonance techniques and biochemical assays to comprehensively characterize the interactions and dynamics of the XRCC4 and XLF CTRs at atomic resolution. We show that the CTRs of XRCC4 and XLF are intrinsically disordered and form a network of multivalent heterotypic and homotypic interactions that promotes robust cellular NHEJ activity. Importantly, we demonstrate that the multivalent interactions of these CTRs led to the formation of XLF and X4L4 condensates in vitro which can recruit relevant effectors and critically stimulate DNA end ligation. Our work highlights the role of disordered regions in the mechanism and dynamics of NHEJ and lays the groundwork for the investigation of NHEJ protein disorder and its associated condensates inside cells with implications in cancer biology, immunology and the development of genome editing strategies.
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Affiliation(s)
- Duc-Duy Vu
- Département de Chimie, LBM, CNRS UMR 7203, École Normale Supérieure, PSL University, Sorbonne University, Paris, France
| | - Alessio Bonucci
- Aix Marseille Univ, CNRS UMR 7281, BIP Bioénergétique et Ingénierie des Protéines, IMM, Marseille, France
| | - Manon Brenière
- Cancer Research Center of Marseille, Department of Genome Integrity, CNRS UMR7258, Inserm U1068, Institut Paoli-Calmettes, Aix Marseille Univ, Marseille, France
| | - Metztli Cisneros-Aguirre
- Department of Cancer Genetics and Epigenetics, Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of the City of Hope, 1500 E Duarte Rd., Duarte, CA 91010 USA
| | - Philippe Pelupessy
- Département de Chimie, LBM, CNRS UMR 7203, École Normale Supérieure, PSL University, Sorbonne University, Paris, France
| | - Ziqing Wang
- Département de Chimie, LBM, CNRS UMR 7203, École Normale Supérieure, PSL University, Sorbonne University, Paris, France
| | - Ludovic Carlier
- Département de Chimie, LBM, CNRS UMR 7203, École Normale Supérieure, PSL University, Sorbonne University, Paris, France
| | - Guillaume Bouvignies
- Département de Chimie, LBM, CNRS UMR 7203, École Normale Supérieure, PSL University, Sorbonne University, Paris, France
| | - Patricia Cortes
- Department of Molecular, Cellular and Biomedical Sciences, CUNY School of Medicine at City College of New York, 160 Convent Avenue, New York, NY 10029, USA
| | - Aneel K Aggarwal
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA
| | - Martin Blackledge
- University Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), Grenoble, France
| | - Zoher Gueroui
- PASTEUR, Département de Chimie, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, Paris, France
| | - Valérie Belle
- Aix Marseille Univ, CNRS UMR 7281, BIP Bioénergétique et Ingénierie des Protéines, IMM, Marseille, France
| | - Jeremy M Stark
- Department of Cancer Genetics and Epigenetics, Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of the City of Hope, 1500 E Duarte Rd., Duarte, CA 91010 USA
| | - Mauro Modesti
- Cancer Research Center of Marseille, Department of Genome Integrity, CNRS UMR7258, Inserm U1068, Institut Paoli-Calmettes, Aix Marseille Univ, Marseille, France
| | - Fabien Ferrage
- Département de Chimie, LBM, CNRS UMR 7203, École Normale Supérieure, PSL University, Sorbonne University, Paris, France
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20
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Barroso-Gomila O, Mayor U, Barrio R, Sutherland JD. SUMO-ID: A Strategy for the Identification of SUMO-Dependent Proximal Interactors. Methods Mol Biol 2023; 2602:177-189. [PMID: 36446975 DOI: 10.1007/978-1-0716-2859-1_13] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Posttranslational modifications by the ubiquitin-like family (UbL) of proteins determine the biological fate of a substrate, including new interaction partners. In the case of the small ubiquitin-like modifier (SUMO), this is achieved in part through its non-covalent interaction with SUMO-interacting motifs (SIMs) found in some proteins. Investigating such partner-complex formation is particularly challenging due to the fast dynamics and reversibility of SUMO modifications and the low affinity of SUMO-SIM interactions. Here, we present a detailed protocol of SUMO-ID, a technology that merges promiscuous proximity biotinylation by TurboID enzyme and protein-fragment complementation strategy to specifically biotinylate SUMO-dependent interactors of particular substrates. When coupled to streptavidin-affinity purification and mass spectrometry, SUMO-ID efficiently identifies SUMO-dependent interactors of a given protein. The methodology describes all the steps from SUMO-ID cell line generation to LC-MS sample preparation to study SUMO-dependent interactors of a particular protein. The protocol is generic and therefore adaptable to study other UbL-dependent interactors, such as ubiquitin.
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Affiliation(s)
- Orhi Barroso-Gomila
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Derio, Spain
| | - Ugo Mayor
- Ikerbasque, Basque Foundation for Science, Bilbao, Spain
- Biochemistry and Molecular Biology Department, University of the Basque Country (UPV/EHU), Leioa, Spain
| | - Rosa Barrio
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Derio, Spain.
| | - James D Sutherland
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Derio, Spain.
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21
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Ilic D, Magnussen HM, Tirard M. Stress - Regulation of SUMO conjugation and of other Ubiquitin-Like Modifiers. Semin Cell Dev Biol 2022; 132:38-50. [PMID: 34996712 DOI: 10.1016/j.semcdb.2021.12.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 12/22/2021] [Accepted: 12/23/2021] [Indexed: 12/14/2022]
Abstract
Stress is unavoidable and essential to cellular and organismal evolution and failure to adapt or restore homeostasis can lead to severe diseases or even death. At the cellular level, stress drives a plethora of molecular changes, of which variations in the profile of protein post-translational modifications plays a key role in mediating the adaptative response of the genome and proteome to stress. In this context, post-translational modification of proteins by ubiquitin-like modifiers, (Ubl), notably SUMO, is an essential stress response mechanism. In this review, aiming to draw universal concepts of the Ubls stress response, we will decipher how stress alters the expression level, activity, specificity and/or localization of the proteins involved in the conjugation pathways of the various type-I Ubls, and how this result in the modification of particular Ubl targets that will translate an adaptive physiological stress response and allow cells to restore homeostasis.
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Affiliation(s)
- Dragana Ilic
- Department of Epigenetics, Max Planck Institute of Immunobiology and Epigenetics, D-79108 Freiburg; Faculty of Biology, University of Freiburg, D-79104 Freiburg; Department of Molecular Neurobiology, Max Planck Institute of Experimental Medicine, D-37075 Göttingen
| | - Helge M Magnussen
- MRC Protein Phosphorylation and Ubiquitination Unit, Sir James Black Center, School of Life Sciences, University of Dundee, Dundee, Scotland, UK
| | - Marilyn Tirard
- Department of Molecular Neurobiology, Max Planck Institute of Experimental Medicine, D-37075 Göttingen.
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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: 27] [Impact Index Per Article: 13.5] [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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Site-specific proteomic strategies to identify ubiquitin and SUMO modifications: Challenges and opportunities. Semin Cell Dev Biol 2022; 132:97-108. [PMID: 34802913 DOI: 10.1016/j.semcdb.2021.11.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 11/08/2021] [Accepted: 11/08/2021] [Indexed: 12/14/2022]
Abstract
Ubiquitin and SUMO modify thousands of substrates to regulate most cellular processes. System-wide identification of ubiquitin and SUMO substrates provides global understanding of their cellular functions. In this review, we discuss the biological importance of site-specific modifications by ubiquitin and SUMO regulating the DNA damage response, protein quality control and cell cycle progression. Furthermore we discuss the machinery responsible for these modifications and methods to purify and identify ubiquitin and SUMO modified sites by mass spectrometry. We provide a framework to aid in the selection of appropriate purification, digestion and acquisition strategies suited to answer different biological questions. We highlight opportunities in the field for employing innovative technologies, as well as discuss challenges and long-standing questions in the field that are difficult to address with the currently available tools, emphasizing the need for further innovation.
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24
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Oravcová M, Nie M, Zilio N, Maeda S, Jami-Alahmadi Y, Lazzerini-Denchi E, Wohlschlegel JA, Ulrich HD, Otomo T, Boddy MN. The Nse5/6-like SIMC1-SLF2 complex localizes SMC5/6 to viral replication centers. eLife 2022; 11:e79676. [PMID: 36373674 PMCID: PMC9708086 DOI: 10.7554/elife.79676] [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: 04/22/2022] [Accepted: 11/09/2022] [Indexed: 11/16/2022] Open
Abstract
The human SMC5/6 complex is a conserved guardian of genome stability and an emerging component of antiviral responses. These disparate functions likely require distinct mechanisms of SMC5/6 regulation. In yeast, Smc5/6 is regulated by its Nse5/6 subunits, but such regulatory subunits for human SMC5/6 are poorly defined. Here, we identify a novel SMC5/6 subunit called SIMC1 that contains SUMO interacting motifs (SIMs) and an Nse5-like domain. We isolated SIMC1 from the proteomic environment of SMC5/6 within polyomavirus large T antigen (LT)-induced subnuclear compartments. SIMC1 uses its SIMs and Nse5-like domain to localize SMC5/6 to polyomavirus replication centers (PyVRCs) at SUMO-rich PML nuclear bodies. SIMC1's Nse5-like domain binds to the putative Nse6 orthologue SLF2 to form an anti-parallel helical dimer resembling the yeast Nse5/6 structure. SIMC1-SLF2 structure-based mutagenesis defines a conserved surface region containing the N-terminus of SIMC1's helical domain that regulates SMC5/6 localization to PyVRCs. Furthermore, SLF1, which recruits SMC5/6 to DNA lesions via its BRCT and ARD motifs, binds SLF2 analogously to SIMC1 and forms a separate Nse5/6-like complex. Thus, two Nse5/6-like complexes with distinct recruitment domains control human SMC5/6 localization.
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Affiliation(s)
- Martina Oravcová
- Department of Molecular Medicine, The Scripps Research InstituteLa JollaUnited States
| | - Minghua Nie
- Department of Molecular Medicine, The Scripps Research InstituteLa JollaUnited States
| | | | - Shintaro Maeda
- Department of Integrative Structural and Computational Biology, The Scripps Research InstituteLa JollaUnited States
| | - Yasaman Jami-Alahmadi
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los AngelesLos AngelesUnited States
| | | | - James A Wohlschlegel
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los AngelesLos AngelesUnited States
| | | | - Takanori Otomo
- Department of Integrative Structural and Computational Biology, The Scripps Research InstituteLa JollaUnited States
- San Diego Biomedical Research InstituteSan DiegoUnited States
| | - Michael N Boddy
- Department of Molecular Medicine, The Scripps Research InstituteLa JollaUnited States
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25
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James Sanford E, Bustamante Smolka M. A field guide to the proteomics of post-translational modifications in DNA repair. Proteomics 2022; 22:e2200064. [PMID: 35695711 PMCID: PMC9950963 DOI: 10.1002/pmic.202200064] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 05/19/2022] [Accepted: 05/30/2022] [Indexed: 12/15/2022]
Abstract
All cells incur DNA damage from exogenous and endogenous sources and possess pathways to detect and repair DNA damage. Post-translational modifications (PTMs), in the past 20 years, have risen to ineluctable importance in the study of the regulation of DNA repair mechanisms. For example, DNA damage response kinases are critical in both the initial sensing of DNA damage as well as in orchestrating downstream activities of DNA repair factors. Mass spectrometry-based proteomics revolutionized the study of the role of PTMs in the DNA damage response and has canonized PTMs as central modulators of nearly all aspects of DNA damage signaling and repair. This review provides a biologist-friendly guide for the mass spectrometry analysis of PTMs in the context of DNA repair and DNA damage responses. We reflect on the current state of proteomics for exploring new mechanisms of PTM-based regulation and outline a roadmap for designing PTM mapping experiments that focus on the DNA repair and DNA damage responses.
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Key Words
- LC-MS/MS, technology, bottom-up proteomics, technology, signal transduction, cell biology
- phosphoproteomics, technology, post-translational modification analysis, technology, post-translational modifications, cell biology, mass spectrometry
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Affiliation(s)
- Ethan James Sanford
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853
| | - Marcus Bustamante Smolka
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853,Corresponding author:
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26
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Vertegaal ACO. Signalling mechanisms and cellular functions of SUMO. Nat Rev Mol Cell Biol 2022; 23:715-731. [PMID: 35750927 DOI: 10.1038/s41580-022-00500-y] [Citation(s) in RCA: 103] [Impact Index Per Article: 51.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/23/2022] [Indexed: 12/22/2022]
Abstract
Sumoylation is an essential post-translational modification that is catalysed by a small number of modifying enzymes but regulates thousands of target proteins in a dynamic manner. Small ubiquitin-like modifiers (SUMOs) can be attached to target proteins as one or more monomers or in the form of polymers of different types. Non-covalent readers recognize SUMO-modified proteins via SUMO interaction motifs. SUMO simultaneously modifies groups of functionally related proteins to regulate predominantly nuclear processes, including gene expression, the DNA damage response, RNA processing, cell cycle progression and proteostasis. Recent progress has increased our understanding of the cellular and pathophysiological roles of SUMO modifications, extending their functions to the regulation of immunity, pluripotency and nuclear body assembly in response to oxidative stress, which partly occurs through the recently characterized mechanism of liquid-liquid phase separation. Such progress in understanding the roles and regulation of sumoylation opens new avenues for the targeting of SUMO to treat disease, and indeed the first drug blocking sumoylation is currently under investigation in clinical trials as a possible anticancer agent.
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Affiliation(s)
- Alfred C O Vertegaal
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, Netherlands.
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27
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Oliveira FRMB, Soares ES, Harms C, Cimarosti HI, Sordi R. SUMOylation in peripheral tissues under low perfusion-related pathological states. J Cell Biochem 2022; 123:1133-1147. [PMID: 35652521 DOI: 10.1002/jcb.30293] [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: 12/08/2021] [Revised: 05/12/2022] [Accepted: 05/18/2022] [Indexed: 11/06/2022]
Abstract
SUMOylation is described as a posttranslational protein modification (PTM) that is involved in the pathophysiological processes underlying several conditions related to ischemia- and reperfusion-induced damage. Increasing evidence suggests that, under low oxygen levels, SUMOylation might be part of an endogenous mechanism, which is triggered by injury to protect cells within the central nervous system. However, the role of ischemia-induced SUMOylation in the periphery is still unclear. This article summarizes the results of recent studies regarding SUMOylation profiles in several diseases characterized by impaired blood flow to the cardiorenal, gastrointestinal, and respiratory systems. Our review shows that although ischemic injury per se does not always increase SUMOylation levels, as seen in strokes, it seems that in most cases the positive modulation of protein SUMOylation after peripheral ischemia might be a protective mechanism. This complex relationship warrants further investigation, as the role of SUMOylation during hypoxic conditions differs from organ to organ and is still not fully elucidated.
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Affiliation(s)
- Filipe R M B Oliveira
- Department of Pharmacology, School of Biological Sciences, Federal University of Santa Catarina (UFSC), Florianopolis, Santa Catarina, Brazil.,Postgraduate Program in Pharmacology, Federal University of Santa Catarina, Santa Catarina, Brazil
| | - Ericks S Soares
- Department of Pharmacology, School of Biological Sciences, Federal University of Santa Catarina (UFSC), Florianopolis, Santa Catarina, Brazil.,Postgraduate Program in Pharmacology, Federal University of Santa Catarina, Santa Catarina, Brazil
| | - Christoph Harms
- Klinik und Hochschulambulanz für Neurologie mit Experimenteller Neurologie, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany.,Centre for Stroke Research, Charité-Universitätsmedizin Berlin, Berlin, Germany.,German Centre for Cardiovascular Research (DZHK), Partner Site Berlin, Berlin, Germany.,Einstein Centre for Neuroscience, Berlin, Germany
| | - Helena I Cimarosti
- Department of Pharmacology, School of Biological Sciences, Federal University of Santa Catarina (UFSC), Florianopolis, Santa Catarina, Brazil.,Postgraduate Program in Pharmacology, Federal University of Santa Catarina, Santa Catarina, Brazil.,Postgraduate Program in Neuroscience, Federal University of Santa Catarina, Santa Catarina, Brazil
| | - Regina Sordi
- Department of Pharmacology, School of Biological Sciences, Federal University of Santa Catarina (UFSC), Florianopolis, Santa Catarina, Brazil.,Postgraduate Program in Pharmacology, Federal University of Santa Catarina, Santa Catarina, Brazil
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28
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Brüninghoff K, Wulff S, Dörner W, Geiss-Friedlander R, Mootz HD. A Photo-Crosslinking Approach to Identify Class II SUMO-1 Binders. Front Chem 2022; 10:900989. [PMID: 35707458 PMCID: PMC9191277 DOI: 10.3389/fchem.2022.900989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 04/25/2022] [Indexed: 11/13/2022] Open
Abstract
The small ubiquitin-like modifier (SUMO) is involved in various cellular processes and mediates known non-covalent protein-protein interactions by three distinct binding surfaces, whose interactions are termed class I to class III. While interactors for the class I interaction, which involves binding of a SUMO-interacting motif (SIM) to a hydrophobic groove in SUMO-1 and SUMO-2/3, are widely abundant, only a couple of examples have been reported for the other two types of interactions. Class II binding is conveyed by the E67 loop region on SUMO-1. Many previous studies to identify SUMO binders using pull-down or microarray approaches did not strategize on the SUMO binding mode. Identification of SUMO binding partners is further complicated due to the typically transient and low affinity interactions with the modifier. Here we aimed to identify SUMO-1 binders selectively enriched for class II binding. Using a genetically encoded photo-crosslinker approach, we have designed SUMO-1 probes to covalently capture class II SUMO-1 interactors by strategically positioning the photo-crosslinking moiety on the SUMO-1 surface. The probes were validated using known class II and class I binding partners. We utilized the probe with p-benzoyl-phenylalanine (BzF, also termed BpF or Bpa) at the position of Gln69 to identify binding proteins from mammalian cell extracts using mass spectrometry. By comparison with results obtained with a similarly designed SUMO-1 probe to target SIM-mediated binders of the class I type, we identified 192 and 96 proteins specifically enriched by either probe, respectively. The implicated preferential class I or class II binding modes of these proteins will further contribute to unveiling the complex interplay of SUMO-1-mediated interactions.
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Affiliation(s)
- Kira Brüninghoff
- Institute of Biochemistry, University of Münster, Münster, Germany
| | - Stephanie Wulff
- Institute of Biochemistry, University of Münster, Münster, Germany
| | - Wolfgang Dörner
- Institute of Biochemistry, University of Münster, Münster, Germany
| | - Ruth Geiss-Friedlander
- Institute of Molecular Medicine and Cell Research, University of Freiburg, Freiburg, Germany
| | - Henning D. Mootz
- Institute of Biochemistry, University of Münster, Münster, Germany
- *Correspondence: Henning D. Mootz,
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29
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Cabello-Lobato MJ, Jenner M, Cisneros-Aguirre M, Brüninghoff K, Sandy Z, da Costa I, Jowitt T, Loch C, Jackson S, Wu Q, Mootz H, Stark J, Cliff M, Schmidt C. Microarray screening reveals two non-conventional SUMO-binding modules linked to DNA repair by non-homologous end-joining. Nucleic Acids Res 2022; 50:4732-4754. [PMID: 35420136 PMCID: PMC9071424 DOI: 10.1093/nar/gkac237] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 03/03/2022] [Accepted: 03/25/2022] [Indexed: 11/25/2022] Open
Abstract
SUMOylation is critical for numerous cellular signalling pathways, including the maintenance of genome integrity via the repair of DNA double-strand breaks (DSBs). If misrepaired, DSBs can lead to cancer, neurodegeneration, immunodeficiency and premature ageing. Using systematic human proteome microarray screening combined with widely applicable carbene footprinting, genetic code expansion and high-resolution structural profiling, we define two non-conventional and topology-selective SUMO2-binding regions on XRCC4, a DNA repair protein important for DSB repair by non-homologous end-joining (NHEJ). Mechanistically, the interaction of SUMO2 and XRCC4 is incompatible with XRCC4 binding to three other proteins important for NHEJ-mediated DSB repair. These findings are consistent with SUMO2 forming a redundant NHEJ layer with the potential to regulate different NHEJ complexes at distinct levels including, but not limited to, XRCC4 interactions with XLF, LIG4 and IFFO1. Regulation of NHEJ is not only relevant for carcinogenesis, but also for the design of precision anti-cancer medicines and the optimisation of CRISPR/Cas9-based gene editing. In addition to providing molecular insights into NHEJ, this work uncovers a conserved SUMO-binding module and provides a rich resource on direct SUMO binders exploitable towards uncovering SUMOylation pathways in a wide array of cellular processes.
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Affiliation(s)
- Maria Jose Cabello-Lobato
- Manchester Cancer Research Centre (MCRC), Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, 555 Wilmslow Road, Manchester M20 4GJ, UK
| | - Matthew Jenner
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, UK
- Warwick Integrative Synthetic Biology (WISB) Centre, University of Warwick, Coventry CV4 7AL, UK
| | - Metztli Cisneros-Aguirre
- Department of Cancer Genetics and Epigenetics, Irell and Manella Graduate School of Biological Sciences Beckman Research Institute of the City of Hope, 1500 E Duarte Rd, Duarte, CA 91010, USA
| | - Kira Brüninghoff
- Institute of Biochemistry, University of Muenster, Corrensstraße 36, 48149 Muenster, Germany
| | - Zac Sandy
- Manchester Cancer Research Centre (MCRC), Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, 555 Wilmslow Road, Manchester M20 4GJ, UK
| | - Isabelle C da Costa
- Manchester Cancer Research Centre (MCRC), Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, 555 Wilmslow Road, Manchester M20 4GJ, UK
| | - Thomas A Jowitt
- Wellcome Trust Centre for Cell-Matrix Research, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | | | - Stephen P Jackson
- Wellcome/Cancer Research UK Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge CB2 1QN, UK
| | - Qian Wu
- Astbury Centre for Structural Molecular Biology, School of Molecular & Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Henning D Mootz
- Institute of Biochemistry, University of Muenster, Corrensstraße 36, 48149 Muenster, Germany
| | - Jeremy M Stark
- Department of Cancer Genetics and Epigenetics, Irell and Manella Graduate School of Biological Sciences Beckman Research Institute of the City of Hope, 1500 E Duarte Rd, Duarte, CA 91010, USA
| | - Matthew J Cliff
- Manchester Institute of Biotechnology (MIB) and School of Chemistry, University of Manchester, Manchester M1 7DN, UK
| | - Christine K Schmidt
- Manchester Cancer Research Centre (MCRC), Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, 555 Wilmslow Road, Manchester M20 4GJ, UK
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30
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Insights in Post-Translational Modifications: Ubiquitin and SUMO. Int J Mol Sci 2022; 23:ijms23063281. [PMID: 35328702 PMCID: PMC8952880 DOI: 10.3390/ijms23063281] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 03/15/2022] [Accepted: 03/16/2022] [Indexed: 12/23/2022] Open
Abstract
Both ubiquitination and SUMOylation are dynamic post-translational modifications that regulate thousands of target proteins to control virtually every cellular process. Unfortunately, the detailed mechanisms of how all these cellular processes are regulated by both modifications remain unclear. Target proteins can be modified by one or several moieties, giving rise to polymers of different morphology. The conjugation cascades of both modifications comprise a few activating and conjugating enzymes but close to thousands of ligating enzymes (E3s) in the case of ubiquitination. As a result, these E3s give substrate specificity and can form polymers on a target protein. Polymers can be quickly modified forming branches or cleaving chains leading the target protein to its cellular fate. The recent development of mass spectrometry(MS) -based approaches has increased the understanding of ubiquitination and SUMOylation by finding essential modified targets in particular signaling pathways. Here, we perform a concise overview comprising from the basic mechanisms of both ubiquitination and SUMOylation to recent MS-based approaches aimed to find specific targets for particular E3 enzymes.
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31
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Lee D, Apelt K, Lee SO, Chan HR, Luijsterburg MS, Leung JWC, Miller K. ZMYM2 restricts 53BP1 at DNA double-strand breaks to favor BRCA1 loading and homologous recombination. Nucleic Acids Res 2022; 50:3922-3943. [PMID: 35253893 PMCID: PMC9023290 DOI: 10.1093/nar/gkac160] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 02/11/2022] [Accepted: 02/22/2022] [Indexed: 12/14/2022] Open
Abstract
An inability to repair DNA double-strand breaks (DSBs) threatens genome integrity and can contribute to human diseases, including cancer. Mammalian cells repair DSBs mainly through homologous recombination (HR) and nonhomologous end-joining (NHEJ). The choice between these pathways is regulated by the interplay between 53BP1 and BRCA1, whereby BRCA1 excludes 53BP1 to promote HR and 53BP1 limits BRCA1 to facilitate NHEJ. Here, we identify the zinc-finger proteins (ZnF), ZMYM2 and ZMYM3, as antagonizers of 53BP1 recruitment that facilitate HR protein recruitment and function at DNA breaks. Mechanistically, we show that ZMYM2 recruitment to DSBs and suppression of break-associated 53BP1 requires the SUMO E3 ligase PIAS4, as well as SUMO binding by ZMYM2. Cells deficient for ZMYM2/3 display genome instability, PARP inhibitor and ionizing radiation sensitivity and reduced HR repair. Importantly, depletion of 53BP1 in ZMYM2/3-deficient cells rescues BRCA1 recruitment to and HR repair of DSBs, suggesting that ZMYM2 and ZMYM3 primarily function to restrict 53BP1 engagement at breaks to favor BRCA1 loading that functions to channel breaks to HR repair. Identification of DNA repair functions for these poorly characterized ZnF proteins may shed light on their unknown contributions to human diseases, where they have been reported to be highly dysregulated, including in several cancers.
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Affiliation(s)
- Doohyung Lee
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Katja Apelt
- Department of Human Genetics, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, the Netherlands
| | - Seong-Ok Lee
- Department of Radiation Oncology, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Hsin-Ru Chan
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Martijn S Luijsterburg
- Department of Human Genetics, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, the Netherlands
| | - Justin W C Leung
- Department of Radiation Oncology, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Kyle M Miller
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
- Livestrong Cancer Institutes, Dell Medical School, The University of Texas at Austin, Austin, TX 78712, USA
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32
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Koike M, Yutoku Y, Koike A. Feline XRCC4 undergoes rapid Ku-dependent recruitment to DNA damage sites. FEBS Open Bio 2022; 12:798-810. [PMID: 35000298 PMCID: PMC8972062 DOI: 10.1002/2211-5463.13363] [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: 07/22/2021] [Revised: 11/30/2021] [Accepted: 01/07/2022] [Indexed: 11/16/2022] Open
Abstract
Radiation and chemotherapy resistance remain some of the greatest challenges in human and veterinary cancer therapies. XRCC4, an essential molecule for nonhomologous end joining repair, is a promising target for radiosensitizers. Genetic variants and mutations of XRCC4 contribute to cancer susceptibility, and XRCC4 is also the causative gene of microcephalic primordial dwarfism (MPD) in humans. The development of clinically effective molecular‐targeted drugs requires accurate understanding of the functions and regulatory mechanisms of XRCC4. In this study, we cloned and sequenced the cDNA of feline XRCC4. Comparative analysis indicated that sequences and post‐translational modification sites that are predicted to be involved in regulating the localization of human XRCC4, including the nuclear localization signal, are mostly conserved in feline XRCC4. All examined target amino acids responsible for human MPD are completely conserved in feline XRCC4. Furthermore, we found that the localization of feline XRCC4 dynamically changes during the cell cycle. Soon after irradiation, feline XRCC4 accumulated at laser‐induced DNA double‐strand break (DSB) sites in both the interphase and mitotic phase, and this accumulation was dependent on the presence of Ku. Additionally, XRCC4 superfamily proteins XLF and PAXX accumulated at the DSB sites. Collectively, these findings suggest that mechanisms regulating the spatiotemporal localization of XRCC4 are crucial for XRCC4 function in humans and cats. Our findings contribute to elucidating the functions of XRCC4 and the role of abnormal XRCC4 in diseases, including cancers and MPD, and may help in developing XRCC4‐targeted drugs, such as radiosensitizers, for humans and cats.
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Affiliation(s)
- Manabu Koike
- Institute for Quantum Medical Science, National Institutes for Quantum and Radiological Science and Technology, 4-9-1 Anagawa, Inage-ku, Chiba, 263-8555, Japan.,Department of Regulatory Biology, Faculty of Science, Saitama University, Saitama, Saitama, 338-8570, Japan
| | - Yasutomo Yutoku
- Institute for Quantum Medical Science, National Institutes for Quantum and Radiological Science and Technology, 4-9-1 Anagawa, Inage-ku, Chiba, 263-8555, Japan
| | - Aki Koike
- Institute for Quantum Medical Science, National Institutes for Quantum and Radiological Science and Technology, 4-9-1 Anagawa, Inage-ku, Chiba, 263-8555, Japan
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33
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Ellis N, Zhu J, Yagle MK, Yang WC, Huang J, Kwako A, Seidman MM, Matunis MJ. RNF4 Regulates the BLM Helicase in Recovery From Replication Fork Collapse. Front Genet 2021; 12:753535. [PMID: 34868226 PMCID: PMC8633118 DOI: 10.3389/fgene.2021.753535] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 10/25/2021] [Indexed: 12/01/2022] Open
Abstract
Sumoylation is an important enhancer of responses to DNA replication stress and the SUMO-targeted ubiquitin E3 ligase RNF4 regulates these responses by ubiquitylation of sumoylated DNA damage response factors. The specific targets and functional consequences of RNF4 regulation in response to replication stress, however, have not been fully characterized. Here we demonstrated that RNF4 is required for the restart of DNA replication following prolonged hydroxyurea (HU)-induced replication stress. Contrary to its role in repair of γ-irradiation-induced DNA double-strand breaks (DSBs), our analysis revealed that RNF4 does not significantly impact recognition or repair of replication stress-associated DSBs. Rather, using DNA fiber assays, we found that the firing of new DNA replication origins, which is required for replication restart following prolonged stress, was inhibited in cells depleted of RNF4. We also provided evidence that RNF4 recognizes and ubiquitylates sumoylated Bloom syndrome DNA helicase BLM and thereby promotes its proteosome-mediated turnover at damaged DNA replication forks. Consistent with it being a functionally important RNF4 substrate, co-depletion of BLM rescued defects in the firing of new replication origins observed in cells depleted of RNF4 alone. We concluded that RNF4 acts to remove sumoylated BLM from collapsed DNA replication forks, which is required to facilitate normal resumption of DNA synthesis after prolonged replication fork stalling and collapse.
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Affiliation(s)
- Nathan Ellis
- University of Arizona Cancer Center, University of Arizona, Tucson, AZ, United States
| | - Jianmei Zhu
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, United States
| | - Mary K Yagle
- University of Arizona Cancer Center, University of Arizona, Tucson, AZ, United States
| | - Wei-Chih Yang
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, United States
| | - Jing Huang
- Laboratory of Molecular Gerontology, National Institute on Aging, Baltimore, MD, United States
| | - Alexander Kwako
- University of Arizona Cancer Center, University of Arizona, Tucson, AZ, United States
| | - Michael M Seidman
- Laboratory of Molecular Gerontology, National Institute on Aging, Baltimore, MD, United States
| | - Michael J Matunis
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, United States
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34
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Dhingra N, Zhao X. Advances in SUMO-based regulation of homologous recombination. Curr Opin Genet Dev 2021; 71:114-119. [PMID: 34333341 PMCID: PMC8671156 DOI: 10.1016/j.gde.2021.07.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 07/07/2021] [Accepted: 07/09/2021] [Indexed: 10/20/2022]
Abstract
Homologous Recombination (HR) is a critical DNA repair mechanism for a range of genome lesions. HR is responsible for mending DNA double strand breaks (DSBs) using intact template DNA. In addition, many HR proteins help cope with DNA lesions generated from DNA replication and telomere deficiency. The functions of HR proteins are often regulated by protein modifications that can quickly and reversibly adjust substrate proteins' attributes. Sumoylation is one of the prevalent modifications that affects all steps of the HR processes and exerts diverse regulation on substrates. This review aims to summarize the most recent advances in our understanding of SUMO-based HR regulation and highlight some key questions that remain to be elucidated.
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Affiliation(s)
- Nalini Dhingra
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Xiaolan Zhao
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
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35
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Barroso-Gomila O, Trulsson F, Muratore V, Canosa I, Merino-Cacho L, Cortazar AR, Pérez C, Azkargorta M, Iloro I, Carracedo A, Aransay AM, Elortza F, Mayor U, Vertegaal ACO, Barrio R, Sutherland JD. Identification of proximal SUMO-dependent interactors using SUMO-ID. Nat Commun 2021; 12:6671. [PMID: 34795231 PMCID: PMC8602451 DOI: 10.1038/s41467-021-26807-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 10/19/2021] [Indexed: 12/13/2022] Open
Abstract
The fast dynamics and reversibility of posttranslational modifications by the ubiquitin family pose significant challenges for research. Here we present SUMO-ID, a technology that merges proximity biotinylation by TurboID and protein-fragment complementation to find SUMO-dependent interactors of proteins of interest. We develop an optimized split-TurboID version and show SUMO interaction-dependent labelling of proteins proximal to PML and RANGAP1. SUMO-dependent interactors of PML are involved in transcription, DNA damage, stress response and SUMO modification and are highly enriched in SUMO Interacting Motifs, but may only represent a subset of the total PML proximal proteome. Likewise, SUMO-ID also allow us to identify interactors of SUMOylated SALL1, a less characterized SUMO substrate. Furthermore, using TP53 as a substrate, we identify SUMO1, SUMO2 and Ubiquitin preferential interactors. Thus, SUMO-ID is a powerful tool that allows to study the consequences of SUMO-dependent interactions, and may further unravel the complexity of the ubiquitin code.
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Affiliation(s)
- Orhi Barroso-Gomila
- grid.420175.50000 0004 0639 2420Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801 A, 48160 Derio, Spain
| | - Fredrik Trulsson
- grid.10419.3d0000000089452978Cell and Chemical Biology, Leiden University Medical Center (LUMC), 2333 ZA Leiden, The Netherlands
| | - Veronica Muratore
- grid.420175.50000 0004 0639 2420Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801 A, 48160 Derio, Spain
| | - Iñigo Canosa
- grid.420175.50000 0004 0639 2420Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801 A, 48160 Derio, Spain
| | - Laura Merino-Cacho
- grid.420175.50000 0004 0639 2420Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801 A, 48160 Derio, Spain
| | - Ana Rosa Cortazar
- grid.420175.50000 0004 0639 2420Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801 A, 48160 Derio, Spain ,grid.413448.e0000 0000 9314 1427CIBERONC, Instituto de Salud Carlos III, C/ Monforte de Lemos 3-5, Pabellón 11, Planta 0, 28029 Madrid, Spain
| | - Coralia Pérez
- grid.420175.50000 0004 0639 2420Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801 A, 48160 Derio, Spain
| | - Mikel Azkargorta
- grid.420175.50000 0004 0639 2420Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801 A, 48160 Derio, Spain ,grid.413448.e0000 0000 9314 1427CIBERehd, Instituto de Salud Carlos III, C/ Monforte de Lemos 3-5, Pabellón 11, Planta 0, 28029 Madrid, Spain ,grid.413448.e0000 0000 9314 1427ProteoRed-ISCIII, Instituto de Salud Carlos III, C/ Monforte de Lemos 3-5, Pabellón 11, Planta 0, 28029 Madrid, Spain
| | - Ibon Iloro
- grid.420175.50000 0004 0639 2420Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801 A, 48160 Derio, Spain ,grid.413448.e0000 0000 9314 1427CIBERehd, Instituto de Salud Carlos III, C/ Monforte de Lemos 3-5, Pabellón 11, Planta 0, 28029 Madrid, Spain ,grid.413448.e0000 0000 9314 1427ProteoRed-ISCIII, Instituto de Salud Carlos III, C/ Monforte de Lemos 3-5, Pabellón 11, Planta 0, 28029 Madrid, Spain
| | - Arkaitz Carracedo
- grid.420175.50000 0004 0639 2420Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801 A, 48160 Derio, Spain ,grid.413448.e0000 0000 9314 1427CIBERONC, Instituto de Salud Carlos III, C/ Monforte de Lemos 3-5, Pabellón 11, Planta 0, 28029 Madrid, Spain ,grid.424810.b0000 0004 0467 2314Ikerbasque, Basque Foundation for Science, 48011 Bilbao, Spain ,grid.11480.3c0000000121671098Biochemistry and Molecular Biology Department, University of the Basque Country (UPV/EHU), E-48940 Leioa, Spain
| | - Ana M. Aransay
- grid.420175.50000 0004 0639 2420Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801 A, 48160 Derio, Spain ,grid.413448.e0000 0000 9314 1427CIBERehd, Instituto de Salud Carlos III, C/ Monforte de Lemos 3-5, Pabellón 11, Planta 0, 28029 Madrid, Spain
| | - Felix Elortza
- grid.420175.50000 0004 0639 2420Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801 A, 48160 Derio, Spain ,grid.413448.e0000 0000 9314 1427CIBERehd, Instituto de Salud Carlos III, C/ Monforte de Lemos 3-5, Pabellón 11, Planta 0, 28029 Madrid, Spain ,grid.413448.e0000 0000 9314 1427ProteoRed-ISCIII, Instituto de Salud Carlos III, C/ Monforte de Lemos 3-5, Pabellón 11, Planta 0, 28029 Madrid, Spain
| | - Ugo Mayor
- grid.424810.b0000 0004 0467 2314Ikerbasque, Basque Foundation for Science, 48011 Bilbao, Spain ,grid.11480.3c0000000121671098Biochemistry and Molecular Biology Department, University of the Basque Country (UPV/EHU), E-48940 Leioa, Spain
| | - Alfred C. O. Vertegaal
- grid.10419.3d0000000089452978Cell and Chemical Biology, Leiden University Medical Center (LUMC), 2333 ZA Leiden, The Netherlands
| | - Rosa Barrio
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801 A, 48160, Derio, Spain.
| | - James D. Sutherland
- grid.420175.50000 0004 0639 2420Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801 A, 48160 Derio, Spain
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Yau TY, Sander W, Eidson C, Courey AJ. SUMO Interacting Motifs: Structure and Function. Cells 2021; 10:cells10112825. [PMID: 34831049 PMCID: PMC8616421 DOI: 10.3390/cells10112825] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 10/14/2021] [Accepted: 10/14/2021] [Indexed: 11/16/2022] Open
Abstract
Small ubiquitin-related modifier (SUMO) is a member of the ubiquitin-related protein family. SUMO modulates protein function through covalent conjugation to lysine residues in a large number of proteins. Once covalently conjugated to a protein, SUMO often regulates that protein’s function by recruiting other cellular proteins. Recruitment frequently involves a non-covalent interaction between SUMO and a SUMO-interacting motif (SIM) in the interacting protein. SIMs generally consist of a four-residue-long hydrophobic stretch of amino acids with aliphatic non-polar side chains flanked on one side by negatively charged amino acid residues. The SIM assumes an extended β-strand-like conformation and binds to a conserved hydrophobic groove in SUMO. In addition to hydrophobic interactions between the SIM non-polar core and hydrophobic residues in the groove, the negatively charged residues in the SIM make favorable electrostatic contacts with positively charged residues in and around the groove. The SIM/SUMO interaction can be regulated by the phosphorylation of residues adjacent to the SIM hydrophobic core, which provide additional negative charges for favorable electrostatic interaction with SUMO. The SUMO interactome consists of hundreds or perhaps thousands of SIM-containing proteins, but we do not fully understand how each SUMOylated protein selects the set of SIM-containing proteins appropriate to its function. SIM/SUMO interactions have critical functions in a large number of essential cellular processes including the formation of membraneless organelles by liquid–liquid phase separation, epigenetic regulation of transcription through histone modification, DNA repair, and a variety of host–pathogen interactions.
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Loh D, Reiter RJ. Melatonin: Regulation of Biomolecular Condensates in Neurodegenerative Disorders. Antioxidants (Basel) 2021; 10:1483. [PMID: 34573116 PMCID: PMC8465482 DOI: 10.3390/antiox10091483] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 09/10/2021] [Accepted: 09/13/2021] [Indexed: 12/12/2022] Open
Abstract
Biomolecular condensates are membraneless organelles (MLOs) that form dynamic, chemically distinct subcellular compartments organizing macromolecules such as proteins, RNA, and DNA in unicellular prokaryotic bacteria and complex eukaryotic cells. Separated from surrounding environments, MLOs in the nucleoplasm, cytoplasm, and mitochondria assemble by liquid-liquid phase separation (LLPS) into transient, non-static, liquid-like droplets that regulate essential molecular functions. LLPS is primarily controlled by post-translational modifications (PTMs) that fine-tune the balance between attractive and repulsive charge states and/or binding motifs of proteins. Aberrant phase separation due to dysregulated membrane lipid rafts and/or PTMs, as well as the absence of adequate hydrotropic small molecules such as ATP, or the presence of specific RNA proteins can cause pathological protein aggregation in neurodegenerative disorders. Melatonin may exert a dominant influence over phase separation in biomolecular condensates by optimizing membrane and MLO interdependent reactions through stabilizing lipid raft domains, reducing line tension, and maintaining negative membrane curvature and fluidity. As a potent antioxidant, melatonin protects cardiolipin and other membrane lipids from peroxidation cascades, supporting protein trafficking, signaling, ion channel activities, and ATPase functionality during condensate coacervation or dissolution. Melatonin may even control condensate LLPS through PTM and balance mRNA- and RNA-binding protein composition by regulating N6-methyladenosine (m6A) modifications. There is currently a lack of pharmaceuticals targeting neurodegenerative disorders via the regulation of phase separation. The potential of melatonin in the modulation of biomolecular condensate in the attenuation of aberrant condensate aggregation in neurodegenerative disorders is discussed in this review.
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Affiliation(s)
- Doris Loh
- Independent Researcher, Marble Falls, TX 78654, USA
| | - Russel J. Reiter
- Department of Cellular and Structural Biology, UT Health Science Center, San Antonio, TX 78229, USA
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Sumoylation regulates the assembly and activity of the SMN complex. Nat Commun 2021; 12:5040. [PMID: 34413305 PMCID: PMC8376998 DOI: 10.1038/s41467-021-25272-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 07/26/2021] [Indexed: 11/09/2022] Open
Abstract
SMN is a ubiquitously expressed protein and is essential for life. SMN deficiency causes the neurodegenerative disease spinal muscular atrophy (SMA), the leading genetic cause of infant mortality. SMN interacts with itself and other proteins to form a complex that functions in the assembly of ribonucleoproteins. SMN is modified by SUMO (Small Ubiquitin-like Modifier), but whether sumoylation is required for the functions of SMN that are relevant to SMA pathogenesis is not known. Here, we show that inactivation of a SUMO-interacting motif (SIM) alters SMN sub-cellular distribution, the integrity of its complex, and its function in small nuclear ribonucleoproteins biogenesis. Expression of a SIM-inactivated mutant of SMN in a mouse model of SMA slightly extends survival rate with limited and transient correction of motor deficits. Remarkably, although SIM-inactivated SMN attenuates motor neuron loss and improves neuromuscular junction synapses, it fails to prevent the loss of sensory-motor synapses. These findings suggest that sumoylation is important for proper assembly and function of the SMN complex and that loss of this post-translational modification impairs the ability of SMN to correct selective deficits in the sensory-motor circuit of SMA mice.
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